Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020822.1 Corchorus olitorius cultivar O-4 contig20855, 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: 60597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4398 original size:15 final size:17
Alignment explanation
Indices: 4364--4401 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
4354 TAAACCTCCG
*
4364 AATTTTGTATGTTAATC
1 AATTTTGTATGATAATC
4381 AATTTTGT-TGAT-ATC
1 AATTTTGTATGATAATC
4396 AATTTT
1 AATTTT
4402 ACTAATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (17 bp):
AATTTTGTATGATAATC
Found at i:13345 original size:2 final size:2
Alignment explanation
Indices: 13329--13367 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
13319 CCTACGATCC
*
13329 AT AT AT GAT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13368 CTTATCCGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:13441 original size:42 final size:43
Alignment explanation
Indices: 13382--13472 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
13372 TCCGCATCTC
13382 GCATTTTTAACCAAAAAAA-GTGATGGTTAGTACTCGATTTCG
1 GCATTTTTAACCAAAAAAACGTGATGGTTAGTACTCGATTTCG
13424 GCATTTTTAACCAAAAAAACGTGATGGTTAGTACTCGATTTCG
1 GCATTTTTAACCAAAAAAACGTGATGGTTAGTACTCGATTTCG
13467 GCATTT
1 GCATTT
13473 GCTAAAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 19 0.40
43 29 0.60
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (43 bp):
GCATTTTTAACCAAAAAAACGTGATGGTTAGTACTCGATTTCG
Found at i:14123 original size:321 final size:322
Alignment explanation
Indices: 13474--14135 Score: 815
Period size: 321 Copynumber: 2.1 Consensus size: 322
13464 TCGGCATTTG
* * * * *
13474 CTAAAATTGACCCGAAAAATTTTTCCCAATTTTTTCTGCCACACTACTTAGAAAAAACTATATAA
1 CTAAAAATGACCCGAAAAATTTTTCCCAATTTTTTCTGCAACAATACTCAGAAAAAACAATATAA
* *
13539 TTCAATACCAAAAAGATTAAAAGTTTTTCACGCTTCTAATATCATTTATCCAACTTTTTTCCTAA
66 TTCAACACCAAAAAGATTAAAAGTTTTTCACGCTTCTAATATCATTTATCCAACTTTTTTCCGAA
* *
13604 TTAATTTCTAATTAAATCGAAATAAGAATCAGATGCTCGTAAAAACAAACCCTTATATACAATGT
131 TTAATTTCTAATTAAATCGAAACAAGAATCAGATACTCGTAAAAACAAACCCTTATATACAATGT
* * * * *
13669 GGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTTGCGCCCAAAATCGTGCAAAA
196 AGCTGACATATGGTTAGATAAATATAAATATTTCAAGGAGTCTTTGCGCCCAAAATCATGCAAAA
* * * *
13734 TGGAGTCGGCCTCTGGATCGTGTTGTTAGTCTAAAACCATGATGGTTAGTACACGATTTCGA
261 TGGAGCCGGCCTCCGGATCGTGTTGTTAGTCAAAAACCATGATGGTTAATACACGATTTCGA
* * *
13796 CTAAAAATAGACCCGAAAATTTTTATCTCAA-TTTTT-TGCAACAATACTCATAAAAAA-AATAT
1 CTAAAAAT-GACCCGAAAAATTTT-TCCCAATTTTTTCTGCAACAATACTCAGAAAAAACAATAT
** * * *
13858 AATTCAACGTCAAAAAGATTGAAAGGATTTTT-ACGCTTCTAAATATCGTTT-TCCCA-TTTTTT
64 AATTCAACACCAAAAAGATT-AAAAG-TTTTTCACGCTTCT-AATATCATTTATCCAACTTTTTT
* * * *
13920 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATCCTTATAT-C
126 CCGAATTAATTTCTAATTAAATCGAAACAAGAATCAGATACTCGTAAAAACAAACCCTTATATAC
**
13984 GAATGTAGCTGACATATGGTTAGATAAATATATAA-ATTTTTAGGAGTCTTTGCGCCCAAAATCA
191 -AATGTAGCTGACATATGGTTAGATAAATATA-AATATTTCAAGGAGTCTTTGCGCCCAAAATCA
* * *
14048 TTCAAAATTGAGCCGGGCTCCGGAATGCGT-TT-TTAG-CAAAAAACCATGATGGTTAATACACG
254 TGCAAAATGGAGCCGGCCTCCGG-AT-CGTGTTGTTAGTC-AAAAACCATGATGGTTAATACACG
* *
14110 ATTTTGG
316 ATTTCGA
14117 CTAAAAACTGACCCGAAAA
1 CTAAAAA-TGACCCGAAAA
14136 GTTTATACTC
Statistics
Matches: 292, Mismatches: 37, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
320 2 0.01
321 202 0.69
322 47 0.16
323 36 0.12
324 5 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (322 bp):
CTAAAAATGACCCGAAAAATTTTTCCCAATTTTTTCTGCAACAATACTCAGAAAAAACAATATAA
TTCAACACCAAAAAGATTAAAAGTTTTTCACGCTTCTAATATCATTTATCCAACTTTTTTCCGAA
TTAATTTCTAATTAAATCGAAACAAGAATCAGATACTCGTAAAAACAAACCCTTATATACAATGT
AGCTGACATATGGTTAGATAAATATAAATATTTCAAGGAGTCTTTGCGCCCAAAATCATGCAAAA
TGGAGCCGGCCTCCGGATCGTGTTGTTAGTCAAAAACCATGATGGTTAATACACGATTTCGA
Found at i:15687 original size:655 final size:645
Alignment explanation
Indices: 14356--16300 Score: 2393
Period size: 663 Copynumber: 2.9 Consensus size: 645
14346 CATCTCGCAT
* * * * * * *
14356 TTTTAA-CCAAAAAAATGTGATGGTTAATATACGATTTTCGGCTAAAATTTTGCACAAACTAACC
1 TTTTAAGCC-AAAAACTGTGATGATTAGTACATGA-TTTCGGCTAAAATTTTGCAAAAACTGACC
* *
14420 CGAAAAAAATTTCATAAATTTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAAAAAA
64 CGAAAAAAATTTCCTCAA-TTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGC-AAAAA
* * * *
14485 AGATTGAATGACATTTCACGCTTCTAATATCGGTTTACCTATTTTTTCCGAATTAATTTTTAGTA
127 AGATTGAATGAC--TT-----TTC--ATCTCGGTTTACATATTTTTT-CGAATTAATTTCTAATA
* *
14550 AAATCGAAAAATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGCCTTATGTTTAG
182 AAATCGAAAAATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTG-CTTATATTTGG
*
14615 TTAGATGGATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTC
246 TTAGATGAATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTC
* * *
14680 CCGGAATGCGTTTTTCGCAAAAAAAACAGTGAT-GTTATATACACAATTTCAGCTAAAATTTTGC
311 CCGGAATGCGTTTTTAG-AAAAAAAACAGTGATGGTTA-ATACACGATTTCAGCTAAAATTTTGA
* *
14744 AAAAACTGACCCAAAAAAAATTTTCCTCATTTTTCGCCACAACACTTTTAAAAAATATATAACTC
374 AAAAACTGA-CCAGAAAAAATTTTCCTCATTTTTCGCCACAACACTCTTAAAAAATATATAACTC
* ** * * * *
14809 AATGTAAAAATGATTAAAGGGTTTTCACGCTTCTAATATAGTTTTTCCTATTTTTTTTAGATTTA
438 AATGCAAAAAAAATTAAAGGCTTTTCACGCTTCTAATATCG----T-C--TTTTTTTTCGAATTA
* * * * * *
14874 ATTTCAAATAAAATCAAAACAAGATTTTGATGATTGTAAAAACAAATCATTAAATCCGACGTGGA
496 ATTTCTAATAAAATCAAAACAAGATTATGATGATTGTAAAAACAAATCCTTAAATCCAATGT-GC
*
14939 TGAGATTTGGTTATATGGATATATAGATATTTCAGTGTGTCTTGGTGTTAAAAATCATGCAAAAC
560 TGAGATTT-GTTATATGGATATATAGATATTTCAGTGTGTCTTGGTGTTAAAAATAATGCAAAAC
*
15004 GCAGACGGGACCTCGGAACGCT
624 GCAGACGGGACCTCGGAACGCG
* *
15026 TTTTAAGTCAAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCG
1 TTTTAAGCCAAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
* * * *
15091 AAAAAAATTTCCTCAATTTTTTGCCACAACACTCGTAAAAAATATATAATTCAATTCAAAAAAGA
66 AAAAAAATTTCCTCAATTTTTTGTCACAACACTC-TTAAAAATCTATAATTCAATGCAAAAAAGA
* * *
15156 TTGAATGACTTTTCA-CTCGTTTTACATATTTTTTCTGAATTCATTTCTAATAAGATCGAAAAAT
130 TTGAATGACTTTTCATCTCGGTTTACATATTTTTTC-GAATTAATTTCTAATAAAATCGAAAAAT
* ** * * *
15220 GATTCTGATGGTCGTAAAAATAAATCTTTAAATTCAATTTCGCTTATATTTGGTTAGATGAATAT
194 GATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGT-GCTTATATTTGGTTAGATGAATAT
* *
15285 AGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGTCCCGGAATGCATT
258 AGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTCCCGGAATGCGTT
*
15350 TTTAGAAAAAAAAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGAAAAAAGTGA
323 TTTAG-----AAAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGAAAAAACTGA
* * * * * * *
15415 CCTGAAAAAATTCTCCTCATTTTTTCACCACAACACTGTTACAAATTATATAACTCAATACAAAA
383 CCAGAAAAAATTTTCCTCA-TTTTTCGCCACAACACTCTTAAAAAATATATAACTCAATGCAAAA
* * * **
15480 AAAAATGAAGAGTTTTTCACTATTCTAATATCGT-TTTTTTTTCGAATTAATTTCTAATAAAATC
447 AAAATTAAAG-GCTTTTCACGCTTCTAATATCGTCTTTTTTTTCGAATTAATTTCTAATAAAATC
*
15544 AAAACAAGATTCTGATGATTGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGA-TTGAATTAT
511 AAAACAAGATTATGATGATTGTAAAAACAAATCCTTAAATCCAATGT-GCTGAGATTTG--TTAT
* * * * *
15608 ATGGACAAATAAATATTTCAGTGTGTGTTGGTGTTAAAAATAATGCAAAATTG-AGACAGGG-CC
573 ATGGATATATAGATATTTCAGTGTGTCTTGGTGTTAAAAATAATGCAAAA-CGCAGAC-GGGACC
* *
15671 TCTGAACTCG
636 TCGGAACGCG
* *
15681 TTTTAAGCCGAAAACTGTGATGTTTAGTACATGATTTCGGCTAAAATTTTGC-AAAACTGACCCG
1 TTTTAAGCCAAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
* *
15745 AAAAATATTTCCTCAATTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAGAAAAGAT
66 AAAAAAATTTCCTCAATTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAAAAAAGAT
15810 TGAATGACTTTTCACGCTTCAAATATCGGTTTACCA-ATTTTTTACGAATTAATTTCTAATAAAA
131 TGAATGACTTTTCA----TC-----TCGGTTTA-CATATTTTTT-CGAATTAATTTCTAATAAAA
* *
15874 TCGCAAAATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGATTATATTTGGTTA
185 TCGAAAAATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGT-GCTTATATTTGGTTA
* * *
15939 GAT-AGATATAGATATTTCAGTGTCTCTCGGCACCAAAAATCAAGCAAAACTGAGCCGGGGTCCC
249 GATGA-ATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTCCC
* *
16003 GGAATACGTTTTTAG-CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTT-ACAAA
313 GGAATGCGTTTTTAGAAAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGA-AAA
* * *
16066 AACTGACCCGAAAAAAGTTTTCCTCATTTTCCGCCACAACACTCTCAAAAAATATATAACTCAAT
377 AACTGACCAGAAAAAA-TTTTCCTCATTTTTCGCCACAACACTCTTAAAAAATATATAACTCAAT
*
16131 GCAAAAAAAATTAAAGGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTCGAATTAATT
441 GCAAAAAAAATTAAA-GGCTTTTCACGCTTCTAATATCG----T-CT-TTTTTTTCGAATTAATT
*
16196 TCTAATAAAATCAAAACAAGATTATGATGATTGTAAAAACAAATCCTTAAATCTAATGTGACTGA
499 TCTAATAAAATCAAAACAAGATTATGATGATTGTAAAAACAAATCCTTAAATCCAATGTG-CTGA
* *
16261 GATTTGTTATATGGATATATAGATATTTTAGTGTATCTTG
563 GATTTGTTATATGGATATATAGATATTTCAGTGTGTCTTG
16301 AATTAAATTA
Statistics
Matches: 1109, Mismatches: 126, Indels: 87
0.84 0.10 0.07
Matches are distributed among these distances:
653 42 0.04
654 45 0.04
655 187 0.17
656 5 0.00
657 123 0.11
658 171 0.15
659 3 0.00
661 20 0.02
662 93 0.08
663 210 0.19
664 83 0.07
665 3 0.00
666 2 0.00
668 34 0.03
669 61 0.06
670 26 0.02
671 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (645 bp):
TTTTAAGCCAAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
AAAAAAATTTCCTCAATTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAAAAAAGAT
TGAATGACTTTTCATCTCGGTTTACATATTTTTTCGAATTAATTTCTAATAAAATCGAAAAATGA
TTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGCTTATATTTGGTTAGATGAATATAGA
TATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTCCCGGAATGCGTTTTT
AGAAAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGAAAAAACTGACCAGAAAA
AATTTTCCTCATTTTTCGCCACAACACTCTTAAAAAATATATAACTCAATGCAAAAAAAATTAAA
GGCTTTTCACGCTTCTAATATCGTCTTTTTTTTCGAATTAATTTCTAATAAAATCAAAACAAGAT
TATGATGATTGTAAAAACAAATCCTTAAATCCAATGTGCTGAGATTTGTTATATGGATATATAGA
TATTTCAGTGTGTCTTGGTGTTAAAAATAATGCAAAACGCAGACGGGACCTCGGAACGCG
Found at i:16132 original size:332 final size:329
Alignment explanation
Indices: 14363--16300 Score: 1772
Period size: 332 Copynumber: 5.8 Consensus size: 329
14353 CATTTTTAAC
* * * *
14363 CAAAAAA-ATGTGATGGTTAATATACGATTTTCGGCTAAAATTTTGCACAAACTAACCCGAAAAA
1 CAAAAAACA-GTGATGGTTAATACACGA-TTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAA
* * * * * * * *
14427 AATTTCATAAATTTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAAAAAAAGATTGA
64 ATTTTCCT-CA-TTTTTCGCCACAACACTCTAAAAAATATATAACTCAATGC-AAAAAAGATTGA
* * * *
14492 ATGACATTTCACGCTTCTAATATCGGTTTACCTATTTTTTCCGAATTAATTTTTAGTAAAATCGA
126 ATGACTTTTCACGCTTCTAATATCGGTTTACCAATTTTTT-CGAATTAATTTCTAATAAAATC-A
* * * * * *
14557 AAA-ATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGCCTTATGTTTAGTTAGAT
189 AAACAAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGAT
* *
14621 GGATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGCCGGGGTCCCGGAA
254 AGATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGACGGGGTCCCGGAA
* *
14686 TGCGTTTTTCG
319 TACGTTTTTAG
* *
14697 CAAAAAAAACAGTGAT-GTTATATACACAATTTCAGCTAAAATTTTGCAAAAACTGACCCAAAAA
1 C--AAAAAACAGTGATGGTTA-ATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCC-GAAA
* * *
14761 AAATTTTCCTCATTTTTCGCCACAACACTTTTAAAAAATATATAACTCAATGTAAAAATGATT-A
62 AAATTTTCCTCATTTTTCGCCACAACAC-TCTAAAAAATATATAACTCAATGCAAAAAAGATTGA
* ** * * * * * * *
14825 AAGGGTTTTCACGCTTCTAATATAGTTTTTCCTATTTTTTTTAGATTTAATTTCAAATAAAATCA
126 ATGACTTTTCACGCTTCTAATATCGGTTTACC-A-ATTTTTTCGAATTAATTTCTAATAAAATCA
* * * * * * * * *
14890 AAACAAGATTTTGATGATTGTAAAAACAAATCATTAAATCCGACGTGGATGAGATTTGGTTATAT
189 AAACAAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGAT
* * ** * *
14955 GGATATATAGATATTTCAGTGTGTCTTGGTGTTAAAAATCATGCAAAAC-GCAGAC-GGGACCTC
254 --AGATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTG-AGACGGGGTCC-C
15018 GG-A-ACGCTTTTTAAG
315 GGAATACG-TTTTT-AG
* * * * * *
15033 TC-AAAAACTGTGATGATTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAAA
1 -CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAA
* * * *
15097 ATTTCCTCAATTTTTTGCCACAACACTCGTAAAAAATATATAATTCAATTCAAAAAAGATTGAAT
65 TTTTCCTC-ATTTTTCGCCACAACACTC-TAAAAAATATATAACTCAATGCAAAAAAGATTGAAT
* * *
15162 GACTTTTCA-----C-----TCGTTTTA-CATATTTTTTCTGAATTCATTTCTAATAAGATCGAA
128 GACTTTTCACGCTTCTAATATCGGTTTACCA-ATTTTTTC-GAATTAATTTCTAATAAAATC-AA
* * * * * * *
15216 AA-ATGATTCTGATGGTCGTAAAAATAAATCTTTAAATTCAATTTCGCTTATATTTGGTTAGAT-
190 AACAAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGATA
*
15279 GAATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGTCCCGGAA
255 G-ATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGACGGGGTCCCGGAA
* *
15344 TGCATTTTTAG
319 TACGTTTTTAG
* * * *
15355 AAAAAAAAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGAAAAAAGTGACCTGA
1 ------CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGA
* * * * * * * *
15420 AAAAATTCTCCTCATTTTTTCACCACAACACTGTTACAAATTATATAACTCAATACAAAAAAAAA
60 AAAAATTTTCCTCA-TTTTTCGCCACAACACT-CTAAAAAATATATAACTCAATGCAAAAAAGAT
* **
15485 TGAA-GAGTTTTTCACTATTCTAATATC-GTTT-----TTTTTTCGAATTAATTTCTAATAAAAT
123 TGAATGA-CTTTTCACGCTTCTAATATCGGTTTACCAATTTTTTCGAATTAATTTCTAATAAAAT
* * * * *
15543 CAAAACAAGATTCTGATGATTGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGA-TTGAATTA
187 CAAAACAAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTG-GTTA
* * * * * * ** * *
15607 TATGGACAAATAAATATTTCAGTGTGTGTTGGTGTTAAAAAT-AATGCAAAATTGAGACAGGG-C
251 GAT--AGATATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAA-GCAAAACTGAGACGGGGTC
* *
15670 CTCTGAACT-CGTTTTAAG
313 C-CGGAA-TACGTTTTTAG
** * * * * *
15688 CCGAAAACTGTGATGTTTAGTACATGATTTCGGCTAAAATTTTGC-AAAACTGACCCG-AAAAAT
1 CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAAT
* * * * * *
15751 ATTTCCTCAATTTTTTGTCACAACACTCTTAAAAATCTATAATTCAATGCAGAAAAGATTGAATG
66 -TTTCCTC-ATTTTTCGCCACAACACTCTAAAAAATATATAACTCAATGCAAAAAAGATTGAATG
* *
15816 ACTTTTCACGCTTCAAATATCGGTTTACCAATTTTTTACGAATTAATTTCTAATAAAATCGCAAA
129 ACTTTTCACGCTTCTAATATCGGTTTACCAATTTTTT-CGAATTAATTTCTAATAAAATC-AAAA
* * * *
15881 -ATGATTCTGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGATTATATTTGGTTAGATAGA
192 CAAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGATAGA
* * * *
15945 TATAGATATTTCAGTGTCTCTCGGCACCAAAAATCAAGCAAAACTGAGCCGGGGTCCCGGAATAC
257 TATAGATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGACGGGGTCCCGGAATAC
16010 GTTTTTAG
322 GTTTTTAG
*
16018 CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTACAAAAACTGACCCGAAAAAAG
1 CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAA-
* * * *
16083 TTTTCCTCATTTTCCGCCACAACACTCTCAAAAAATATATAACTCAATGCAAAAAAAATTAAAGG
65 TTTTCCTCATTTTTCGCCACAACACTCT-AAAAAATATATAACTCAATGCAAAAAAGATTGAATG
* * * * *
16148 GCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTCGAATTAATTTCTAATAAAATCAAAAC
129 ACTTTTCACGCTTCTAATATCGGTTTACC-AATTTTTTCGAATTAATTTCTAATAAAATCAAAAC
* * * * * * * *
16213 AAGATTATGATGATTGTAAAAACAAATCCTTAAATCTAATGTGACTGAGATTT-GTTATATGGAT
193 AAGATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGAT--AG
* *
16277 ATATAGATATTTTAGTGTATCTTG
256 ATATAGATATTTCAGTGTGTCTTG
16301 AATTAAATTA
Statistics
Matches: 1276, Mismatches: 251, Indels: 155
0.76 0.15 0.09
Matches are distributed among these distances:
322 49 0.04
323 20 0.02
324 65 0.05
325 58 0.05
326 36 0.03
327 40 0.03
328 110 0.09
329 1 0.00
330 98 0.08
331 112 0.09
332 210 0.16
333 135 0.11
334 178 0.14
335 81 0.06
336 76 0.06
337 5 0.00
338 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (329 bp):
CAAAAAACAGTGATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAAT
TTTCCTCATTTTTCGCCACAACACTCTAAAAAATATATAACTCAATGCAAAAAAGATTGAATGAC
TTTTCACGCTTCTAATATCGGTTTACCAATTTTTTCGAATTAATTTCTAATAAAATCAAAACAAG
ATTCTGATGATCGTAAAAACAAATCCTTAAATCCAATGTGGCTTATATTTGGTTAGATAGATATA
GATATTTCAGTGTGTCTTGGCGCCAAAAATCAAGCAAAACTGAGACGGGGTCCCGGAATACGTTT
TTAG
Found at i:19228 original size:40 final size:40
Alignment explanation
Indices: 19184--19590 Score: 599
Period size: 40 Copynumber: 10.2 Consensus size: 40
19174 TACACGGCAC
* *
19184 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
19224 ATTCACATCCAAATTTTCCAATTGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
19264 CATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
1 -ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * * *
19305 ATTCACATTCAACTTTCCCAATCAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* * * *
19345 AATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
19385 ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
* *
19424 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
19464 ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
*
19503 ATTCACATCCAACA-TTTCCAAATAACATTGAACTTGCCTT
1 ATTCACATCCAA-ATTTTCCAATTAACATTGAACTTGCCTT
19543 ATTCACATCCAAA-TTTCCAA-TAGACATTGAACTTGCCTT
1 ATTCACATCCAAATTTTCCAATTA-ACATTGAACTTGCCTT
19582 AATTCACAT
1 -ATTCACAT
19591 TGGCCCTCAA
Statistics
Matches: 341, Mismatches: 21, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
38 2 0.01
39 96 0.28
40 204 0.60
41 39 0.11
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (40 bp):
ATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
Found at i:19424 original size:79 final size:78
Alignment explanation
Indices: 19184--19590 Score: 625
Period size: 79 Copynumber: 5.1 Consensus size: 78
19174 TACACGGCAC
* * * **
19184 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTTCCAATTGA
1 ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAA-TTTCCAATAAA
19249 CATTGAACTTGCCTT
64 CATTGAACTTGCCTT
* * * *
19264 CATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTTATTCACATTCAACTTTCCCAATCA
1 -ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTT-CCAATAA
19329 ACATTGAACTTGCCTT
63 ACATTGAACTTGCCTT
* *
19345 AATCACATCCAACTTTCCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
1 ATTCACATCCAAATTT-CCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
19410 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
19424 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
1 ATTCACATCC-AAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
19489 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
*
19503 ATTCACATCCAACATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAGAC
1 ATTCACATCCAA-ATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAAC
19568 ATTGAACTTGCCTT
65 ATTGAACTTGCCTT
19582 AATTCACAT
1 -ATTCACAT
19591 TGGCCCTCAA
Statistics
Matches: 306, Mismatches: 15, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
78 2 0.01
79 171 0.56
80 63 0.21
81 70 0.23
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (78 bp):
ATTCACATCCAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACA
TTGAACTTGCCTT
Found at i:19456 original size:119 final size:117
Alignment explanation
Indices: 19184--19590 Score: 577
Period size: 119 Copynumber: 3.4 Consensus size: 117
19174 TACACGGCAC
* * * * * *
19184 ATTCACATTCAAATTTTCCAATTGACATTGAACTTGCCTTATTCACATCCAAATTTTCCAATTGA
1 ATTCACATCCAAA-TTTCCAAATAACATTGAACTTGCCTTAATCACATCCAAA-TTTCCAAATAA
*
19249 CATTGAACTTGCCTTCATTCACATCCAAATTTTCCAATTAACATTGAACTTGCCTT
64 CATTGAACTTGCCTT-ATTCACATCCAAA-TTTCCAATAAACATTGAACTTGCCTT
* * * *
19305 ATTCACATTCAACTTTCCCAATCAACATTGAACTTGCCTTAATCACATCCAACTTTCCCAAATAA
1 ATTCACATCCAAATTTCCAAAT-AACATTGAACTTGCCTTAATCACATCCAAATTT-CCAAATAA
19370 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
*
19424 ATTCACATCCAAAATTTCCAAATAACATTGAACTTGCCTTATTCACATCCAAATTTCC-AATAAA
1 ATTCACATCC-AAATTTCCAAATAACATTGAACTTGCCTTAATCACATCCAAATTTCCAAAT-AA
19488 CATTGAACTTGCCTTATTCACATCCAACATTTCCAA-ATAACATTGAACTTGCCTT
64 CATTGAACTTGCCTTATTCACATCCAA-ATTTCCAATA-AACATTGAACTTGCCTT
19543 ATTCACATCCAAATTTCC-AATAGACATTGAACTTGCCTTAATTCACAT
1 ATTCACATCCAAATTTCCAAATA-ACATTGAACTTGCCTTAA-TCACAT
19591 TGGCCCTCAA
Statistics
Matches: 263, Mismatches: 15, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
117 7 0.03
118 57 0.22
119 106 0.40
120 33 0.13
121 60 0.23
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (117 bp):
ATTCACATCCAAATTTCCAAATAACATTGAACTTGCCTTAATCACATCCAAATTTCCAAATAACA
TTGAACTTGCCTTATTCACATCCAAATTTCCAATAAACATTGAACTTGCCTT
Found at i:22726 original size:2 final size:2
Alignment explanation
Indices: 22719--22790 Score: 74
Period size: 2 Copynumber: 36.5 Consensus size: 2
22709 AAGTTTTAAG
* * * * *
22719 AT AT AT AT AT GT GT GT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
22761 AT AT AC AT AT AT AT AT AT AT A- AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22791 CCAATAATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:22756 original size:16 final size:16
Alignment explanation
Indices: 22737--22790 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
22727 ATGTGTGTAT
*
22737 ATATATATATATACAC
1 ATATATATATATACAA
*
22753 ATATATATATATACAT
1 ATATATATATATACAA
22769 ATATATATATATA-AA
1 ATATATATATATACAA
22784 ATATATA
1 ATATATA
22791 CCAATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATATATATACAA
Found at i:23886 original size:14 final size:14
Alignment explanation
Indices: 23867--23904 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
23857 ACACAAAAAG
23867 TACATATATATACA
1 TACATATATATACA
23881 TACATATAT-TACA
1 TACATATATATACA
*
23894 TA-ATACATATA
1 TACATATATATA
23905 TACAAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TACATATATATACA
Found at i:36532 original size:6 final size:6
Alignment explanation
Indices: 36484--36531 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
36474 CAGCTTGAAG
* *
36484 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA GCAGCA GCAGCA
1 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA
36532 GTAATAGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.46, C:0.33, G:0.21, T:0.00
Consensus pattern (6 bp):
ACAGCA
Found at i:44337 original size:2 final size:2
Alignment explanation
Indices: 44330--44363 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44320 TCCATTGATC
44330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44364 GTCTCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46081 original size:47 final size:46
Alignment explanation
Indices: 46028--46121 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
46018 CAATTTTCTA
*
46028 TGCTTTTACATTAAATTGACAAATACTACTATTAGGTAAGTATAGTT
1 TGCTTTTACATTAAATTGACAAATACCACTATTAGGT-AGTATAGTT
*
46075 TGCTTTTACTTTAAATTGACAAATACCACTATTAGGTAGTATAGTT
1 TGCTTTTACATTAAATTGACAAATACCACTATTAGGTAGTATAGTT
46121 T
1 T
46122 TTAATGCACT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 10 0.22
47 35 0.78
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (46 bp):
TGCTTTTACATTAAATTGACAAATACCACTATTAGGTAGTATAGTT
Found at i:46560 original size:16 final size:16
Alignment explanation
Indices: 46524--46560 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
46514 TTGAATTGAA
*
46524 TAAATTATTAAAAAAT
1 TAAATTATAAAAAAAT
46540 T-AATTATAAAAAAAT
1 TAAATTATAAAAAAAT
46555 TAAATT
1 TAAATT
46561 CAAGTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTATAAAAAAAT
Found at i:48424 original size:16 final size:16
Alignment explanation
Indices: 48399--48480 Score: 74
Period size: 16 Copynumber: 4.8 Consensus size: 16
48389 AATTTCACAT
*
48399 AATAATAATATAATAG
1 AATAAAAATATAATAG
48415 AATAAAAATATAATAG
1 AATAAAAATATAATAG
* *
48431 AATAAAATTATAGTATAT
1 AATAAAAATATA--ATAG
48449 AATATAATTACATATAATAG
1 AATA-AA--A-ATATAATAG
*
48469 AATAAAATTATA
1 AATAAAAATATA
48481 GTAAATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
16 30 0.56
17 1 0.02
18 7 0.13
19 4 0.07
20 7 0.13
21 1 0.02
22 4 0.07
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (16 bp):
AATAAAAATATAATAG
Found at i:48510 original size:54 final size:54
Alignment explanation
Indices: 48397--48512 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
48387 CAAATTTCAC
*
48397 ATAATAA-TAATATAATAGAATAAAAATATAATAGAATAAAATTATAGTATATA
1 ATAATAATTAATATAATAGAATAAAAATATAATAGAATAAAATTATACTATATA
* * *
48450 AT-ATAATTACATATAATAGAATAAAATTATAGTA-AAT-ATATGTATACTATATA
1 ATAATAATTA-ATATAATAGAATAAAAATATAATAGAATAAAAT-TATACTATATA
*
48503 GTAATAATTA
1 ATAATAATTA
48513 TGTAGTAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
52 7 0.13
53 18 0.33
54 29 0.54
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (54 bp):
ATAATAATTAATATAATAGAATAAAAATATAATAGAATAAAATTATACTATATA
Found at i:51912 original size:3 final size:3
Alignment explanation
Indices: 51904--51949 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
51894 ATTGCAACCT
* * * *
51904 CAG CAG CAG CAG CAG CAG CCG CCG CCG CCG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
51950 CCAACTCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.24, C:0.43, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:60125 original size:22 final size:22
Alignment explanation
Indices: 60100--60153 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
60090 ATTTGATTAT
*
60100 AAAATATTGATTGATGTAAAA-A
1 AAAATATT-ATTGATATAAAATA
*
60122 AAAATATTTTTGATATAAAATA
1 AAAATATTATTGATATAAAATA
60144 AAAATATTAT
1 AAAATATTAT
60154 AATAATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAATATTATTGATATAAAATA
Found at i:60367 original size:2 final size:2
Alignment explanation
Indices: 60360--60405 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
60350 ATTATTTGTC
60360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60401 AT AT A
1 AT AT A
60406 AAAGTATGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.