Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017035.1 Corchorus olitorius cultivar O-4 contig17068, 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: 46171
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:466 original size:31 final size:31
Alignment explanation
Indices: 431--535 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 31
421 AGTGGATGGA
*
431 CTTATTTGAGATTTTTCGCGAAGTTGGGGCC
1 CTTATTTGAGATTTTTCGCAAAGTTGGGGCC
** *
462 CTTATTTGA-CCTTTTC-CAAAGTTCGGGCC
1 CTTATTTGAGATTTTTCGCAAAGTTGGGGCC
* * * *
491 CTTATTTGATATTTATGGCAAAGTTCGGGGAC
1 CTTATTTGAGATTTTTCGCAAAGTT-GGGGCC
523 C-TATTTGAGATTT
1 CTTATTTGAGATTT
536 CAGCCGTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.33
30 8 0.13
31 27 0.45
32 5 0.08
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (31 bp):
CTTATTTGAGATTTTTCGCAAAGTTGGGGCC
Found at i:9447 original size:2 final size:2
Alignment explanation
Indices: 9410--9567 Score: 66
Period size: 2 Copynumber: 76.0 Consensus size: 2
9400 AAGATTATCT
*
9410 TA TA CTA TA CTA TA CTA TA CTA TA CTA TA CTA TA TA TA TA GA GTA
1 TA TA -TA TA -TA TA -TA TA -TA TA -TA TA -TA TA TA TA TA TA -TA
* *
9455 TA GTA TA TA TA TA T- TA -A T- TA -A GA T- TA TC T- TA 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
9492 TA TA TA CTA TA CTA TA TA TA GTA TA TA GTA TA GTA TA GTA TA GTA
1 TA TA TA -TA TA -TA TA TA TA -TA TA TA -TA TA -TA TA -TA TA -TA
*
9537 TA GTA TA -A GA TA -A TA TA TA T- TA TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9568 AACAATAAAT
Statistics
Matches: 125, Mismatches: 5, Indels: 52
0.69 0.03 0.29
Matches are distributed among these distances:
1 10 0.08
2 84 0.67
3 31 0.25
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:9461 original size:5 final size:5
Alignment explanation
Indices: 9410--9447 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
9400 AAGATTATCT
9410 TATAC TATAC TATAC TATAC TATAC TATAC TATA- TATA
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATA
9448 TAGAGTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAC
Found at i:9483 original size:74 final size:73
Alignment explanation
Indices: 9394--9538 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 73
9384 TTTATGTTCG
*
9394 TTAATTAAGATTATCTTATACTATA-CTATACTATACTATACTATACTATATA-TATAGAGTATA
1 TTAATTAAGATTATCTTATA-TATATATATACTATACTATA-TATACTATATAGTAT--AGTATA
9457 GTATA-TATATA
62 GTATAGTATATA
*
9468 TTAATTAAGATTATCTTATATATATATATACTATACTATATATAGTATATAGTATAGTATAGTAT
1 TTAATTAAGATTATCTTATATATATATATACTATACTATATATACTATATAGTATAGTATAGTAT
9533 AGTATA
66 AGTATA
9539 GTATAAGATA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
72 11 0.17
73 18 0.27
74 37 0.56
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (73 bp):
TTAATTAAGATTATCTTATATATATATATACTATACTATATATACTATATAGTATAGTATAGTAT
AGTATATA
Found at i:9502 original size:5 final size:4
Alignment explanation
Indices: 9484--9567 Score: 59
Period size: 5 Copynumber: 20.0 Consensus size: 4
9474 AAGATTATCT
9484 TATA TATA TATA TACTA TACTA TATA TAGTA TATA GTATA GTATA GTATA
1 TATA TATA TATA TA-TA TA-TA TATA TA-TA TATA -TATA -TATA -TATA
*
9534 GTATA GTATA -AGA TA-A TATA TAT- TATA T-TA TATA
1 -TATA -TATA TATA TATA TATA TATA TATA TATA TATA
9568 AACAATAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
3 11 0.15
4 24 0.33
5 37 0.51
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:9509 original size:7 final size:6
Alignment explanation
Indices: 9410--9567 Score: 66
Period size: 7 Copynumber: 25.3 Consensus size: 6
9400 AAGATTATCT
*
9410 TATACTA TACTATA CTATACTA TACTATA CTATATA TATAGA GTATAGTA
1 TATA-TA TA-TATA -TATA-TA TA-TATA -TATATA TATATA -TATA-TA
* *
9460 TATATA TAT-TA -AT-TA -AGAT- TATCT- TATATA TATATA TACTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA-TATA
*
9503 CTATATA TAGTATA TAGTATA GTATAGTA TAGTATA GTATA-A GATA-A
1 -TATATA TA-TATA TA-TATA -TATA-TA TA-TATA -TATATA TATATA
9550 TATATA T-TATA T-TATA TA
1 TATATA TATATA TATATA TA
9568 AACAATAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 39
0.73 0.05 0.23
Matches are distributed among these distances:
4 5 0.04
5 26 0.21
6 23 0.19
7 49 0.40
8 21 0.17
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:9736 original size:12 final size:12
Alignment explanation
Indices: 9704--9729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9694 ATTCTCATAA
9704 ATATTTTTATTT
1 ATATTTTTATTT
9716 ATATTTTTATTT
1 ATATTTTTATTT
9728 AT
1 AT
9730 TTATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATATTTTTATTT
Found at i:10427 original size:87 final size:89
Alignment explanation
Indices: 10278--10447 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 89
10268 CATGGTTGGA
* *
10278 TTTTCTTAAAAATTGGGAGATTTGACTTAGTACATAATTGTTATATGAATTCATAACATGAGTAA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAATACATAATTGTTATATGAATTCATAACATGAGTAA
* *
10343 GATAT-TTTTTTTAACCGATAACT
66 AACATATTTTTTTAACCGATAACT
* *
10366 TTTTCTTAAAGATT-GAAGATTTGACTTAATACATAATTGTTATATGAATTCATGAA-GTGAGTA
1 TTTTCTTAAAAATTGGAAGATTTGACTTAATACATAATTGTTATATGAATTCAT-AACATGAGTA
10429 AAACATCATTTTTTTAACC
65 AAACAT-ATTTTTTTAACC
10448 CTGCAAACCA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
87 47 0.64
88 15 0.21
89 11 0.15
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (89 bp):
TTTTCTTAAAAATTGGAAGATTTGACTTAATACATAATTGTTATATGAATTCATAACATGAGTAA
AACATATTTTTTTAACCGATAACT
Found at i:11831 original size:229 final size:227
Alignment explanation
Indices: 11430--11886 Score: 860
Period size: 229 Copynumber: 2.0 Consensus size: 227
11420 ACATTAATGT
11430 TAGTAGCTATAAAATATCAAATCCAAAGGATCATTGGCTTAATTCTAAGATTATGAAAATAGAGA
1 TAGTAGCTATAAAATATCAAATCCAAAGGATCATTGGCTTAATTCTAAGATTATGAAAATAGAGA
*
11495 GAGCTAATTAATACCCTATCCCTTCATTAAGGTGAAAAATATGTCTCAATTAAGGTTATAATTTA
66 GAGCTAATTAACACCCTATCCCTTCATTAAGGTGAAAAATATGTCTCAATTAAGGTTATAATTTA
11560 TCTATTCTAAAAATATTTTAATAGCTAAGTAACATGAGATATAAAAAAAAAAAAAAGTGACAACT
131 TCTATTCTAAAAATATTTTAATAGCTAAGTAACATGAGATAT--AAAAAAAAAAAAGTGACAACT
* *
11625 ATGAGATTGTTAGAGTGAAACCACGTTCCACCAG
194 ATGAGATTCTTAGAGTAAAACCACGTTCCACCAG
11659 TAGTAGCTATAAAATATCAAATCCAAAGGATCATTGGCTTAATTCTAAGATTATGAAAATAGAGA
1 TAGTAGCTATAAAATATCAAATCCAAAGGATCATTGGCTTAATTCTAAGATTATGAAAATAGAGA
*
11724 GAGCTAATTAACACCCTATTCCTTCATTAAGGTGAAAAATATGTCTCAATTAAGGTTATAATTTA
66 GAGCTAATTAACACCCTATCCCTTCATTAAGGTGAAAAATATGTCTCAATTAAGGTTATAATTTA
11789 TCTATTCTAAAAATATTTTAATAGCTAAGTAACATGAGATATAAAAAAAAAAAAGTGACAACTAT
131 TCTATTCTAAAAATATTTTAATAGCTAAGTAACATGAGATATAAAAAAAAAAAAGTGACAACTAT
11854 GAGATTCTTAGAGTAAAACCACGTTCCACCAG
196 GAGATTCTTAGAGTAAAACCACGTTCCACCAG
11886 T
1 T
11887 CCAACCGCAA
Statistics
Matches: 224, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
227 54 0.24
229 170 0.76
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (227 bp):
TAGTAGCTATAAAATATCAAATCCAAAGGATCATTGGCTTAATTCTAAGATTATGAAAATAGAGA
GAGCTAATTAACACCCTATCCCTTCATTAAGGTGAAAAATATGTCTCAATTAAGGTTATAATTTA
TCTATTCTAAAAATATTTTAATAGCTAAGTAACATGAGATATAAAAAAAAAAAAGTGACAACTAT
GAGATTCTTAGAGTAAAACCACGTTCCACCAG
Found at i:14430 original size:15 final size:17
Alignment explanation
Indices: 14404--14436 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
14394 ATCTACCTAC
14404 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
14420 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
14436 C
1 C
14437 TCACATTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:14821 original size:19 final size:18
Alignment explanation
Indices: 14794--14829 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14784 TTTATCCTCT
*
14794 AATGGGTAGTTTTATTTAA
1 AATGAGTAGTTTT-TTTAA
14813 AATGAGTAGTTTTTTTA
1 AATGAGTAGTTTTTTTA
14830 TTTTGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (18 bp):
AATGAGTAGTTTTTTTAA
Found at i:19347 original size:149 final size:149
Alignment explanation
Indices: 19141--19434 Score: 412
Period size: 149 Copynumber: 2.0 Consensus size: 149
19131 TTTATTTGGC
* * *
19141 TGTCTATCTGCAAAAGTGCTCAATAACGTGTGCATGTTTGTACATGTTTCTAGAACCTTGTCTGT
1 TGTCTATCTGCAAAAGTGCACAATAACGTGTGCATGTCTGTACATGTTTCTAGAACCTTATCTGT
* * * * *
19206 GTATCTAGATATTAAACTCCTTGCTATGTGCTTTAGAGTTCAGAACA-TTATTACGT-GATAGTT
66 GTATCTAGATATTAAACACCTTGCTATGTGCTTTAGAGTCCAGAACATTTATGACATAAATAGTT
*
19269 TATCACTCTTTTGGCCCTG
131 TATCACTCCTTTGGCCCTG
* * *
19288 TGTCTATCTGCACAAGTGCACAATCACATGTGTGGATGTCTGTACATGTTTCTAGAACCTTATCT
1 TGTCTATCTGCAAAAGTGCACAAT-A-ACGTGTGCATGTCTGTACATGTTTCTAGAACCTTATCT
* ** *
19353 GTGTATTTAGATATTGGACACCTTGCTATGTGCTTTAGAGTCCTGAACATTTATGACATAAATAG
64 GTGTATCTAGATATTAAACACCTTGCTATGTGCTTTAGAGTCCAGAACATTTATGACATAAATAG
19418 TTTATCACTCCTTTGGC
129 TTTATCACTCCTTTGGC
19435 TTTCCATGCA
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
147 22 0.17
148 1 0.01
149 77 0.61
150 7 0.06
151 20 0.16
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (149 bp):
TGTCTATCTGCAAAAGTGCACAATAACGTGTGCATGTCTGTACATGTTTCTAGAACCTTATCTGT
GTATCTAGATATTAAACACCTTGCTATGTGCTTTAGAGTCCAGAACATTTATGACATAAATAGTT
TATCACTCCTTTGGCCCTG
Found at i:21662 original size:5 final size:5
Alignment explanation
Indices: 21654--21697 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
21644 TACTAAAAAG
* * *
21654 AGAAA AGAAA AG-CA GGAAA AGAAT AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
21698 GAGCTCTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 2 0.06
5 30 0.94
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:36842 original size:22 final size:23
Alignment explanation
Indices: 36812--36854 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
36802 TTTTGATGAT
36812 TTCCTTATGAAATTTTAATAATC
1 TTCCTTATGAAATTTTAATAATC
36835 TTCC-TATGAAATTTTAATAA
1 TTCCTTATGAAATTTTAATAA
36855 CGATACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (23 bp):
TTCCTTATGAAATTTTAATAATC
Found at i:36863 original size:22 final size:22
Alignment explanation
Indices: 36817--36870 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
36807 ATGATTTCCT
* *
36817 TATGAAATTTTAATAATCTTCC
1 TATGAAATTTTAATAATCATAC
36839 TATGAAATTTTAATAA-CGATAC
1 TATGAAATTTTAATAATC-ATAC
*
36861 TATGGAATTT
1 TATGAAATTT
36871 CAAGAACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTAATAATCATAC
Found at i:36901 original size:22 final size:22
Alignment explanation
Indices: 36875--36923 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
36865 GAATTTCAAG
* *
36875 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
36897 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
36919 AACCT
1 AACCT
36924 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:36976 original size:23 final size:22
Alignment explanation
Indices: 36905--37311 Score: 256
Period size: 22 Copynumber: 18.7 Consensus size: 22
36895 TTAACCTTCT
* *
36905 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
36927 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTCAC
*
36949 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
36972 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * **
36993 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTCAC
* *
37016 TATGAAAATTT-AAAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
* *
37037 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATT-TTGA-TAACCTCAC
* * * *
37059 TCTGAAAATTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
37081 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
37103 TATGAAATTTTGATAATCCTTC-C
1 TATGAAATTTTGATAA-CC-TCAC
* *
37126 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
37149 TAT-ACAATTTTGATAACCTC-C
1 TATGA-AATTTTGATAACCTCAC
*
37170 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
*
37191 ----AAATTTTGATAACTTTC-C
1 TATGAAATTTTGATAAC-CTCAC
** *
37209 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
37231 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
37253 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
37275 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
37297 TATGAAATTTTGATA
1 TATGAAATTTTGATA
37312 TCTTGCCTGA
Statistics
Matches: 302, Mismatches: 53, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
16 11 0.04
18 2 0.01
20 3 0.01
21 26 0.09
22 195 0.65
23 60 0.20
24 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:37006 original size:22 final size:23
Alignment explanation
Indices: 36946--37012 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
36936 TTGAAGACCT
*
36946 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATATTGATAACCAA
* * **
36969 CACTATGAGATGTTGATAACCTC
1 CACTATGAAATATTGATAACCAA
*
36992 CA-TATGATATATTGATAACCA
1 CACTATGAAATATTGATAACCA
37013 CGTTATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
CACTATGAAATATTGATAACCAA
Found at i:37257 original size:82 final size:84
Alignment explanation
Indices: 37107--37311 Score: 202
Period size: 82 Copynumber: 2.4 Consensus size: 84
37097 CCTCGCTATG
* *
37107 AAATTTTGATAATCCTTCCTATAAAATTTTGATAAACCTCCCTATACAATTTTGATAACCTCCTT
1 AAATTTTGATAATCCTTCCTATAAAATTTTGATAAACCTCACTATACAATTTTGATAACCTCCCT
*
37172 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGAAAACTAC
* * ** * * *
37191 AAATTTTGATAA-CTTTCCTATGATTTTTTGAT-AACCTCATTATGA-AATTTTGTTAATCTCCC
1 AAATTTTGATAATCCTTCCTATAAAATTTTGATAAACCTCACTAT-ACAATTTTGATAACCTCCC
*
37253 TATGAAATTTTGAAAACTAAAC
65 TATGAAATCTTGAAAACT--AC
* *
37275 TATGAAATTTTGATAA-CCTTCATATGAAATTTTGATA
1 ----AAATTTTGATAATCCTTCCTATAAAATTTTGATA
37312 TCTTGCCTGA
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
82 39 0.40
83 17 0.17
84 14 0.14
88 28 0.29
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (84 bp):
AAATTTTGATAATCCTTCCTATAAAATTTTGATAAACCTCACTATACAATTTTGATAACCTCCCT
ATGAAATCTTGAAAACTAC
Found at i:37461 original size:22 final size:22
Alignment explanation
Indices: 37432--37487 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
37422 TGGAAATCAC
*
37432 ATTT-TGAAAATTTGATAACCT
1 ATTTATGAAAATTTAATAACCT
*
37453 ATTTATGAAATTTTAATAACCT
1 ATTTATGAAAATTTAATAACCT
* *
37475 CTCTAT-AAAATTT
1 ATTTATGAAAATTT
37488 TGTTGACCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTTATGAAAATTTAATAACCT
Found at i:37488 original size:22 final size:22
Alignment explanation
Indices: 37438--37664 Score: 92
Period size: 22 Copynumber: 10.4 Consensus size: 22
37428 TCACATTTTG
* *
37438 AAAA-TTTGATAACCTATTTAT
1 AAAATTTTGATAACCTCTCTAT
* *
37459 GAAATTTTAATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* * *
37481 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* * *
37503 GAAATTTTGATAATCACAT-TAT
1 AAAATTTTGATAACCTC-TCTAT
** *
37525 GTAATTTTGATAACCTCGT-TTT
1 AAAATTTTGATAACCTC-TCTAT
* * *** *
37547 GAATTTTTGATAATAACACTAT
1 AAAATTTTGATAACCTCTCTAT
*
37569 -AAATTTTGATAATCT-TCT-T
1 AAAATTTTGATAACCTCTCTAT
* *
37588 ATAAATTTTGATAATCTGATATCTAT
1 A-AAATTTTGATAA-C--CTCTCTAT
* * *
37614 GAAATTTCGATAACCACTCTAT
1 AAAATTTTGATAACCTCTCTAT
* *
37636 GAGA-TTTGATAACCT-TCTAT
1 AAAATTTTGATAACCTCTCTAT
*
37656 CAAATTTTG
1 AAAATTTTG
37665 GTACTCCTTA
Statistics
Matches: 153, Mismatches: 42, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
19 1 0.01
20 9 0.06
21 40 0.26
22 85 0.56
23 1 0.01
24 2 0.01
25 14 0.09
26 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:37569 original size:88 final size:87
Alignment explanation
Indices: 37411--37576 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 87
37401 AAAAATACCA
* **
37411 CTATGAAATTTTGGAAATCACATTTTGAAAATTTGATAACCTATTTATGAAATTTTAATAACCTC
1 CTATGAAATTTTGGAAATCACATTATGAAAATTTGATAACCTATTTATGAAATTTTAATAACAAC
*
37476 TCTATAAAATTTTGTTGACCCCT
66 ACTAT-AAATTTTGTTGACCCCT
* * * * * *
37499 CTATGAAATTTT-GATAATCACATTATGTAATTTTGATAACCTCGTTT-TGAATTTTTGATAATA
1 CTATGAAATTTTGGA-AATCACATTATGAAAATTTGATAACCT-ATTTATGAAATTTTAATAACA
37562 ACACTATAAATTTTG
64 ACACTATAAATTTTG
37577 ATAATCTTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
87 10 0.15
88 53 0.80
89 3 0.05
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (87 bp):
CTATGAAATTTTGGAAATCACATTATGAAAATTTGATAACCTATTTATGAAATTTTAATAACAAC
ACTATAAATTTTGTTGACCCCT
Found at i:37595 original size:43 final size:43
Alignment explanation
Indices: 37504--37602 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 43
37494 CCCCTCTATG
* * * *
37504 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTTTT
1 AAATTTTGATAATAACACTATGAAATTTTGATAACCTCGTTAT
* *
37547 GAATTTTTGATAATAACACTAT-AAATTTTGATAATCTTC-TTAT
1 -AAATTTTGATAATAACACTATGAAATTTTGATAA-CCTCGTTAT
37590 AAATTTTGATAAT
1 AAATTTTGATAAT
37603 CTGATATCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 12 0.26
43 14 0.30
44 21 0.45
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (43 bp):
AAATTTTGATAATAACACTATGAAATTTTGATAACCTCGTTAT
Found at i:39029 original size:538 final size:539
Alignment explanation
Indices: 38012--39088 Score: 1687
Period size: 538 Copynumber: 2.0 Consensus size: 539
38002 TAGGCTCGTT
* * * *
38012 TGAGTCCATGAAATCCGAAATGTCAAGTCAGATGTTTTAAAGTCTAAATTTGATATTTTTAGACC
1 TGAGTCCATGAAATCCGAAATGTCAAGCCAGATGTTTTAAAGTCTAAATCTAATATTCTTAGACC
* * *
38077 CAATTCGTTAATATGGAAGCCCAAAGAATGAATCCAAGTCCAATCAGTAATTATGATGCAGTAAT
66 CAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATAATGCAGTAAT
*
38142 GATTCAGCCCTGATACGGCATTGTTAAATCCTAATTAAAGGAGGACTTCACAAGAGCAGTTTTGG
131 GATTCAGCCCTGATACAGCATTGTTAAATCCTAATTAAAGGAGGACTTCACAAGAGCAGTTTTGG
* *
38207 AAGAAATTTCATAACTTTTGATTCAAAGCTCAGAAAAATGCAAATGAGGTACCGTTGAAAAGAGG
196 AAGAAAATTCATAACTTTTGATGCAAAGCTCAGAAAAATGCAAATGAGGTACCGTTGAAAAGAGG
** * *
38272 ATTTTGACATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCAGTGGATGATTT
261 ATTCCGACATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCAGTAGACGATTT
* * * *
38337 TACCCTTGAAATTTCTGGATAGAATTGATCTTCTCCTAAATTGACTTTGAGAATGTTTTAGACGA
326 TACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACTGACTTGGAGAATGTTTTAGACGA
* *
38402 AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCATGTTAGATTCTAATTCATGAGG
391 AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCATGTTAGATTCTAATTAATGAGC
*
38467 ATAATCTAAATTGCCATTATTTTAATAGTGGAATGATTAAAATATTATTTAATAAT-GCAATTTA
456 ATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTA
38531 GAAATATATTTGAAAAAAA
521 GAAATATATTTGAAAAAAA
* * *
38550 TGAGTCCATGAAGTCC-AAATTGTCAAGCCATAT-TTATTGAAGTCTAAATCTAATATTCTTAGA
1 TGAGTCCATGAAATCCGAAA-TGTCAAGCCAGATGTT-TTAAAGTCTAAATCTAATATTCTTAGA
* *
38613 CCCAATTCGTTAATATGGAAGCCCAAAGAAGGAGTCCAAATCCAATTAGTAATTATAATGCAGTA
64 CCCAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATAATGCAGTA
** ** * *
38678 ATGATTCAGCGGTGATGTAGCATTGTTAAATCCTATTTAAATGAGGACTTCACAAGAGCAGTTTT
129 ATGATTCAGCCCTGATACAGCATTGTTAAATCCTAATTAAAGGAGGACTTCACAAGAGCAGTTTT
* * *
38743 GGAAGAAAATTCATAACTTTTGATGCAGAA-TTCAGAAAAATGCAAATGAGGTACCTTTGGAAAG
194 GGAAGAAAATTCATAACTTTTGATGCA-AAGCTCAGAAAAATGCAAATGAGGTACCGTTGAAAAG
*
38807 AGGATTCCGAGATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCAGTAGACGA
258 AGGATTCCGACATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCAGTAGACGA
* *
38872 TTTTGCCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACTGACTTGGAGAATGTTTTGGA
323 TTTTACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACTGACTTGGAGAATGTTTTAGA
* * *
38937 CGAAAATTCAGAT-CTTGAAGATGATGTGGGGCATCCCTATTGGCCATGTTGGATTCTAATTAAT
388 CGAAAATTCAGATGC-TAAAAATGATGTGGGGCATCCCTATTGGCCATGTTAGATTCTAATTAAT
* * *
39001 GAGCATAATCTACATTTCCATTATTTTAATATTGGAATAATTAAAATATTATTTAATAATGGCAA
452 GAGCATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAA
39066 TTTAGAAATATATTTGAAAAAAA
517 TTTAGAAATATATTTGAAAAAAA
39089 GGCTACAATC
Statistics
Matches: 490, Mismatches: 44, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
537 6 0.01
538 455 0.93
539 29 0.06
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (539 bp):
TGAGTCCATGAAATCCGAAATGTCAAGCCAGATGTTTTAAAGTCTAAATCTAATATTCTTAGACC
CAATTCGTTAATATGGAAGCCCAAAGAAGGAATCCAAATCCAATCAGTAATTATAATGCAGTAAT
GATTCAGCCCTGATACAGCATTGTTAAATCCTAATTAAAGGAGGACTTCACAAGAGCAGTTTTGG
AAGAAAATTCATAACTTTTGATGCAAAGCTCAGAAAAATGCAAATGAGGTACCGTTGAAAAGAGG
ATTCCGACATCTACAACTTTTATGTTTATCTCGAGACCTAATTCTGCCGTTTCAGTAGACGATTT
TACCCTTAAAATTTCTGGACAGAATTGATCTTCTCCTAAACTGACTTGGAGAATGTTTTAGACGA
AAATTCAGATGCTAAAAATGATGTGGGGCATCCCTATTGGCCATGTTAGATTCTAATTAATGAGC
ATAATCTAAATTGCCATTATTTTAATAGTGGAATAATTAAAATATTATTTAATAATGGCAATTTA
GAAATATATTTGAAAAAAA
Found at i:39370 original size:21 final size:21
Alignment explanation
Indices: 39335--39376 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39325 GGTGTGTGTG
*
39335 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
39357 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
39377 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:40263 original size:21 final size:21
Alignment explanation
Indices: 40228--40269 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40218 TGTGTGTGTG
*
40228 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
40250 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
40270 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:41194 original size:21 final size:21
Alignment explanation
Indices: 41165--41206 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41155 TTCTGGCTAA
*
41165 GCTTCAGAATCAGGAGCAAAT
1 GCTTCAGAATCAAGAGCAAAT
*
41186 GCTTTAGAATCAAGAGCAAAT
1 GCTTCAGAATCAAGAGCAAAT
41207 ACAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
GCTTCAGAATCAAGAGCAAAT
Found at i:41606 original size:152 final size:152
Alignment explanation
Indices: 41330--41636 Score: 524
Period size: 152 Copynumber: 2.0 Consensus size: 152
41320 ACAGCGGAAT
*
41330 TGGTGGTGGCGTTAATAAGCAGCAGCACTATGCAACGAGACAAACAAGACTGGAGTTTCCTCGTT
1 TGGTGGTGGCGTTAATAAACAGCAGCACTATGCAACGAGACAAACAAGACTGGAGTTTCCTCGTT
* * * *
41395 TCGATGGCGAAAACTCAACTGGATGGCTCTTTCATTGCAAACAATTCTTCGATCTTGACCACAAA
66 TCAATGGCGAAAACTCAACTGAATGACTCTTTCATTGCAAACAATTCTTCCATCTTGACCACAAA
41460 CCTGCAGATCTTAAGGTTAAGA
131 CCTGCAGATCTTAAGGTTAAGA
* *
41482 TGGTGGTGGCGTTAATAAACAGTAGCACTATGCAACGAGACAAACAAGACTGGAGTTTCCTTGTT
1 TGGTGGTGGCGTTAATAAACAGCAGCACTATGCAACGAGACAAACAAGACTGGAGTTTCCTCGTT
* * *
41547 TCAATGGCGAAAACTTAACTGAATGACTCTTTCGTTGCAAACAATTCTTCCATCTTGACCACACA
66 TCAATGGCGAAAACTCAACTGAATGACTCTTTCATTGCAAACAATTCTTCCATCTTGACCACAAA
41612 CCTGCAGATCTTAAGGTTAAGA
131 CCTGCAGATCTTAAGGTTAAGA
41634 TGG
1 TGG
41637 GTTCCATGAA
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 145 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (152 bp):
TGGTGGTGGCGTTAATAAACAGCAGCACTATGCAACGAGACAAACAAGACTGGAGTTTCCTCGTT
TCAATGGCGAAAACTCAACTGAATGACTCTTTCATTGCAAACAATTCTTCCATCTTGACCACAAA
CCTGCAGATCTTAAGGTTAAGA
Found at i:42894 original size:33 final size:30
Alignment explanation
Indices: 42827--42902 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 30
42817 AACTATTGCG
* * *
42827 TCAAGGACGTTTTGTCCCCAAACTTCCACAT
1 TCAA-GACATTTTGCCCCCAAACTTCCAAAT
42858 TCAAGACATTTTGCCCCCTAAACTTTCCCAAAT
1 TCAAGACATTTTGCCCCC-AAAC-TT-CCAAAT
42891 TCAAGACATTTT
1 TCAAGACATTTT
42903 ACTCCCTGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 12 0.31
31 8 0.21
32 2 0.05
33 17 0.44
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (30 bp):
TCAAGACATTTTGCCCCCAAACTTCCAAAT
Done.