Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007046.1 Corchorus capsularis cultivar CVL-1 contig07067, 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: 63036
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:592 original size:18 final size:17
Alignment explanation
Indices: 551--593 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
541 ATTTGTTTGC
*
551 TTGTCTTTAGTTTTGTT
1 TTGTTTTTAGTTTTGTT
*
568 TAAGTTTTTAGTTTTTGTT
1 T-TGTTTTTAG-TTTTGTT
587 TTGTTTT
1 TTGTTTT
594 CTAGCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72
Consensus pattern (17 bp):
TTGTTTTTAGTTTTGTT
Found at i:2379 original size:12 final size:12
Alignment explanation
Indices: 2362--2392 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2352 GTTGTGGCCG
2362 GATGGCCCGTGC
1 GATGGCCCGTGC
*
2374 GATGGCTCGTGC
1 GATGGCCCGTGC
2386 GATGGCC
1 GATGGCC
2393 GGCTGTGGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.29, G:0.42, T:0.19
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:2434 original size:42 final size:42
Alignment explanation
Indices: 2345--2436 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
2335 AAAGGGTCGA
* * *
2345 ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGCTCGTGCG
1 ATGGCCGGCTGTGGCCGGATGGCCCGTGCGATGGCCCATGCG
*
2387 ATGGCCGGCTGTGGCCGGATGGCCCGTGCGATGTCCCATGC-
1 ATGGCCGGCTGTGGCCGGATGGCCCGTGCGATGGCCCATGCG
2428 ATTGGCCGG
1 A-TGGCCGG
2437 TCATGGCCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.09, C:0.28, G:0.42, T:0.21
Consensus pattern (42 bp):
ATGGCCGGCTGTGGCCGGATGGCCCGTGCGATGGCCCATGCG
Found at i:3638 original size:30 final size:30
Alignment explanation
Indices: 3602--3658 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3592 CATCTTCAAG
*
3602 TCCATGATAAGCCTTGGGCGCATCATTACT
1 TCCATGATAAGCCTTGCGCGCATCATTACT
3632 TCCATGATAAGCCTTGCGCGCATCATT
1 TCCATGATAAGCCTTGCGCGCATCATT
3659 CCCTCTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGCGCGCATCATTACT
Found at i:4185 original size:33 final size:33
Alignment explanation
Indices: 4106--4169 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
4096 ATTAGCATCC
* * *
4106 AAAATAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
*
4139 AAAACAGATTTAGTGTCATCGCAAACAACAC
1 AAAACAGATTTAGTGTCATCACAAACAACAC
4170 TCAAATTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:4197 original size:33 final size:33
Alignment explanation
Indices: 4106--4198 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 33
4096 ATTAGCATCC
* * *
4106 AAAATAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
* *
4139 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * *
4171 CAAATTAGGTTTAGTATTATCACAAACA
1 -AAAACAGATTTAGTATCATCACAAACA
4199 CTATCTAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
32 2 0.04
33 47 0.96
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:5891 original size:13 final size:14
Alignment explanation
Indices: 5873--5902 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5863 TCTTGTTGAA
5873 TTTATTTTTAT-TT
1 TTTATTTTTATATT
5886 TTTATTTTTATATT
1 TTTATTTTTATATT
5900 TTT
1 TTT
5903 CAATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTTTATATT
Found at i:6873 original size:21 final size:21
Alignment explanation
Indices: 6849--6888 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6839 ATCTAGTCAT
6849 CGGA-CCAATAGGCATCTTCAA
1 CGGATCCAAT-GGCATCTTCAA
*
6870 CGGATCGAATGGCATCTTC
1 CGGATCCAATGGCATCTTC
6889 TTGGTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.23
Consensus pattern (21 bp):
CGGATCCAATGGCATCTTCAA
Found at i:11558 original size:33 final size:33
Alignment explanation
Indices: 11518--11592 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
11508 AGCACAAGTG
* * * *
11518 ACCGGCCATGCGACTTGGAGATGCCGGGCCAAA
1 ACCGGCCACGCGACATGGACATGCCCGGCCAAA
*
11551 ACCGGCCACGCGACATGGCCATGCCCGGCCAAA
1 ACCGGCCACGCGACATGGACATGCCCGGCCAAA
11584 ACCGGCCAC
1 ACCGGCCAC
11593 ATGACTCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGGCCAAA
Found at i:11604 original size:33 final size:33
Alignment explanation
Indices: 11538--11629 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
11528 CGACTTGGAG
* **
11538 ATGCCGGGCCAAAACCGGCCACGCGACATGGCC
1 ATGCCCGGCCAAAACCGGCCACATGACATGGCC
11571 ATGCCCGGCCAAAACCGGCCACATGAC-TCGGCC
1 ATGCCCGGCCAAAACCGGCCACATGACAT-GGCC
* * *
11604 AAGCCCGGCCATAACCGACCACATGA
1 ATGCCCGGCCAAAACCGGCCACATGA
11630 TCCTTTAGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.27, C:0.40, G:0.25, T:0.08
Consensus pattern (33 bp):
ATGCCCGGCCAAAACCGGCCACATGACATGGCC
Found at i:12659 original size:10 final size:9
Alignment explanation
Indices: 12646--12680 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
12636 AGTTATATCG
12646 AAAAATATAA
1 AAAAATA-AA
12656 AAAAATAAA
1 AAAAATAAA
12665 ACAAAATAAA
1 A-AAAATAAA
12675 AAAAAT
1 AAAAAT
12681 TTCGACCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:14237 original size:33 final size:33
Alignment explanation
Indices: 14190--14273 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
14180 AATTGTGATG
*
14190 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* * *
14223 AAAATAATTTTGTTTTGGTTGATCATAGCATTG
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* *
14256 CAAATAAATCTGTTTTGG
1 AAAATAATTCTGTTTTGG
14274 GTGACGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
AAAATAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:16080 original size:33 final size:33
Alignment explanation
Indices: 16038--16126 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
16028 CGACTTGGAG
* *
16038 ATGCTCGGCCAACACCGGCCACGCGACAT-GGCC
1 ATGCCCGGCCAACACCGGCCACACGAC-TCGGCC
* *
16071 ATGCCCGGCC-ACAATCGGCCACATGACTCGGCC
1 ATGCCCGGCCAAC-ACCGGCCACACGACTCGGCC
*
16104 ATGCCCGG-CAATAACCGGCCACA
1 ATGCCCGGCCAA-CACCGGCCACA
16127 TGATCCTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 4 0.09
33 42 0.91
ACGTcount: A:0.24, C:0.42, G:0.25, T:0.10
Consensus pattern (33 bp):
ATGCCCGGCCAACACCGGCCACACGACTCGGCC
Found at i:16127 original size:33 final size:33
Alignment explanation
Indices: 16067--16129 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
16057 CACGCGACAT
* *
16067 GGCCATGCCCGGCCACAATCGGCCACATGACTC
1 GGCCATGCCCGGCAACAACCGGCCACATGACTC
*
16100 GGCCATGCCCGGCAATAACCGGCCACATGA
1 GGCCATGCCCGGCAACAACCGGCCACATGA
16130 TCCTTTAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.24, C:0.40, G:0.25, T:0.11
Consensus pattern (33 bp):
GGCCATGCCCGGCAACAACCGGCCACATGACTC
Found at i:20724 original size:30 final size:30
Alignment explanation
Indices: 20688--20750 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
20678 TGTTCAAGGG
20688 GGAGGGAATGATGCGCCCAAAG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAAGACTTATCAT
*
20718 GGAGGGAATGATGCGCCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCAAAGACTTATCAT
20748 GGA
1 GGA
20751 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAAGACTTATCAT
Found at i:24923 original size:443 final size:441
Alignment explanation
Indices: 24099--24979 Score: 1397
Period size: 443 Copynumber: 2.0 Consensus size: 441
24089 GGCAAAATAT
* * *
24099 TAAATGCGTATATCGAAAAATACGCGAATCTTAAGAAAACCAAGGAAAGGCACCATCGAAATTTA
1 TAAATGCATATATCGAAAAATACGCGAATCATAAGAAAACCAAGGAAAAGCACCATCGAAATTTA
* * * *
24164 AGTGTCATAAAAACAAGTAAAGTCTTGTTTGCACATTTTTATTTTGACAGCAGAAAATAAATGCA
66 AGTATCATAAAAACAAGTAAAGTCTTGTTTGCACATTTTAATTTTGAAAGCAGAAAATAAATACA
* * **
24229 CTAGTTAAAATGCTGAATGCGAAAGGCCAGAATCGCTCCCCAATTTTCCCACGTGACTGATCTAC
131 CTAGTTAAAATGCTGAATGCGAAAAGCCAGAATCACTCCCCAATTTTCCCACAAGACTGATCTAC
24294 ATCATCACCTGAAAACAGGTGAAATAATCTAATAAGTACAACAACTCAGCAAGTGACAGACATCC
196 ATCATCACCTGAAAACAGGTGAAATAATCTAATAAGTACAACAACTCAGCAAGTGACAGACATCC
**
24359 CCATAGTTCGATCGAGTACGTTAAAACATAGGCCAAATCATATCATATAGTTGATCGAATATAAT
261 CCATAGTTCGATCGAAAACGTTAAAACATAGGCCAAATCATATCATATAGTTGATCGAATATAAT
24424 AAGACATTTCAAAAATATAGTTTCATATCATATATCCACAAAACATTTACAAAGCAATACAAACT
326 AAGACATTTCAAAAATATAGTTTCATATCATATATCCACAAAACATTTACAAAGCAATACAAACT
*
24489 TGTCTCCCATAACAGATTAGGGCCACATTTAACCCCTATGACATAGGTCGA
391 TGTCTCCCATAACAGACTAGGGCCACATTTAACCCCTATGACATAGGTCGA
* *
24540 TAAATGCATATATCGAAAAATATGCGAATCATAAGAAAACCTAGGAAAAGCACCATCGAAATTTA
1 TAAATGCATATATCGAAAAATACGCGAATCATAAGAAAACCAAGGAAAAGCACCATCGAAATTTA
* *
24605 AGTATCATAAAAACAAGTAAAGTCTTGTTTTGCACAATCTTTAATTTT-AAAGTAGGAAATAAAT
66 AGTATCATAAAAACAAGTAAAGTCTTG-TTTGCAC-AT-TTTAATTTTGAAAGCAGAAAATAAAT
* ** * *
24669 ACGCTAGTTAAAATTTTGAATGCGAAAAGCCGGAATCACTCCCCTATTTTCCCACAAGA-TAGAT
128 ACACTAGTTAAAATGCTGAATGCGAAAAGCCAGAATCACTCCCCAATTTTCCCACAAGACT-GAT
* * * *
24733 TTACATCATCACCTGAAAACATGTGAAATAATCTAATAAGTGCAACGACTCAGCAAGTGACAGAC
192 CTACATCATCACCTGAAAACAGGTGAAATAATCTAATAAGTACAACAACTCAGCAAGTGACAGAC
** * *
24798 ATCCCTTTAGTTGGATCGAAAACGTTAAAACATAGGCCACATCATATCATATAGTTGATCGAATA
257 ATCCCCATAGTTCGATCGAAAACGTTAAAACATAGGCCAAATCATATCATATAGTTGATCGAATA
* * *
24863 TAATAAGACATTTCAAAAGTATAGTTTCATATCATATATCGACAAAACATTTGCAAAGCAATACA
322 TAATAAGACATTTCAAAAATATAGTTTCATATCATATATCCACAAAACATTTACAAAGCAATACA
*
24928 AACTTGTCTCCCATAACAGACTAGGGCCACATTTAACCCCTGTGACATAGGT
387 AACTTGTCTCCCATAACAGACTAGGGCCACATTTAACCCCTATGACATAGGT
24980 TAGAAGTTCA
Statistics
Matches: 401, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
441 86 0.21
442 8 0.02
443 299 0.75
444 8 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (441 bp):
TAAATGCATATATCGAAAAATACGCGAATCATAAGAAAACCAAGGAAAAGCACCATCGAAATTTA
AGTATCATAAAAACAAGTAAAGTCTTGTTTGCACATTTTAATTTTGAAAGCAGAAAATAAATACA
CTAGTTAAAATGCTGAATGCGAAAAGCCAGAATCACTCCCCAATTTTCCCACAAGACTGATCTAC
ATCATCACCTGAAAACAGGTGAAATAATCTAATAAGTACAACAACTCAGCAAGTGACAGACATCC
CCATAGTTCGATCGAAAACGTTAAAACATAGGCCAAATCATATCATATAGTTGATCGAATATAAT
AAGACATTTCAAAAATATAGTTTCATATCATATATCCACAAAACATTTACAAAGCAATACAAACT
TGTCTCCCATAACAGACTAGGGCCACATTTAACCCCTATGACATAGGTCGA
Found at i:27324 original size:18 final size:17
Alignment explanation
Indices: 27301--27336 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
27291 CTCAACCTAA
27301 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
27319 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
27336 A
1 A
27337 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:29347 original size:92 final size:94
Alignment explanation
Indices: 29225--29412 Score: 335
Period size: 95 Copynumber: 2.0 Consensus size: 94
29215 AATGTGGCAT
29225 TCTTTTTCATCCATTATTATTATAGCTTAGTTAATTTTTAAT-TTT-ATCATCCTTCTTGAAAAA
1 TCTTTTTCATCCATTATTATTATAGCTTAGTTAATTTTTAATATTTCATCATCCTTCTTGAAAAA
29288 TAATTAAAGCTTCGCACATGTTAAAAATG
66 TAATTAAAGCTTCGCACATGTTAAAAATG
*
29317 TCTTTTTCATCCATTATTATTATAGCTTAGTTAATTTTTAATAATTTCATTATCCTTCTTGAAAA
1 TCTTTTTCATCCATTATTATTATAGCTTAGTTAATTTTTAAT-ATTTCATCATCCTTCTTGAAAA
*
29382 ATAATTAAAGTTTCGCACATGTTAAAAATG
65 ATAATTAAAGCTTCGCACATGTTAAAAATG
29412 T
1 T
29413 GGCCCTCTTT
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
92 42 0.46
94 3 0.03
95 46 0.51
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (94 bp):
TCTTTTTCATCCATTATTATTATAGCTTAGTTAATTTTTAATATTTCATCATCCTTCTTGAAAAA
TAATTAAAGCTTCGCACATGTTAAAAATG
Found at i:29814 original size:107 final size:105
Alignment explanation
Indices: 29585--29847 Score: 397
Period size: 107 Copynumber: 2.5 Consensus size: 105
29575 AATTTTTCTA
* ** *
29585 ACCCTTAAAATAAAATTTTAATTTTAATTT-GAGCTAAACTTAGTG-AATTAATTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTTTATATTTTA
*
29648 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
29688 ACCCTTAAAATGAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGA-TTTGTATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA-ATTTTATATTTT
*
29752 ATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 ATTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
29795 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
29848 GGCTAACTTA
Statistics
Matches: 144, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
103 26 0.18
104 13 0.09
105 36 0.25
106 2 0.01
107 67 0.47
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTTTATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:30319 original size:2 final size:2
Alignment explanation
Indices: 30312--30343 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30302 AGCATGATTG
30312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30344 ATGAGATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34275 original size:8 final size:8
Alignment explanation
Indices: 34262--34295 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
34252 CGTTCTTGAA
34262 AAAAATTC
1 AAAAATTC
34270 AAAAATTC
1 AAAAATTC
34278 AAAAACTTC
1 AAAAA-TTC
34287 AAAAATTC
1 AAAAATTC
34295 A
1 A
34296 TAGCCGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:34287 original size:17 final size:17
Alignment explanation
Indices: 34261--34295 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34251 ACGTTCTTGA
34261 AAAAAATTCAAAAATTC
1 AAAAAATTCAAAAATTC
*
34278 AAAAACTTCAAAAATTC
1 AAAAAATTCAAAAATTC
34295 A
1 A
34296 TAGCCGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAATTCAAAAATTC
Found at i:35173 original size:30 final size:30
Alignment explanation
Indices: 35137--35195 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35127 CAAGGAGGAG
*
35137 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGC-ACCAAGGACTTATCATGGAA
35167 GGAATGATGCACCAAGGACTTATCATGGA
1 GGAATGATGCACCAAGGACTTATCATGGA
35196 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (30 bp):
GGAATGATGCACCAAGGACTTATCATGGAA
Found at i:39062 original size:18 final size:18
Alignment explanation
Indices: 39041--39094 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
39031 TCGCGAGTTT
* * *
39041 GATCAATATTACCTTTTC
1 GATCAAAATTACCTCTGC
*
39059 GATCAAAATTGCCTCTGC
1 GATCAAAATTACCTCTGC
*
39077 GATCAAAATTATCTCTGC
1 GATCAAAATTACCTCTGC
39095 CAAAACCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (18 bp):
GATCAAAATTACCTCTGC
Found at i:44577 original size:33 final size:33
Alignment explanation
Indices: 44537--44637 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
44527 AGCATAAGTG
**
44537 ACCGGCCACGCGATTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCAGC-CAAC
* * *
44570 ACCGGCCATGCAACATGGAGATGCCCAGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
** *
44603 ACCGGCCACGCGACATGGCCATGCCCGGCC-AC
1 ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
44635 ACC
1 ACC
44638 CAGCCACATG
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
32 4 0.07
33 50 0.89
34 2 0.04
ACGTcount: A:0.23, C:0.41, G:0.27, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCAGCCAAC
Found at i:44678 original size:33 final size:33
Alignment explanation
Indices: 44619--44682 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
44609 CACGCGACAT
*
44619 GGCCATGCCCGGCCACACCCAGCCACATGACTC
1 GGCCATGCCCGGCCACAACCAGCCACATGACTC
*
44652 GGCCATGCCCGGCCACAACCGGCCACATGAC
1 GGCCATGCCCGGCCACAACCAGCCACATGAC
44683 CCTTTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.47, G:0.23, T:0.08
Consensus pattern (33 bp):
GGCCATGCCCGGCCACAACCAGCCACATGACTC
Found at i:45582 original size:8 final size:8
Alignment explanation
Indices: 45569--45602 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
45559 ACCCTTCTTG
45569 AAAAATTC
1 AAAAATTC
45577 AAAAATTC
1 AAAAATTC
*
45585 AGAAACTTC
1 A-AAAATTC
45594 AAAAATTC
1 AAAAATTC
45602 A
1 A
45603 TAGCTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:47187 original size:33 final size:33
Alignment explanation
Indices: 47150--47321 Score: 251
Period size: 33 Copynumber: 5.3 Consensus size: 33
47140 TGAAAACAAA
47150 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
47183 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* **
47216 TCTGTTTTGGTTGAACATAGCATTAAAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
*
47249 TTTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * * *
47282 CCTGTTTTGGTAGAT-A-A-CATTGAAAATAAA
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
47312 TCTGTTTTGG
1 TCTGTTTTGG
47322 GTGACGAAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
30 20 0.16
31 1 0.01
32 1 0.01
33 104 0.83
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:47191 original size:66 final size:66
Alignment explanation
Indices: 47117--47321 Score: 177
Period size: 66 Copynumber: 3.2 Consensus size: 66
47107 TGATACTAAA
* * * * **
47117 TCTGTTTTGGATGCTAATTGTGA-TGAAAACAAATCTGTTTTGGTTGATCATAGCATTGCAAATA
1 TCTGTTTTGGATGATAATAG-CATTGAAAACAAATCTGTTTTGGTTGAACATAGCATTAAAAATA
47181 AT
65 AT
* * * * *
47183 TCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGAACATAGCATTAAAAATAA
1 TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGAACATAGCATTAAAAATAA
47248 T
66 T
* * * * * * * *
47249 TTTGTTTTGGTTGATCATAGCATTGCAAA-TAATCCTGTTTTGG-T--AGATAACATTGAAAATA
1 TCTGTTTTGGATGATAATAGCATTGAAAACAAAT-CTGTTTTGGTTGAACATAGCATTAAAAATA
*
47310 AA
65 AT
47312 TCTGTTTTGG
1 TCTGTTTTGG
47322 GTGACGAAAA
Statistics
Matches: 118, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
63 24 0.20
65 4 0.03
66 90 0.76
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (66 bp):
TCTGTTTTGGATGATAATAGCATTGAAAACAAATCTGTTTTGGTTGAACATAGCATTAAAAATAA
T
Found at i:48798 original size:33 final size:33
Alignment explanation
Indices: 48758--48865 Score: 121
Period size: 33 Copynumber: 3.3 Consensus size: 33
48748 AGCATAAGTG
* *
48758 ACCGGCCACGCGACTTGGAGATGCCC-GCGTAAC
1 ACCGGCCACGCGACATGGAGATGCCCGGC-CAAC
* *
48791 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
* **
48824 ACCGGCCACGCAACATGGCCATGCCCGGCC-AC
1 ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
48856 ACCCGGCCAC
1 A-CCGGCCAC
48866 ATGACTCGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCCAAC
Found at i:48875 original size:23 final size:23
Alignment explanation
Indices: 48849--48893 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
48839 TGGCCATGCC
*
48849 CGGCCACACCCGGCCACATGACT
1 CGGCCACAACCGGCCACATGACT
48872 CGGCCACAACCGGCCACATGAC
1 CGGCCACAACCGGCCACATGAC
48894 CCTTTAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.47, G:0.22, T:0.07
Consensus pattern (23 bp):
CGGCCACAACCGGCCACATGACT
Found at i:48877 original size:13 final size:12
Alignment explanation
Indices: 48858--48894 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
48848 CCGGCCACAC
48858 CCGGCCACATGA
1 CCGGCCACATGA
48870 CTCGGCCACA--A
1 C-CGGCCACATGA
48881 CCGGCCACATGA
1 CCGGCCACATGA
48893 CC
1 CC
48895 CTTTAGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 4 0.18
13 8 0.36
ACGTcount: A:0.24, C:0.46, G:0.22, T:0.08
Consensus pattern (12 bp):
CCGGCCACATGA
Found at i:52679 original size:8 final size:7
Alignment explanation
Indices: 52651--52690 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
52641 GGCAACCCAA
52651 TTTTAA-
1 TTTTAAT
52657 TTTTAAT
1 TTTTAAT
52664 TTTTAAT
1 TTTTAAT
*
52671 TTTTAAA
1 TTTTAAT
*
52678 TTTTATT
1 TTTTAAT
52685 TTTTAA
1 TTTTAA
52691 GGTTTTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:53487 original size:21 final size:22
Alignment explanation
Indices: 53449--53492 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
53439 GAAGCAAATT
53449 TTGAAGAAGCAAAAGTCGACTAG
1 TTGAAGAAGC-AAAGTCGACTAG
53472 TTGAAGAAGC-AAGTCGACTAG
1 TTGAAGAAGCAAAGTCGACTAG
53493 CCTACAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (22 bp):
TTGAAGAAGCAAAGTCGACTAG
Found at i:57214 original size:16 final size:17
Alignment explanation
Indices: 57195--57227 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57185 AATGTCATGG
57195 TGAATGAATGAA-CAAA
1 TGAATGAATGAAGCAAA
*
57211 TGAATGTATGAAGCAAA
1 TGAATGAATGAAGCAAA
57228 ATATGGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (17 bp):
TGAATGAATGAAGCAAA
Done.