Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016380.1 Corchorus olitorius cultivar O-4 contig16413, 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: 79350
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:620 original size:338 final size:339
Alignment explanation
Indices: 4--2220 Score: 2467
Period size: 338 Copynumber: 6.6 Consensus size: 339
1 GGT
*
4 TTTTCCTTTTTTTTCCGAATT-ATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATAAAACC
1 TTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACC
* * * *
68 AACTCCTTAAATCTAAGGAGGCTAAGATTTGGTTAAATGAATTTAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * * * * **
133 TGCCAAAAATCAAGGAAAACTG-AGTCGTGGCCCCAGAACGCATTTTTACTTTTAAGCCAAAAGT
130 TGCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAAC
* * * *
197 CATGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACGGAACCGAAAATTTTTTCCTCA
195 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCA
*
262 ATTCTTTGCCAAAATACTCCTAAAAGATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCA
260 ATTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCA
*
327 CACTTCAAATAACGA
325 CACTTCAAATAATGA
*
342 TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAACCA
1 TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACCA
*
407 AATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTTCT
66 AATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
* *
472 TCCAAAAATCAAGCAAAACT-AACTCGGGGCCTCGGAACGCATTTTGACTTTTAAGCCAAAAACC
131 GCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAACC
* * *
536 GTGATGGTTAGTACACGATTTCGTCTAAAATTTTGCAAAAACTGACCCGAAAATTTCTTCCTTAA
196 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAA
* * * * * *
601 TTCTTTTCCAGAATACTCCTAAAAAGTATATAAATCAGCGCTAAAAATATTAACATGCTTTTCAC
261 TTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCAC
* *
666 AGTTCAAATATTGA
326 ACTTCAAATAATGA
* *
680 CATGTCC-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACC
1 -TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACC
* * *
744 AAATCCTTAACTCTAAAGAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * * **
809 TGCCAAAAATCAAGCAAAACTGAGC-CGGGGTCCCGAAACGCATTTTTTCTTTTAAGCCAAAAAC
130 TGCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAAC
* * *
873 CGTGATGGTTAGTATACGATTTCGGCTAAAATTTAGCAAAAACTAACCCCGAAAATTTTTTTCCT
195 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGA-CCCGAAAA-TTTTTTCCT
* * *
938 CGATTCATTGCCAAAATACTCCTAAAAAATATATAAATCAGCGTCAAAAAGATTGACATGCTTTT
258 CAATTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTT
*
1003 CACACTTCAAAT-ATTA
323 CACACTTCAAATAATGA
*
1019 TTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAACCGAAACAAGATTCAGATGCTCATAAAACC
1 -TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACC
* *
1084 AACTCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * *
1149 TGCCAAAAATCAAGCAAAACTGAGCT-GGGGCCCCGGAACGCATTTTTACTTTTAAGCCAAAAGC
130 TGCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAAC
* *
1213 CGTGATGGTTAGTACACGATCTCGGCTAAAATTTTGCAAAAACTGACCCGAAACTTTTTTCCTCA
195 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCA
* * *
1278 ATTCTTTGCCAAAATACCCCCAAAAAATATATAAATCAGCGCCCAAAAAGATTGACATTCTTTTC
260 ATTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCG-CCAAAAAGATTGACATGCTTTTC
* * *
1343 GCAATTCAAATATTG-
324 ACACTTCAAATAATGA
* *
1358 TTTTCCTTTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCA-AGTGGTCATAAAATC
1 TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA-TGCTCATAAAACC
* * ** * * * *
1421 AAATCCTTAAATCTAATGTGGCTGAGATCAGGTAAGATTAATGTAGATATTTCACGGAGTCTTTC
65 AAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * * * *
1486 TGCCCAAAATCAAGCAAAACTGAGC-CGGGTCCCCTGAACG-----TG--TTTTTAGCCAAAAAC
130 TGCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAAC
* * * **
1543 CGTGATGGTTAGTAAACGATTTTGGCTAAAATTTTGCAAAGAAAACTCACCTAAAAATTTTTT-C
195 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC--A-AAAACTGACCCGAAAATTTTTTCC
* * * ** *
1607 TCAATT-TCTTGCCACAATACT-CAAAAGAAATATATAATTCAATGCCAAAAAAAAAATTGA-AG
257 TCAATTCT-TTGCCAAAATACTCCTAAA-AAATATATAAATCAGCGCC---AAAAAGATTGACA-
* * * ** *
1669 GGTTTTTCAC-GTTCCTGAT-ATCGT
316 TGCTTTTCACACTT-CAAATAAT-GA
* * * *
1693 TTTTCCATTTTTTTCCAAATTTATTTCTGATTAAATCGAAACAAGATTTAGATGCTCATACAAA-
1 TTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA-AAAC
* * * * * *
1757 CAAATACTTAAATCCAATGTGGTTGAGATTTGGTTAAATGAATATAGATATTTCAAGGAGTCTTT
64 CAAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
* * * * * *
1822 AC-GCCAAACATCATGCAATACTGAA-TCGGGGTCCCGGAATGC---GTG---TTT-AGCCAAAA
129 -CTGCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAA
* * * *
1878 A-C---------AGTACACAATTTTGTCTAAAATTTTGCAAAAACTGACCCAAAAATTTTTTCCT
193 ACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCT
** * * *** *
1933 CAATTCTTTGCCAAAATACTCAGAAAAAATATAGAATTCAATACCAAAAAGATTGACAGGCTTTT
258 CAATTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTT
* **
1998 CACACTTCTAATATTATTT
323 CACACTTC-AA-ATAATGA
** * * * * *
2017 TTTTTTTCTTTTTTGCGAATT-ATTTCCAACTAAATCGAATA-AATATTCAGATGCTCATAAAAA
1 TTTTCCT-TTTTTTCCGAATTAATTTCTAATTAAATCGAA-ACAAGATTCAGATGCTCATAAAAC
* ** * *
2080 CAAATCCTTAAATAC-AATGTTGCTTG-GATTTGGTTCGATGAATATAGATATTTCAAGGAGTTT
64 CAAATCCTTAAAT-CTAAGGAGGC-TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* * ** * * * *
2143 TTATGCCAAAAAAACAAGTGAAACTG-AGTCGAGGCCCCGAAACGC-----G--TTTTTAGCCAA
127 TTCTGCC-AAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAA
2200 AAACCGTGATGGTTAGTACAC
191 AAACCGTGATGGTTAGTACAC
2221 AACCAAAAAC
Statistics
Matches: 1619, Mismatches: 200, Indels: 124
0.83 0.10 0.06
Matches are distributed among these distances:
322 24 0.01
323 96 0.06
324 76 0.05
325 40 0.02
326 4 0.00
327 24 0.01
330 47 0.03
331 7 0.00
332 34 0.02
333 22 0.01
334 27 0.02
335 6 0.00
336 9 0.01
337 281 0.17
338 571 0.35
339 59 0.04
340 292 0.18
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (339 bp):
TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACCA
AATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
GCCAAAAATCAAGCAAAACTGAACTCGGGGCCCCGGAACGCATTTTGACTTTTAAGCCAAAAACC
GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAA
TTCTTTGCCAAAATACTCCTAAAAAATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTCAC
ACTTCAAATAATGA
Found at i:1371 original size:678 final size:668
Alignment explanation
Indices: 4--3246 Score: 2892
Period size: 678 Copynumber: 4.8 Consensus size: 668
1 GGT
* *
4 TTTTCCTTTTTTTTCCGAATT-ATTTCTAATTAAATTGAAACAAGATTCAGATGCTCATAAAACC
1 TTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAC
* * * * *
68 AACTCCTTAAATCTAAGGAGGCTAAGATTTGGTTAAATGAATTTAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * * * **
133 TGCCAAAAATCAAGGAAAACTGAGTCGTGG-CCCCAGAACGCATTTTTACTTTTAAGCCAAAAGT
130 TGCCAAAAATCAAGCAAAACTGAGTCGGGGTCCCGA-AACGC-TTTTT-TTTTTAAGCCAAAAAC
* * * * *
197 CATGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACGGAA-CCGAAAATTTTTTCCTC
192 CGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAAAAAC-TAACCCGAAAATTTTTTTCTC
* * *
261 AATTCTTTGCCAAAATACTCCTAAAAGATATATAAATCAGCGCCAAAAAGATTGACATGCTTTTC
256 AATTCTTTGCCAAAATACTCCAAAAAAATATATAAATCAGCGACAAAAAGATTGACATGCTTTTC
* * * *
326 ACACTTCAAATAACGATTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTA
321 ACACTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* *
391 GATGCTCATAAAACCAAATCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATATAGATAT
386 GATGCTCATAAAAACAAATCCTTAAATCTAAGGTGGCTGAGATTTGGTTAGATGAATATAGATAT
* * * *
456 TTCAAGAAGTCTTTCTTCCAAAAATCAAGCAAAACT-AACTCGGGGCCTCGGAACGCATTTTGAC
451 TTCAAGGAGTCTTTCTGCCAAAAATCAAGCAAAACTGAGCTCGGGGCCCCGGAACGC-----G--
* *
520 TTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGTCTAAAATTTTGCAAAAACTGACCCG
509 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
* * * * * * * * *
585 AAAATTTCTTCCTTAATTCTTTTCCAGAATACTCCTAAAAAGTATATAAATCAGCGCTAAAAATA
574 AAAATTTTTTCCTCAATTCTTTGCCAAAATACTCCCAAAAAATATATAAATCAGAGCCAAAAAGA
* * *
650 TTAACATGCTTTTCACAGTTCAAATATTGA
639 TTGACAGGCTTTTCACACTTCAAATATTGA
* * *
680 CATGTCC-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAACC
1 -TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAC
* * *
744 AAATCCTTAACTCTAAAGAGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
*
809 TGCCAAAAATCAAGCAAAACTGAGCCGGGGTCCCGAAACGCATTTTTTCTTTTAAGCCAAAAACC
130 TGCCAAAAATCAAGCAAAACTGAGTCGGGGTCCCGAAACGC-TTTTTT-TTTTAAGCCAAAAACC
* *
874 GTGATGGTTAGTATACGATTTCGGCTAAAATTTAGCAAAAACTAACCCCGAAAATTTTTTTCCTC
193 GTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTAA-CCCGAAAATTTTTTT-CTC
* * * *
939 GATTCATTGCCAAAATACTCCTAAAAAATATATAAATCAGCGTCAAAAAGATTGACATGCTTTTC
256 AATTCTTTGCCAAAATACTCCAAAAAAATATATAAATCAGCGACAAAAAGATTGACATGCTTTTC
* ** *
1004 ACACTTCAAATATTATTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAACCGAAACAAGATTCA
321 ACACTTCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * *
1069 GATGCTCATAAAACCAACTCCTTAAATCTAAGGAGGCTGAGATTTGGTTAGATGAATAAAGATAT
386 GATGCTCATAAAAACAAATCCTTAAATCTAAGGTGGCTGAGATTTGGTTAGATGAATATAGATAT
*
1134 TTCAAGGAGTCTTTCTGCCAAAAATCAAGCAAAACTGAGCT-GGGGCCCCGGAACGCATTTTTAC
451 TTCAAGGAGTCTTTCTGCCAAAAATCAAGCAAAACTGAGCTCGGGGCCCCGGAACGC----GT--
* *
1198 TTTTAAGCCAAAAGCCGTGATGGTTAGTACACGATCTCGGCTAAAATTTTGCAAAAACTGACCCG
510 TTTT-AGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
* * *
1263 AAACTTTTTTCCTCAATTCTTTGCCAAAATACCCCCAAAAAATATATAAATCAGCGCCCAAAAAG
574 AAAATTTTTTCCTCAATTCTTTGCCAAAATACTCCCAAAAAATATATAAATCAGAG-CCAAAAAG
** * *
1328 ATTGACATTCTTTTCGCAATTCAAATATTG-
638 ATTGACAGGCTTTTCACACTTCAAATATTGA
* *
1358 TTTTCCTTTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCA-AGTGGTCATAAAATC
1 TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA-TGCTCATAAAAAC
* ** * * * *
1421 AAATCCTTAAATCTAATGTGGCTGAGATCAGGTAAGATTAATGTAGATATTTCACGGAGTCTTTC
65 AAATCCTTAAATCTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
* * *
1486 TGCCCAAAATCAAGCAAAACTGAG-CCGGGTCCCCTG-AACG----TGTTTTT-AGCCAAAAACC
130 TGCCAAAAATCAAGCAAAACTGAGTCGGGGT-CCC-GAAACGCTTTTTTTTTTAAGCCAAAAACC
* * * *
1544 GTGATGGTTAGTAAACGATTTTGGCTAAAATTTTGCAAAGAAAACTCA-CCTAAAAATTTTTTCT
193 GTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGC--A-AAAACTAACCCGAAAATTTTTTTCT
* * * * * *
1608 CAATT-TCTTGCCACAATACT-CAAAAGAAATATATAATTCAATGCCAAAAAAAAAATTGA-AGG
255 CAATTCT-TTGCCAAAATACTCCAAAA-AAATATATAAATC-A-G-CGACAAAAAGATTGACA-T
* * * * * *
1670 GTTTTTCAC-GTTCCTGATATCGTTTTTCCATTTTTTTCCAAATTTATTTCTGATTAAATCGAAA
314 GCTTTTCACACTT-CTAATATCGTTTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * * * * *
1734 CAAGATTTAGATGCTCATACAAACAAATACTTAAATCCAATGTGGTTGAGATTTGGTTAAATGAA
377 CAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCTAAGGTGGCTGAGATTTGGTTAGATGAA
* * * * * *
1799 TATAGATATTTCAAGGAGTCTTTAC-GCCAAACATCATGCAATACTGA-ATCGGGGTCCCGGAAT
442 TATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCAAGCAAAACTGAGCTCGGGGCCCCGGAAC
* * * *
1862 GCGTGTTTAGCCAAAAA-C---------AGTACACAATTTTGTCTAAAATTTTGCAAAAACTGAC
506 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGAC
* ** * * *
1917 CCAAAAATTTTTTCCTCAATTCTTTGCCAAAATACTCAGAAAAAATATAGAATTCA-ATACCAAA
571 CCGAAAATTTTTTCCTCAATTCTTTGCCAAAATACTCCCAAAAAATATATAAATCAGA-GCCAAA
*
1981 AAGATTGACAGGCTTTTCACACTTCTAATATTATT-T
635 AAGATTGACAGGCTTTTCACACTTC-AA-A-TATTGA
** * * * *
2017 TTTTTTTCTTTTTTGCGAATT-ATTTCCAACTAAATCGAATA-AATATTCAGATGCTCATAAAAA
1 TTTTCCT-TTTTTTCCGAATTAATTTCTAATTAAATCGAA-ACAAGATTCAGATGCTCATAAAAA
* ** * *
2080 CAAATCCTTAAATAC-AATGTTGCTTGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTT
64 CAAATCCTTAAAT-CTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* * ** * *
2144 TATGCCAAAAAAACAAGTGAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
128 TCTGCC-AAAAATCAAGCAAAACTGAGTCGGGGTCCCGAAACGC-TTTTT------------T--
* * * *
2209 TGGTTAGTACACAACCAAAAACCGTGATGGTTAGTACACAATTTCGTCTAAAATTGACCCGGTTT
177 T--TT--T--A-AGCCAAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAA-T-------TTT
** * * * * *
2274 CGGCCAAAAACCGACACGAAAAATTTTTTTCTCACTTTTTTGCCAAAATACTCCGAAAAATTATA
227 --G-CAAAAACTAACCCG-AAAATTTTTTTCTCAATTCTTTGCCAAAATACTCCAAAAAAATATA
** * * * *
2339 TATGTTAACGACAAAAAGTTTGACAGGCTTTTCACACTTCTAATATCGTTTTTCC-TTTTTTCCG
288 TAAATCAGCGACAAAAAGATTGACATGCTTTTCACACTTCTAATATCGTTTTTCCTTTTTTTCCG
* * *
2403 AACTT-ATTTTTAATTAAACCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAA
353 AA-TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCTAA
* * * * *
2467 -TTGGTTGAGATTTGATTCGATTG-ATATAGTTATTTCAAGGAGTCTTTCTGCCAAAAATCAAGC
417 GGTGGCTGAGATTTGGTTAGA-TGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAAGC
* ** * * ** *
2530 AAAACTGAG-TCGGGTCCTTGAAACGCGTTTTTAGCCAAAAACCTTGATAATTAGTAAACGATTT
481 AAAACTGAGCTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
* *
2594 CGGC--------T--AAAAACTGACCC-AAAA-TTTTTCTCTCAAATT-TTTGCCACAAT--TCT
546 CGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTC-CTC-AATTCTTTGCCAAAATACTCC
* * * * * * * *
2644 CAGAAAAATATATAATTCAAAGGCAAAAAGATTGACAGGCTGTTCACACTT-TAGTATCGT
609 CA-AAAAATATATAAATCAGAGCCAAAAAGATTGACAGGCTTTTCACACTTCAAATATTGA
* * * *
2704 TTTTCTTTTTTTTCTGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
1 TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACA
* * * * * * * * *
2769 AATCCTAAAATCCAATGTGACTGAGATTTGG-TACGATTAAAATGGATATTTCAAGGATTTTTTA
66 AATCCTTAAATCTAATGTGGCTAAGATTTGGTTA-GATGAATATAGATATTTCAAGGAGTCTTT-
* * * *
2833 C-GCCAAAAAAACATGCAAAACTGAGTC-GGGTCCCAAAACGC----GTTTTT-AGCCAAAAAAC
129 CTGCC-AAAAATCAAGCAAAACTGAGTCGGGGTCCCGAAACGCTTTTTTTTTTAAGCC-AAAAAC
*
2891 CGTGATGGTTACTAAACGATTTCGGC--------T--AAAAACTGAA-CCGAAAATTTTTTTTCT
192 CGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAAAAACT-AACCCGAAAA-TTTTTTTCT
* * * * * *
2945 CAATT-TTATGCCACAATACT-CAAAAAAAAATTATAATTCAACGTCAAAAAGATTGGC-TGGC-
255 CAATTCTT-TGCCAAAATACTCCAAAAAAATA-TATAAATCAGCGACAAAAAGATTGACAT-GCT
* * *
3006 TTTCACACTTCTAATATCGTTTTTCATTTTTTCTTTTCCGAATTAATTTCTAATTAAATTGAAAT
317 TTTCACACTTCTAATATCGTTTTTC---CTTT-TTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * *
3071 AAGATTCAGATGCTCATAAAAACAAATCCTTAAATAC-AATGTGTCTGTGATTTGGTTCGATGAA
378 AAGATTCAGATGCTCATAAAAACAAATCCTTAAAT-CTAAGGTGGCTGAGATTTGGTTAGATGAA
* * * * * * *** *
3135 TATAGATATTTCAAGGAGTATTTATGCCAAAAACCATGCGAAACTAAG-TCAATGCCCCGAAACG
442 TATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCAAGCAAAACTGAGCTCGGGGCCCCGGAACG
* * * *
3199 TGTTTTTAGCCAAAAACCGTAATGGTTAATACAGGATTTCGGCTAAAA
507 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
3247 ACTGACCCGA
Statistics
Matches: 2132, Mismatches: 305, Indels: 286
0.78 0.11 0.11
Matches are distributed among these distances:
638 38 0.02
639 54 0.03
640 1 0.00
642 4 0.00
643 63 0.03
644 104 0.05
656 26 0.01
657 84 0.04
658 1 0.00
659 12 0.01
660 124 0.06
661 32 0.02
662 3 0.00
663 1 0.00
665 2 0.00
666 2 0.00
667 9 0.00
668 3 0.00
669 5 0.00
670 75 0.04
671 17 0.01
672 7 0.00
673 39 0.02
674 139 0.07
675 17 0.01
676 198 0.09
677 162 0.08
678 347 0.16
679 35 0.02
680 1 0.00
682 2 0.00
684 1 0.00
686 28 0.01
687 116 0.05
688 37 0.02
689 4 0.00
690 48 0.02
691 19 0.01
692 99 0.05
693 64 0.03
694 3 0.00
695 35 0.02
696 12 0.01
697 3 0.00
698 38 0.02
699 6 0.00
702 12 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (668 bp):
TTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACA
AATCCTTAAATCTAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
GCCAAAAATCAAGCAAAACTGAGTCGGGGTCCCGAAACGCTTTTTTTTTTAAGCCAAAAACCGTG
ATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAATTTTTTTCTCAATTC
TTTGCCAAAATACTCCAAAAAAATATATAAATCAGCGACAAAAAGATTGACATGCTTTTCACACT
TCTAATATCGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
TCATAAAAACAAATCCTTAAATCTAAGGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
GGAGTCTTTCTGCCAAAAATCAAGCAAAACTGAGCTCGGGGCCCCGGAACGCGTTTTTAGCCAAA
AACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCC
TCAATTCTTTGCCAAAATACTCCCAAAAAATATATAAATCAGAGCCAAAAAGATTGACAGGCTTT
TCACACTTCAAATATTGA
Found at i:2234 original size:27 final size:27
Alignment explanation
Indices: 2196--2249 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2186 GCGTTTTTAG
2196 CCAAAAACCGTGATGGTTAGTACACAA
1 CCAAAAACCGTGATGGTTAGTACACAA
2223 CCAAAAACCGTGATGGTTAGTACACAA
1 CCAAAAACCGTGATGGTTAGTACACAA
2250 TTTCGTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
CCAAAAACCGTGATGGTTAGTACACAA
Found at i:3206 original size:326 final size:316
Alignment explanation
Indices: 2271--3531 Score: 1214
Period size: 325 Copynumber: 3.9 Consensus size: 316
2261 ATTGACCCGG
* * * * * ** *
2271 TTTCGGCCAAAAACCGACACGAAAAATTTTTTTCTCACTTTTTTGCCAAAATACTC-CGAAAAAT
1 TTTCGGCTAAAAACTGAC-CGAAAATTTTTTTTCTCA-ATTTTTGCCACAATACTCAAAAAAAAA
* * *
2335 TATATATGTTAACGACAAAAAGTTTGACAGGCTTTTCACACTTCTAATATCGTTTTTC-CTTTTT
64 TATA-AT-TCAACGACAAAAAGATTGACAGGC-TTTCACACTTCTAATATCGTTTTTCTTTTTTT
* *
2399 TCCGAACTT-ATTTTTAATTAAACCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
126 TCCGAA-TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
* * * * *
2463 CTAAT-TGGT-TGAGATTTGATTCGATTG-ATATAGTTATTTCAAGGAGTCTTTCTGCCAAAAAT
190 C-AATGT-GTCTGAGATTTGGTTCGA-TGAATATAGATATTTCAAGGAGTATTTATGCCAAAAAA
* ** * ** *
2525 CAAGCAAAACTGAGTCGGGTCCTTGAAACGCGTTTTTAGCCAAAAACCTTGATAATTAGTAAACG
252 CATGCAAAACTGAGTCGGG-CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATAAACG
2590 A
316 A
* * * * *
2591 TTTCGGCTAAAAACTGACCCAAAA-TTTTTCTCTCAAATTTTTGCCACAATTCTCAGAAAAATAT
1 TTTCGGCTAAAAACTGACCGAAAATTTTTTTTCTC-AATTTTTGCCACAATACTCAAAAAAAAAT
* * * *
2655 ATAATTCAAAGGCAAAAAGATTGACAGGCTGTTCACACTT-TAGTATCGTTTTTCTTTTTTTTCT
65 ATAATTCAACGACAAAAAGATTGACAGGCT-TTCACACTTCTAATATCGTTTTTCTTTTTTTTCC
* *
2719 GAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAAAATCCAA
129 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CAA
* * * * * * * *
2784 TGTGACTGAGATTTGGTACGATTAAAATGGATATTTCAAGGATTTTTTACGCCAAAAAAACATGC
193 TGTGTCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTATGCC-AAAAAACATGC
* * *
2849 AAAACTGAGTCGGGTCCCAAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTACTAAACGA
257 AAAACTGAGTCGGGCCCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAATAAACGA
2910 TTTCGGCTAAAAACTGAACCGAAAATTTTTTTTCTCAATTTTATGCCACAATACTCAAAAAAAAA
1 TTTCGGCTAAAAACTG-ACCGAAAATTTTTTTTCTCAATTTT-TGCCACAATACTCAAAAAAAAA
* * *
2975 TTATAATTCAACGTCAAAAAGATTGGCTGGCTTTCACACTTCTAATATCGTTTTTCATTTTTTCT
64 -TATAATTCAACGACAAAAAGATTGACAGGCTTTCACACTTCTAATATCGTTTTTC---TTTT-T
* * *
3040 TTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTCAGATGCTCATAAAAACAAATCCTTAAA
124 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* *
3105 TACAATGTGTCTGTGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTATGCCAAAAACC
189 T-CAATGTGTCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTATGCCAAAAAAC
* * ** * * * *
3170 ATGCGAAACTAAGTCAATGCCCCGAAACGTGTTTTTAGCCAAAAACCGTAATGGTTAATACAGGA
253 ATGCAAAACTGAGTC-GGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATAAACGA
* *
3235 TTTCGGCTAAAAACTGACCCGAAATTTATTTTTTTTCCTAAATTCTTT-CCAACAATACTGAAAA
1 TTTCGGCTAAAAACTGA-CCGAAA---ATTTTTTTT-CTCAATT-TTTGCC-ACAATACTCAAAA
** * * * ** * * **
3299 AAGTATATAATTCAACGCCCAAAAAAATTGA-AGGGTTCTCACGGTTTTAGTATCGTTTTTCCGT
59 AAAAATATAATTCAACG-ACAAAAAGATTGACAGGCTT-TCACACTTCTAATATCGTTTTTCTTT
** * * * * *** **
3363 TTTTTCTAAATTTATTTCTTATTAAATCGAAATAAAATTCAGATGCTCGTTTTAACAAATAGTTA
122 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * *
3428 AATCAAATGTAG-CTGAGATCTAGTTAGATGAATATAGATATTTC-AGGAACTTTTTATGTCAAA
187 AATC-AATGT-GTCTGAGATTTGGTTCGATGAATATAGATATTTCAAGG-AGTATTTATGCCAAA
* * * * * * *
3491 AAACATGAAAAATTGAGACGGGCTCCGGAACACATTTTTAG
249 AAACATGCAAAACTGAGTCGGGCCCCGAAACGCGTTTTTAG
3532 TTAAAAAAAT
Statistics
Matches: 780, Mismatches: 128, Indels: 62
0.80 0.13 0.06
Matches are distributed among these distances:
316 16 0.02
317 95 0.12
318 80 0.10
319 74 0.09
320 29 0.04
321 37 0.05
322 40 0.05
324 20 0.03
325 179 0.23
326 130 0.17
328 27 0.03
329 51 0.07
330 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (316 bp):
TTTCGGCTAAAAACTGACCGAAAATTTTTTTTCTCAATTTTTGCCACAATACTCAAAAAAAAATA
TAATTCAACGACAAAAAGATTGACAGGCTTTCACACTTCTAATATCGTTTTTCTTTTTTTTCCGA
ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAATGT
GTCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTATGCCAAAAAACATGCAAAA
CTGAGTCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATAAACGA
Found at i:3725 original size:23 final size:24
Alignment explanation
Indices: 3699--3747 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3689 TTTATACGTT
3699 TTTCC-TTCTTTTAT-CAGAATTTA
1 TTTCCATT-TTTTATCCAGAATTTA
*
3722 TTTCCATTTTTTTTCCAGAATTTA
1 TTTCCATTTTTTATCCAGAATTTA
3746 TT
1 TT
3748 ACCAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTCCATTTTTTATCCAGAATTTA
Found at i:5920 original size:16 final size:16
Alignment explanation
Indices: 5899--5929 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5889 ATAACCACAA
*
5899 ACAATTAAGGAAAAAG
1 ACAATTAAAGAAAAAG
5915 ACAATTAAAGAAAAA
1 ACAATTAAAGAAAAA
5930 CCTTTTCCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (16 bp):
ACAATTAAAGAAAAAG
Found at i:7959 original size:42 final size:43
Alignment explanation
Indices: 7871--7959 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 43
7861 TTAATGATTC
*
7871 TCTTATTGGATATTTAGTGTCTTAGACATACAGAGAATTGCTATTA
1 TCTTATTGGATATTTAGTGTCTTAG--A-ACAGAGAATTACTATTA
* *
7917 TCTTATTGGATATTTAGTGTCTTAG-ACAGAGTATTATTATTA
1 TCTTATTGGATATTTAGTGTCTTAGAACAGAGAATTACTATTA
7959 T
1 T
7960 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 15 0.38
46 25 0.62
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (43 bp):
TCTTATTGGATATTTAGTGTCTTAGAACAGAGAATTACTATTA
Found at i:16660 original size:14 final size:16
Alignment explanation
Indices: 16635--16666 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16625 CAAAGTGAAA
16635 CATCCTATAATTA-AT
1 CATCCTATAATTACAT
16650 CATCC-ATAATTACAT
1 CATCCTATAATTACAT
16665 CA
1 CA
16667 CAGACTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (16 bp):
CATCCTATAATTACAT
Found at i:28252 original size:22 final size:22
Alignment explanation
Indices: 28227--28282 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
28217 CCTCGTTATT
28227 AAATTTTGATAAC-TTTACTATG
1 AAATTTTGATAACATTTA-TATG
*
28249 AAATTTTAATAACATTTATATG
1 AAATTTTGATAACATTTATATG
*
28271 AAAATTTGATAA
1 AAATTTTGATAA
28283 TCACACAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAACATTTATATG
Found at i:28341 original size:44 final size:44
Alignment explanation
Indices: 28243--28349 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
28233 TGATAACTTT
** * * *
28243 ACTATGAAATTTTAATAACATTTATATGAAAATTTGATAATCAC
1 ACTATGAAATTTTAATAACATCCATATAAAAATTTGAGAACCAC
* * * * *
28287 ACAATAAAATTTTAATAATATCCCTATAAAAATTTGAGAACCCC
1 ACTATGAAATTTTAATAACATCCATATAAAAATTTGAGAACCAC
*
28331 ACTATGAAATTTTGATAAC
1 ACTATGAAATTTTAATAAC
28350 CTTCCAATTA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (44 bp):
ACTATGAAATTTTAATAACATCCATATAAAAATTTGAGAACCAC
Found at i:28385 original size:13 final size:13
Alignment explanation
Indices: 28367--28391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28357 TTACCATATC
28367 AATTTTTGATAAA
1 AATTTTTGATAAA
28380 AATTTTTGATAA
1 AATTTTTGATAA
28392 CATCCTTGTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTTTTGATAAA
Found at i:28723 original size:24 final size:24
Alignment explanation
Indices: 28691--28736 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28681 TCAAAATAGG
28691 TTAAGGCTTACTTTGGCATTGAAA
1 TTAAGGCTTACTTTGGCATTGAAA
*
28715 TTAAGGCTTAGTTTGGCATTGA
1 TTAAGGCTTACTTTGGCATTGA
28737 GGTTGCAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (24 bp):
TTAAGGCTTACTTTGGCATTGAAA
Found at i:29117 original size:16 final size:15
Alignment explanation
Indices: 29096--29138 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
29086 CCAGACCTAA
29096 GTTTTGAAAAATGTTG
1 GTTTTGAAAAATG-TG
*
29112 GTTTTGAAGAA-GTG
1 GTTTTGAAAAATGTG
*
29126 CTTTTGAAAAATG
1 GTTTTGAAAAATG
29139 CTTTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.40
Consensus pattern (15 bp):
GTTTTGAAAAATGTG
Found at i:29523 original size:362 final size:365
Alignment explanation
Indices: 29093--29810 Score: 1015
Period size: 362 Copynumber: 1.9 Consensus size: 365
29083 AAACCAGACC
* * *
29093 TAAGTTTTGAAAAATGTTGGTTTTGAAGAAGTGCTTTTGAAAAATGCTTTTTAAATTTTGGGTTG
1 TAAGTTTTGAAAAATGTTGGTTTTGAAGAAATGCTTTTGAAAAATGCTTTTTAAAATTGGGGTTG
* *
29158 AAAAATGTAATTAATGTTTGGTATTGTTGTAGAAAAATGTGGTTGAGAGATAAAATGTCTAAGAA
66 AAAAATGTAATTAATGTTTGGTATTGTTGTAGAAAAATATGGTTGAGAGATAAAATGTCTAAAAA
* *
29223 GGGTACTAATTAAAATAGAAATAGAAAAAAA-ATTTAAGAGAGTTTAGTCATTTAATATCTAAAA
131 GGGTACTAATTAAAATAGAAATA-AAAAAAATATTTAAAAGAGTTTAGTAATTTAATATCTAAAA
* *
29287 GCACTATTGAAAACGCAAAAGCATCT-AA-A-A-A-TT-A-GCTTTTGAGGTGGAAATTAGCTTT
195 GCACTATTG-AAACGCAAAAGCACCTAAAGATATAGTTGATGCTTTTGAGGTGAAAATTAGCTTT
*
29345 TGACACAAATCATGACTTATTTAATATTGTGTTTGAGGTGAAAAGTAACTTTTTTTTTATCTCCA
259 TGACACAAACCATGACTTATTTAATATTGTGTTTGAGGTGAAAAGTAA---TTTTTTTATCTCCA
29410 AACTCAATTCCAAACCAAGCCTAAGGCTTAATTTGATATTGAGGT
321 AACTCAATTCCAAACCAAGCCTAAGGCTTAATTTGATATTGAGGT
29455 TAAGTTTTGAAAAA-GCTTGGTTTTGAAGAAATGCTTTT-AAAAAGTGCTTTTTAAAATTGGGGT
1 TAAGTTTTGAAAAATG-TTGGTTTTGAAGAAATGCTTTTGAAAAA-TGCTTTTTAAAATTGGGGT
*
29518 TGAAAAATGTAATTAATGTTTGGTATTGTTGTAGAAAAATATGGTTGAGAGATAAAATGTTTAAA
64 TGAAAAATGTAATTAATGTTTGGTATTGTTGTAGAAAAATATGGTTGAGAGATAAAATGTCTAAA
* ** *
29583 AAGGGTACTAATTAAAATGGAGTTAAAAAAAATATTTAAAAGAGTTTAGTAATTTAATGTCTAAA
129 AAGGGTACTAATTAAAATAGAAATAAAAAAAATATTTAAAAGAGTTTAGTAATTTAATATCTAAA
* *
29648 AGCACTTTTGAAACGCAAAAGCACCTAAAGATTAGTTTTTGAGGTTGACTTGGCTTTTGCGGTGA
194 AGCACTATTGAAACGCAAAAGCACCTAAAGA-TA-----T-A-GTTGA--T-GCTTTTGAGGTGA
**
29713 AAATTAGCTTTTGACACAAACCATGACTTATTTGGTATTGTGTTTGAGGTGAAAAGTAATTTTTT
248 AAATTAGCTTTTGACACAAACCATGACTTATTTAATATTGTGTTTGAGGTGAAAAGTAATTTTTT
* *
29778 TATCTTCAAACTCAATTCCAAACCAAGCGTAAG
313 TATCTCCAAACTCAATTCCAAACCAAGCCTAAG
29811 TGACACAGTC
Statistics
Matches: 314, Mismatches: 21, Indels: 28
0.87 0.06 0.08
Matches are distributed among these distances:
361 28 0.09
362 176 0.56
363 1 0.00
365 1 0.00
372 1 0.00
374 2 0.01
375 1 0.00
376 37 0.12
379 67 0.21
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.35
Consensus pattern (365 bp):
TAAGTTTTGAAAAATGTTGGTTTTGAAGAAATGCTTTTGAAAAATGCTTTTTAAAATTGGGGTTG
AAAAATGTAATTAATGTTTGGTATTGTTGTAGAAAAATATGGTTGAGAGATAAAATGTCTAAAAA
GGGTACTAATTAAAATAGAAATAAAAAAAATATTTAAAAGAGTTTAGTAATTTAATATCTAAAAG
CACTATTGAAACGCAAAAGCACCTAAAGATATAGTTGATGCTTTTGAGGTGAAAATTAGCTTTTG
ACACAAACCATGACTTATTTAATATTGTGTTTGAGGTGAAAAGTAATTTTTTTATCTCCAAACTC
AATTCCAAACCAAGCCTAAGGCTTAATTTGATATTGAGGT
Found at i:30766 original size:16 final size:16
Alignment explanation
Indices: 30745--30778 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30735 GCGGAAAACG
30745 AAGCTTACTCGGGGGT
1 AAGCTTACTCGGGGGT
30761 AAGCTTACTCGGGGGT
1 AAGCTTACTCGGGGGT
30777 AA
1 AA
30779 AATTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (16 bp):
AAGCTTACTCGGGGGT
Found at i:31812 original size:1 final size:1
Alignment explanation
Indices: 31806--31832 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31796 GAAAAGCAGC
31806 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
31833 ATGCGTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35769 original size:2 final size:2
Alignment explanation
Indices: 35764--35815 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
35754 CTCTCTCTCT
35764 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
35806 -A GCA CA CA CA
1 CA -CA CA CA CA
35816 AACAAGCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.48, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40395 original size:7 final size:7
Alignment explanation
Indices: 40380--40410 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40370 TGTCTCATGA
*
40380 TGATTGC
1 TGATGGC
40387 TGATGGC
1 TGATGGC
40394 TGATGGC
1 TGATGGC
40401 TGATGGC
1 TGATGGC
40408 TGA
1 TGA
40411 CAGAAGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.39, T:0.32
Consensus pattern (7 bp):
TGATGGC
Found at i:41473 original size:9 final size:9
Alignment explanation
Indices: 41469--41512 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
41459 TTCAATCCCC
41469 ACAATTCCT
1 ACAATTCCT
41478 ACAATTCCT
1 ACAATTCCT
41487 ACAATTCCT
1 ACAATTCCT
*
41496 ACAATCCCT
1 ACAATTCCT
41505 ACAATTCC
1 ACAATTCC
41513 CTCCATTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (9 bp):
ACAATTCCT
Found at i:41490 original size:18 final size:18
Alignment explanation
Indices: 41461--41512 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
41451 AACATGCCTT
*
41461 CAATCCCCACAATTCCTA
1 CAATCCCTACAATTCCTA
*
41479 CAATTCCTACAATTCCTA
1 CAATCCCTACAATTCCTA
41497 CAATCCCTACAATTCC
1 CAATCCCTACAATTCC
41513 CTCCATTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (18 bp):
CAATCCCTACAATTCCTA
Found at i:41491 original size:27 final size:27
Alignment explanation
Indices: 41461--41512 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
41451 AACATGCCTT
*
41461 CAATCCCCACAATTCCTACAATTCCTA
1 CAATCCCCACAATCCCTACAATTCCTA
* *
41488 CAATTCCTACAATCCCTACAATTCC
1 CAATCCCCACAATCCCTACAATTCC
41513 CTCCATTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (27 bp):
CAATCCCCACAATCCCTACAATTCCTA
Found at i:43046 original size:15 final size:15
Alignment explanation
Indices: 43028--43090 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
43018 ATCATTTTCT
43028 TCCTCATCCTCATCC
1 TCCTCATCCTCATCC
* * *
43043 TCCTCTTCCTCTTCT
1 TCCTCATCCTCATCC
** *
43058 TCCTTGTCGTCATCC
1 TCCTCATCCTCATCC
43073 TCCTCATGCC-CATCC
1 TCCTCAT-CCTCATCC
43088 TCC
1 TCC
43091 ATGTGGCTAT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
15 35 0.97
16 1 0.03
ACGTcount: A:0.08, C:0.49, G:0.05, T:0.38
Consensus pattern (15 bp):
TCCTCATCCTCATCC
Found at i:44257 original size:16 final size:15
Alignment explanation
Indices: 44236--44268 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
44226 TTCCATACAA
44236 AAAAGAAACAAAAAAG
1 AAAAGAAA-AAAAAAG
44252 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
44267 AA
1 AA
44269 GCTATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:52256 original size:6 final size:6
Alignment explanation
Indices: 52245--52270 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52235 GGAAGCATCA
52245 TCAGAG TCAGAG TCAGAG TCAGAG TC
1 TCAGAG TCAGAG TCAGAG TCAGAG TC
52271 CGATTCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (6 bp):
TCAGAG
Found at i:66907 original size:15 final size:15
Alignment explanation
Indices: 66884--66920 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
66874 CTGAAGCTGC
*
66884 TTTTTTGGCTGGGGG
1 TTTTCTGGCTGGGGG
*
66899 TTTTCTGGCTGGTGG
1 TTTTCTGGCTGGGGG
66914 TTTTCTG
1 TTTTCTG
66921 CATGCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.38, T:0.51
Consensus pattern (15 bp):
TTTTCTGGCTGGGGG
Found at i:68598 original size:20 final size:20
Alignment explanation
Indices: 68573--68610 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
68563 AAAAATCTTC
68573 AATTGTTCAAAGGAAACAAA
1 AATTGTTCAAAGGAAACAAA
*
68593 AATTGTTCAAGGGAAACA
1 AATTGTTCAAAGGAAACA
68611 GAGAAGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (20 bp):
AATTGTTCAAAGGAAACAAA
Found at i:76390 original size:27 final size:27
Alignment explanation
Indices: 76353--76406 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
76343 ACATGTAAAC
76353 AAAAAAAAAAGGAATAGATTACTTATA
1 AAAAAAAAAAGGAATAGATTACTTATA
*
76380 AAAAAAAAAAGGAATAGATTAGTTATA
1 AAAAAAAAAAGGAATAGATTACTTATA
76407 GTTGTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.13, T:0.22
Consensus pattern (27 bp):
AAAAAAAAAAGGAATAGATTACTTATA
Done.