Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008253.1 Corchorus capsularis cultivar CVL-1 contig08274, 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: 54230
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3806 original size:30 final size:30
Alignment explanation
Indices: 3772--3828 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3762 CATCTTCAAG
*
3772 TCCATGATAAGTCCTT-GGCGCTTCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
3802 TCCATGATAAGCCTTGGGCGCATCATT
1 TCCATGATAAGCCTTGGGCGCATCATT
3829 TGGGCTGCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:6153 original size:15 final size:15
Alignment explanation
Indices: 6128--6166 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6118 TGCTTTTATC
**
6128 AATTGATTTTCTCTTT
1 AATT-ATTTTCTAGTT
6144 AATTATTTTCTAGTT
1 AATTATTTTCTAGTT
6159 AATTATTT
1 AATTATTT
6167 ATTTGTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (15 bp):
AATTATTTTCTAGTT
Found at i:6550 original size:196 final size:195
Alignment explanation
Indices: 6217--6568 Score: 652
Period size: 196 Copynumber: 1.8 Consensus size: 195
6207 TTTCTAGGTT
*
6217 AGAATTTCTTTTGTAAGATTTAACTTTGATTCGTACCTTCCCTGTGGATTCGACCCCTACTTGCC
1 AGAATTTCTTTTGTAAGATTTAACTTTGATTCGTACCTTCCCTATGGATTCGACCCCTACTTGCC
6282 CTAGCTATATAGTTAATCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAACG
66 CTAGCTATATAGTTAATCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAACG
*
6347 ACCGATCACAATTTTGGCGCCGTTGCCGGGGAAGGTTTACGTAATTGAAGGCAAATTATTACTTG
131 ACCGATCACAATTTTGGCACCGTTGCCGGGGAAGGTTTACGTAATTGAAGGCAAATTATTACTTG
6412 AGAATTTCTTTTGTAAGATTTAACTTTGATTCGTACCTTCCCTATGGATTCGACCCCCTACTTGC
1 AGAATTTCTTTTGTAAGATTTAACTTTGATTCGTACCTTCCCTATGGATTCGA-CCCCTACTTGC
*
6477 CCTAGCTA-AGTAGTTAATCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATGAA
65 CCTAGCTATA-TAGTTAATCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAA
6541 CGACCGATCACAATTTTGGCACCGTTGC
129 CGACCGATCACAATTTTGGCACCGTTGC
6569 ATGCCAAATA
Statistics
Matches: 152, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
195 53 0.35
196 99 0.65
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (195 bp):
AGAATTTCTTTTGTAAGATTTAACTTTGATTCGTACCTTCCCTATGGATTCGACCCCTACTTGCC
CTAGCTATATAGTTAATCTATTTGTTATTGGTTTGTGGGGAATTTATCTTGTGATTTGATCAACG
ACCGATCACAATTTTGGCACCGTTGCCGGGGAAGGTTTACGTAATTGAAGGCAAATTATTACTTG
Found at i:18644 original size:15 final size:15
Alignment explanation
Indices: 18619--18657 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
18609 TGCTTTTATC
**
18619 AATTGATTTTCTCTTT
1 AATT-ATTTTCTAGTT
18635 AATTATTTTCTAGTT
1 AATTATTTTCTAGTT
18650 AATTATTT
1 AATTATTT
18658 ATTTCTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (15 bp):
AATTATTTTCTAGTT
Found at i:29702 original size:27 final size:26
Alignment explanation
Indices: 29672--29747 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
29662 AAGTGGACTT
29672 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCT-AATGCA
* * *
29699 AAAATGACCAGAATGCCCCTAGTGTA
1 AAAATGACCAAAATGCCCCTAATGCA
*
29725 AGAATGACCAAAATGCCCC-AATG
1 AAAATGACCAAAATGCCCCTAATG
29748 TGACCTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 3 0.07
26 21 0.49
27 19 0.44
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTAATGCA
Found at i:34542 original size:2 final size:2
Alignment explanation
Indices: 34535--34561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34525 CTAGAGTGTC
34535 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 T
34562 TGATTTTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34975 original size:22 final size:22
Alignment explanation
Indices: 34933--34976 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34923 TATTCATATG
*
34933 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
34955 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
34977 TTTATGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:35181 original size:45 final size:45
Alignment explanation
Indices: 35123--35208 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
35113 AAGATCTCAA
* *
35123 TATGAAATTTTGATAA-CTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAAGC-T-CCATATGAAATATTGATAACCAACAC
* *
35168 TATGAGATGTTGATAAGCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAAGCTCCATATGAAATATTGATAACCA
35209 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 3 0.09
45 31 0.89
46 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAAGCTCCATATGAAATATTGATAACCAACAC
Found at i:35272 original size:22 final size:22
Alignment explanation
Indices: 35247--35508 Score: 107
Period size: 22 Copynumber: 12.1 Consensus size: 22
35237 GAATTGTTAG
*
35247 TAATCATACTCTGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* *
35269 TAATCACACTATGAAATTGTGA
1 TAATCATACTATGAAATTTTGA
* *
35291 TAA-CCTCGCTATGAAATTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
35313 TAAATCTTCCTATAAAATTTTGA
1 T-AATCATACTATGAAATTTTGA
* * *
35336 TAA-CTTTCTTATGAAATCTTGA
1 TAATCATAC-TATGAAATTTTGA
35358 TAA-C-TAC----AAATTTTGA
1 TAATCATACTATGAAATTTTGA
* * **
35374 TAA-CCTCCCTATGATTTTTTGA
1 TAATCAT-ACTATGAAATTTTGA
* * *
35396 TAACCTTATTATGAAATTTT-A
1 TAATCATACTATGAAATTTTGA
*
35417 TTAATC-TCCCTATGAAATTTTGA
1 -TAATCAT-ACTATGAAATTTTGA
* ** *
35440 TAACCCCATTATGAAATTTTGA
1 TAATCATACTATGAAATTTTGA
* * *
35462 -AAACTAAACTATGAGATTTTGA
1 TAATC-ATACTATGAAATTTTGA
* * *
35484 TAACCTTTCATATGAAATTTTGA
1 TAATCATAC-TATGAAATTTTGA
35507 TA
1 TA
35509 TCCTCCCTAA
Statistics
Matches: 182, Mismatches: 40, Indels: 35
0.71 0.16 0.14
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
18 1 0.01
21 12 0.07
22 118 0.65
23 36 0.20
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCATACTATGAAATTTTGA
Found at i:35428 original size:44 final size:44
Alignment explanation
Indices: 35258--35527 Score: 179
Period size: 44 Copynumber: 6.3 Consensus size: 44
35248 AATCATACTC
* * * * *
35258 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCCCATTATGAAATTTTGATAACCTCCCTA
* * * * *
35302 TGAAATTTTGATAAATCTTCC--TATAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGAT-AA-C-CCCATTATGAAATTTTGATAACCTCCCTA
* *
35347 TGAAATCTTGATAA---C--TA-CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCCCATTATGAAATTTTGATAACCTCCCTA
** ** *
35385 TGATTTTTTGATAACCTTATTATGAAATTTT-ATTAATCTCCCTA
1 TGAAATTTTGATAACCCCATTATGAAATTTTGA-TAACCTCCCTA
* **
35429 TGAAATTTTGATAACCCCATTATGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCCCATTATGAAATTTTGATAACCT-CCCTA
* * *
35473 TGAGATTTTGATAACCTTTCA-TATGAAATTTTGATATCCTCCCTA
1 TGAAATTTTGATAACC--CCATTATGAAATTTTGATAACCTCCCTA
35518 --AAATTTTGAT
1 TGAAATTTTGAT
35528 TACTCTATAA
Statistics
Matches: 177, Mismatches: 34, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
38 28 0.16
39 3 0.02
43 16 0.09
44 76 0.43
45 48 0.27
46 5 0.03
47 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (44 bp):
TGAAATTTTGATAACCCCATTATGAAATTTTGATAACCTCCCTA
Found at i:35749 original size:22 final size:22
Alignment explanation
Indices: 35609--35862 Score: 115
Period size: 22 Copynumber: 11.4 Consensus size: 22
35599 GAAATACCAC
* * * *
35609 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCTCCT
* * *
35631 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCT
* *
35653 TGTGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCCT
* * *
35675 TATAAAATTTTGTTGACC-CCT
1 TATGAAATTTTGATAACCTCCT
* * * *
35696 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAACCTCCT
*
35719 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-CT
** *
35742 T-TGAAATTTTGATTGATAACAACAT
1 TATGAAA--TT--TTGATAACCTCCT
* *
35767 TATGAAATTTTGATAATCTGATCT
1 TATGAAATTTTGATAACCT--CCT
* * * *
35791 CTATGAAATTTCGATAATCACTT
1 -TATGAAATTTTGATAACCTCCT
* *
35814 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTCCT
* *
35834 TATCAAATTTTGGT-A-CTCCT
1 TATGAAATTTTGATAACCTCCT
35854 TATGAAATT
1 TATGAAATT
35863 GAGACTTTTA
Statistics
Matches: 171, Mismatches: 48, Indels: 28
0.69 0.19 0.11
Matches are distributed among these distances:
19 3 0.02
20 14 0.08
21 15 0.09
22 96 0.56
23 5 0.03
24 5 0.03
25 19 0.11
26 14 0.08
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:35920 original size:22 final size:22
Alignment explanation
Indices: 35886--35987 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
35876 ACTTCATATG
35886 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
* * * *
35908 AAATTTTGATAACCTCCCCATG
1 AAATTTTGATAACCACACTATA
* * *
35930 AAATATT-AGTAACCTC-CTAATG
1 AAATTTTGA-TAACCACACT-ATA
* *
35952 AAATTTTGTTAACAACACTATA
1 AAATTTTGATAACCACACTATA
35974 AAATTCTT-ATAACC
1 AAATT-TTGATAACC
35988 TTGCTATGAC
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.03
22 56 0.90
23 4 0.06
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:36104 original size:24 final size:22
Alignment explanation
Indices: 36050--36107 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
36040 AATTAACCAC
36050 CCTATGAAATTTCAATAATCAA
1 CCTATGAAATTTCAATAATCAA
*
36072 CCTAAGAAATTTCAATAA-CATA
1 CCTATGAAATTTCAATAATCA-A
36094 GTCCTATGAAATTT
1 --CCTATGAAATTT
36108 TGATAACCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.06
22 18 0.58
24 11 0.35
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (22 bp):
CCTATGAAATTTCAATAATCAA
Found at i:36128 original size:22 final size:22
Alignment explanation
Indices: 36097--36252 Score: 122
Period size: 22 Copynumber: 7.0 Consensus size: 22
36087 TAACATAGTC
36097 CTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* *
36119 CTGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
36141 CTATATGAAATTTTGATAACTTC-CA
1 C--TATGAAATTTTGATAAC--CACA
* * *
36166 -TACGAAATTTTGGTAAGCACA
1 CTATGAAATTTTGATAACCACA
* *
36187 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
36208 CTCATGAAATTATAATAATCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
36231 TTATGGAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
36253 TAGAGACAAG
Statistics
Matches: 103, Mismatches: 22, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 77 0.75
23 2 0.02
24 15 0.15
25 2 0.02
26 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:36217 original size:44 final size:43
Alignment explanation
Indices: 36097--36218 Score: 145
Period size: 46 Copynumber: 2.7 Consensus size: 43
36087 TAACATAGTC
* *
36097 CTATGAAATTTTGATAACCACACTGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTC-CTATGAAATTTTGGTAACCACA
* * *
36141 CTATATGAAATTTTGATAACTTCCATACGAAATTTTGGTAAGCACA
1 C--TATGAAATTTTGATAACCTCC-TATGAAATTTTGGTAACCACA
*
36187 CTATGGAATTTTGATAACCTCCTCATGAAATT
1 CTATGAAATTTTGATAACCTCCT-ATGAAATT
36219 ATAATAATCA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.02
44 27 0.41
45 1 0.02
46 37 0.56
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCCTATGAAATTTTGGTAACCACA
Found at i:37442 original size:30 final size:31
Alignment explanation
Indices: 37401--37464 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
37391 GACAATTTAT
* *
37401 AAATATGTTTTAAAAA-AAGGGTACAATTGG
1 AAATATATTTTAAAAATAAGGGTACAATCGG
37431 AAATATATTTTAAAAATAAGGGTACAATCGG
1 AAATATATTTTAAAAATAAGGGTACAATCGG
37462 AAA
1 AAA
37465 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (31 bp):
AAATATATTTTAAAAATAAGGGTACAATCGG
Found at i:39435 original size:16 final size:16
Alignment explanation
Indices: 39414--39454 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39404 TCGGGTTGGA
** *
39414 TTTGGGTTAAGTTAGT
1 TTTGGGTTAAGGAAAT
39430 TTTGGGTTAAGGAAAT
1 TTTGGGTTAAGGAAAT
39446 TTTGGGTTA
1 TTTGGGTTA
39455 TAAGGGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (16 bp):
TTTGGGTTAAGGAAAT
Found at i:40009 original size:41 final size:41
Alignment explanation
Indices: 39932--40015 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
39922 AGGACTAGTA
* *
39932 ATAATAGTAATATAATATGAGAATATGTATAATATATATAT
1 ATAATAATAATATAATATGAGAATATGTATAATATATACAT
*
39973 ATAATAATAATAATAATATGAGAATTAT-TAT-CTATATACAT
1 ATAATAATAAT-ATAATATGAGAA-TATGTATAATATATACAT
40014 AT
1 AT
40016 TTTTATACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 20 0.53
42 15 0.39
43 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (41 bp):
ATAATAATAATATAATATGAGAATATGTATAATATATACAT
Found at i:46798 original size:11 final size:10
Alignment explanation
Indices: 46780--46813 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
46770 GAAGTTCGTG
46780 TTTTGAAGAT
1 TTTTGAAGAT
46790 TTCTTGAAGAT
1 TT-TTGAAGAT
46801 ATTTTGAAGAT
1 -TTTTGAAGAT
46812 TT
1 TT
46814 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:47965 original size:3 final size:3
Alignment explanation
Indices: 47957--48020 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
47947 TCCCACTCTT
* *
47957 TTA TTA TTA TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
48004 TTA TTG TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
48021 CCCTTTTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:48056 original size:28 final size:28
Alignment explanation
Indices: 48024--48077 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
48014 TATTATTCCC
* *
48024 TTTTTGCTTCACTTCATTTCTTATCCTT
1 TTTTTACTTCACTTCATTTCTCATCCTT
* *
48052 TTTTTACTTCATTTCGTTTCTCATCC
1 TTTTTACTTCACTTCATTTCTCATCC
48078 ATTTCCTCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.11, C:0.26, G:0.04, T:0.59
Consensus pattern (28 bp):
TTTTTACTTCACTTCATTTCTCATCCTT
Found at i:50707 original size:35 final size:34
Alignment explanation
Indices: 50668--51442 Score: 785
Period size: 35 Copynumber: 22.7 Consensus size: 34
50658 CAGTAATAAG
*
50668 TAACTTAATTCAGGGCAATTAAGTAAGTCAGTGAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AA
50703 TAACTTAATTCAGGGTAATTAAGTAAGTCAG---
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
50734 CAACTTAATTCAGGGTAATTAAGTAAGT-AATAGG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTA-A
*
50768 TAACTTAACTCAGGGTAATTAAGT---T-AGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
50798 GTAGCTTAATTCAGGGTAATTAAGTAGAGTCAGTTAG
1 -TAACTTAATTCAGGGTAATTAAGTA-AGTCAG-TAA
* * * *
50835 TAACTTAGTTCAGGGAAATTAAGCAAGGCAG---
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
50866 TAACTTAATTCAGGGTAATTAAGTAATTTAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
50900 TCAACTTAATTCAGGGTGATTAAGCAAGTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
50935 TCAACTTAGTTCAGGGTAATTAACTGAGTCAGTAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
50970 TCAACCTTAATTCAAGGTAATTAAGT-AGTTCAATGAG
1 T-AA-CTTAATTCAGGGTAATTAAGTAAG-TCAGT-AA
* *
51007 TAACTTAATTCAGGGTAATAAAGTAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAA
* *
51042 TAACTTAATTCAGGGTAATTAAGTGAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAA
* * *
51077 TAACTTAATTCAGGGTAATTAATTGAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAA
* *
51112 CAACTTAATTCAGGGTAATTAAGTCAGTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * * *
51146 TTAACTTAATTCAGGGTGATTAAGTAATTCAATTA
1 -TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
51181 TTACTTTAATTCAGGGTAATTAAGTAATTTAGTAA
1 TAAC-TTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
51216 TCAACTTAATTTAGGGTAATTAAGTCAGT-A--AA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
51248 TAGCTTAATTCAGGGTAATTAAGTAAGTCAATAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
51282 GTAACTTAATTCAGGGTAATTAAGTCAGT-A--AA
1 -TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * * *
51314 TAGCTTAATTCAAGGTAATTAAGCAAGTCAGTTAG
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAA
*
51349 TAACTTAATTCAGGGTAATTAAGTAAGTCAATAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
51383 GTAACTTAATTCAGGGTAATTAAGTAAGTCATTGA
1 -TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
51418 TCGACTTAATTCAGGGTAATTAAGT
1 T-AACTTAATTCAGGGTAATTAAGT
51443 TTAGTAAGTA
Statistics
Matches: 629, Mismatches: 78, Indels: 66
0.81 0.10 0.09
Matches are distributed among these distances:
30 1 0.00
31 126 0.20
32 7 0.01
34 35 0.06
35 404 0.64
36 52 0.08
37 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (34 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
Found at i:51175 original size:18 final size:18
Alignment explanation
Indices: 51117--51240 Score: 71
Period size: 16 Copynumber: 7.1 Consensus size: 18
51107 GTTAGCAACT
51117 TAATTCAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
* * *
51135 TCAGTCA--GTAATTAACT
1 TAATTCAGGGTAATTAA-G
*
51152 TAATTCAGGGTGATTAAG
1 TAATTCAGGGTAATTAAG
* * **
51170 TAATTCA--ATTATTACTT
1 TAATTCAGGGTAATTA-AG
51187 TAATTCAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
* * *
51205 TAATTTA--GTAATCAACT
1 TAATTCAGGGTAATTAA-G
*
51222 TAATTTAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
51240 T
1 T
51241 CAGTAAATAG
Statistics
Matches: 77, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
16 20 0.26
17 19 0.25
18 19 0.25
19 19 0.25
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (18 bp):
TAATTCAGGGTAATTAAG
Done.