Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017279.1 Corchorus olitorius cultivar O-4 contig17312, 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: 41156
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:36 original size:21 final size:22
Alignment explanation
Indices: 10--52 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1 GTTCTTTTG
10 TCTTTTTCTAACT-TTTTCTTT
1 TCTTTTTCTAACTCTTTTCTTT
*
31 TCTTTTTCTAATTCTTTTCTTT
1 TCTTTTTCTAACTCTTTTCTTT
53 CATTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTTTTTCTAACTCTTTTCTTT
Found at i:58 original size:21 final size:21
Alignment explanation
Indices: 13--58 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3 TCTTTTGTCT
*
13 TTTTCTAACTTTTTCTTTTCT
1 TTTTCTAACTTTTTCTTTTCA
*
34 TTTTCTAATTCTTTTC-TTTCA
1 TTTTCTAACT-TTTTCTTTTCA
55 TTTT
1 TTTT
59 TTCTTTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTAACTTTTTCTTTTCA
Found at i:3028 original size:12 final size:12
Alignment explanation
Indices: 3013--3233 Score: 74
Period size: 12 Copynumber: 19.2 Consensus size: 12
3003 TAAAAAAAGT
*
3013 AATAGACAAATA
1 AATAGATAAATA
*
3025 AATAAATAAATA
1 AATAGATAAATA
*
3037 AATAGAAAAATA
1 AATAGATAAATA
*
3049 AGTA-A-AAAT-
1 AATAGATAAATA
3058 AATAGATAAATAA
1 AATAGATAAAT-A
*
3071 AAAAGATAAATA
1 AATAGATAAATA
** * *
3083 GGTATATAGAT-
1 AATAGATAAATA
3094 AATAAGATAAATA
1 AAT-AGATAAATA
** * *
3107 GTTAGGTAAAAA
1 AATAGATAAATA
* *
3119 AAAAG-TAGAT-
1 AATAGATAAATA
3129 AATAG-TAAATA
1 AATAGATAAATA
3140 AATAGAT-AATA
1 AATAGATAAATA
** * *
3151 GCTAAATTAATA
1 AATAGATAAATA
3163 AATA-A-AAGGATA
1 AATAGATAA--ATA
3175 AATAG-TAAATA
1 AATAGATAAATA
*
3186 AATTGAT-AATA
1 AATAGATAAATA
** * *
3197 GTTAAATTAATA
1 AATAGATAAATA
*
3209 AATA-AAAATATA
1 AATAGATAA-ATA
3221 AATAG-TAAATA
1 AATAGATAAATA
3232 AA
1 AA
3234 AAAAAATCTT
Statistics
Matches: 149, Mismatches: 43, Indels: 35
0.66 0.19 0.15
Matches are distributed among these distances:
9 3 0.02
10 14 0.09
11 44 0.30
12 75 0.50
13 13 0.09
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.25
Consensus pattern (12 bp):
AATAGATAAATA
Found at i:3029 original size:4 final size:4
Alignment explanation
Indices: 3020--3082 Score: 56
Period size: 4 Copynumber: 15.2 Consensus size: 4
3010 AGTAATAGAC
* * *
3020 AAAT AAAT AAAT AAAT AAAT AGAA- AAAT AAGT AAAA ATAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT
*
3069 AAAA AAGAT AAAT A
1 AAAT AA-AT AAAT A
3083 GGTATATAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
3 2 0.04
4 37 0.79
5 8 0.17
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:3162 original size:19 final size:18
Alignment explanation
Indices: 3124--3167 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
3114 AAAAAAAAAG
3124 TAGATAATAGTAAATAAA
1 TAGATAATAGTAAATAAA
*
3142 TAGATAATAGCTAAATTAA
1 TAGATAATAG-TAAATAAA
*
3161 TAAATAA
1 TAGATAA
3168 AAGGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (18 bp):
TAGATAATAGTAAATAAA
Found at i:3165 original size:27 final size:27
Alignment explanation
Indices: 3134--3214 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
3124 TAGATAATAG
*
3134 TAAATAAATAGATAATAGCTAAATTAA
1 TAAATAAATAGATAATAGATAAATTAA
*
3161 TAAATAAA-AG------GATAAA-TAG
1 TAAATAAATAGATAATAGATAAATTAA
* *
3180 TAAATAAATTGATAATAGTTAAATTAA
1 TAAATAAATAGATAATAGATAAATTAA
3207 TAAATAAA
1 TAAATAAA
3215 AATATAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
19 10 0.24
20 6 0.15
26 7 0.17
27 18 0.44
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (27 bp):
TAAATAAATAGATAATAGATAAATTAA
Found at i:3185 original size:46 final size:46
Alignment explanation
Indices: 3125--3233 Score: 175
Period size: 46 Copynumber: 2.4 Consensus size: 46
3115 AAAAAAAAGT
3125 AGAT-AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
* * *
3170 GGATAAATAGTAAATAAATTGATAATAGTTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
*
3216 ATATAAATAGTAAATAAA
1 AGATAAATAGTAAATAAA
3234 AAAAAATCTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
45 3 0.05
46 55 0.95
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.28
Consensus pattern (46 bp):
AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
Found at i:3193 original size:19 final size:19
Alignment explanation
Indices: 3161--3203 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3151 GCTAAATTAA
3161 TAAATAAAAGGATAAATAG-
1 TAAATAAAAGGAT-AATAGT
**
3180 TAAATAAATTGATAATAGT
1 TAAATAAAAGGATAATAGT
3199 TAAAT
1 TAAAT
3204 TAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (19 bp):
TAAATAAAAGGATAATAGT
Found at i:13166 original size:42 final size:43
Alignment explanation
Indices: 13118--13207 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 43
13108 TATTATCTTA
* *
13118 ATTCTA-CTCCATCTCTGGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
13160 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
13205 ATT
1 ATT
13208 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 6 0.14
45 37 0.86
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
Found at i:14409 original size:30 final size:30
Alignment explanation
Indices: 14375--14434 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
14365 TACTTTGTCA
*
14375 ATTTATTTCGATCCTGCTTTAGGATCATTG
1 ATTTATTACGATCCTGCTTTAGGATCATTG
*
14405 ATTTATTACGATCCTGGTTTAGGATCATTG
1 ATTTATTACGATCCTGCTTTAGGATCATTG
14435 CTTTGTCGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (30 bp):
ATTTATTACGATCCTGCTTTAGGATCATTG
Found at i:14483 original size:30 final size:30
Alignment explanation
Indices: 14447--14761 Score: 504
Period size: 30 Copynumber: 10.5 Consensus size: 30
14437 TTGTCGGTTT
*
14447 ATTTTAATCCTGGTTAAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
*
14477 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
** *
14507 ATTTTAATCCCAGTTGAGGATCATTACTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
* * *
14537 ATTTTAATCCTAGTTGAGGATCGTTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
*
14567 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
*
14597 ATTTTAATCTTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
*
14627 ATTTTAATCCTGGTTGAGGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
14657 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
* * *
14687 ATTTTAATCTTGGTTGACGATCATTGCTTT
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
14717 ATTTTAATCCTGGTTGAGGATCATTGCTTC
1 ATTTTAATCCTGGTTGAGGATCATTGCTTC
14747 ATTTTAATCCTGGTT
1 ATTTTAATCCTGGTT
14762 TATGATCTTT
Statistics
Matches: 262, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 262 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (30 bp):
ATTTTAATCCTGGTTGAGGATCATTGCTTC
Found at i:17589 original size:6 final size:6
Alignment explanation
Indices: 17578--17604 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17568 TAACTAATTT
17578 TTGGAA TTGGAA TTGGAA TTGGAA TTG
1 TTGGAA TTGGAA TTGGAA TTGGAA TTG
17605 AACTAGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (6 bp):
TTGGAA
Found at i:18856 original size:24 final size:24
Alignment explanation
Indices: 18824--18882 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
18814 CTTGGCTGTC
*
18824 GTTGCAATCCTGGATTTGATTGAG
1 GTTGCAATCCTGGATTTGACTGAG
*
18848 GTTGCAATCTTGGATTTGACTGAG
1 GTTGCAATCCTGGATTTGACTGAG
* *
18872 GCTGGAATCCT
1 GTTGCAATCCT
18883 CTACTTGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (24 bp):
GTTGCAATCCTGGATTTGACTGAG
Found at i:21094 original size:42 final size:42
Alignment explanation
Indices: 21041--21130 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
21031 TAATCACAAT
*
21041 TTGAAAGTAACGATTCAAAGAAGAAGAAGAAGAAAATAGAGA
1 TTGAAAATAACGATTCAAAGAAGAAGAAGAAGAAAATAGAGA
21083 TTGAAAATAACGATTCAAAGAAGAAGAAGAAGAAAATAGAGA
1 TTGAAAATAACGATTCAAAGAAGAAGAAGAAGAAAATAGAGA
21125 TTGAAA
1 TTGAAA
21131 GTACCTATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (42 bp):
TTGAAAATAACGATTCAAAGAAGAAGAAGAAGAAAATAGAGA
Found at i:21282 original size:9 final size:9
Alignment explanation
Indices: 21268--21297 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
21258 GAGAAGCCGG
21268 GAGAGAAGA
1 GAGAGAAGA
21277 GAGAGAAGA
1 GAGAGAAGA
21286 GAGAGAAGA
1 GAGAGAAGA
21295 GAG
1 GAG
21298 GTGAGATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (9 bp):
GAGAGAAGA
Found at i:30760 original size:21 final size:21
Alignment explanation
Indices: 30716--30760 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30706 GGCGCCCACA
*
30716 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAAGACCCAGG
*
30737 TGGTTTG-CTTGAAGACCTAGG
1 TGGTTTGTC-TGAAGACCCAGG
30758 TGG
1 TGG
30761 GCAGTGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (21 bp):
TGGTTTGTCTGAAGACCCAGG
Found at i:30844 original size:76 final size:76
Alignment explanation
Indices: 30695--30847 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 76
30685 GGCTGTCCAC
* * * * *
30695 GACTCTCCCTGGGCGCCCACATGGTTTGTCTGAAGACCCATGTGGTTTGCTTGAAGACCTAGGTG
1 GACTCTACCTGGGCGCCCACATGGTTTGTCTGAAGACCCATGTGATTTGCCTGAACACCTAGGTA
30760 GGCAGTGTCAT
66 GGCAGTGTCAT
* * * *
30771 GACTCTACCTGGGTGCCCACATGGTTTGTTTGAGGACCCATGTGATTTGCCTGATCACCTAGGTA
1 GACTCTACCTGGGCGCCCACATGGTTTGTCTGAAGACCCATGTGATTTGCCTGAACACCTAGGTA
**
30836 GGTTGTGTCAT
66 GGCAGTGTCAT
30847 G
1 G
30848 GCTCGACACC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (76 bp):
GACTCTACCTGGGCGCCCACATGGTTTGTCTGAAGACCCATGTGATTTGCCTGAACACCTAGGTA
GGCAGTGTCAT
Found at i:31352 original size:49 final size:49
Alignment explanation
Indices: 31196--31453 Score: 156
Period size: 49 Copynumber: 5.2 Consensus size: 49
31186 GTCTAATCAA
* ** * *
31196 AAGGACATTTTTGTAAAAAGCAAGAAAAAATTTACGCCTTCCGACTAGG
1 AAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGCCTAGG
* * * ** *
31245 AAGGGC-GTTTTAGGAAATA-TAAGTAAGAAAATTAGTGCCTTTTTCGACC--GG
1 AAGGGCATTTTTGGGAAA-AGCAAG-AA-AAAATTAACGCC--TTCCG-CCTAGG
* *
31296 AGAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAATGCCTTCCGCCTGGG
1 A-AGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGCCTAGG
* * * *
31346 AAGGGCATTTTAGGAAAAAGCAAG--AAAATTAGCGCCTTTCGACC--GG
1 AAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCG-CCTAGG
* * * * *
31392 AAAGGGCGTTTTTGGGAAAATG-TAGTAAAAATTAACGTCTTCCGTCTAGG
1 -AAGGGCATTTTTGGGAAAA-GCAAGAAAAAATTAACGCCTTCCGCCTAGG
*
31442 AAGGGCGTTTTT
1 AAGGGCATTTTT
31454 TTTGGCAAAA
Statistics
Matches: 162, Mismatches: 29, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
46 2 0.01
47 32 0.20
48 16 0.10
49 59 0.36
50 14 0.09
51 14 0.09
52 12 0.07
53 13 0.08
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (49 bp):
AAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGCCTAGG
Found at i:31434 original size:96 final size:100
Alignment explanation
Indices: 31195--31452 Score: 319
Period size: 96 Copynumber: 2.6 Consensus size: 100
31185 GGTCTAATCA
* ** *
31195 AAAGGACATTTTTGTAAAAAGCAAGAAAAAATTTACGCCTTCCGACTAGGAAGGGCGTTTTAGGA
1 AAAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGACTAGGAAGGGCGTTTTAGGA
* *
31260 AATATAAGTAAGAAAATTAGTGCCTTTTTCGACCGG
66 AATATAAGCAAGAAAATTAGCGCC-TTTTCGACCGG
* * * * *
31296 AGAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAATGCCTTCCGCCTGGGAAGGGCATTTTAGG-
1 AAAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGACTAGGAAGGGCGTTTTAGGA
31360 AA-A-AAGCAAGAAAATTAGCGCC-TTTCGACCGG
66 AATATAAGCAAGAAAATTAGCGCCTTTTCGACCGG
* * * * *
31392 AAAGGGCGTTTTTGGGAAAATG-TAGTAAAAATTAACGTCTTCCGTCTAGGAAGGGCGTTTT
1 AAAGGGCATTTTTGGGAAAA-GCAAGAAAAAATTAACGCCTTCCGACTAGGAAGGGCGTTTT
31453 TTTTGGCAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
96 60 0.44
97 1 0.01
98 17 0.12
99 1 0.01
100 2 0.01
101 55 0.40
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (100 bp):
AAAGGGCATTTTTGGGAAAAGCAAGAAAAAATTAACGCCTTCCGACTAGGAAGGGCGTTTTAGGA
AATATAAGCAAGAAAATTAGCGCCTTTTCGACCGG
Found at i:32524 original size:21 final size:21
Alignment explanation
Indices: 32500--32570 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
32490 CTTAGGCAAT
32500 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
*
32521 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGAAACCTTC
32542 TCCAATGAGCTTGAAA-CTTGC
1 TCCAATGAGCTTGAAACCTT-C
32563 TCCAATGA
1 TCCAATGA
32571 TCTCCTAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:35331 original size:21 final size:21
Alignment explanation
Indices: 35305--35345 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35295 AATAAAACCC
35305 TAGTACCACTTAG-CTCCAATT
1 TAGTACCACTT-GTCTCCAATT
35326 TAGTACCACTTGTCTCCAAT
1 TAGTACCACTTGTCTCCAAT
35346 AGGGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (21 bp):
TAGTACCACTTGTCTCCAATT
Found at i:35837 original size:25 final size:24
Alignment explanation
Indices: 35800--35846 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
35790 CTAGAAAATT
35800 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
35826 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
35847 AATAGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:35856 original size:28 final size:26
Alignment explanation
Indices: 35800--35856 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
35790 CTAGAAAATT
* *
35800 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGAA
35826 TGAAAAACTTGATGATAGATGA-ATAGAA
1 TGAAAAACTT--TGATAGATGAGAT-GAA
35854 TGA
1 TGA
35857 TAGATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 14 0.54
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGAA
Found at i:36744 original size:21 final size:21
Alignment explanation
Indices: 36720--36790 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
36710 CTTAGGCAAT
36720 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGAAACCTTC
36741 TCCAATGAGCTT-AGAACCTTC
1 TCCAATGAGCTTGA-AACCTTC
* *
36762 TCCAATGTGCTTGGAA-CTTGC
1 TCCAATGAGCTTGAAACCTT-C
36783 TCCAATGA
1 TCCAATGA
36791 TCTCCTAGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.09
21 40 0.91
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACCTTC
Found at i:37263 original size:22 final size:21
Alignment explanation
Indices: 37227--37269 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
37217 CTGAGGAAGG
37227 AGTGAATCAAAGAC-AGACAA
1 AGTGAATCAAAGACAAGACAA
37247 AGTGCAATCAAAAGACAAGACAA
1 AGTG-AATC-AAAGACAAGACAA
37270 CAATCATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 6 0.30
23 6 0.30
ACGTcount: A:0.56, C:0.16, G:0.19, T:0.09
Consensus pattern (21 bp):
AGTGAATCAAAGACAAGACAA
Found at i:38034 original size:68 final size:68
Alignment explanation
Indices: 37924--38061 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
37914 AATTTCCTTC
* *
37924 TTCCTTCCTTTAAATCCATTTTTGGCTTTGGGCTTGTGTACTTGGGTCAAGAGTGTTCATTTGGG
1 TTCCTTCCTTTAAACCCATTTTTGGCTTTGGGCTTGTATACTTGGGTCAAGAGTGTTCATTTGGG
37989 CCA
66 CCA
* *
37992 TTCCTTCTTTTAAACCCATTTTTGGCTTTGGGCTTGTATACTTGGGTCTAGAGTGTTCATTTGGG
1 TTCCTTCCTTTAAACCCATTTTTGGCTTTGGGCTTGTATACTTGGGTCAAGAGTGTTCATTTGGG
38057 CCA
66 CCA
38060 TT
1 TT
38062 GCATTTCTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.44
Consensus pattern (68 bp):
TTCCTTCCTTTAAACCCATTTTTGGCTTTGGGCTTGTATACTTGGGTCAAGAGTGTTCATTTGGG
CCA
Found at i:41018 original size:29 final size:30
Alignment explanation
Indices: 40986--41052 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
40976 ATGCAATTTG
40986 GGATATAACGTTAC-AAAACAAGCAATTAA
1 GGATATAACGTTACAAAAACAAGCAATTAA
*
41015 GGATATAACGTTACGAAAAACGAGCAATTAA
1 GGATATAACGTTAC-AAAAACAAGCAATTAA
41046 GGATATA
1 GGATATA
41053 GTCCGTTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
31 21 0.60
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (30 bp):
GGATATAACGTTACAAAAACAAGCAATTAA
Done.