Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006559.1 Corchorus capsularis cultivar CVL-1 contig06580, 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: 59030
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:594 original size:15 final size:15
Alignment explanation
Indices: 571--607 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
561 GGTGATTTGA
*
571 TGCTTTCATAGGAGT
1 TGCTCTCATAGGAGT
586 TGCTCTCATAGGAGT
1 TGCTCTCATAGGAGT
601 TGCTCTC
1 TGCTCTC
608 GTTGCACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (15 bp):
TGCTCTCATAGGAGT
Found at i:3450 original size:11 final size:11
Alignment explanation
Indices: 3436--3460 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3426 AAAAGGTAGT
3436 AAAAAGAAAAA
1 AAAAAGAAAAA
3447 AAAAAGAAAAA
1 AAAAAGAAAAA
3458 AAA
1 AAA
3461 GAGAGAACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:3690 original size:25 final size:26
Alignment explanation
Indices: 3657--3708 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
3647 AAGCTCATAC
*
3657 ATGAAATGCGGCGCAAC-ACAACACA
1 ATGAAATGCGGCGCAACGACAAAACA
*
3682 ATGAGATGCGGCGCAACGACAAAACA
1 ATGAAATGCGGCGCAACGACAAAACA
3708 A
1 A
3709 GCATAACACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (26 bp):
ATGAAATGCGGCGCAACGACAAAACA
Found at i:3857 original size:29 final size:29
Alignment explanation
Indices: 3825--3884 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
3815 AAAAATTGTG
* *
3825 AAATTGCCGCAAGTACCCAAAATTCCAAA
1 AAATTGCCGCAACTACCCAAAATTACAAA
**
3854 AAATTGCCGCAACTAGTCAAAATTACAAA
1 AAATTGCCGCAACTACCCAAAATTACAAA
3883 AA
1 AA
3885 CCCCGTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.18
Consensus pattern (29 bp):
AAATTGCCGCAACTACCCAAAATTACAAA
Found at i:3948 original size:46 final size:46
Alignment explanation
Indices: 3853--3948 Score: 104
Period size: 46 Copynumber: 2.1 Consensus size: 46
3843 AAAATTCCAA
* * *
3853 AAAATTGCCGCAACTAGTCAAAATTACAAAAACCCCGTAACTAGCC
1 AAAATTGCCGCAACTAGTCAAAATTACAAAAACCCCGCAACAAGAC
* * * **
3899 AAAATTGTCGCAACTAG-CAAAAATTGCAAGAATTCCGCAACAAGAC
1 AAAATTGCCGCAACTAGTC-AAAATTACAAAAACCCCGCAACAAGAC
3945 AAAA
1 AAAA
3949 GGCACTGCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.17
Consensus pattern (46 bp):
AAAATTGCCGCAACTAGTCAAAATTACAAAAACCCCGCAACAAGAC
Found at i:22398 original size:39 final size:40
Alignment explanation
Indices: 22358--22502 Score: 197
Period size: 39 Copynumber: 3.6 Consensus size: 40
22348 CCCAATAATC
22358 AAAGTCCTCAAACACATATAACACAGAGGCATCTATATC-
1 AAAGTCCTCAAACACATATAACACAGAGGCATCTATATCT
* * * *
22397 AAAGTCCTCAAACACATGTAACACAGGGGCAATTCTCTTTCT
1 AAAGTCCTCAAACACATATAACACAGAGGC-A-TCTATATCT
22439 AAAGTCCTCAAACACATATAACACAGAGGCATCTATA-CT
1 AAAGTCCTCAAACACATATAACACAGAGGCATCTATATCT
*
22478 AAAGTCC-CTAAACACATACAACACA
1 AAAGTCCTC-AAACACATATAACACA
22503 AGGGCAATTT
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.01
39 52 0.56
40 5 0.05
41 7 0.08
42 28 0.30
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.21
Consensus pattern (40 bp):
AAAGTCCTCAAACACATATAACACAGAGGCATCTATATCT
Found at i:22443 original size:81 final size:81
Alignment explanation
Indices: 22358--22517 Score: 252
Period size: 81 Copynumber: 2.0 Consensus size: 81
22348 CCCAATAATC
**
22358 AAAGTCCTCAAACACATATAACACAGAGGCATCTATA-TCAAAGT-CCTCAAACACATGTAACAC
1 AAAGTCCTCAAACACATATAACACAGAGGCATCTATACT-AAAGTCCCT-AAACACATACAACAC
*
22421 AGGGGCAATTCTCTTTCT
64 AAGGGCAATTCTCTTTCT
22439 AAAGTCCTCAAACACATATAACACAGAGGCATCTATACTAAAGTCCCTAAACACATACAACACAA
1 AAAGTCCTCAAACACATATAACACAGAGGCATCTATACTAAAGTCCCTAAACACATACAACACAA
*
22504 GGGCAATTTTCTTT
66 GGGCAATTCTCTTT
22518 TCTACATGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
81 69 0.95
82 4 0.05
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (81 bp):
AAAGTCCTCAAACACATATAACACAGAGGCATCTATACTAAAGTCCCTAAACACATACAACACAA
GGGCAATTCTCTTTCT
Found at i:26513 original size:21 final size:21
Alignment explanation
Indices: 26488--26573 Score: 127
Period size: 21 Copynumber: 4.1 Consensus size: 21
26478 TTTTTTGTCA
*
26488 AAATTTTGATGGCCAAACCCC
1 AAATTTTGATGGTCAAACCCC
*
26509 AAATTTTGATGGTGAAACCCC
1 AAATTTTGATGGTCAAACCCC
**
26530 AAATTTTGATTATCAAACCCC
1 AAATTTTGATGGTCAAACCCC
*
26551 AAATTTTGATGGTCAAATCCC
1 AAATTTTGATGGTCAAACCCC
26572 AA
1 AA
26574 TTGAAGCACC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (21 bp):
AAATTTTGATGGTCAAACCCC
Found at i:26622 original size:132 final size:132
Alignment explanation
Indices: 26442--26699 Score: 381
Period size: 132 Copynumber: 2.0 Consensus size: 132
26432 ATCTTTTCAG
* *
26442 TTGAAGCACCCACCACATTTTTTGCCCAAAACTGTGTTTTTTGTCAAAATTTTGATGGCCAAACC
1 TTGAAGCACCCACCACATTTTTTGCCCAAAACTGTGTTTTTTGCCAAAATTTTGATGACCAAACC
* * * * * **
26507 CCAAATTTTGATGGTGAAACCCCAAATTTTGATTATCAAACCCCAAATTTTGATGGTCAAATCCC
66 CAAAAATTTGATAGTCAAACCCCAAATTTTGATGATCAAACCCCAAAGCTTGATGGTCAAATCCC
26572 AA
131 AA
**
26574 TTGAAGCACCCACCACATTTTTTGCCCAAAACTGTGTTTTTTGCCAAAATTTTGATGATGAAACC
1 TTGAAGCACCCACCACATTTTTTGCCCAAAACTGTGTTTTTTGCCAAAATTTTGATGACCAAACC
* * * *
26639 TAAAAATTTGATAGTCAAACCCCAAATTTTGATGGTCAAACCCTAAAGCTTGATTGTCAAA
66 CAAAAATTTGATAGTCAAACCCCAAATTTTGATGATCAAACCCCAAAGCTTGATGGTCAAA
26700 CAACAAAATT
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 111 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (132 bp):
TTGAAGCACCCACCACATTTTTTGCCCAAAACTGTGTTTTTTGCCAAAATTTTGATGACCAAACC
CAAAAATTTGATAGTCAAACCCCAAATTTTGATGATCAAACCCCAAAGCTTGATGGTCAAATCCC
AA
Found at i:26658 original size:21 final size:21
Alignment explanation
Indices: 26617--26743 Score: 98
Period size: 21 Copynumber: 6.0 Consensus size: 21
26607 GTGTTTTTTG
* *
26617 CCAAAATTTTGAT-GATGAAAC
1 CCAAAAATTTGATAG-TCAAAC
*
26638 CTAAAAATTTGATAGTCAAAC
1 CCAAAAATTTGATAGTCAAAC
* * *
26659 CCCAAATTTTGATGGTCAAAC
1 CCAAAAATTTGATAGTCAAAC
* ** *
26680 CCTAAAGCTTGATTGTCAAA-
1 CCAAAAATTTGATAGTCAAAC
*
26700 CAACAAAATTTGAT-GATCAAAC
1 CCA-AAAATTTGATAG-TCAAAC
*
26722 CCCAAAATTTGATAGTCAAAC
1 CCAAAAATTTGATAGTCAAAC
26743 C
1 C
26744 ATGTTAAACC
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.02
21 79 0.94
22 3 0.04
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (21 bp):
CCAAAAATTTGATAGTCAAAC
Found at i:26680 original size:42 final size:41
Alignment explanation
Indices: 26620--26744 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 41
26610 TTTTTTGCCA
* *
26620 AAATTTTGATGATGAAACCTAAAAATTTGATAGTCAAACCCC
1 AAATTTTGATGATCAAACCT-AAAATTTGATAGTCAAACCAC
* ** * *
26662 AAATTTTGATGGTCAAACCCTAAAGCTTGATTGTCAAACAAC
1 AAATTTTGATGATCAAA-CCTAAAATTTGATAGTCAAACCAC
* *
26704 AAAATTTGATGATCAAACCCCAAAATTTGATAGTCAAACCA
1 AAATTTTGATGATCAAA-CCTAAAATTTGATAGTCAAACCA
26745 TGTTAAACCT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 65 0.96
43 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.27
Consensus pattern (41 bp):
AAATTTTGATGATCAAACCTAAAATTTGATAGTCAAACCAC
Found at i:26828 original size:21 final size:21
Alignment explanation
Indices: 26802--26863 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
26792 TGTGTTTTTG
* *
26802 CCCAAATTTTGATGGTCAAAC
1 CCCAAATTTTGATAGTAAAAC
*
26823 CCCAAATTTTGGTAGTAAAAC
1 CCCAAATTTTGATAGTAAAAC
* *
26844 CTCAAAATTTGATAGCTAAA
1 CCCAAATTTTGATAG-TAAA
26864 TCATGTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (21 bp):
CCCAAATTTTGATAGTAAAAC
Found at i:26952 original size:122 final size:122
Alignment explanation
Indices: 26694--26923 Score: 295
Period size: 122 Copynumber: 1.9 Consensus size: 122
26684 AAGCTTGATT
* * *
26694 GTCAAACAACAAAATTTGAT-GATCAAACCCCAAAATTTGATAGTCAAACCATGTTAAACCTTAT
1 GTCAAACAACAAATTTTGGTAG-TAAAACCCCAAAATTTGATAGTCAAACCATGTTAAACCTTAT
* * * ** *
26758 CAATTGAAGCACCCACCACGTTTTTGTCCAAAACTGTGTTTTTGCCCAAATTTTGATG
65 CAATTGAAGCACCCAACACATTTTTGTCCAAAACTGTGTCTAAGCCCAAATTTTGAAG
** * *
26816 GTCAAACCCCAAATTTTGGTAGTAAAACCTCAAAATTTGATAG-CTAAATCATGTTAAACCTTAT
1 GTCAAACAACAAATTTTGGTAGTAAAACCCCAAAATTTGATAGTC-AAACCATGTTAAACCTTAT
26880 CAATTGAAGCACCCAACACATTTTTG-CCTAAAACTGTGTCTAAG
65 CAATTGAAGCACCCAACACATTTTTGTCC-AAAACTGTGTCTAAG
26924 GCAAATTATA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
121 3 0.03
122 89 0.96
123 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (122 bp):
GTCAAACAACAAATTTTGGTAGTAAAACCCCAAAATTTGATAGTCAAACCATGTTAAACCTTATC
AATTGAAGCACCCAACACATTTTTGTCCAAAACTGTGTCTAAGCCCAAATTTTGAAG
Found at i:28137 original size:2 final size:2
Alignment explanation
Indices: 28117--28159 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
28107 GATATGATTG
*
28117 AT AT AT -T AT TT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28157 AT A
1 AT A
28160 GTGAGGGTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:29240 original size:26 final size:26
Alignment explanation
Indices: 29204--29270 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
29194 GCCATGATAG
29204 TGTGATGAGATCTTGCTGGTAAGATCC
1 TGTG-TGAGATCTTGCTGGTAAGATCC
29231 TGTGTGAGATCTTGCTGGTAAGATCC
1 TGTGTGAGATCTTGCTGGTAAGATCC
*
29257 TGTGTGAGGTCTTG
1 TGTGTGAGATCTTG
29271 TGTTGTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 35 0.90
27 4 0.10
ACGTcount: A:0.18, C:0.13, G:0.33, T:0.36
Consensus pattern (26 bp):
TGTGTGAGATCTTGCTGGTAAGATCC
Found at i:31839 original size:37 final size:37
Alignment explanation
Indices: 31788--31872 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
31778 AGGAATTGCG
* * *
31788 GAAACTGCAATAAATAGAAACAATTTCCAGAATTGTA
1 GAAAATGCAATAAATAGAAACAATTTCCAGAACTGCA
* *
31825 GAAAATGCAGTAAATAGAAACAATTTTCAGAACTGCA
1 GAAAATGCAATAAATAGAAACAATTTCCAGAACTGCA
31862 GAAAATTGCAA
1 GAAAA-TGCAA
31873 AATGAAATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 37 0.90
38 4 0.10
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.22
Consensus pattern (37 bp):
GAAAATGCAATAAATAGAAACAATTTCCAGAACTGCA
Found at i:32026 original size:14 final size:14
Alignment explanation
Indices: 32007--32047 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
31997 TTTGTCCTTG
*
32007 TTTTAACATGTTCA
1 TTTTAACATGTCCA
32021 TTTTAACTTATGTCCA
1 TTTTAAC--ATGTCCA
32037 TTTTAACATGT
1 TTTTAACATGT
32048 ATGCCTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (14 bp):
TTTTAACATGTCCA
Found at i:43660 original size:19 final size:18
Alignment explanation
Indices: 43636--43671 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43626 TGAAGATTTC
43636 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
43655 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
43672 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:48494 original size:22 final size:21
Alignment explanation
Indices: 48469--48525 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
48459 AAAATCAAAA
*
48469 GGATTTGTTTGAAAAATTAGGG
1 GGATTTGTTTGAAAAA-TAAGG
* *
48491 GGATTTCTTTGGAAAATAAGG
1 GGATTTGTTTGAAAAATAAGG
*
48512 GGATTGGTTTGAAA
1 GGATTTGTTTGAAA
48526 GGGAAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.35
Consensus pattern (21 bp):
GGATTTGTTTGAAAAATAAGG
Found at i:48928 original size:2 final size:2
Alignment explanation
Indices: 48888--48913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48878 CATGCTGCTG
48888 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48914 TATCAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50159 original size:60 final size:58
Alignment explanation
Indices: 50072--50227 Score: 158
Period size: 55 Copynumber: 2.7 Consensus size: 58
50062 GGCTAATTGT
* ** * *
50072 TCAAATA-GGACCTTAATGTATTAAAAAATGTTCAATTTAGGCCTTATGCTTTTAATTTGA
1 TCAAATATGGACC-TAACGTATGCAAAAATG-TCAA-TAAGGACTTATGCTTTTAATTTGA
* *
50132 TCAAATATGGACCTAACGTATGCAAAAATG---ATAAGGACTTATGCTTTTTATTTGG
1 TCAAATATGGACCTAACGTATGCAAAAATGTCAATAAGGACTTATGCTTTTAATTTGA
* *
50187 TCAAATATGGCCCTAACGTATGCTAAAATGCTCAAATAAGG
1 TCAAATATGGACCTAACGTATGCAAAAATG-TC-AATAAGG
50228 CCCCAAAATC
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
55 48 0.59
56 1 0.01
60 27 0.33
61 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (58 bp):
TCAAATATGGACCTAACGTATGCAAAAATGTCAATAAGGACTTATGCTTTTAATTTGA
Found at i:50369 original size:60 final size:59
Alignment explanation
Indices: 50275--50390 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 59
50265 CAACAGGTCT
50275 TTATTTGAGCATTTTCGCTAATGTTAGGGCCATATTTAACC-AAATTAAAAGCATGAATCC
1 TTATTTGAGCATTTTCGCTAA-GTTAGGGCCATATTTAACCAAAATT-AAAGCATGAATCC
* *
50335 TTATTTGAGCATTTTTGCATACA-TTAGGGTCATATTTAACCAAAATTAAAGCATGA
1 TTATTTGAGCATTTTCGC-TA-AGTTAGGGCCATATTTAACCAAAATTAAAGCATGA
50391 GGTCTAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
60 43 0.84
61 7 0.14
62 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (59 bp):
TTATTTGAGCATTTTCGCTAAGTTAGGGCCATATTTAACCAAAATTAAAGCATGAATCC
Found at i:50409 original size:60 final size:60
Alignment explanation
Indices: 50298--50420 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
50288 TTCGCTAATG
* * * *
50298 TTAGGGCCATATTTAACCAAATTAAAAGCATGAATCCTTATTTGAGCATTTTTGCATACA
1 TTAGGGCCATATTTAACCAAATTAAAAGCATGAATCCTAAATTGAACATTTTTACATACA
* * *
50358 TTAGGGTCATATTTAACCAAAATT-AAAGCATGAGGT-CTAAATTGAATATTTTTACATACA
1 TTAGGGCCATATTTAACC-AAATTAAAAGCATGA-ATCCTAAATTGAACATTTTTACATACA
50418 TTA
1 TTA
50421 AGAACTAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 48 0.89
61 6 0.11
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (60 bp):
TTAGGGCCATATTTAACCAAATTAAAAGCATGAATCCTAAATTGAACATTTTTACATACA
Found at i:51282 original size:146 final size:149
Alignment explanation
Indices: 51076--51386 Score: 380
Period size: 146 Copynumber: 2.1 Consensus size: 149
51066 AAATTTGACT
* * *
51076 TTAATGAGAAATGACAAATTAAATTTATTACTGCATAAGGTAAAAAGAAGGAATAGAAGTTTAAT
1 TTAATGAGAAATGACAAATTAAATTCATTACTGCATAAGCTAAAAAGAAGGAATAAAAGTTTAAT
* * *
51141 G-A-AATCACTTAATGAGACATGACGTTTTGGCATTTTAATT-TTGATGTTGGATTAAAGA-TTT
66 GAATAATAACTTAATGAGACATGACGTTTTGCCATTTT-ATTATTGATGTTGAATTAAAGATTTT
* * *
51202 GCCGAGGAAAATCAAGTATG
130 GCAGAAGAAAATAAAGTATG
* * * * * *
51222 TTAATGAGAAATGACAAATTCAATTCATTATTGCAT-ATCTCAAAATGGAGGAATAAAAGTTTTA
1 TTAATGAGAAATGACAAATTAAATTCATTACTGCATAAGCT-AAAAAGAAGGAATAAAAGTTTAA
* *
51286 TGTAATAATAATTTAATGAGATATGACGTTTTGCCATTTTATTATTGATGTTGAATTAAAGATTT
65 TG-AATAATAACTTAATGAGACATGACGTTTTGCCATTTTATTATTGATGTTGAATTAAAGATTT
* *
51351 TGTAGAAGAAAATAAATTATG
129 TGCAGAAGAAAATAAAGTATG
*
51372 TTAATGAGACATGAC
1 TTAATGAGAAATGAC
51387 TTGTAGTTGT
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
145 2 0.01
146 54 0.39
148 4 0.03
149 47 0.34
150 32 0.23
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.35
Consensus pattern (149 bp):
TTAATGAGAAATGACAAATTAAATTCATTACTGCATAAGCTAAAAAGAAGGAATAAAAGTTTAAT
GAATAATAACTTAATGAGACATGACGTTTTGCCATTTTATTATTGATGTTGAATTAAAGATTTTG
CAGAAGAAAATAAAGTATG
Found at i:51490 original size:32 final size:32
Alignment explanation
Indices: 51453--51515 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
51443 TTTATGTATT
*
51453 GTTTACATTATGGTGTTGGTGTGAAAAAAGTG
1 GTTTACATTATGGTGCTGGTGTGAAAAAAGTG
*
51485 GTTTACATTGTGGTGCTGGTGTGAAAAAAGT
1 GTTTACATTATGGTGCTGGTGTGAAAAAAGT
51516 AGAAGTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.37
Consensus pattern (32 bp):
GTTTACATTATGGTGCTGGTGTGAAAAAAGTG
Found at i:56205 original size:22 final size:22
Alignment explanation
Indices: 56180--56221 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
56170 TCGAATACAT
56180 ATTTATTTACTGTAGAAATAAA
1 ATTTATTTACTGTAGAAATAAA
*
56202 ATTTGTTTACTGTAGAAATA
1 ATTTATTTACTGTAGAAATA
56222 TTATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTATTTACTGTAGAAATAAA
Found at i:56227 original size:22 final size:22
Alignment explanation
Indices: 56173--56227 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
56163 CTTAATGTCG
56173 AATACATATTTATTTACTGTAGA
1 AATA-ATATTTATTTACTGTAGA
* *
56196 AATAAAATTTGTTTACTGTAGA
1 AATAATATTTATTTACTGTAGA
*
56218 AATATTATTT
1 AATAATATTT
56228 CAATTAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
AATAATATTTATTTACTGTAGA
Found at i:57745 original size:9 final size:10
Alignment explanation
Indices: 57711--57746 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
57701 AATTATATCG
57711 AAAAATATCAA
1 AAAAATAT-AA
57722 AAAAATATAA
1 AAAAATATAA
57732 AAAAA-ATAA
1 AAAAATATAA
57741 AAAAAT
1 AAAAAT
57747 TCAACCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 7 0.29
11 8 0.33
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATATAA
Done.