Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009798.1 Corchorus capsularis cultivar CVL-1 contig09819, 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: 65666
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1015 original size:195 final size:195
Alignment explanation
Indices: 666--1038 Score: 581
Period size: 195 Copynumber: 1.9 Consensus size: 195
656 ACAAAAAGAA
* *
666 GCGCCAAAATGGCTAACATTTTTTGTGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGT
1 GCGCCAAAATGGCTAACAGTTTTTGTGACGATATTTCGTAGCCACTAATTAATTGAATTGTTAGT
** **
731 GACATGATTTGTCGTCACAAAAGTTACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAA
66 GACACAACATGTCGTCACAAAAGTTACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAA
* *
796 TGAAACTTTTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATTCGTGCCATATCCATGTTG
131 TGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAATATCATTCGTGCCATATCCATGTTG
861 GCGCCAAAATGGCTAAC-GTTTTTGTGACGATATTGT-GTAGCCACTAATTAATTGAATTGTTAG
1 GCGCCAAAATGGCTAACAGTTTTTGTGACGATATT-TCGTAGCCACTAATTAATTGAATTGTTAG
* * * *
924 TGACACAACATGTCGTCACAAAATGTTACACACAAATGTGACGAGGTACTTTTTTGTCACA-AAC
65 TGACACAACATGTCGTCACAAAA-GTTACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAA-
*
988 AAATGAAACTTGTAGTGACCAATATAGGTTTTGCCACAAAAAATATCATTC
128 AAATGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAATATCATTC
1039 CCGCCAAATA
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
194 63 0.39
195 99 0.61
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (195 bp):
GCGCCAAAATGGCTAACAGTTTTTGTGACGATATTTCGTAGCCACTAATTAATTGAATTGTTAGT
GACACAACATGTCGTCACAAAAGTTACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAA
TGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAATATCATTCGTGCCATATCCATGTTG
Found at i:1085 original size:195 final size:194
Alignment explanation
Indices: 690--1089 Score: 520
Period size: 195 Copynumber: 2.1 Consensus size: 194
680 AACATTTTTT
* ** **
690 GTGACGATATTTCGTAGCCACTAATTAGTTGAATTGTTAGTGACATGATTTGTCGTCACAAAAGT
1 GTGACGATATTTCGTAGCCACTAATTAATTGAATTGTTAGTGACACAACATGTCGTCACAAAAGT
*
755 TACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAATGAAACTTTTAGTGACCAATATAG
66 TACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAG
* ** * * * * * **
820 GTTTGGCCACAAAAAGTATCATTCGTGCCATATCCATGTTGGCGCCAAAATGGCTAACGTTTTT
131 GTTTGGCCACAAAAAATATCATTCCCGCCAAATACATATTGGCGCCAAAATGACTAACGTATCA
884 GTGACGATATTGT-GTAGCCACTAATTAATTGAATTGTTAGTGACACAACATGTCGTCACAAAAT
1 GTGACGATATT-TCGTAGCCACTAATTAATTGAATTGTTAGTGACACAACATGTCGTCACAAAA-
* * * *
948 GTTACACACAAATGTGACGAGGTACTTTTTTGTCACA-AACAAATGAAACTTGTAGTGACCAATA
64 GTTACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAA-AAATGAAACTTGTAGTGACCAATA
* * * *
1012 TAGGTTTTGCCACAAAAAATATCATTCCCGCCAAATACGTATTGGCGCCAAACTGATTAA-GCTA
128 TAGGTTTGGCCACAAAAAATATCATTCCCGCCAAATACATATTGGCGCCAAAATGACTAACG-TA
1076 TCA
192 TCA
1079 GTGACGA-ATTT
1 GTGACGATATTT
1090 TTAATGACAA
Statistics
Matches: 178, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
193 1 0.01
194 62 0.35
195 115 0.65
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (194 bp):
GTGACGATATTTCGTAGCCACTAATTAATTGAATTGTTAGTGACACAACATGTCGTCACAAAAGT
TACACACAAAAGTGACCAGGTAATTTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAG
GTTTGGCCACAAAAAATATCATTCCCGCCAAATACATATTGGCGCCAAAATGACTAACGTATCA
Found at i:1361 original size:35 final size:35
Alignment explanation
Indices: 1322--1884 Score: 675
Period size: 35 Copynumber: 16.1 Consensus size: 35
1312 TCTTGTAGTG
* *
1322 TGAGATCAACTCTGATCGTTGGAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCTTGAAAACTTCTTGAAA
*
1357 TGAGATCAACTCTGA-CCTCTAAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
* * *
1392 TGAGATCAACTCTGATCATTGGAAACTTCTTGGAA
1 TGAGATCAACTCTGATCCTTGAAAACTTCTTGAAA
*
1427 TGAGATCAACTCTGA-CCTCTGAAAACTTCTTGCAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
* * *
1462 TGAGATCAACTCT-AACTTCTAAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
** * *
1497 TGAGATCAACTCTGATTGTTGGAAACTTCTTGGAA
1 TGAGATCAACTCTGATCCTTGAAAACTTCTTGAAA
1532 TGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
*
1567 TGAGATCAACTCTGAT-CTTCGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATCCTT-GAAAACTTCTTGAAA
*
1602 TGAGATCAACTCTGA-CCTCTAAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
1637 TGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAACTTCTTGAAA
* *
1672 TCAGATCAACTCTGAT-CTTCGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATCCTT-GAAAACTTCTTGAAA
*
1707 TGAGATCAACTCTGATCGTTGAAAACTTC-TGAAGA
1 TGAGATCAACTCTGATCCTTGAAAACTTCTTGAA-A
* *
1742 TGAGATCAACTCTGATCGTTGGAAACTTCTTGAAA
1 TGAGATCAACTCTGATCCTTGAAAACTTCTTGAAA
* *
1777 TGAGATCAACTCCGAT-CTTCGAAAACTTCTTGGAA
1 TGAGATCAACTCTGATCCTT-GAAAACTTCTTGAAA
* * *
1812 TGAGATCAACTTTGATCGC-TGGAAACTTCTTGGAA
1 TGAGATCAACTCTGATC-CTTGAAAACTTCTTGAAA
*
1847 TGAGATCAACTCTGAT-CTCT-AAAAGCTTTTTGAAA
1 TGAGATCAACTCTGATCCT-TGAAAA-CTTCTTGAAA
1882 TGA
1 TGA
1885 CCGCACTGGA
Statistics
Matches: 463, Mismatches: 44, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
33 1 0.00
34 16 0.03
35 433 0.94
36 12 0.03
37 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (35 bp):
TGAGATCAACTCTGATCCTTGAAAACTTCTTGAAA
Found at i:1504 original size:105 final size:104
Alignment explanation
Indices: 1322--1884 Score: 760
Period size: 105 Copynumber: 5.4 Consensus size: 104
1312 TCTTGTAGTG
* * * *
1322 TGAGATCAACTCTGATCGT-TGGAAACTTCTTGAAATGAGATCAACTCTGA-CCTCTAAAAACTT
1 TGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCT-ATCTTC-GAAAACTT
* *
1385 CTTGAAATGAGATCAACTCTGATCATTGGAAACTTCTTGGAA
63 CTTGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAA
* * *
1427 TGAGATCAACTCTGACCTCTGAAAACTTCTTGCAATGAGATCAACTCTAACTTCTAAAAACTTCT
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTATCTTC-GAAAACTTCT
* *
1492 TGAAATGAGATCAACTCTGATTGTTGGAAACTTCTTGGAA
65 TGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAA
1532 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCTTCGAAAACTTCT
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCT-ATCTTCGAAAACTTCT
* ** *
1597 TGGAATGAGATCAACTCTGA-CCTCTAAAAACTTCTTGAAA
65 TGGAATGAGATCAACTCTGATCGT-TGGAAACTTCTTGGAA
*
1637 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATCAGATCAACTCTGATCTTCGAAAACTTCT
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCT-ATCTTCGAAAACTTCT
* *
1702 TGGAATGAGATCAACTCTGATCGTTGAAAACTTC-TGAAGA
65 TGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGA-A
* * *
1742 TGAGATCAACTCTGATCGT-TGGAAACTTCTTGAAATGAGATCAACTCCGATCTTCGAAAACTTC
1 TGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGATCAACT-CTATCTTCGAAAACTTC
* *
1806 TTGGAATGAGATCAACTTTGATCGCTGGAAACTTCTTGGAA
64 TTGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAA
* *
1847 TGAGATCAACTCTGATCTCT-AAAAGCTTTTTGAAATGA
1 TGAGATCAACTCTGACCTCTGAAAA-CTTCTTGAAATGA
1885 CCGCACTGGA
Statistics
Matches: 417, Mismatches: 30, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
104 12 0.03
105 392 0.94
106 13 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (104 bp):
TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTATCTTCGAAAACTTCTT
GGAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAA
Found at i:22286 original size:19 final size:19
Alignment explanation
Indices: 22262--22301 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
22252 TTGCCCCTCT
*
22262 TCTCTCTCTTCCCACTAAG
1 TCTCTCTCCTCCCACTAAG
*
22281 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCTCCCACTAAG
22300 TC
1 TC
22302 AAGATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.45, G:0.05, T:0.38
Consensus pattern (19 bp):
TCTCTCTCCTCCCACTAAG
Found at i:25423 original size:12 final size:12
Alignment explanation
Indices: 25408--25438 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25398 TTATTATTGG
25408 TTTTGGTTTTGT
1 TTTTGGTTTTGT
*
25420 TTTTTGTTTTGT
1 TTTTGGTTTTGT
25432 TTTTGGT
1 TTTTGGT
25439 GAGATGGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (12 bp):
TTTTGGTTTTGT
Found at i:30543 original size:121 final size:120
Alignment explanation
Indices: 30327--30610 Score: 356
Period size: 121 Copynumber: 2.4 Consensus size: 120
30317 TGTAATATCC
* * *
30327 TATGAGGCACATTGCATCACCTATACATGTGACGTTCAGATTTTCATCACGAATAGTGAAACATT
1 TATGACGCACATTGCATCACCTATACATGTGACGTTCAGATTTCCATCACGAATAATGAAACATT
* * * * *
30392 TTCCTCATTTTTTGTGACAATCAACTATTGTAAGTGACCTTATAT-TGTAGTCTTT
66 TTCCACATTTTTTATGACAATCAACAATTGTAAGTGACCTTATATGT-TAATATTT
* ** * * *
30447 TATGACGCACATTGCGTCATGTATACATGTGACGTTTCCGATTTCCGTCACGAATAATGGAACAT
1 TATGACGCACATTGCATCACCTATACATGTGACG-TTCAGATTTCCATCACGAATAATGAAACAT
* *
30512 TTTCCACATTTTTTATGACAATCAACAATTGTCAGTGACGTTATATGTTAATATTT
65 TTTCCACATTTTTTATGACAATCAACAATTGTAAGTGACCTTATATGTTAATATTT
* * *
30568 TATGACG-AAATTTGCATCACCTATACATGTGACATTCACATTT
1 TATGACGCACA-TTGCATCACCTATACATGTGACGTTCAGATTT
30611 TCGTCACATA
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
120 39 0.28
121 98 0.71
122 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (120 bp):
TATGACGCACATTGCATCACCTATACATGTGACGTTCAGATTTCCATCACGAATAATGAAACATT
TTCCACATTTTTTATGACAATCAACAATTGTAAGTGACCTTATATGTTAATATTT
Found at i:35306 original size:16 final size:16
Alignment explanation
Indices: 35304--35356 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
35294 GAAAAATGAA
*
35304 AAAAATAAATAAACTG
1 AAAAATAAATAAAATG
* *
35320 AAAAAGAAATGAAATG
1 AAAAATAAATAAAATG
* *
35336 AAAATTAAGTAAAATG
1 AAAAATAAATAAAATG
35352 AAAAA
1 AAAAA
35357 AGGACAAAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAAATG
Found at i:35310 original size:18 final size:18
Alignment explanation
Indices: 35287--35357 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 18
35277 TATTAAAAGG
35287 AAAATAAGA-AAAATGAAA
1 AAAATAA-ATAAAATGAAA
*
35305 AAAATAAATAAACTG--A
1 AAAATAAATAAAATGAAA
* *
35321 AAAAGAAATGAAATG--A
1 AAAATAAATAAAATGAAA
* *
35337 AAATTAAGTAAAATGAAA
1 AAAATAAATAAAATGAAA
35355 AAA
1 AAA
35358 GGACAAAACG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
16 25 0.60
17 1 0.02
18 16 0.38
ACGTcount: A:0.72, C:0.01, G:0.11, T:0.15
Consensus pattern (18 bp):
AAAATAAATAAAATGAAA
Found at i:39682 original size:372 final size:372
Alignment explanation
Indices: 38997--39683 Score: 1365
Period size: 372 Copynumber: 1.8 Consensus size: 372
38987 CAAGATTCAC
38997 TGTTTGACGGGTGAGACATCAATCCCTCAACTGCCTTATGAGTATGATGCCAAGTCATATGCTCT
1 TGTTTGACGGGTGAGACATCAATCCCTCAACTGCCTTATGAGTATGATGCCAAGTCATATGCTCT
39062 GCTATGGCTTTCGAGGCATACAGCCTTTGCAATCTCGGAGTAAGGGGCAAATACCAAAGAACCAG
66 GCTATGGCTTTCGAGGCATACAGCCTTTGCAATCTCGGAGTAAGGGGCAAATACCAAAGAACCAG
39127 TTGCGATATTCTTTTTTGCTTCAGATTGTCCTGCCTACCCCGACGTTCTCTGTATCTAGGCTTTA
131 TTGCGATATTCTTTTTTGCTTCAGATTGTCCTGCCTACCCCGACGTTCTCTGTATCTAGGCTTTA
39192 AACAAAACTTGCAAGAAGTTAAATCCGAGTCCACTTTTCAAGACAACATGCATCCTCCGAGGCAA
196 AACAAAACTTGCAAGAAGTTAAATCCGAGTCCACTTTTCAAGACAACATGCATCCTCCGAGGCAA
39257 GCATCGTATTTGACAACAGGCAACCCCAAGTCACGCACTAACTTCTTATGCTGGTGAGACATCAA
261 GCATCGTATTTGACAACAGGCAACCCCAAGTCACGCACTAACTTCTTATGCTGGTGAGACATCAA
39322 TCCCTCAGCTGCCTTATGAGGGATGATGCCAAGTCATATGCAAGTTT
326 TCCCTCAGCTGCCTTATGAGGGATGATGCCAAGTCATATGCAAGTTT
*
39369 TGTTTGACGGGTGAGACATCAATCCCTCAGCTGCCTTATGAGTATGATGCCAAGTCATATGCTCT
1 TGTTTGACGGGTGAGACATCAATCCCTCAACTGCCTTATGAGTATGATGCCAAGTCATATGCTCT
39434 GCTATGGCTTTCGAGGCATACAGCCTTTGCAATCTCGGAGTAAGGGGCAAATACCAAAGAACCAG
66 GCTATGGCTTTCGAGGCATACAGCCTTTGCAATCTCGGAGTAAGGGGCAAATACCAAAGAACCAG
39499 TTGCGATATTCTTTTTTGCTTCAGATTGTCCTGCCTACCCCGACGTTCTCTGTATCTAGGCTTTA
131 TTGCGATATTCTTTTTTGCTTCAGATTGTCCTGCCTACCCCGACGTTCTCTGTATCTAGGCTTTA
39564 AACAAAACTTGCAAGAAGTTAAATCCGAGTCCACTTTTCAAGACAACATGCATCCTCCGAGGCAA
196 AACAAAACTTGCAAGAAGTTAAATCCGAGTCCACTTTTCAAGACAACATGCATCCTCCGAGGCAA
39629 GCATCGTATTTGACAACAGGCAACCCCAAGTCACGCACTAACTTCTTATGCTGGT
261 GCATCGTATTTGACAACAGGCAACCCCAAGTCACGCACTAACTTCTTATGCTGGT
39684 AGAAATCTGG
Statistics
Matches: 314, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
372 314 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (372 bp):
TGTTTGACGGGTGAGACATCAATCCCTCAACTGCCTTATGAGTATGATGCCAAGTCATATGCTCT
GCTATGGCTTTCGAGGCATACAGCCTTTGCAATCTCGGAGTAAGGGGCAAATACCAAAGAACCAG
TTGCGATATTCTTTTTTGCTTCAGATTGTCCTGCCTACCCCGACGTTCTCTGTATCTAGGCTTTA
AACAAAACTTGCAAGAAGTTAAATCCGAGTCCACTTTTCAAGACAACATGCATCCTCCGAGGCAA
GCATCGTATTTGACAACAGGCAACCCCAAGTCACGCACTAACTTCTTATGCTGGTGAGACATCAA
TCCCTCAGCTGCCTTATGAGGGATGATGCCAAGTCATATGCAAGTTT
Found at i:46243 original size:2 final size:2
Alignment explanation
Indices: 46236--46278 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
46226 ATAATTTTTC
*
46236 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
46279 AAAGTACGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:46582 original size:109 final size:109
Alignment explanation
Indices: 46370--46645 Score: 421
Period size: 109 Copynumber: 2.5 Consensus size: 109
46360 ACTATTATAG
* *
46370 TTTTATTCTACTTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACT
1 TTTTATTCTAC-TAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACT
*
46435 TTCTTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
60 TTATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
46485 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
46550 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
*
46594 CTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
46646 TAAAGTTTTT
Statistics
Matches: 154, Mismatches: 6, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 7 0.05
109 121 0.79
110 3 0.02
111 2 0.01
114 10 0.06
115 11 0.07
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:53043 original size:17 final size:16
Alignment explanation
Indices: 53023--53072 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
53013 TTTCGTTATT
53023 TTTCTTTTAATTTTTCG
1 TTTCTTTT-ATTTTTCG
* *
53040 TTTCTTTTGTTTTTAG
1 TTTCTTTTATTTTTCG
53056 TTTACTTTTTATTTTTC
1 TTT-C-TTTTATTTTTC
53073 TTAGTTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.33
17 9 0.33
18 9 0.33
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTCTTTTATTTTTCG
Found at i:53047 original size:22 final size:23
Alignment explanation
Indices: 52990--53052 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
52980 TACTTAAGAA
*
52990 TTTC-TTACCTTTATCTTTTAATT
1 TTTCGTTATCTTT-TCTTTTAATT
53013 TTTCGTTAT-TTTTCTTTTAATT
1 TTTCGTTATCTTTTCTTTTAATT
*
53035 TTTCGTT-TCTTTTGTTTT
1 TTTCGTTATCTTTTCTTTT
53053 TAGTTTACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 25 0.69
23 7 0.19
24 3 0.08
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (23 bp):
TTTCGTTATCTTTTCTTTTAATT
Found at i:53058 original size:16 final size:17
Alignment explanation
Indices: 53023--53071 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
53013 TTTCGTTATT
*
53023 TTTCTTTTAATTTTTCG
1 TTTCTTTTAATTTTTAG
*
53040 TTTCTTTT-GTTTTTAG
1 TTTCTTTTAATTTTTAG
*
53056 TTTACTTTTTATTTTT
1 TTT-CTTTTAATTTTT
53072 CTTAGTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTCTTTTAATTTTTAG
Found at i:62122 original size:735 final size:738
Alignment explanation
Indices: 60698--62176 Score: 2770
Period size: 735 Copynumber: 2.0 Consensus size: 738
60688 GCATGTGGAA
* *
60698 AAGTAAATCTTAATGTTGGTGCTATGGTTCTTCACAGGGTGAATGTTTGATTAGGAACAATAGAG
1 AAGTTAATCTTAATGTTGGTGCTATGATTCTTCACAGGGTGAATGTTTGATTAGGAACAATAGAG
60763 ATTAATCGTCAGCAAGATGCGGGTTAATTCTTCTTAGCATGTTGGAGGGTTCGAGTATTCCTCTC
66 ATTAATCGTCAGCAAGATGCGGGTTAATTCTTCTTAGCATGTTGGAGGGTTCGAGTATTCCTCTC
*
60828 CTATACCAATTATTTAAATGGAGTTGTTTTAAGGTATTAAGAGGATTACTTTGTTTCGATGAAAG
131 CTATACCAATTATTTAAATGGAGTTGTTTTAAGATATTAAGAGGATTACTTTGTTTCGATGAAAG
*
60893 TTGATGTCTACGTCTTAGGCTATATACCGATTTGGAGTGATTTATGATTCTTAATTGATTGCAAT
196 TTGACGTCTACGTCTTAGGCTATATACCGATTTGGAGTGATTTATGATTCTTAATTGATTGCAAT
*
60958 CTAAGCCAAATTTATGTTTAGTGTCCATGATCCATGATTCACTTGATCAAAGTAGTTGCCTAAAG
261 CTAAGCCAAATTTATGTTTAGAGTCCATGATCCATGATTCACTTGATCAAAGTAGTTGCCTAAAG
* **
61023 GAGAAGAAGTATGTTTTTATTCATTGTTTTTTCTCTGACTCTCTATTTTAAATCTTTAGTTTAGA
326 GAGAAGAAGCATGTTTTTATTCATTGTTTTTTCTAAGACTCTCTATTTTAAATCTTTAGTTTAGA
*
61088 TTTCTTTTATTGTTTTCTAGTTTAATTAATCTATTTTGAAAAACCCAAAAATATCTTTTCTCGGT
391 TTTCTTTTATTGTTTTCTAGTTTAATTAATCTATTTTGAAAAACCCAAAAATATCTTTTCTAGGT
61153 TAGATTTTCTTCTGTAAGATTTAACTTTGATTCATACCTTCCTTGTGGATTCGACCCCTACTTGC
456 TAGATTTTCTTCTGTAAGATTTAACTTTGATTCATACCTTCCTTGTGGATTCGACCCCTACTTGC
61218 CCTAGCTAAGCAGTTATTCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAAC
521 CCTAGCTAAGCAGTTATTCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAAC
61283 GACCGGTCACAATTTTGCGCCGTTGCCAGGGAAGGTTACGTAATTGAAGGCGAATTATTACTTAA
586 GACCGGTCACAATTTTGCGCCGTTGCCAGGGAAGGTTACGTAATTGAAGGCGAATTATTACTTAA
* *
61348 GAATTTCTTACCTTTATCTTTTATATTTTTTCGTTATTTTTCTTTTCAATTTTTAGTTTAGTTAA
651 GAATTTCTAACCTTTATCTTTTATATTTTTTCATTATTTTTCTTTTCAATTTTTAGTTTAGTTAA
*
61413 TTTTTCCTTAGTTTTTATTTTTC
716 TTTTTCCTTACTTTTTATTTTTC
61436 AAGTTAATCTTAATGCTT-GTGCTATGATTCTTCACAGGGTGAATGTTTGATTAGGAACAATAGA
1 AAGTTAATCTTAATG-TTGGTGCTATGATTCTTCACAGGGTGAATGTTTGATTAGGAACAATAGA
*
61500 GATTAATCGTCAGCGAGATGCGGGTTAATTCTTCTTAGCATGTTGGAGGG-TCGAGTATTCCTCT
65 GATTAATCGTCAGCAAGATGCGGGTTAATTCTTCTTAGCATGTTGGAGGGTTCGAGTATTCCTCT
61564 CCTATACCAATTATTTAAATGGAGTTG-TTTAAGATATTAAGAGGATTACTTTGTTTCGATGAAA
130 CCTATACCAATTATTTAAATGGAGTTGTTTTAAGATATTAAGAGGATTACTTTGTTTCGATGAAA
61628 GTTGACGTCTACGTCTTAGGCTATATACCGATTTGGAGTGATTTATGATTCTTAATTGATTGCAA
195 GTTGACGTCTACGTCTTAGGCTATATACCGATTTGGAGTGATTTATGATTCTTAATTGATTGCAA
61693 TCTAAGCCAAATTTATGTTT-GAGTCCATGATCCATGATTCACTTGATCAAAGTAGTTGCCTAAA
260 TCTAAGCCAAATTTATGTTTAGAGTCCATGATCCATGATTCACTTGATCAAAGTAGTTGCCTAAA
61757 GGAGAAGAAGCATGTTTTTATTCATTGTTTTTTCTAAGACTCTCTATTTTAAATCTTTAGTTTAG
325 GGAGAAGAAGCATGTTTTTATTCATTGTTTTTTCTAAGACTCTCTATTTTAAATCTTTAGTTTAG
61822 ATTTCTTTTATTGTTTTCTAGTTTAATTAATCTATTTTGAAAAACCCAAAAATATCTTTTCTAGG
390 ATTTCTTTTATTGTTTTCTAGTTTAATTAATCTATTTTGAAAAACCCAAAAATATCTTTTCTAGG
61887 TTAGATTTTCTTCTGTAAGATTTAACTTTGATTCATACCTTCCTTGTGGATTCGACCCCTACTTG
455 TTAGATTTTCTTCTGTAAGATTTAACTTTGATTCATACCTTCCTTGTGGATTCGACCCCTACTTG
61952 CCCTAGCTAAGCAGTTATTCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAA
520 CCCTAGCTAAGCAGTTATTCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAA
*
62017 CGACCGGTCACAATTTTGGCGCCGTTGCCGGGGAAGGTTACGTAATTGAAGGCGAATTATTACTT
585 CGACCGGTCACAATTTT-GCGCCGTTGCCAGGGAAGGTTACGTAATTGAAGGCGAATTATTACTT
62082 AAGAATTTCTAACCTTTATCTTTTATA-TTTTTCATTATTTTTCTTTTCAATTTTTAGTTTAGTT
649 AAGAATTTCTAACCTTTATCTTTTATATTTTTTCATTATTTTTCTTTTCAATTTTTAGTTTAGTT
*
62146 AATTTTTTCTTACTTTTTATTTTTC
714 AATTTTTCCTTACTTTTTATTTTTC
62171 AAGTTA
1 AAGTTA
62177 CTTGTTATTC
Statistics
Matches: 724, Mismatches: 15, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
735 381 0.53
736 192 0.27
737 41 0.06
738 108 0.15
739 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (738 bp):
AAGTTAATCTTAATGTTGGTGCTATGATTCTTCACAGGGTGAATGTTTGATTAGGAACAATAGAG
ATTAATCGTCAGCAAGATGCGGGTTAATTCTTCTTAGCATGTTGGAGGGTTCGAGTATTCCTCTC
CTATACCAATTATTTAAATGGAGTTGTTTTAAGATATTAAGAGGATTACTTTGTTTCGATGAAAG
TTGACGTCTACGTCTTAGGCTATATACCGATTTGGAGTGATTTATGATTCTTAATTGATTGCAAT
CTAAGCCAAATTTATGTTTAGAGTCCATGATCCATGATTCACTTGATCAAAGTAGTTGCCTAAAG
GAGAAGAAGCATGTTTTTATTCATTGTTTTTTCTAAGACTCTCTATTTTAAATCTTTAGTTTAGA
TTTCTTTTATTGTTTTCTAGTTTAATTAATCTATTTTGAAAAACCCAAAAATATCTTTTCTAGGT
TAGATTTTCTTCTGTAAGATTTAACTTTGATTCATACCTTCCTTGTGGATTCGACCCCTACTTGC
CCTAGCTAAGCAGTTATTCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAAC
GACCGGTCACAATTTTGCGCCGTTGCCAGGGAAGGTTACGTAATTGAAGGCGAATTATTACTTAA
GAATTTCTAACCTTTATCTTTTATATTTTTTCATTATTTTTCTTTTCAATTTTTAGTTTAGTTAA
TTTTTCCTTACTTTTTATTTTTC
Done.