Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1329
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: 38386
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:915 original size:15 final size:16
Alignment explanation
Indices: 897--928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
887 TTTATTGAGG
897 AATTAA-TTATTTTTA
1 AATTAATTTATTTTTA
912 AATTAATTTATTTTTA
1 AATTAATTTATTTTTA
928 A
1 A
929 CAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTAATTTATTTTTA
Found at i:1291 original size:35 final size:36
Alignment explanation
Indices: 1247--1323 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
1237 ATAATTAATT
*
1247 ATTTTTTAATATTTTAA-TAAGATTATAAAATCATA
1 ATTTTTTAATATTCTAATTAAGATTATAAAATCATA
* *
1282 ATTTTTTAATATTCTAATTACGATTATAAAATTATA
1 ATTTTTTAATATTCTAATTAAGATTATAAAATCATA
1318 ATTTTT
1 ATTTTT
1324 AAAATTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 16 0.42
36 22 0.58
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (36 bp):
ATTTTTTAATATTCTAATTAAGATTATAAAATCATA
Found at i:1849 original size:2 final size:2
Alignment explanation
Indices: 1842--1866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1832 AAAATACCAC
1842 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
1867 CAGAGATGTT
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:4359 original size:33 final size:33
Alignment explanation
Indices: 4317--4383 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
4307 CATCCAATTG
4317 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
1 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
4350 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
1 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
4383 A
1 A
4384 ACCCTTTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (33 bp):
AGAAAGGCTACTACCGAAGCCACAAGTATATAC
Found at i:6495 original size:13 final size:13
Alignment explanation
Indices: 6479--6508 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6469 ATACATTGTT
6479 CATTATATCGATA
1 CATTATATCGATA
*
6492 CATTGTATCGATA
1 CATTATATCGATA
6505 CATT
1 CATT
6509 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:8455 original size:51 final size:51
Alignment explanation
Indices: 8387--8554 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 51
8377 TCGAAAATAA
* *
8387 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
* *** * * *
8438 CGGGGTTGGAGTATCCCCGATTA-AAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGA-G-AAATCAATATTTTGGAAATAAAGC
* *
8490 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
* *
8541 TGAGGTTGGAGTAT
1 CGGGGTTGGAGTAT
8555 TCCCTCGGAA
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
50 1 0.01
51 52 0.55
52 40 0.43
53 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGC
Found at i:8565 original size:31 final size:28
Alignment explanation
Indices: 8530--8586 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 28
8520 TCAATATTTT
8530 GGAAATAAAGTTGAGGTTGGAGTATTCCCTC
1 GGAAATAAAG--G-GGTTGGAGTATTCCCTC
*
8561 GGAAATAACGGGGTTGGAGTATTCCC
1 GGAAATAAAGGGGTTGGAGTATTCCC
8587 GATGATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 15 0.60
29 1 0.04
31 9 0.36
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (28 bp):
GGAAATAAAGGGGTTGGAGTATTCCCTC
Found at i:11103 original size:32 final size:32
Alignment explanation
Indices: 11062--11123 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
11052 TTTCCAAATG
***
11062 TATCGATACAAAGATCCATGTATCGATACAAT
1 TATCGATACAAAGAAAAATGTATCGATACAAT
*
11094 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
11124 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (32 bp):
TATCGATACAAAGAAAAATGTATCGATACAAT
Found at i:11167 original size:19 final size:18
Alignment explanation
Indices: 11143--11210 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
11133 CAGTAGCTAA
11143 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
11162 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
11177 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
11194 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
11211 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:11183 original size:13 final size:13
Alignment explanation
Indices: 11165--11189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11155 ACAATACTTA
11165 TGTATCGATACAT
1 TGTATCGATACAT
11178 TGTATCGATACA
1 TGTATCGATACA
11190 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11187 original size:32 final size:32
Alignment explanation
Indices: 11146--11208 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11136 TAGCTAATTA
*
11146 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
11178 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
11209 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:11272 original size:21 final size:21
Alignment explanation
Indices: 11246--11323 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
11236 GTTGGGACCC
11246 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
11267 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
11287 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
11308 TGTATCGATACATTTG
1 TGTATCGATACATTTG
11324 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:11310 original size:41 final size:40
Alignment explanation
Indices: 11246--11327 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
11236 GTTGGGACCC
* *
11246 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
11287 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
11327 T
1 T
11328 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:11908 original size:55 final size:54
Alignment explanation
Indices: 11804--12552 Score: 988
Period size: 55 Copynumber: 13.5 Consensus size: 54
11794 AAGAGGAAAA
* * * * * * *
11804 TAAAGTGTATCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTT
1 TAAAG-GTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
11859 TGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
11914 TAAGAGGTGTCCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTT
1 TAA-AGGTGTCCTGCTCTTTGA-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** *
11969 TGAAA-ATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
1 T-AAAGGT-----G--TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
12030 TAAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
* *
12085 TGAAAGGTGTCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
12140 TGAGAGGTGTCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTT
12195 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
12251 TGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
12306 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
12361 TGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
12416 TAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
12471 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
12526 TAAGAGGTGTCCTGCTCTTTGAGGACT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT
12553 AAAAAGCGGA
Statistics
Matches: 631, Mismatches: 38, Indels: 50
0.88 0.05 0.07
Matches are distributed among these distances:
54 17 0.03
55 500 0.79
56 64 0.10
57 3 0.00
59 1 0.00
61 44 0.07
62 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (54 bp):
TAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:12429 original size:331 final size:332
Alignment explanation
Indices: 11838--12552 Score: 1170
Period size: 331 Copynumber: 2.1 Consensus size: 332
11828 AGTAAAAAGT
* *
11838 GCCACCAACTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAAC
1 GCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAAC
*
11902 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAGGGACTGAAAGGTGCCACCAACTTGTGTAGGC
65 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAGGGACTGAAAGGCGCCACCAACTTGTGTAGGC
11967 TTTGAAAATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTA
130 TTT----ATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTA
12032 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
191 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCC
* *
12097 TGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGA
256 TGCTCTTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGA
12162 GGACTAGAAGGC
321 GGACTAGAAGGC
12174 GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAAC
1 GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAAC
* * *
12239 TTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTT-GAGGACTGGAAGGCGCCACCAACTTGTGTGGG
65 TTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAG-GGACTGAAAGGCGCCACCAACTTGTGTAGG
* * ** * * *
12303 C-TT-TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA
129 CTTTATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAA
12366 GGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTG
194 GGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTG
*
12430 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGG
258 CTCTTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGG
*
12495 ACTGGAAGGC
323 ACTAGAAGGC
12505 GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
1 GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
12553 AAAAAGCGGA
Statistics
Matches: 358, Mismatches: 17, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
330 2 0.01
331 233 0.65
335 2 0.01
336 46 0.13
337 75 0.21
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (332 bp):
GCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACT
TGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAGGGACTGAAAGGCGCCACCAACTTGTGTAGGCT
TTATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGG
TGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTC
TTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
AGAAGGC
Found at i:13558 original size:13 final size:12
Alignment explanation
Indices: 13534--13580 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
13524 CTTTTCTCTC
*
13534 TTTTTCTTTGTT
1 TTTTTTTTTGTT
13546 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
**
13559 TTTTTTTTCCTT
1 TTTTTTTTTGTT
13571 TTTTTTTTTG
1 TTTTTTTTTG
13581 CTCTTTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:13587 original size:13 final size:13
Alignment explanation
Indices: 13531--13588 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
13521 TTTCTTTTCT
*
13531 CTCTTTTTCTTTG
1 CTCTTTTTTTTTG
*
13544 -TTTTGTTTTTTTG
1 CTCTT-TTTTTTTG
*
13557 -T-TTTTTTTTTC
1 CTCTTTTTTTTTG
*
13568 CTTTTTTTTTTTG
1 CTCTTTTTTTTTG
13581 CTCTTTTT
1 CTCTTTTT
13589 GTTGAAGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 7 0.19
12 6 0.16
13 24 0.65
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (13 bp):
CTCTTTTTTTTTG
Found at i:27636 original size:36 final size:35
Alignment explanation
Indices: 27610--27685 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 35
27600 AATTAATTAT
* *
27610 TTTTTTAATATTTTAATTAAGATTATAAAATCATAA
1 TTTTATAATATTCTAATTAAGATTATAAAAT-ATAA
*
27646 TTTTATAATATTCTAATTACGATTATAAAATTATAA
1 TTTTATAATATTCTAATTAAGATTATAAAA-TATAA
27682 TTTT
1 TTTT
27686 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 35 0.97
37 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (35 bp):
TTTTATAATATTCTAATTAAGATTATAAAATATAA
Found at i:28218 original size:2 final size:2
Alignment explanation
Indices: 28211--28237 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28201 AAAATACCAC
28211 AT 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 AT A
28238 CAGAGATGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30092 original size:33 final size:33
Alignment explanation
Indices: 30050--30116 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
30040 CATCCAATTG
30050 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
1 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
30083 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
1 AGAAAGGCTACTACCGAAGCCACAAGTATATAC
30116 A
1 A
30117 ACCCTTTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (33 bp):
AGAAAGGCTACTACCGAAGCCACAAGTATATAC
Found at i:32228 original size:13 final size:13
Alignment explanation
Indices: 32212--32241 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
32202 ATACATTGTT
32212 CATTATATCGATA
1 CATTATATCGATA
*
32225 CATTGTATCGATA
1 CATTATATCGATA
32238 CATT
1 CATT
32242 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:34516 original size:13 final size:13
Alignment explanation
Indices: 34498--34523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34488 CAATTTTTTG
34498 TGTATCGATACAT
1 TGTATCGATACAT
34511 TGTATCGATACAT
1 TGTATCGATACAT
34524 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:35263 original size:21 final size:21
Alignment explanation
Indices: 35222--35265 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35212 CTCTCCTTTA
* *
35222 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
35243 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
35264 TC
1 TC
35266 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:35297 original size:86 final size:86
Alignment explanation
Indices: 35193--35449 Score: 487
Period size: 86 Copynumber: 3.0 Consensus size: 86
35183 CTCCCCCTTA
35193 ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
1 ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
35258 AGTAATTCATATCAAAAATTC
66 AGTAATTCATATCAAAAATTC
** *
35279 ATAATTTAATTCATGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
1 ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
35344 AGTAATTCATATCAAAAATTC
66 AGTAATTCATATCAAAAATTC
35365 ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
1 ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
35430 AGTAATTCATATCAAAAATT
66 AGTAATTCATATCAAAAATT
35450 TATTTGCACA
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 165 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (86 bp):
ATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTCTCCCCCTTAATCA
AGTAATTCATATCAAAAATTC
Found at i:35349 original size:21 final size:21
Alignment explanation
Indices: 35308--35351 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35298 CTCTCCTTTA
* *
35308 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
35329 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
35350 TC
1 TC
35352 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:35435 original size:21 final size:21
Alignment explanation
Indices: 35394--35437 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35384 CTCTCCTTTA
* *
35394 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
35415 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
35436 TC
1 TC
35438 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:37267 original size:13 final size:13
Alignment explanation
Indices: 37249--37286 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
37239 ATAATCACCC
37249 TGTATCGATACAA
1 TGTATCGATACAA
*
37262 TGTATCGATATAA
1 TGTATCGATACAA
37275 TGTATCGATACA
1 TGTATCGATACA
37287 TTGAATTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Done.