Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_305
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: 97668
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:3475 original size:21 final size:21
Alignment explanation
Indices: 3451--3492 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3441 TCATCAGATC
3451 TACACCTTGA-GACATCGGGGG
1 TACACCTTGACGA-ATCGGGGG
**
3472 TACAGGTTGACGAATCGGGGG
1 TACACCTTGACGAATCGGGGG
3493 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (21 bp):
TACACCTTGACGAATCGGGGG
Found at i:5756 original size:30 final size:30
Alignment explanation
Indices: 5722--5781 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5712 CTTTAATACG
* *
5722 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTACCCCTA
* *
5752 AACTTTTGCATAATTACACTTTTACCCCTA
1 AACTTTGGCAAAATTACACTTTTACCCCTA
5782 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTACCCCTA
Found at i:8559 original size:50 final size:50
Alignment explanation
Indices: 8504--8797 Score: 326
Period size: 50 Copynumber: 5.8 Consensus size: 50
8494 ACCGAAGCTC
* *
8504 TCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATGTGACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * *
8554 TCTGGTACACATAGTAGCCTGCAATTAGTACTACACAAGTGACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* * * * * * *
8604 TCCGATACACGTAGTAGCCTGGA-TATAGTACTACACACGTGA-TTGAAGCTA
1 TCTGGTACACATAGTAGCCTGCACT-TAGTACTACACATGTGACCT-AA-CAA
* * * **
8655 TCAGGTACGCATAGTAGCCTGCACTTAGTTCTACACATGCAACCTAACAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
8705 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
* *
8754 -CTGTCTTAAACACATAGTAGCCTGCACATAGTACTACACATGTG
1 TCTG--GT--ACACATAGTAGCCTGCACTTAGTACTACACATGTG
8798 TTCTCACAAC
Statistics
Matches: 205, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
48 3 0.01
49 4 0.02
50 127 0.62
51 35 0.17
52 36 0.18
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAACAA
Found at i:8674 original size:101 final size:101
Alignment explanation
Indices: 8513--8746 Score: 276
Period size: 101 Copynumber: 2.3 Consensus size: 101
8503 CTCTGGTACG
* * * * *
8513 CATAGTAGCCTGCACTTAGTATTACACATGTGACCT-AA-CAATCTGGTACACATAGTAGCCTGC
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGCTATCAGGTACACATAGTAGCCTGC
** *
8576 AATTAGTACTACACAAGTGACCTAACCATCCGATACA
65 AATTAGTACTACACAAGCAACCTAACAATCCGATACA
* * *
8613 CGTAGTAGCCTGGA-TATAGTACTACACACGTGATTGAAGCTATCAGGTACGCATAGTAGCCTGC
1 CATAGTAGCCTGCACT-TAGTACTACACACGTGATTGAAGCTATCAGGTACACATAGTAGCCTGC
* * * * *
8677 ACTTAGTTCTACACATGCAACCTAACAATCTGGTACA
65 AATTAGTACTACACAAGCAACCTAACAATCCGATACA
*
8714 CATAGTAGCCTGCACTTAGTACTACACATGTGA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA
8747 CCTAAAACTG
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
99 2 0.02
100 29 0.26
101 79 0.71
102 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (101 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGCTATCAGGTACACATAGTAGCCTGCA
ATTAGTACTACACAAGCAACCTAACAATCCGATACA
Found at i:8742 original size:26 final size:26
Alignment explanation
Indices: 8710--8794 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
8700 AACAATCTGG
8710 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
** **
8736 TACACAT-GT-GACCTAAAACTGTCTTA-
1 TACACATAGTAG-CCT-GCACT-TAGTAC
* *
8762 AACACATAGTAGCCTGCACATAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
8788 TACACAT
1 TACACAT
8795 GTGTTCTCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
24 1 0.02
25 8 0.19
26 24 0.57
27 8 0.19
28 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACTTAGTAC
Found at i:27168 original size:47 final size:47
Alignment explanation
Indices: 27097--27482 Score: 646
Period size: 47 Copynumber: 8.2 Consensus size: 47
27087 CCCTTCGGGA
* * * * * *
27097 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
27144 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27191 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27238 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27285 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27379 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27426 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27473 CTTATCACAT
1 CTTATCACAT
27483 TCATCACATC
Statistics
Matches: 324, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 324 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27175 original size:25 final size:25
Alignment explanation
Indices: 27147--27225 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
27137 ACTCGGCCCT
27147 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
27172 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
*
27194 ATCACATATATACATTTTCACATTC
1 ATCACATATATACACTTTCACATTC
27219 ATCACAT
1 ATCACAT
27226 CGGCCATTAG
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 11 0.29
23 5 0.13
24 5 0.13
25 17 0.45
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:27354 original size:141 final size:140
Alignment explanation
Indices: 27097--27577 Score: 713
Period size: 141 Copynumber: 3.5 Consensus size: 140
27087 CCCTTCGGGA
* * * * * * * *
27097 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
* * *
27162 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATTTTCACATTCATCACATC
66 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACA-TTTCACATTCATCACATC
27227 GGCCATTAGGC
130 GGCCATTAGGC
* *
27238 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
27303 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACA-TTTCACATTCATCACATC
27368 GGCCATTAGGC
130 GGCCATTAGGC
27379 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
27444 TTTCACATTCACCACATCGGCCATTAGG------C-C---T-T--A--TCACATTCATCACATCG
66 TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACATTTCACATTCATCACATCG
27494 GCCATTAGGC
131 GCCATTAGGC
*
27504 CTTATCACATATATACACTTTCACATTCACCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
27569 TTTCACATT
66 TTTCACATT
27578 TATTCAAATA
Statistics
Matches: 325, Mismatches: 15, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
125 100 0.31
128 1 0.00
130 1 0.00
131 1 0.00
134 1 0.00
135 1 0.00
141 220 0.68
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (140 bp):
CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACATTTCACATTCATCACATCG
GCCATTAGGC
Found at i:27484 original size:31 final size:31
Alignment explanation
Indices: 27446--27513 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
27436 ATATACACTT
27446 TCACATTCACCACATCGGCCATTAGGCCTTA
1 TCACATTCACCACATCGGCCATTAGGCCTTA
*
27477 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCACCACATCGGCCATTAGGCCTTA
27508 TCACAT
1 TCACAT
27514 ATATACACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.34, G:0.12, T:0.28
Consensus pattern (31 bp):
TCACATTCACCACATCGGCCATTAGGCCTTA
Found at i:27504 original size:125 final size:125
Alignment explanation
Indices: 27352--27577 Score: 443
Period size: 125 Copynumber: 1.8 Consensus size: 125
27342 ATATACACTT
27352 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGG
27417 CCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTA
66 CCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTA
27477 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGG
*
27542 CTATTAGGCCTTATCACATATATACACTTTCACATT
66 CCATTAGGCCTTATCACATATATACACTTTCACATT
27578 TATTCAAATA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 100 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (125 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGG
CCATTAGGCCTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTA
Found at i:27528 original size:47 final size:47
Alignment explanation
Indices: 27477--27577 Score: 184
Period size: 47 Copynumber: 2.1 Consensus size: 47
27467 TTAGGCCTTA
*
27477 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACACTT
*
27524 TCACATTCACCACATCGGCTATTAGGCCTTATCACATATATACACTT
1 TCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACACTT
27571 TCACATT
1 TCACATT
27578 TATTCAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
TCACATTCACCACATCGGCCATTAGGCCTTATCACATATATACACTT
Found at i:34277 original size:37 final size:38
Alignment explanation
Indices: 34217--34289 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
34207 AGTACGCACT
*
34217 ATCGAGCCAAACCATACCTTTATATTGAATGAAGCTCA
1 ATCGAGCCAAACCATACCTTTATACTGAATGAAGCTCA
* *
34255 ATCGAG-CAAATCATA-CTATTATACTGAATGGAGCT
1 ATCGAGCCAAACCATACCT-TTATACTGAATGAAGCT
34290 TAACTAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 2 0.06
37 23 0.74
38 6 0.19
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (38 bp):
ATCGAGCCAAACCATACCTTTATACTGAATGAAGCTCA
Found at i:38604 original size:15 final size:15
Alignment explanation
Indices: 38584--38613 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38574 TGTATCAATC
38584 ATGTTTCACATATAT
1 ATGTTTCACATATAT
38599 ATGTTTCACATATAT
1 ATGTTTCACATATAT
38614 GTATATATAT
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:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
ATGTTTCACATATAT
Found at i:40189 original size:56 final size:56
Alignment explanation
Indices: 40129--40268 Score: 208
Period size: 56 Copynumber: 2.5 Consensus size: 56
40119 CCAGACAGGG
* * *
40129 TCTTACTCACACACATATATTAGAGTCACATATCGATGCCAACGTATTAAACGTGA
1 TCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGA
* *
40185 TCTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGG
1 TCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGA
* *
40241 TCTTACTCGCACATCACATATCGGAATC
1 TCTTACTCGCACA-CATATATCAGAATC
40269 CTATGTCATG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 64 0.83
57 13 0.17
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (56 bp):
TCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGA
Found at i:40687 original size:12 final size:12
Alignment explanation
Indices: 40664--40699 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
40654 TTTAATTATG
40664 TTATA-ATA-TA
1 TTATATATATTA
40674 TTATATATATTA
1 TTATATATATTA
40686 TTATATATATTA
1 TTATATATATTA
40698 TT
1 TT
40700 TACTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.21
11 3 0.12
12 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATTA
Found at i:40706 original size:19 final size:22
Alignment explanation
Indices: 40664--40706 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
40654 TTTAATTATG
*
40664 TTATAATATATTATATATATTA
1 TTATAATATATTATATATACTA
40686 TTAT-ATATATTAT-T-TACTA
1 TTATAATATATTATATATACTA
40705 TT
1 TT
40707 TTACATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 9 0.45
22 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAATATATTATATATACTA
Found at i:40714 original size:21 final size:21
Alignment explanation
Indices: 40669--40714 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40659 TTATGTTATA
*
40669 ATATATTATATATATTATTAT
1 ATATATTATATATATTATTAC
*
40690 ATATATTATTTACTATT-TTAC
1 ATATATTATATA-TATTATTAC
40711 ATAT
1 ATAT
40715 TTAACCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTATATATATTATTAC
Found at i:41833 original size:30 final size:30
Alignment explanation
Indices: 41799--41859 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41789 TTCCCGAGCC
41799 TAGGGGAAAAAGTGTAAATATGAAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGAAAAAGTT
* * * * *
41829 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGAAAAAGTT
41859 T
1 T
41860 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGAAAAAGTT
Found at i:42445 original size:68 final size:64
Alignment explanation
Indices: 42357--42637 Score: 244
Period size: 64 Copynumber: 4.3 Consensus size: 64
42347 CGGGATGCAT
42357 ACCATGT-GTACAAGAGAGCTACAAGACATTACGAGGTAGCTAGGTCGCATGGGTGATACTAAGT
1 ACCATGTAG-ACAAGAGAGCTAC--GACA-TA-GAGGTAGCTAGGTCGCATGGGTGATACTAAGT
42421 GTAC
61 GTAC
* ** * * *
42425 ACTATGTAGACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGGGTGATACTATGTGTAC
1 ACCATGTAGACAAGAGAGCTACGACATAGAGGTAGCTAGGTCGCATGGGTGATACTAAGTGTAC
* * * * * * * * * *
42489 ACCATGTAGACAAGAGAGCTACGAGATAAATGTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGG
1 ACCATGTAGACAAGAGAGCTACGACATAGAGGTAGCTAGGTCGCATGGGTGATACTAAGT---GT
42554 AC
63 AC
* * * * * * * *
42556 ACCATGTAAACAAAAGAGCTACGAGATA-AAGTGGCTAGGTCACATGGGTGGTACTAAGTGTTC
1 ACCATGTAGACAAGAGAGCTACGACATAGAGGTAGCTAGGTCGCATGGGTGATACTAAGTGTAC
42619 ACCATGT-GTACAAGAGAGC
1 ACCATGTAG-ACAAGAGAGC
42638 CAAAATTATG
Statistics
Matches: 178, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
63 18 0.10
64 84 0.47
65 2 0.01
66 25 0.14
67 29 0.16
68 19 0.11
69 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (64 bp):
ACCATGTAGACAAGAGAGCTACGACATAGAGGTAGCTAGGTCGCATGGGTGATACTAAGTGTAC
Found at i:42471 original size:64 final size:63
Alignment explanation
Indices: 42392--42637 Score: 278
Period size: 64 Copynumber: 3.8 Consensus size: 63
42382 ACATTACGAG
* *
42392 GTAGCTAGGTCGCATGGGTGATACTAAGTGTACACTATGTAGACAAGAGAGCTACGGGATATAT
1 GTAGCTAGGTCGCATGGGTGATACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATA-AT
*
42456 GTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAAAT
1 GTAGCTAGGTCGCATGGGTGATACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGAT-AAT
* * * * * * * * *
42520 GTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGGACACCATGTAAACAAAAGAGCTACGAGATAA
1 GTAGCTAGGTCGCATGGGTGATACTAAGT---GTACACCATGTAGACAAGAGAGCTACGAGATAA
*
42585 A
63 T
* * * *
42586 GTGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 GTAGCTAGGTCGCATGGGTGATACTAAGTGTACACCATGTAG-ACAAGAGAGC
42638 CAAAATTATG
Statistics
Matches: 153, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
63 18 0.12
64 82 0.54
65 1 0.01
66 24 0.16
67 28 0.18
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (63 bp):
GTAGCTAGGTCGCATGGGTGATACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAAT
Found at i:46649 original size:131 final size:131
Alignment explanation
Indices: 46411--46805 Score: 585
Period size: 131 Copynumber: 3.0 Consensus size: 131
46401 ATAATTATTC
* * * ** * *
46411 ATTTAAAAATTCTTAAAAACGAAGGAAATGTTCGATGTTTGGCAATTCAGGAAATCGTCGTTCCC
1 ATTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGT-G--CCC
* * *
46476 TATCGTGCTGGGTTGCGATTTCCCGTTCGTTCAAAACAATCAAATATTCCTTTGGAATATCACTC
63 TATCGTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTC
46541 ATGT
128 ATGT
* *
46545 CTTTAAAAACTCTTCAAAATGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
1 ATTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
*
46610 CGTGCTAGGTTGCGATTTCCTGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTCATG
66 CGTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTCATG
46675 T
131 T
46676 ATTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
1 ATTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
* * * * * *
46741 C-TGCTGGGTTGCGATCTCCTGTTTGTTCGAAATAACCGAATATTCCTTTAGAATTTCACTCATG
66 CGTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTCATG
46805 T
131 T
46806 TCTCTAAATT
Statistics
Matches: 239, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
130 57 0.24
131 132 0.55
133 1 0.00
134 49 0.21
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (131 bp):
ATTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
CGTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCAAATATTCCTTTGGAATTTCACTCATG
T
Found at i:47338 original size:30 final size:30
Alignment explanation
Indices: 47304--47438 Score: 166
Period size: 30 Copynumber: 4.5 Consensus size: 30
47294 TAAATCTTAG
*
47304 CCTTTTCCACCACCAACTCCACTAGCCACT
1 CCTTTTCCACCACCAACTCCACTAGCCACA
47334 CCTTTTCCACCACCAACTCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
*
47364 CCTTTTCCACCACCAAATCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
* ** * *
47394 -CTTGCTCCATTACCTACTCCACTAACCACA
1 CCTT-TTCCACCACCAACTCCACTAGCCACA
*
47424 -CTTGCTCCACCACCA
1 CCTT-TTCCACCACCA
47439 CTTGTACCTA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 3 0.03
30 90 0.97
ACGTcount: A:0.26, C:0.48, G:0.04, T:0.22
Consensus pattern (30 bp):
CCTTTTCCACCACCAACTCCACTAGCCACA
Found at i:47966 original size:23 final size:23
Alignment explanation
Indices: 47929--48056 Score: 70
Period size: 23 Copynumber: 5.5 Consensus size: 23
47919 CTTTTTTTGT
47929 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
47952 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
47974 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* *
47997 TATTACGTATATA-TATT-ATACTA
1 TATTA--TATATATTCTTAATATTA
* *
48020 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
*
48045 TATTATTTATAT
1 TATTATATATAT
48057 ATTTTTTTTC
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
21 8 0.10
22 15 0.19
23 25 0.32
24 8 0.10
25 22 0.28
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:48009 original size:25 final size:24
Alignment explanation
Indices: 47972--48061 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 24
47962 ATTCTTTTAA
* *
47972 TATATTAGGTATAT-TTTAAATTC
1 TATATTATGTATATATTTTAATTC
* * *
47995 TATATTACGTATATATATT-ATAC
1 TATATTATGTATATATTTTAATTC
*
48018 TATTTTATGTATATATCTTTAATAT-
1 TATATTATGTATATAT-TTTAAT-TC
*
48043 TATATTATTTATATATTTT
1 TATATTATGTATATATTTT
48062 TTTTCTACAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
23 30 0.57
24 7 0.13
25 16 0.30
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATTATGTATATATTTTAATTC
Found at i:48124 original size:25 final size:25
Alignment explanation
Indices: 48094--48142 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
48084 GTATATCTTA
**
48094 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
48119 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
48143 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:48327 original size:24 final size:24
Alignment explanation
Indices: 48295--48354 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
48285 TAATTATTAT
*
48295 TATTCTAATATTTTGATATTTT-GA
1 TATTTTAATATTTT-ATATTTTAGA
*
48319 TATTTTAATATTTTATATTTTATA
1 TATTTTAATATTTTATATTTTAGA
*
48343 TATTTTATTATT
1 TATTTTAATATT
48355 CACATCATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.22
24 25 0.78
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (24 bp):
TATTTTAATATTTTATATTTTAGA
Found at i:48338 original size:7 final size:8
Alignment explanation
Indices: 48302--48343 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
48292 TATTATTCTA
48302 ATATTTTG
1 ATATTTTG
48310 ATATTTTG
1 ATATTTTG
*
48318 ATATTTTA
1 ATATTTTG
48326 ATATTTT-
1 ATATTTTG
48333 ATATTTT-
1 ATATTTTG
48340 ATAT
1 ATAT
48344 ATTTTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 11 0.33
8 22 0.67
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (8 bp):
ATATTTTG
Found at i:48345 original size:16 final size:16
Alignment explanation
Indices: 48302--48350 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
48292 TATTATTCTA
*
48302 ATATTTTGATAT-TTTG
1 ATATTTT-ATATATTTT
48318 ATATTTTA-ATATTTT
1 ATATTTTATATATTTT
48333 ATATTTTATATATTTT
1 ATATTTTATATATTTT
48349 AT
1 AT
48351 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 2 0.07
15 12 0.40
16 16 0.53
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
ATATTTTATATATTTT
Found at i:61766 original size:47 final size:47
Alignment explanation
Indices: 61715--61984 Score: 416
Period size: 47 Copynumber: 5.7 Consensus size: 47
61705 TTAGGATTCT
* * *
61715 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
*
61762 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
61809 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
61856 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
61903 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
61950 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
61985 TCCCGAAGGG
Statistics
Matches: 207, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.00
47 206 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:62213 original size:36 final size:37
Alignment explanation
Indices: 62103--62254 Score: 234
Period size: 37 Copynumber: 4.1 Consensus size: 37
62093 CCGAGCTCTA
62103 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
*
62140 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
*
62177 AAGACCCGATGACTACGTGTGGGGA-TTTGTCCGGGT
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
* * * * *
62213 AAGACCCGATAACTTCATGTGGAGATTATGTTCGGGT
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
62250 AAGAC
1 AAGAC
62255 TTCGTAATAA
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 32 0.30
37 75 0.70
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
Found at i:62249 original size:73 final size:74
Alignment explanation
Indices: 62103--62254 Score: 234
Period size: 73 Copynumber: 2.1 Consensus size: 74
62093 CCGAGCTCTA
* * * *
62103 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGTAAGACCCGATGACTACGTGTGGGGATTT
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGTAAGACCCGATAACTACATGTGGAGATTA
62168 TGTCCGGGT
66 TGTCCGGGT
* *
62177 AAGACCCGATGACTACGTGTGGGGA-TTTGTCCGGGTAAGACCCGATAACTTCATGTGGAGATTA
1 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGTAAGACCCGATAACTACATGTGGAGATTA
*
62241 TGTTCGGGT
66 TGTCCGGGT
62250 AAGAC
1 AAGAC
62255 TTCGTAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 47 0.66
74 24 0.34
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (74 bp):
AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGTAAGACCCGATAACTACATGTGGAGATTA
TGTCCGGGT
Found at i:64851 original size:14 final size:14
Alignment explanation
Indices: 64832--64858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
64822 CGCTGAGGTA
64832 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
64846 TTTTCAATTTCTG
1 TTTTCAATTTCTG
64859 GTCTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:65033 original size:89 final size:89
Alignment explanation
Indices: 64694--65209 Score: 874
Period size: 89 Copynumber: 5.8 Consensus size: 89
64684 TGTTCCAAAG
* *
64694 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGTTGAGGTATTTTCAATTTTTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
*
64759 TTCCAATTTCTGCTCTTC-AAAAA
66 TTTCAATTTCTGCTCTTCAAAAAA
* *
64782 ATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
*
64847 TTTCAATTTCTGGTCTTCAAAAAAA
66 TTTCAATTTCTGCTCTTC-AAAAAA
* * *
64872 ATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
64937 TTTCAATTTCAT-CTCTTCAAAAAA
66 TTTCAATTTC-TGCTCTTCAAAAAA
*
64961 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
*
65026 TTCCAATTTCTGCTCTTCAAAAAA
66 TTTCAATTTCTGCTCTTCAAAAAA
*
65050 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
65115 TTTCAATTTCTGCTCTTCAAAAAA
66 TTTCAATTTCTGCTCTTCAAAAAA
*
65139 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
*
65204 CTTCAA
66 TTTCAA
65210 AAAAATCAAC
Statistics
Matches: 403, Mismatches: 21, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
88 78 0.19
89 242 0.60
90 82 0.20
91 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (89 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGCT
TTTCAATTTCTGCTCTTCAAAAAA
Found at i:65050 original size:178 final size:175
Alignment explanation
Indices: 64694--65300 Score: 961
Period size: 178 Copynumber: 3.5 Consensus size: 175
64684 TGTTCCAAAG
* *
64694 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGTTGAGGTATTTTCAATTTTTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
* *
64759 TTCCAATTTCTGCTCTTC-AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
66 TTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
*
64823 GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGGTCTTCAAAAAAA
131 GCTGAGGTATTTTC-ATTTCTG--TTTCAATTTCTGCTCTTC-AAAAAA
*
64872 ATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
64937 TTTCAATTTCAT-CTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
66 TTTCAATTTC-TGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
65001 CGCTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAA
130 CGCTGAGGTATTTTC-ATTTCTG-TTT-CAATTTCTGCTCTTCAAAAAA
*
65050 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
65115 TTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
66 TTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
65180 GCTGAGGTA---T--TTTC-G-----ATTTCTGCTCTTCAAAAAA
131 GCTGAGGTATTTTCATTTCTGTTTCAATTTCTGCTCTTCAAAAAA
65214 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTG-T
* *
65279 TTTTCAATTTATGCTTTTCAAA
65 TTTTCAATTTCTGCTCTTCAAA
65301 TTCTGCTTTT
Statistics
Matches: 411, Mismatches: 13, Indels: 23
0.92 0.03 0.05
Matches are distributed among these distances:
164 81 0.20
165 21 0.05
171 1 0.00
172 4 0.01
175 1 0.00
177 1 0.00
178 221 0.54
179 81 0.20
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (175 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
TTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
GCTGAGGTATTTTCATTTCTGTTTCAATTTCTGCTCTTCAAAAAA
Found at i:65119 original size:14 final size:14
Alignment explanation
Indices: 65100--65126 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65090 CGCTGAGGTA
65100 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
65114 TTTTCAATTTCTG
1 TTTTCAATTTCTG
65127 CTCTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:65169 original size:267 final size:251
Alignment explanation
Indices: 64694--65438 Score: 967
Period size: 267 Copynumber: 2.8 Consensus size: 251
64684 TGTTCCAAAG
*
64694 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGTTGAGGTATTTTCAATTTTTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGCT
*
64759 TTCCAATTTCTGCTCTTCAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
66 TTCCAATTTCTGCTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
64824 CTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGGTCTTCAAAAAAAATCAACTCATATTGCGA
131 CTGAGGTATTTTCAATTTCTGTTTTTCAATTTCT-GTCTTC-AAAAAAATCAACTCATATTGCGA
*
64889 GAGGCGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTTTTTCAATTTCAT-CTCT
194 GAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC-------G-------ATTTC-TGCTCT
64953 TCAAAAAA
244 TCAAAAAA
* *
64961 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGCT
65026 TTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
66 TTCCAATTTCTGCTCTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
65091 GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGA
130 GCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTG-TCTTCAAAAAAATCAACTCATATTGCGA
65156 GAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCTCTTCAAAAAA
194 GAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCTCTTCAAAAAA
65214 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTG--
* * * *
65279 TTTTCAATTTATGCTTTTCAAATTCTGCTTTTTAAAAAATCAACTCATATTGCTAGAGGTGAGTT
64 ----C---TT-T-C----CAATTTCTGCTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
** * ** *
65344 GAGCCTC-GGGTCACATG-TCGAGGTATTTTCAAAATCTGTTTTTCAAATTAAGT-TTCAAAGAA
116 GAGCCTCAGGG-CAC--GCT-GAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTCTTCAAAAAA
* *
65406 ACCAACTCATATGGCGAGAGGTGAGTTGAGCCT
177 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
65439 TAGCTCACGT
Statistics
Matches: 437, Mismatches: 19, Indels: 44
0.87 0.04 0.09
Matches are distributed among these distances:
252 1 0.00
253 78 0.18
259 1 0.00
260 1 0.00
262 2 0.00
263 1 0.00
264 1 0.00
266 3 0.01
267 221 0.51
268 99 0.23
269 29 0.07
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (251 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGCT
TTCCAATTTCTGCTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGTCTTCAAAAAAATCAACTCATATTGCGAGA
GGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCTCTTCAAAAAA
Found at i:65237 original size:75 final size:75
Alignment explanation
Indices: 65114--65273 Score: 311
Period size: 75 Copynumber: 2.1 Consensus size: 75
65104 CAATTTCTGT
65114 TTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
65179 CGCTGAGGTA
66 CGCTGAGGTA
*
65189 TTTTCGATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
65254 CGCTGAGGTA
66 CGCTGAGGTA
65264 TTTTCAATTT
1 TTTTCAATTT
65274 TTGTTTTTTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (75 bp):
TTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
CGCTGAGGTA
Found at i:65296 original size:15 final size:15
Alignment explanation
Indices: 65264--65311 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65254 CGCTGAGGTA
* *
65264 TTTTCAATTTTTGTT
1 TTTTCAATTTATGCT
65279 TTTTCAATTTATGC-
1 TTTTCAATTTATGCT
* *
65293 TTTTCAAATTCTGCT
1 TTTTCAATTTATGCT
65308 TTTT
1 TTTT
65312 AAAAAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTCAATTTATGCT
Found at i:66201 original size:30 final size:30
Alignment explanation
Indices: 66167--66301 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
66157 TAAATCTTAG
*
66167 CCTTTTCCGCCACCAACTCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
*
66197 CCTTTTCCACCACCAACTCCACTAGCCACT
1 CCTTTTCCACCACCAACTCCACTAGCCACA
*
66227 CCTTTTCCACCACCAAATCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
* ** * *
66257 -CTTGCTCCATTACCTACTCCACTAACCACA
1 CCTT-TTCCACCACCAACTCCACTAGCCACA
*
66287 -CTTGCTCCACCACCA
1 CCTT-TTCCACCACCA
66302 CTTGTACCTA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 3 0.03
30 88 0.97
ACGTcount: A:0.25, C:0.48, G:0.04, T:0.22
Consensus pattern (30 bp):
CCTTTTCCACCACCAACTCCACTAGCCACA
Found at i:66885 original size:27 final size:27
Alignment explanation
Indices: 66855--66973 Score: 75
Period size: 27 Copynumber: 4.5 Consensus size: 27
66845 ATTTTAAATT
66855 CTATATTACGTATATATATATTTTATA
1 CTATATTACGTATATATATATTTTATA
* * * *
66882 CTATTTTA--TGTATATATCTTTAATA
1 CTATATTACGTATATATATATTTTATA
* ** *
66907 TTATATTATTTATATATATATTTTTCTA
1 CTATATTACGTATATATATA-TTTTATA
* * * *
66935 C-ATGTTATCTTATGTATATATCTTA-A
1 CTATATTA-CGTATATATATATTTTATA
*
66961 CTATATTATGTAT
1 CTATATTACGTAT
66974 GTATTTTTAA
Statistics
Matches: 68, Mismatches: 19, Indels: 11
0.69 0.19 0.11
Matches are distributed among these distances:
25 20 0.29
26 5 0.07
27 28 0.41
28 15 0.22
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (27 bp):
CTATATTACGTATATATATATTTTATA
Found at i:66895 original size:25 final size:25
Alignment explanation
Indices: 66804--67010 Score: 88
Period size: 25 Copynumber: 8.2 Consensus size: 25
66794 ATTATATTTC
* *
66804 TTAATATTATATTATATATAT-TAT
1 TTAATACTATATTATGTATATATAT
* *
66828 TT--TAATATATTAGGTATAT-T-T
1 TTAATACTATATTATGTATATATAT
* * *
66849 TAAATTCTATATTACGTATATATATAT
1 TTAATACTATATTA--TGTATATATAT
* * *
66876 TTTATACTATTTTATGTATATATCT
1 TTAATACTATATTATGTATATATAT
* *
66901 TTAATATTATATTATTTATATATATATTTT
1 TTAATACTATATTA--TGTATATATA---T
** * *
66931 TCTACATGTTATCTTATGTATATAT-C
1 T-TA-ATACTATATTATGTATATATAT
* *
66957 TT-A-ACTATATTATGTATGTATTT
1 TTAATACTATATTATGTATATATAT
* * *
66980 TTAACACTATATTATGTACATATTT
1 TTAATACTATATTATGTATATATAT
67005 TTAATA
1 TTAATA
67011 TTATCACGTA
Statistics
Matches: 136, Mismatches: 31, Indels: 31
0.69 0.16 0.16
Matches are distributed among these distances:
21 2 0.01
22 29 0.21
23 11 0.08
24 3 0.02
25 49 0.36
26 2 0.01
27 19 0.14
30 10 0.07
31 2 0.01
32 9 0.07
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:66917 original size:30 final size:30
Alignment explanation
Indices: 66877--66958 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
66867 TATATATATT
*
66877 TTATACTATTTTATGTATATATCTTTAATA
1 TTATATTATTTTATGTATATATCTTTAATA
* **
66907 TTATATTA-TTTATATATATAT-TTTTCTA
1 TTATATTATTTTATGTATATATCTTTAATA
* * *
66935 -CATGTTATCTTATGTATATATCTT
1 TTATATTATTTTATGTATATATCTT
66959 AACTATATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 14 0.33
30 7 0.17
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (30 bp):
TTATATTATTTTATGTATATATCTTTAATA
Found at i:67187 original size:16 final size:15
Alignment explanation
Indices: 67163--67210 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
67153 TAATTATTAT
*
67163 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
67179 TATTTTAATATTTTA
1 TATTTTAATATTTTA
67194 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
67210 T
1 T
67211 TATTCACATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:67198 original size:7 final size:8
Alignment explanation
Indices: 67163--67214 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
67153 TAATTATTAT
*
67163 TATTCTAA
1 TATTTTAA
*
67171 TATTTTGA
1 TATTTTAA
67179 TATTTTAA
1 TATTTTAA
67187 TATTTT-A
1 TATTTTAA
67194 TATTTTATA
1 TATTTTA-A
*
67203 TATTTTAT
1 TATTTTAA
67211 TATT
1 TATT
67215 CACATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:73144 original size:28 final size:28
Alignment explanation
Indices: 73112--73181 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
73102 ATAGTAAGTC
*
73112 CGCACACTTAGTGCT-TAATAGTCAAACT
1 CGCACACTTAGTGCTATAA-AATCAAACT
*
73140 CGCACACTTAGTGCTATAAAATTAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
73168 CGCACACTTAGTGC
1 CGCACACTTAGTGC
73182 CAATCTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:80854 original size:26 final size:28
Alignment explanation
Indices: 80823--80889 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 28
80813 ATAGTAAGTC
80823 CGCACACTTAGTGCT-TA-ATATCAAACT
1 CGCACACTTAGTGCTATACA-ATCAAACT
*
80850 C-CACACTTA-TGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
80876 CGCACACTTAGTGC
1 CGCACACTTAGTGC
80890 CAATCTCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 4 0.11
26 18 0.51
27 10 0.29
28 3 0.09
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:88528 original size:28 final size:28
Alignment explanation
Indices: 88496--88566 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
88486 TATATAGTAA
88496 TCGCACACTTAGTGCT-TA-ATAGTCAAAC
1 TCGCACACTTAGTGCTATACA-A-TCAAAC
*
88524 TCGCACACTTAGTGCTATACAATTAAAC
1 TCGCACACTTAGTGCTATACAATCAAAC
88552 TCGCACACTTAGTGC
1 TCGCACACTTAGTGC
88567 CAATCTCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 36 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (28 bp):
TCGCACACTTAGTGCTATACAATCAAAC
Found at i:95533 original size:55 final size:53
Alignment explanation
Indices: 95466--95720 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 53
95456 ATTAGGGTTT
*
95466 AAGGATACCATGTAAGACCATG-CTAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * * *
95521 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * * *
95576 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* *
95629 AAGGATACCATGTAAGACAATGTCAAGACATGGAAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTCTAAGGC
* * *
95678 AAGGATACCAAGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGG-AATTGGTAAG
95721 GTACCCGCGT
Statistics
Matches: 167, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
49 36 0.22
50 2 0.01
52 7 0.04
53 40 0.24
54 11 0.07
55 66 0.40
56 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:95672 original size:108 final size:110
Alignment explanation
Indices: 95473--95673 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
95463 TTTAAGGATA
* *
95473 CCATGTAAGACCATGCTAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* * *
95538 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CAATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
* * *
95583 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
95645 ACAATGTCAAGACATGGAAATGGTAAGTT
65 ACAATGTCAAGACATGGAAATGATAAGTT
95674 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 7 0.09
110 25 0.31
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CAATGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:95932 original size:16 final size:16
Alignment explanation
Indices: 95911--95941 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95901 ATAAATTTGA
95911 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
95927 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
95942 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Done.