Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007769.1 Corchorus capsularis cultivar CVL-1 contig07790, 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: 48412
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:1284 original size:332 final size:334
Alignment explanation
Indices: 1--1376 Score: 1912
Period size: 332 Copynumber: 4.1 Consensus size: 334
*
1 AACGATTTCGGCTAAAAATTTT-C-AAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGACTAA
1 AACGATTTCGGCT-AAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAA
* *
64 AATACTCACTAAATATATATATAATTTAACACCAAAAAATTTGAATGACTTTTCGAGCTTTTCAT
65 AATACTCACGAAATATATA-A-AATTTAACACC-AAAAATTTGAAGGACTTTTCGAGCTTTTCAT
* *
129 ATCGTTTTTCATA-TTTTTCTGAATTAATTTTTAATTAAACCGAAACAAGATTCAGATACTCGTA
127 ATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
193 AAAACATATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATATATATTTCAAAGAGT
192 AAAACAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGT
* * *
258 CTCGACG-CAAATAATCATGCAAAACTGAGTCGGAA-CCCTGGAACGCGTTTTTAGGGAAAAAAA
257 CTCGACGCCAAA-AATCATGCAAAACTGAGAC-GAAGCCCCGAAACGCGTTTTTA--GAAAAAAA
**
321 AATTGTGATGGTTAGTA
318 AACCGTGATGGTTAGTA
*
338 CACGATTTCGGCTAAAATTTTGC-AAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAAA
1 AACGATTTCGGCTAAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAAA
* ** * *
402 ATACCCATTAAATATATAGAATTT-ACGCCCAAAAATTTGAAGGACTTTTCGAGCTTTTCATATC
66 ATACTCACGAAATATATAAAATTTAAC-ACCAAAAATTTGAAGGACTTTTCGAGCTTTTCATATC
* *
466 GTTTTTCATATTTTTTCTGAATTAATTTTTACTTAAATCGAAACAAGATTCAGATTCTCGTAAAA
130 GTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
531 ACAAATCCTTAAATTCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
195 ACAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTC
* * *
596 GATGCCAAAAATCAAGCAAAACTGAGACGGAGCCCCGAAACGCGTTTTTAGCAAAAAAAAACCGT
260 GACGCCAAAAATCATGCAAAACTGAGACGAAGCCCCGAAACGCGTTTTTAG-AAAAAAAAACCGT
*
661 GATTGTTAGTA
324 GATGGTTAGTA
* *
672 TACGATTTCGGCTAAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTCTGGCTAAA
1 AACGATTTCGGCTAAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAAA
** * * * * * *
737 ATTTTTCAAAGAAAAAATTTTTGGGCTATAATTTAATAACAAAAAATTTGAAGGACTTTTCGAGC
66 A-TACTC-ACG---AAA--TAT---ATAAAATTTAA-CACCAAAAATTTGAAGGACTTTTCGAGC
* * *
802 TTTTCATATCGTTTTTCATATTTTTTTTAAATTAATTTTTAATTAAATCGAAACAAGATTCAAAT
120 TTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGAT
**
867 GCTCGTAAAATTAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
185 GCTCGTAAAAACAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
* * * * *
932 AAAGAGGCTCGACGCCAAAAATCATGCAAAACTGAGTCGAAGCCCTGGAACGCGTTTTTAG-TAA
250 AAAGAGTCTCGACGCCAAAAATCATGCAAAACTGAGACGAAGCCCCGAAACGCGTTTTTAGAAAA
** *
996 AAAAATTGTTATGGTTAGTA
315 AAAAACCGTGATGGTTAGTA
*
1016 AACGATTTCGGCTAAAATTTTGCAAAAAAATGTTCCGAAAAA-TTTTCTTCAATTTTTGGCTAAA
1 AACGATTTCGGCTAAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAAA
** *
1080 ATACTCACGAAATATATAAAATTTAATGCCAAAAATTCGAAGGACTTTTCGAGCTTTTCATATCG
66 ATACTCACGAAATATATAAAATTTAACACCAAAAATTTGAAGGACTTTTCGAGCTTTTCATATCG
1145 TTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
131 TTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
*
1210 CAAATCCTTAAATGCATTGTGGCTAAGATTTGA-TACGATGAATATAGATATTT-AAAGGAGTCT
196 CAAATCCTTAAATGCATTGTGGCTGAGATTTGATTA-GATGAATATAGATATTTCAAA-GAGTCT
* * * * *
1273 CGACACCAAAAATCATACAAAATTGAGACGGAGCCCCGAAACGCGTTTTTAG-CAAAAAAACCGT
259 CGACGCCAAAAATCATGCAAAACTGAGACGAAGCCCCGAAACGCGTTTTTAGAAAAAAAAACCGT
1337 GATGGTTAGTA
324 GATGGTTAGTA
* *
1348 CACGATTTCGGCAAAAATTTTGCAAAAAA
1 AACGATTTCGGCTAAAATTTTGCAAAAAA
1377 TGACGAGTTT
Statistics
Matches: 928, Mismatches: 90, Indels: 47
0.87 0.08 0.04
Matches are distributed among these distances:
331 5 0.01
332 240 0.26
333 10 0.01
334 90 0.10
335 196 0.21
336 16 0.02
337 70 0.08
338 3 0.00
340 3 0.00
341 2 0.00
342 5 0.01
343 22 0.02
344 58 0.06
345 7 0.01
346 201 0.22
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (334 bp):
AACGATTTCGGCTAAAATTTTGCAAAAAAATGTCCCGAAAAATTTTTCTTCAATTTTTGGCTAAA
ATACTCACGAAATATATAAAATTTAACACCAAAAATTTGAAGGACTTTTCGAGCTTTTCATATCG
TTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAAGAGTCTCG
ACGCCAAAAATCATGCAAAACTGAGACGAAGCCCCGAAACGCGTTTTTAGAAAAAAAAACCGTGA
TGGTTAGTA
Found at i:1582 original size:251 final size:250
Alignment explanation
Indices: 1129--1625 Score: 789
Period size: 251 Copynumber: 2.0 Consensus size: 250
1119 AAGGACTTTT
1129 CGAGCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
1 CGAGCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
*
1194 CAGATGCTCGTAAAAACAAATCCTTAAATGCATTGTGGCTAAGATTTGATACGATGAATATAGAT
66 CAGATACTCGTAAAAACAAATCCTTAAATGCATTGTGGCTAAGATTTGATACGATGAATATAGAT
* * * *
1259 ATTTAAAGGAGTCTCGACACCAAAAATCATACAAAATTGAGACGGAGCCCCGAAACGCGTTTTTA
131 ATTTAAAGCAGTCTCGACACCAAAAATCATACAAAACTGAGACGAAGCCACGAAACGCGTTTTTA
1324 GCAAAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGA
196 GC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGA
* *
1380 CGAGTTTTTTATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
1 CGAGCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
* * * *
1445 TAGATACTCGTAGAAACAAATTCTTAAATGCATTGTGGCTGAGATTTGATTA-GATGAATATAGA
66 CAGATACTCGTAAAAACAAATCCTTAAATGCATTGTGGCTAAGATTTGA-TACGATGAATATAGA
** *
1509 TATTTAAAGCAGTCTCGATGCCAAAAATCATGCAAAACTGAGACGAAGCCACGAAACGCGTTTTT
130 TATTTAAAGCAGTCTCGACACCAAAAATCATACAAAACTGAGACGAAGCCACGAAACGCGTTTTT
** * ** *
1574 AGCAAAAAATGGTGATGGTTAGTACACTATTTCGGGTAAAATTTTGTAAAAA
195 AGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAA
1626 CAAATCATGC
Statistics
Matches: 225, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
250 43 0.19
251 180 0.80
252 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (250 bp):
CGAGCTTTTCATATCGTTTTTCATATTTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATT
CAGATACTCGTAAAAACAAATCCTTAAATGCATTGTGGCTAAGATTTGATACGATGAATATAGAT
ATTTAAAGCAGTCTCGACACCAAAAATCATACAAAACTGAGACGAAGCCACGAAACGCGTTTTTA
GCAAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAAATGA
Found at i:1694 original size:94 final size:94
Alignment explanation
Indices: 1533--1719 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 94
1523 TCGATGCCAA
*
1533 AAATCATGCAAAACTGAGACGAAGCCACGAAACGCGTTTTTAGCAAAAAATGGTGATGGTTAGTA
1 AAATCATGCAAAACTGAGACGAAGCCACGAAACGCGTTTTTAGCAAAAAATCGTGATGGTTAGTA
* * *
1598 CACTATTTCGGGTAAAATTTTGTAAAAAC
66 CACGATTTCGGCTAAAATTTTGCAAAAAC
* *
1627 AAATCATGCAAAACTGAGACGAATCCCCGAAACGCGTTTTTAGCAAAAAATCGTGATGGTTAGTA
1 AAATCATGCAAAACTGAGACGAAGCCACGAAACGCGTTTTTAGCAAAAAATCGTGATGGTTAGTA
1692 CACGATTTCGGCTAAAATTTTGCAAAAA
66 CACGATTTCGGCTAAAATTTTGCAAAAA
1720 ATGACCCAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (94 bp):
AAATCATGCAAAACTGAGACGAAGCCACGAAACGCGTTTTTAGCAAAAAATCGTGATGGTTAGTA
CACGATTTCGGCTAAAATTTTGCAAAAAC
Found at i:3031 original size:13 final size:12
Alignment explanation
Indices: 3013--3094 Score: 53
Period size: 12 Copynumber: 6.7 Consensus size: 12
3003 CTATCGTACG
3013 TAAGATAGTAAGA
1 TAAGATA-TAAGA
3026 TAAGATATAAGA
1 TAAGATATAAGA
*
3038 TTTAA-A-AAAAGA
1 --TAAGATATAAGA
* * *
3050 -AAAAAAAAAGA
1 TAAGATATAAGA
3061 TAAGATATAAGA
1 TAAGATATAAGA
*
3073 TATATATAGTAAGA
1 TA-AGATA-TAAGA
3087 TAAGATAT
1 TAAGATAT
3095 GCATTGCACG
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
9 2 0.04
10 1 0.02
11 6 0.11
12 21 0.38
13 16 0.29
14 10 0.18
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (12 bp):
TAAGATATAAGA
Found at i:6072 original size:21 final size:21
Alignment explanation
Indices: 6048--6091 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6038 TCTAAACCTT
6048 TAAATATG-ACCAAATTGGACC
1 TAAAT-TGCACCAAATTGGACC
*
6069 TAAATTGCACCAAATTGGGCC
1 TAAATTGCACCAAATTGGACC
6090 TA
1 TA
6092 TTTTGGACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
TAAATTGCACCAAATTGGACC
Found at i:12051 original size:29 final size:29
Alignment explanation
Indices: 12009--12101 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
11999 CTAATGTGGC
** * *
12009 TCCAAAATGCAAGTTTAGGGGGAAAAATG
1 TCCAAAATTAAAGTTTAGGGAGAAAAACG
* * *
12038 TCCAAAATTAAAGTTTATGAAGCAAAACG
1 TCCAAAATTAAAGTTTAGGGAGAAAAACG
* * *
12067 TCTAAAATTAAAGTTTATGGAGCAAAACG
1 TCCAAAATTAAAGTTTAGGGAGAAAAACG
*
12096 CCCAAA
1 TCCAAA
12102 TCGTACAAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (29 bp):
TCCAAAATTAAAGTTTAGGGAGAAAAACG
Found at i:14641 original size:165 final size:161
Alignment explanation
Indices: 14447--14742 Score: 420
Period size: 165 Copynumber: 1.8 Consensus size: 161
14437 CGACTAAACC
* * *
14447 AAATGTGTACCCTTCTTTATTTATGGTGGAGCAACTCATTCAATTTTTTGTTGTATAGCATAGGA
1 AAATGTGGACCCTTCTTTATTTATGGTGGAGCAACCCATTCAATTCTTTGTTGTATAG---A--A
14512 CTTTCGTCCAAC-TATAT-AAAGTAGAAGTAAACAGTTGCATGCTTTCGACTTTTT-TTTTCATG
61 CTTTCGT--AACATATATAAAAGTAGAAGTAAACAGTTGCATGCTTTCGACTTTTTATTTTCATG
14574 ATCAATAACAATCTCTCTTTATTTCATTGATACGACTA
124 ATCAATAACAATCTCTCTTTATTTCATTGATACGACTA
*
14612 AAATGTGGACTCTTCTTTACTTT-TGGTGGAGCAACCCATTCAATTCTTTGTTGTATAGAACTTT
1 AAATGTGGACCCTTCTTTA-TTTATGGTGGAGCAACCCATTCAATTCTTTGTTGTATAGAACTTT
* *
14676 CGTAACTATATATACAAAGTAGAAGTAAATAGTTGCATGCTTTCGATTTTTTATTTTCATGATCA
65 CGTAAC-ATATATA-AAAGTAGAAGTAAACAGTTGCATGCTTTCGACTTTTTATTTTCATGATCA
14741 AT
128 AT
14743 TAATCATCGA
Statistics
Matches: 119, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
158 3 0.03
160 13 0.11
162 36 0.30
163 14 0.12
165 50 0.42
166 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (161 bp):
AAATGTGGACCCTTCTTTATTTATGGTGGAGCAACCCATTCAATTCTTTGTTGTATAGAACTTTC
GTAACATATATAAAAGTAGAAGTAAACAGTTGCATGCTTTCGACTTTTTATTTTCATGATCAATA
ACAATCTCTCTTTATTTCATTGATACGACTA
Found at i:22799 original size:15 final size:15
Alignment explanation
Indices: 22775--22859 Score: 53
Period size: 15 Copynumber: 5.7 Consensus size: 15
22765 TTTCTCTTCT
* *
22775 TCTTCCTCCTCGTCC
1 TCTTCATCCTCCTCC
22790 TCTTCATCCTCCTCC
1 TCTTCATCCTCCTCC
* * * *
22805 TCCTCATCTTCTTCT
1 TCTTCATCCTCCTCC
* * *
22820 TCTTCATCATCATCG
1 TCTTCATCCTCCTCC
* * *
22835 TCTTCAGCTTCCTTC
1 TCTTCATCCTCCTCC
*
22850 TCTTCCTCCT
1 TCTTCATCCT
22860 TTCCTCTAAC
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.07, C:0.45, G:0.04, T:0.45
Consensus pattern (15 bp):
TCTTCATCCTCCTCC
Found at i:22799 original size:18 final size:18
Alignment explanation
Indices: 22772--22809 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
22762 CACTTTCTCT
* *
22772 TCTTCTTCCTCCTCGTCC
1 TCTTCATCCTCCTCCTCC
22790 TCTTCATCCTCCTCCTCC
1 TCTTCATCCTCCTCCTCC
22808 TC
1 TC
22810 ATCTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.53, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCATCCTCCTCCTCC
Found at i:26323 original size:13 final size:13
Alignment explanation
Indices: 26305--26330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26295 CATAAGTAAG
26305 CAGTTCTTATTTA
1 CAGTTCTTATTTA
26318 CAGTTCTTATTTA
1 CAGTTCTTATTTA
26331 TTGTTGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CAGTTCTTATTTA
Found at i:26421 original size:22 final size:22
Alignment explanation
Indices: 26396--26439 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
26386 AAAGTCCTCT
26396 AATTACATAAAAGCCCAAAATA
1 AATTACATAAAAGCCCAAAATA
26418 AATTACATAAAAGCCCAAAATA
1 AATTACATAAAAGCCCAAAATA
26440 GGAAGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (22 bp):
AATTACATAAAAGCCCAAAATA
Found at i:32772 original size:163 final size:163
Alignment explanation
Indices: 32491--32786 Score: 468
Period size: 163 Copynumber: 1.8 Consensus size: 163
32481 TGAAAAAATA
* **
32491 AAAAAATTCTGCTGCCGGGATTTGAACCCGGATTCCATATATCCTGAAGGAATTACCAAGTGTTA
1 AAAAAATTCCGCTGCCGGGATTTGAACCCGGATTCCATATATCCTGAAGGAATTACCAAGTACTA
* * **
32556 CAATGGATTCTATTTGTTATAGGATTGCAAACAATTTGATTTAACAAACTTTAGTCCCAAAGACT
66 CAACGGATTCTATTTGTTACAAAATTGCAAACAATTTGATTTAACAAACTTTAGTCCCAAA-ACT
32621 CCTAGCAAATAAACAAACGTTGTAATAAATATTT
130 CCTAGCAAATAAACAAACGTTGTAATAAATATTT
* *
32655 AAAATATTCCGCTGCCGGGATTTGAACCCGGATTCCATATATCC-GAAGGAATTGCCAAGTACTA
1 AAAAAATTCCGCTGCCGGGATTTGAACCCGGATTCCATATATCCTGAAGGAATTACCAAGTACTA
* * *
32719 CAACGGATTCTGTTTGTTACAAAATTGCAAACAATTTTATTTAACAAACTTTAGTCCCACAACTC
66 CAACGGATTCTATTTGTTACAAAATTGCAAACAATTTGATTTAACAAACTTTAGTCCCAAAACTC
32784 CTA
131 CTA
32787 ATGCCTTCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
162 7 0.06
163 71 0.59
164 42 0.35
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (163 bp):
AAAAAATTCCGCTGCCGGGATTTGAACCCGGATTCCATATATCCTGAAGGAATTACCAAGTACTA
CAACGGATTCTATTTGTTACAAAATTGCAAACAATTTGATTTAACAAACTTTAGTCCCAAAACTC
CTAGCAAATAAACAAACGTTGTAATAAATATTT
Found at i:34162 original size:2 final size:2
Alignment explanation
Indices: 34155--34181 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34145 AAACACAATA
34155 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
34182 ATAGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39699 original size:25 final size:25
Alignment explanation
Indices: 39665--39716 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
39655 TGTGTATCCA
*
39665 AAATATGCAAAACATATTTCATACT
1 AAATATGCAAAACACATTTCATACT
39690 AAATATGCAAAACACATTTCATACT
1 AAATATGCAAAACACATTTCATACT
39715 AA
1 AA
39717 TGGTATTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (25 bp):
AAATATGCAAAACACATTTCATACT
Found at i:41384 original size:22 final size:24
Alignment explanation
Indices: 41343--41386 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41333 CCCTCACTTG
*
41343 TTTAATAATATAATATAATTATTA
1 TTTAAAAATATAATATAATTATTA
41367 TTTAAAAATA-AATA-AATTAT
1 TTTAAAAATATAATATAATTAT
41387 GTGACTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 4 0.21
24 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAAATATAATATAATTATTA
Found at i:42449 original size:19 final size:20
Alignment explanation
Indices: 42425--42476 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 20
42415 ACAATGCGTC
42425 TAGGTTTAATTTAGTTA-TT
1 TAGGTTTAATTTAGTTAGTT
42444 TAGGTTTAATTTAGTTAGTT
1 TAGGTTTAATTTAGTTAGTT
42464 TAGTAGTTTAATT
1 TAG--GTTTAATT
42477 ACCGTGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.57
20 5 0.17
22 8 0.27
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (20 bp):
TAGGTTTAATTTAGTTAGTT
Found at i:43302 original size:65 final size:65
Alignment explanation
Indices: 43222--43349 Score: 229
Period size: 65 Copynumber: 2.0 Consensus size: 65
43212 ATAATGGAGC
* *
43222 TCATATCACTGAGAAAAAACCAAAAGGAAAACGAAAAAGATTAAAAGAATAGAGAAATATAGAGT
1 TCATATCACTAAGAAAAAACCAAAAGGAAAACGAAAAAGATTAAAAGAACAGAGAAATATAGAGT
*
43287 TCATATCACTAAGAAAAAACCAAAAGGAAAACGAAAAAGGTTAAAAGAACAGAGAAATATAGA
1 TCATATCACTAAGAAAAAACCAAAAGGAAAACGAAAAAGATTAAAAGAACAGAGAAATATAGA
43350 TTTAGTAAGC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (65 bp):
TCATATCACTAAGAAAAAACCAAAAGGAAAACGAAAAAGATTAAAAGAACAGAGAAATATAGAGT
Done.