Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022357.1 Corchorus olitorius cultivar O-4 contig22390, 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: 18933
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1151 original size:22 final size:23
Alignment explanation
Indices: 1126--1206 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 23
1116 ATTTTCTGAC
1126 TTTGGGCTTTTC-TTTTATTTAA
1 TTTGGGCTTTTCTTTTTATTTAA
*
1148 TTTGGGCCCTTTTCTTTATTCTTTACA
1 TTTGGG--CTTTTCTTT-TTATTTA-A
* * *
1175 GTTGGGC-TTCCTTTTTATATAA
1 TTTGGGCTTTTCTTTTTATTTAA
1197 TTTGGGCTTT
1 TTTGGGCTTT
1207 GTTGAGAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
22 13 0.28
23 7 0.15
24 12 0.26
25 3 0.06
26 6 0.13
27 6 0.13
ACGTcount: A:0.12, C:0.15, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTGGGCTTTTCTTTTTATTTAA
Found at i:1875 original size:52 final size:52
Alignment explanation
Indices: 1818--1953 Score: 236
Period size: 52 Copynumber: 2.6 Consensus size: 52
1808 TCAATTTAAG
1818 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTATTCAATCCAGCTC
1 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTATTCAATCCAGCTC
* * * *
1870 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAGGTATTCCATTCAGCTC
1 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTATTCAATCCAGCTC
1922 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTT
1 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTT
1954 TAAGTTTTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTCAAAGTATTCAATCCAGCTC
Found at i:2018 original size:36 final size:37
Alignment explanation
Indices: 1922--2112 Score: 130
Period size: 36 Copynumber: 5.2 Consensus size: 37
1912 CATTCAGCTC
* *
1922 TTTTCAAATTGGGAAAGTTCCCA-ACAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATTCAAGTTTTAAAG
* *
1958 TTTTAAAATCGGGAAAGTTCCCATTC-AGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATTCAAGTTTT-AAAG
* ***
1995 -TTTCAAATTGGGAAAGTTCCCATT-AGGTTTTAGTTTTTTT
1 TTTTCAAATTGGGAAAGTTCCCATTCAAGTTTTA-----AAG
* * *
2035 TTTTTAAATTGGGAGAGTTCCCA-TCAGGTTTT--AG
1 TTTTCAAATTGGGAAAGTTCCCATTCAAGTTTTAAAG
*
2069 TTTTCAATTTAGGGAAAGTTCCCA-TCAA-TTTTCAAAG
1 TTTTCAAATT-GGGAAAGTTCCCATTCAAGTTTT-AAAG
*
2106 TATTCAA
1 TTTTCAA
2113 TTTAGCCGGT
Statistics
Matches: 122, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
34 12 0.10
35 16 0.13
36 54 0.44
37 12 0.10
40 1 0.01
41 27 0.22
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATTCAAGTTTTAAAG
Found at i:5138 original size:14 final size:13
Alignment explanation
Indices: 5114--5158 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
5104 TTTTCCAAAA
*
5114 AAAAAATGTTTTC
1 AAAAAAGGTTTTC
5127 AAGAAAAGGTTTTC
1 AA-AAAAGGTTTTC
*
5141 AAAAATGAGTTTTC
1 AAAAAAG-GTTTTC
5155 AAAA
1 AAAA
5159 GGTTTTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (13 bp):
AAAAAAGGTTTTC
Found at i:5863 original size:21 final size:20
Alignment explanation
Indices: 5823--5861 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5813 GTCCCTAAAT
* *
5823 AAAAATTGTTTTTTCAAAAG
1 AAAAAATGTTTTCTCAAAAG
5843 AAAAAATGTTTTCTCAAAA
1 AAAAAATGTTTTCTCAAAA
5862 AGGTTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
AAAAAATGTTTTCTCAAAAG
Found at i:6278 original size:13 final size:13
Alignment explanation
Indices: 6260--6285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6250 GATTGTGAAT
6260 GTTTTGAAAATGA
1 GTTTTGAAAATGA
6273 GTTTTGAAAATGA
1 GTTTTGAAAATGA
6286 ATTGCATTCC
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GTTTTGAAAATGA
Found at i:7235 original size:35 final size:35
Alignment explanation
Indices: 7196--7479 Score: 255
Period size: 35 Copynumber: 8.6 Consensus size: 35
7186 TCAAGTTGAC
*
7196 CCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
* **
7231 CCAGGGCGATCTTTCTTCAGTTAGCTTCAATTGAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
* * *
7266 CCAGAGCGATCTTGCTTCA---AG-TT-GA-C---
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
* *
7292 CCAGGGCGGTCTTTCCTCAGTTAGTTTCAATCAAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
* * *
7327 CCAGGGCGATCATTCTTCAGTTTA-CTTCAATCGAT
1 CCAGGGCGATCTTTCTTCAG-TTAGTTTCAATCAAT
* * *
7362 CCAGAGCGATCTTGCTTCA---AG-TT-GA-C---
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
*
7388 CCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
* *
7423 CCAGGGCGATCTTTCTTCAGTTAGTTTCAACCGAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
*
7458 CCAGGGCGATCATTCTTCAGTT
1 CCAGGGCGATCTTTCTTCAGTT
7480 TACTTTAATT
Statistics
Matches: 199, Mismatches: 30, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
26 31 0.16
29 5 0.03
30 6 0.03
31 7 0.04
32 4 0.02
35 143 0.72
36 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (35 bp):
CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCAAT
Found at i:7282 original size:25 final size:26
Alignment explanation
Indices: 7254--7304 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
7244 TCTTCAGTTA
*
7254 GCTTCAA-TTGATCCAGAGCGATCTT
1 GCTTCAAGTTGACCCAGAGCGATCTT
* *
7279 GCTTCAAGTTGACCCAGGGCGGTCTT
1 GCTTCAAGTTGACCCAGAGCGATCTT
7305 TCCTCAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (26 bp):
GCTTCAAGTTGACCCAGAGCGATCTT
Found at i:7296 original size:61 final size:61
Alignment explanation
Indices: 7231--7345 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
7221 TTCAATCAAT
* **
7231 CCAGGGCGATCTTTCTTCAGTTAGCTTCAATTGATCCAGAGCGATC-TTGCTTCAAGTTGAC
1 CCAGGGCGATCTTTCCTCAGTTAGCTTCAATCAATCCAGAGCGATCATT-CTTCAAGTTGAC
* * *
7292 CCAGGGCGGTCTTTCCTCAGTTAGTTTCAATCAATCCAGGGCGATCATTCTTCA
1 CCAGGGCGATCTTTCCTCAGTTAGCTTCAATCAATCCAGAGCGATCATTCTTCA
7346 GTTTACTTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
61 45 0.96
62 2 0.04
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (61 bp):
CCAGGGCGATCTTTCCTCAGTTAGCTTCAATCAATCCAGAGCGATCATTCTTCAAGTTGAC
Found at i:7317 original size:96 final size:96
Alignment explanation
Indices: 7177--7476 Score: 514
Period size: 96 Copynumber: 3.1 Consensus size: 96
7167 AATCTAAGTT
7177 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
1 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
*
7242 TTTCTTCAGTTAGCTTCAATTGATCCAGAGC
66 TTTCTTCAGTTAGCTTCAATCGATCCAGAGC
*
7273 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCCTCAGTTAGTTTCAATCAATCCAGGGCGATC
1 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
*
7338 ATTCTTCAGTTTA-CTTCAATCGATCCAGAGC
66 TTTCTTCAG-TTAGCTTCAATCGATCCAGAGC
7369 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
1 GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
* * *
7434 TTTCTTCAGTTAGTTTCAACCGATCCAGGGC
66 TTTCTTCAGTTAGCTTCAATCGATCCAGAGC
7465 GATCATT-CTTCA
1 GATC-TTGCTTCA
7477 GTTTACTTTA
Statistics
Matches: 193, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
95 3 0.02
96 185 0.96
97 5 0.03
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (96 bp):
GATCTTGCTTCAAGTTGACCCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAATCCAGGGCGATC
TTTCTTCAGTTAGCTTCAATCGATCCAGAGC
Found at i:7494 original size:35 final size:35
Alignment explanation
Indices: 7388--7502 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
7378 TCAAGTTGAC
* *
7388 CCAGGGCGGTCTTTCTTCAGTTAGTTTCAATCAAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCGAT
*
7423 CCAGGGCGATCTTTCTTCAGTTAGTTTCAACCGAT
1 CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCGAT
* * *
7458 CCAGGGCGATCATTCTTCAGTTTACTTT-AATTGAT
1 CCAGGGCGATCTTTCTTCAG-TTAGTTTCAATCGAT
*
7493 CCAGAGCGAT
1 CCAGGGCGAT
7503 TTTTTTTCTT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 65 0.92
36 6 0.08
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (35 bp):
CCAGGGCGATCTTTCTTCAGTTAGTTTCAATCGAT
Found at i:7600 original size:22 final size:22
Alignment explanation
Indices: 7572--7650 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
7562 GGTGGCCTTT
* *
7572 CTTCAATTTTAATACATCAATG
1 CTTCAATTTCAATACATCAAAG
* *
7594 CTTCAATTTCAATTCTTCAAAG
1 CTTCAATTTCAATACATCAAAG
* * *
7616 CTTCAATTTCAATTCTTCAAAA
1 CTTCAATTTCAATACATCAAAG
*
7638 CATCAATTTCAAT
1 CTTCAATTTCAAT
7651 TCTTCAAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (22 bp):
CTTCAATTTCAATACATCAAAG
Found at i:7633 original size:14 final size:15
Alignment explanation
Indices: 7588--7681 Score: 54
Period size: 14 Copynumber: 6.3 Consensus size: 15
7578 TTTTAATACA
*
7588 TCAATGCTTCAA-TT
1 TCAATTCTTCAAGTT
*
7602 TCAATTCTTCAAAGCT
1 TCAATTCTTC-AAGTT
*
7618 TCAA-T-TTCAATTCT
1 TCAATTCTTCAAGT-T
** *
7632 TCAAAACATCAA-TT
1 TCAATTCTTCAAGTT
7646 TCAATTCTTCAAGATT
1 TCAATTCTTCAAG-TT
7662 TCAAATT-TTCAAGTAT
1 TC-AATTCTTCAAGT-T
7678 TCAA
1 TCAA
7682 AACTTCAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
13 2 0.03
14 27 0.44
15 7 0.11
16 22 0.35
17 4 0.06
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.40
Consensus pattern (15 bp):
TCAATTCTTCAAGTT
Found at i:7651 original size:22 final size:22
Alignment explanation
Indices: 7596--7657 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
7586 CATCAATGCT
* *
7596 TCAATTTCAATTCTTCAAAGCT
1 TCAATTTCAATTCTTCAAAACA
7618 TCAATTTCAATTCTTCAAAACA
1 TCAATTTCAATTCTTCAAAACA
7640 TCAATTTCAATTCTTCAA
1 TCAATTTCAATTCTTCAA
7658 GATTTCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (22 bp):
TCAATTTCAATTCTTCAAAACA
Found at i:7665 original size:22 final size:21
Alignment explanation
Indices: 7594--7689 Score: 102
Period size: 22 Copynumber: 4.3 Consensus size: 21
7584 TACATCAATG
7594 CTTCAATTTCAATTCTTCAAA
1 CTTCAATTTCAATTCTTCAAA
7615 GCTTCAATTTCAATTCTTCAAAA
1 -CTTCAATTTCAATTCTTC-AAA
*
7638 CATCAATTTCAATTCTTCAAGA
1 CTTCAATTTCAATTCTTCAA-A
* * *
7660 TTTCAAATTTTCAAGTATTCAAAA
1 CTTC-AA-TTTCAATTCTTC-AAA
7684 CTTCAA
1 CTTCAA
7690 ATTCTGAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
21 2 0.03
22 38 0.60
23 7 0.11
24 14 0.22
25 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (21 bp):
CTTCAATTTCAATTCTTCAAA
Found at i:7680 original size:24 final size:24
Alignment explanation
Indices: 7600--7713 Score: 74
Period size: 24 Copynumber: 4.9 Consensus size: 24
7590 AATGCTTCAA
* * *
7600 TTTCAATTCTTCAAAGCTTC-AA-
1 TTTCAAGTATTCAAAACTTCAAAT
* * *
7622 TTTCAATTCTTCAAAACATC-AA-
1 TTTCAAGTATTCAAAACTTCAAAT
* * * *
7644 TTTCAATTCTTCAAGATTTCAAAT
1 TTTCAAGTATTCAAAACTTCAAAT
7668 TTTCAAGTATTCAAAACTTCAAAT
1 TTTCAAGTATTCAAAACTTCAAAT
* * * *
7692 TCTGAAATATTCAAAGCTTCAA
1 TTTCAAGTATTCAAAACTTCAA
7714 TTCTCCAATG
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 37 0.48
23 2 0.03
24 38 0.49
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (24 bp):
TTTCAAGTATTCAAAACTTCAAAT
Found at i:7682 original size:16 final size:17
Alignment explanation
Indices: 7643--7674 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7633 CAAAACATCA
7643 ATTTC-AATTCTTCAAG
1 ATTTCAAATTCTTCAAG
7659 ATTTCAAATT-TTCAAG
1 ATTTCAAATTCTTCAAG
7675 TATTCAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTTCAAATTCTTCAAG
Found at i:7863 original size:54 final size:54
Alignment explanation
Indices: 7783--8135 Score: 406
Period size: 54 Copynumber: 6.6 Consensus size: 54
7773 TCAAGTGGCG
* *
7783 TAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTATAATGGTT
1 TAAGTTTATCTTC-AAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
* * * **
7838 TAGGTTTAACTTCAAGTGATCCAGTGCGATCGTTC-AGAAAG-TTACCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTA-CAGTGGTT
** * * *
7891 TAAACTTATCATCAAGCGATCTAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
** * * * *
7945 TAAGTCAATCTTCGAGTGATACAGTGCGGTCAGTCAAGAAAGTTTACAATGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
* **
7999 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCGATCAATCAAGTTTACAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
* * * ** *
8053 TAAATTTATCTTCAAGTGATCCAGCGCGATCGTTC-AGAAAGTTTCCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
* *
8106 TAAATTTATCTTTAAGTGATCCAGTGCGGT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGT
8136 TAGTCAAGGA
Statistics
Matches: 248, Mismatches: 47, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
52 3 0.01
53 79 0.32
54 152 0.61
55 14 0.06
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (54 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTT
Found at i:8094 original size:161 final size:161
Alignment explanation
Indices: 7790--8178 Score: 464
Period size: 161 Copynumber: 2.4 Consensus size: 161
7780 GCGTAAGTTT
* * *
7790 ATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTATAATGGTTTAGGTTTAACTTCAAGT
1 ATCTTC-AAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACAATGGTTTAGGTTTATCTTCAAGT
* * * *
7855 GATCCAGTGCGATCGTTCAGAAAGTTACCAGTGGTTTAAACTTATCATCAAGCGATCTAGTGCGG
65 GATCCAGTGCGATCGATCAGAAAGTTACCAGTGGTTTAAACTTATCATCAAGCGATCCAGCGCGA
*
7920 TCAATCAAGAAAGTTTACAGTGGTTTAAGTCA
130 TCAATCAAGAAAGTTTACAGTGGTTTAAATCA
* * *
7952 ATCTTCGAGTGATACAGTGCGGTCAGTCAAGAAAGTTTACAATGGTTTAAGTTTATCTTCAAGTG
1 ATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACAATGGTTTAGGTTTATCTTCAAGTG
* * * *
8017 ATCCAGTGCGGTCGATCA-ATCAAGTTTA-CAGTGGTTTAAATTTATCTTCAAGTGATCCAGCGC
66 ATCCAGTGCGATCGATCAGA--AAG-TTACCAGTGGTTTAAACTTATCATCAAGCGATCCAGCGC
** * **
8080 GATCGTTC-AGAAAGTTTCCAGTGGTTTAAATTT
128 GATCAATCAAGAAAGTTTACAGTGGTTTAAATCA
* * * ** *
8113 ATCTTTAAGTGATCCAGTGCGGTTAGTCAAGGAAGATTT-CAAT-GACTGGGTTTATCTTCAAGT
1 ATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAG-TTTACAATGGTTTAGGTTTATCTTCAAGT
8176 GAT
65 GAT
8179 TCGGCTTCAA
Statistics
Matches: 194, Mismatches: 29, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
160 20 0.10
161 124 0.64
162 47 0.24
163 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (161 bp):
ATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTACAATGGTTTAGGTTTATCTTCAAGTG
ATCCAGTGCGATCGATCAGAAAGTTACCAGTGGTTTAAACTTATCATCAAGCGATCCAGCGCGAT
CAATCAAGAAAGTTTACAGTGGTTTAAATCA
Found at i:8188 original size:15 final size:15
Alignment explanation
Indices: 8168--8197 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8158 CTGGGTTTAT
8168 CTTCAAGTGATTCGG
1 CTTCAAGTGATTCGG
8183 CTTCAAGTGATTCGG
1 CTTCAAGTGATTCGG
8198 TAAGTCAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (15 bp):
CTTCAAGTGATTCGG
Found at i:14791 original size:21 final size:21
Alignment explanation
Indices: 14765--14835 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
14755 CGCCCATTCA
14765 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGTTAAGC
14786 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGTTAAGC
* *
14807 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGTTAAGC
14828 CCGTGCCA
1 CCGTGCCA
14836 TCGCCATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (21 bp):
CCGTGCCACCACCGGTTAAGC
Found at i:15241 original size:15 final size:14
Alignment explanation
Indices: 15221--15250 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15211 ATCTTTTTAA
15221 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
15236 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
15250 T
1 T
15251 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:16729 original size:29 final size:31
Alignment explanation
Indices: 16676--16736 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
16666 CGAAGTTCGT
*
16676 ATTTGAAGACCATTTGAAGACTTATTTGAAG
1 ATTTGAAGACCATTTGAAGACTTATTTCAAG
*
16707 ATTTGAAGA-C-TTTGAAGATTTATTTCAAG
1 ATTTGAAGACCATTTGAAGACTTATTTCAAG
16736 A
1 A
16737 GGAAGAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.64
30 1 0.04
31 9 0.32
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
ATTTGAAGACCATTTGAAGACTTATTTCAAG
Done.