Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015044.1 Corchorus capsularis cultivar CVL-1 contig15065, 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: 15788
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:548 original size:22 final size:22
Alignment explanation
Indices: 506--549 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
496 TATTCATATG
* *
506 AAATTATGATAATCTCTCTATT
1 AAATTATAATAATCTCACTATT
528 AAATTATAATAAT-TACACTATT
1 AAATTATAATAATCT-CACTATT
550 TTTTATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTATAATAATCTCACTATT
Found at i:775 original size:22 final size:22
Alignment explanation
Indices: 665--1148 Score: 213
Period size: 22 Copynumber: 22.3 Consensus size: 22
655 GAAATTCGGT
* * *
665 TAACCTCCTTAAGGAATTTTGA
1 TAACCTCCATATGAAATTTTGA
*
687 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTCCATATGAAATTTTGA
*
709 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
** * *
731 TAACCAACACTATGAGATGTTGA
1 TAACCTCCA-TATGAAATTTTGA
* *
754 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
* ** * *
776 TAACCACGTTATGAAAATTTAA
1 TAACCTCCATATGAAATTTTGA
*
798 AAACCTCCATATG-AATTGTT-A
1 TAACCTCCATATGAAATT-TTGA
*
819 GTAA--TCACACTCTGAAATTTTGA
1 -TAACCTC-CA-TATGAAATTTTGA
* * *
842 TAATCATAC-TATGAAATTGTGA
1 TAA-CCTCCATATGAAATTTTGA
864 TAACCTCGC-TATGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* *
886 TAAATCTTCC-TATAAAATTTT-A
1 T-AA-CCTCCATATGAAATTTTGA
* * * *
908 TTAACTTTCTTATGAAATCTTGA
1 -TAACCTCCATATGAAATTTTGA
*
931 TAA----C-TA-CAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* **
947 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCATATGAAATTTTGA
*
969 TAACCT-CATTATGAAATTTTGT
1 TAACCTCCA-TATGAAATTTTGA
* *
991 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * *
1013 TCTACATAC-TATGAAATTTTGA
1 T-AACCTCCATATGAAATTTTGA
* *
1035 TAACC-CTCTTGTGAAATTTTGA
1 TAACCTC-CATATGAAATTTTGA
* **
1057 -AAACTAAACTATGAAATTTTGA
1 TAACCTCCA-TATGAAATTTTGA
*
1079 TAACCTTCATATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* *
1101 TATCCTCC--CTGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
* * * *
1121 TTA-CTCCATAATAAAAATTTAA
1 TAACCTCCAT-ATGAAATTTTGA
1143 TAACCT
1 TAACCT
1149 TCCTAATTTG
Statistics
Matches: 346, Mismatches: 78, Indels: 75
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 4 0.01
20 15 0.04
21 24 0.07
22 233 0.67
23 51 0.15
24 4 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:1278 original size:22 final size:22
Alignment explanation
Indices: 1228--1279 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1218 ATCACATTTG
1228 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
1249 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
1271 AAAATTTTG
1 AAAATTTTG
1280 TTGACCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:1297 original size:22 final size:22
Alignment explanation
Indices: 1226--1372 Score: 73
Period size: 22 Copynumber: 6.5 Consensus size: 22
1216 TAATCACATT
* * *
1226 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
1248 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
1270 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
*
1292 TGAAATAAATTTTGATAATCCGATCTCTA
1 TG----AAATTTTGATAA-CC--CCTCTA
* * * *
1321 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
1343 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
*
1363 TCAAATTTTG
1 TGAAATTTTG
1373 GTACTCCTAA
Statistics
Matches: 96, Mismatches: 21, Indels: 17
0.72 0.16 0.13
Matches are distributed among these distances:
20 7 0.07
21 11 0.11
22 47 0.49
24 1 0.01
25 11 0.11
26 10 0.10
27 2 0.02
29 7 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:1426 original size:22 final size:22
Alignment explanation
Indices: 1393--1449 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1383 TGAAATTGAG
*
1393 ACTTTT-ATAACCTT-CATATGA
1 ACTTTTGATAACCTTAC-TATAA
*
1414 ACTTTTGATAACCATACTATAA
1 ACTTTTGATAACCTTACTATAA
*
1436 AATTTTGATAACCT
1 ACTTTTGATAACCT
1450 CCCCATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.20
22 23 0.77
23 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (22 bp):
ACTTTTGATAACCTTACTATAA
Found at i:1460 original size:22 final size:22
Alignment explanation
Indices: 1435--1492 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1425 CCATACTATA
*
1435 AAATTTTGATAACCTCCCCATG
1 AAATTTTGATAACCTCCCAATG
* *
1457 AAATATT-AGTAACCTCCTAATG
1 AAATTTTGA-TAACCTCCCAATG
*
1479 AAATTTTGTTAACC
1 AAATTTTGATAACC
1493 ACATTATGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCAATG
Found at i:1501 original size:22 final size:21
Alignment explanation
Indices: 1476--1530 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1466 TAACCTCCTA
1476 ATGAAATTTTGTTAACCACATT
1 ATGAAATTTTG-TAACCACATT
* *
1498 ATGAAATTCTTGTAACCTCGTT
1 ATGAAATT-TTGTAACCACATT
*
1520 ATGACATTTTG
1 ATGAAATTTTG
1531 ATAATCTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (21 bp):
ATGAAATTTTGTAACCACATT
Found at i:1634 original size:24 final size:22
Alignment explanation
Indices: 1577--1635 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1567 AATTAATCAC
*
1577 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTAATAACCAA
* * *
1599 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC--AA
1623 CCTATGAAATTTT
1 CCTATGAAATTTT
1636 GGTAACTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 17 0.59
24 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (22 bp):
CCTATGAAATTTTAATAACCAA
Found at i:1929 original size:19 final size:20
Alignment explanation
Indices: 1898--1935 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1888 ATTGACATTT
1898 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
1917 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
1936 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:4563 original size:27 final size:27
Alignment explanation
Indices: 4533--4586 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4523 ATTGGCCACT
4533 GTACTAAATGCAGAGCCAATAAGGTTA
1 GTACTAAATGCAGAGCCAATAAGGTTA
*
4560 GTACTAAATGCAGAGCTAATAAGGTTA
1 GTACTAAATGCAGAGCCAATAAGGTTA
4587 ACCTGTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (27 bp):
GTACTAAATGCAGAGCCAATAAGGTTA
Found at i:5842 original size:20 final size:20
Alignment explanation
Indices: 5817--5856 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5807 GGCCAATCCC
5817 TTATATAAGGCCAAGGCCAT
1 TTATATAAGGCCAAGGCCAT
5837 TTATATAAGGCCAAGGCCAT
1 TTATATAAGGCCAAGGCCAT
5857 GACTTGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
TTATATAAGGCCAAGGCCAT
Found at i:13710 original size:22 final size:21
Alignment explanation
Indices: 13660--13711 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
13650 TGATCCCATC
*
13660 ATGAAATTTTGATAACCTCCT
1 ATGAAATTTTGATAACCTACT
*
13681 ATGAAATTTTGATAACGGTACT
1 ATGAAATTTTGATAAC-CTACT
*
13703 ATGGAATTT
1 ATGAAATTT
13712 CAAGAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (21 bp):
ATGAAATTTTGATAACCTACT
Found at i:13958 original size:22 final size:22
Alignment explanation
Indices: 13914--13973 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
13904 GAATTGTTAG
* * * *
13914 TAATCACACTTTAAAATTTTGA
1 TAATCACACTATGAAACTGTGA
13936 TAATCACACTATGAAACTGTGA
1 TAATCACACTATGAAACTGTGA
*
13958 TAA-CATCGCTATGAAA
1 TAATCA-CACTATGAAA
13974 TTTTGATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (22 bp):
TAATCACACTATGAAACTGTGA
Found at i:13980 original size:22 final size:20
Alignment explanation
Indices: 13927--14219 Score: 135
Period size: 22 Copynumber: 13.6 Consensus size: 20
13917 TCACACTTTA
*
13927 AAATTTTGATAATCACACTATG
1 AAATTTTGATAA-CTC-CTATG
* *
13949 AAACTGTGATAACATCGCTATG
1 AAATTTTGATAAC-TC-CTATG
* * *
13971 AAATTTTGATTAATCTTTCTGTA
1 AAATTTTGA-TAA-C-TCCTATG
* *
13994 AAATTTTAATAAGCCTCCCTATA
1 AAATTTTGATAA--CT-CCTATG
*
14017 AAATTTTGATAACTTTCTTATG
1 AAATTTTGATAAC--TCCTATG
* *
14039 AAATCTTGATAA---CTA-C
1 AAATTTTGATAACTCCTATG
14055 AAATTTTGATAAGCTCCTTATG
1 AAATTTTGATAA-CTCC-TATG
** *
14077 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAA-CTC-CTATG
*
14099 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAA-CT-CCTATG
* *
14121 AAATTTTGATCTACATACTATG
1 AAATTTTGAT-AAC-TCCTATG
14143 AAATTTTGATAACTCTCTTATG
1 AAATTTTGATAACTC-C-TATG
* *
14165 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAACT--CCTATG
* *
14187 AAAATTTGATAACCTTCATATG
1 AAATTTTGATAA-C-TCCTATG
14209 AAATTTTGATA
1 AAATTTTGATA
14220 TCCTCACTGA
Statistics
Matches: 205, Mismatches: 43, Indels: 46
0.70 0.15 0.16
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
20 2 0.01
21 7 0.03
22 144 0.70
23 36 0.18
24 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTTTGATAACTCCTATG
Found at i:14186 original size:66 final size:66
Alignment explanation
Indices: 14080--14225 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
14070 CCTTATGATT
* * ** * *
14080 TTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAC-TATGA
1 TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAAATTTGAT-AACATACATATGA
14144 AA
65 AA
* *
14146 TTTTGATAACTCTC-TTATGAAATTTTG-AAAACTAAACTATGAAAATTTGATAACCTTCATATG
1 TTTTGATAAC-CTCATTATGAAATTTTGTAAAACT-AACTATGAAAATTTGATAACATACATATG
14209 AAA
64 AAA
*
14212 TTTTGATATCCTCA
1 TTTTGATAACCTCA
14226 CTGAATTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
65 11 0.16
66 53 0.79
67 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (66 bp):
TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAAATTTGATAACATACATATGAA
A
Found at i:14273 original size:20 final size:19
Alignment explanation
Indices: 14209--14276 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
14199 CCTTCATATG
*
14209 AAATTTTGATATCCTCACT
1 AAATTTTGATATCCTCCCT
* *
14228 GAATTTTGATATCCTCCTT
1 AAATTTTGATATCCTCCCT
* *
14247 GAATTTTGGTATCCTCCCT
1 AAATTTTGATATCCTCCCT
14266 AAAATTTTGAT
1 -AAATTTTGAT
14277 TACTCCATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 33 0.80
20 8 0.20
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (19 bp):
AAATTTTGATATCCTCCCT
Found at i:14414 original size:22 final size:22
Alignment explanation
Indices: 14383--14599 Score: 131
Period size: 22 Copynumber: 9.7 Consensus size: 22
14373 AATCAGATTT
*
14383 TGAAAATTTGATAACCACTTTA
1 TGAAATTTTGATAACCACTTTA
14405 TGAAATTTTGATAA-CATCTTTA
1 TGAAATTTTGATAACCA-CTTTA
* * * * *
14427 TAAAAATTTTGTTGACCCCTCTA
1 T-GAAATTTTGATAACCACTTTA
* *
14450 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCACTTTA
* * *
14472 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCAC-TTTA
* **
14494 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCACTTTA
*
14516 TGAAATTTTTGATAA--TCTTCATA
1 TGAAA-TTTTGATAACCACTT--TA
*
14539 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-C-CA-CTTTA
* * *
14563 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCACTTTA
*
14585 TGAGA-TTTGATAACC
1 TGAAATTTTGATAACC
14600 TTCTATCAAA
Statistics
Matches: 148, Mismatches: 33, Indels: 29
0.70 0.16 0.14
Matches are distributed among these distances:
21 21 0.14
22 79 0.53
23 30 0.20
24 4 0.03
25 11 0.07
26 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCACTTTA
Found at i:14523 original size:44 final size:43
Alignment explanation
Indices: 14383--14530 Score: 129
Period size: 45 Copynumber: 3.3 Consensus size: 43
14373 AATCAGATTT
* * * *
14383 TGAAAATTTGATAACCACTTTATGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCACCTT-TGAAATTTTGATAACAACATTA
* * *
14427 TAAAAATTTTGTTGACC-CCTCTATGAAATTTTGATAATC-ACATTA
1 T-GAAATTTTGATAACCACCT-T-TGAAATTTTGATAA-CAACATTA
* * *
14472 TGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCAC-CTTTGAAATTTTGATAACAACATTA
14516 TGAAATTTTTGATAA
1 TGAAA-TTTTGATAA
14531 TCTTCATATA
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 37 0.44
45 43 0.51
46 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (43 bp):
TGAAATTTTGATAACCACCTTTGAAATTTTGATAACAACATTA
Found at i:14526 original size:89 final size:90
Alignment explanation
Indices: 14357--14526 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 90
14347 AAAAATACCA
* * * *
14357 CTATGAAAATTTTTGTAATCAGATTTTGAAAATTTGATAACCACTTTATGAAATTTTGATAACAT
1 CTATGAAAATTTTTGTAATCACATTATGAAAATTTGATAACCACCTTATGAAATTTTGATAACAA
**
14422 CTTTATAAAAATTTTGTTGACCCCT
66 CACTATAAAAATTTTGTTGACCCCT
* * *
14447 CTATG-AAA-TTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CTATGAAAATTTTTG-TAATCACATTATGAAAATTTGATAACCAC-CTTATGAAATTTTGATAAC
* *
14509 AACACTATGAAATTTTTG
64 AACACTATAAAAATTTTG
14527 ATAATCTTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
88 5 0.07
89 55 0.82
90 7 0.10
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (90 bp):
CTATGAAAATTTTTGTAATCACATTATGAAAATTTGATAACCACCTTATGAAATTTTGATAACAA
CACTATAAAAATTTTGTTGACCCCT
Found at i:14667 original size:22 final size:22
Alignment explanation
Indices: 14403--14748 Score: 103
Period size: 22 Copynumber: 15.4 Consensus size: 22
14393 ATAACCACTT
*
14403 TATGAAATTTTGATAACATCTTTA
1 TATGAAATTTTGATAAC--CTTCA
* * * *
14427 TA-AAAATTTTGTTGACCCCTC-
1 TATGAAATTTTGAT-AACCTTCA
* *
14448 TATGAAATTTTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
* *
14469 TTATGTAATTTTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* **
14492 TTTGAAATTTTGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
*
14513 CTATGAAATTTTTGATAATCTTCA
1 -TATGAAA-TTTTGATAACCTTCA
* *
14537 TAT-AAATTTTGATAATCATATCTT
1 TATGAAATTTTGATAA-CCT-TC-A
*
14561 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAA-C-CTTCA
*
14583 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* * *
14603 TATCAAAATTTTGGTACTCCTT-A
1 TAT-GAAATTTTGATA-ACCTTCA
*
14626 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
14652 TATGAAATTTTGATAACCAT-A
1 TATGAAATTTTGATAACCTTCA
* * *
14673 CTATAAAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * *
14696 GATGAAGTATT-AGTAACCTTC-
1 TATGAAATTTTGA-TAACCTTCA
* *
14717 TAATGAAATTTTGTTAACC-ACA
1 T-ATGAAATTTTGATAACCTTCA
14739 CTATGAAATT
1 -TATGAAATT
14749 CGTATAACCT
Statistics
Matches: 237, Mismatches: 52, Indels: 68
0.66 0.15 0.19
Matches are distributed among these distances:
19 1 0.00
20 7 0.03
21 31 0.13
22 127 0.54
23 30 0.13
24 12 0.05
25 17 0.07
26 6 0.03
27 6 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:14876 original size:24 final size:23
Alignment explanation
Indices: 14821--14951 Score: 85
Period size: 22 Copynumber: 5.8 Consensus size: 23
14811 TTAACCACCA
* *
14821 TATGAAATTTCAATAACC-AAGC
1 TATGAAATTTTAATAACCTAATC
*
14843 TAAGAAATTTTAATAACCTAATCC
1 TATGAAATTTTAATAACCTAAT-C
** *
14867 TATGAAATTTTGGTAA-CTACTC
1 TATGAAATTTTAATAACCTAATC
**
14889 TATGAAATTTTGGTAACC-ACA-C
1 TATGAAATTTTAATAACCTA-ATC
**
14911 TATGAAATTTTGGTAACC-ACA-C
1 TATGAAATTTTAATAACCTA-ATC
* *
14933 TATGGAATTTTGATAACCT
1 TATGAAATTTTAATAACCT
14952 CCTCATGGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
22 73 0.78
23 7 0.07
24 14 0.15
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (23 bp):
TATGAAATTTTAATAACCTAATC
Found at i:14894 original size:22 final size:22
Alignment explanation
Indices: 14866--14950 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
14856 TAACCTAATC
* *
14866 CTATGAAATTTTGGTAACTACT
1 CTATGAAATTTTGGTAACCACA
14888 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
14910 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
14932 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
14951 TCCTCATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:14959 original size:22 final size:21
Alignment explanation
Indices: 14864--14963 Score: 103
Period size: 22 Copynumber: 4.6 Consensus size: 21
14854 AATAACCTAA
14864 TCCTATGAAATTTTGGTAA-C
1 TCCTATGAAATTTTGGTAACC
14884 TACTCTATGAAATTTTGGTAACC
1 T-C-CTATGAAATTTTGGTAACC
*
14907 ACACTATGAAATTTTGGTAACC
1 TC-CTATGAAATTTTGGTAACC
* * *
14929 ACACTATGGAATTTTGATAACC
1 TC-CTATGAAATTTTGGTAACC
*
14951 TCCTCATGGAATT
1 TCCT-ATGAAATT
14964 ATAATAACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 66 0.93
23 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
TCCTATGAAATTTTGGTAACC
Found at i:15023 original size:18 final size:18
Alignment explanation
Indices: 15000--15052 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
14990 TGATATAATG
15000 AAATAATTTATAATTAAA
1 AAATAATTTATAATTAAA
**
15018 AAATAATGGAATAATTAAA
1 AAATAAT-TTATAATTAAA
*
15037 AATATTATTTAGTAAT
1 AA-ATAATTTA-TAAT
15053 GGCAATTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AAATAATTTATAATTAAA
Done.