Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016091.1 Corchorus capsularis cultivar CVL-1 contig16112, 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: 28275
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:2380 original size:11 final size:11
Alignment explanation
Indices: 2366--2403 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2356 ATTCATAACA
2366 AATTTATAATT
1 AATTTATAATT
2377 AATTTATAATT
1 AATTTATAATT
2388 -ATTTGATAATT
1 AATTT-ATAATT
*
2399 TATTT
1 AATTT
2404 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:4150 original size:228 final size:227
Alignment explanation
Indices: 3866--4317 Score: 870
Period size: 228 Copynumber: 2.0 Consensus size: 227
3856 TATAAAAAAA
3866 TTTTGGAACCCTAAATAAGAAAATTGGTAGCCTTCACTATTGATGAAAGTTTACTAAATCTTTTT
1 TTTTGGAACCCTAAATAAGAAAATTGGTAGCCTTCACTATTGATGAAAGTTTACTAAATCTTTTT
3931 TAATAACTCTAAATAAGAAATATGATAACCAAAATTACAAAAAATGTAAGGTTATCGAATTAGTT
66 TAATAACTCTAAATAAGAAATATGATAACCAAAATTACAAAAAATGTAAGGTTATCGAATTAGTT
3996 GATAGTACTATACATCTTTTATGCTCATTATAGGTTTTTCAGTAACTTTT-AGGAAGAAAAAATG
131 GATAGTACTATACATCTTTTATGCTCATTATAGGTTTTTCAGTAACTTTTGA-GAAGAAAAAATG
4060 GTAAATATATAAGAATGTAAGGATTGGTAATTT
195 GTAAATATATAAGAATGTAAGGATTGGTAATTT
4093 TTTTGGAACCCTAAATAAGAAAAATTGGTAGCCTTCACTATTGATGAAAGTTTACTAAATCTTTT
1 TTTTGGAACCCTAAATAAG-AAAATTGGTAGCCTTCACTATTGATGAAAGTTTACTAAATCTTTT
4158 TTAATAACTCTAAATAAGAAATATGATAACCAAAATTACAAAAAATGTAAGGTTATCGAATTAGT
65 TTAATAACTCTAAATAAGAAATATGATAACCAAAATTACAAAAAATGTAAGGTTATCGAATTAGT
*
4223 TGATAGTACTATACCTCTTTTATGCTCATTATAGGTTTTTCAGTAACTTTTGAGAAGAAAAAATG
130 TGATAGTACTATACATCTTTTATGCTCATTATAGGTTTTTCAGTAACTTTTGAGAAGAAAAAATG
4288 GTAAATATATAAGAATGTAAGGATTGGTAA
195 GTAAATATATAAGAATGTAAGGATTGGTAA
4318 ATATATACAA
Statistics
Matches: 222, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
227 19 0.09
228 202 0.91
229 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (227 bp):
TTTTGGAACCCTAAATAAGAAAATTGGTAGCCTTCACTATTGATGAAAGTTTACTAAATCTTTTT
TAATAACTCTAAATAAGAAATATGATAACCAAAATTACAAAAAATGTAAGGTTATCGAATTAGTT
GATAGTACTATACATCTTTTATGCTCATTATAGGTTTTTCAGTAACTTTTGAGAAGAAAAAATGG
TAAATATATAAGAATGTAAGGATTGGTAATTT
Found at i:5068 original size:24 final size:25
Alignment explanation
Indices: 5026--5099 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 25
5016 TATAATTAAG
*
5026 TAATAGATAACTATAAAAAAATAAAAA
1 TAATAGATAA--ATAAAAAGATAAAAA
*
5053 TAATAGATAAATAAAAAGATAAATA
1 TAATAGATAAATAAAAAGATAAAAA
* *
5078 -AATATATAAACAAAAAGATAAA
1 TAATAGATAAATAAAAAGATAAA
5100 TAAGTATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 20 0.47
25 13 0.30
27 10 0.23
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (25 bp):
TAATAGATAAATAAAAAGATAAAAA
Found at i:5074 original size:12 final size:12
Alignment explanation
Indices: 5038--5102 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 12
5028 ATAGATAACT
*
5038 ATAAAAAAATAA
1 ATAAAAAGATAA
5050 A-AATAATAGATAA
1 ATAA-AA-AGATAA
5063 ATAAAAAGATAA
1 ATAAAAAGATAA
* *
5075 ATAAATATATAA
1 ATAAAAAGATAA
*
5087 ACAAAAAGATAA
1 ATAAAAAGATAA
5099 ATAA
1 ATAA
5103 GTATGTAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 2 0.05
12 31 0.72
13 8 0.19
14 2 0.05
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (12 bp):
ATAAAAAGATAA
Found at i:5078 original size:4 final size:4
Alignment explanation
Indices: 5038--5140 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
5028 ATAGATAACT
* * * *
5038 ATAA AAAA ATAA AAATA ATAG ATAA ATAA A-AA GATAA ATAA ATAT ATAA
1 ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA
* * * * * * *
5087 ACAA A-AA GATAA ATAA GTAT GTAA A-CA A-AA ATAT ATAT ATAA ATAA
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
5133 ATAA ATAA
1 ATAA ATAA
5141 TAGCTTAATA
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
3 8 0.11
4 61 0.80
5 7 0.09
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:5211 original size:17 final size:17
Alignment explanation
Indices: 5189--5228 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5179 AGATAGATAA
*
5189 ATAATAGTATTAAATAG
1 ATAATAGTACTAAATAG
5206 ATAATAGTACTAAATAG
1 ATAATAGTACTAAATAG
5223 ATAATA
1 ATAATA
5229 ATAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAATAGTACTAAATAG
Found at i:5231 original size:27 final size:26
Alignment explanation
Indices: 5201--5276 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 26
5191 AATAGTATTA
*
5201 AATAGATAATAGTACTAAATAGATAAT
1 AATA-ATAATAGTACTAAATAGATAAG
5228 AATAAATAATAGTTAC-AAATAGATAAG
1 AAT-AATAATAG-TACTAAATAGATAAG
*
5255 AA-AATGA-A-TACTAAATAGATAA
1 AATAATAATAGTACTAAATAGATAA
5277 AAAAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 3 0.07
23 10 0.23
24 1 0.02
25 4 0.09
27 22 0.50
28 4 0.09
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.26
Consensus pattern (26 bp):
AATAATAATAGTACTAAATAGATAAG
Found at i:5299 original size:26 final size:26
Alignment explanation
Indices: 5269--5330 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5259 TGAATACTAA
*
5269 ATAGATA-AAAAAAACTAAGTAGATAG
1 ATAGATAGAAAAAAA-TAAATAGATAG
* *
5295 ATAGATAGATAATAATAAATAGATAG
1 ATAGATAGAAAAAAATAAATAGATAG
5321 ATA-A-AGAAAA
1 ATAGATAGAAAA
5331 TGATTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
26 20 0.65
27 5 0.16
ACGTcount: A:0.63, C:0.02, G:0.15, T:0.21
Consensus pattern (26 bp):
ATAGATAGAAAAAAATAAATAGATAG
Found at i:6877 original size:54 final size:54
Alignment explanation
Indices: 6787--7217 Score: 577
Period size: 54 Copynumber: 8.1 Consensus size: 54
6777 ATCTTTCTGA
* *
6787 AATGACCGCACCGGATCAATTCGAGATCAAGTCTGACCACCGAAAACTTCTT-G
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * * * **
6840 AGACGACCACACCGTATCAATTGGAGATCAACTCTGACCACCAAAAACTTCTTTA
1 A-ATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * * * *
6895 AATGACCGCACCGG-CCTATTCGAGATCAACTCTGACCACTGAAAATTTCTT-G
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * * * * *
6947 AGACGACCACGCCAGATCAATTGGGGGTCAACTCTGACCACCG-AAACTTCTTGG
1 A-ATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* *
7001 AATGACCGCACCAGATCAATTCGAGATCAACTCTGACCACCGAAAAC-TCTTGG
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* *
7054 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGATAATTTCTTGG
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* *
7108 AATGACCGCACCGGATCAAATGGAGATCAACTCTAACCACCGAAAACTTCTTGG
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
7162 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTC-TGG
1 AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
7215 AAT
1 AAT
7218 AAGATCAACT
Statistics
Matches: 327, Mismatches: 44, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.00
53 139 0.43
54 186 0.57
55 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (54 bp):
AATGACCGCACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
Found at i:7216 original size:107 final size:108
Alignment explanation
Indices: 6787--7217 Score: 595
Period size: 107 Copynumber: 4.0 Consensus size: 108
6777 ATCTTTCTGA
*
6787 AATGACCGCACCGGATCAATTCGAGATCAAGTCTGACCACCGAAAACTTCTTGAGACGACCACAC
1 AATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTTCTTGAGACGACCACAC
* * **
6852 CGTATCAATTGGAGATCAACTCTGACCACCAAAAACTTCTTTA
66 CGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * * * *
6895 AATGACCGCACCGG-CCTATTCGAGATCAACTCTGACCACTGAAAATTTCTTGAGACGACCACGC
1 AATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTTCTTGAGACGACCACAC
* * *
6959 CAGATCAATTGGGGGTCAACTCTGACCACCG-AAACTTCTTGG
66 CGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * *
7001 AATGACCGCACCAGATCAATTCGAGATCAACTCTGACCACCGAAAAC-TCTTG-GAATGACCGCA
1 AATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTTCTTGAG-ACGACCACA
* *
7064 CCGGATCAATTGGAGATCAACTCTGACCACCGATAATTTCTTGG
65 CCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
* * * * *
7108 AATGACCGCACCGGATCAAATGGAGATCAACTCTAACCACCGAAAACTTCTTG-GAATGACCGCA
1 AATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTTCTTGAG-ACGACCACA
7172 CCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTC-TGG
65 CCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
7215 AAT
1 AAT
7218 AAGATCAACT
Statistics
Matches: 287, Mismatches: 32, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
105 1 0.00
106 62 0.22
107 156 0.54
108 68 0.24
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (108 bp):
AATGACCGCACCGGATCAATTCGAGATCAACTCTGACCACCGAAAACTTCTTGAGACGACCACAC
CGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGG
Found at i:7269 original size:35 final size:35
Alignment explanation
Indices: 7205--7426 Score: 283
Period size: 35 Copynumber: 6.4 Consensus size: 35
7195 TGACCACCGA
*
7205 AAACTTC-TGGAATAAGATCAACTCTGATCGTTGG
1 AAACTTCTTGGAATGAGATCAACTCTGATCGTTGG
* * * *
7239 GAACTTCTTAGAATGAGATCAACT-TAGATCGTCGA
1 AAACTTCTTGGAATGAGATCAACTCT-GATCGTTGG
*
7274 AAACCTTC-TAGAATGAGATCAACTCTGATCGTTGG
1 AAA-CTTCTTGGAATGAGATCAACTCTGATCGTTGG
*
7309 AAACTTCTTGGAATGAGATCAACTCTGATC-TTCGA
1 AAACTTCTTGGAATGAGATCAACTCTGATCGTT-GG
*
7344 AAACTTCTTGGAATGAGATCAACTCTAATCGTTGG
1 AAACTTCTTGGAATGAGATCAACTCTGATCGTTGG
* *
7379 AAACTTCTTGGAATGAGACCAACTCTGATC-TTCGA
1 AAACTTCTTGGAATGAGATCAACTCTGATCGTT-GG
7414 AAACTTCTTGGAA
1 AAACTTCTTGGAA
7427 GATCACACTG
Statistics
Matches: 165, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
34 15 0.09
35 143 0.87
36 7 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (35 bp):
AAACTTCTTGGAATGAGATCAACTCTGATCGTTGG
Found at i:7300 original size:70 final size:69
Alignment explanation
Indices: 7184--7426 Score: 353
Period size: 70 Copynumber: 3.5 Consensus size: 69
7174 GGATCAATTG
* ** * * *
7184 GAGATCAACTCTGACCACCGAAAACTTCTGGAATAAGATCAACTCTGATCGTTGGGAACTTCTTA
1 GAGATCAACTCTGATCTTCGAAAACTTCTGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTG
7249 GAAT
66 GAAT
* *
7253 GAGATCAACT-TAGATCGTCGAAAACCTTCTAGAATGAGATCAACTCTGATCGTTGGAAACTTCT
1 GAGATCAACTCT-GATCTTCGAAAA-CTTCTGGAATGAGATCAACTCTGATCGTTGGAAACTTCT
7317 TGGAAT
64 TGGAAT
*
7323 GAGATCAACTCTGATCTTCGAAAACTTCTTGGAATGAGATCAACTCTAATCGTTGGAAACTTCTT
1 GAGATCAACTCTGATCTTCGAAAACTTC-TGGAATGAGATCAACTCTGATCGTTGGAAACTTCTT
7388 GGAAT
65 GGAAT
*
7393 GAGACCAACTCTGATCTTCGAAAACTTCTTGGAA
1 GAGATCAACTCTGATCTTCGAAAACTTC-TGGAA
7427 GATCACACTG
Statistics
Matches: 159, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
68 1 0.01
69 23 0.14
70 134 0.84
71 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (69 bp):
GAGATCAACTCTGATCTTCGAAAACTTCTGGAATGAGATCAACTCTGATCGTTGGAAACTTCTTG
GAAT
Found at i:8373 original size:17 final size:17
Alignment explanation
Indices: 8353--8385 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8343 TTTTCTCTCT
8353 TTTTTGTTTTGTTTTGC
1 TTTTTGTTTTGTTTTGC
*
8370 TTTTTGTTTTTTTTTG
1 TTTTTGTTTTGTTTTG
8386 GACCTTTCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (17 bp):
TTTTTGTTTTGTTTTGC
Found at i:11054 original size:2 final size:2
Alignment explanation
Indices: 11047--11073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11037 AAATAACGAA
11047 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
11074 CATACTAAAT
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:14557 original size:10 final size:10
Alignment explanation
Indices: 14537--14579 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
14527 ATAGATAACT
14537 ATAAAAA-AA
1 ATAAAAATAA
14546 ATAAAAATAA
1 ATAAAAATAA
14556 ATAAAAATAA
1 ATAAAAATAA
14566 A-AGATAAATAA
1 ATA-A-AAATAA
14577 ATA
1 ATA
14580 TATAAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.27
10 14 0.47
11 7 0.23
12 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:14572 original size:17 final size:16
Alignment explanation
Indices: 14537--14577 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
14527 ATAGATAACT
14537 ATAAA-AAAAATAAAA
1 ATAAATAAAAATAAAA
14552 ATAAATAAAAATAAAA
1 ATAAATAAAAATAAAA
14568 GATAAATAAA
1 -ATAAATAAA
14578 TATATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.21
16 10 0.42
17 9 0.38
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
ATAAATAAAAATAAAA
Found at i:14596 original size:24 final size:23
Alignment explanation
Indices: 14536--14631 Score: 81
Period size: 24 Copynumber: 4.3 Consensus size: 23
14526 AATAGATAAC
* *
14536 TATAAAAAAAATAAAAATAAATA
1 TATAAAAAAAAGATAAATAAATA
*
14559 -A-AAATAAAAGATAAATAAATA
1 TATAAAAAAAAGATAAATAAATA
**
14580 TATAAACAAAAAGATAAATACTTA
1 TATAAA-AAAAAGATAAATAAATA
* * * *
14604 TGTAAACAAAA-ATATATATATA
1 TATAAAAAAAAGATAAATAAATA
14626 TATAAA
1 TATAAA
14632 TAAATAAATA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
21 17 0.29
22 15 0.26
23 7 0.12
24 19 0.33
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (23 bp):
TATAAAAAAAAGATAAATAAATA
Found at i:14713 original size:17 final size:17
Alignment explanation
Indices: 14691--14730 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
14681 AGATAGATAA
*
14691 ATAATAGTATTAAATAG
1 ATAATAGTACTAAATAG
14708 ATAATAGTACTAAATAG
1 ATAATAGTACTAAATAG
14725 ATAATA
1 ATAATA
14731 ATAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (17 bp):
ATAATAGTACTAAATAG
Found at i:14733 original size:27 final size:27
Alignment explanation
Indices: 14703--14755 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
14693 AATAGTATTA
*
14703 AATAGATAATAG-TACTAAATAGATAAT
1 AATAAATAATAGTTAC-AAATAGATAAT
14730 AATAAATAATAGTTACAAATAGATAA
1 AATAAATAATAGTTACAAATAGATAA
14756 GAAAATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (27 bp):
AATAAATAATAGTTACAAATAGATAAT
Found at i:14779 original size:44 final size:45
Alignment explanation
Indices: 14683--14779 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
14673 AAAATAAAAG
* * * *
14683 ATAGATAAATAATAGTATTAAATAGATAATAGTACTAAATAGATA
1 ATAGATAAATAATAGTATCAAATAGATAAGAGAAATAAATAGATA
*
14728 ATA-ATAAATAATAGT-TACAAATAGATAAGA-AAATGAATAG-TAA
1 ATAGATAAATAATAGTAT-CAAATAGATAAGAGAAATAAATAGAT-A
14771 ATAGATAAA
1 ATAGATAAA
14780 ACAAAAAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 12 0.27
44 28 0.64
45 3 0.07
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (45 bp):
ATAGATAAATAATAGTATCAAATAGATAAGAGAAATAAATAGATA
Found at i:16939 original size:2 final size:2
Alignment explanation
Indices: 16932--16960 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16922 CTTTAACTAG
16932 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 T
16961 TGCTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.