Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009177.1 Corchorus capsularis cultivar CVL-1 contig09198, 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: 83604
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:37 original size:26 final size:25
Alignment explanation
Indices: 1--229 Score: 273
Period size: 26 Copynumber: 8.7 Consensus size: 25
1 ATATAGTTGCATATTCAGTAGGGCTC
1 ATATAGTTGCATATTCAGTAGGGC-C
*
27 ATATAGTTGCATATTCATTAGGGCTC
1 ATATAGTTGCATATTCAGTAGGGC-C
53 ATATAGTTGCATATTCAGTAGGGGCC
1 ATATAGTTGCATATTCAGTA-GGGCC
*
79 ATAGAGTTGCATATTCAGTAGGGGCC
1 ATATAGTTGCATATTCAGTA-GGGCC
*
105 ATACAGTTGCATATTCAGTAGGGGCC
1 ATATAGTTGCATATTCAGTA-GGGCC
*
131 ATATAGCTGCATATTCAGTAGGG-C
1 ATATAGTTGCATATTCAGTAGGGCC
*
155 -TCATAGTTGCATATTCTGTAGGGCTC
1 AT-ATAGTTGCATATTCAGTAGGGC-C
*
181 ATATAGTTGCATTGCATATTTAGTAGGAGCC
1 ATATA---G--TTGCATATTCAGTAGG-GCC
212 ATATAGTTGCATATTCAG
1 ATATAGTTGCATATTCAG
230 CAGTCATGTA
Statistics
Matches: 181, Mismatches: 11, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.01
24 20 0.11
25 3 0.02
26 128 0.71
27 5 0.03
28 1 0.01
29 1 0.01
31 20 0.11
32 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
ATATAGTTGCATATTCAGTAGGGCC
Found at i:196 original size:31 final size:31
Alignment explanation
Indices: 161--223 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 31
151 GGGCTCATAG
161 TTGCATATTCT-GTAGG-GCTCATATAGTTGCA
1 TTGCATATT-TAGTAGGAGC-CATATAGTTGCA
192 TTGCATATTTAGTAGGAGCCATATAGTTGCA
1 TTGCATATTTAGTAGGAGCCATATAGTTGCA
223 T
1 T
224 ATTCAGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.90
32 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (31 bp):
TTGCATATTTAGTAGGAGCCATATAGTTGCA
Found at i:1876 original size:321 final size:320
Alignment explanation
Indices: 1154--2629 Score: 1803
Period size: 321 Copynumber: 4.6 Consensus size: 320
1144 CTCAGTTTAA
* * * * *
1154 GGCTAAAAACGCGTTTCAGGGG-CTTGACTCAGTTTTGCATGATTTTTGGCGTAAAAACTCCTTG
1 GGCTAAAAACGC-ATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCC-TG
* *** * *
1218 -AAA-TATCTATATTCTTCGAACCAAATCTCAGTAAAATTGGATTTAACGATTTGTATTTACGGG
64 CAAATTA-CTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGGG
* * *
1281 CATCTGAATCTTATTT-GATTTAATTTGAAATTAATTTGAAAAAAATGGAAAAACAATATTAGAA
128 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATGGAAAAACGATATTAGAA
* * **
1345 GCGTGAAAAAAGCCTTCAATATTTTTGGTATTGAATTATATTTTATTTATGAGTATTATGGAAAA
193 GCGTG--AAAAGCCTTCAATCTTTTTGGCATTGAATTATATAGTATTTATGAGTATTATGGAAAA
*
1410 GAATTGAGAAAAAAGTTGTCAGGTCAGTTTTT------AATC-TGT-CT-A-C-TCACGGTTTTT
256 GAATTGAGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTT
* *
1464 GGCTAAAAACGCATTCCGGGGCCCTGGCTCA-TTTTGCATGATTTTTGGCGTAAACACTTCTTCA
1 GGCTAAAAACGCATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCCTGCA
* * * * * *
1528 AATAACTATATTCATCGAGTTAAATCCCAATCAAATTTGATTTAACGATTTATTTTTACGAGCAT
66 AATTACTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGGGCAT
1593 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATGGAAAAACGATATTAGAAGCG
131 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATGGAAAAACGATATTAGAAGCG
* * *
1658 TGAAAATCCTTCAATCTTTTTGGCATTGAATTACATAGTATTTATGAGTATTATGGTCAAAGAAT
196 TGAAAAGCCTTCAATCTTTTTGGCATTGAATTATATAGTATTTATGAGTATTATGG-AAAAGAAT
*
1723 TGAGAAAAAAGTTTTCATGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTT
260 TGAGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTT
* *
1784 GGCTAAAAACGCAATCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTGCA
1 GGCTAAAAACGCATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCCTGCA
*
1849 AATTACTATATTCATCGAGTTAAATCCCAGCCAAATTGGATTTAACGATTTGTATTTACGGGCAT
66 AATTACTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGGGCAT
*
1914 CTGAATCTTGTTTCAATTTAATTAGAAATTAATTTGAAAAAAAATGGAAAAACGATATTAGAAGC
131 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTTG-AAAAAAATGGAAAAACGATATTAGAAGC
* ** * * * * *
1979 GTGATAAGCCTTCAATCTTTTTGGCATTGAATTATATTTTATTTTTGAGTATTGTAGCAAGGAAT
195 GTGAAAAGCCTTCAATCTTTTTGGCATTGAATTATATAGTATTTATGAGTATTATGGAAAAGAAT
* *
2044 TGTGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACTAACCATTACGGTTTTT
260 TGAGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTT
** *
2105 GGCTAAAAACGCATTCCGAAGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCCTTCA
1 GGCTAAAAACGCATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCCTGCA
* * * * *
2170 AATAACTATATTCATCGAGTTAAATCCCAGTCAAATTTGATTTAACGATTTGTTTTTATGAGCAT
66 AATTACTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGGGCAT
* *
2235 CTGAATCTTGTTTCGATTT-ATTAGAAATT-ATTTGGAAAAAAAATGGAAAAACGATATCAGAAT
131 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTT-G-AAAAAAATGGAAAAACGATATTAGAAG
* * * * * * * *
2298 CATGAAAAACCCTCCAATCTTTTTGTCGTTGAATTATATAGT-TTTAAAGTGTATTGTGGTAAAA
194 CGTG-AAAAGCCTTCAATCTTTTTGGCATTGAATTATATAGTATTT-ATGAGTATTATGG-AAAA
* * * * * * *
2362 AAATTGGGGAAAAAA-TTTCCAGGTCAATTTTTAGCCGAAATCGTGCACTAAAAACATCACGGTT
256 GAATT-GAGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACT--AACCATCACGGTT
2426 TTT
318 TTT
* * * * * * * * ** *
2429 GGCTAAAAACACGTTTCAGGG-TCTCGACTTAGTTTTGCATGATTTTTGGTCTTAATGACCCCTT
1 GGCTAAAAACGCATTCCGGGGCCCT-GGCTCAGTTTTGCATGATTTTTGG-CGTAAACACTCC-T
* * *** * **
2493 G--AA-TATCTATTTTCTTCGAACCAAATCCCAGCCAAATTGGATTTAATAATTTGTATTTACGG
63 GCAAATTA-CTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGG
*
2555 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTTATTTGAAAAAAATGGAAAAACGATATTAGA
127 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATGGAAAAACGATATTAGA
2620 AGCGTGAAAA
192 AGCGTGAAAA
2630 ACAACAAAAA
Statistics
Matches: 1014, Mismatches: 121, Indels: 49
0.86 0.10 0.04
Matches are distributed among these distances:
308 49 0.05
309 131 0.13
310 71 0.07
315 4 0.00
316 3 0.00
317 2 0.00
318 1 0.00
319 5 0.00
320 84 0.08
321 364 0.36
322 113 0.11
323 15 0.01
324 148 0.15
325 19 0.02
326 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (320 bp):
GGCTAAAAACGCATTCCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGCGTAAACACTCCTGCA
AATTACTATATTCATCGAGTTAAATCCCAGTCAAATTGGATTTAACGATTTGTATTTACGGGCAT
CTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAAATGGAAAAACGATATTAGAAGCG
TGAAAAGCCTTCAATCTTTTTGGCATTGAATTATATAGTATTTATGAGTATTATGGAAAAGAATT
GAGAAAAAAGTTTTCAGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTT
Found at i:3470 original size:40 final size:40
Alignment explanation
Indices: 3421--3499 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
3411 ATTTGATTTT
* * *
3421 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
3461 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGA
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGA
3500 AGACTTGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 15 0.44
41 18 0.53
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:3534 original size:99 final size:100
Alignment explanation
Indices: 3411--3600 Score: 258
Period size: 104 Copynumber: 1.9 Consensus size: 100
3401 TGAGAGTTTG
* * * * *
3411 ATTTGATTTTATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTG-ATAATTTAATTCAAGG
1 ATTTGATTTGATTCGATTCAAGGGTCTG-ATGACTTGATCTCGAATTGAATAATTTAACTCAAGG
3474 GTCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
65 GTCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
* *
3510 ATTTGATTTGATTCGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATAATAATTTGACTCA
1 ATTTGATTTGATTCGATTCAAGGGTC--TGATGACTTGATCTCGAATTG--AATAATTTAACTCA
3575 AGGGTCTTGACGACTTGATCTTGAAT
62 AGGGTCTTGACGACTTGATCTTGAAT
3601 AAACAACTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
99 23 0.29
101 17 0.22
102 1 0.01
104 37 0.47
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (100 bp):
ATTTGATTTGATTCGATTCAAGGGTCTGATGACTTGATCTCGAATTGAATAATTTAACTCAAGGG
TCTTGACGACTTGATCTTGAATTGAAGACTTGGGA
Found at i:3839 original size:91 final size:88
Alignment explanation
Indices: 3677--3897 Score: 298
Period size: 91 Copynumber: 2.5 Consensus size: 88
3667 TCTTTGATAA
* * * * *
3677 TTTGGAAGAAGAATCCTCCACATACGTGGATCTTCTTTCAATAATTTCCCAATATCTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
* *
3742 AGTAATTCTGCAATAATTGGATCTTC
66 AGTAATTCT-C--CAATTGAATCTTC
* * *
3768 TTTGAAGGAAGAATACTCCACCTACATGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
3833 AGTAATTCTCCAATTGAATCTTC
66 AGTAATTCTCCAATTGAATCTTC
** *
3856 TTTGAAAGAAGAATTTTCCACATACGTGAATCTTCTTTCAAT
1 TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAAT
3898 CTTCTTAAGC
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
88 47 0.41
90 1 0.01
91 66 0.58
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (88 bp):
TTTGAAAGAAGAATACTCCACATACGTGGATCTTCTTTCAATAACTCCCCAATAACTGGGTCTTC
AGTAATTCTCCAATTGAATCTTC
Found at i:3964 original size:16 final size:16
Alignment explanation
Indices: 3943--3992 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
3933 TCTGAAATAT
3943 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
*
3959 TTCAGAACTTTTCTGC
1 TTCAGAGCTTTTCTGC
3975 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
3991 TT
1 TT
3993 TCTGAATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Found at i:4665 original size:73 final size:73
Alignment explanation
Indices: 4570--4761 Score: 359
Period size: 73 Copynumber: 2.6 Consensus size: 73
4560 GCGAGATGAA
*
4570 TGAG-GAAATTAATCACTCTATTTTTAGATGAAAAAAATTTTAAAAATTAACACTCTAAAAAGAG
1 TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAATTTAAAAAATTAACACTCTAAAAAGAG
4634 AGACTTTT
66 AGACTTTT
4642 TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAATTTAAAAAATTAACACTCTAAAAAGAG
1 TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAATTTAAAAAATTAACACTCTAAAAAGAG
4707 AGACTTTT
66 AGACTTTT
*
4715 TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAAATTAAAAAA
1 TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAATTTAAAAAA
4762 AGTTATCATT
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
72 4 0.03
73 113 0.97
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (73 bp):
TGAGAGAAATTAATCACTCTATTTTTAGATGAAAAAAATTTAAAAAATTAACACTCTAAAAAGAG
AGACTTTT
Found at i:12504 original size:2 final size:2
Alignment explanation
Indices: 12493--12528 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
12483 TTATTACTAT
12493 TA TA -A TA TA TA TA 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 TA T
12529 TTTGTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13219 original size:6 final size:6
Alignment explanation
Indices: 13209--13241 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
13199 TTCTAATTCT
*
13209 AATTAT AATTAA AATTAA AATTAA AATTAA AAT
1 AATTAA AATTAA AATTAA AATTAA AATTAA AAT
13242 GTTGCTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:13317 original size:12 final size:12
Alignment explanation
Indices: 13297--13329 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
13287 TTGCTCGATG
13297 TTGGGCTTGGTC
1 TTGGGCTTGGTC
*
13309 TTGGTCTTGGTC
1 TTGGGCTTGGTC
13321 TTGGGCTTG
1 TTGGGCTTG
13330 AGCTTAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.39, T:0.45
Consensus pattern (12 bp):
TTGGGCTTGGTC
Found at i:15433 original size:6 final size:6
Alignment explanation
Indices: 15422--15463 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
15412 GGCACCGGGG
*
15422 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACACAAA CCCAA
1 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA AC-CAAA ACCAA
15464 TTCCCTCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAA
Found at i:18532 original size:9 final size:9
Alignment explanation
Indices: 18511--18540 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18501 AAAAAAAAAA
18511 AAAACAAAC
1 AAAACAAAC
18520 -AAACAAAC
1 AAAACAAAC
18528 AAAACAAAC
1 AAAACAAAC
18537 AAAA
1 AAAA
18541 ATTTAAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAACAAAC
Found at i:27979 original size:2 final size:2
Alignment explanation
Indices: 27972--27999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27962 AAGTAACTAC
27972 AT 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 AT
28000 TTCAAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33954 original size:111 final size:112
Alignment explanation
Indices: 33789--34013 Score: 443
Period size: 112 Copynumber: 2.0 Consensus size: 112
33779 GTATTACTAC
33789 GTTGAGTAGTATTTGTAATTGTAACAATGGATACCCCTACGGC-TTTTTTTTTTTTTTGGCGTCA
1 GTTGAGTAGTATTTGTAATTGTAACAATGGATACCCCTACGGCATTTTTTTTTTTTTTGGCGTCA
33853 ACGTTTATACACTAAAAAAATTAGCTACGCATGACATATACTATATA
66 ACGTTTATACACTAAAAAAATTAGCTACGCATGACATATACTATATA
33900 GTTGAGTAGTATTTGTAATTGTAACAATGGATACCCCTACGGCATTTTTTTTTTTTTTGGCGTCA
1 GTTGAGTAGTATTTGTAATTGTAACAATGGATACCCCTACGGCATTTTTTTTTTTTTTGGCGTCA
33965 ACGTTTATACACTAAAAAAATTAGCTACGCATGACATATACTATATA
66 ACGTTTATACACTAAAAAAATTAGCTACGCATGACATATACTATATA
34012 GT
1 GT
34014 AATAATGTAA
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 43 0.38
112 70 0.62
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (112 bp):
GTTGAGTAGTATTTGTAATTGTAACAATGGATACCCCTACGGCATTTTTTTTTTTTTTGGCGTCA
ACGTTTATACACTAAAAAAATTAGCTACGCATGACATATACTATATA
Found at i:35100 original size:2 final size:2
Alignment explanation
Indices: 35088--35149 Score: 78
Period size: 2 Copynumber: 33.0 Consensus size: 2
35078 GGAATATTGT
* *
35088 TA TA T- TA TA TA TA TA TA TA TA TA TG TA -A TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35128 TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
35150 CTACTATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
1 4 0.08
2 48 0.92
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35125 original size:25 final size:24
Alignment explanation
Indices: 35093--35149 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
35083 ATTGTTATAT
*
35093 TATA-TATATATATATATATGTAA
1 TATATTATATATATATATATATAA
*
35116 TATATCTATATATATATATATATAT
1 TATAT-TATATATATATATATATAA
35141 TATATTATA
1 TATATTATA
35150 CTACTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 22 0.73
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATTATATATATATATATATAA
Found at i:35351 original size:15 final size:16
Alignment explanation
Indices: 35331--35360 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35321 ATAAAAGTCG
35331 TTAATTATCC-GAAAT
1 TTAATTATCCAGAAAT
35346 TTAATTATCCAGAAA
1 TTAATTATCCAGAAA
35361 AAAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (16 bp):
TTAATTATCCAGAAAT
Found at i:39342 original size:2 final size:2
Alignment explanation
Indices: 39335--39359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39325 TTTTTCATGA
39335 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 A
39360 GTGGTCCGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40645 original size:2 final size:2
Alignment explanation
Indices: 40633--40684 Score: 56
Period size: 2 Copynumber: 26.0 Consensus size: 2
40623 TAAATAAATA
40633 AT AT A- AT AT AT AT AT AT AT AT AT AT AT ACT ACT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT
40674 ACT AT AT AT AT
1 A-T AT AT AT AT
40685 TAGTACGGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.07
2 35 0.78
3 7 0.16
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:64007 original size:27 final size:27
Alignment explanation
Indices: 63950--64010 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
63940 TTTTAGAGGC
* * *
63950 ATCCATAGTTGTTTTTGGAACAGAGAC
1 ATCCATAATTGTTTTTGGAACAAAGAA
*
63977 ATCCATAATT-TTTTTGGGTACAAAGAA
1 ATCCATAATTGTTTTT-GGAACAAAGAA
64004 ATCCATA
1 ATCCATA
64011 GTTATCGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (27 bp):
ATCCATAATTGTTTTTGGAACAAAGAA
Found at i:64373 original size:15 final size:15
Alignment explanation
Indices: 64353--64382 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
64343 TAACATGGGA
64353 AAATTATTAAATTTT
1 AAATTATTAAATTTT
64368 AAATTATTAAATTTT
1 AAATTATTAAATTTT
64383 TAAAATATAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTATTAAATTTT
Found at i:64377 original size:8 final size:8
Alignment explanation
Indices: 64353--64386 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
64343 TAACATGGGA
64353 AAATTATT
1 AAATTATT
64361 AAATT-TT
1 AAATTATT
64368 AAATTATT
1 AAATTATT
*
64376 AAATTTTT
1 AAATTATT
64384 AAA
1 AAA
64387 ATATAAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTATT
Found at i:75383 original size:6 final size:7
Alignment explanation
Indices: 75366--75397 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
75356 AGATTTTTTT
75366 AAAAAAG
1 AAAAAAG
75373 AAAAAAG
1 AAAAAAG
75380 AAAAAAG
1 AAAAAAG
75387 -AAAAAG
1 AAAAAAG
75393 AAAAA
1 AAAAA
75398 CTTGCTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:75385 original size:14 final size:13
Alignment explanation
Indices: 75366--75397 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
75356 AGATTTTTTT
75366 AAAAAAGAAAAAAG
1 AAAAAAG-AAAAAG
75380 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
75393 AAAAA
1 AAAAA
75398 CTTGCTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:80592 original size:2 final size:2
Alignment explanation
Indices: 80585--80609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
80575 TCAAATTGTT
80585 TA 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 T
80610 TCATATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80780 original size:4 final size:4
Alignment explanation
Indices: 80766--80797 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
80756 CTTCATTATG
*
80766 ATTT GTTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
80798 TTGAGAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
ATTT
Done.