Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014750.1 Corchorus capsularis cultivar CVL-1 contig14771, 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: 97547
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6628 original size:39 final size:39
Alignment explanation
Indices: 6585--6666 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
6575 GCATTTACAG
** * *
6585 AAGGTGGCGCGTGGGTTTAATGTTGATCCTGTGAGTGAA
1 AAGGTGGCGCGTGGACTTAATGTTGATCATGCGAGTGAA
* * *
6624 AAGGTGGTGCGTGGACTTAATTTTGATCATGCGAGTGAG
1 AAGGTGGCGCGTGGACTTAATGTTGATCATGCGAGTGAA
6663 AAGG
1 AAGG
6667 CGCGTGGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.29
Consensus pattern (39 bp):
AAGGTGGCGCGTGGACTTAATGTTGATCATGCGAGTGAA
Found at i:11372 original size:54 final size:54
Alignment explanation
Indices: 11290--11401 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
11280 GGTACCCCCC
*
11290 TGAGCCTGGCTGGATCAAAGTTAATGGAGATGTGGCTTTTAATCCTGCTAGTGA
1 TGAGCCTGGCTGGATCAAAGTTAATGGAGATGGGGCTTTTAATCCTGCTAGTGA
11344 TGAGCCTGGCTGGATCAAAGTTAATGGAGATGGGGCTTTTAATCCTGCTAGTGA
1 TGAGCCTGGCTGGATCAAAGTTAATGGAGATGGGGCTTTTAATCCTGCTAGTGA
11398 TGAG
1 TGAG
11402 GTTGGGATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.30
Consensus pattern (54 bp):
TGAGCCTGGCTGGATCAAAGTTAATGGAGATGGGGCTTTTAATCCTGCTAGTGA
Found at i:22502 original size:14 final size:14
Alignment explanation
Indices: 22483--22510 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22473 GGTCTTATTG
22483 CCCCCCCCACCCCC
1 CCCCCCCCACCCCC
22497 CCCCCCCCACCCCC
1 CCCCCCCCACCCCC
22511 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (14 bp):
CCCCCCCCACCCCC
Found at i:24932 original size:5 final size:5
Alignment explanation
Indices: 24922--24950 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
24912 CATATCTCAC
24922 TATCT TATCT TATCT TATCT TATCT TATC
1 TATCT TATCT TATCT TATCT TATCT TATC
24951 CTACTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (5 bp):
TATCT
Found at i:26488 original size:100 final size:100
Alignment explanation
Indices: 26316--26605 Score: 492
Period size: 100 Copynumber: 2.9 Consensus size: 100
26306 TATACAATAT
* * * *
26316 ACTATCAA-TGTAAAATTTGAACTCTACAAGCGGGTTAAGAAGTTGGCACATGCACATTTTCTTG
1 ACTATCAAGTGTAAATTTTGGACTCTATAAGCGGGTTAAGAAGTTGACACATGCACATTTTCTTG
*
26380 ATTAATTTTGTTTTTAAAATTTAAAACTATTCCAC
66 ATTAATTTTGTTTTTAAAATTCAAAACTATTCCAC
* *
26415 ACTATCAAGTGTAAATTTTGGACTCTATAAGCCGGTTAAGAAGTTGACACATGTACATTTTCTTG
1 ACTATCAAGTGTAAATTTTGGACTCTATAAGCGGGTTAAGAAGTTGACACATGCACATTTTCTTG
26480 ATTAATTTTGTTTTTAAAATTCAAAACTATTCCAC
66 ATTAATTTTGTTTTTAAAATTCAAAACTATTCCAC
*
26515 ACTATCAAGTGTAAATTTTGGACTCTATAAGCGGGTTAAGAAGTTGACACATACACATTTTCTTG
1 ACTATCAAGTGTAAATTTTGGACTCTATAAGCGGGTTAAGAAGTTGACACATGCACATTTTCTTG
*
26580 ATTAATTTTGTTTTTGAAATTCAAAA
66 ATTAATTTTGTTTTTAAAATTCAAAA
26606 GTACCCGGTA
Statistics
Matches: 179, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
99 8 0.04
100 171 0.96
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (100 bp):
ACTATCAAGTGTAAATTTTGGACTCTATAAGCGGGTTAAGAAGTTGACACATGCACATTTTCTTG
ATTAATTTTGTTTTTAAAATTCAAAACTATTCCAC
Found at i:38540 original size:4 final size:4
Alignment explanation
Indices: 38531--38560 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
38521 TGTTAAATCA
38531 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
38561 TAATTATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:41076 original size:2 final size:2
Alignment explanation
Indices: 41071--41109 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41061 TATATATATA
41071 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41110 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:41114 original size:2 final size:2
Alignment explanation
Indices: 41109--41139 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41099 TGTGTGTGTG
41109 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
41140 GAAACAAATT
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:43419 original size:20 final size:19
Alignment explanation
Indices: 43394--43434 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
43384 CCTAATGTGC
43394 AATTATTTTATTTGACTT-AT
1 AATTATTTT-TTT-ACTTGAT
43414 AATTATTTTTTTACTTGAT
1 AATTATTTTTTTACTTGAT
43433 AA
1 AA
43435 ATGTAACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTATTTTTTTACTTGAT
Found at i:44029 original size:25 final size:24
Alignment explanation
Indices: 44001--44048 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43991 GTTACAAGCT
* *
44001 TTTCCATGGAAAAAAATACTCATAA
1 TTTCCATAG-AAAAAATACACATAA
*
44026 TTTCCCTAGAAAAAATACACATA
1 TTTCCATAGAAAAAATACACATA
44049 TTTATCCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (24 bp):
TTTCCATAGAAAAAATACACATAA
Found at i:53147 original size:52 final size:52
Alignment explanation
Indices: 53069--53172 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
53059 ACTATTTAAT
53069 TGATACTTAAAATTAATAAGTAGCTAATTAGAGTTATGAGATGGGATTCGAC
1 TGATACTTAAAATTAATAAGTAGCTAATTAGAGTTATGAGATGGGATTCGAC
*
53121 TGATACTTAAAATTAATAAGTAGCTAATTAGAGTTATTAGATGGGATTCGAC
1 TGATACTTAAAATTAATAAGTAGCTAATTAGAGTTATGAGATGGGATTCGAC
53173 CTCATGTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (52 bp):
TGATACTTAAAATTAATAAGTAGCTAATTAGAGTTATGAGATGGGATTCGAC
Found at i:53405 original size:90 final size:90
Alignment explanation
Indices: 53252--53431 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
53242 ATCCCGACTA
53252 TACTCACTCTTGCTAAGCATATGGCATAAGACTCCAAGAGCTTCTGATCTTCCAATTTTAATTGC
1 TACTCACTCTTGCTAAGCATATGGCATAAGACTCCAAGAGCTTCTGATCTTCCAATTTTAATTGC
53317 AATGTGCAATGCAGTCTCGTCTTTT
66 AATGTGCAATGCAGTCTCGTCTTTT
*
53342 TACTCACTCTTGCTAAGCATATGGCATAAGACTCCAAGAGCTTCTGATCTTCCATTTTTAATTGC
1 TACTCACTCTTGCTAAGCATATGGCATAAGACTCCAAGAGCTTCTGATCTTCCAATTTTAATTGC
53407 AATGTGCAATGCAGTCTCGTCTTTT
66 AATGTGCAATGCAGTCTCGTCTTTT
53432 GTTGTTGTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (90 bp):
TACTCACTCTTGCTAAGCATATGGCATAAGACTCCAAGAGCTTCTGATCTTCCAATTTTAATTGC
AATGTGCAATGCAGTCTCGTCTTTT
Found at i:54508 original size:14 final size:14
Alignment explanation
Indices: 54489--54517 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54479 GTTTTGTGTG
54489 ATATAAAAAGTCTT
1 ATATAAAAAGTCTT
54503 ATATAAAAAGTCTT
1 ATATAAAAAGTCTT
54517 A
1 A
54518 CAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (14 bp):
ATATAAAAAGTCTT
Found at i:72065 original size:15 final size:15
Alignment explanation
Indices: 72045--72083 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
72035 GTATTTCTTA
*
72045 GGAAAGAAATGGAAC
1 GGAAAGAAATAGAAC
* *
72060 GGAAAGAAGTAGCAC
1 GGAAAGAAATAGAAC
72075 GGAAAGAAA
1 GGAAAGAAA
72084 GTAGGAGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.08, G:0.33, T:0.05
Consensus pattern (15 bp):
GGAAAGAAATAGAAC
Found at i:72094 original size:16 final size:15
Alignment explanation
Indices: 72058--72087 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
72048 AAGAAATGGA
72058 ACGGAAAGAAGTAGC
1 ACGGAAAGAAGTAGC
72073 ACGGAAAGAAAGTAG
1 ACGGAAAG-AAGTAG
72088 GAGGGAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.10, G:0.33, T:0.07
Consensus pattern (15 bp):
ACGGAAAGAAGTAGC
Found at i:72435 original size:30 final size:33
Alignment explanation
Indices: 72401--72472 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 33
72391 ACAAGTATAC
72401 AAATTTTGCCTGATCT-TTTT-TTTT-CCAACA
1 AAATTTTGCCTGATCTGTTTTATTTTGCCAACA
* * *
72431 AAATTTTGCCTGGTGTGTTTTATTTTGGCAACA
1 AAATTTTGCCTGATCTGTTTTATTTTGCCAACA
72464 AAATTTTGC
1 AAATTTTGC
72473 TTGGTGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.39
31 4 0.11
32 4 0.11
33 14 0.39
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (33 bp):
AAATTTTGCCTGATCTGTTTTATTTTGCCAACA
Found at i:72468 original size:33 final size:30
Alignment explanation
Indices: 72401--72481 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 30
72391 ACAAGTATAC
* *
72401 AAATTTTGCCTGATCTTTTTTTTTCCAACA
1 AAATTTTGCCTGGTGTTTTTTTTTCCAACA
*
72431 AAATTTTGCCTGGTGTGTTTTATTTTGGCAACA
1 AAATTTTGCCTGGTGT-TTTT-TTTT-CCAACA
*
72464 AAATTTTGCTTGGTGTTT
1 AAATTTTGCCTGGTGTTT
72482 AAGTCCCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.32
31 4 0.09
32 6 0.14
33 20 0.45
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (30 bp):
AAATTTTGCCTGGTGTTTTTTTTTCCAACA
Found at i:72959 original size:16 final size:15
Alignment explanation
Indices: 72940--72982 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
72930 TTCCTCCCTA
*
72940 TTTCCTTTCTATTTCC
1 TTTCCTTTCTACTT-C
*
72956 TTTCCTTCCTACTTC
1 TTTCCTTTCTACTTC
*
72971 TTTCCTCTCTAC
1 TTTCCTTTCTAC
72983 CAAATACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTCCTTTCTACTTC
Found at i:72960 original size:27 final size:26
Alignment explanation
Indices: 72924--72974 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
72914 TATGATTTCC
*
72924 TTTCCCTTCCTCCCTATTTCCTTTCTA
1 TTTCCCTTCCTCCCTACTT-CTTTCTA
* *
72951 TTTCCTTTCCTTCCTACTTCTTTC
1 TTTCCCTTCCTCCCTACTTCTTTC
72975 CTCTCTACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTCCCTTCCTCCCTACTTCTTTCTA
Found at i:72975 original size:31 final size:32
Alignment explanation
Indices: 72918--72981 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
72908 AGGAAATATG
* *
72918 ATTTCCTTTCCCTTCCTCCCTATTTCCTTTCT
1 ATTTCCTTTCCCTTCCTACCTATTTCCTCTCT
* *
72950 ATTTCCTTT-CCTTCCTACTTCTTTCCTCTCT
1 ATTTCCTTTCCCTTCCTACCTATTTCCTCTCT
72981 A
1 A
72982 CCAAATACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTCCTTTCCCTTCCTACCTATTTCCTCTCT
Found at i:76115 original size:22 final size:22
Alignment explanation
Indices: 76031--76348 Score: 103
Period size: 22 Copynumber: 14.3 Consensus size: 22
76021 AGGTTATACG
* *
76031 AATTTCATAGTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
76053 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* * *
76075 TACTTCAT-TGGGAGGTTATCAA
1 AATTTCATAT-GAAGGTTATCAA
76097 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
76118 AAGTCTCAATTTCAT-AAGGAATACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
* *
76145 AATTTGATA-GAAGGTCATC-A
1 AATTTCATATGAAGGTTATCAA
* *
76165 AATCTCATA-G-AGTGATTATCGA
1 AATTTCATATGAAG-G-TTATCAA
*
76187 AATTTCATAAAGATAGGATTATCAA
1 AATTTCAT-ATGA-AGG-TTATCAA
*
76212 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
* **
76233 AATTTTATA-GTATTGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
* *
76255 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
* * *
76277 AATTACATAATG-CGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* *
76299 AATTTCATA-GAGGGGTTAACAA
1 AATTTCATATGA-AGGTTATCAA
*
76321 AATTT--TATAAAGAGATTATCAA
1 AATTTCATATGAAG-G-TTATCAA
76343 AATTTC
1 AATTTC
76349 GCAGAGGGGT
Statistics
Matches: 223, Mismatches: 42, Indels: 61
0.68 0.13 0.19
Matches are distributed among these distances:
19 2 0.01
20 15 0.07
21 29 0.13
22 133 0.60
23 8 0.04
24 5 0.02
25 19 0.09
26 8 0.04
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:76296 original size:44 final size:44
Alignment explanation
Indices: 76248--76393 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
76238 TATAGTATTG
* * * *
76248 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGCGA
1 TTATCAAAATTTCAAAGAGAGGTTAACAAAATTACATAAAGAGA
* * **
76292 TTATCAAAATTTCATAGAGGGGTTAACAAAATTTTATAAAGAGA
1 TTATCAAAATTTCAAAGAGAGGTTAACAAAATTACATAAAGAGA
** * * *
76336 TTATCAAAATTTCGCAGAGGGGTCAACAAAAATT-TATAAAGATG-
1 TTATCAAAATTTCAAAGAGAGGTTAAC-AAAATTACATAAAGA-GA
*
76380 TTATCAAATTTTCA
1 TTATCAAAATTTCA
76394 CAAACGTACA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 80 0.92
45 7 0.08
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (44 bp):
TTATCAAAATTTCAAAGAGAGGTTAACAAAATTACATAAAGAGA
Found at i:81276 original size:53 final size:53
Alignment explanation
Indices: 81192--81294 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
81182 GCCACGTGTC
* ** *
81192 ACTTTTTGTTACACGTGGAGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGAGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
81245 ACTTTTTGGTACACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGAGTGACACATGTCACTTTTTGGTACACGTGGC
81295 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGAGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:81606 original size:24 final size:24
Alignment explanation
Indices: 81579--81630 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
81569 TCTCTTTTGG
81579 TGTGAAGAGTTTTTT-TTTTTT-TTT
1 TGTGAA-A-TTTTTTATTTTTTCTTT
81603 TGTGAAATTTTTTGATTTTTTCTTT
1 TGTGAAATTTTTT-ATTTTTTCTTT
81628 TGT
1 TGT
81631 TTTTATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.24
23 1 0.04
24 12 0.48
25 6 0.24
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.69
Consensus pattern (24 bp):
TGTGAAATTTTTTATTTTTTCTTT
Found at i:87831 original size:16 final size:14
Alignment explanation
Indices: 87798--87836 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
87788 AACGAGAATT
87798 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
87812 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
*
87826 AAAGAGAGGAG
1 AGAGAG-GGAG
87837 CGGCAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (14 bp):
AGAGAGGGAGAAGG
Found at i:92644 original size:45 final size:45
Alignment explanation
Indices: 92580--92668 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
92570 ACTCTTACTA
92580 TTGATAATGCTGAGAATAGTCAGAAGAGTCATCTGGACAAACCCG
1 TTGATAATGCTGAGAATAGTCAGAAGAGTCATCTGGACAAACCCG
* *
92625 TTGATAATGGTGAGAATAGTCAGAAGAGTCATCTGGACAGACCC
1 TTGATAATGCTGAGAATAGTCAGAAGAGTCATCTGGACAAACCC
92669 ATGATTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (45 bp):
TTGATAATGCTGAGAATAGTCAGAAGAGTCATCTGGACAAACCCG
Done.