Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009209.1 Corchorus capsularis cultivar CVL-1 contig09230, 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: 65703
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1083 original size:331 final size:330
Alignment explanation
Indices: 1--2759 Score: 3126
Period size: 331 Copynumber: 8.3 Consensus size: 330
* * * * * ** * * *
1 GATTTGTTTTTACAAACATCTAAATCTTGTTTCGTTTTGATTTGAAATTAATTTGTAAAAAAAAA
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCG-GAAAAAATA
* * *
66 GGTAAA-ACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTTTTGGCATTGGATTATATATTTTT
65 -GCAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTT
* * * * *
130 TACGAGTATTGTGGACAAAAATAAAGGAAAAAAATTTCGGGTCAG-TTTTG-AAAAATTTTAGGC
129 TACGAGTAATGTGGCCAAAAATTAAGG-AAAAATTTTTGGGTCAGTTTTTGCAAAAATTTT--GC
* * ** * * *
193 -GAAATCGTGTACTAACGATCACAGTTTTTAGCTAAAAGTGTGTTTCGGGTCCCCGGCTCAGTTT
191 TGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCG-TTCCGGTCCCCGACTCAGTTT
* * * * * *
257 TTCATGATTTTTTGCACCAAGACTCACTAAAATACCTATATTCATTTAACCAAGTCTCAGCCACA
255 TGCATGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACA
*
322 TTTGATTTAAG
320 TTGGATTTAAG
* * ** * *
333 GATTTCTTTTTATGAGTGTCTGAATCATGTTTCGATTTAATCAGAAATTAATTCTG-AAAAATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* * * *
397 GAAATACGATATTAGAAGCGTGAAAAG-CCTTCATTCTTTTTGGCATTGAATTATAAATTTCTTA
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTTA
* *
461 CGAGTAATGTGGCC-AAAATTGAGGAAAACTTTTTAGGGTCAGTTTTTGCAAAAATTTTGCTGAA
131 CGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTT-GGGTCAGTTTTTGCAAAAATTTTGCTGAA
* ** *
525 ATCGTGTACTAACCATCAGAGTTTTTGGCTAAGAAA-AAGTTCTGGATCCCCGACTCAGTTTTGC
195 ATCGTGTACTAACCATCACAGTTTTTGGCTAA-AAACGCGTTCCGG-TCCCCGACTCAGTTTTGC
* * * * * *
589 ATGATTTTTGGCGCCAAGACTGACTAAAATATGTGTATTCAACGAA-CAAATCTCAGCAACATTG
258 ATGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG
653 GATTTAAG
323 GATTTAAG
* * *
661 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATATAATCAGCAATTAATTCGAAAAAAATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* * * * * *
726 CAAATATGATATTAGAAGCATGAAAATCCCTTCATTCTTATTCGCATTGAATTATAAATTTCTTA
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTTA
* * * * *
791 CGAGTACTATGGCCAAAAATTGAGGAAAAATTTTTTGGTCAGTTTTTGCAAACATTTTGCTGAAA
131 CGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTGGGTCAGTTTTTGCAAAAATTTTGCTGAAA
* * * *
856 TCGTCTACTAACCATCACAGTTTTTAGCTATAAACGCGTTCCGGTGCCCCGACT-ATATTTTGCA
196 TCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGT-CCCCGACTCA-GTTTTGCA
* * * *
920 TGATTTTTGGCGCCATGATTCAGTTAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
259 TGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
*
985 ATTTAAT
324 ATTTAAG
* * * *
992 GTTTTGTTTTTACGAGCATCTAAATCATGTTTCGATATAATCAGAAATTAATTTGGAAAAAATAC
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* ** * *
1057 CAAATATGATATTAGAAGCGTGAAAATACCTTCATTCTAATTGGAATTGAATTATATATTTTTTA
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTTA
* * * * * *
1122 CTAGTATTATGGCCAAAAATTGAGGAAAATATTTTTGGGTCAGTTTTTGAAAAAATTTAGCTGAA
131 CGAGTAATGTGGCCAAAAATTAAGGAAAA-ATTTTTGGGTCAGTTTTTGCAAAAATTTTGCTGAA
** *
1187 ATCGTGTACT-ACCATCACAGTTTTTTCCTAAAAACGCGTTCCGGGTCCTCGACTCAGTTTTGCA
195 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCC-GGTCCCCGACTCAGTTTTGCA
* * * * *
1251 TGATTTTTTTGCGCCAAGACTCACTGAAATACCTATATTCATCTAACCAAGTCTCAGCCACATTT
259 TGA-TTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTG
1316 GATTTAAG
323 GATTTAAG
* * * * * * *
1324 GATTTCTCTTTATGAGTATCTGAATCATGTTTTGATTTAATCAGAAATTAATTCTG-AAAAATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* * * * **
1388 GAAATACGATATTAGAAGCGTGAAAAGCCCTCCATTCATT-TCGGCATTGAATTATAAATTCCTT
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTC-TTATTGGCATTGAATTATATATTTTTT
* * * *
1452 ACGAGTAATGTGGCCAAAAATTGAGGAAAACTTTTTCGGATTAGTTTTTGCAAAAATTTTGCTGA
130 ACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTT-GGGTCAGTTTTTGCAAAAATTTTGCTGA
* * *
1517 AATCGTGTACTAACCATCACAGTTTTTTTTAGCTAAAAACGCGTTTCGGTGCCCCGACT-ATATT
194 AATCGTGTACTAACCATCACAG---TTTTTGGCTAAAAACGCGTTCCGGT-CCCCGACTCA-GTT
* ** * ** * *
1581 TTGCATGATTTTTGGCGTCATTATTTGCTTAAATATCTATATTCATCTAATCAAATCTCAGCCAC
254 TTGCATGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCAC
1646 ATTGGATTTAAG
319 ATTGGATTTAAG
* * ** * * **
1658 AATTCGTTTTTACGAGCATCCGAATCATGTTTCGATATAATCAGAAATTAATTGGGGGAAAATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* ** * * *
1723 CAAATATGATATTAGAAATGTGAACATCCCTTCATTCTTATTGGAATTGAATTATATATTTTTTA
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTTA
* ** *
1788 CGAGTATTGTGGCCAAAAATTAAGG-AAAATTTTCCAGGTCAGTTTTTGCAAAAATTTAGCTGAA
131 CGAGTAATGTGGCCAAAAATTAAGGAAAAATTTT-TGGGTCAGTTTTTGCAAAAATTTTGCTGAA
* * * * *
1852 ATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGTGTTCCGGATTCCCGACCCAGTTTTGCA
195 ATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGG-TCCCCGACTCAGTTTTGCA
* * * * *
1917 TGATTTTTGGCGCCAAGATTCACTAAAATATGTGTATTCATCTAACCAAATCTCAACTACATTGG
259 TGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
1982 ATTTAAG
324 ATTTAAG
* * * *
1989 GATTTGTTTTTACGTGCATC-AGAATAATGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAT-
1 GATTTGTTTTTACGAGCATCTA-AATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATA
* * * * * *
2052 GGAAATACAATATTTGAAGCGTGAAAAGCCTTTCATTCTTTTTGGCATTGAATTATATATTTTAT
65 GCAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTT
*
2117 ACGAGTAATGTGGCCAAAATTTAAGGAAAAAATTTTT-GGTCAGTTTTTG-AAAAATTTTAGGC-
130 ACGAGTAATGTGGCCAAAAATTAAGG-AAAAATTTTTGGGTCAGTTTTTGCAAAAATTTT--GCT
* * * * *
2179 GAAATCTTGTACTAACCATCACAATTTTTGGCTAAAAACGCATCTCGGGTCACC-AGCTCAGTTT
192 GAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGT-TCCGGTCCCCGA-CTCAGTTT
* * * * * *
2243 TGCATGATTTTTGTCGCCAAGACTCACTGAAATATCTATAATCCTTTAACCAAATATCAGCCACA
255 TGCATGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACA
*
2308 TTGGATTTAGG
320 TTGGATTTAAG
* ** * * *
2319 GAATACTTTTTACGAGCATCTGAATAATGTTTCGATTTATTCAGAAATTAATTCGGAAAAAATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* *
2384 CAAATACGATATTAGAAGCGTGAAAAACCCTTCAATCTT-TTAGGCATTGAAATT-TATATTTTT
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATT-GGCATTG-AATTATATATTTTT
*
2447 TACCAGTAATGTGGCCAAAAATTAAGGAAAAAATTTTTGGGTCAGTTTTTG-AAAAATTTTAGGC
129 TACGAGTAATGTGGCCAAAAATTAAGG-AAAAATTTTTGGGTCAGTTTTTGCAAAAATTTT--GC
* * *
2511 -GAAATCGTCTACTAACCATCACAGTTTTTGGCTAAAAACGTGTTTCGAGTCCCC-AGCTCAGTT
191 TGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCG-GTCCCCGA-CTCAGTT
* * * * * **
2574 TTGCATAATTTTTGCCGTCAAGAGTCACTGAAATA-CATATATTTGTCTAACCAAATCTCAGCCA
254 TTGCATGATTTTTGGCGCCAAGACTCACTAAAATATC-TATATTCATCTAACCAAATCTCAGCCA
*
2638 CATTTGATTTAAG
318 CATTGGATTTAAG
* * * * *
2651 GATTTGTTTTTACGAGCATCTAATTTATGTTTCGATTTAGTCAGAAATTAATTCGTAAAATATAG
1 GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
* * *
2716 CAAATACAATATTAGAAGTGTGAAAA-CCCTTCATTCTTTTTGGC
66 CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGC
2760 CAAAAATTGA
Statistics
Matches: 2068, Mismatches: 313, Indels: 93
0.84 0.13 0.04
Matches are distributed among these distances:
327 7 0.00
328 92 0.04
329 186 0.09
330 459 0.22
331 610 0.29
332 439 0.21
334 159 0.08
335 116 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
GATTTGTTTTTACGAGCATCTAAATCATGTTTCGATTTAATCAGAAATTAATTCGGAAAAAATAG
CAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCTTATTGGCATTGAATTATATATTTTTTA
CGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTGGGTCAGTTTTTGCAAAAATTTTGCTGAAA
TCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGTCCCCGACTCAGTTTTGCATG
ATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAT
TTAAG
Found at i:4978 original size:334 final size:332
Alignment explanation
Indices: 3711--6130 Score: 2638
Period size: 334 Copynumber: 7.3 Consensus size: 332
3701 ATAAGAAGCG
* * *
3711 TGAATTATATTTTTTTTACGAGAATTGTGGCCAAAATTTGAGGAAAATTTTTTCCGGTCAGTTTT
1 TGAATTATA-TATTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTT-CGGTCAGTTTT
* * *
3776 TGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTTGGCT-GAAA--TGTTCCGA
64 TGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAG-TTTTTTGGCTAAAAACGAGTTCCGG
* * ** *
3838 GGTCTCGACTATATTTTGCAAAATTTTTGGCGCCAAGATTCATTGAAATATCTATATTCATCT-A
128 GGCCCCGACTATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCTAA
* * * * *
3902 CGAAAATCTCAACTACATTGGATTTAAGGGTTTGTTTTTACGAGAATCTGAATCATGTTTCGATT
193 C-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATT
* * * *
3967 TAATTAGAAATTAATTTGG-AAAAAATAACAAATACGATATTAGAAGCGTCAAAAGCCCTTCATA
257 TAATCAGAAATTAATTCGGAAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTCATA
4031 CTTTTTGGCAT
322 CTTTTTGGCAT
* * * * *
4042 TGGATTATATGTTTTTTACGAGTATTGTGGCCAAAACTCGAGGAAAATTTTTTCGGATAAGTTTT
1 TGAATTATAT-ATTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTCGG-TCAGTTTT
* * *
4107 TGCCAAAATTTAGCTAAAATCGTGTACTAACCATCACAGTTTTTTGGCTGAAAACGCA-TTCCGG
64 TGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACG-AGTTCCGG
** * * * * *
4171 GGCCTTGACTATATTTTGCATGGTTTTTGGCACCAAGATTTAATGAAATATCTACATTCATCTAA
128 GGCCCCGACTATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCTAA
* * * * * * * *
4236 CAAAATCTCAGCCACATTGGATTTAAGGATCTCTTTTTGCGAAGTATCTAAACCTTGTTTCGATT
193 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG-AGCATCTGAATCATGTTTCGATT
*
4301 TAATCAGAAATTAATTCGGAAAAAAATTATG-AAATACGATATTAGAAGCGTGAAAAGTCCTTCA
257 TAATCAGAAATTAATTCGGAAAAAAA-TA-GCAAATACGATATTAGAAGCGTGAAAAGCCCTTCA
* * *
4365 TTCTTGTTGGTAT
320 TACTTTTTGGCAT
* *
4378 TGAATTATATATTTTTTTACGAGAATTGTGGCCAAAAATTGAGGAAAA-CTTTTCGGGTCAGTTT
1 TGAATTATATA--TTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTC-GGTCAGTTT
* *
4442 TTGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTTGGTTGAAAACGCA-TTCC
63 TTGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAG-TTTTTTGGCTAAAAACG-AGTTCC
* * *
4506 GGGGCCTCGACTATATTTTGCAAGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATTT
126 GGGGCCCCGACTATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCT
* * * *
4571 AACAAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCAAGTTTCGGT
191 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGAT
* * *
4636 TTAATCAGAAATTAATTCGGTAAAAAAATAGCAAATACGATATTGGAAACGTGAAAAGCCGTTCA
256 TTAATCAGAAATTAATTCGG-AAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTCA
*
4701 TACTTTTTAGCAT
320 TACTTTTTGGCAT
* *
4714 TGAATTATATATTTTTATGAGTATTGTGGCCAACAATTGAGGAAAATTTTTTCGGTTCAGTTTTT
1 TGAATTATATATTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTCGG-TCAGTTTTT
* * * *
4779 GCAAAAATTTAGCTGAAATTGTATACTAATCATCACAGTTGTTTTTGGCTAAAAACGAGTTCTGG
65 GCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAG-T-TTTTTGGCTAAAAACGAGTTCCGG
*
4844 GGCCCCGACTATATTTTGCATGA-TTTTGACGCCAAGATTCACTGAAATAT-TATATTCATCTAA
128 GGCCCCGACTATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCTAA
* * ** *
4907 CCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTC
193 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTT
* * * *
4972 AATCAGAAATTAATTCGG--GAAAATAGGAAATACGATATTAGAAACGTCAAAAGCCCTTCATTA
258 AATCAGAAATTAATTCGGAAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTCA-TA
5035 -TTTTTGGCAT
322 CTTTTTGGCAT
* * * *
5045 TGAAATATATACTTTTGACGAGTATTGTGGCCAAAAAATTGCGGAAAATTTTTTCGG-CATAGGT
1 TGAATTATATA-TTTTTACGAGTATTGTGGCC-AAAAATTGAGGAAAATTTTTTCGGTC--AGTT
** * * * *
5109 TTTGCAAAGTTTTAAC--CAACCGTGTACTAACCATCACAG-TTTTT-GC-----ACGCGTTCCG
62 TTTGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGAGTTCCG
* * * * * * *
5165 AGGCCCC-AGCTCA-GTTTTGCATGGTTTTTGGCGGCAAAACTCACTAAAATATCTATATTCATC
127 GGGCCCCGA-CT-ATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATC
* * ** *
5228 TAACCAAATCTCAGCCACTTTGGATTTAAGGATTCTCTTTTTATAAGTATCTGAATCATGTTTCG
190 TAACCAAATCTCAGCCACATTGGATTTAAGGATT-TGTTTTTACGAGCATCTGAATCATGTTTCG
* * *
5293 ATTTAATTAGAAATTAATTTGGAAAAAAATA-CGAAATACGATATTAGAAGCGTTAAAAGCCCTT
254 ATTTAATCAGAAATTAATTCGGAAAAAAATAGC-AAATACGATATTAGAAGCGTGAAAAGCCCTT
* *
5357 CAT-TTTTTTGGTAT
318 CATACTTTTTGGCAT
* * * * * *
5371 TGAGTTATATATTTTTTTACAAGTATTGTGGCTAAAAATTGAGGAAAATTATTTCTGGTTAGCTT
1 TGAATTATATA--TTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTC-GGTCAGTTT
* *
5436 TTGCAAAAATTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGCAG-TCCA
63 TTGCAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACG-AGTTCCG
* * * ** * *
5500 GGTCCCTG-CTCA-GTTTTGCATGATTTTTGGCGCCAAGACACACAGAAATATCCATATTCATCT
127 GGGCCCCGACT-ATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCT
* * *
5563 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTCCAAACATCTGAATCATGTTTCGAT
191 AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGAT
* * *
5628 TTAATCAGAAATTAATTCGGAAAAAAAATAGCAAATATGATATTAGTAGCGTGAAAATCCCTTCA
256 TTAATCAGAAATTAATTCGG-AAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTCA
* *
5693 TTCTTATTGGCAT
320 TACTTTTTGGCAT
* **
5706 TGAATTATATAAATTTTACGAGTATTGTGGGAAAAAAATTGAGGAAAATTTTTTCAGGTCAGTTT
1 TGAATTATAT-ATTTTTACGAGTATTGT-GGCCAAAAATTGAGGAAAATTTTTTC-GGTCAGTTT
* * * *
5771 TTGCAAAAATTTAACTGAAATCGTGTATTAACAACCATCACAG-TTTTTAGCTAAAAACGCGTTC
63 TTGCAAAAATTTAGCTGAAATCGTGTACT---AACCATCACAGTTTTTTGGCTAAAAACGAGTTC
** * * * * * *
5835 CGGATCCCCGGCTCA-GTTTTACATGATTTTTGGCGCCAAGACTCA-T----TATGTGTATTCAT
125 CGGGGCCCCGACT-ATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCAT
** * * * * *
5894 CTAACCAAATCTCAGTTACATTGGATGTAAGGATTTGTTTTTACAAACATCTCAATCATATTTCG
189 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
5959 ATTTAATCATAAATTAATTCGG--AAAAATAGAAAATACGATATTAGAAACATGAAAAG-CTTTC
254 ATTTAATCAGAAATTAATTCGGAAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTC
*
6021 ATTCTTTTTGGCAT
319 ATACTTTTTGGCAT
* * * * ** *
6035 CGAATTATATATTTTTTTA-GAGTATTGTGGCAAAAAATTGAGAAAAATATTTTCAGAACAATTT
1 TGAATTATATA--TTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTC-GGTCAGTTT
* * * *
6099 TTACAATAATTTTAACTAAAATCGTGTACTAA
63 TTGCAA-AAATTTAGCTGAAATCGTGTACTAA
6131 TTATTAGTAT
Statistics
Matches: 1794, Mismatches: 233, Indels: 129
0.83 0.11 0.06
Matches are distributed among these distances:
321 1 0.00
322 25 0.01
323 23 0.01
324 41 0.02
325 43 0.02
326 57 0.03
327 58 0.03
328 62 0.03
329 60 0.03
330 50 0.03
331 169 0.09
332 20 0.01
333 266 0.15
334 293 0.16
335 169 0.09
336 231 0.13
337 183 0.10
338 43 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
TGAATTATATATTTTTACGAGTATTGTGGCCAAAAATTGAGGAAAATTTTTTCGGTCAGTTTTTG
CAAAAATTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTTGGCTAAAAACGAGTTCCGGGGC
CCCGACTATATTTTGCATGATTTTTGGCGCCAAGATTCACTGAAATATCTATATTCATCTAACCA
AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAAT
CAGAAATTAATTCGGAAAAAAATAGCAAATACGATATTAGAAGCGTGAAAAGCCCTTCATACTTT
TTGGCAT
Found at i:12297 original size:21 final size:20
Alignment explanation
Indices: 12260--12298 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12250 TTTAGAAGCA
*
12260 ATTAATTAAAAGCATTAAAC
1 ATTAATTAAAAACATTAAAC
12280 ATTAATTAAAAACAATTAA
1 ATTAATTAAAAAC-ATTAA
12299 GGAAGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAAACATTAAAC
Found at i:12392 original size:74 final size:74
Alignment explanation
Indices: 12310--12456 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
12300 GAAGGGAATG
*
12310 TGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTTTAGTCA
1 TGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCA
12375 TCC-GAAAAC
66 -CCTGAAAAC
*
12384 TGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCA
1 TGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCA
12449 CCTGAAAA
66 CCTGAAAA
12457 GTGTGAAAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 2 0.03
74 68 0.97
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.20
Consensus pattern (74 bp):
TGTAATTACGAAAAAGGGTAGAAGCAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTCA
CCTGAAAAC
Found at i:12758 original size:33 final size:33
Alignment explanation
Indices: 12716--12833 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 33
12706 TAGTACCGGT
* *
12716 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
12749 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
12782 GCCGCCCCAGGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG-T-AGG
*
12815 GCCGCCCCAGGGGGACGGC
1 GCCGCCCCAGGGGGGCGGC
12834 ACCGGTGGGG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 71 0.97
34 1 0.01
35 1 0.01
ACGTcount: A:0.12, C:0.35, G:0.42, T:0.11
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:24275 original size:24 final size:22
Alignment explanation
Indices: 24232--24275 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
24222 ACTGTGGCCG
*
24232 TGAGATTCGGCCATAGTGGTCA
1 TGAGATTCGGCCATAATGGTCA
24254 TGAGATTCGGCCACATAATGGT
1 TGAGATTCGG-C-CATAATGGT
24276 ACACAGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (22 bp):
TGAGATTCGGCCATAATGGTCA
Found at i:24482 original size:22 final size:22
Alignment explanation
Indices: 24417--24483 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
24407 GGGTTAGTAT
*
24417 GTGGCCGTGAGATTCGGCCATA
1 GTGGCCGTGAGATTCGGCCATG
*
24439 GTGGCCGTGGGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
*
24461 GTGGTCGTGAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
24483 G
1 G
24484 CTACTTTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.13, C:0.21, G:0.42, T:0.24
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATG
Found at i:25007 original size:17 final size:17
Alignment explanation
Indices: 24985--25029 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
24975 TCTTTTGGAG
24985 TCTTGTCTACTTGAGAC
1 TCTTGTCTACTTGAGAC
**
25002 TCTTGTCT-C-CAAGAC
1 TCTTGTCTACTTGAGAC
25017 TCTTGTCTACTTG
1 TCTTGTCTACTTG
25030 CTTGAGACTC
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (17 bp):
TCTTGTCTACTTGAGAC
Found at i:27937 original size:27 final size:27
Alignment explanation
Indices: 27896--27960 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
27886 CCGAATATGC
*
27896 TCCCTCTGTTCCTTTTTAATTG-TCTCTT
1 TCCCT-TGTTTCTTTTTAATTGTTC-CTT
27924 TCCCTTGTTTCTTTTTAATTGTTCCTT
1 TCCCTTGTTTCTTTTTAATTGTTCCTT
*
27951 TCCATTGTTT
1 TCCCTTGTTT
27961 TCCAGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.60
Consensus pattern (27 bp):
TCCCTTGTTTCTTTTTAATTGTTCCTT
Found at i:31262 original size:3 final size:3
Alignment explanation
Indices: 31256--31304 Score: 53
Period size: 3 Copynumber: 14.7 Consensus size: 3
31246 ATAAAACCCG
31256 GAA GAA GAA GAA GAAA GAA GAAA GAA GAAA GAA GAAA GAA GAAA GAA
1 GAA GAA GAA GAA G-AA GAA G-AA GAA G-AA GAA G-AA GAA G-AA GAA
31303 GA
1 GA
31305 TTGCTCATCG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 26 0.63
4 15 0.37
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31275 original size:7 final size:7
Alignment explanation
Indices: 31257--31304 Score: 89
Period size: 7 Copynumber: 7.0 Consensus size: 7
31247 TAAAACCCGG
31257 AAGAAG-
1 AAGAAGA
31263 AAGAAGA
1 AAGAAGA
31270 AAGAAGA
1 AAGAAGA
31277 AAGAAGA
1 AAGAAGA
31284 AAGAAGA
1 AAGAAGA
31291 AAGAAGA
1 AAGAAGA
31298 AAGAAGA
1 AAGAAGA
31305 TTGCTCATCG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:33682 original size:14 final size:15
Alignment explanation
Indices: 33653--33693 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
33643 TATCTAACCT
33653 AAAAGAAAAATGAAA
1 AAAAGAAAAATGAAA
*
33668 AAAAAAAAAAT-AAA
1 AAAAGAAAAATGAAA
*
33682 AGAAGAAAAATG
1 AAAAGAAAAATG
33694 GTTATAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAATGAAA
Found at i:36210 original size:13 final size:13
Alignment explanation
Indices: 36192--36218 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36182 GCATAATGCC
36192 TAACTATATAGAA
1 TAACTATATAGAA
36205 TAACTATATAGAA
1 TAACTATATAGAA
36218 T
1 T
36219 GACTTCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
TAACTATATAGAA
Found at i:42664 original size:26 final size:26
Alignment explanation
Indices: 42634--42687 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
42624 TGTGTGGTTC
42634 AAAA-GAAGACAAACATGGT-GAATTAT
1 AAAAGGAA-ACAAACAT-GTAGAATTAT
*
42660 AAAAGGAAACAAAGATGTAGAATTAT
1 AAAAGGAAACAAACATGTAGAATTAT
42686 AA
1 AA
42688 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 2 0.08
26 20 0.80
27 3 0.12
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.19
Consensus pattern (26 bp):
AAAAGGAAACAAACATGTAGAATTAT
Found at i:44590 original size:261 final size:261
Alignment explanation
Indices: 44126--44648 Score: 1037
Period size: 261 Copynumber: 2.0 Consensus size: 261
44116 TACGTTACTC
44126 TTCTTCTCATTTTTAAAACTTTAAATTCTTGTTATACCAACATGCTCAAAAAATAGAAACAGACC
1 TTCTTCTCATTTTTAAAACTTTAAATTCTTGTTATACCAACATGCTCAAAAAATAGAAACAGACC
44191 AATCACTATATAATTTAAATAAATTTTTAACTTAATTAATTTTAAAAAATATGAATAATTAATGA
66 AATCACTATATAATTTAAATAAATTTTTAACTTAATTAATTTTAAAAAATATGAATAATTAATGA
*
44256 TTAGACAATTTATTTTAACTTTTAAACTTGATAATAATACTTTTGTTAGTTTATATTTTAATTGA
131 TTAGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTGTTAGTTTATATTTTAATTGA
44321 AAATTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTCAATTAAATAAAA
196 AAATTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTCAATTAAATAAAA
44386 A
261 A
44387 TTCTTCTCATTTTTAAAACTTTAAATTCTTGTTATACCAACATGCTCAAAAAATAGAAACAGACC
1 TTCTTCTCATTTTTAAAACTTTAAATTCTTGTTATACCAACATGCTCAAAAAATAGAAACAGACC
44452 AATCACTATATAATTTAAATAAATTTTTAACTTAATTAATTTTAAAAAATATGAATAATTAATGA
66 AATCACTATATAATTTAAATAAATTTTTAACTTAATTAATTTTAAAAAATATGAATAATTAATGA
44517 TTAGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTGTTAGTTTATATTTTAATTGA
131 TTAGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTGTTAGTTTATATTTTAATTGA
44582 AAATTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTCAATTAAATAAAA
196 AAATTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTCAATTAAATAAAA
44647 A
261 A
44648 T
1 T
44649 AGTGTTTTCA
Statistics
Matches: 261, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
261 261 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.40
Consensus pattern (261 bp):
TTCTTCTCATTTTTAAAACTTTAAATTCTTGTTATACCAACATGCTCAAAAAATAGAAACAGACC
AATCACTATATAATTTAAATAAATTTTTAACTTAATTAATTTTAAAAAATATGAATAATTAATGA
TTAGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTGTTAGTTTATATTTTAATTGA
AAATTTTAAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATTGAATTCAATTAAATAAAA
A
Found at i:44837 original size:70 final size:70
Alignment explanation
Indices: 44761--44985 Score: 297
Period size: 70 Copynumber: 3.1 Consensus size: 70
44751 TAACTAAAAT
*
44761 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
44826 AGTTG
66 AGTTG
*
44831 AGTAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
44896 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * * *
44909 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAAAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
44974 AGTTG
66 AGTTG
44979 AGTAAAA
1 AGTAAAA
44986 CTATAAAAAC
Statistics
Matches: 137, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
70 64 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 62 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:44838 original size:78 final size:77
Alignment explanation
Indices: 44755--44993 Score: 341
Period size: 78 Copynumber: 3.2 Consensus size: 77
44745 TTTTTTTAAC
*
44755 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
44820 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
44833 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
44898 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * * *
44911 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAAAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
44969 TTTTTAGTTGAG
66 TTTTTAGTTGAG
44981 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
44994 ACCTAAACAG
Statistics
Matches: 152, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 54 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 87 0.57
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:45137 original size:1 final size:1
Alignment explanation
Indices: 45131--45157 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
45121 CAATTTTACA
45131 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
45158 GTAGGAGATC
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:53133 original size:19 final size:19
Alignment explanation
Indices: 53109--53149 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53099 GGATTTTTTT
*
53109 TTTTGGAGCGTTCTACCGC
1 TTTTGGAGCGTACTACCGC
*
53128 TTTTGGAGCGTACTATCGC
1 TTTTGGAGCGTACTACCGC
53147 TTT
1 TTT
53150 GCGGTCATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTTGGAGCGTACTACCGC
Found at i:53186 original size:47 final size:47
Alignment explanation
Indices: 53113--53211 Score: 144
Period size: 47 Copynumber: 2.1 Consensus size: 47
53103 TTTTTTTTTT
* * * * *
53113 GGAGCGTTCTACCGCTTTTGGAGCGTACTATCGCTTTGCGGTCATTG
1 GGAGCGTACTACCGCTATTGGAGCGTACTACCACTTCGCGGTCATTG
*
53160 GGAGCGTACTACCGCTATTGGGGCGTACTACCACTTCGCGGTCATTG
1 GGAGCGTACTACCGCTATTGGAGCGTACTACCACTTCGCGGTCATTG
53207 GGAGC
1 GGAGC
53212 ACTCCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.28
Consensus pattern (47 bp):
GGAGCGTACTACCGCTATTGGAGCGTACTACCACTTCGCGGTCATTG
Found at i:53320 original size:27 final size:25
Alignment explanation
Indices: 53263--53312 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
53253 AATGGGCGTA
*
53263 CGGCGCTCTCTTGATGGTGGGCGCG
1 CGGCGCTCTCTTGATGGTGGGCACG
*
53288 CGGCGCTTTCTTGTTATGGTGGGCA
1 CGGCGCTCTCTTG--ATGGTGGGCA
53313 TGTGGCGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.06, C:0.24, G:0.40, T:0.30
Consensus pattern (25 bp):
CGGCGCTCTCTTGATGGTGGGCACG
Found at i:53385 original size:26 final size:26
Alignment explanation
Indices: 53355--53701 Score: 228
Period size: 26 Copynumber: 12.8 Consensus size: 26
53345 GACGCCCTCT
* * * *
53355 TCCAAGATTGATGTACGTCGCTCTCT
1 TCCAAAATGGATGTACGGCGCTCTCG
* *
53381 TCCAAGATGGTGTATGTACAGCGCTCTCG
1 TCCAAAAT-G-G-ATGTACGGCGCTCTCG
*
53410 TCCAAAATGGTGGATGTACGACGCTCAT-G
1 TCCAAAA---TGGATGTACGGCGCTC-TCG
* * *
53439 TCCAAAATGGTTGTACGACGCTCTCT
1 TCCAAAATGGATGTACGGCGCTCTCG
*
53465 TCCAAGATGGATGTACGGCGCTCTCG
1 TCCAAAATGGATGTACGGCGCTCTCG
53491 TCCAAAATGGTGGATGTACGGCGCTCAT-G
1 TCCAAAA---TGGATGTACGGCGCTC-TCG
* *
53520 TCCAAAATGGTTGTACGGCGCTCTCT
1 TCCAAAATGGATGTACGGCGCTCTCG
* *
53546 TCCAAGATGGTTGTACGGCG--CTCG
1 TCCAAAATGGATGTACGGCGCTCTCG
*
53570 TCCAAAATGGTGGATGTATGGCGCTCATC-
1 TCCAAAA---TGGATGTACGGCGCTC-TCG
*
53599 -CAAAATAGTGGATGTACGGCG--CTCG
1 TCCAAA-A-TGGATGTACGGCGCTCTCG
53624 TCCAAAATAGTGGATGTACGGCG--CTCG
1 TCC-AAA-A-TGGATGTACGGCGCTCTCG
** *
53651 TCCAAAATGGTGGATGTATAGCGCTCTCT
1 TCCAAAA---TGGATGTACGGCGCTCTCG
*
53680 TCCAAGATGGATGTACGGCGCT
1 TCCAAAATGGATGTACGGCGCT
53702 TTTCTTCCAA
Statistics
Matches: 264, Mismatches: 30, Indels: 54
0.76 0.09 0.16
Matches are distributed among these distances:
24 11 0.04
25 4 0.02
26 102 0.39
27 62 0.23
28 5 0.02
29 73 0.28
30 5 0.02
31 1 0.00
32 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (26 bp):
TCCAAAATGGATGTACGGCGCTCTCG
Found at i:53509 original size:81 final size:79
Alignment explanation
Indices: 53366--53745 Score: 401
Period size: 81 Copynumber: 4.6 Consensus size: 79
53356 CCAAGATTGA
* * *
53366 TGTACGTCGCTCTCTTCCAAGATGGTGTATGTACAGCGCTCTCGTCCAAAATGGTGGATGTACGA
1 TGTACGGCGCTCTCTTCCAAGAT-G-G-ATGTAC-G-GCGCTCGTCCAAAATGGTGGATGTACGG
53431 CGCTCATGTCCAAAATGGT
61 CGCTCATGTCCAAAATGGT
*
53450 TGTACGACGCTCTCTTCCAAGATGGATGTACGGCGCTCTCGTCCAAAATGGTGGATGTACGGCGC
1 TGTACGGCGCTCTCTTCCAAGATGGATGTACGGCG--CTCGTCCAAAATGGTGGATGTACGGCGC
53515 TCATGTCCAAAATGGT
64 TCATGTCCAAAATGGT
* *
53531 TGTACGGCGCTCTCTTCCAAGATGGTTGTACGGCGCTCGTCCAAAATGGTGGATGTATGGCGCTC
1 TGTACGGCGCTCTCTTCCAAGATGGATGTACGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTC
*
53596 A--TCCAAAATAGTGGA
66 ATGTCC-AAA-A-TGGT
* * **
53611 TGTACGGCGCTCGTC--CAAAATAGTGGATGTACGGCGCTCGTCCAAAATGGTGGATGTATAGCG
1 TGTACGGCGCTC-TCTTC-CAAGA-TGGATGTACGGCGCTCGTCCAAAATGGTGGATGTACGGCG
* * *
53674 CTC-TCTTCCAAGATGGA
63 CTCAT-GTCCAAAATGGT
* * * *
53691 TGTACGGCGCTTTTCTTCCAAGATGATGGATGTACAGCGCTCGTCCGACATGGTG
1 TGTACGGCGC-TCTCTTCC-A-A-GATGGATGTACGGCGCTCGTCCAAAATGGTG
53746 AGCGTGCTCC
Statistics
Matches: 261, Mismatches: 18, Indels: 35
0.83 0.06 0.11
Matches are distributed among these distances:
77 3 0.01
78 3 0.01
79 34 0.13
80 35 0.13
81 127 0.49
82 5 0.02
83 31 0.12
84 23 0.09
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (79 bp):
TGTACGGCGCTCTCTTCCAAGATGGATGTACGGCGCTCGTCCAAAATGGTGGATGTACGGCGCTC
ATGTCCAAAATGGT
Found at i:53676 original size:27 final size:27
Alignment explanation
Indices: 53381--53668 Score: 267
Period size: 27 Copynumber: 10.7 Consensus size: 27
53371 GTCGCTCTCT
* * *
53381 TCCAAGATGGTGTATGTACAGCGCTCTCG
1 TCCAAAATGGTGGATGTAC-G-GCGCTCG
*
53410 TCCAAAATGGTGGATGTACGACGCTCATG
1 TCCAAAATGGTGGATGTACGGCGCTC--G
*
53439 TCCAAAATGGT---TGTACGACGCTC-
1 TCCAAAATGGTGGATGTACGGCGCTCG
* *
53462 TCTTC-CAA-GATGGATGTACGGCGCTCTCG
1 TC--CAAAATGGTGGATGTACGGCG--CTCG
53491 TCCAAAATGGTGGATGTACGGCGCTCATG
1 TCCAAAATGGTGGATGTACGGCGCTC--G
*
53520 TCCAAAATGGT---TGTACGGCGCTCTCT
1 TCCAAAATGGTGGATGTACGGCG--CTCG
*
53546 TCCAAGATGGT---TGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACGGCGCTCG
* *
53570 TCCAAAATGGTGGATGTATGGCGCTCA
1 TCCAAAATGGTGGATGTACGGCGCTCG
*
53597 TCCAAAATAGTGGATGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACGGCGCTCG
*
53624 TCCAAAATAGTGGATGTACGGCGCTCG
1 TCCAAAATGGTGGATGTACGGCGCTCG
53651 TCCAAAATGGTGGATGTA
1 TCCAAAATGGTGGATGTA
53669 TAGCGCTCTC
Statistics
Matches: 221, Mismatches: 19, Indels: 40
0.79 0.07 0.14
Matches are distributed among these distances:
23 4 0.02
24 15 0.07
25 1 0.00
26 48 0.22
27 87 0.39
28 9 0.04
29 57 0.26
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (27 bp):
TCCAAAATGGTGGATGTACGGCGCTCG
Found at i:53906 original size:29 final size:29
Alignment explanation
Indices: 53872--54203 Score: 233
Period size: 29 Copynumber: 11.3 Consensus size: 29
53862 ATCTTGGGGT
*
53872 AGTACTACCACTTCGTGAGTTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* *
53901 AGTACTACCATTTCGTGGGCTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
*
53930 AGTACTACCACTTCGTGAGTTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* * *
53959 AGTACTACCGCTTTGTGAACTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* *
53988 AGTACTACCACTTTGTGAACTTT-G-GGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* **** ***
54015 CGTACTACCACCTT--TTTTTTTTTTTGGG
1 AGTACTACCA-CTTCGTGAGCTTTGGAGGG
** * * ** *
54043 TTTCCCATGACTTGGT-ATTTTTTGCCTTTGGAGGG
1 AGTACTACCACTTCGTGA------G-CTTTGGAGGG
* **
54078 AGTACTACCACTTCGTGAGTTTTATAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* * **
54107 CGTACTACCACTTCTTGCTCTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
* * *
54136 AGTACTACCACTTCTTGAACTTTGGAGAG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
*
54165 AGTACTACCACTTTGTGAGCTTTGGAGGG
1 AGTACTACCACTTCGTGAGCTTTGGAGGG
*
54194 CGTACTACCA
1 AGTACTACCA
54204 TTTCTTGCCC
Statistics
Matches: 235, Mismatches: 55, Indels: 26
0.74 0.17 0.08
Matches are distributed among these distances:
26 4 0.02
27 15 0.06
28 11 0.05
29 188 0.80
30 1 0.00
35 15 0.06
36 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (29 bp):
AGTACTACCACTTCGTGAGCTTTGGAGGG
Found at i:54189 original size:148 final size:148
Alignment explanation
Indices: 53920--54189 Score: 368
Period size: 148 Copynumber: 1.8 Consensus size: 148
53910 ATTTCGTGGG
* *
53920 CTTTGGAGGGAGTACTACCACTTCGTGAGTTTTGGAGGGAGTACTACCGCTTTGTGAACTTTGGA
1 CTTTGGAGGGAGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTTTGTGAACTTTGGA
* * ****
53985 GGGAGTACTACCACTTTGTGAACTTTGGGGCGTACTACCACCTTTTTTTTTTTTTGGGTTTCCCA
66 GGGAGTACTACCACTTTGTGAACTTTGGGGAGTACTACCACCTTTTGTGAGCTTTGGGTTTCCCA
54050 TGACTTGGTATTTTTTGC
131 TGACTTGGTATTTTTTGC
* * **
54068 CTTTGGAGGGAGTACTACCACTTCGTGAGTTTTATAGGGCGTACTACCACTTCT-TGCTCTTTGG
1 CTTTGGAGGGAGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTT-TGTGAACTTTGG
54132 AGGGAGTACTACCACTTCT-TGAACTTTGGAGAGAGTACTACCA-C-TTTGTGAGCTTTGG
65 AGGGAGTACTACCACTT-TGTGAACTTTGG-G-GAGTACTACCACCTTTTGTGAGCTTTGG
54190 AGGGCGTACT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
148 92 0.87
149 4 0.04
150 10 0.09
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (148 bp):
CTTTGGAGGGAGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTTTGTGAACTTTGGA
GGGAGTACTACCACTTTGTGAACTTTGGGGAGTACTACCACCTTTTGTGAGCTTTGGGTTTCCCA
TGACTTGGTATTTTTTGC
Found at i:54241 original size:206 final size:206
Alignment explanation
Indices: 53872--54244 Score: 543
Period size: 206 Copynumber: 1.8 Consensus size: 206
53862 ATCTTGGGGT
* * *
53872 AGTACTACCACTTCGTGAGTTTTGGAGGGAGTACTACCATTTCGTGGGCTTTGGAGGGAGTACTA
1 AGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTTCGTGCGCTTTGGAGGGAGTACTA
** * *
53937 CCACTTCGTGAGTTTTGGAGGGAGTACTACCGCTTTGTGAACTTTGGAGGGAGTACTACCACTTT
66 CCACTTCGTGAACTTTGGAGAGAGTACTACCACTTTGTGAACTTTGGAGGGAGTACTACCACTTT
* *
54002 GTGAACTTTGGGGCGTACTACCACCTTTTTTTTTTTTTGGGTTTCCCATGACTTGGTATTTTTTG
131 GTGAACTTCGGGGCGTACTACCACCTCTTTTTTTTTTTGGGTTTCCCATGACTTGGTATTTTTTG
54067 CCTTTGGAGGG
196 CCTTTGGAGGG
* * * *
54078 AGTACTACCACTTCGTGAGTTTTATAGGGCGTACTACCACTTCTTGCTCTTTGGAGGGAGTACTA
1 AGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTTCGTGCGCTTTGGAGGGAGTACTA
* * *
54143 CCACTTCTTGAACTTTGGAGAGAGTACTACCACTTTGTGAGCTTTGGAGGGCGTACTACCA-TTT
66 CCACTTCGTGAACTTTGGAGAGAGTACTACCACTTTGTGAACTTTGGAGGGAGTACTACCACTTT
* **
54207 CTTGCCCCTTCGGGGCGTACTACCACC-CTTTTTTTTTT
131 -GTG-AACTTCGGGGCGTACTACCACCTCTTTTTTTTTT
54245 GCATCTGCTC
Statistics
Matches: 146, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
205 3 0.02
206 124 0.85
207 19 0.13
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (206 bp):
AGTACTACCACTTCGTGAGTTTTAGAGGGAGTACTACCACTTCGTGCGCTTTGGAGGGAGTACTA
CCACTTCGTGAACTTTGGAGAGAGTACTACCACTTTGTGAACTTTGGAGGGAGTACTACCACTTT
GTGAACTTCGGGGCGTACTACCACCTCTTTTTTTTTTTGGGTTTCCCATGACTTGGTATTTTTTG
CCTTTGGAGGG
Found at i:54638 original size:20 final size:20
Alignment explanation
Indices: 54610--54647 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54600 AAATTTTATC
54610 TAGGCTGTATGCCTTTGGGG
1 TAGGCTGTATGCCTTTGGGG
*
54630 TAGGTTGTATGCCTTTGG
1 TAGGCTGTATGCCTTTGG
54648 AAATTTTATC
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:0.11, C:0.13, G:0.37, T:0.39
Consensus pattern (20 bp):
TAGGCTGTATGCCTTTGGGG
Found at i:54658 original size:48 final size:48
Alignment explanation
Indices: 54584--54695 Score: 197
Period size: 48 Copynumber: 2.3 Consensus size: 48
54574 ATTCTATCTT
*
54584 GGCTGTATGCCTTTGGAAATTTTATCTAGGCTGTATGCCTTTGGGGTA
1 GGCTGTATGCCTTTGGAAATTTTATCTAGACTGTATGCCTTTGGGGTA
* *
54632 GGTTGTATGCCTTTGGAAATTTTATCTAGACTTTATGCCTTTGGGGTA
1 GGCTGTATGCCTTTGGAAATTTTATCTAGACTGTATGCCTTTGGGGTA
54680 GGCTGTATGCCTTTGG
1 GGCTGTATGCCTTTGG
54696 GGGGTGCCCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (48 bp):
GGCTGTATGCCTTTGGAAATTTTATCTAGACTGTATGCCTTTGGGGTA
Found at i:54806 original size:58 final size:58
Alignment explanation
Indices: 54719--54968 Score: 306
Period size: 58 Copynumber: 4.3 Consensus size: 58
54709 TAGGTTGTGA
* * * * * * * *
54719 GACCAAGGGATGCTTGTTTTTCTTCTTGCACGTGTGGGGGATGCCCA-TTGGATCGTGT
1 GACCGAGGGATGCTCGATTTTCTTATTACATGAGTGGGGGATGCCCACTTGG-CCGTGT
* * * *
54777 GACCGAGGGATGCTCGGTTTTCTTATTGCATGAGTGGGGGATGCCCACTGGGCCATGT
1 GACCGAGGGATGCTCGATTTTCTTATTACATGAGTGGGGGATGCCCACTTGGCCGTGT
* *
54835 GACCAAGGGATGCTCGATTTAT-TTATTACATGAGTGGGGGATGCCCACTTGGCCGTGC
1 GACCGAGGGATGCTCGATTT-TCTTATTACATGAGTGGGGGATGCCCACTTGGCCGTGT
** * *
54893 GACCGAGGGATGCTCGATCGTCTTATTACATGAGTGGGAGATGCCCACTTGGTCGTGT
1 GACCGAGGGATGCTCGATTTTCTTATTACATGAGTGGGGGATGCCCACTTGGCCGTGT
54951 GACCGAGGGATGCTCGAT
1 GACCGAGGGATGCTCGAT
54969 CGATATTGCT
Statistics
Matches: 168, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
57 1 0.01
58 163 0.97
59 4 0.02
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (58 bp):
GACCGAGGGATGCTCGATTTTCTTATTACATGAGTGGGGGATGCCCACTTGGCCGTGT
Done.