Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001574.1 Hibiscus syriacus cultivar Beakdansim tig00003126_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1705968
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 7
Found at i:506397 original size:259 final size:260
Alignment explanation
Indices: 505742--509026 Score: 3728
Period size: 259 Copynumber: 12.8 Consensus size: 260
505732 TAGCGGTTTT
* * * *
505742 GTTCAAGCTATTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGGCGTGTATCATAAACCTT
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
* * * ** *
505807 AATTTTT-TGTTAAAATTGGTGGAAATTTATGAAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
66 ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* *
505871 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTAATTTTCCTCTGATATTCAAGAACACGACAGCG
131 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
*
505936 TGCATAAAAAAGCAATGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCTT
196 TGCATAAAAAA-CAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTT
506001 C
260 C
* * * *
506002 TTTCAAGCTATTT-GTTC-TTTTTTATCTTGTTATCATGAACTTGGTGACGTGCATCATAAACCC
1 GTTCAAGCT-TTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCC
* * *
506065 TATTTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTATCGAGTTTCGTTCAATCTTTTGAT
65 TA-TTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGAT
* * *
506130 TGTTCTTGGTGTTAATTTTCTATGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACGT-GACA
129 TGTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAAC-TCGACA
*
506194 GCGT-AAGTAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGA-GTACTGAG
193 GCGTGCA-TAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAG
506257 CTTC
257 CTTC
* *
506261 GTTCAAGCTTTTTGTTCTTTTTTTCTCTTGTTATCAA-AAGCTTGGCGACGTGCATCAGAAACCC
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAA-CTTGGCGACGTGCATCATAAACCC
* * * * * *
506325 TATTTTTTCTATTAAAATTGTTGGAATTTTATGGAAAGTATCGAACTTCGTTCAATCTTTTGATT
65 TATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATT
*
506390 GTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
130 GTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* *
506455 GTGCAT-AAAAACATTGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTACGAGGTACTGAGCTT
195 GTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTT
506519 C
260 C
* * *
506520 GTTCAAGCTTTTCGTTCTTTTTTCCTCTTGTTATCAAGAACTTGGTGATGTGCATCATAAACCCT
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
* * ** *
506585 A-TTTTTATGTT-AAATTGGTGGACATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
66 ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* * * *
506648 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTACTTTTCCTGTGATATTCAAGAACTCGACAACA
131 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
* * * * * * *
506713 TGCATAAAAAGCACTGTTTTTGAAAATTAATGGTAAGTTGTGGAAATTTTGAGGTACAGATCTTC
196 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
* * * *
506778 TTTCAAGCTATTCGTTC-TTTTTTATATTGTTATCAAG-ACTTGGCGACGTGCATCATAAACCCT
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
*
506841 ATTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
66 ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* * *
506906 TTCTTGGCGTTAATTTTCTACGCTTGTGTTATA-TTTTCCTCTGATATTCAAGAACTCGACAACG
131 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
506970 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
196 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
* *
507035 TTTCAAGCCTTTT-GTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCATAAACC
1 GTTCAAG-CTTTTCGTTC-TTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACC
* * * * *
507099 CTATTTTTCCTGTTAAAATTGGTGGAAATTTATGGAAAGCACCGAACTTCATGT-AATCTTTTGA
64 CTATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGT-TCAATCTTTTGA
* * *
507163 TTGTTCTTGGAGTTAATTTTCTACGCTTTTGTTTTATTTTTCCTCTAATATTCAAGAACTCGACA
128 TTGTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACA
* * * * *
507228 GCGTGCATATAAAACACTATTTTTGAAAATTAGTGGTAATTTTTGGAAATTTTGAGGTACTGAGC
193 GCGTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGC
507293 TTC
258 TTC
*
507296 GTTCAAGCTTTTCGTTCTTTTTTCCTCTTGTTATCAAGAACTT-GCTGACGTGCATCATAAACCC
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGC-GACGTGCATCATAAACCC
* ** * *
507360 TATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCATTCAATCTTTTCATT
65 TATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATT
* * * *
507425 GTTCTTGGCATTAATTTTCTACGTTTTTGTTCTATTTTTCCTCCGATATTTAAGAACTCGACAGC
130 GTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* * * *
507490 GAGCATAAAAAACACTGTTTTTGAAAATTAGTGGTAAGTTGTAGAAA-TTCGAGGTACTGAGCTT
195 GTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTT
507554 C
260 C
* * * * *
507555 TTTCAAGCTATTCGTTC-TTTTTTATCTTGTTATCAAGAACTTGACGACGTGCATCAGAAACCCT
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
* * * *
507619 ATTTTTTATGTTGAAATTGATGGAAATTTATGGAATGTACCGAGCTTCGTTCAATATTTTGATTG
66 ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* * * *
507684 TTCTGGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTCTG-TAGT
131 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTC-GACAGC
*
507748 GTGCGA-AAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTAAGCT
195 GTGC-ATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCT
507812 TC
259 TC
* * *
507814 GTTCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAAACCC
1 GTTCAAGCTTTTCGTTC-TTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCC
* * * * * * *
507879 TATTTTTTCTATTGAAATTAGTGGAAATTTATGAAAAGTACCGAACTTTGTTTAATATTTTGATT
65 TATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATT
* * *
507944 GTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGGCAAC
130 GTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* * * * * *
508009 GTGCATAAAAAATATTGTTTTTGAAAATTATTGGTAATTTGTGGAAATTTTGAGGTATTGAGTTT
195 GTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTT
508074 C
260 C
* * * *
508075 GTTCAAGCTTTTCATTC-TTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATTAGAAACTCT
1 GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
*
508139 ATTTTTTCTATTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
66 ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* * * *
508204 TTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATCTTTAGGAACT-------G
131 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
*** * * * * * * * * **
508262 TTTTTGAAAATC---G--TTGGAAATTTA-TGGAAATTT-T---AATGTACTAAG--CTTTG-TT
196 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAAT-TTCGAGGTACTGAGCTT
508314 C
260 C
*** ** * * * * **
508315 ---CATCTTTTTGTTCT-TTTCTTTCTTTGGTTTTCAAGAACTTGGCGACGTTTATCATAAACCC
1 GTTCAAGCTTTTCGT-TCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCC
* * * * * * * * *
508376 TGTTTTTCCAT-CT-AAATTAGTGGAAATTTGTGAAAAGTACTGAGTTTCGTTCAATCTTTTAAT
65 TATTTTTTC-TGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGAT
* * **** * * * * * *
508439 TGTTATTGGTGTTAATTTTCTGTATTTTTGTTATATTCTTCCTCTTATAATCAATAACTCGGCAG
129 TGTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAG
* * * ** * * *
508504 CGTGTAT-AAAAGCATTGTTTTTG-AAA--A----CCA---GTGGAAATTCCGAGGTATTGAGAT
194 CGTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCT
508558 TC
259 TC
* * * * * * * *
508560 GCTCAAGTTTTTCGTTTTTTTCTTTCTCTGGTTATCAAGGACTTTGCGACGTGCATAAAAAACCC
1 GTTCAAGCTTTTCGTTCTTTT-TTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCC
* * *** * *
508625 TATTTTTTC-GTTGAAATTGGTAGAAATTTGTGGAAAGTATTTAGCTGCGTCCAATCTTTTGATT
65 TATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATT
* * * * * * * *
508689 GTTATTGGAGTTAATTTTC-ATCGTTTTTGTTATATTCTTCCTGTGATAATCAAGAACCCGACAG
130 GTTCTTGGCGTTAATTTTCTA-CGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAG
* * * * * * *** * *
508753 CGTGCATCAAAAATATTATTTTTG-AAACTAATTAAAATTTGT-GAAAATTCAGAGGTGCTGAGC
194 CGTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTC-GAGGTACTGAGC
508816 TTC
258 TTC
* * * ** *
508819 GTTCAAGCTTTTCATTCTTTTCTATCTCTGGTTATCAAGAACTTGATGATGTGCATCA-AATACC
1 GTTCAAGCTTTTCGTTCTTTT-TTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAA-ACC
* * * * * * ** * *
508883 CTATTTTTCCTTTTAAAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTTGTTCAACCTTTTGAT
64 CTATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGAT
* * * * ** * *
508948 TGTTCTTGGCATTAATTTTCTACGTTTTTATTCTATTCTT-CAGTGATAATCAACAACTCGACAG
129 TGTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAG
*
509012 CGTGCATTAAAAACA
194 CGTGCATAAAAAACA
509027 CTCCTTTTTT
Statistics
Matches: 2599, Mismatches: 349, Indels: 155
0.84 0.11 0.05
Matches are distributed among these distances:
237 96 0.04
238 46 0.02
239 1 0.00
240 4 0.00
241 2 0.00
242 8 0.00
243 11 0.00
244 6 0.00
245 5 0.00
246 9 0.00
247 12 0.00
248 15 0.01
249 145 0.06
250 16 0.01
252 8 0.00
256 26 0.01
257 234 0.09
258 405 0.16
259 606 0.23
260 497 0.19
261 447 0.17
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (260 bp):
GTTCAAGCTTTTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
ATTTTTTCTGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
Found at i:507623 original size:778 final size:777
Alignment explanation
Indices: 505742--509028 Score: 4151
Period size: 778 Copynumber: 4.3 Consensus size: 777
505732 TAGCGGTTTT
* * * *
505742 GTTCAAGCTATTCGTTCTTTTTTTCTCTTGTTATCAAGAACTTGGC-GGCGTGTATCATAAACCT
1 GTTCAAGCTTTTCGTTC-TTTTTTCTCTTGTTATCAAGAACTT-GCTGACGTGCATCATAAACCC
* *
505806 TAATTTTT-TGTTAAAATTGGTGGAAATTTATGAAAAGTACTAAGCTTCGTTCAATCTTTTCATT
64 TATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATT
* * *
505870 GTTCTTGGCGTTAATTTTCTACGCTTTTGTTCTAATTTTCCTCTGATATTCAAGAACACGACAGC
129 GTTCTTGGCATTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* *
505935 GTGCATAAAAAAGCAATGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCT
194 GAGCATAAAAAA-CACTGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCT
* * *
506000 TCTTTCAAGCTATTTGTTCTTTTTTATCTTGTTATCATGAACTTGGTGACGTGCATCATAAACCC
258 TCTTTCAAGCTATTCGTTCTTTTTTATCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCC
* *
506065 TATTTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTATCGAGTTTCGTTCAATCTTTTGAT
323 TA-TTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGAT
* *
506130 TGTTCTTGGTGTTAATTTTCTATGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACGT-GACA
387 TGTTCTTGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAAC-TCGACA
*
506194 GCGT-AAGTAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGA-GTACTGAG
451 GCGTGCA-TAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAG
* *
506257 CTTCGTTCAAGCTTTTTGTTC-TTTTTTTCTCTTGTTATCAAAAGCTTGGCGACGTGCATCAGAA
515 CTTCGTTCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAA
* * *
506321 ACCCTATTTTTTCTATTAAAATTGTTGGAATTTTATGGAAAGTATCGAACTTCGTTCAATCTTTT
580 ACCCTATTTTTTCTATTAAAATTGGTGGAAATTTATGGAAAGTACCGAACTTCGTT-AATCTTTT
506386 GATTGTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGA
644 GATTGTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGA
* **
506451 CAGCGTGCATAAAAACATTGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTACGAGGTACTGAG
709 CAGCGTGCATAAAAACATTATTTTTGAAAATTAGTGGTAATTTGTGGAAATTTTGAGGTACTGAG
506516 CTTC
774 CTTC
* *
506520 GTTCAAGCTTTTCGTTCTTTTTTCCTCTTGTTATCAAGAACTTGGTGATGTGCATCATAAACCCT
1 GTTCAAGCTTTTCGTTCTTTTTT-CTCTTGTTATCAAGAACTTGCTGACGTGCATCATAAACCCT
* *
506585 A-TTTTTATGTT-AAATTGGTGGACATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
65 ATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
* * * *
506648 TTCTTGGCGTTAATTTTCTACGCTTTTGTTCTACTTTTCCTGTGATATTCAAGAACTCGACAAC-
130 TTCTTGGCATTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
* * * * *
506712 ATGCATAAAAAGCACTGTTTTTGAAAATTAATGGTAAGTTGTGGAAATTTTGAGGTACAGATCTT
195 A-GCATAAAAAACACTGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCTT
*
506777 CTTTCAAGCTATTCGTTCTTTTTTATATTGTTATCAAG-ACTTGGCGACGTGCATCATAAACCCT
259 CTTTCAAGCTATTCGTTCTTTTTTATCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCT
506841 ATTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
324 ATTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
* *
506906 TTCTTGGCGTTAATTTTCTACGCTTGTGTTATA-TTTTCCTCTGATATTCAAGAACTCGACAACG
389 TTCTTGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTCGACAGCG
506970 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
454 TGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTC
* * *
507035 TTTCAAGCCTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCATAAACCC
519 GTTCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAAACCC
* * * *
507100 TATTTTTCCTGTTAAAATTGGTGGAAATTTATGGAAAGCACCGAACTTCATGTAATCTTTTGATT
584 TATTTTTTCTATTAAAATTGGTGGAAATTTATGGAAAGTACCGAACTTCGT-TAATCTTTTGATT
* *
507165 GTTCTTGGAGTTAATTTTCTACGCTTTTGTTTTATTTTTCCTCTAATATTCAAGAACTCGACAGC
648 GTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* *
507230 GTGCATATAAAACACTATTTTTGAAAATTAGTGGTAATTTTTGGAAATTTTGAGGTACTGAGCTT
713 GTGCATA-AAAACATTATTTTTGAAAATTAGTGGTAATTTGTGGAAATTTTGAGGTACTGAGCTT
507295 C
777 C
507296 GTTCAAGCTTTTCGTTCTTTTTTCCTCTTGTTATCAAGAACTTGCTGACGTGCATCATAAACCCT
1 GTTCAAGCTTTTCGTTCTTTTTT-CTCTTGTTATCAAGAACTTGCTGACGTGCATCATAAACCCT
*
507361 ATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCATTCAATCTTTTCATTG
65 ATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
* * *
507426 TTCTTGGCATTAATTTTCTACGTTTTTGTTCTATTTTTCCTCCGATATTTAAGAACTCGACAGCG
130 TTCTTGGCATTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCG
*
507491 AGCATAAAAAACACTGTTTTTGAAAATTAGTGGTAAGTTGTAGAAA-TTCGAGGTACTGAGCTTC
195 AGCATAAAAAACACTGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCTTC
* *
507555 TTTCAAGCTATTCGTTCTTTTTTATCTTGTTATCAAGAACTTGACGACGTGCATCAGAAACCCTA
260 TTTCAAGCTATTCGTTCTTTTTTATCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCTA
* * *
507620 TTTTTTATGTTGAAATTGATGGAAATTTATGGAATGTACCGAGCTTCGTTCAATATTTTGATTGT
325 TTTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTGT
* * *
507685 TCTGGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTCTG-TAGTG
390 TCTTGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTC-GACAGCG
*
507749 TGCGA-AAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTAAGCTT
454 TGC-ATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTT
507813 CGTTCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAAACC
518 CGTTCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAAACC
* * * * *
507878 CTATTTTTTCTATTGAAATTAGTGGAAATTTATGAAAAGTACCGAACTTTGTTTAATATTTTGAT
583 CTATTTTTTCTATTAAAATTGGTGGAAATTTATGGAAAGTACCGAACTTCG-TTAATCTTTTGAT
* *
507943 TGTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGGCAA
647 TGTTCTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAG
* * * * *
508008 CGTGCATAAAAAATATTGTTTTTGAAAATTATTGGTAATTTGTGGAAATTTTGAGGTATTGAGTT
712 CGTGCAT-AAAAACATTATTTTTGAAAATTAGTGGTAATTTGTGGAAATTTTGAGGTACTGAGCT
508073 TC
776 TC
* * * *
508075 GTTCAAGCTTTTCATTCTTTTTTCTCTTGTTATCAAGAACTTGGC-GACGTGCATTAGAAACTCT
1 GTTCAAGCTTTTCGTTCTTTTTTCTCTTGTTATCAAGAACTT-GCTGACGTGCATCATAAACCCT
* * ** *
508139 ATTTTTTCTATTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTG
65 ATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTG
*
508204 TTCTTGG-AGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATCTT-------T----A--
130 TTCTTGGCA-TTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGC
* * * * ** * *
508255 G-G--------A-ACTGTTTTTGAAAA-TCGTTGGAAATTTATGGAAATTTTAATGTACTAAGCT
194 GAGCATAAAAAACACTGTTTTTGAAAATTAG-TGGTAAGTTGTGGAAATTTCGAGGTACTGAGCT
* * * * * **
508309 T-TGTTCCATCTTTTTGTTCTTTTCTT-TCTTTGGTTTTCAAGAACTTGGCGACGTTTATCATAA
258 TCT-TTCAAGCTATTCGTTCTTTT-TTATC-TT-GTTATCAAGAACTTGGCGACGTGCATCATAA
* * * * * * * *
508372 ACCCTGTTTTTCCAT-CT-AAATTAGTGGAAATTTGTGAAAAGTACTGAGTTTCGTTCAATCTTT
319 ACCCTATTTTT-TATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTT
* * * **** * * * *
508435 TAATTGTTATTGGTGTTAATTTTCTGTATTTTTGTTATATTCTTCCTCTTATAATCAATAACTCG
383 TGATTGTTCTTGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTCG
* * * * ** * *
508500 GCAGCGTGTAT-AAAAGCATTGTTTTTG-AAA--A----CCA---GTGGAAATTCCGAGGTATTG
448 ACAGCGTGCATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTG
* * * ** * *
508554 AGATTCGCTCAAG-TTTTTCGTT-TTTTTCTTTCTCTGGTTATCAAGGACTTTGCGACGTGCATA
513 AGCTTCGTTCAAGCTTTTT-GTTCTTTTT-TTTCTCTTGTTATCAAAAACTTGGCGACGTGCATC
* * * * *** * * *
508617 AAAAACCCTATTTTTTC-GTTGAAATTGGTAGAAATTTGTGGAAAGTATTTAGCTGCGTCCAATC
576 AAAAACCCTATTTTTTCTATTAAAATTGGTGGAAATTTATGGAAAGTACCGAACTTCGT-TAATC
* * * * * *
508681 TTTTGATTGTTATTGGAGTTAATTTTC-ATCGTTTTTGTTATATTCTTCCTGTGATAATCAAGAA
640 TTTTGATTGTTCTTGGAGTTAATTTTCTA-CGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAA
* * * * *** * **
508745 CCCGACAGCGTGCATCAAAAATATTATTTTTG-AAACTAATTAAAATTTGTGAAAATTCAGAGGT
704 CTCGACAGCGTGCAT-AAAAACATTATTTTTGAAAATTAGTGGTAATTTGTGGAAATTTTGAGGT
*
508809 GCTGAGCTTC
768 ACTGAGCTTC
* * * *
508819 GTTCAAGCTTTTCATTCTTTTCTATCTCTGGTTATCAAGAACTTGATGATGTGCATCA-AATACC
1 GTTCAAGCTTTTCGTTCTTTT-T-TCTCTTGTTATCAAGAACTTGCTGACGTGCATCATAA-ACC
* * * * * * * * * *
508883 CTATTTTTCCTTTTAAAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTTGTTCAACCTTTTGAT
63 CTATTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCAT
* * * ** * *
508948 TGTTCTTGGCATTAATTTTCTACGTTTTTATTCTATTCTT-CAGTGATAATCAACAACTCGACAG
128 TGTTCTTGGCATTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAG
* *
509012 CGTGCATTAAAAACACT
193 CGAGCATAAAAAACACT
509029 CCTTTTTTTT
Statistics
Matches: 2218, Mismatches: 229, Indels: 134
0.86 0.09 0.05
Matches are distributed among these distances:
744 54 0.02
745 135 0.06
746 198 0.09
747 1 0.00
749 1 0.00
752 1 0.00
753 1 0.00
754 2 0.00
755 30 0.01
756 49 0.02
757 99 0.04
758 38 0.02
759 3 0.00
764 1 0.00
765 1 0.00
767 2 0.00
768 3 0.00
771 1 0.00
772 1 0.00
773 77 0.03
774 120 0.05
775 197 0.09
776 201 0.09
777 192 0.09
778 459 0.21
779 347 0.16
780 4 0.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (777 bp):
GTTCAAGCTTTTCGTTCTTTTTTCTCTTGTTATCAAGAACTTGCTGACGTGCATCATAAACCCTA
TTTTTTCTGTTAAAATTGGTGGAAATTTATGGAAAGTACTAAGCTTCGTTCAATCTTTTCATTGT
TCTTGGCATTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCGA
GCATAAAAAACACTGTTTTTGAAAATTAGTGGTAAGTTGTGGAAATTTCGAGGTACTGAGCTTCT
TTCAAGCTATTCGTTCTTTTTTATCTTGTTATCAAGAACTTGGCGACGTGCATCATAAACCCTAT
TTTTTATGTTGAAATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTGTT
CTTGGCGTTAATTTTCTACGCTTTTGTTATATTTTTCCTCTGATATTCAAGAACTCGACAGCGTG
CATAAAAAACAATGTTTTTGAAAATTAGTGGTAATTTGTGGAAATTTCGAGGTACTGAGCTTCGT
TCAAGCTTTTTGTTCTTTTTTTTCTCTTGTTATCAAAAACTTGGCGACGTGCATCAAAAACCCTA
TTTTTTCTATTAAAATTGGTGGAAATTTATGGAAAGTACCGAACTTCGTTAATCTTTTGATTGTT
CTTGGAGTTAATTTTCTACGCTTTTGTTCTATTTTTCCTCTGATATTCAAGAACTCGACAGCGTG
CATAAAAACATTATTTTTGAAAATTAGTGGTAATTTGTGGAAATTTTGAGGTACTGAGCTTC
Found at i:508455 original size:237 final size:236
Alignment explanation
Indices: 508024--508459 Score: 547
Period size: 237 Copynumber: 1.8 Consensus size: 236
508014 TAAAAAATAT
* * * * * *
508024 TGTTTTTGAAAATTATTGGTAATTTGTGGAAATTTTGAGGTATTGAGTTTCGTTCAAGCTTTTCA
1 TGTTTTTGAAAATCATTGGAAATTTATGGAAATTTTAAGGTACTAAGTTTCGTTCAAGCTTTTCA
* * * *
508089 TTCTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATTAGAAACTCTATTTTTTCTATTGAA
66 TTCTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCAGAAACCCTAGTTTTTCCATTGAA
* * * *
508154 ATTGGTGGAAATTTATGGAAAGTACCGAGCTTCGTTCAATCTTTTGATTGTTCTTGGAGTTAATT
131 ATTAGTGGAAATTTATGAAAAGTACCGAGCTTCGTTCAATCTTTTAATTGTTATTGGAGTTAATT
508219 TTCTACGCTTTTGTTCTATTTTTCCTCTGATCTTTAGGAAC
196 TTCTACGCTTTTGTTCTATTTTTCCTCTGATCTTTAGGAAC
* * * * *
508260 TGTTTTTGAAAATCGTTGGAAATTTATGGAAATTTTAATGTACTAAGCTTT-GTTCCATCTTTTT
1 TGTTTTTGAAAATCATTGGAAATTTATGGAAATTTTAAGGTACTAAG-TTTCGTTCAAGCTTTTC
* * ** *
508324 GTTCTTTTCTT-TCTTTGGTTTTCAAGAACTTGGCGACGTTTATCATAAACCCT-GTTTTTCCAT
65 ATTCTTTT-TTCTC-TT-GTTATCAAGAACTTGGCGACGTGCATCAGAAACCCTAGTTTTTCCAT
* * * *
508387 CT-AAATTAGTGGAAATTTGTGAAAAGTACTGAGTTTCGTTCAATCTTTTAATTGTTATTGGTGT
127 -TGAAATTAGTGGAAATTTATGAAAAGTACCGAGCTTCGTTCAATCTTTTAATTGTTATTGGAGT
508451 TAATTTTCT
191 TAATTTTCT
508460 GTATTTTTGT
Statistics
Matches: 167, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
236 58 0.35
237 78 0.47
238 31 0.19
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (236 bp):
TGTTTTTGAAAATCATTGGAAATTTATGGAAATTTTAAGGTACTAAGTTTCGTTCAAGCTTTTCA
TTCTTTTTTCTCTTGTTATCAAGAACTTGGCGACGTGCATCAGAAACCCTAGTTTTTCCATTGAA
ATTAGTGGAAATTTATGAAAAGTACCGAGCTTCGTTCAATCTTTTAATTGTTATTGGAGTTAATT
TTCTACGCTTTTGTTCTATTTTTCCTCTGATCTTTAGGAAC
Found at i:508724 original size:249 final size:252
Alignment explanation
Indices: 508319--509026 Score: 725
Period size: 249 Copynumber: 2.8 Consensus size: 252
508309 TTGTTCCATC
* * * ** * *
508319 TTTTT-GTTCTTTTCTTTCTTTGGTTTTCAAGAACTTGGCGACGTTTATCATAAACCCTGTTTTT
1 TTTTTCGTTCTTTTCTTTCTCTGGTTATCAAGAACTTTGCGACGTGCATCAAAAACCCTATTTTT
* * *
508383 CCATCTAAATTAGTGGAAATTTGTGAAAAGTACTGAGTTTCGTTCAATCTTTTAATTGTTATTGG
66 CCAT-TAAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTCGTTCAATCTTTTGATTGTTATTGG
* * * * * *
508448 TGTTAATTTTCT-GTATTTTTGTTATATTCTTCCTCTTATAATCAATAACTCGGCAGCGTGTAT-
130 AGTTAATTTTCTCG--TTTTTGTTATATTCTTCCTGTGATAATCAACAACTCGACAGCGTGCATC
* * ** * * *
508511 AAAAGCATTGTTTTTG-A-AA-ACCA-GTGGAAATTCCGAGGTATTGAGATTCGCTCAAG
193 AAAAACATTATTTTTGAACAATAAAATGTGAAAATTCAGAGGTACTGAGATTCGCTCAAG
* * *
508567 TTTTTCGTTTTTTTCTTTCTCTGGTTATCAAGGACTTTGCGACGTGCATAAAAAACCCTATTTTT
1 TTTTTCGTTCTTTTCTTTCTCTGGTTATCAAGAACTTTGCGACGTGCATCAAAAACCCTATTTTT
* * * * * * * *
508632 TCGTTGAAATTGGTAGAAATTTGTGGAAAGTATTTAGCTGCGTCCAATCTTTTGATTGTTATTGG
66 CCATT-AAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTCGTTCAATCTTTTGATTGTTATTGG
* *
508697 AGTTAATTTTCATCGTTTTTGTTATATTCTTCCTGTGATAATCAAGAACCCGACAGCGTGCATCA
130 AGTTAATTTTC-TCGTTTTTGTTATATTCTTCCTGTGATAATCAACAACTCGACAGCGTGCATCA
* * * *
508762 AAAATATTATTTTTGAAACTAATTAAAATTTGTGAAAATTCAGAGGTGCTGAGCTTCGTTCAAG
194 AAAACATTATTTTTG-AAC-AA-TAAAA--TGTGAAAATTCAGAGGTACTGAGATTCGCTCAAG
* * * * * *
508826 CTTTTCATTCTTTTCTATCTCTGGTTATCAAGAAC-TTGATGATGTGCATCAAATACCCTATTTT
1 TTTTTCGTTCTTTTCTTTCTCTGGTTATCAAGAACTTTG-CGACGTGCATCAAAAACCCTATTTT
* * * *
508890 TCCTTTTAAAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTTGTTCAACCTTTTGATTGTTCTT
65 TCC-ATT-AAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTCGTTCAATCTTTTGATTGTTATT
* * *
508955 GGCA-TTAATTTTCTACGTTTTTATTCTATTCTT-CAGTGATAATCAACAACTCGACAGCGTGCA
128 GG-AGTTAATTTTCT-CGTTTTTGTTATATTCTTCCTGTGATAATCAACAACTCGACAGCGTGCA
*
509018 TTAAAAACA
191 TCAAAAACA
509027 CTCCTTTTTT
Statistics
Matches: 375, Mismatches: 67, Indels: 25
0.80 0.14 0.05
Matches are distributed among these distances:
248 6 0.02
249 153 0.41
250 14 0.04
251 1 0.00
252 1 0.00
254 2 0.01
256 2 0.01
258 3 0.01
259 115 0.31
260 77 0.21
261 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (252 bp):
TTTTTCGTTCTTTTCTTTCTCTGGTTATCAAGAACTTTGCGACGTGCATCAAAAACCCTATTTTT
CCATTAAATTAGTGGAAATTTGTGAAAAGTATTGAGCTTCGTTCAATCTTTTGATTGTTATTGGA
GTTAATTTTCTCGTTTTTGTTATATTCTTCCTGTGATAATCAACAACTCGACAGCGTGCATCAAA
AACATTATTTTTGAACAATAAAATGTGAAAATTCAGAGGTACTGAGATTCGCTCAAG
Found at i:510170 original size:24 final size:24
Alignment explanation
Indices: 510143--510203 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
510133 TGATGACATG
510143 ACATTATCTTAATGTGTCACGTTA
1 ACATTATCTTAATGTGTCACGTTA
510167 ACATTATCTTAATGTGTCACGTTA
1 ACATTATCTTAATGTGTCACGTTA
510191 ACATTATCGTTAA
1 ACATTATC-TTAA
510204 ATTTTTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 32 0.89
25 4 0.11
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (24 bp):
ACATTATCTTAATGTGTCACGTTA
Found at i:514035 original size:13 final size:14
Alignment explanation
Indices: 514002--514037 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
513992 ATTGCTTACA
514002 ACATAACACTTAAT
1 ACATAACACTTAAT
*
514016 GCATAACACTT-AT
1 ACATAACACTTAAT
514029 ACATAACAC
1 ACATAACAC
514038 CCTTCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (14 bp):
ACATAACACTTAAT
Found at i:520543 original size:131 final size:131
Alignment explanation
Indices: 520308--520545 Score: 386
Period size: 131 Copynumber: 1.8 Consensus size: 131
520298 ATAATTCTAA
* *
520308 GAGAGAAAACGATAATATCTAATTATTTTAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* * * *
520373 ACCATTTATTACTCCGATCGAAATGAATATATATCACTATTTCGTCTTAAAATTCAATATTGATT
66 ACCATTTATCACTCCAACCGAAATGAAAATATATCACTATTTCGTCTTAAAATTCAATATTGATT
520438 T
131 T
* *
520439 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACTTCTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* *
520504 ATCATTTATCACTCCAACCGAAATGAAAATATATTACTATTT
66 ACCATTTATCACTCCAACCGAAATGAAAATATATCACTATTT
520546 TCAATATTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 97 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
ACCATTTATCACTCCAACCGAAATGAAAATATATCACTATTTCGTCTTAAAATTCAATATTGATT
T
Found at i:521056 original size:18 final size:18
Alignment explanation
Indices: 521035--521069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
521025 CACTACCAAT
*
521035 ATATTTTATACATGTATA
1 ATATTTAATACATGTATA
*
521053 ATATTTAATGCATGTAT
1 ATATTTAATACATGTAT
521070 TATTCATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (18 bp):
ATATTTAATACATGTATA
Found at i:521839 original size:16 final size:16
Alignment explanation
Indices: 521773--521840 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
521763 AGATTTCCTC
* *
521773 TCTTCTTTTTCTTTTC
1 TCTTTTTTTTCTTTTT
*
521789 TCTATTTTTTGCTTTGGTT
1 TCT-TTTTTTTCTTT--TT
*
521808 T-TTTTTTTTCAATTTT
1 TCTTTTTTTTC-TTTTT
521824 TCTTTTTTTTCTTTTT
1 TCTTTTTTTTCTTTTT
521840 T
1 T
521841 TAAAACCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
16 11 0.27
17 25 0.61
18 3 0.07
19 2 0.05
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (16 bp):
TCTTTTTTTTCTTTTT
Found at i:522362 original size:3 final size:3
Alignment explanation
Indices: 522339--522409 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
522329 AAGAAATAAA
522339 AAC AA- AAC AA- AAC AA- AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
522384 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
522410 TAATAATAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 6 0.09
3 59 0.91
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:522414 original size:3 final size:3
Alignment explanation
Indices: 522408--522457 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
522398 CAACAACAAC
522408 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
522456 AA
1 AA
522458 CTCGGATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:523016 original size:42 final size:41
Alignment explanation
Indices: 522932--523025 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 41
522922 ATAGATGGCT
* *
522932 CGAAGGACTTATCATCTTGCTCGAAAAGCTTATATATAACC
1 CGAAGGACTTATCATCATGATCGAAAAGCTTATATATAACC
* *
522973 CGAAGGATTTAATCATCATGATC-AAAAGACTTAT-TGATGACC
1 CGAAGGACTT-ATCATCATGATCGAAAAG-CTTATAT-ATAACC
*
523015 CGAATGACTTA
1 CGAAGGACTTA
523026 CCAATTTTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGATCGAAAAGCTTATATATAACC
Found at i:523469 original size:41 final size:41
Alignment explanation
Indices: 523439--523528 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
523429 GGATGGCTCG
523439 AAGGACTTATCATCT-TACTCGAAAGGCTTATAGATGACCCA
1 AAGGACTTATCAT-TGTACTCGAAAGGCTTATAGATGACCCA
* * * * *
523480 AAGGATTTATCATTGTACTTGAAAGACTTACTA-ATGTCCTA
1 AAGGACTTATCATTGTACTCGAAAGGCTTA-TAGATGACCCA
523521 AAGGACTT
1 AAGGACTT
523529 CATAAGTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 1 0.02
41 38 0.93
42 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (41 bp):
AAGGACTTATCATTGTACTCGAAAGGCTTATAGATGACCCA
Found at i:523487 original size:251 final size:249
Alignment explanation
Indices: 522760--523511 Score: 871
Period size: 254 Copynumber: 3.0 Consensus size: 249
522750 AAGACTAATA
* * *
522760 GATGGCCCGAAGGACTTACTAATTTTGGAAATAGATTACTAGGTAAGAAAC-TTTGAAAATTGTT
1 GATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTG-AAATCGTT
*
522824 TTCTTACTTTTCAAAAATTTCAATTTTCAG-----ATGAGAAACTTTGGAAATCGTTTTCTCATT
65 TTCTTA-TTTTCAAAAATTTCAATTTTCAGATTAAATGAGAAACTTTGGAAATCATTTTCTCATT
* * * *
522884 TTTCGAAAACGTTTGAAAGCATCCTGCCCGAAGGTCTTATAGATGGCTCGAAGGACTTATCATCT
129 TTTC-AAAACATTTGAAAACAT-CTGCTC-AAGGTCTTATGGATGGCTCGAAGGACTTATCATCT
* * ** *
522949 TGCTCGAAAAGCTTATATATAACCCGAAGGATTTAATCATCATGATCAAAAGACTTATT
191 TGCTCGAAAGGCTTATATATAACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACT
* * *
523008 GATGACCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGTTT
1 GATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTGAAATCGTTT
523073 TCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTGGAAATCATTTTCTCATT
66 TCTTA-TTTTCAAAAATTTCAATTTTCAGA-TTAAATGAGAAACTTTGGAAATCATTTTCTCA-T
* ** * * *
523138 TTTTGAAAAACACGTGAAAA-ATTCTGCCTGAAGG-CTTTGTGGATGGC-CTGAAGGTCTTATCA
128 TTTT-CAAAACATTTGAAAACA-TCTG-CTCAAGGTC-TTATGGATGGCTC-GAAGGACTTATCA
* * * *
523200 TCTTGCTCGAAAGGCTTGTATATAATCCGGAGGATTTAATTATCATGCTTGAAAGACTTACT
188 TCTTGCTCGAAAGGCTTATATATAACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACT
** *
523262 GATGGCCCGAAGGACTTACCAATTCGGGAAATAGTTTACCAGGTAAGAAACTTTTGAAATCGTTT
1 GATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTGAAATCGTTT
* *
523327 TC-T-TTTTCAAAAATTTCAATTTTCAGATCTAAATGAGAAACTTTGGAAATAAATTTTCTCATG
66 TCTTATTTTCAAAAATTTCAATTTTCAGAT-TAAATGAGAAACTTTGGAAAT-CATTTTCTCATT
**** * *
523390 TTTCAATTTTTTTTAAAACATCATACTTCAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTT
129 TTTCAAAACATTTGAAAACATC-TGC-TCAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTT
* * * * ** *
523455 ACTCGAAAGGCTTATAGATGACCCAAAGGATTT-ATCATTGTACTTGAAAGACTTACT
192 GCTCGAAAGGCTTATATATAACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACT
523512 AATGTCCTAA
Statistics
Matches: 427, Mismatches: 57, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
248 84 0.20
249 3 0.01
250 31 0.07
251 108 0.25
252 11 0.03
253 3 0.01
254 170 0.40
255 17 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (249 bp):
GATGGCCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTGAAATCGTTT
TCTTATTTTCAAAAATTTCAATTTTCAGATTAAATGAGAAACTTTGGAAATCATTTTCTCATTTT
TCAAAACATTTGAAAACATCTGCTCAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTC
GAAAGGCTTATATATAACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACT
Found at i:528257 original size:14 final size:14
Alignment explanation
Indices: 528234--528291 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 14
528224 AAGATATAGC
*
528234 AAAAAAATAGAAAG
1 AAAAAGATAGAAAG
528248 AAAAAGATAG-AA-
1 AAAAAGATAGAAAG
528260 AAAAAG--AGAAAG
1 AAAAAGATAGAAAG
528272 AAAAAGATAGAAAAG
1 AAAAAGATAG-AAAG
528287 AAAAA
1 AAAAA
528292 AAAGGAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 12 0.32
13 2 0.05
14 11 0.29
15 9 0.24
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAAAGATAGAAAG
Found at i:528269 original size:24 final size:23
Alignment explanation
Indices: 528229--528383 Score: 130
Period size: 24 Copynumber: 6.8 Consensus size: 23
528219 AAGTAAAGAT
528229 ATAGCAAAAAAATAGAAAGAAAAAG
1 ATAG-AAAAAAA-AGAAAGAAAAAG
528254 ATAGAAAAAAAGAGAAAGAAAAAG
1 ATAGAAAAAAA-AGAAAGAAAAAG
* *
528278 ATAGAAAAGAAAAAAAAGGAAAA-
1 ATAGAAAA-AAAAGAAAGAAAAAG
*
528301 ATAGAAAAAAAAGAAA-AAACAG
1 ATAGAAAAAAAAGAAAGAAAAAG
*
528323 --A-AAAAAAAA-ATA-AAAAAG
1 ATAGAAAAAAAAGAAAGAAAAAG
* *
528341 AGAGAAAAAAAGGAAAAGAAAAAG
1 ATAGAAAAAAAAG-AAAGAAAAAG
528365 A-A-AAAAAGAGAAGAAAGAA
1 ATAGAAAAA-A-AAGAAAGAA
528384 GAAATAAAAT
Statistics
Matches: 109, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.06
19 8 0.07
20 2 0.02
21 10 0.09
22 12 0.11
23 18 0.17
24 45 0.41
25 7 0.06
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (23 bp):
ATAGAAAAAAAAGAAAGAAAAAG
Found at i:528271 original size:6 final size:6
Alignment explanation
Indices: 528244--528387 Score: 61
Period size: 6 Copynumber: 23.2 Consensus size: 6
528234 AAAAAAATAG
* *
528244 AAAGAA AAAGATA GAA-AA AAAGAG AAAGAA AAAGATAGA AAAGAA AAA-AA
1 AAAGAA AAAGA-A AAAGAA AAAGAA AAAGAA AAAG--A-A AAAGAA AAAGAA
* *
528294 AGGAA-AA ATAGAA AAA-AA AGAA-AA AACAGAA AAA-AA AAATAAA AAAGAGA
1 A--AAGAA AAAGAA AAAGAA A-AAGAA AA-AGAA AAAGAA AAA-GAA AAAGA-A
* *
528344 GAA-AA AAAGGA AAAGAA AAAGAA AAA-AA GAGAAGAA AGAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -A-AAGAA A-AAGAA A
528388 TAAAATCGAT
Statistics
Matches: 109, Mismatches: 11, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
5 21 0.19
6 49 0.45
7 31 0.28
8 3 0.03
9 5 0.05
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:528318 original size:18 final size:18
Alignment explanation
Indices: 528259--528392 Score: 99
Period size: 19 Copynumber: 6.9 Consensus size: 18
528249 AAAAGATAGA
528259 AAAAAAGAGAAAGAAAAAG
1 AAAAAAGAGAAA-AAAAAG
*
528278 ATAGAAA-AGAAAAAAAAG
1 A-AAAAAGAGAAAAAAAAG
* *
528296 GAAAAATAGAAAAAAAAG
1 AAAAAAGAGAAAAAAAAG
* *
528314 AAAAAACAGAAAAAAAAAAT
1 -AAAAA-AGAGAAAAAAAAG
528334 AAAAAAGAGAGAAAAAAAGG
1 AAAAAAGAGA-AAAAAAA-G
*
528354 AAAAGAAAAAGAAAAAAAGAG
1 -AAA-AAAGAGAAAAAAA-AG
*
528375 AAGAAAGAAGAAATAAAA
1 AAAAAAG-AGAAA-AAAA
528393 TCGATCAAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
17 4 0.04
18 21 0.23
19 25 0.27
20 21 0.23
21 14 0.15
22 7 0.08
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:528326 original size:8 final size:9
Alignment explanation
Indices: 528244--528392 Score: 118
Period size: 9 Copynumber: 15.2 Consensus size: 9
528234 AAAAAAATAG
528244 AAAGAAAAA
1 AAAGAAAAA
*
528253 GATAGAAAAA
1 -AAAGAAAAA
528263 AAGAGAAAGAA
1 AA-AGAAA-AA
* *
528274 AAAGATAGA
1 AAAGAAAAA
528283 AAAGAAAAA
1 AAAGAAAAA
*
528292 AAAGGAAAA
1 AAAGAAAAA
*
528301 ATAGAAAAA
1 AAAGAAAAA
528310 AAAGAAAAA
1 AAAGAAAAA
*
528319 ACAGAAAAA
1 AAAGAAAAA
*
528328 AAAAATAAAA
1 AAAGA-AAAA
528338 AAGAGAGAAAA
1 AA-AGA-AAAA
528349 AAAGGAAAAGAA
1 AAA-G-AAA-AA
528361 AAAGAAAAA
1 AAAGAAAAA
528370 AAGAGAAGAAA
1 AA-AGAA-AAA
*
528381 GAAGAAATAA
1 AAAGAAA-AA
528391 AA
1 AA
528393 TCGATCAAAT
Statistics
Matches: 112, Mismatches: 17, Indels: 20
0.75 0.11 0.13
Matches are distributed among these distances:
9 48 0.43
10 38 0.34
11 20 0.18
12 6 0.05
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:528385 original size:20 final size:21
Alignment explanation
Indices: 528246--528392 Score: 92
Period size: 20 Copynumber: 7.0 Consensus size: 21
528236 AAAAATAGAA
528246 AGAA-AAAGATAGAAAAAAAG
1 AGAAGAAAGATAGAAAAAAAG
*
528266 AGAAAGAAAAAGATAGAAAAGAAAA
1 AG-AAG--AAAGATAGAAAA-AAAG
* *
528291 AAAAGGAAAAATAGAAAAAAA-
1 AGAA-GAAAGATAGAAAAAAAG
* *
528312 AGAA-AAA-ACAGAAAAAAAAA
1 AGAAGAAAGATAG-AAAAAAAG
* * *
528332 ATAAAAAAGAGAGAAAAAAAGG
1 AGAAGAAAGATAGAAAAAAA-G
*
528354 AAAAGAAA-A-AGAAAAAAAG
1 AGAAGAAAGATAGAAAAAAAG
528373 AGAAGAAAGA-AGAAATAAAA
1 AGAAGAAAGATAGAAA-AAAA
528393 TCGATCAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
18 3 0.03
19 18 0.17
20 20 0.19
21 20 0.19
22 12 0.12
23 11 0.11
24 14 0.14
25 5 0.05
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (21 bp):
AGAAGAAAGATAGAAAAAAAG
Found at i:529058 original size:28 final size:28
Alignment explanation
Indices: 528998--529059 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
528988 CGCAAGAAGC
528998 CAACCTGAAACACATTACCTGCCCAAAT
1 CAACCTGAAACACATTACCTGCCCAAAT
* * *
529026 TAACCTGAAACACATTACCTTCCCAAGT
1 CAACCTGAAACACATTACCTGCCCAAAT
529054 CAACCT
1 CAACCT
529060 AAGCTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.35, G:0.06, T:0.21
Consensus pattern (28 bp):
CAACCTGAAACACATTACCTGCCCAAAT
Found at i:530916 original size:20 final size:20
Alignment explanation
Indices: 530891--530951 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
530881 TTTCTTGATG
530891 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
530911 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
530930 ATGCTTAAGTCCTTCGGGCCAT
1 A-G--TAAGTCCTTCGGGCCAT
530952 TTATAAGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.12
20 14 0.44
22 11 0.34
23 3 0.09
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:530925 original size:263 final size:261
Alignment explanation
Indices: 530279--531321 Score: 1477
Period size: 263 Copynumber: 4.0 Consensus size: 261
530269 AATCATTACT
* **
530279 TTGACGTGGGGGCATATTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAG
1 TTGATGTGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAG
* * * * *
530344 CTTTATTTTTAAGGTTTTATTGATGAGTAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGTATGA
66 CTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
530409 TGCTTAAGTCATTCAGGCCATTTATAAGTCTTTTGAGCAAGATGATAAGTCCTTCGGGCTATCCA
131 TGCTTAAGTCATTCAGGCCATTTATAAGTCTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCA
* * *
530474 TAAG--ATCTTCGGCAAGATGTTTTCAACATTTATGGTACTCGATTCATCACATATGGAGTTAAA
196 TAAGACAT-TTGGGCAAGATGTTTTCAACATTTCTGGTACTCGATTCATCACATATGGAGTTGAA
530537 TC
260 TC
*
530539 TTGATGT-GGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAATTAAG
1 TTGATGTGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAG
* * *
530603 CTTGATTTTCAAGGTTTTCTTGATGAGTAAATCCTTCGGGCCATCAGTAAGTATTTCGAGCATGA
66 CTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGA
* * *
530668 TGCTTAAGTCATTCAGGCCATTTATAAATCTTTCGAGCGAGATGATAAGACCTTCAGGCCATCCA
131 TGCTTAAGTCATTCAGGCCATTTATAAGTCTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCA
* * * *
530733 TAAGACCTTTGGGTAGGATGTTTTCAACATTTCTGGTACTTGATTCATCACATATGGAGTTGAAT
196 TAAGACATTTGGGCAAGATGTTTTCAACATTTCTGGTACTCGATTCATCACATATGGAGTTGAAT
530798 C
261 C
* *
530799 TTGATGTGGGGGCACGTTACCCAAACAACATGAAATTTTCAAAAGAATTTTTTAATAACAAACTA
1 TTGATGTGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAA-TTTTT-ATAAGAAACTA
* *
530864 AACTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
64 AGCTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
530929 GATGCTTAAGTCCTTCGGGCCATTTATAAGTTTTTCGAGCAAGATGATAAGACCTTTGGGCCATC
129 GATGCTTAAGTCATTCAGGCCATTTATAAGTCTTTCGAGCAAGATGATAAGACCTTCGGGCCATC
*
530994 CATAAGACATTTGGGCAAAATGTTTTCAACATTT-TCGGTACTCGATTCATCACATATGGAGTTG
194 CATAAGACATTTGGGCAAGATGTTTTCAACATTTCT-GGTACTCGATTCATCACATATGGAGTTG
531058 AATC
258 AATC
* * * * *
531062 TCGATGTGGGGGAACGTTACCCAAACAACTTGATATTTTTAAAATAATTTTTATAAGAAACTAAG
1 TTGATGTGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAG
* * * * *
531127 CTTGATTTTTAAGGTTTTCTTGACGAGTAAGTCTTTCAGGCCATCTGTAAATCTTTCGAGCATGA
66 CTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGA
* * * * *
531192 TGCTTAACTCCTAC-GAGCCATTTATAAGTATTTCGAGCAAGATGATAAGACATTCGGGCCATCC
131 TGCTTAAGTCATTCAG-GCCATTTATAAGTCTTTCGAGCAAGATGATAAGACCTTCGGGCCATCC
*** ** ** *
531256 ATAAGACA-TTCATCTTGGATGTTTTCAACATTTCTAATACTCGATTTATCACATATGGAGTTGA
195 ATAAGACATTTGGGC-AAGATGTTTTCAACATTTCTGGTACTCGATTCATCACATATGGAGTTGA
531320 AT
259 AT
531322 TAGAAATACC
Statistics
Matches: 703, Mismatches: 71, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
259 174 0.25
260 69 0.10
261 217 0.31
262 12 0.02
263 231 0.33
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (261 bp):
TTGATGTGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAG
CTTGATTTTCAAGGTTTTCTTGATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAGTCATTCAGGCCATTTATAAGTCTTTCGAGCAAGATGATAAGACCTTCGGGCCATCCA
TAAGACATTTGGGCAAGATGTTTTCAACATTTCTGGTACTCGATTCATCACATATGGAGTTGAAT
C
Found at i:530945 original size:42 final size:40
Alignment explanation
Indices: 530887--530999 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 40
530877 AGGTTTTCTT
*
530887 GATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCAA
* * *
530929 GATGCTTAAGTCCTTCGGGCCATTTATAAGTTTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCA-TCATAAGTCTTTCGAGCAA
* *
530971 GATGATAAGACCTTTGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCAT-CATAAG
531000 ACATTTGGGC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 19 0.32
42 38 0.63
43 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
GATGATAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCAA
Found at i:532142 original size:2 final size:2
Alignment explanation
Indices: 532135--532163 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
532125 AAACAAGCAA
532135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
532164 CACATTAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:538233 original size:18 final size:18
Alignment explanation
Indices: 538197--538232 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
538187 GTAAATAAAT
*
538197 TAATAAGCTAATGCAAAA
1 TAATAAGCAAATGCAAAA
538215 TAATAATGCAAATGCAAA
1 TAATAA-GCAAATGCAAA
538233 TGCAAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
TAATAAGCAAATGCAAAA
Found at i:539742 original size:14 final size:15
Alignment explanation
Indices: 539717--539747 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
539707 TTAAAAAAAG
539717 AAAAATTCGATTTTT
1 AAAAATTCGATTTTT
539732 AAAAATT-GATTTTT
1 AAAAATTCGATTTTT
539746 AA
1 AA
539748 GAGACCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (15 bp):
AAAAATTCGATTTTT
Found at i:542224 original size:21 final size:20
Alignment explanation
Indices: 542193--542234 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
542183 AAAGGCCTAT
*
542193 AAAAGAAATAAATCAAAATA
1 AAAAGAAATAAAACAAAATA
542213 AAAAGAAAATAAAACAAAATA
1 AAAAG-AAATAAAACAAAATA
542234 A
1 A
542235 TAATAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAGAAATAAAACAAAATA
Found at i:542911 original size:21 final size:21
Alignment explanation
Indices: 542862--542935 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
542852 CTTTTGATAT
*
542862 TAGAGAGTATGGATACTCAAC
1 TAGAGAGTATGGATACTCAAA
* *
542883 TAGGGAGTGTGGATACTCAAA
1 TAGAGAGTATGGATACTCAAA
* **
542904 TTGAGAGTATAAATACTCAAA
1 TAGAGAGTATGGATACTCAAA
* *
542925 CAAAGAGTATG
1 TAGAGAGTATG
542936 AAGACTTTGG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (21 bp):
TAGAGAGTATGGATACTCAAA
Found at i:543110 original size:17 final size:18
Alignment explanation
Indices: 543088--543132 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
543078 ATATATACGT
543088 TATTATATATAT-AATAA
1 TATTATATATATAAATAA
*
543105 TATTATAT-TATAAATAT
1 TATTATATATATAAATAA
*
543122 TATTATTTATA
1 TATTATATATA
543133 AAAACTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 19 0.79
18 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATATATATAAATAA
Found at i:550660 original size:15 final size:15
Alignment explanation
Indices: 550640--550672 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
550630 CAAAGTTGAT
550640 AGATTCTCTTTTCAA
1 AGATTCTCTTTTCAA
*
550655 AGATTCTTTTTTCAA
1 AGATTCTCTTTTCAA
550670 AGA
1 AGA
550673 CGAAAGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (15 bp):
AGATTCTCTTTTCAA
Found at i:551674 original size:40 final size:41
Alignment explanation
Indices: 551618--551720 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 41
551608 GTATGAAAGC
* * *
551618 CTTCACAGAGGAGTAGTGAAGCAATCCAA-TC-ATTCTCAGT
1 CTTCACGGAAGAGTAGTGAAGCAATCCAACTCGAGTCTCA-T
* * * *
551658 TTTCACGGAAGAGTAGTGAAGTAATCTAATCTCGAGTCTGAT
1 CTTCACGGAAGAGTAGTGAAGCAATCCAA-CTCGAGTCTCAT
551700 CTTCACGGAAGAGTAGTGAAG
1 CTTCACGGAAGAGTAGTGAAG
551721 TGGATTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
40 24 0.46
42 23 0.44
43 5 0.10
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTCACGGAAGAGTAGTGAAGCAATCCAACTCGAGTCTCAT
Found at i:553258 original size:30 final size:29
Alignment explanation
Indices: 553202--553258 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
553192 GGTAGAATTA
* *
553202 TATATTTAGTCCCTTAAATATTTTTAGTT
1 TATATTTAGTCCCATAAATATATTTAGTT
553231 TATATTTCAGTCCCATATAATA-ATTTAG
1 TATATTT-AGTCCCATA-AATATATTTAG
553259 GGTAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 13 0.54
31 4 0.17
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (29 bp):
TATATTTAGTCCCATAAATATATTTAGTT
Found at i:553366 original size:24 final size:23
Alignment explanation
Indices: 553339--553389 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
553329 GTTTTAAATA
* *
553339 ATTATTATTATTATATGATTAATT
1 ATTATTAGTATTATAGGATT-ATT
*
553363 ATTATTAGTATTTTAGGATTATT
1 ATTATTAGTATTATAGGATTATT
553386 ATTA
1 ATTA
553390 CACAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (23 bp):
ATTATTAGTATTATAGGATTATT
Found at i:553865 original size:20 final size:21
Alignment explanation
Indices: 553840--553885 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
553830 ACCCAACTTT
*
553840 AATATCGATACTAGATGAA-C
1 AATATCGATACTACATGAATC
553860 AATATCGATACTACATGAATC
1 AATATCGATACTACATGAATC
553881 AATAT
1 AATAT
553886 AAATTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (21 bp):
AATATCGATACTACATGAATC
Found at i:554371 original size:120 final size:120
Alignment explanation
Indices: 554075--554625 Score: 444
Period size: 123 Copynumber: 4.5 Consensus size: 120
554065 TTTTTTGTTG
** ** * * * * ** * *
554075 TTTTTTAAACAAACGTCGCAATAGACCAGTGCATTAGTGACATTTTAAAATGTAAATGCCATAAA
1 TTTTTTAAACAAACACCGCAATAGATTAGTGCATTAATGGCGTTTTTAAATACAAACGCCACAAA
* * * ***
554140 ATGATAACATTAGCGATGTTTTTCTAGAAACGCCGCTATAGCCTCGTCGTTTGTGGTA
66 ATGGTAACATTAGCGACGTTTTTCTAGAAAC-CCGCTATAGCCTC-T-GTTTATAACA
* * * *
554198 TTTTTTAAATAAACATCGCAATTA-ATTAGTGCATTAATGGCGTGTTTAAATACAAACGCCACTA
1 TTTTTTAAACAAACACCGCAA-TAGATTAGTGCATTAATGGCGTTTTTAAATACAAACGCCACAA
* *
554262 AATGGTAACATTAGTGACGTTTTTCTAGAAACATCGCTATAGCCT-TGTTTATAACA
65 AATGGTAACATTAGCGACGTTTTTCTAGAAAC-CCGCTATAGCCTCTGTTTATAACA
* *
554318 TTTTTTAAACAAACACCACAATAGATTAGTGCATTAATAGCGTTTTTAAATACAAACGCCACAAA
1 TTTTTTAAACAAACACCGCAATAGATTAGTGCATTAATGGCGTTTTTAAATACAAACGCCACAAA
* * ** * * **
554383 ATGGTAACATTAGCAACATTTTTCTAGAAACGCTACTATAGCCTCATCTTTTTTTCA
66 ATGGTAACATTAGCGACGTTTTTCTAGAAAC-CCGCTATAGCCTC-TGTTTATAACA
* * *
554440 TTTTTTAAACAAACGCCGTAATAGATCT-GTGCATTGATGGCGTTTTTAAATACAAACGCCACAA
1 TTTTTTAAACAAACACCGCAATAGAT-TAGTGCATTAATGGCGTTTTTAAATACAAACGCCACAA
* * * * * * * * * **
554504 AAAGGATAACATTAGTGGCATTTTCCCAGTAACACCGCTATATACTCATCT-TTTGTGGCA
65 AATGG-TAACATTAGCGACGTTTTTCTAGAAAC-CCGCTATA-GC-C-TCTGTTTATAACA
* * * * * * *
554564 TTGTTTTTAAAGAAACACCACAATAGGTCAGTGCATTAGTGGTGTTTTTAAATATAAACGCC
1 -T-TTTTTAAACAAACACCGCAATAGATTAGTGCATTAATGGCGTTTTTAAATACAAACGCC
554626 GCAATATGTC
Statistics
Matches: 347, Mismatches: 69, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
119 2 0.01
120 99 0.29
121 1 0.00
122 68 0.20
123 115 0.33
124 9 0.03
125 3 0.01
126 50 0.14
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (120 bp):
TTTTTTAAACAAACACCGCAATAGATTAGTGCATTAATGGCGTTTTTAAATACAAACGCCACAAA
ATGGTAACATTAGCGACGTTTTTCTAGAAACCCGCTATAGCCTCTGTTTATAACA
Found at i:554545 original size:243 final size:248
Alignment explanation
Indices: 554076--554625 Score: 564
Period size: 243 Copynumber: 2.2 Consensus size: 248
554066 TTTTTGTTGT
** * * * * * ** * *
554076 TTTTTAAACAAACGTCGCAATAGACCAGTGCATTAGT-GACATTTTAAAATGTAAATGCCATAAA
1 TTTTTAAACAAACACCACAATAGATCAGTGCATTAATAG-CGTTTTTAAATACAAACGCCACAAA
* ** * *
554140 ATGATAACATTAGCGATGTTTTTCTAGAAACGCCGCTATAGCCTCGTCGTTTGTGGTATTTTTTA
65 ATGATAACATTAGCAACATTTTTCTAGAAACGCCACTATAGCCTCATCGTTTGTGGTATTTTTTA
* * * *
554205 AATAAACATCGCAATTAATTAGTGCATTAATGGCGTGTTTAAATACAAACGCCACTAAATGGTAA
130 AACAAACACCGCAATTAATTAGTGCATTAATGGCGTGTTTAAATACAAACGCCACAAAAAGGTAA
* * * * *
554270 CATTAGTGACGTTTTTCTAGAAACATCGCTATA-GC-C-T-TGTTTATAACA-T-
195 CATTAGTGACATTTTCCCAGAAACACCGCTATATACTCATCT-TTTATAACATTG
*
554319 TTTTTAAACAAACACCACAATAGATTAGTGCATTAATAGCGTTTTTAAATACAAACGCCACAAAA
1 TTTTTAAACAAACACCACAATAGATCAGTGCATTAATAGCGTTTTTAAATACAAACGCCACAAAA
* * **
554384 TGGTAACATTAGCAACATTTTTCTAGAAACGCTACTATAGCCTCATC-TTT-TTTTCATTTTTTA
66 TGATAACATTAGCAACATTTTTCTAGAAACGCCACTATAGCCTCATCGTTTGTGGT-ATTTTTTA
* * * *
554447 AACAAACGCCGTAA-TAGATCT-GTGCATTGATGGCGTTTTTAAATACAAACGCCACAAAAAGGA
130 AACAAACACCGCAATTA-AT-TAGTGCATTAATGGCGTGTTTAAATACAAACGCCACAAAAAGG-
* * * **
554510 TAACATTAGTGGCATTTTCCCAGTAACACCGCTATATACTCATCTTTTGTGGCATTG
192 TAACATTAGTGACATTTTCCCAGAAACACCGCTATATACTCATCTTTTATAACATTG
* * * * * *
554567 TTTTTAAAGAAACACCACAATAGGTCAGTGCATTAGTGGTGTTTTTAAATATAAACGCC
1 TTTTTAAACAAACACCACAATAGATCAGTGCATTAATAGCGTTTTTAAATACAAACGCC
554626 GCAATATGTC
Statistics
Matches: 250, Mismatches: 46, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
241 4 0.02
242 60 0.24
243 122 0.49
244 2 0.01
245 1 0.00
246 7 0.03
247 2 0.01
248 52 0.21
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (248 bp):
TTTTTAAACAAACACCACAATAGATCAGTGCATTAATAGCGTTTTTAAATACAAACGCCACAAAA
TGATAACATTAGCAACATTTTTCTAGAAACGCCACTATAGCCTCATCGTTTGTGGTATTTTTTAA
ACAAACACCGCAATTAATTAGTGCATTAATGGCGTGTTTAAATACAAACGCCACAAAAAGGTAAC
ATTAGTGACATTTTCCCAGAAACACCGCTATATACTCATCTTTTATAACATTG
Found at i:554611 original size:41 final size:41
Alignment explanation
Indices: 554565--554658 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 41
554555 TTTGTGGCAT
*
554565 TGTTTTTAAAGAAACACCACAATAGGTCAGTGCATTAGTGG
1 TGTTTTTAAAGAAACACCACAATAGGTCAGTACATTAGTGG
* * * * *
554606 TGTTTTTAAATATAAACGCCGCAATATGTCAGTATATTAGTGG
1 TGTTTTT-AA-AGAAACACCACAATAGGTCAGTACATTAGTGG
554649 TGTTTTTAAA
1 TGTTTTTAAA
554659 TACAAACGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 8 0.18
42 4 0.09
43 33 0.73
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (41 bp):
TGTTTTTAAAGAAACACCACAATAGGTCAGTACATTAGTGG
Found at i:554613 original size:126 final size:121
Alignment explanation
Indices: 554010--554625 Score: 391
Period size: 123 Copynumber: 5.0 Consensus size: 121
554000 ATCTCGAAAA
* *** * * ** ***
554010 CCACAAAATGGTAACATTAGCAGTGTTTTTCTAGAAACGCTGTTATAACCTCATCTTTTTTGTTG
1 CCACAAAAAGGTAACATTAGCAACATTTTCCCAGAAACGCTACTAT-ACCTCATC-TTTTTGGCA
** * * * * * ** *
554075 TTTTTTAAACAAACGTCGCAATAGACCAGTGCATTAGTGACATTTTAAAATGTAAATG
64 TTTTTTAAACAAACACCACAATAGATCAGTGCATTAGTGGCGTTTTTAAATACAAACG
* * * * ** * * ** * * *
554133 CCATAAAATGATAACATTAGCGATGTTTTTCTAGAAACGCCGCTATAGCCTCGTCGTTTGTGGTA
1 CCACAAAAAGGTAACATTAGCAACATTTTCCCAGAAACGCTACTATA-CCTCATC-TTTTTGGCA
* * * * * *
554198 TTTTTTAAATAAACATCGCAATTA-ATTAGTGCATTAATGGCGTGTTTAAATACAAACG
64 TTTTTTAAACAAACACCACAA-TAGATCAGTGCATTAGTGGCGTTTTTAAATACAAACG
* * ** * * * * * * * **
554256 CCACTAAATGGTAACATTAGTGACGTTTTTCTAGAAAC-ATCGCTATAGCCT--TGTTTATAACA
1 CCACAAAAAGGTAACATTAGCAACATTTTCCCAGAAACGCT-ACTATA-CCTCATCTTTTTGGCA
* * *
554318 TTTTTTAAACAAACACCACAATAGATTAGTGCATTAATAGCGTTTTTAAATACAAACG
64 TTTTTTAAACAAACACCACAATAGATCAGTGCATTAGTGGCGTTTTTAAATACAAACG
* * * **
554376 CCACAAAATGGTAACATTAGCAACATTTTTCTAGAAACGCTACTATAGCCTCATCTTTTTTTCAT
1 CCACAAAAAGGTAACATTAGCAACATTTTCCCAGAAACGCTACTATA-CCTCATCTTTTTGGCAT
* ** *
554441 TTTTTAAACAAACGCCGTAATAGATCTGTGCATT-GATGGCGTTTTTAAATACAAACG
65 TTTTTAAACAAACACCACAATAGATCAGTGCATTAG-TGGCGTTTTTAAATACAAACG
***
554498 CCACAAAAAGGATAACATTAGTGGCATTTTCCCAGTAACACCGCTA-TATA-CTCATCTTTTGTG
1 CCACAAAAAGG-TAACATTAGCAACATTTTCCCAG-AA-A-CGCTACTATACCTCATCTTTT-TG
* * * *
554561 GCATTGTTTTTAAAGAAACACCACAATAGGTCAGTGCATTAGTGGTGTTTTTAAATATAAACG
61 GCA-T-TTTTTAAACAAACACCACAATAGATCAGTGCATTAGTGGCGTTTTTAAATACAAACG
554624 CC
1 CC
554626 GCAATATGTC
Statistics
Matches: 404, Mismatches: 73, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
119 2 0.00
120 98 0.24
121 2 0.00
122 68 0.17
123 166 0.41
124 7 0.02
125 6 0.01
126 54 0.13
127 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (121 bp):
CCACAAAAAGGTAACATTAGCAACATTTTCCCAGAAACGCTACTATACCTCATCTTTTTGGCATT
TTTTAAACAAACACCACAATAGATCAGTGCATTAGTGGCGTTTTTAAATACAAACG
Found at i:554637 original size:43 final size:43
Alignment explanation
Indices: 554584--554672 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
554574 AGAAACACCA
* *
554584 CAATAGGTCAGTGCATTAGTGGTGTTTTTAAATATAAACGCCG
1 CAATAGGTCAGTACATTAGTGGTGTTTTTAAATACAAACGCCG
* *
554627 CAATATGTCAGTATATTAGTGGTGTTTTTAAATACAAACGCCG
1 CAATAGGTCAGTACATTAGTGGTGTTTTTAAATACAAACGCCG
554670 CAA
1 CAA
554673 ATTTTAAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (43 bp):
CAATAGGTCAGTACATTAGTGGTGTTTTTAAATACAAACGCCG
Found at i:558141 original size:2 final size:2
Alignment explanation
Indices: 558134--558178 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
558124 TATGTTTGTT
558134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558176 TA T
1 TA T
558179 TGTACACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560523 original size:12 final size:13
Alignment explanation
Indices: 560506--560543 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
560496 CATCCCGACT
560506 TTATTATTATT-A
1 TTATTATTATTAA
560518 TTATTATTATTAA
1 TTATTATTATTAA
560531 TTAATTAATTATT
1 TT-ATT-ATTATT
560544 GCAGGCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.48
13 3 0.13
14 3 0.13
15 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:562612 original size:27 final size:27
Alignment explanation
Indices: 562531--562612 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
562521 GTCGATACGA
*
562531 TCGTTCATAAACTTATTATGAATTCTG
1 TCGTTCATAAACTTATTATGAATTCAG
* * * * * *
562558 TGGGTT-ACACACTTAGTGTCG-ATACAG
1 T-CGTTCATAAACTTATTAT-GAATTCAG
562585 TCGTTCATAAACTTATTATGAATTCAG
1 TCGTTCATAAACTTATTATGAATTCAG
562612 T
1 T
562613 GGGTTGCACA
Statistics
Matches: 38, Mismatches: 13, Indels: 8
0.64 0.22 0.14
Matches are distributed among these distances:
26 4 0.11
27 30 0.79
28 4 0.11
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (27 bp):
TCGTTCATAAACTTATTATGAATTCAG
Found at i:562907 original size:54 final size:54
Alignment explanation
Indices: 562504--562899 Score: 578
Period size: 54 Copynumber: 7.3 Consensus size: 54
562494 TTGAATTTCA
* * *
562504 TGGGTTACACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
* * * *
562558 TGGGTTACACACTTAGTGTCGATACAGTCGTTCATAAACTTATTATGAATTCAG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
* * * *
562612 TGGGTTGCACACTTAGTACCGATACGATCCTTCATAAACTTATTATAAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
*
562666 TGGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
* * * * *
562720 CGAGTTGAACACTTAGTGCCGATAAGGTCGTTCATAAACTTATTATGAATTATG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
* *
562774 TGGGTTGCACACTTAGCGTCGATAC-GTCCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGT-CGTTCATAAACTTATTATGAATTCTG
* * *
562828 TGGGTTGCACATTTAGTGCCGATACGGTCGTTCAAAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
562882 TGGGTTGCACACTTAGTG
1 TGGGTTGCACACTTAGTG
562900 TTGATACGTT
Statistics
Matches: 306, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.01
54 302 0.99
55 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTG
Found at i:564174 original size:22 final size:21
Alignment explanation
Indices: 564123--564179 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
564113 TACCAATCCA
*
564123 TTTTTGGT-ATATTGGATTGG
1 TTTTTGGTGATATTAGATTGG
564143 TTTATTGGTGATATTAGATTGAG
1 TTT-TTGGTGATATTAGATTG-G
* *
564166 TTTTAGGTGTTATT
1 TTTTTGGTGATATT
564180 GAGTTCATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 5 0.16
22 19 0.61
23 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.54
Consensus pattern (21 bp):
TTTTTGGTGATATTAGATTGG
Found at i:564397 original size:22 final size:23
Alignment explanation
Indices: 564342--564400 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
564332 ACCCGACTGA
564342 ACTGTTGACTTTGATCAGAGTTG
1 ACTGTTGACTTTGATCAGAGTTG
* * *
564365 ACCGTTTACTTTGAT-TG-GTATG
1 ACTGTTGACTTTGATCAGAGT-TG
564387 ACTGTTGACTTTGA
1 ACTGTTGACTTTGA
564401 CCAAAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (23 bp):
ACTGTTGACTTTGATCAGAGTTG
Found at i:565813 original size:90 final size:90
Alignment explanation
Indices: 565660--565839 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
565650 GACCTAACAC
* *
565660 ATCCTTTTATATTCGAGTTACCCTAATCACATTAGGGATTTTATTATTTCAAATTAATTAAATCT
1 ATCCTTTTATATCCAAGTTACCCTAATCACATTAGGGATTTTATTATTTCAAATTAATTAAATCT
*
565725 ATATTTAATTAATTGGAATTTAATA
66 ATATTTAATTAATTGGAATTAAATA
*
565750 ATCCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCT
1 ATCCTTTTATATCCAAGTTACCCTAATCACATTAGGGATTTTATTATTTCAAATTAATTAAATCT
565815 ATATTTAATTAATTGGAATTAAATA
66 ATATTTAATTAATTGGAATTAAATA
565840 TTCAGGATTA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (90 bp):
ATCCTTTTATATCCAAGTTACCCTAATCACATTAGGGATTTTATTATTTCAAATTAATTAAATCT
ATATTTAATTAATTGGAATTAAATA
Found at i:579369 original size:22 final size:21
Alignment explanation
Indices: 579319--579369 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
579309 ACCAATCAGG
* *
579319 TTTTGGT-ATATTGGATTGGT
1 TTTTGGTGATATTAGATTGAT
579339 TTATTGGTGATATTAGATTGAT
1 TT-TTGGTGATATTAGATTGAT
579361 TTTTAGGTG
1 TTTT-GGTG
579370 TAATTGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 7 0.27
22 17 0.65
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (21 bp):
TTTTGGTGATATTAGATTGAT
Found at i:581516 original size:29 final size:29
Alignment explanation
Indices: 581471--581536 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
581461 GATACCACAT
* *
581471 TAGAAAAGTTGAGTGTCTATCACGTTAGC
1 TAGAAAAGCTGAATGTCTATCACGTTAGC
581500 TAGAAAAGCTGAATGTCTATCACGTTAGC
1 TAGAAAAGCTGAATGTCTATCACGTTAGC
581529 TAGAAAAG
1 TAGAAAAG
581537 TTATACACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (29 bp):
TAGAAAAGCTGAATGTCTATCACGTTAGC
Found at i:583936 original size:54 final size:54
Alignment explanation
Indices: 583853--584149 Score: 443
Period size: 54 Copynumber: 5.5 Consensus size: 54
583843 TTTCAATTTC
* * * *
583853 ATGGGTTGCACACTTAGTGCCGATACGGTCGTTTATAAACATATTATTAATTCT
1 ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
* * * * * *
583907 ATGGGTTGCACACTTAGTTTTGATTCGGTCATTCAAAAACTTATTATGAATTCC
1 ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
* * *
583961 GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCC
1 ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
584015 ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-T
1 ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
*
584068 CGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
1 -ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
*
584123 GTGGGTTGCACACTTAGTGTCGATACG
1 ATGGGTTGCACACTTAGTGTCGATACG
584150 TGAAAATACA
Statistics
Matches: 220, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
54 219 1.00
55 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (54 bp):
ATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCT
Found at i:587969 original size:13 final size:13
Alignment explanation
Indices: 587951--587989 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
587941 GTCATAAATC
*
587951 TATGACACGCATT
1 TATGACGCGCATT
*
587964 TATGACGTGCATT
1 TATGACGCGCATT
587977 TATGACGCGCATT
1 TATGACGCGCATT
587990 GTGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:588046 original size:98 final size:98
Alignment explanation
Indices: 587924--588139 Score: 236
Period size: 98 Copynumber: 2.2 Consensus size: 98
587914 TAAATCTCAT
* * * * * *
587924 ATGACACGCAATTGTGTGTCATAAATCTATGACACGCATTTATGACGTGCATTTATGACGCGCAT
1 ATGACACACATTTGTGTGTCATAAATCTATGACACGCATTTACGACGTACATTTACGACGCACAT
* * * * *
587989 TGTGCGTCATTGAAGCCCCCATCA-TAAATGAAG
66 TGCGCGTAATTGAAGCACACATCATTAAA-AAAG
* * * * **
588022 ATGACACACATTTGTGTGTTATAAATTTATGACATGCATTTACGACTTACATTTACGACTTACAT
1 ATGACACACATTTGTGTGTCATAAATCTATGACACGCATTTACGACGTACATTTACGACGCACAT
* *
588087 TGCGTGTAATTGAAGTACACATCATTAAAAAAG
66 TGCGCGTAATTGAAGCACACATCATTAAAAAAG
*
588120 ATGACACACATTTGTATGTC
1 ATGACACACATTTGTGTGTC
588140 GTGCTTGTAT
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
98 92 0.96
99 4 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (98 bp):
ATGACACACATTTGTGTGTCATAAATCTATGACACGCATTTACGACGTACATTTACGACGCACAT
TGCGCGTAATTGAAGCACACATCATTAAAAAAG
Found at i:588074 original size:13 final size:13
Alignment explanation
Indices: 588058--588087 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
588048 TTATGACATG
588058 CATTTACGACTTA
1 CATTTACGACTTA
588071 CATTTACGACTTA
1 CATTTACGACTTA
588084 CATT
1 CATT
588088 GCGTGTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:589219 original size:12 final size:12
Alignment explanation
Indices: 589202--589232 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
589192 ATATATTGAT
589202 AATCAAATGAAA
1 AATCAAATGAAA
589214 AATCAAATGAAA
1 AATCAAATGAAA
*
589226 AAACAAA
1 AATCAAA
589233 CCCGAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:589767 original size:39 final size:40
Alignment explanation
Indices: 589722--589838 Score: 110
Period size: 48 Copynumber: 2.8 Consensus size: 40
589712 TCCCTCTTCA
*
589722 GTGTCCCTTCTCCTTTCTCCTCTTCCTTTTTCC-TTTGCG
1 GTGTCCCTTCTCCTTTCTCCTCTTCCTTTTTCCGTGTGCG
** * *
589761 GTGTCCCTTCTTTCCCCTCTTCCTTTTCTTTCTTTTTTTCCGTGTTCG
1 GTGTCCCTTC--T--CCT-TT-CTCCTC-TTC-CTTTTTCCGTGTGCG
589809 GTGTCCCTTCTCCTTTCTCCTCTTCCTTTT
1 GTGTCCCTTCTCCTTTCTCCTCTTCCTTTT
589839 CAACAAGTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
39 10 0.16
40 4 0.07
41 4 0.07
42 4 0.07
43 5 0.08
44 5 0.08
45 4 0.07
46 4 0.07
47 7 0.11
48 14 0.23
ACGTcount: A:0.00, C:0.37, G:0.09, T:0.54
Consensus pattern (40 bp):
GTGTCCCTTCTCCTTTCTCCTCTTCCTTTTTCCGTGTGCG
Found at i:592707 original size:24 final size:24
Alignment explanation
Indices: 592680--592749 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
592670 AACACACACC
592680 TCATATTATAAAAACTCACACATT
1 TCATATTATAAAAACTCACACATT
* * *
592704 TCATATTA-ACAACACACACACCCTT
1 TCATATTATA-AAAACTCACA-CATT
592729 T-ATATTATAAAAACTCACACA
1 TCATATTATAAAAACTCACACA
592750 CATTTTCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.05
24 30 0.81
25 5 0.14
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (24 bp):
TCATATTATAAAAACTCACACATT
Found at i:592765 original size:24 final size:24
Alignment explanation
Indices: 592680--592775 Score: 70
Period size: 24 Copynumber: 3.8 Consensus size: 24
592670 AACACACACC
* *
592680 TCATATTATAAAAACTCACACA-TT
1 TCATATTA-AAACACACACACATTT
*
592704 TCATATTAACAACACACACACCCTTT
1 TCATATTAA-AACACACACA-CATTT
* *
592730 AT-ATTATAAAAACTCACACACATTT
1 -TCA-TATTAAAACACACACACATTT
*
592755 TCATATTAAAAGAGCACACAC
1 TCATATTAAAACA-CACACAC
592776 CCTTTATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
23 1 0.02
24 24 0.43
25 13 0.23
26 12 0.21
27 6 0.11
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (24 bp):
TCATATTAAAACACACACACATTT
Found at i:592777 original size:51 final size:50
Alignment explanation
Indices: 592682--592812 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 50
592672 CACACACCTC
592682 ATATTATAAAAACT--CACACATTTCATATTAACAACACACACACCCTTT
1 ATATTATAAAAACTCACACACATTTCATATTAACAACACACACACCCTTT
*
592730 ATATTATAAAAACTCACACACATTTTCATATTAA-AAGAGCACACACCCTTT
1 ATATTATAAAAACTCACACACA-TTTCATATTAACAACA-CACACACCCTTT
* *
592781 ATATTATAATAAGTAACACACACATTTCATAT
1 ATATTATAAAAACT--CACACACATTTCATAT
592813 ATACATTAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
48 14 0.19
50 9 0.12
51 35 0.47
52 8 0.11
53 8 0.11
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (50 bp):
ATATTATAAAAACTCACACACATTTCATATTAACAACACACACACCCTTT
Found at i:592784 original size:24 final size:26
Alignment explanation
Indices: 592682--592789 Score: 86
Period size: 26 Copynumber: 4.3 Consensus size: 26
592672 CACACACCTC
*
592682 ATATTATAAAAACTCACACA---TTT
1 ATATTATAAAAACGCACACACCCTTT
* *
592705 CATA-T-TAACAACACACACACCCTTT
1 -ATATTATAAAAACGCACACACCCTTT
* **
592730 ATATTATAAAAACTCACACACATTTT
1 ATATTATAAAAACGCACACACCCTTT
*
592756 CATATTA-AAAGA-GCACACACCCTTT
1 -ATATTATAAAAACGCACACACCCTTT
592781 ATATTATAA
1 ATATTATAA
592790 TAAGTAACAC
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
22 12 0.18
23 1 0.01
24 12 0.18
25 16 0.24
26 20 0.30
27 6 0.09
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (26 bp):
ATATTATAAAAACGCACACACCCTTT
Found at i:592875 original size:25 final size:26
Alignment explanation
Indices: 592796--592881 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 26
592786 ATAATAAGTA
*
592796 ACACACACATTTCATATATACATTAAAC
1 ACACACACATTACATATAT--ATTAAAC
* **
592824 ACACACATGCATTGCATA-ATAAAAAAC
1 ACACACA--CATTACATATATATTAAAC
592851 ACACACACA-TACATATATATTAAAC
1 ACACACACATTACATATATATTAAAC
592876 ACACAC
1 ACACAC
592882 GTACTGCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
24 5 0.10
25 15 0.31
27 12 0.24
28 7 0.14
29 2 0.04
30 8 0.16
ACGTcount: A:0.50, C:0.26, G:0.02, T:0.22
Consensus pattern (26 bp):
ACACACACATTACATATATATTAAAC
Found at i:592925 original size:33 final size:29
Alignment explanation
Indices: 592874--593040 Score: 125
Period size: 29 Copynumber: 5.9 Consensus size: 29
592864 TATATATTAA
*
592874 ACACACACGTACTGCATAATAAAATAAGCATAT
1 ACACACACTTACTGCATAATAAAA-AA--A-AT
*
592907 ACACACACTTACTACATAAT-AAAAAAAT
1 ACACACACTTACTGCATAATAAAAAAAAT
592935 ACACACACTTACTGCATAAT--AAAAAA-
1 ACACACACTTACTGCATAATAAAAAAAAT
* * * **
592961 CCACACAC--A-TGAAT-ATATATTAAAT
1 ACACACACTTACTGCATAATAAAAAAAAT
** * *
592986 ACACACACTTACTATATAATAGAAAAAAG
1 ACACACACTTACTGCATAATAAAAAAAAT
**
593015 ACACACACTTGTTGCATAATAAAAAA
1 ACACACACTTACTGCATAATAAAAAA
593041 TCTTTTATAT
Statistics
Matches: 108, Mismatches: 19, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
22 2 0.02
23 4 0.04
24 5 0.05
25 7 0.06
26 7 0.06
27 7 0.06
28 24 0.22
29 29 0.27
31 2 0.02
32 3 0.03
33 18 0.17
ACGTcount: A:0.52, C:0.20, G:0.05, T:0.22
Consensus pattern (29 bp):
ACACACACTTACTGCATAATAAAAAAAAT
Found at i:592936 original size:28 final size:28
Alignment explanation
Indices: 592905--593040 Score: 120
Period size: 28 Copynumber: 5.0 Consensus size: 28
592895 AAATAAGCAT
592905 ATACACACACTTACTACATAATAAAAAA
1 ATACACACACTTACTACATAATAAAAAA
*
592933 ATACACACACTTACTGCATAATAAAAAA
1 ATACACACACTTACTACATAATAAAAAA
** * * **
592961 CCACACACA-TGA--ATAT-AT-ATTAA
1 ATACACACACTTACTACATAATAAAAAA
*
592984 ATACACACACTTACTATATAATAGAAAAA
1 ATACACACACTTACTACATAATA-AAAAA
* ** *
593013 AGACACACACTTGTTGCATAATAAAAAA
1 ATACACACACTTACTACATAATAAAAAA
593041 TCTTTTATAT
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
23 10 0.12
24 4 0.05
25 2 0.02
26 4 0.05
27 4 0.05
28 39 0.46
29 21 0.25
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
ATACACACACTTACTACATAATAAAAAA
Found at i:597667 original size:54 final size:54
Alignment explanation
Indices: 597600--598064 Score: 643
Period size: 54 Copynumber: 8.6 Consensus size: 54
597590 AAGCTCTTTT
* * * *
597600 TGAATTTTATGGGTTGCACACTTAGTGTCGATATGGTCGTTTATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* * * * *
597654 TGAATTATGTGGGTTGTACACTTAGTTTCGATACGGTCCTTCATAAAATTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* *
597708 TGAATTCTGTGGGTTGCACACTTAGTGCCGA-ACGGTCCTTCATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* *
597761 TGAATTCCGTGGGTTGCACACTTAGTG-CTGATACGATCGTTCATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACTTATTA
* *
597815 TGAATTCTGTGGGTTGCACACTTAGTGCCGA-ACGGTCCTTCATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* *
597868 TGAATTCCGTGGGTTGCACACTTAGTG-CTGATACGATCGTTCATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACTTATTA
* * * *
597922 TGAATT-TCATGGGTTTCACACTTAGTGTCGATACGATCGTTCAAAAACTTATTA
1 TGAATTCT-GTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* *
597976 TGAATTTTGTGGGTTGCACACTTAGTGTCGATATGGTCGTTCATAAACTTATTA
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
* *
598030 TGAATTATGTGGATTGCACACTTAGTGTCGATACG
1 TGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
598065 TGAAAATGTA
Statistics
Matches: 369, Mismatches: 34, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.01
53 97 0.26
54 267 0.72
55 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (54 bp):
TGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTA
Found at i:597782 original size:107 final size:108
Alignment explanation
Indices: 597600--598064 Score: 634
Period size: 107 Copynumber: 4.3 Consensus size: 108
597590 AAGCTCTTTT
* * * * * * **
597600 TGAATTTTATGGGTTGCACACTTAGTGTCGATATGGTCGTTTATAAACTTATTATGAATTATGTG
1 TGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCCTTCATAAACTTATTATGAATTCCGTG
* * * * *
597665 GGTTGTACACTTAGT-TTCGATACGGTCCTTCATAAAATTATTA
66 GGTTGCACACTTAGTGCT-GATACGATCGTTCATAAACTTATTA
597708 TGAATTCTGTGGGTTGCACACTTAGTGCCGA-ACGGTCCTTCATAAACTTATTATGAATTCCGTG
1 TGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCCTTCATAAACTTATTATGAATTCCGTG
597772 GGTTGCACACTTAGTGCTGATACGATCGTTCATAAACTTATTA
66 GGTTGCACACTTAGTGCTGATACGATCGTTCATAAACTTATTA
597815 TGAATTCTGTGGGTTGCACACTTAGTGCCGA-ACGGTCCTTCATAAACTTATTATGAATTCCGTG
1 TGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCCTTCATAAACTTATTATGAATTCCGTG
597879 GGTTGCACACTTAGTGCTGATACGATCGTTCATAAACTTATTA
66 GGTTGCACACTTAGTGCTGATACGATCGTTCATAAACTTATTA
* * * * * * **
597922 TGAATT-TCATGGGTTTCACACTTAGTGTCGATACGATCGTTCAAAAACTTATTATGAATTTTGT
1 TGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCCTTCATAAACTTATTATGAATTCCGT
* *
597986 GGGTTGCACACTTAGTG-TCGATATGGTCGTTCATAAACTTATTA
65 GGGTTGCACACTTAGTGCT-GATACGATCGTTCATAAACTTATTA
* * *
598030 TGAATTATGTGGATTGCACACTTAGTGTCGATACG
1 TGAATTCTGTGGGTTGCACACTTAGTGCCGATACG
598065 TGAAAATGTA
Statistics
Matches: 326, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
106 1 0.00
107 198 0.61
108 126 0.39
109 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (108 bp):
TGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCCTTCATAAACTTATTATGAATTCCGTG
GGTTGCACACTTAGTGCTGATACGATCGTTCATAAACTTATTA
Found at i:597913 original size:161 final size:162
Alignment explanation
Indices: 597608--598064 Score: 679
Period size: 161 Copynumber: 2.8 Consensus size: 162
597598 TTTGAATTTT
* * * *
597608 ATGGGTTGCACACTTAGTGTCGATATGGTCGTTTATAAACTTATTATGAATTATGTGGGTTGTAC
1 ATGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTATGTGGGTTGCAC
* * *
597673 ACTTAGTTTCGATACGGTCCTTCATAAAATTATTATGAATTCTGTGGGTTGCACACTTAGTGCCG
66 ACTTAGTGTCGATACGGTCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCTG
*
597738 A-ACGGTCCTTCATAAACTTATTATGAATTCC
131 ATACGATCCTTCATAAACTTATTATGAATTCC
* *
597769 GTGGGTTGCACACTTAGTG-CTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCA
1 ATGGGTTGCACACTTAGTGTC-GATACGATCGTTCATAAACTTATTATGAATTATGTGGGTTGCA
* *
597833 CACTTAGTGCCGA-ACGGTCCTTCATAAACTTATTATGAATTCCGTGGGTTGCACACTTAGTGCT
65 CACTTAGTGTCGATACGGTCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCT
* *
597897 GATACGATCGTTCATAAACTTATTATGAATTTC
130 GATACGATCCTTCATAAACTTATTATGAATTCC
* * *
597930 ATGGGTTTCACACTTAGTGTCGATACGATCGTTCAAAAACTTATTATGAATTTTGTGGGTTGCAC
1 ATGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTATGTGGGTTGCAC
* * * *
597995 ACTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATTATGTGGATTGCACACTTAGTG-TC
66 ACTTAGTGTCGATACGGTCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCT-
598059 GATACG
130 GATACG
598065 TGAAAATGTA
Statistics
Matches: 267, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
160 51 0.19
161 165 0.62
162 51 0.19
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (162 bp):
ATGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTATGTGGGTTGCAC
ACTTAGTGTCGATACGGTCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCTG
ATACGATCCTTCATAAACTTATTATGAATTCC
Found at i:600888 original size:17 final size:17
Alignment explanation
Indices: 600866--600899 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
600856 GCCTATTCTA
600866 GATATAAAACACAAAAT
1 GATATAAAACACAAAAT
* *
600883 GATATAATACATAAAAT
1 GATATAAAACACAAAAT
600900 AGTTAATCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
GATATAAAACACAAAAT
Found at i:605667 original size:18 final size:18
Alignment explanation
Indices: 605644--605685 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
605634 ACATGGCATC
605644 TACATTGCATTTACTTTT
1 TACATTGCATTTACTTTT
605662 TACATTGCATTTACTTTT
1 TACATTGCATTTACTTTT
605680 TACATT
1 TACATT
605686 TCCTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.55
Consensus pattern (18 bp):
TACATTGCATTTACTTTT
Found at i:609873 original size:106 final size:106
Alignment explanation
Indices: 609678--609874 Score: 261
Period size: 106 Copynumber: 1.9 Consensus size: 106
609668 TGTAAGTTGG
* * * *
609678 ACTCAAGACGACACAAGTTCAAATTCACAATGAATGGACGGCTGGTTGTCAGAAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAAATTCACAATGAAGGGACGGCTGGCTGTCAGAAAACAATTTCCC
*
609743 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGTTATTGA
66 AATTCCAGAGCCAATTTAAACTTCACAGCGAAGGTTATTGA
* * * *
609784 ACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGGCTGGCTGTCA-ACAAACAATTTCC
1 ACTCAAGACAACACAAGCTCAAATTCACAATGAAGGGACGGCTGGCTGTCAGA-AAACAATTTCC
* * * *
609848 TAGTTCCGGAGCCAATTTCAACTTCAC
65 CAATTCCAGAGCCAATTTAAACTTCAC
609875 GACGGAGGAT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 1 0.01
106 76 0.99
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGCTCAAATTCACAATGAAGGGACGGCTGGCTGTCAGAAAACAATTTCCC
AATTCCAGAGCCAATTTAAACTTCACAGCGAAGGTTATTGA
Found at i:611678 original size:41 final size:39
Alignment explanation
Indices: 611633--611709 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
611623 GGGCTCATTT
* *
611633 TTTTTATTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTATCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
* *
611674 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTATCTTATTTCTAACTAAAGCCCCCCACTTTC
611710 GGTGAAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.31
40 1 0.03
41 21 0.66
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.48
Consensus pattern (39 bp):
TTTTTATCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:611889 original size:9 final size:9
Alignment explanation
Indices: 611877--611934 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
611867 CCTTATCTTA
611877 TTTATTTAT
1 TTTATTTAT
611886 TTTATTTAT
1 TTTATTTAT
611895 TTTATTT-T
1 TTTATTTAT
*
611903 TTTCCTTTTAT
1 TTT--ATTTAT
611914 TTTATTCTA-
1 TTTATT-TAT
611923 TTTATCTTAT
1 TTTAT-TTAT
611933 TT
1 TT
611935 GTTTTCTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 4 0.10
9 25 0.61
10 8 0.20
11 4 0.10
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:611900 original size:14 final size:14
Alignment explanation
Indices: 611869--611939 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
611859 CTTTTTTTCC
*
611869 TTATCTTATTTA-T
1 TTATTTTATTTATT
611882 TTATTTTATTTATT
1 TTATTTTATTTATT
*
611896 TTATTTT-TTTCCTT
1 TTATTTTATTT-ATT
611910 TTATTTTATTCTA-T
1 TTATTTTATT-TATT
* *
611924 TTATCTTATTTGTT
1 TTATTTTATTTATT
611938 TT
1 TT
611940 CTTTACCTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 15 0.31
14 30 0.62
15 2 0.04
16 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:612875 original size:10 final size:10
Alignment explanation
Indices: 612860--612901 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
612850 TTTTCTTGCC
612860 ATTTTTTTTT
1 ATTTTTTTTT
612870 ATTTTTTTTT
1 ATTTTTTTTT
* *
612880 ATTTCTATTT
1 ATTTTTTTTT
612890 ATTTTTATTTT
1 ATTTTT-TTTT
612901 A
1 A
612902 CTAATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:612888 original size:16 final size:15
Alignment explanation
Indices: 612860--612901 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
612850 TTTTCTTGCC
612860 ATTTTT-TTTTATTT
1 ATTTTTATTTTATTT
*
612874 TTTTTTATTTCTATTT
1 ATTTTTATTT-TATTT
612890 ATTTTTATTTTA
1 ATTTTTATTTTA
612902 CTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 14 0.58
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTTATTTTATTT
Found at i:612889 original size:26 final size:26
Alignment explanation
Indices: 612833--612900 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
612823 CTAACCATGT
* *
612833 TTTTTTCTCTTATGTTTTTTTCTTGCCA
1 TTTTTT-T-TTATTTTTTTTTATTGCCA
* *
612861 TTTTTTTTTATTTTTTTTTATTTCTA
1 TTTTTTTTTATTTTTTTTTATTGCCA
*
612887 TTTATTTTTATTTT
1 TTTTTTTTTATTTT
612901 ACTAATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 28 0.80
27 1 0.03
28 6 0.17
ACGTcount: A:0.10, C:0.09, G:0.03, T:0.78
Consensus pattern (26 bp):
TTTTTTTTTATTTTTTTTTATTGCCA
Found at i:616431 original size:21 final size:21
Alignment explanation
Indices: 616365--616424 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
616355 TCAAGAACAA
616365 AAAAGAAAAGAAGCAAAAAAG
1 AAAAGAAAAGAAGCAAAAAAG
*
616386 AAAA-AACAATAA-CAAAAAAG
1 AAAAGAA-AAGAAGCAAAAAAG
616406 AAAAGAAAAGAAGCAAAAA
1 AAAAGAAAAGAAGCAAAAA
616425 TCAAAAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.78, C:0.07, G:0.13, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAGAAGCAAAAAAG
Found at i:618052 original size:37 final size:36
Alignment explanation
Indices: 617946--618055 Score: 96
Period size: 37 Copynumber: 3.0 Consensus size: 36
617936 ACTCAAGATT
* *
617946 GTTTTTCTTAAAACAAATTTCATCTCCCCGTGAGACA
1 GTTTTTCTTAAAACAAATTTTATCT-CCCTTGAGACA
* ** * * *
617983 ATTTCTT-TTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTT-TTCTTAAAAC-AAATTTTATCTCCCTTGAGACA
*
618020 GTTTTTCTTAAAACAAAATTTTTTCTCCCTTGAGAC
1 GTTTTTCTTAAAAC-AAATTTTATCTCCCTTGAGAC
618056 CATTTCTCAT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
36 2 0.04
37 43 0.78
38 10 0.18
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAATTTTATCTCCCTTGAGACA
Found at i:618829 original size:216 final size:216
Alignment explanation
Indices: 618590--619238 Score: 932
Period size: 216 Copynumber: 3.0 Consensus size: 216
618580 ATATCACGCC
*
618590 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACCACTTTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTC
*
618655 AATTTCATTCACAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTC
66 AATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTC
* *
618720 AACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCAA
131 AACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAA
*
618785 CTTCACAGCAAAGGATATTGG
196 CTTCACAGCGAAGGATATTGG
*
618806 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAAACCACTTTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTC
* * *
618871 AGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAACACAAGTTC
66 AATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTC
* * * *
618936 AACTTCACAACGAAGGCACGGCTGGTTGTCAGCAAATAATTTCCCAATTTCAGAGCCAATTTCAA
131 AACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAA
*
619001 CTTCATAGCGAAGGATATTGG
196 CTTCACAGCGAAGGATATTGG
* * * * *
619022 ACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGATGGCTGGTTGTCAACAAA-CAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTT-T
* * * * *
619086 CAA--T--TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCGAGAAAACACAAGCT
65 CAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
* * * * * * * * *
619147 CAACTTCATAGCGAAGGGGTGGCTGGCTGTCAACAAACAATTTCCTAGTTCCGGAGCCAATTTTA
130 CAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCA
*
619212 AATTCAC-GACGAAGGATATTGG
195 ACTTCACAG-CGAAGGATATTGG
619234 ACTCG
1 ACTCG
619239 GAACAATACT
Statistics
Matches: 387, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
211 1 0.00
212 124 0.32
214 1 0.00
215 5 0.01
216 256 0.66
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (216 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTC
AATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTC
AACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAA
CTTCACAGCGAAGGATATTGG
Found at i:618841 original size:106 final size:106
Alignment explanation
Indices: 618670--619238 Score: 773
Period size: 106 Copynumber: 5.3 Consensus size: 106
618660 CATTCACAGT
618670 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
618735 GGATGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
*
618776 CAATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * * * *
618841 GGACGGCTGGTTGCCAACAAACCACTTT-TCAGTTTCATTCAGAGT
66 GGACGGCTGGTTGTCAACAAA-CAATTTCCCA--AT--TTCAGAGC
* *
618886 CAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
618951 GCACGGCTGGTTGTCAGCAAATAATTTCCCAATTTCAGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* * *
618992 CAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
*
619057 GGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* * * * * *
619098 CAATTTCAACTTCACAACGAAGGATATTGAACTCGAGAAAACACAAGCTCAACTTCATAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
** * * * * *
619163 GGGTGGCTGGCTGTCAACAAACAATTTCCTAGTTCCGGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
* *
619204 CAATTTTAAATTCAC-GACGAAGGATATTGGACTCG
1 CAATTTCAACTTCACAG-CGAAGGATATTGGACTCG
619239 GAACAATACT
Statistics
Matches: 412, Mismatches: 44, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
106 312 0.76
107 3 0.01
108 2 0.00
109 4 0.01
110 91 0.22
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (106 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGC
Found at i:619184 original size:322 final size:324
Alignment explanation
Indices: 618590--619184 Score: 935
Period size: 322 Copynumber: 1.8 Consensus size: 324
618580 ATATCACGCC
* * * *
618590 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGCACGGCTGGTTGTCAGCAAACCAATTTCC
* *
618655 AATTTCATTCACAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTC
66 AA-TT-ATTCACAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTC
* *
618720 AACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCAA
129 AAATTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAA
* * * *
618785 CTTCACAGCAAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
194 CTTCACAACAAAGGATATTGAACTCGAGAAAACACAAGCTCAACTTCACAACGAAGGGACGGCTG
*
618850 GTTGCCAACAAACCACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTG
259 GCTGCCAACAAACCACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTG
618915 G
324 G
*
618916 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGCACGGCTGGTTGTCAGCAAA-TAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGCACGGCTGGTTGTCAGCAAACCAATTT-C
* *
618980 CAA-T-TTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCAAGACAACACAAGTTCA
65 CAATTATTCACAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCA
*
619043 AATTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
130 AATTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAAC
* * * **
619108 TTCACAACGAAGGATATTGAACTCGAGAAAACACAAGCTCAACTTCATAGCGAAGGGGTGGCTGG
195 TTCACAACAAAGGATATTGAACTCGAGAAAACACAAGCTCAACTTCACAACGAAGGGACGGCTGG
*
619173 CTGTCAACAAAC
260 CTGCCAACAAAC
619185 AATTTCCTAG
Statistics
Matches: 245, Mismatches: 23, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
322 183 0.75
324 1 0.00
325 4 0.02
326 57 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (324 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGCACGGCTGGTTGTCAGCAAACCAATTTCC
AATTATTCACAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAA
ATTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTACCCAATTTCAGAGCCAATTTCAACT
TCACAACAAAGGATATTGAACTCGAGAAAACACAAGCTCAACTTCACAACGAAGGGACGGCTGGC
TGCCAACAAACCACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGG
Found at i:620547 original size:17 final size:18
Alignment explanation
Indices: 620521--620560 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
620511 ATTATATGGA
620521 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
620537 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
620555 TATTAT
1 TATTAT
620561 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:621014 original size:41 final size:39
Alignment explanation
Indices: 620969--621045 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
620959 GCTCATTTTT
* *
620969 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
621010 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
621046 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:621254 original size:18 final size:18
Alignment explanation
Indices: 621233--621273 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
621223 TTCCTTTTAT
*
621233 TTTATTCTCTTTATCTTA
1 TTTATTCTCTTTACCTTA
* *
621251 TTTATTTTCTTTACCTTG
1 TTTATTCTCTTTACCTTA
621269 TTTAT
1 TTTAT
621274 CTAACACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTCTCTTTACCTTA
Found at i:622570 original size:45 final size:44
Alignment explanation
Indices: 622486--622570 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 44
622476 GAGAATAAAT
* * * *
622486 AAATGGGGTTCAAGATGAAAACCTGTAAAGGGAGTCTTGAAACC
1 AAATGAGGTTCAAGATGAAAACCCGCAAAGGGAGGCTTGAAACC
* *
622530 AAATGAGGTCTCAAGTTGAAAACCCGCAAAGGGTGGCTTGA
1 AAATGAGGT-TCAAGATGAAAACCCGCAAAGGGAGGCTTGA
622571 GAGTTATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 8 0.24
45 26 0.76
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.20
Consensus pattern (44 bp):
AAATGAGGTTCAAGATGAAAACCCGCAAAGGGAGGCTTGAAACC
Found at i:624164 original size:137 final size:136
Alignment explanation
Indices: 623721--624310 Score: 696
Period size: 135 Copynumber: 4.4 Consensus size: 136
623711 ATGAATCAAA
* * * *
623721 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATTTCCAGATCTGATTTTCTCTCA
1 CTCGATTCAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATTTTCCCTCA
*
623786 AGAAGCAGTGAAACAGATCC-CTATTTTCTTT-CAGATTTGATCTTCCCTGAGGAACAGTGGAAC
66 AGAAGCAGTGGAACAGATCCTCT-TTTT-TTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAAC
*
623849 AAGTCTCC
129 AAGTCTGC
* *
623857 CTCGATTCAA-TTTCCCCGAAGAACAGTGGAATGCATCAACATTTCCAGATATGATTTTCCCTCA
1 CTCGATTCAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATTTTCCCTCA
* * * * * * *
623921 AGAATCAGCGGAACATAT-ATCTCTTTTTTCCAGATTTGA---TCCTTGAGGAACATTGGAACAA
66 AGAAGCAGTGGAACAGATCCTCTTTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAA
*
623982 GTTTGC
131 GTCTGC
* * **
623988 CTTGATTAAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTTTAGATATGATTTTCCCTCA
1 CTCGATTCAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATTTTCCCTCA
* * * * * *
624053 AGAAGTAGTGGAACAGATCCGTCTTTTTTTTTCAGATTTGATTTTCCATGAGGAACAGTTGAAGA
66 AGAAGCAGTGGAACAGATCC-TCTTTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACA
624118 AGTCTGC
130 AGTCTGC
* * * * *
624125 CTCGATTCAATTTTCCCTGAAGAATAGTGAAATGAATCAACATTT-CTGAATCTAATTTTCCCTC
1 CTCGATTCAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAG-ATATGATTTTCCCTC
* * *
624189 AAGAAACAGTGGAACAGATCCTC-TTTTTTTCCAGACTTGATCTTCCCTAAGGAACAGTGGAACA
65 AAGAAGCAGTGGAACAGATCCTCTTTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACA
624253 AGTCTGC
130 AGTCTGC
* * * * * * *
624260 CCCAATAC-ATTCTTCTCTAAAGAGCAGTGGAATTAATCAACATTTCCAGAT
1 CTCGATTCAATT-TTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGAT
624311 TTCTTTTCAC
Statistics
Matches: 382, Mismatches: 61, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
131 32 0.08
132 64 0.17
133 3 0.01
134 33 0.09
135 139 0.36
136 15 0.04
137 96 0.25
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (136 bp):
CTCGATTCAATTTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATTTTCCCTCA
AGAAGCAGTGGAACAGATCCTCTTTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAA
GTCTGC
Found at i:632283 original size:3 final size:3
Alignment explanation
Indices: 632257--632332 Score: 98
Period size: 3 Copynumber: 25.0 Consensus size: 3
632247 ATTTTTTAGT
* * * *
632257 TTA TTT TTA TTT TTA TTT TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
632305 TTA TACA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA
632333 AATAAATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
3 60 0.97
4 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:633702 original size:22 final size:22
Alignment explanation
Indices: 633677--633725 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
633667 ATTATTTATT
*
633677 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
633699 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
633721 TATTA
1 TATTA
633726 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:633724 original size:11 final size:10
Alignment explanation
Indices: 633656--633725 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 10
633646 GCTTTTTAAT
633656 TTATTTTAATCA
1 TTATTTT-AT-A
*
633668 TTATTTATTTA
1 TTATTT-TATA
*
633679 TTATTTTGTTA
1 TTATTTT-ATA
633690 TTACTTTTATA
1 TTA-TTTTATA
633701 TTATTTTATTA
1 TTATTTTA-TA
633712 TTATTTTCATA
1 TTATTTT-ATA
633723 TTA
1 TTA
633726 GTCACATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.12
11 32 0.63
12 12 0.24
13 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTATTTTATA
Found at i:634036 original size:115 final size:115
Alignment explanation
Indices: 633903--634113 Score: 307
Period size: 115 Copynumber: 1.8 Consensus size: 115
633893 TACATTTTAA
* ** * * *
633903 TATTTATTTTTTTATTAATATTGAAGGAAATAGTTGTCTTAAAGCAACTAGAAACCCTTTTCTAA
1 TATTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTAA
*
633968 TATTTTTAAATAAATAAATATCTTATTATATTAAAATAATTTTTTATTAT
66 TATTTCTAAATAAATAAATATCTTATTATATTAAAATAATTTTTTATTAT
* * *
634018 TATTTATTTAATTT-TTAATATCAAAAGAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTG
1 TATTTATTT-ATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTA
*
634082 ATATTTCTAAATAAATAAATATGTTATTATAT
65 ATATTTCTAAATAAATAAATATCTTATTATAT
634114 ATATATATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
115 81 0.96
116 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.45
Consensus pattern (115 bp):
TATTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTAA
TATTTCTAAATAAATAAATATCTTATTATATTAAAATAATTTTTTATTAT
Found at i:639511 original size:22 final size:22
Alignment explanation
Indices: 639493--639537 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
639483 ATGATCCATT
639493 ACTAATTAGTAAATTATCCTCA
1 ACTAATTAGTAAATTATCCTCA
639515 ACTAATTAGTAAATTATCCTCA
1 ACTAATTAGTAAATTATCCTCA
639537 A
1 A
639538 ATTACAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
ACTAATTAGTAAATTATCCTCA
Found at i:643261 original size:13 final size:13
Alignment explanation
Indices: 643243--643277 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
643233 TCAACACCCC
*
643243 ACCCGACCTGTTG
1 ACCCGACCCGTTG
643256 ACCCGACCCGTTG
1 ACCCGACCCGTTG
643269 ACCCGACCC
1 ACCCGACCC
643278 AATCTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:646166 original size:63 final size:63
Alignment explanation
Indices: 646093--646214 Score: 167
Period size: 63 Copynumber: 1.9 Consensus size: 63
646083 CTAATGTGAC
* * *
646093 TCTTAGGTAGGCTCTATGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GACCCTAAGATATGT
1 TCTTAGGTAGGCCCTACGGCCCTGAAATCTA-TCTCGGGTAGGCCCT-CAGACCCTAAGATATGT
* *
646156 TCTTAGGTAGGCCCTACGGCCCTGAAATCTATCTTGGGTAGGCTCTCAGACCCTAAGAT
1 TCTTAGGTAGGCCCTACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGACCCTAAGAT
646215 GTTCCCTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.28
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGACCCTAAGATATGT
Found at i:652572 original size:18 final size:18
Alignment explanation
Indices: 652545--652605 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
652535 ATCGGTCACA
*
652545 ACCCGCCTCGACCTGTTG
1 ACCCGACTCGACCTGTTG
*
652563 ACCCGACTCGACCTGTTA
1 ACCCGACTCGACCTGTTG
* * *
652581 ACCCGACCCGATCTATTG
1 ACCCGACTCGACCTGTTG
652599 ACCCGAC
1 ACCCGAC
652606 CCGTTGACCG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.20, C:0.43, G:0.18, T:0.20
Consensus pattern (18 bp):
ACCCGACTCGACCTGTTG
Found at i:653576 original size:32 final size:32
Alignment explanation
Indices: 653531--653591 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
653521 AGGGTTTGTG
**
653531 CAAGATATTAGAAT-TCTATTAAGGAATCATTT
1 CAAGATAAGAGAATGTC-ATTAAGGAATCATTT
*
653563 CAAGATAAGAGAATGTCCTTAAGGAATCA
1 CAAGATAAGAGAATGTCATTAAGGAATCA
653592 GCTCAACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (32 bp):
CAAGATAAGAGAATGTCATTAAGGAATCATTT
Found at i:656860 original size:13 final size:13
Alignment explanation
Indices: 656844--656868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
656834 GACTCGACTT
656844 GTTGACCCGACCC
1 GTTGACCCGACCC
656857 GTTGACCCGACC
1 GTTGACCCGACC
656869 GGATCGTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
GTTGACCCGACCC
Found at i:659832 original size:30 final size:30
Alignment explanation
Indices: 659760--659832 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
659750 CTAATGTGAC
*
659760 TCTTAGGTAGGCTTTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGC-TTGCGGCCCTAAGATCAT
**
659791 TCTCGGGTAGGC-TGCGGCCCTAAGAT-ATGT
1 TCTTAGGTAGGCTTGCGGCCCTAAGATCA--T
659821 TCTTAGGTAGGC
1 TCTTAGGTAGGC
659833 CCAACGACCC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 13 0.37
30 11 0.31
31 10 0.29
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.30
Consensus pattern (30 bp):
TCTTAGGTAGGCTTGCGGCCCTAAGATCAT
Found at i:668092 original size:6 final size:6
Alignment explanation
Indices: 668081--668117 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
668071 ATTAATTATT
* *
668081 TATTAA TATTAA TATTAA TATTAA TACTAA TACTAA T
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA T
668118 TTTATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (6 bp):
TATTAA
Found at i:669722 original size:2 final size:2
Alignment explanation
Indices: 669715--669739 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
669705 TAAATATTTG
669715 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
669740 TGTGGTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:676862 original size:36 final size:36
Alignment explanation
Indices: 676791--676944 Score: 142
Period size: 36 Copynumber: 4.4 Consensus size: 36
676781 TGTTGAGATT
* * * *
676791 GTTTTTCTCGAAACAAAGTTCTGTCTCACTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* *
676828 GTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* **
676864 GTTTCTCTTGAAACATAA-----AC-CT-TTGAGATT
1 GTTTCTCTTGAAACA-AATTTTGTCTCTCTTGAGACA
*
676894 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
676930 GTTTCTCTTTAAACA
1 GTTTCTCTTGAAACA
676945 TAAACTTTGA
Statistics
Matches: 98, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.02
30 22 0.22
31 2 0.02
32 1 0.01
34 1 0.01
35 2 0.02
36 51 0.52
37 17 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:676905 original size:66 final size:66
Alignment explanation
Indices: 676828--677075 Score: 390
Period size: 66 Copynumber: 3.8 Consensus size: 66
676818 ACTTGAGACA
* *
676828 GTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACTGTTTCTCTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
676893 T
66 T
* *
676894 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTTAAACATAAA-CTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
*
676958 A
66 T
* **
676959 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACATAAACAATTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
677024 T
66 T
* * *
677025 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGGCAGTTTCTCTTGAAACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
677076 AATTATCACT
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
65 61 0.37
66 105 0.63
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGAT
T
Found at i:676981 original size:131 final size:131
Alignment explanation
Indices: 676820--677075 Score: 413
Period size: 131 Copynumber: 2.0 Consensus size: 131
676810 TCTGTCTCAC
* *
676820 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACTGTTTCTCTTGAAACATAAACC
1 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * *
676885 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTTAAACATAAAC
66 ATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
676950 T
131 T
* * *
676951 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACATAAACA
1 TTGAGACAGTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTCTTGAAACATAAACA
*
677016 ATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGGCAGTTTCTCTTGAAACA
66 ATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
677076 AATTATCACT
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 114 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (131 bp):
TTGAGACAGTTTCTCTTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTCTTGAAACATAAACA
ATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
T
Found at i:677588 original size:276 final size:276
Alignment explanation
Indices: 677078--677626 Score: 735
Period size: 276 Copynumber: 2.0 Consensus size: 276
677068 TTGAAACAAA
* *
677078 TTATCACTAAAGATGGCTAGACGTCCTCATCACGTAGAAAAAATGTCATCCATCAATCAGATCTC
1 TTATCACTAAAGATGGCTAGACGTCCTCATCACGTAGAAAAAATGTCATCCACCAACCAGATCTC
* *
677143 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCACGCTTTCTCATCATGTAGGAATCGTGTT
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCACGCTTTCTCATCATGTAGGAAACATGTT
* * * * * *
677208 GTCTCTAATTATCCCTAAAGATGGTTAGACGTCCTCATCACGTAGGAACAATGTCATCCACTGAC
131 ATCTCCAATTATCCATAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGAC
* ** * * *
677273 CAGATCTCCTCATCGTGTAGGAGTAGCGCCAACCTTAGATAACAAAACTTCCTCATCAAATAGGA
196 CAGATATCCTCATCACGTAGGAGCAACACCAACCTTAGATAACAAAACTTCCTCATCAAATAGGA
677338 ACTGTGTTGTCTCTAT
261 ACTGTGTTGTCTCTAT
* * * * *
677354 TTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
1 TTATCACTAAAGATGGCTAGACGTCCTCATCACGTAGAAAAAATGTCATCCACCAACCAGATCTC
* *
677419 TTCATCACATAGGAGCAACGTCATCCTTAGATAATCA-GACTTTCTCATCACT-TAGGAAACATG
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCACG-CTTTCTCATCA-TGTAGGAAACATG
* * * *
677482 TTATCTCCCATTTATCCATAAAGATGGCTAGATGTCTTC-TCATATAGGAACAATGTCATCCACC
129 TTATCT-CCAATTATCCATAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACC
* * ** * * * *
677546 GATCAGATATCCTCATCACGTAGGAGCAACATCATTCTTAGATAACCAGATTTCCTCATCACATA
193 GACCAGATATCCTCATCACGTAGGAGCAACACCAACCTTAGATAACAAAACTTCCTCATCAAATA
677611 GGAACTGTGTTGTCTC
258 GGAACTGTGTTGTCTC
677627 CAAATTTACC
Statistics
Matches: 235, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
275 1 0.00
276 207 0.88
277 27 0.11
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (276 bp):
TTATCACTAAAGATGGCTAGACGTCCTCATCACGTAGAAAAAATGTCATCCACCAACCAGATCTC
CTCATCACATAGGAGCAACGTCATCCTTAGATAACCACGCTTTCTCATCATGTAGGAAACATGTT
ATCTCCAATTATCCATAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGAC
CAGATATCCTCATCACGTAGGAGCAACACCAACCTTAGATAACAAAACTTCCTCATCAAATAGGA
ACTGTGTTGTCTCTAT
Found at i:677627 original size:138 final size:137
Alignment explanation
Indices: 677078--677626 Score: 654
Period size: 138 Copynumber: 4.0 Consensus size: 137
677068 TTGAAACAAA
* * * * * *
677078 TTATCACTAAAGATGGCTAGACGTCCTCATCACGTAGAAAAAATGTCATCCATCAATCAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
* **
677143 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCACGCTTTCTCATCATGTAGGAA-TCGTGT
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCA-GATTTCTCATCACATAGGAACT-GTGT
*
677207 TGTCTCTAA
129 TGTCTCTAT
* *
677216 TTATCCCTAAAGATGGTTAGACGTCCTCATCACGTAGGAACAATGTCATCCACTGACCAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
*** * * * * * * * *
677281 CTCATCGTGTAGGAGTAGCGCCAACCTTAGATAACAAAACTTCCTCATCAAATAGGAACTGTGTT
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCAGA-TTTCTCATCACATAGGAACTGTGTT
677346 GTCTCTAT
130 GTCTCTAT
*
677354 TTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
* * * *
677419 TTCATCACATAGGAGCAACGTCATCCTTAGATAATCAGACTTTCTCATCACTTAGGAAAC-ATGT
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCAGA-TTTCTCATCACATAGG-AACTGTGT
* *
677483 TATCTCCCAT
129 TGTCT-CTAT
* * * ** * *
677493 TTATCCATAAAGATGGCTAGATGTCTTC-TCATATAGGAACAATGTCATCCACCGATCAGATATC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
* * *
677557 CTCATCACGTAGGAGCAACATCATTCTTAGATAACCAGATTTCCTCATCACATAGGAACTGTGTT
66 CTCATCACATAGGAGCAACGTCATCCTTAGATAACCAGATTT-CTCATCACATAGGAACTGTGTT
677622 GTCTC
130 GTCTC
677627 CAAATTTACC
Statistics
Matches: 349, Mismatches: 56, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
137 7 0.02
138 309 0.89
139 33 0.09
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (137 bp):
TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCTC
CTCATCACATAGGAGCAACGTCATCCTTAGATAACCAGATTTCTCATCACATAGGAACTGTGTTG
TCTCTAT
Found at i:680426 original size:25 final size:23
Alignment explanation
Indices: 680392--680442 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
680382 TAATTGTTAA
*
680392 TTTTTCAAATAAAATTCATAATTGT
1 TTTTTAAAATAAAATT--TAATTGT
* *
680417 TTTTTAAAATGATATTTAATTGT
1 TTTTTAAAATAAAATTTAATTGT
680440 TTT
1 TTT
680443 CAAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
25 13 0.57
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (23 bp):
TTTTTAAAATAAAATTTAATTGT
Found at i:686907 original size:23 final size:23
Alignment explanation
Indices: 686875--686974 Score: 101
Period size: 23 Copynumber: 4.3 Consensus size: 23
686865 GAGTTGAGGG
* * *
686875 TTCTACGTGGTTCTTCGGGACAA
1 TTCTATGTGGTCCTTCAGGACAA
*
686898 TTCTATGTGGTCCTTCAGGACAT
1 TTCTATGTGGTCCTTCAGGACAA
* * *
686921 TTCTACGTGATCCTTCAGAACAA
1 TTCTATGTGGTCCTTCAGGACAA
* * * *
686944 TACTATGTGGTCCTTCGGGATAT
1 TTCTATGTGGTCCTTCAGGACAA
686967 TTCTATGT
1 TTCTATGT
686975 AGCACATCGG
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCAGGACAA
Found at i:686944 original size:46 final size:46
Alignment explanation
Indices: 686875--686971 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
686865 GAGTTGAGGG
* * * * *
686875 TTCTACGTGGTTCTTCGGGACAATTCTATGTGGTCCTTCAGGACAT
1 TTCTACGTGATCCTTCAGAACAATACTATGTGGTCCTTCAGGACAT
* *
686921 TTCTACGTGATCCTTCAGAACAATACTATGTGGTCCTTCGGGATAT
1 TTCTACGTGATCCTTCAGAACAATACTATGTGGTCCTTCAGGACAT
686967 TTCTA
1 TTCTA
686972 TGTAGCACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (46 bp):
TTCTACGTGATCCTTCAGAACAATACTATGTGGTCCTTCAGGACAT
Found at i:695015 original size:22 final size:22
Alignment explanation
Indices: 694985--695039 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
694975 TATTAAGGGG
*
694985 GTATTGATACCCTAATAGAGCA
1 GTATCGATACCCTAATAGAGCA
* *
695007 GTATCGATACCCTAATAGGGTA
1 GTATCGATACCCTAATAGAGCA
695029 GTATCGATACC
1 GTATCGATACC
695040 ATAAGCAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
GTATCGATACCCTAATAGAGCA
Found at i:695573 original size:79 final size:79
Alignment explanation
Indices: 695442--695843 Score: 531
Period size: 79 Copynumber: 5.1 Consensus size: 79
695432 AAACTAATGA
*
695442 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATAAGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
695507 GGTATATTATCGGC
66 GGTACATTATCGGC
*
695521 ATAAAAGAATAATGCATAAGGGTGCATTTGAT-GCATGAAAGGATGCCTTAGCTGATATGTATAT
1 ATAAAAGAATAATGCATAAGGGTGCATTAG-TGGCATGAAAGGATGCCTTAGCTGATATGTATAT
** *
695585 GCTTATATTATCGGC
65 GGGTACATTATCGGC
* * * * *
695600 ATAAAATAATAATGCATACGGGTGCATTAGTGGCATGAAATGATGCGTTAGCTGATATGTATACG
1 ATAAAAGAATAATGCATAAGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
* *
695665 GGTACAATATCAGC
66 GGTACATTATCGGC
* * *
695679 ATAACAGAATAATGCATATGGGTGCATTAGTGGCATGAAATGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATAAGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
695744 GGTACATTATCGGC
66 GGTACATTATCGGC
* ** * * *
695758 ATAACAA-AATAATGCA-AATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATA
1 ATAA-AAGAATAATGCATAA-GGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATA
* **
695821 TGGGTGCATTATCAAC
64 TGGGTACATTATCGGC
695837 ATAAAAG
1 ATAAAAG
695844 TATGCTATAA
Statistics
Matches: 284, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
78 4 0.01
79 278 0.98
80 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATAAGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCGGC
Found at i:697092 original size:2 final size:2
Alignment explanation
Indices: 697085--697113 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
697075 GATGTCAGAA
697085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
697114 GCTTTTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:699224 original size:18 final size:20
Alignment explanation
Indices: 699201--699255 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
699191 AATTTAATTT
699201 GGGTATCGATACC-TAG-AG
1 GGGTATCGATACCATAGAAG
699219 GGGTATC-AGTACCATAGCATAG
1 GGGTATCGA-TACCATAG-A-AG
699241 GGGTATCGATACCAT
1 GGGTATCGATACCAT
699256 TGTGAGGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.03
18 11 0.35
19 3 0.10
22 15 0.48
23 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (20 bp):
GGGTATCGATACCATAGAAG
Found at i:699795 original size:79 final size:79
Alignment explanation
Indices: 699664--700021 Score: 574
Period size: 79 Copynumber: 4.5 Consensus size: 79
699654 AAACTAATGA
*
699664 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
699729 GGTACATTATCGGT
66 GGTACATTATCGGC
* *
699743 ATAAAAGAATAATGCATACGGGTGCATTTGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
* *
699808 CGTACATTATCGGA
66 GGTACATTATCGGC
* * *
699822 ATAAAAGAATAATGCATATGGGTGCATTAGTTGCATGAAATGATGCCTTAGCTTATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
699887 GGTACTTTATCGGC
66 GGTACATTATCGGC
* *
699901 ATAACAA-AATAATGCATATGGGTGCATTAGTGGCATGAAATGATGCCTTAACTGATATGTATAT
1 ATAA-AAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATAT
699965 GGGTACATTATCGGC
65 GGGTACATTATCGGC
* *
699980 ATAACAGAATAATGCATATGGGTGCATTATTGGCATGAAAGG
1 ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGG
700022 CAAGCAAAAA
Statistics
Matches: 257, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
78 1 0.00
79 254 0.99
80 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCGGC
Found at i:703757 original size:37 final size:40
Alignment explanation
Indices: 703700--703799 Score: 116
Period size: 37 Copynumber: 2.6 Consensus size: 40
703690 TTAAAGCTTG
* * * *
703700 TGTTTCGAGGAAAACTATCTCAAGTGATAT-GAAA-TT-T
1 TGTTTCGAGGGAAACAATCTCAAGTGAGATAAAAATTTCT
*
703737 TGTTTCAAGGGAAACAATCTCAAGTGAGATAAAAATTTCT
1 TGTTTCGAGGGAAACAATCTCAAGTGAGATAAAAATTTCT
* *
703777 TGTTTCGAGTGAAACAATTTCAA
1 TGTTTCGAGGGAAACAATCTCAA
703800 AATTTGTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
37 26 0.50
38 3 0.06
39 2 0.04
40 21 0.40
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (40 bp):
TGTTTCGAGGGAAACAATCTCAAGTGAGATAAAAATTTCT
Found at i:703827 original size:106 final size:106
Alignment explanation
Indices: 703633--703832 Score: 235
Period size: 106 Copynumber: 1.9 Consensus size: 106
703623 GACAAAAAAT
* * * * ** *
703633 TTTCAAGAGAAACAATCTCAAGTGAGATGAAATTTTCCTTTTTTGAGTGGAATGATCTTAAAGCT
1 TTTCAAGAGAAACAATCTCAAGTGAGATAAAAATTTCCTTTTTCGAGTGAAACAATCTTAAAACT
* *
703698 TGTGTTTCGAGGAAAACTATCTCAAGTGATATGAAATTTTG
66 TGTATTTCAAGGAAAACTATCTCAAGTGATATGAAATTTTG
*
703739 TTTCAAGGGAAACAATCTCAAGTGAGATAAAAATTT-CTTGTTTCGAGTGAAACAAT-TTCAAAA
1 TTTCAAGAGAAACAATCTCAAGTGAGATAAAAATTTCCTT-TTTCGAGTGAAACAATCTT-AAAA
* * *
703802 TTTGTATTTCAA-GAGAAAGTGTCTCAAGTGA
64 CTTGTATTTCAAGGA-AAACTATCTCAAGTGA
703833 GATAATTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
105 7 0.09
106 71 0.91
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (106 bp):
TTTCAAGAGAAACAATCTCAAGTGAGATAAAAATTTCCTTTTTCGAGTGAAACAATCTTAAAACT
TGTATTTCAAGGAAAACTATCTCAAGTGATATGAAATTTTG
Found at i:703957 original size:67 final size:66
Alignment explanation
Indices: 703731--703978 Score: 288
Period size: 63 Copynumber: 3.8 Consensus size: 66
703721 AAGTGATATG
* * * * *
703731 AAATTT-TGTTTCAAGGGAAACAATCTCAAGTGAGATAAAAATTTCTTGTTTCGAGTGAAACAAT
1 AAATTTGTATTTCAAGAGAAACTATCTCAAGTGAGAT-AAAA-TT-TTGTTTTGAATGAAACAAT
703795 TTCA
63 TTCA
* * **
703799 AAATTTGTATTTCAAGAGAAAGTGTCTCAAGTGAGAT--AATTTT-TTTTGAATGAAATGATTTC
1 AAATTTGTATTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTTGAATGAAACAATTTC
703861 A
66 A
*
703862 AAATTTGTATTTCAAGAGAAAATATCTCAAGTGAGATAAAAATTTTGTTTTGAATGAAACAATTT
1 AAATTTGTATTTCAAGAGAAACTATCTCAAGTGAGAT-AAAATTTTGTTTTGAATGAAACAATTT
703927 CA
65 CA
* * * * * *
703929 AACTTTGTGTTTCAAGGGAAACTGTCTCAAGTGAGATGAACTTTTGTTTT
1 AAATTTGTATTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTT
703979 AAGGGAAACA
Statistics
Matches: 155, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
63 51 0.33
64 2 0.01
65 2 0.01
66 19 0.12
67 50 0.32
68 6 0.04
69 25 0.16
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (66 bp):
AAATTTGTATTTCAAGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTTGAATGAAACAATTTC
A
Found at i:709040 original size:139 final size:140
Alignment explanation
Indices: 708684--709150 Score: 536
Period size: 139 Copynumber: 3.4 Consensus size: 140
708674 GAAGGCTCTA
* * * *
708684 TATTAACCCTAAT-AATTCTTTAACAAATTATTGAACCAAAT-A-ATCAAAATGGAACCTCAAGC
1 TATTAA-CCTAATCAA-T-TTTAACCAATTATTGAATCGAATAATATTAAAATGGAACCTCAAG-
** * * * * * *
708746 ATAAAATTGATGACCAAATAAAAAATTCTCTTAAATTAAAGGACTAAATATGAAATTAATCCTAT
62 A-AAAAGCGACGACCAAATTAAGAATTCCCTTAAATTAAAGGACTAAATATGAAATTAAGCCTAA
* *
708811 AGTGGAGGCTTTAA-
126 AGTGGAAGCTCTAAT
* * * *
708825 TATTAACCCTAACCAATTTTAGCCAATTATTGGATCAAAT-A-ATTAAAATGGAACCTCAAGAAA
1 TATTAA-CCTAATCAATTTTAACCAATTATTGAATCGAATAATATTAAAATGGAACCTCAAGAAA
* *
708888 AAGCGAGGACCAAATTAAGAATTCCCTTAAATTAAAGGACTAAATATGAAATTAAGCCTAAAGTA
65 AAGCGACGACCAAATTAAGAATTCCCTTAAATTAAAGGACTAAATATGAAATTAAGCCTAAAGTG
708953 GAAGCTCTAAT
130 GAAGCTCTAAT
* * * ** *
708964 TATTAA-CTAATTAATTTTAACCAATTGTTGAATCGAATAATATTAAAATGGAACTTTGAGCAAA
1 TATTAACCTAATCAATTTTAACCAATTATTGAATCGAATAATATTAAAATGGAACCTCAAGAAAA
* *
709028 AGCGACGACCAAATTAAGAATTCCCCTAAATTAAAGGACTAAATATAAAATTAAGCCTAAAGTGG
66 AGCGACGACCAAATTAAGAATTCCCTTAAATTAAAGGACTAAATATGAAATTAAGCCTAAAGTGG
*
709093 ATGCTCTAAT
131 AAGCTCTAAT
* * *
709103 TATTAACCTAGTCAATTTTAACCAAATATTGAATGGAATAAT-TTAAAA
1 TATTAACCTAATCAATTTTAACCAATTATTGAATCGAATAATATTAAAA
709151 GTTTAGGGAC
Statistics
Matches: 284, Mismatches: 37, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
137 26 0.09
138 67 0.24
139 108 0.38
140 68 0.24
141 13 0.05
142 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (140 bp):
TATTAACCTAATCAATTTTAACCAATTATTGAATCGAATAATATTAAAATGGAACCTCAAGAAAA
AGCGACGACCAAATTAAGAATTCCCTTAAATTAAAGGACTAAATATGAAATTAAGCCTAAAGTGG
AAGCTCTAAT
Found at i:710406 original size:55 final size:55
Alignment explanation
Indices: 710276--710415 Score: 156
Period size: 55 Copynumber: 2.5 Consensus size: 55
710266 GCCCGATTTG
* * * * * *
710276 TTTTCTCAAGCGCCGTACATGGCCGCTAGTCAAATAATCTCAGATGTCTATATTG
1 TTTTCTCAAGCACCATACATGGCTGCTAGTCAAATAATCACAGATGTCGATATTA
* * * *
710331 TTTTCTCAATCATCACACATGACTGCTAGTCAAATAATCACAGATGTACGA-ATTA
1 TTTTCTCAAGCACCATACATGGCTGCTAGTCAAATAATCACAGATGT-CGATATTA
**
710386 TTTTCTTGAGCACCATACATGGCTGCTAGT
1 TTTTCTCAAGCACCATACATGGCTGCTAGT
710416 AGGTCTTATT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
55 66 0.97
56 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (55 bp):
TTTTCTCAAGCACCATACATGGCTGCTAGTCAAATAATCACAGATGTCGATATTA
Found at i:710915 original size:38 final size:38
Alignment explanation
Indices: 710873--710950 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
710863 AAAAACCGAT
710873 TTGGTTTTTCCCAGCTCTTGAGCTTCTCACTCTCTCAA
1 TTGGTTTTTCCCAGCTCTTGAGCTTCTCACTCTCTCAA
710911 TTGGTTTTTCCCAGCTCTTGAGCTTCTCACTCTCTCAA
1 TTGGTTTTTCCCAGCTCTTGAGCTTCTCACTCTCTCAA
710949 TT
1 TT
710951 TTATCTCTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.13, C:0.31, G:0.13, T:0.44
Consensus pattern (38 bp):
TTGGTTTTTCCCAGCTCTTGAGCTTCTCACTCTCTCAA
Found at i:711397 original size:5 final size:5
Alignment explanation
Indices: 711387--711563 Score: 354
Period size: 5 Copynumber: 35.4 Consensus size: 5
711377 GACTGTGAAG
711387 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
711437 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
711487 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
711537 TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
711564 GGGTAAATTA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 172 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:719746 original size:31 final size:31
Alignment explanation
Indices: 719689--719756 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
719679 TGGAAAGATA
* *
719689 AAAGAAATAGTTTAAGGAAATGAATGAAAAG-
1 AAAGAAATAGTCTAAGAAAATGAATG-AAAGC
*
719720 AAAGAAATGGTCTAAGAAAA-GTAATGAAAGC
1 AAAGAAATAGTCTAAGAAAATG-AATGAAAGC
719751 AAAGAA
1 AAAGAA
719757 GGAATAGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (31 bp):
AAAGAAATAGTCTAAGAAAATGAATGAAAGC
Found at i:725681 original size:18 final size:18
Alignment explanation
Indices: 725658--725702 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
725648 TTCATGCATC
725658 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
*
725676 TAGTTCATTGAATAATGT
1 TAGTTCATTGAATAAAGT
725694 TAGTTCATT
1 TAGTTCATT
725703 AATCAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:727337 original size:19 final size:19
Alignment explanation
Indices: 727309--727355 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
727299 TATGTTTTAA
727309 TATGCCTCATTTATTATAT
1 TATGCCTCATTTATTATAT
*
727328 TATGCTTCATTTATTATAT
1 TATGCCTCATTTATTATAT
727347 TATGCCTCA
1 TATGCCTCA
727356 CTAAGTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (19 bp):
TATGCCTCATTTATTATAT
Done.