Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023641.1 Corchorus olitorius cultivar O-4 contig23674, 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: 93122
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7428 original size:29 final size:28
Alignment explanation
Indices: 7391--7555 Score: 186
Period size: 29 Copynumber: 5.7 Consensus size: 28
7381 AGAGTATGCA
* *
7391 AAAAATGACCAAACTGCCCCAGAATGTGT
1 AAAAATGACCAAAATGCCCCAG-ATGTGC
* * *
7420 AAAAATGACCATAATGCCCCTGGATGGGC
1 AAAAATGACCAAAATGCCCC-AGATGTGC
* *
7449 AAAATTGACCAAAATGCCCCTAGATGCGC
1 AAAAATGACCAAAATGCCCC-AGATGTGC
7478 AAAAATGACCAAAATGCCCCTAGATGTGC
1 AAAAATGACCAAAATGCCCC-AGATGTGC
* * * *
7507 AAAAATAACCAAACTGCCCTAGGATATGC
1 AAAAATGACCAAAATGCCCCA-GATGTGC
7536 AAAAATGACCAAAATGCCCC
1 AAAAATGACCAAAATGCCCC
7556 TGAGCAAGCA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
28 1 0.01
29 114 0.98
30 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCAGATGTGC
Found at i:7467 original size:58 final size:57
Alignment explanation
Indices: 7391--7557 Score: 217
Period size: 58 Copynumber: 2.9 Consensus size: 57
7381 AGAGTATGCA
* *
7391 AAAAATGACCAAACTGCCCCAGAATGTGTAAAAATGACCATAATGCCCCTGGATGGGC
1 AAAAATGACCAAACTGCCCCAG-ATGTGCAAAAATGACCAAAATGCCCCTGGATGGGC
* * * * *
7449 AAAATTGACCAAAATGCCCCTAGATGCGCAAAAATGACCAAAATGCCCCTAGATGTGC
1 AAAAATGACCAAACTGCCCC-AGATGTGCAAAAATGACCAAAATGCCCCTGGATGGGC
* * *
7507 AAAAATAACCAAACTGCCCTAGGATATGCAAAAATGACCAAAATGCCCCTG
1 AAAAATGACCAAACTGCCCCA-GATGTGCAAAAATGACCAAAATGCCCCTG
7558 AGCAAGCAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
57 1 0.01
58 90 0.97
59 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (57 bp):
AAAAATGACCAAACTGCCCCAGATGTGCAAAAATGACCAAAATGCCCCTGGATGGGC
Found at i:7525 original size:87 final size:87
Alignment explanation
Indices: 7391--7585 Score: 238
Period size: 87 Copynumber: 2.2 Consensus size: 87
7381 AGAGTATGCA
* * * * *
7391 AAAAATGACCAAACTGCCCC-AGAATGTGTAAAAATGACCATAATGCCCCT-GGATGGGCAAAAT
1 AAAAATGACCAAAATGCCCCTAGAATGTGCAAAAATAACCATAATG-CCCTAGGATAGGCAAAAA
7454 TGACCAAAATGCCCCTAGATGC-GC
65 TGACCAAAATGCCCCT-GA-GCAGC
*
7478 AAAAATGACCAAAATGCCCCTAG-ATGTGCAAAAATAACCA-AACTGCCCTAGGATATGCAAAAA
1 AAAAATGACCAAAATGCCCCTAGAATGTGCAAAAATAACCATAA-TGCCCTAGGATAGGCAAAAA
7541 TGACCAAAATGCCCCTGAGCAAGC
65 TGACCAAAATGCCCCTGAGC-AGC
* *
7565 AAAAATGACTAAAATACCCCT
1 AAAAATGACCAAAATGCCCCT
7586 GAGCGTGCGA
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
85 2 0.02
86 8 0.08
87 83 0.87
88 2 0.02
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.16
Consensus pattern (87 bp):
AAAAATGACCAAAATGCCCCTAGAATGTGCAAAAATAACCATAATGCCCTAGGATAGGCAAAAAT
GACCAAAATGCCCCTGAGCAGC
Found at i:7566 original size:29 final size:30
Alignment explanation
Indices: 7420--7589 Score: 151
Period size: 29 Copynumber: 5.8 Consensus size: 30
7410 CAGAATGTGT
* *
7420 AAAAATGACCATAATGCCCCTG-G-ATGGGC
1 AAAAATGACCAAAATGCCCCTGAGCAT-AGC
* *
7449 AAAATTGACCAAAATGCCCCT-AG-ATGCGC
1 AAAAATGACCAAAATGCCCCTGAGCAT-AGC
*
7478 AAAAATGACCAAAATGCCCCT-AG-ATGTGC
1 AAAAATGACCAAAATGCCCCTGAGCAT-AGC
* * *
7507 AAAAATAACCAAACTG-CCCT-AGGATATGC
1 AAAAATGACCAAAATGCCCCTGAGCATA-GC
7536 AAAAATGACCAAAATGCCCCTGAGCA-AGC
1 AAAAATGACCAAAATGCCCCTGAGCATAGC
* *
7565 AAAAATGACTAAAATACCCCTGAGC
1 AAAAATGACCAAAATGCCCCTGAGC
7590 GTGCGAATGG
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.05
29 109 0.89
30 5 0.04
31 3 0.02
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (30 bp):
AAAAATGACCAAAATGCCCCTGAGCATAGC
Found at i:10468 original size:71 final size:71
Alignment explanation
Indices: 10371--10550 Score: 211
Period size: 71 Copynumber: 2.5 Consensus size: 71
10361 ATTGTCTTGG
* * * *
10371 TCATGGTAGACTGAACCATGGGATGAGGAACGCTAGGTAGGAA-ACCTTTGGCTGCCTTAGCCAC
1 TCATGGTAGTCTAAACCATGTGATGAGGAAAGCTAGGTA-GAAGACCTTTGGCTGCCTTAGCCAC
*
10435 ATCTTAA
65 AACTTAA
* * * * *
10442 TGATGGTAGTCTAAACCATGTGATGAGGAAGGCTAAGTAGAAGACCTTTGGCTGGCTTTGCCACA
1 TCATGGTAGTCTAAACCATGTGATGAGGAAAGCTAGGTAGAAGACCTTTGGCTGCCTTAGCCACA
*
10507 ACTTAG
66 ACTTAA
* *
10513 TCAAGGTAGAT-TAAACAATGTGATGAGGAAAGCTAGGT
1 TCATGGTAG-TCTAAACCATGTGATGAGGAAAGCTAGGT
10551 GAGAGTACTA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
70 3 0.03
71 88 0.96
72 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (71 bp):
TCATGGTAGTCTAAACCATGTGATGAGGAAAGCTAGGTAGAAGACCTTTGGCTGCCTTAGCCACA
ACTTAA
Found at i:15891 original size:21 final size:22
Alignment explanation
Indices: 15852--15892 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15842 TCAATGCTTT
**
15852 AGGAATGCAAGAGGGATTTCAA
1 AGGAATGCAAGAGCCATTTCAA
15874 AGGAA-GCAAGAGCCATTTC
1 AGGAATGCAAGAGCCATTTC
15893 CAAGAAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (22 bp):
AGGAATGCAAGAGCCATTTCAA
Found at i:20757 original size:4 final size:4
Alignment explanation
Indices: 20748--20774 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20738 CTCTTTGAAA
20748 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
20775 AAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:27895 original size:25 final size:25
Alignment explanation
Indices: 27864--27911 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
27854 CTGTTTTATG
27864 TTTTGCGTCA-AAGAAAAAAAAATAT
1 TTTTGCGTCATAA-AAAAAAAAATAT
27889 TTTTGCGTCATAAAAAAAAAAAT
1 TTTTGCGTCATAAAAAAAAAAAT
27912 TTGTCCCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (25 bp):
TTTTGCGTCATAAAAAAAAAAATAT
Found at i:31705 original size:18 final size:17
Alignment explanation
Indices: 31666--31705 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
31656 CTGCATGCAT
31666 CATAATCTTAATATATG
1 CATAATCTTAATATATG
31683 C-TAATCTTAATATATG
1 CATAATCTTAATATATG
31699 CCATAAT
1 -CATAAT
31706 TTTTTCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.71
17 2 0.10
18 4 0.19
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (17 bp):
CATAATCTTAATATATG
Found at i:38545 original size:21 final size:21
Alignment explanation
Indices: 38521--38566 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
38511 ATGCAGTTCT
*
38521 AGTCAACTGAAGTGAAGTTTC
1 AGTCAACTCAAGTGAAGTTTC
* *
38542 AGTCGATTCAAGTGAAGTTTC
1 AGTCAACTCAAGTGAAGTTTC
38563 AGTC
1 AGTC
38567 GATTGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (21 bp):
AGTCAACTCAAGTGAAGTTTC
Found at i:38567 original size:21 final size:21
Alignment explanation
Indices: 38530--38570 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
38520 TAGTCAACTG
38530 AAGTGAAGTTTCAGTCGATTC
1 AAGTGAAGTTTCAGTCGATTC
38551 AAGTGAAGTTTCAGTCGATT
1 AAGTGAAGTTTCAGTCGATT
38571 GAAAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (21 bp):
AAGTGAAGTTTCAGTCGATTC
Found at i:40421 original size:30 final size:30
Alignment explanation
Indices: 40385--40444 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40375 GCGGCTCCTT
40385 GGGCTTTCTCCTCCAAATCTTCAACAATTC
1 GGGCTTTCTCCTCCAAATCTTCAACAATTC
40415 GGGCTTTCTCCTCCAAATCTTCAACAATTC
1 GGGCTTTCTCCTCCAAATCTTCAACAATTC
40445 TTCAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (30 bp):
GGGCTTTCTCCTCCAAATCTTCAACAATTC
Found at i:43694 original size:23 final size:22
Alignment explanation
Indices: 43664--43709 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
43654 GATGATATCG
43664 CAACTTTGCTTCTCCTTGGTCGA
1 CAACTTTGCTTCTCCTT-GTCGA
43687 CAACTTTGCTTCTCCTTGTCGA
1 CAACTTTGCTTCTCCTTGTCGA
43709 C
1 C
43710 TTGCCTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.13, C:0.33, G:0.15, T:0.39
Consensus pattern (22 bp):
CAACTTTGCTTCTCCTTGTCGA
Found at i:50854 original size:19 final size:18
Alignment explanation
Indices: 50821--50856 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
50811 TTGAGATATT
50821 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
50839 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
50857 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:56129 original size:21 final size:20
Alignment explanation
Indices: 56091--56134 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
56081 TCATGCTTTG
*
56091 CGGCATGGCTGGGTCATGGC
1 CGGCATGGCTGGGCCATGGC
* *
56111 CGGCTATGGCTTGGCCATGTC
1 CGGC-ATGGCTGGGCCATGGC
56132 CGG
1 CGG
56135 GCCATGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.23
Consensus pattern (20 bp):
CGGCATGGCTGGGCCATGGC
Found at i:68857 original size:19 final size:19
Alignment explanation
Indices: 68807--68857 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
68797 TGTAAGATTT
68807 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
68825 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
68844 TTAATAATTAATTA
1 TTAATAATTAATTA
68858 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:69230 original size:13 final size:13
Alignment explanation
Indices: 69212--69237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69202 AAGTTAACAA
69212 CAAAAATCATCAC
1 CAAAAATCATCAC
69225 CAAAAATCATCAC
1 CAAAAATCATCAC
69238 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:70811 original size:22 final size:22
Alignment explanation
Indices: 70762--70812 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
70752 AAATATTACC
* **
70762 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
70784 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
70807 A-AATTA
1 ATAATTA
70813 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:82157 original size:19 final size:19
Alignment explanation
Indices: 82107--82157 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
82097 TGTAAGATTT
82107 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* * *
82125 TAAAAAAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
82144 TTAATAATTAATTA
1 TTAATAATTAATTA
82158 ATTTCAGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:83492 original size:24 final size:24
Alignment explanation
Indices: 83465--83523 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
83455 ACAGGAAATG
83465 CGGGTCGCGACCTGGCCATGGACC
1 CGGGTCGCGACCTGGCCATGGACC
83489 CGGGTCGCGACCTGGCCATGGACC
1 CGGGTCGCGACCTGGCCATGGACC
83513 CGGGTCGCGAC
1 CGGGTCGCGAC
83524 GCGCGATCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.12, C:0.37, G:0.39, T:0.12
Consensus pattern (24 bp):
CGGGTCGCGACCTGGCCATGGACC
Found at i:84703 original size:2 final size:2
Alignment explanation
Indices: 84696--84729 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
84686 AATTACCTAC
84696 TA TA TA TA TA -A 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 TA TA T
84730 CCATTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86827 original size:144 final size:151
Alignment explanation
Indices: 86556--86846 Score: 443
Period size: 144 Copynumber: 2.0 Consensus size: 151
86546 GTTTATCATT
* *
86556 TTTGTATTCATTAAATAGTGAGATTTATTATTATTATTATAAAATAATTATATTATATAGTATAT
1 TTTGTATGCATTAAATAGTGAGA-TTATTATTATTACTATAAAATAATTATATTATATAGTATAT
*
86621 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAACAAGTACACATACCAAACAATACAA
65 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAACAAGCACACATACCAAACAATACAA
86686 AATACAATGAACTATTGAATTC
130 AATACAATGAACTATTGAATTC
*
86708 TTTGTATGCATTAAATAGTGAG-TT-TTATTATTACTATAAAATAATTCTATTATATA-T-TA-T
1 TTTGTATGCATTAAATAGTGAGATTATTATTATTACTATAAAATAATTATATTATATAGTATATT
** *
86768 -TT-TTAATTGTGTGGTTTATTCAATTGAACCTATTAAGGAAGCACACATACCAAATAATACAAA
66 ATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAACAAGCACACATACCAAACAATACAAA
* *
86831 ATGCAATGAATTATTG
131 ATACAATGAACTATTG
86847 GATTTAAATA
Statistics
Matches: 130, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
144 71 0.55
145 2 0.02
146 1 0.01
147 2 0.02
148 1 0.01
149 30 0.23
150 2 0.02
152 21 0.16
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (151 bp):
TTTGTATGCATTAAATAGTGAGATTATTATTATTACTATAAAATAATTATATTATATAGTATATT
ATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAACAAGCACACATACCAAACAATACAAA
ATACAATGAACTATTGAATTC
Found at i:86923 original size:109 final size:109
Alignment explanation
Indices: 86762--86979 Score: 355
Period size: 109 Copynumber: 2.0 Consensus size: 109
86752 TTCTATTATA
* * *
86762 TATTATTTTTAATTGTGTGGTTTATTCAATTGAACCTATTAAGGAAGCACACATACCAAATAATA
1 TATTATTGTTAATTGTGTGGTTTATTCAATTGAACCTATTAAAGAAGCACACATACCAAACAATA
* * *
86827 CAAAATGCAATGAATTATTGGATTTAAATAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
* *
86871 TATTATTGTTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTGTTAATTGTGTGGTTTATTCAATTGAACCTATTAAAGAAGCACACATACCAAACAATA
*
86936 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
86980 AAAATGACTA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (109 bp):
TATTATTGTTAATTGTGTGGTTTATTCAATTGAACCTATTAAAGAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAACACC
Found at i:88708 original size:12 final size:12
Alignment explanation
Indices: 88688--88721 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
88678 ATTTACAGAG
88688 AAAAA-AAAACA
1 AAAAACAAAACA
*
88699 AAAAACAAAAAA
1 AAAAACAAAACA
88711 AAAAACAAAAC
1 AAAAACAAAAC
88722 TTAAAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACAAAACA
Found at i:88720 original size:24 final size:24
Alignment explanation
Indices: 88688--88745 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
88678 ATTTACAGAG
88688 AAAAA-AAAACAAAAAACAAAAAA
1 AAAAACAAAACAAAAAACAAAAAA
** * *
88711 AAAAACAAAACTTAAAACCACAAA
1 AAAAACAAAACAAAAAACAAAAAA
*
88735 AAGAACAAAAC
1 AAAAACAAAAC
88746 GGAAGAAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.03
Consensus pattern (24 bp):
AAAAACAAAACAAAAAACAAAAAA
Found at i:93086 original size:2 final size:2
Alignment explanation
Indices: 93079--93111 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93069 TTCCCAAATC
93079 AT AT AT 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 AT AT AT A
93112 CTACATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.