Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014208.1 Corchorus olitorius cultivar O-4 contig14241, 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: 22689
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:56 original size:26 final size:25
Alignment explanation
Indices: 14--69 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
4 CTTCAGTTTA
14 CTTCAATTGATCCAGGGCGATCTTT
1 CTTCAATTGATCCAGGGCGATCTTT
* *
39 CTTCAAGTTGA-CCTAGGGTGGTCTTT
1 CTTCAA-TTGATCC-AGGGCGATCTTT
65 CTTCA
1 CTTCA
70 CTTTATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
CTTCAATTGATCCAGGGCGATCTTT
Found at i:137 original size:16 final size:16
Alignment explanation
Indices: 106--156 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
96 TCAATGCTCC
* *
106 ATTCTTCAATTATTCA
1 ATTCTCCAATTCTTCA
122 ATGT-TCCAATTCTTCA
1 AT-TCTCCAATTCTTCA
*
138 ATTCTCCAATGCTTCA
1 ATTCTCCAATTCTTCA
154 ATT
1 ATT
157 TACTTCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTCTCCAATTCTTCA
Found at i:139 original size:8 final size:8
Alignment explanation
Indices: 106--156 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
96 TCAATGCTCC
106 ATTCTTCA
1 ATTCTTCA
*
114 ATTATTCA
1 ATTCTTCA
*
122 ATGT-TCCA
1 AT-TCTTCA
130 ATTCTTCA
1 ATTCTTCA
*
138 ATTCTCCA
1 ATTCTTCA
*
146 ATGCTTCA
1 ATTCTTCA
154 ATT
1 ATT
157 TACTTCAAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 1 0.03
8 32 0.94
9 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (8 bp):
ATTCTTCA
Found at i:147 original size:24 final size:24
Alignment explanation
Indices: 97--156 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
87 TGGGGGTATT
* *
97 CAATGCTCC-ATTCTTCAATTATT
1 CAATGTTCCAATTCTTCAATTATC
*
120 CAATGTTCCAATTCTTCAATTCTC
1 CAATGTTCCAATTCTTCAATTATC
144 CAATGCTT-CAATT
1 CAATG-TTCCAATT
157 TACTTCAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.25
24 22 0.69
25 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.42
Consensus pattern (24 bp):
CAATGTTCCAATTCTTCAATTATC
Found at i:366 original size:37 final size:38
Alignment explanation
Indices: 298--375 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 38
288 GTGGTTTAAG
298 TTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGAAAA
1 TTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGAAAA
*
336 TTTCCTAAAGGTGATCC-AGTGCGGTCAATCAAGAAAA
1 TTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGAAAA
373 TTT
1 TTT
376 ACAGTGGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 23 0.59
38 16 0.41
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (38 bp):
TTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGAAAA
Found at i:448 original size:54 final size:54
Alignment explanation
Indices: 346--458 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
336 TTTCCTAAAG
* *
346 GTGATCCAGTGCGGTCAATCAAGAAAATTTACAGTGGTTTAAGTTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGGTTTAAGCTTATCTTCAA
* * * * * *
400 GTGATCCAGTACGGTTAGTCAAGGAAGTTTTCAG-GGATTTAGGCTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGG-TTTAAGCTTATCTTCAA
454 GTGAT
1 GTGAT
459 TCGGTGAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (54 bp):
GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGGTTTAAGCTTATCTTCAA
Found at i:555 original size:42 final size:42
Alignment explanation
Indices: 456--659 Score: 286
Period size: 42 Copynumber: 4.9 Consensus size: 42
446 ATCTTCAAGT
* *
456 GATTCGGTGAATCAGATGACTCGAGGTAGCATCTTCAA--GT
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
* * *
496 GATTTGGTTAATCAGATGACTCGGGGTAGCATCTTCAAGCAG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
* **
538 GATTTGGTGAATCAGATGACTCGGGGTATTATCTTCAAGCGG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
* *
580 GATTCGGTGAATCAGATGACTCGGTGTAGCATCTTCAAGTGG
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
**
622 GATTCGGTGAATCAGATGACTCGATGTAGCATCTTCAA
1 GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAA
660 TATTGGAATT
Statistics
Matches: 147, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 35 0.24
42 112 0.76
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
GATTCGGTGAATCAGATGACTCGGGGTAGCATCTTCAAGCGG
Found at i:1081 original size:26 final size:26
Alignment explanation
Indices: 1052--1131 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
1042 GGCATTAGGG
1052 TCAC-CTAGGGGGCATTTTGGTCATTT
1 TCACACTA-GGGGCATTTTGGTCATTT
* **
1078 TCACACTAAGGGCATCCTGGTCATTT
1 TCACACTAGGGGCATTTTGGTCATTT
* * *
1104 GCACATTCAGGGCCATTTTGGTCATTT
1 TCACACT-AGGGGCATTTTGGTCATTT
1131 T
1 T
1132 AAGTCCACTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
26 24 0.57
27 18 0.43
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
TCACACTAGGGGCATTTTGGTCATTT
Found at i:8021 original size:77 final size:77
Alignment explanation
Indices: 7894--8047 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
7884 AGCCGAAATC
7894 TGAAAAATATCTAAGAAAAAATTGTGCATTGCTATTTGCTAGAAATGCGAACTTCATTGAGGAAA
1 TGAAAAATATCTAAGAAAAAATTGTGCATTGCTATTTGCTAGAAATGCGAACTTCATTGAGGAAA
7959 TTTATCAAACAG
66 TTTATCAAACAG
*
7971 TGAAAAATATCTAAGAAAAAATTGTGCATTGCTATTTGCTAGAAATGCGAATTTCATTGAGGAAA
1 TGAAAAATATCTAAGAAAAAATTGTGCATTGCTATTTGCTAGAAATGCGAACTTCATTGAGGAAA
8036 TTTATCAAACAG
66 TTTATCAAACAG
8048 GTATTCTTGA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (77 bp):
TGAAAAATATCTAAGAAAAAATTGTGCATTGCTATTTGCTAGAAATGCGAACTTCATTGAGGAAA
TTTATCAAACAG
Found at i:8839 original size:24 final size:25
Alignment explanation
Indices: 8812--8863 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
8802 GTTCTCCATT
* *
8812 GTTGAGAAAGTGA-TTTGGATTTGA
1 GTTGAGAAACTAAGTTTGGATTTGA
*
8836 GTTGGGAAACTAAGTTTGGATTTGA
1 GTTGAGAAACTAAGTTTGGATTTGA
8861 GTT
1 GTT
8864 TAGAGCAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.33, T:0.38
Consensus pattern (25 bp):
GTTGAGAAACTAAGTTTGGATTTGA
Found at i:9197 original size:100 final size:100
Alignment explanation
Indices: 9024--9224 Score: 357
Period size: 100 Copynumber: 2.0 Consensus size: 100
9014 AGCACGTGCA
*
9024 TATCACGCAAACGGATCCGTCTGAATTTATCCTGAAATGACACAAGCCGATAACATTAGATTCTC
1 TATCACGCAAACGGATCCGTCTGAATTTATCCTGAAATGACACAACCCGATAACATTAGATTCTC
*
9089 AATTGACACAAGAGGTAACTGTAGATTCTGAATTG
66 AATTGACACAAGAGGTAACTGTAGATCCTGAATTG
* *
9124 TATCACGCAAACGGATTCGTCTGAATTTATCCTGAAATGACACAACCCGATAACGTTAGATTCTC
1 TATCACGCAAACGGATCCGTCTGAATTTATCCTGAAATGACACAACCCGATAACATTAGATTCTC
*
9189 AATTGACACAAGAGTTAACTGTAGATCCTGAATTG
66 AATTGACACAAGAGGTAACTGTAGATCCTGAATTG
9224 T
1 T
9225 CGTTTGTGGC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (100 bp):
TATCACGCAAACGGATCCGTCTGAATTTATCCTGAAATGACACAACCCGATAACATTAGATTCTC
AATTGACACAAGAGGTAACTGTAGATCCTGAATTG
Found at i:10851 original size:20 final size:20
Alignment explanation
Indices: 10826--10926 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 20
10816 GAAGAGCTCT
10826 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* *
10846 GCGGT-AAG-GGGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
10863 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* *
10883 GCGGT-AAG-GGGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
*
10900 ACGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
*
10920 ACGGTAA
1 GCGGTAA
10927 GGAGAGCTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
17 11 0.17
18 18 0.27
19 18 0.27
20 19 0.29
ACGTcount: A:0.25, C:0.19, G:0.41, T:0.16
Consensus pattern (20 bp):
GCGGTAAAGAGGGTGCTACC
Found at i:10947 original size:37 final size:37
Alignment explanation
Indices: 10700--10949 Score: 250
Period size: 37 Copynumber: 6.7 Consensus size: 37
10690 GCAGTGATTC
* * * * * *
10700 GTAAGGAGAGCTCTACAGTAAAGAGGATGTTGCCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* * * * ** * *
10737 GTAAGGAGAGTTTCTACGATGAAGAGGGTGCCGCAGCA
1 GTAAGGAGAG-CTCTGCGGTAAAGAGGGTGCTACCGCG
* * * *
10775 GTAAGGAGAGCTCAGCGGTAAAGAGGGTGTTATCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
*
10812 AT-AGGAAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGG-AGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
*
10849 GTAAGGGGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* * *
10886 GTAAGGGGAGCTCTACGGTAAAGAGGGTGCTACCACG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* *
10923 GTAAGGAGAGCTCTGCGATGAAGAGGG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGG
10950 CTATCGCAAA
Statistics
Matches: 179, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
36 3 0.02
37 144 0.80
38 32 0.18
ACGTcount: A:0.28, C:0.16, G:0.38, T:0.17
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
Found at i:11025 original size:30 final size:30
Alignment explanation
Indices: 10977--11037 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
10967 TTGCTGCAAC
* * *
10977 GTGTTTGGTAAAGCGAGTCTTGCGGCAAAA
1 GTGTTTCGCAAAGCGAGTCATGCGGCAAAA
* *
11007 GTGTTTCGCAAAGTGAGTCATGCGGTAAAA
1 GTGTTTCGCAAAGCGAGTCATGCGGCAAAA
11037 G
1 G
11038 GGGTGCTACC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (30 bp):
GTGTTTCGCAAAGCGAGTCATGCGGCAAAA
Found at i:14061 original size:27 final size:27
Alignment explanation
Indices: 14021--14146 Score: 120
Period size: 27 Copynumber: 4.9 Consensus size: 27
14011 GCGGCTTATG
**
14021 GCTCCCGCTCTTGGGACTTATGCCGTA
1 GCTCCCGCGATTGGGACTTATGCCGTA
*
14048 GCTCCCGCGATTGGGACTTATGACGTA
1 GCTCCCGCGATTGGGACTTATGCCGTA
*
14075 GCT--C-CGA---GGACTTATGTCGTA
1 GCTCCCGCGATTGGGACTTATGCCGTA
* * **
14096 GCTCCCGCGATTGGGCCTTAAGTTGTA
1 GCTCCCGCGATTGGGACTTATGCCGTA
* *
14123 GCTCCCGCGGTTGGGACTCATGCC
1 GCTCCCGCGATTGGGACTTATGCC
14147 AAAGCCTCTT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
21 16 0.20
23 1 0.01
24 6 0.08
25 1 0.01
27 56 0.70
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.27
Consensus pattern (27 bp):
GCTCCCGCGATTGGGACTTATGCCGTA
Found at i:14087 original size:21 final size:21
Alignment explanation
Indices: 14061--14100 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
14051 CCCGCGATTG
14061 GGACTTATGACGTAGCTCCGA
1 GGACTTATGACGTAGCTCCGA
*
14082 GGACTTATGTCGTAGCTCC
1 GGACTTATGACGTAGCTCC
14101 CGCGATTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (21 bp):
GGACTTATGACGTAGCTCCGA
Found at i:14124 original size:48 final size:48
Alignment explanation
Indices: 14034--14127 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
14024 CCCGCTCTTG
*
14034 GGACTTATGCCGTAGCTCCCGCGATTGGGACTTATGACGTAGCTCCGA
1 GGACTTATGCCGTAGCTCCCGCGATTGGGACTTAAGACGTAGCTCCGA
* * **
14082 GGACTTATGTCGTAGCTCCCGCGATTGGGCCTTAAGTTGTAGCTCC
1 GGACTTATGCCGTAGCTCCCGCGATTGGGACTTAAGACGTAGCTCC
14128 CGCGGTTGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.28
Consensus pattern (48 bp):
GGACTTATGCCGTAGCTCCCGCGATTGGGACTTAAGACGTAGCTCCGA
Found at i:14753 original size:20 final size:20
Alignment explanation
Indices: 14728--14865 Score: 96
Period size: 19 Copynumber: 7.3 Consensus size: 20
14718 GAAGAGTTCT
*
14728 GCGGTAAAGAAGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* *
14748 GCGGT-AAG-GGGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
*
14765 GTGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
* **
14785 GCGGT-AAG-GGGAGCT-TT
1 GCGGTAAAGAGGGTGCTACC
* * *
14802 ACGGTAAAAAGGGTGTTACC
1 GCGGTAAAGAGGGTGCTACC
* * *
14822 GCGGT-AAG-GAGAGCT-CT
1 GCGGTAAAGAGGGTGCTACC
14839 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGTGCTACC
14859 GCGGTAA
1 GCGGTAA
14866 GGAGAGCTAT
Statistics
Matches: 84, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
17 15 0.18
18 23 0.27
19 24 0.29
20 22 0.26
ACGTcount: A:0.25, C:0.17, G:0.40, T:0.18
Consensus pattern (20 bp):
GCGGTAAAGAGGGTGCTACC
Found at i:14842 original size:17 final size:18
Alignment explanation
Indices: 14818--14874 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
14808 AAAAGGGTGT
14818 TACCGCGGTAAGGAGAGC
1 TACCGCGGTAAGGAGAGC
* * *
14836 T-CTGCGGTAAAGAGGGTGC
1 TACCGCGGT-AAG-GAGAGC
14855 TACCGCGGTAAGGAGAGC
1 TACCGCGGTAAGGAGAGC
14873 TA
1 TA
14875 TGTGATGAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 6 0.20
18 10 0.33
19 8 0.27
20 6 0.20
ACGTcount: A:0.26, C:0.19, G:0.39, T:0.16
Consensus pattern (18 bp):
TACCGCGGTAAGGAGAGC
Found at i:14888 original size:37 final size:37
Alignment explanation
Indices: 14602--14873 Score: 249
Period size: 37 Copynumber: 7.3 Consensus size: 37
14592 GCAATGTTTT
* * * * * *
14602 GTAAGGAGAACTTTACGGTAAAGAGGATGCTGCCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* * * * * *
14639 GTACGGAGAGTTTCTGCAGTGAAGAGGGTG-TCGCCGCA
1 GTAAGGAGAG-CTCTGCGGTAAAGAGGGTGCT-ACCGCG
* * * * * * **
14677 GTAAGGAAAGCTCAGTGGTAAAGAGGCTGTTATCGTA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* * *
14714 GTAAGAAGAGTTCTGCGGTAAAGAAGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* *
14751 GTAAGGGGAGCTCTGTGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
* * * * *
14788 GTAAGGGGAGCTTTACGGTAAAAAGGGTGTTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
14825 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
14862 GTAAGGAGAGCT
1 GTAAGGAGAGCT
14874 ATGTGATGAA
Statistics
Matches: 187, Mismatches: 45, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
37 159 0.85
38 28 0.15
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.20
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
Found at i:14964 original size:30 final size:29
Alignment explanation
Indices: 14892--14970 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
14882 AAGAGGGCTA
* *
14892 TCGCAAAGTGGGAT-TTGCTGCAAAGTGTT
1 TCGCAAAGTGAG-TCTTGCGGCAAAGTGTT
* * *
14921 TGGTAAAGCGAGTCTTGCGGCAAATGTGTT
1 TCGCAAAGTGAGTCTTGCGGCAAA-GTGTT
14951 TCGCAAAGTGAGTCTTGCGG
1 TCGCAAAGTGAGTCTTGCGG
14971 TAAAAGGGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 1 0.03
29 17 0.43
30 22 0.55
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (29 bp):
TCGCAAAGTGAGTCTTGCGGCAAAGTGTT
Found at i:17278 original size:16 final size:15
Alignment explanation
Indices: 17240--17281 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
17230 ACAGAGGTTG
*
17240 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
17255 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
17270 ACTAGAAAACAA
1 AC-AGAAAACAA
17282 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.