Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1221
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: 58094
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:633 original size:9 final size:11
Alignment explanation
Indices: 604--644 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
594 TATTTATAAT
604 ATTATATTTTA
1 ATTATATTTTA
615 ATTATATTTTA
1 ATTATATTTTA
*
626 ATTATTTTTTA
1 ATTATATTTTA
637 TATTATAT
1 -ATTATAT
645 ATATCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTATATTTTA
Found at i:1754 original size:54 final size:54
Alignment explanation
Indices: 1665--1790 Score: 157
Period size: 54 Copynumber: 2.4 Consensus size: 54
1655 TGTTTGCATG
* * * * *
1665 GAAAA-TCACCCACGGGACATTGATTGATTTTGTGTTGAAGTGT-TCTATGGTTT
1 GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCT-TATGGTTT
*
1718 GAAAAGTCACCCACGGGGCATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
1 GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
* *
1772 GGAAAGTCATCCACGGGAC
1 GAAAAGTCACCCACGGGAC
1791 TATGGCTAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.08
54 56 0.90
55 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (54 bp):
GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
Found at i:3616 original size:51 final size:49
Alignment explanation
Indices: 3540--3638 Score: 126
Period size: 51 Copynumber: 2.0 Consensus size: 49
3530 CGATTTTAGT
* * * *
3540 TTTTTTTATTATCATTATTTATTGTTTGTATTTATTTATTGTGATAATATC
1 TTTTTTTATTATCATTATGTATTGTTT-AATTTATTAATTAT-ATAATATC
* *
3591 TTTTTTTGTTGTCATTATGTATTGTTTAATTTATTAATTATATAATAT
1 TTTTTTTATTATCATTATGTATTGTTTAATTTATTAATTATATAATAT
3639 TCGTTATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 7 0.17
50 11 0.26
51 24 0.57
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (49 bp):
TTTTTTTATTATCATTATGTATTGTTTAATTTATTAATTATATAATATC
Found at i:3679 original size:12 final size:12
Alignment explanation
Indices: 3662--3695 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
3652 TATTAATTAT
3662 ATTATATTTTTA
1 ATTATATTTTTA
3674 ATTATA-TTTTA
1 ATTATATTTTTA
3685 ATTAT-TTTTTA
1 ATTATATTTTTA
3696 TATAATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTATATTTTTA
Found at i:3936 original size:29 final size:30
Alignment explanation
Indices: 3904--3973 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
3894 TATTACGTGA
3904 TAAAAATAATAATATTTTAATAA-T-ATATT
1 TAAAAATAATAATATTTTAATAATTAAT-TT
* *
3933 TAAAAATATTATTATTTTAATAATTAATTT
1 TAAAAATAATAATATTTTAATAATTAATTT
*
3963 TTAAAATAATA
1 TAAAAATAATA
3974 TTAATTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.60
30 12 0.34
31 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAATAATAATATTTTAATAATTAATTT
Found at i:7599 original size:27 final size:27
Alignment explanation
Indices: 7569--7623 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
7559 AAAAATTTTT
7569 TGCGAATTTTAAAGATGGATTTGATTC
1 TGCGAATTTTAAAGATGGATTTGATTC
7596 TGCGAATTTTAAAGATGGATTTGATTC
1 TGCGAATTTTAAAGATGGATTTGATTC
7623 T
1 T
7624 ATCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
TGCGAATTTTAAAGATGGATTTGATTC
Found at i:7631 original size:23 final size:24
Alignment explanation
Indices: 7578--7631 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 24
7568 TTGCGAATTT
**
7578 TAAAGATGGATTTGATTCTGCGAATTT
1 TAAAGATGGATTTGATTCT--G-ATCA
7605 TAAAGATGGATTTGATTCT-ATCA
1 TAAAGATGGATTTGATTCTGATCA
7628 TAAA
1 TAAA
7632 CAATCCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.24
27 19 0.76
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (24 bp):
TAAAGATGGATTTGATTCTGATCA
Found at i:7896 original size:15 final size:15
Alignment explanation
Indices: 7878--7912 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
7868 TCTGTTGCAA
7878 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
7893 AAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAC
*
7908 CAAAA
1 AAAAA
7913 TCGAATCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:7896 original size:16 final size:16
Alignment explanation
Indices: 7877--7912 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7867 ATCTGTTGCA
7877 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
* *
7893 AAAAAACAAAAAAACC
1 AAAAAAAAAAAAAAAC
7909 AAAA
1 AAAA
7913 TCGAATCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Found at i:11198 original size:2 final size:2
Alignment explanation
Indices: 11193--11222 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11183 GTGTGTGTGC
11193 AT 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 AT
11223 TTCATTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11617 original size:30 final size:30
Alignment explanation
Indices: 11576--11636 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
11566 AAAATCATGG
11576 CGTATGCTTAATTTTTTCCTCTGTACTTTT
1 CGTATGCTTAATTTTTTCCTCTGTACTTTT
*
11606 CGTATGTTTAATTTTTTCCTCTGTACTTTT
1 CGTATGCTTAATTTTTTCCTCTGTACTTTT
11636 C
1 C
11637 TTGAGGAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.20, G:0.10, T:0.57
Consensus pattern (30 bp):
CGTATGCTTAATTTTTTCCTCTGTACTTTT
Found at i:14300 original size:11 final size:11
Alignment explanation
Indices: 14284--14319 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14274 AATATCATAT
14284 TTTTAATTATA
1 TTTTAATTATA
*
14295 TTTTAATTATT
1 TTTTAATTATA
14306 TTTTATATTATA
1 TTTTA-ATTATA
14318 TT
1 TT
14320 ATATCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTAATTATA
Found at i:19002 original size:22 final size:22
Alignment explanation
Indices: 18977--19071 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 22
18967 TTAATATCTT
18977 TATTAAGTGTGTTAAGTAAATA
1 TATTAAGTGTGTTAAGTAAATA
* * **
18999 TATTAGGTAG-GTTAGGT-GGTA
1 TATTAAGT-GTGTTAAGTAAATA
*
19020 TGTT-AG-GTG---AGTA-ATA
1 TATTAAGTGTGTTAAGTAAATA
*
19036 TATTAAGTGTGTTAGGTAAATA
1 TATTAAGTGTGTTAAGTAAATA
*
19058 TATTAGGTGTGTTA
1 TATTAAGTGTGTTA
19072 GGTGAACATA
Statistics
Matches: 53, Mismatches: 11, Indels: 18
0.65 0.13 0.22
Matches are distributed among these distances:
16 7 0.13
17 2 0.04
18 4 0.08
19 1 0.02
20 1 0.02
21 8 0.15
22 29 0.55
23 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (22 bp):
TATTAAGTGTGTTAAGTAAATA
Found at i:19072 original size:22 final size:22
Alignment explanation
Indices: 19032--19083 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
19022 TTAGGTGAGT
19032 AATATATTAAGTGTGTTAGGTA
1 AATATATTAAGTGTGTTAGGTA
* *
19054 AATATATTAGGTGTGTTAGGTG
1 AATATATTAAGTGTGTTAGGTA
*
19076 AACATATT
1 AATATATT
19084 TTATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (22 bp):
AATATATTAAGTGTGTTAGGTA
Found at i:20272 original size:48 final size:48
Alignment explanation
Indices: 20183--20276 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
20173 CTCTCCTTGG
* **
20183 TACACCCCTTCAGGAAAAAGGCTAGGATTCTCAGGGGAATTTTATATA
1 TACACCCCTTCAGGAAAAAGGCTAAGATTCTCAGGAAAATTTTATATA
20231 TACACCCCTTCAGGAAAAAGGCTAAGATTCT-ATGGAAAATTTTATA
1 TACACCCCTTCAGGAAAAAGGCTAAGATTCTCA-GGAAAATTTTATA
20277 CACCTGAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 1 0.02
48 41 0.98
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (48 bp):
TACACCCCTTCAGGAAAAAGGCTAAGATTCTCAGGAAAATTTTATATA
Found at i:22906 original size:68 final size:68
Alignment explanation
Indices: 22828--22962 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
22818 ATCAACAAAC
*
22828 TTGGTTGAATAAAAACTCCTCCAAAGCATCAATTCCAACCACATTTCCTTCAAAACCATCAAATC
1 TTGGTTGAATAAAAACTCCTCCAAAGCACCAATTCCAACCACATTTCCTTCAAAACCATCAAATC
22893 AGT
66 AGT
22896 TTGGTTGAATAAAAACTCCTCCAAAGCACCAATTCCAACCACATTTCCTTCAAAACCATCAAATC
1 TTGGTTGAATAAAAACTCCTCCAAAGCACCAATTCCAACCACATTTCCTTCAAAACCATCAAATC
22961 AG
66 AG
22963 CCCCAACTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.25
Consensus pattern (68 bp):
TTGGTTGAATAAAAACTCCTCCAAAGCACCAATTCCAACCACATTTCCTTCAAAACCATCAAATC
AGT
Found at i:31182 original size:20 final size:20
Alignment explanation
Indices: 31157--31202 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31147 AAGAATTGAA
*
31157 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
31177 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
31197 GAGGGA
1 GAGGGA
31203 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:35751 original size:20 final size:20
Alignment explanation
Indices: 35726--35771 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35716 AAGAATTGAA
*
35726 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
35746 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
35766 GAGGGA
1 GAGGGA
35772 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:37114 original size:54 final size:54
Alignment explanation
Indices: 37056--37190 Score: 130
Period size: 54 Copynumber: 2.5 Consensus size: 54
37046 ATTGATTGAT
* *
37056 TTTGTGTTGAAGTGTTCTATGGTTTGAAAAGTCACCCACGGGGCAT-TGACGCAC
1 TTTGTGTTGAAGTGTTCTACGGTTTGAAAAGTCACCCACGGGGC-TGTGACGAAC
* * * * * **
37110 TTTGTGTTGAAATG-CCTTACGGTTTGGAAAGTTATCCACGGGGCTGTGATTAAC
1 TTTGTGTTGAAGTGTTC-TACGGTTTGAAAAGTCACCCACGGGGCTGTGACGAAC
* *
37164 TTTGGGTTGGAAGTGTTCTAGGGTTTG
1 TTTGTGTT-GAAGTGTTCTACGGTTTG
37191 GAATATCACC
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
53 2 0.03
54 48 0.75
55 13 0.20
56 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (54 bp):
TTTGTGTTGAAGTGTTCTACGGTTTGAAAAGTCACCCACGGGGCTGTGACGAAC
Found at i:37237 original size:14 final size:14
Alignment explanation
Indices: 37220--37271 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
37210 TCGTAACACG
37220 TTATAATTTTTATT
1 TTATAATTTTTATT
* *
37234 TTATTATTTTAATT
1 TTATAATTTTTATT
* *
37248 TTTTAATTGTTATT
1 TTATAATTTTTATT
37262 ATATATAATT
1 -T-TATAATT
37272 AATATTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 22 0.76
15 1 0.03
16 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATAATTTTTATT
Found at i:37333 original size:15 final size:15
Alignment explanation
Indices: 37315--37361 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
37305 TACATTATAT
37315 ATTATAAAATATAAA
1 ATTATAAAATATAAA
37330 ATTATTAAAA-ATAAA
1 ATTA-TAAAATATAAA
* *
37345 ATAAAAAAATAATAAA
1 ATTATAAAAT-ATAAA
37361 A
1 A
37362 AATATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 12 0.44
16 11 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTATAAAATATAAA
Found at i:37343 original size:22 final size:22
Alignment explanation
Indices: 37318--37362 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
37308 ATTATATATT
* * *
37318 ATAAAATATAAAATTATTAAAA
1 ATAAAATAAAAAAATAATAAAA
37340 ATAAAATAAAAAAATAATAAAA
1 ATAAAATAAAAAAATAATAAAA
37362 A
1 A
37363 ATATTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
ATAAAATAAAAAAATAATAAAA
Found at i:37362 original size:23 final size:22
Alignment explanation
Indices: 37318--37365 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
37308 ATTATATATT
* * *
37318 ATAAAATATAAAATTATTAAAA
1 ATAAAATAAAAAATAATAAAAA
37340 ATAAAATAAAAAAATAATAAAAA
1 ATAAAAT-AAAAAATAATAAAAA
37363 ATA
1 ATA
37366 TTATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
ATAAAATAAAAAATAATAAAAA
Found at i:44272 original size:2 final size:2
Alignment explanation
Indices: 44265--44291 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44255 TATTAATTAG
44265 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 T
44292 TTATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47341 original size:12 final size:12
Alignment explanation
Indices: 47324--47366 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
47314 TATTTATAAT
47324 ATTATATTTTTA
1 ATTATATTTTTA
47336 ATTATA-TTTTA
1 ATTATATTTTTA
47347 ATTAT-TTTTTA
1 ATTATATTTTTA
47358 TATTATATT
1 -ATTATATT
47367 ATATCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 15 0.54
12 11 0.39
13 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTATATTTTTA
Found at i:47344 original size:35 final size:33
Alignment explanation
Indices: 47305--47382 Score: 84
Period size: 35 Copynumber: 2.3 Consensus size: 33
47295 TCTTATTTAT
* *
47305 TATTTAAAATATTTATAATATTATATTTTTAATTA
1 TATTTAAAATATTTATAATATTATA-TTAT-ATCA
* * * *
47340 TATTTTAATTATTTTTTATATTATATTATATCA
1 TATTTAAAATATTTATAATATTATATTATATCA
47373 TATTTAAAAT
1 TATTTAAAAT
47383 TAAGTTTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 11 0.31
34 3 0.09
35 21 0.60
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
TATTTAAAATATTTATAATATTATATTATATCA
Found at i:48477 original size:54 final size:54
Alignment explanation
Indices: 48388--48513 Score: 157
Period size: 54 Copynumber: 2.4 Consensus size: 54
48378 TGTTTGCATG
* * * * *
48388 GAAAA-TCACCCACGGGACATTGATTGATTTTGTGTTGAAGTGT-TCTATGGTTT
1 GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCT-TATGGTTT
*
48441 GAAAAGTCACCCACGGGGCATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
1 GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
* *
48495 GGAAAGTCATCCACGGGAC
1 GAAAAGTCACCCACGGGAC
48514 TGTGGCTAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.08
54 56 0.90
55 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (54 bp):
GAAAAGTCACCCACGGGACATTGACTCACTTCGTGTTGAAATGTCTTATGGTTT
Found at i:50341 original size:51 final size:49
Alignment explanation
Indices: 50265--50363 Score: 126
Period size: 51 Copynumber: 2.0 Consensus size: 49
50255 CGATTTTAGT
* * * *
50265 TTTTTTTATTATCATTATTTATTGTTTGTATTTATTTATTGTGATAATATC
1 TTTTTTTATTATCATTATGTATTGTTT-AATTTATTAATTAT-ATAATATC
* *
50316 TTTTTTTGTTGTCATTATGTATTGTTTAATTTATTAATTATATAATAT
1 TTTTTTTATTATCATTATGTATTGTTTAATTTATTAATTATATAATAT
50364 TCGTTATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 7 0.17
50 11 0.26
51 24 0.57
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (49 bp):
TTTTTTTATTATCATTATGTATTGTTTAATTTATTAATTATATAATATC
Found at i:50409 original size:11 final size:11
Alignment explanation
Indices: 50387--50420 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
50377 TATTAATTAT
50387 ATTATATTTTTA
1 ATTAT-TTTTTA
50399 ATTATTTTTTA
1 ATTATTTTTTA
50410 ATTATTTTTTA
1 ATTATTTTTTA
50421 TATAATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTTTTTA
Found at i:50661 original size:29 final size:30
Alignment explanation
Indices: 50629--50698 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
50619 TATTACGTGA
50629 TAAAAATAATAATATTTTAATAA-T-ATATT
1 TAAAAATAATAATATTTTAATAATTAAT-TT
* *
50658 TAAAAATATTATTATTTTAATAATTAATTT
1 TAAAAATAATAATATTTTAATAATTAATTT
*
50688 TTAAAATAATA
1 TAAAAATAATA
50699 TTAATTTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.60
30 12 0.34
31 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAATAATAATATTTTAATAATTAATTT
Found at i:54323 original size:27 final size:27
Alignment explanation
Indices: 54293--54347 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54283 CAAAAATTTT
54293 TGCGAATTTTAAAGATGGATTTGATTC
1 TGCGAATTTTAAAGATGGATTTGATTC
54320 TGCGAATTTTAAAGATGGATTTGATTC
1 TGCGAATTTTAAAGATGGATTTGATTC
54347 T
1 T
54348 ATCATAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
TGCGAATTTTAAAGATGGATTTGATTC
Found at i:54355 original size:23 final size:24
Alignment explanation
Indices: 54302--54355 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 24
54292 TTGCGAATTT
**
54302 TAAAGATGGATTTGATTCTGCGAATTT
1 TAAAGATGGATTTGATTCT--G-ATCA
54329 TAAAGATGGATTTGATTCT-ATCA
1 TAAAGATGGATTTGATTCTGATCA
54352 TAAA
1 TAAA
54356 CAATCCATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.24
27 19 0.76
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (24 bp):
TAAAGATGGATTTGATTCTGATCA
Found at i:54621 original size:15 final size:15
Alignment explanation
Indices: 54603--54637 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54593 CTGTTGCAAA
54603 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
54618 AAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAC
*
54633 CAAAA
1 AAAAA
54638 TCGAATCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:54621 original size:16 final size:16
Alignment explanation
Indices: 54602--54637 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54592 TCTGTTGCAA
54602 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAC
* *
54618 AAAAAACAAAAAAACC
1 AAAAAAAAAAAAAAAC
54634 AAAA
1 AAAA
54638 TCGAATCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAC
Done.