Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015015.1 Corchorus capsularis cultivar CVL-1 contig15036, 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: 14115
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:69 original size:2 final size:2
Alignment explanation
Indices: 62--92 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52 AATGAAATCT
62 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93 TGCTACTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3639 original size:3 final size:3
Alignment explanation
Indices: 3633--3662 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3623 TAATAATAAA
3633 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3663 GTACCGACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6448 original size:12 final size:13
Alignment explanation
Indices: 6431--6464 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6421 TGACAAAAAA
6431 AGAGAAATTA-AG
1 AGAGAAATTAGAG
6443 AGAGAAATTAGAG
1 AGAGAAATTAGAG
*
6456 AGAGTAATT
1 AGAGAAATT
6465 GGTATATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (13 bp):
AGAGAAATTAGAG
Found at i:6825 original size:22 final size:22
Alignment explanation
Indices: 6799--6895 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
6789 ATATTCATAC
6799 GAAATTATGATAACCTTCCTAT
1 GAAATTATGATAACCTTCCTAT
*
6821 TAAATTATGATAA--TTACACTAT
1 GAAATTATGATAACCTT-C-CTAT
** *
6843 --TTTTGATGATATCC-T--TAT
1 GAAATT-ATGATAACCTTCCTAT
*
6861 GAAATTTTGATAACCTTCCTAT
1 GAAATTATGATAACCTTCCTAT
6883 GAAATTATGATAA
1 GAAATTATGATAA
6896 TTACACTATT
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
18 3 0.05
19 7 0.12
20 7 0.12
21 7 0.12
22 32 0.57
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (22 bp):
GAAATTATGATAACCTTCCTAT
Found at i:6945 original size:22 final size:22
Alignment explanation
Indices: 6920--7496 Score: 186
Period size: 22 Copynumber: 26.6 Consensus size: 22
6910 ATGACATCCT
6920 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
6942 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
6964 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
6986 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
7007 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
7029 TAAGGAATTTTGA-AGACC-TCAT
1 TATGAAATTTTGATA-ACCTTC-C
7051 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* * **
7072 AAATGAAATTTTGATAATCAACAC
1 -TATGAAATTTTGATAACCTTC-C
7096 TAT-AAGA---TGATAACC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * * *
7114 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
7137 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
7158 ATATG-AATTGTT-AGTAATC-GCAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
7181 TTTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
7203 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
7225 TATGAAATTTTGATAATCCTTCA
1 TATGAAATTTTGATAA-CCTTCC
* * *
7248 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
7271 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
7292 TTATGAAATCTTAATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
7310 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
7331 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
7353 TATGAAA-TTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
7374 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* * *
7396 TATGAGATTTTGAATAACCCTCT
1 TATGAAATTTTG-ATAACCTTCC
* * * **
7419 TCT-AAATTTTGAAAATCTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
7441 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* * *
7463 TATGAAATTGTGATATCCTCCC
1 TATGAAATTTTGATAACCTTCC
7485 T-T-AAATTTTGAT
1 TATGAAATTTTGAT
7497 TACTCCATAA
Statistics
Matches: 406, Mismatches: 110, Indels: 80
0.68 0.18 0.13
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 2 0.00
19 5 0.01
20 17 0.04
21 48 0.12
22 253 0.62
23 64 0.16
24 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6966 original size:62 final size:62
Alignment explanation
Indices: 6799--6950 Score: 268
Period size: 62 Copynumber: 2.5 Consensus size: 62
6789 ATATTCATAC
* * *
6799 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTGATGATATCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
*
6861 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACATCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
6923 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
6951 TCAATAACGA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 86 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
Found at i:7286 original size:46 final size:44
Alignment explanation
Indices: 7185--7286 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 44
7175 TCGCACTTTG
* * *
7185 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAATCACACTATAAAATTGTGATAACCTCCCTATA
* * *
7229 AAATTTTGATAATC-CTTCATATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAATCAC-AC-TATAAAATTGTGAT-AACCTCCCTATA
7275 AAATTTTGATAA
1 AAATTTTGATAA
7287 CCTCCTTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.02
44 15 0.31
45 12 0.24
46 21 0.43
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAATCACACTATAAAATTGTGATAACCTCCCTATA
Found at i:7626 original size:22 final size:22
Alignment explanation
Indices: 7601--7706 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
7591 AATCACATTT
* *
7601 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
7623 TGAAA-TTTGAATAACCTCTCTA
1 TGAAATTTTG-ATAACCTCTCTA
* * * *
7645 TCAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
** *
7667 TGAAATTTTGATAGTCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
*
7689 TGTAATTTTGATAACCTC
1 TGAAATTTTGATAACCTC
7707 GTTTTATGCT
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
21 4 0.06
22 57 0.86
23 5 0.08
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:8506 original size:37 final size:36
Alignment explanation
Indices: 8414--8510 Score: 104
Period size: 38 Copynumber: 2.6 Consensus size: 36
8404 ATCTAAGCTC
* *
8414 AAATAGGACGTTGGAGACGAAAATAAAAAGCAAAATT
1 AAATAGGACGTTGGAAAC-AAAACAAAAAGCAAAATT
** * * *
8451 AAATACAACAATTAGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGAC-GTTGGAAACAAA-ACAAAAAGCAAAATT
8489 AAATAGGACGTTGGAAACAAAA
1 AAATAGGACGTTGGAAACAAAA
8511 AGTTAAATTG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
36 1 0.02
37 20 0.43
38 26 0.55
ACGTcount: A:0.58, C:0.10, G:0.18, T:0.14
Consensus pattern (36 bp):
AAATAGGACGTTGGAAACAAAACAAAAAGCAAAATT
Found at i:12327 original size:31 final size:31
Alignment explanation
Indices: 12292--12353 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
12282 TTATGTTTTT
12292 CAATTATACCCTTATT-TTTAAAACATATTTC
1 CAATTATACCCTT-TTCTTTAAAACATATTTC
* *
12323 CAATTGTACTCTTTTCTTTAAAACATATTTC
1 CAATTATACCCTTTTCTTTAAAACATATTTC
12354 TAAATTACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (31 bp):
CAATTATACCCTTTTCTTTAAAACATATTTC
Found at i:12937 original size:22 final size:21
Alignment explanation
Indices: 12866--13028 Score: 110
Period size: 22 Copynumber: 7.3 Consensus size: 21
12856 TTATCTCTAT
* *
12866 GTGGTTATCAAAATTTTAAAAG
1 GTGGTTATCAAAA-TTTCATAG
* * *
12888 ATGGTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTCAT-AG
*
12910 GAGGTTATCAAAATTTCATAG
1 GTGGTTATCAAAATTTCATAG
*
12931 TGTGGTTACCAAAATTTCATAG
1 -GTGGTTATCAAAATTTCATAG
* * *
12953 TATAGTTAACAAAATTTCATAG
1 -GTGGTTATCAAAATTTCATAG
* * *
12975 GATCAGGTTATTAAAATCTCTTAG
1 G-T--GGTTATCAAAATTTCATAG
**
12999 GTTGGTTATTGAAATTTCATAGG
1 G-TGGTTATCAAAATTTCATA-G
13022 GTGGTTA
1 GTGGTTA
13029 ATTATCACAA
Statistics
Matches: 111, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.05
22 87 0.78
23 2 0.02
24 16 0.14
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (21 bp):
GTGGTTATCAAAATTTCATAG
Found at i:13241 original size:20 final size:23
Alignment explanation
Indices: 13218--13315 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 23
13208 AGGAGTACCA
*
13218 AAATTTGATAGAAG-G-TTATC-
1 AAATTTCATAGAAGTGATTATCG
*
13238 AAATCTCATAG-AGTGATTATCG
1 AAATTTCATAGAAGTGATTATCG
* *
13260 AAATTTCATAGAAATCGGATTATCA
1 AAATTTCATAGAAGT--GATTATCG
** *
13285 AAATTT-ATA-AAAAGATTATCA
1 AAATTTCATAGAAGTGATTATCG
13306 AAATTTCATA
1 AAATTTCATA
13316 TTGTTGTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
19 2 0.03
20 10 0.15
21 19 0.29
22 13 0.20
23 5 0.08
24 3 0.05
25 13 0.20
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (23 bp):
AAATTTCATAGAAGTGATTATCG
Found at i:13370 original size:44 final size:44
Alignment explanation
Indices: 13277--13469 Score: 187
Period size: 44 Copynumber: 4.4 Consensus size: 44
13267 ATAGAAATCG
* * *
13277 GATTATCAAAATTT-ATAAAAAGATTATCAAAATTTCATATTGTT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATG-T
*
13321 G-TTATCAAAATTTCA-AAATGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAA-GAGGTTATCAAAATTTCATAATGT
* * * * * * * *
13364 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
* * * *
13408 GGTTATCAAAATTTCATAAAGAGGTTATTAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
13452 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
13470 GTGCTATTTC
Statistics
Matches: 118, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
43 18 0.15
44 98 0.83
45 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
Found at i:13442 original size:21 final size:22
Alignment explanation
Indices: 13199--13445 Score: 157
Period size: 22 Copynumber: 11.3 Consensus size: 22
13189 TAAAAGTCTC
* *
13199 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
13219 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
13239 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
13261 AATTTCATAGAA-ATCGGATTATCAA
1 AATTTCATA-AAGA--GG-TTATCAA
* *
13286 AATTT-ATAAAAAGATTATCAA
1 AATTTCATAAAGAGGTTATCAA
** **
13307 AATTTCATATTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
13329 AATTTCA-AAATGAGGTTATCAA
1 AATTTCATAAA-GAGGTTATCAA
* * * * *
13351 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
13373 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
13395 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
13417 AATTTCATAAAGAGGTTATTAA
1 AATTTCATAAAGAGGTTATCAA
*
13439 ATTTTCA
1 AATTTCA
13446 AAATGTGATT
Statistics
Matches: 170, Mismatches: 45, Indels: 22
0.72 0.19 0.09
Matches are distributed among these distances:
19 1 0.01
20 19 0.11
21 22 0.13
22 107 0.63
23 5 0.03
24 5 0.03
25 11 0.06
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:13683 original size:43 final size:43
Alignment explanation
Indices: 13589--13686 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
13579 TGAGGGAGGA
**
13589 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGAGAGAT
1 TATCAAAATTTCATATG-AGGTTATCAAAAAATCATAGAGAGAT
* * * *
13633 TAACAAAATTTCATAATG-GGTTATCAAAAAATCATAGGGTGGT
1 TATCAAAATTTCAT-ATGAGGTTATCAAAAAATCATAGAGAGAT
13676 TATCAAAATTT
1 TATCAAAATTT
13687 GTAGTTATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 30 0.65
44 13 0.28
45 3 0.07
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (43 bp):
TATCAAAATTTCATATGAGGTTATCAAAAAATCATAGAGAGAT
Found at i:13742 original size:45 final size:43
Alignment explanation
Indices: 13691--13814 Score: 133
Period size: 45 Copynumber: 2.8 Consensus size: 43
13681 AAATTTGTAG
* *
13691 TTATCAAGATTTCATAAGAAAATTATCAAAATTTTATAGGGAGGT
1 TTATCAA-ATTTCATAAGAAAATTATCAAAATTTTATAGCGA-GA
* * *
13736 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTTATAGCGAGA
1 TTATC-AAATTTCATAAGAA-AATTATCAAAATTTTATAGCGAGA
*
13781 TTATCACAATTTCAT-AGTGAAATTATCAAAATTT
1 TTATCA-AATTTCATAAG-AAAATTATCAAAATTT
13815 CAGAGTGTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
44 15 0.23
45 29 0.44
46 22 0.33
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (43 bp):
TTATCAAATTTCATAAGAAAATTATCAAAATTTTATAGCGAGA
Found at i:13827 original size:44 final size:45
Alignment explanation
Indices: 13691--13828 Score: 120
Period size: 45 Copynumber: 3.1 Consensus size: 45
13681 AAATTTGTAG
* * * * * * *
13691 TTATCAAGATTTCATAAGAA-AATTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGATTTATCAAAATTTCAGAGCGA-GA
* * *
13736 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTTATAGCGAGA
1 TTATCAAAATTTCATAGGAAGATTTATCAAAATTTCAGAGCGAGA
* * *
13781 TTATCACAATTTCATAGTGAA-A-TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAAGATTTATCAAAATTTCAGAGCGAGA
13825 TTAT
1 TTAT
13829 TAGCAATTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
44 22 0.28
45 34 0.43
46 23 0.29
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTTATCAAAATTTCAGAGCGAGA
Found at i:13951 original size:45 final size:44
Alignment explanation
Indices: 13589--13995 Score: 190
Period size: 44 Copynumber: 9.3 Consensus size: 44
13579 TGAGGGAGGA
** *
13589 TATCAAAATTTCATATG-AAGGTTATCAAAATTTCATAGAG-AGAT
1 TATCAAAATTTCATA-GCGTGGTTATCAAAATTTCATAGGGAAG-T
* ** ** **
13633 TAACAAAATTTCATAATG-GGTTATCAAAAAATCATAGGGTGGT
1 TATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGAAGT
* * * * *
13676 TATCAAAA-TT--T---GTAGTTATCAAGATTTCATAAGAAAAT
1 TATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGAAGT
* * * *
13714 TATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATA-GGAAGATT
1 TATCAAAATTTCATAGCGTGG-TTATCAAAATTTCATAGGGAAG--T
* * * * * *
13760 TATCAAAATTTTATAGCGAGATTATCACAATTTCATAGTGAAAT
1 TATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGAAGT
* * * * * * *
13804 TATCAAAATTTCAGAGTGTGATTATTAGCAA-TTCATATGGAGGT
1 TATCAAAATTTCATAGCGTGGTTATCA-AAATTTCATAGGGAAGT
* * * * * * *
13848 TTTTAAATTTTCATAACGTGGTTATCAATATATCATAGGGAGGT
1 TATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGAAGT
* * * * *
13892 TAGCAATATCTCATAGTGTTGGTTATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAGCG-TGGTTATCAAAATTTCATAGGGAAGT
** * * * *
13937 TATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGGT
1 TATCAAAATTTCATAGCGTGGT-TATCAAAATTTCATAGGGAAGT
* *
13981 TAACCAAATTTCATA
1 TATCAAAATTTCATA
13996 AGAAGGTTAA
Statistics
Matches: 273, Mismatches: 73, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
37 1 0.00
38 24 0.09
39 2 0.01
40 1 0.00
41 1 0.00
42 2 0.01
43 27 0.10
44 124 0.45
45 68 0.25
46 23 0.08
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGAAGT
Found at i:14083 original size:22 final size:22
Alignment explanation
Indices: 13589--14083 Score: 155
Period size: 22 Copynumber: 22.7 Consensus size: 22
13579 TGAGGGAGGA
*
13589 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAAGAAGGT
*
13611 TATCAAAATTTCAT-AGAGAGAT
1 TATCAAAATTTCATAAGA-AGGT
*
13633 TAACAAAATTTCATAATG--GGT
1 TATCAAAATTTCATAA-GAAGGT
** * **
13654 TATCAAAAAATCATAGGGTGGT
1 TATCAAAATTTCATAAGAAGGT
*
13676 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAAGAAGGT
* **
13692 TATCAAGATTTCATAAGAAAAT
1 TATCAAAATTTCATAAGAAGGT
* * *
13714 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAAGAAGG-T
* * *
13737 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAAGAAG-GT
* * *
13760 TATCAAAATTTTAT-AGCGAGAT
1 TATCAAAATTTCATAAG-AAGGT
* * *
13782 TATCACAATTTCATAGTGAA-AT
1 TATCAAAATTTCATA-AGAAGGT
* *
13804 TATCAAAATTTCA-GAG-TGTGAT
1 TATCAAAATTTCATAAGAAG-G-T
* * * *
13826 TATTAGCAA-TTCATATGGAGGT
1 TATCA-AAATTTCATAAGAAGGT
* * * *
13848 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCATAA-GAAGGT
* * * *
13870 TATCAATATATCATAGGGAGGT
1 TATCAAAATTTCATAAGAAGGT
* * * * **
13892 TAGCAATATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-AGAAGGT
**
13915 TATCAAAATTTCATTGGGAA-GT
1 TATCAAAATTTCA-TAAGAAGGT
*
13937 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-AGAAGGT
* * * *
13959 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAAGAAGGT
* *
13981 TAACCAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGAAGGT
** * *
14003 TAAAAAAAATT-ATAAAAAGGT
1 TATCAAAATTTCATAAGAAGGT
* * * * **
14024 TCTCGAAATTCCATAATATCGT
1 TATCAAAATTTCATAAGAAGGT
*
14046 TATTAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGAAGGT
14068 TATCAAAATTTCATAA
1 TATCAAAATTTCATAA
14084 TGGGATCATA
Statistics
Matches: 345, Mismatches: 95, Indels: 66
0.68 0.19 0.13
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
19 2 0.01
20 2 0.01
21 39 0.11
22 226 0.66
23 60 0.17
24 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAAGGT
Done.