Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 135 of 228
Found at i:40341709 original size:40 final size:40
Alignment explanation
Indices: 40341664--40341931 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
40341654 GCAAACACAT
*
40341664 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40341704 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
40341744 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
40341784 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40341824 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40341864 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40341904 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40341932 TCCAATGCTC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40345039 original size:51 final size:49
Alignment explanation
Indices: 40344908--40345095 Score: 186
Period size: 51 Copynumber: 3.7 Consensus size: 49
40344898 GAAAGTTATG
* *
40344908 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAG-GTT
1 GTCA-GTGTGTAGTACTATGTGCAGGCTACTATGTGTACC-G---GATAGTATT
* *
40344961 G-CA-TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTT
1 GTCAGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATT
* * *
40345008 GATCATGTGTGTAGTACTATGTGCAGGCTACTACT-TGTATCGGATGGTAATG
1 G-TCA-GTGTGTAGTACTATGTGCAGGCTACTA-TGTGTACCGGATAGT-ATT
*
40345060 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 GTCA-GTGTGTAGTACTATGTGCAGGCTACTATGTG
40345096 AACTGAACAT
Statistics
Matches: 117, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
46 5 0.04
47 3 0.03
49 3 0.03
50 33 0.28
51 67 0.57
52 5 0.04
53 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (49 bp):
GTCAGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTATT
Found at i:40345112 original size:102 final size:101
Alignment explanation
Indices: 40344913--40345112 Score: 251
Period size: 102 Copynumber: 2.0 Consensus size: 101
40344903 TTATGGTCAC
**
40344913 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTTGCATGTGTAGTACTATG
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTATG
* * * *
40344978 TGCAGGCTACTATGCGTACCGGATAGTTTTGATCAT
66 TGCAGGCTACTATGCGAACCGAACAGTATTGATCAT
* * * *
40345014 GTGTGTAGTACTATGTGCAGGCTACTACTTGTATC-GGATGGTAATGGTCACATGTGTAGTACTA
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGAT-A-GGTCACATGTGTAGTACTA
* *
40345078 TGTGCAGGCTACTATGTGAACTGAACA-TCATTGAT
64 TGTGCAGGCTACTATGCGAACCGAACAGT-ATTGAT
40345113 TAGTAAGGTG
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
100 5 0.06
101 35 0.42
102 44 0.52
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTATG
TGCAGGCTACTATGCGAACCGAACAGTATTGATCAT
Found at i:40345188 original size:45 final size:45
Alignment explanation
Indices: 40345102--40345190 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
40345092 TGTGAACTGA
* *
40345102 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCAGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCAGAATCCACCGG
**
40345147 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCAGAATCCACCG
40345191 AGTATCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCAGAATCCACCGG
Found at i:40360097 original size:20 final size:20
Alignment explanation
Indices: 40360074--40360121 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40360064 TTAACTTAGT
*
40360074 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCAAGCTCAAG
* *
40360094 TCAGCTCATTCAAGCTCAAT
1 TCAGCTCACTCAAGCTCAAG
40360114 TCAGCTCA
1 TCAGCTCA
40360122 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (20 bp):
TCAGCTCACTCAAGCTCAAG
Found at i:40360099 original size:10 final size:10
Alignment explanation
Indices: 40360073--40360123 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
40360063 TTTAACTTAG
40360073 TTCAGCTC-A
1 TTCAGCTCAA
*
40360082 CTCGAGCTCAA
1 TTC-AGCTCAA
*
40360093 GTCAGCTC-A
1 TTCAGCTCAA
40360102 TTCAAGCTCAA
1 TTC-AGCTCAA
40360113 TTCAGCTCAA
1 TTCAGCTCAA
40360123 T
1 T
40360124 CTTAACCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 5 0.14
10 23 0.66
11 7 0.20
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:40362832 original size:13 final size:14
Alignment explanation
Indices: 40362816--40362846 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
40362806 AATGAAATCG
40362816 AGAAATGAAA-AAA
1 AGAAATGAAAGAAA
40362829 AGAAATGAAAGAAA
1 AGAAATGAAAGAAA
40362843 AGAA
1 AGAA
40362847 CAAGAAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (14 bp):
AGAAATGAAAGAAA
Found at i:40363808 original size:33 final size:33
Alignment explanation
Indices: 40363771--40363842 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
40363761 TGATCAAGCC
* *
40363771 AGGTAAAATCAAACTTTGTTTCCCTGCTCCAAA
1 AGGTAAAACCAAACTTTATTTCCCTGCTCCAAA
** *
40363804 AGGTAAAACCAAACTTTATTTTTCTGCTCCTAA
1 AGGTAAAACCAAACTTTATTTCCCTGCTCCAAA
40363837 AGGTAA
1 AGGTAA
40363843 GCCTCCTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (33 bp):
AGGTAAAACCAAACTTTATTTCCCTGCTCCAAA
Found at i:40366637 original size:40 final size:40
Alignment explanation
Indices: 40366578--40366845 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
40366568 GAGCATTGGA
* *
40366578 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
40366618 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
40366658 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
40366698 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
40366738 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
40366778 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
40366818 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
40366846 ATGTGTTTGC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:40375418 original size:40 final size:40
Alignment explanation
Indices: 40375373--40375640 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
40375363 GCAAACACAT
*
40375373 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40375413 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
40375453 TTGCCTTCGGGTTTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
40375493 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40375533 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40375573 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40375613 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40375641 TCCAATGCTC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40378420 original size:33 final size:33
Alignment explanation
Indices: 40378383--40378454 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
40378373 TTCAGGAGGC
* *
40378383 TTACCTTTAGGAGCAGAAAAATAAAGTTTGGTT
1 TTACCTTTAGGAGCAGAAAAACAAAGTTTGATT
* **
40378416 TTACCTTTTGGAGCAGGGAAACAAAGTTTGATT
1 TTACCTTTAGGAGCAGAAAAACAAAGTTTGATT
40378449 TTACCT
1 TTACCT
40378455 GGCTTGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (33 bp):
TTACCTTTAGGAGCAGAAAAACAAAGTTTGATT
Found at i:40379408 original size:14 final size:15
Alignment explanation
Indices: 40379363--40379414 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 15
40379353 TCACTCTCAT
*
40379363 TTTCTTTTTCGATTTCT
1 TTTCTTTTTC--TTTCA
40379380 TGTTCTTTTTCTTTCA
1 T-TTCTTTTTCTTTCA
40379396 TTTCTTTTT-TTTCA
1 TTTCTTTTTCTTTCA
40379410 TTTCT
1 TTTCT
40379415 CGATTTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 10 0.30
15 8 0.24
16 5 0.15
17 1 0.03
18 9 0.27
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTCTTTTTCTTTCA
Found at i:40382125 original size:10 final size:10
Alignment explanation
Indices: 40382110--40382160 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
40382100 TTGGGTTAAG
40382110 ATTGAGCTGA
1 ATTGAGCTGA
40382120 ATTGAGCTTGA
1 ATTGAGC-TGA
40382131 A-TGAGCTGA
1 ATTGAGCTGA
*
40382140 CTTGAGCTCG-
1 ATTGAGCT-GA
*
40382150 AGTGAGCTGA
1 ATTGAGCTGA
40382160 A
1 A
40382161 CTAAGTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 4 0.12
10 25 0.74
11 5 0.15
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:40382135 original size:20 final size:20
Alignment explanation
Indices: 40382112--40382160 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40382102 GGGTTAAGAT
*
40382112 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* *
40382132 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
40382152 TGAGCTGAA
1 TGAGCTGAA
40382161 CTAAGTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.27
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40384159 original size:33 final size:34
Alignment explanation
Indices: 40384117--40384191 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 34
40384107 GTAATAAATC
*
40384117 GAAAAAGAAGAAAAAGA-AAAGGCAAGTGA-AAAA
1 GAAAAAGAAGAAAAAGAGAAAGG-AAATGAGAAAA
*
40384150 GAAAAAGAAGAAAAAGAGAATGGAAATGAGAAAA
1 GAAAAAGAAGAAAAAGAGAAAGGAAATGAGAAAA
40384184 GAAAAAGA
1 GAAAAAGA
40384192 GAAGTGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.69, C:0.01, G:0.25, T:0.04
Consensus pattern (34 bp):
GAAAAAGAAGAAAAAGAGAAAGGAAATGAGAAAA
Found at i:40384199 original size:20 final size:20
Alignment explanation
Indices: 40384176--40384214 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40384166 AGAATGGAAA
40384176 TGAGA-AAAGAAAAAGAGAAG
1 TGAGAGAAA-AAAAAGAGAAG
40384196 TGAGAGAAAAAAAAGAGAA
1 TGAGAGAAAAAAAAGAGAA
40384215 AATTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (20 bp):
TGAGAGAAAAAAAAGAGAAG
Found at i:40384208 original size:25 final size:23
Alignment explanation
Indices: 40384149--40384208 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 23
40384139 CAAGTGAAAA
40384149 AGAAAAAGAAGAAAAAGAGAATGG
1 AGAAAAA-AAGAAAAAGAGAATGG
40384173 A-AATGAGAAAAGAAAAAGAGAAGTGAG
1 AGAA--A-AAAAGAAAAAGAGAA-TG-G
40384200 AGAAAAAAA
1 AGAAAAAAA
40384209 AGAGAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
23 2 0.07
24 1 0.03
25 18 0.60
26 5 0.17
27 2 0.07
28 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (23 bp):
AGAAAAAAAGAAAAAGAGAATGG
Found at i:40384268 original size:12 final size:12
Alignment explanation
Indices: 40384252--40384285 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
40384242 AGGAAGTGAA
40384252 AAAAAGAAAATTG
1 AAAAAG-AAATTG
40384265 AAAAAGAAATTG
1 AAAAAGAAATTG
40384277 AAGAAAGAA
1 AA-AAAGAA
40384286 GAGAAATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:40384308 original size:18 final size:17
Alignment explanation
Indices: 40384265--40384320 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
40384255 AAGAAAATTG
*
40384265 AAAAAGAAATTGAAGAAA
1 AAAAAGAAATCG-AGAAA
* *
40384283 GAAGAGAAATCGAGTAAA
1 AAAAAGAAATCGAG-AAA
40384301 AAAAAGAAA-CGAGAGAA
1 AAAAAGAAATCGAGA-AA
40384318 AAA
1 AAA
40384321 GAGGCAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 11 0.35
18 19 0.61
ACGTcount: A:0.68, C:0.04, G:0.21, T:0.07
Consensus pattern (17 bp):
AAAAAGAAATCGAGAAA
Found at i:40394601 original size:23 final size:23
Alignment explanation
Indices: 40394561--40394626 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
40394551 TAAACACGAA
*
40394561 ATTTTGTAAAGCCTTTGTGGCAT
1 ATTTTGTGAAGCCTTTGTGGCAT
* *
40394584 ATTTTGTGAAGTCGTTGTGGCAT
1 ATTTTGTGAAGCCTTTGTGGCAT
*
40394607 ATTCTGTGAAGCCTTTGTGG
1 ATTTTGTGAAGCCTTTGTGG
40394627 TGAGATCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (23 bp):
ATTTTGTGAAGCCTTTGTGGCAT
Found at i:40398291 original size:35 final size:35
Alignment explanation
Indices: 40398264--40398354 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
40398254 ATTGATATTT
* * * *
40398264 TGATTCGTATGTTAAGCGTGCTATTATTCTGGTTA
1 TGATTCGCATGTTAAGCATGCTATTATTATGATTA
* *
40398299 TGATTCGCATGTTAAGCATTCTATTATTTTGATTA
1 TGATTCGCATGTTAAGCATGCTATTATTATGATTA
*
40398334 TGACTT-GCATGTTAAACATGC
1 TGA-TTCGCATGTTAAGCATGC
40398355 CATTGTGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 46 0.96
36 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (35 bp):
TGATTCGCATGTTAAGCATGCTATTATTATGATTA
Found at i:40403618 original size:10 final size:9
Alignment explanation
Indices: 40403596--40403661 Score: 69
Period size: 10 Copynumber: 6.8 Consensus size: 9
40403586 GCTAATAACA
*
40403596 AGCTCAATG
1 AGCTGAATG
*
40403605 AGCTAAATTG
1 AGCTGAA-TG
40403615 AGCTCGAATG
1 AGCT-GAATG
40403625 AGCTTGAATG
1 AGC-TGAATG
40403635 AGCTGAATTG
1 AGCTGAA-TG
40403645 AGCTCGAATG
1 AGCT-GAATG
40403655 AGCTGAA
1 AGCTGAA
40403662 CCGCGTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
9 13 0.26
10 31 0.62
11 6 0.12
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.24
Consensus pattern (9 bp):
AGCTGAATG
Found at i:40403636 original size:30 final size:30
Alignment explanation
Indices: 40403601--40403658 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
40403591 TAACAAGCTC
40403601 AATGAGCTAAATTGAGCTCGAATGAGCTTG
1 AATGAGCTAAATTGAGCTCGAATGAGCTTG
*
40403631 AATGAGCTGAATTGAGCTCGAATGAGCT
1 AATGAGCTAAATTGAGCTCGAATGAGCT
40403659 GAACCGCGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.26
Consensus pattern (30 bp):
AATGAGCTAAATTGAGCTCGAATGAGCTTG
Found at i:40404461 original size:41 final size:41
Alignment explanation
Indices: 40404371--40404463 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 41
40404361 ATACTTTACA
* * * * * * *
40404371 TCTAGCAGGTTTGACGCCGGTGAAATATTTCGGACTTTATG
1 TCTAGCAGGCTTAACGCCGGTGAAACAATTCGAACTATAAG
* *
40404412 TCTGGCAGGCTTAATGCCGGTGAAACAATTCGAACTATAAG
1 TCTAGCAGGCTTAACGCCGGTGAAACAATTCGAACTATAAG
40404453 TCTAGCAGGCT
1 TCTAGCAGGCT
40404464 AAAAGCTGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (41 bp):
TCTAGCAGGCTTAACGCCGGTGAAACAATTCGAACTATAAG
Found at i:40412011 original size:41 final size:41
Alignment explanation
Indices: 40411963--40412042 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
40411953 TGATCGAATG
* *
40411963 TTTCAGACTTTACCTCTAGCAGGTTTGATGCCGGTGAAATA
1 TTTCAGACTTTACCTCTAGCAGGCTTAATGCCGGTGAAATA
**
40412004 TTTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAAA
1 TTTCAGACTTTACCTCTAGCAGGCTTAATGCCGGTGAAA
40412043 CAATTTGGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTCAGACTTTACCTCTAGCAGGCTTAATGCCGGTGAAATA
Found at i:40412062 original size:41 final size:41
Alignment explanation
Indices: 40411963--40412080 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 41
40411953 TGATCGAATG
* ** * * *
40411963 TTTCAGACTTTACCTCTAGCAGGTTTGATGCCGGTGAAATA
1 TTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAAAAA
* *
40412004 TTTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAAACAA
1 TTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAAA-AA
* * *
40412046 TTT-GGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 TTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTG
40412081 TACTAAATCA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
41 62 0.94
42 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (41 bp):
TTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAAAAA
Found at i:40412231 original size:32 final size:32
Alignment explanation
Indices: 40412194--40412288 Score: 81
Period size: 32 Copynumber: 3.0 Consensus size: 32
40412184 TTGAAGAACA
*
40412194 TGTATATACATTCGGTGATAATATTTGTTATG
1 TGTATATACATTCGGTGATAATATTTGTTAAG
* * *
40412226 TGTATA-AGCATTTGGCT-AT-TTATGTT-TAAAG
1 TGTATATA-CATTCGG-TGATAATAT-TTGTTAAG
* *
40412257 TGTATATGCATTCGATGATAATATTTGTTAAG
1 TGTATATACATTCGGTGATAATATTTGTTAAG
40412289 CATATATGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
30 1 0.02
31 22 0.47
32 23 0.49
33 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (32 bp):
TGTATATACATTCGGTGATAATATTTGTTAAG
Found at i:40413168 original size:39 final size:39
Alignment explanation
Indices: 40413091--40413350 Score: 421
Period size: 39 Copynumber: 6.6 Consensus size: 39
40413081 TATATTTACT
* *
40413091 TTTAAGCATATATCATATATTACACATATAATCACATAACA
1 TTTAAGCATATATCACA-A-TACTCATATAATCACATAACA
40413132 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * * *
40413171 TTCAAACATATATCACAATTCTCATATAATCAGATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
40413210 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
40413249 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
40413288 TTTAAGCATATATCACAATACTCATATCATCATATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
40413327 TTTAAGCATATATCATAATACTCA
1 TTTAAGCATATATCACAATACTCA
40413351 AAAACATGTT
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 189 0.92
40 1 0.00
41 16 0.08
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:40417014 original size:4 final size:4
Alignment explanation
Indices: 40417005--40417038 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40416995 AAGTTTTATT
40417005 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
40417039 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:40417046 original size:22 final size:22
Alignment explanation
Indices: 40416988--40417047 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
40416978 AAGTGGCCCA
*
40416988 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
40417012 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
40417033 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
40417048 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:40421480 original size:22 final size:23
Alignment explanation
Indices: 40421455--40421514 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
40421445 TGGACTGAAT
40421455 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
40421477 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
40421499 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
40421515 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:40421482 original size:4 final size:4
Alignment explanation
Indices: 40421464--40421497 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
40421454 TATAAAAATT
40421464 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
40421498 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:40421821 original size:20 final size:20
Alignment explanation
Indices: 40421788--40421855 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
40421778 AAGCACCATA
40421788 GTGCAAT-AGAGGCACAAAT
1 GTGCAATCAGAGGCACAAAT
* *
40421807 GTACAATCGGAGGCACCAAA-
1 GTGCAATCAGAGGCA-CAAAT
40421827 GTGCAAAT-AGAGGCACAAAT
1 GTGC-AATCAGAGGCACAAAT
40421847 GTGCAATCA
1 GTGCAATCA
40421856 AAGGTAGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 13 0.32
20 20 0.50
21 7 0.17
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (20 bp):
GTGCAATCAGAGGCACAAAT
Found at i:40421875 original size:40 final size:40
Alignment explanation
Indices: 40421780--40421859 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
40421770 CTAAATAAAA
* **
40421780 GCACCATAGTGC-AATAGAGGCACAAATGTACAATCGGAG
1 GCACCAAAGTGCAAATAGAGGCACAAATGTACAATCAAAG
*
40421819 GCACCAAAGTGCAAATAGAGGCACAAATGTGCAATCAAAG
1 GCACCAAAGTGCAAATAGAGGCACAAATGTACAATCAAAG
40421859 G
1 G
40421860 TAGTGAAGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 11 0.31
40 25 0.69
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (40 bp):
GCACCAAAGTGCAAATAGAGGCACAAATGTACAATCAAAG
Found at i:40425892 original size:20 final size:20
Alignment explanation
Indices: 40425867--40425905 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40425857 AAGAAGATGA
40425867 TAATATATATTTT-ACTTTAT
1 TAATAT-TATTTTAACTTTAT
40425887 TAATATTATTTTAACTTTA
1 TAATATTATTTTAACTTTA
40425906 AAAATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTATTTTAACTTTAT
Found at i:40425911 original size:20 final size:20
Alignment explanation
Indices: 40425868--40425911 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40425858 AGAAGATGAT
**
40425868 AATATATATTTTACTTTATT
1 AATATATATTTTACTTTAAA
40425888 AATAT-TATTTTAACTTTAAA
1 AATATATATTTT-ACTTTAAA
40425908 AATA
1 AATA
40425912 AAGTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
AATATATATTTTACTTTAAA
Found at i:40437654 original size:16 final size:17
Alignment explanation
Indices: 40437635--40437667 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40437625 TAATCGTAAG
40437635 ATTAA-TTAAATTAATT
1 ATTAATTTAAATTAATT
*
40437651 ATTAATTTAATTTAATT
1 ATTAATTTAAATTAATT
40437668 TGACAGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAATTTAAATTAATT
Found at i:40442841 original size:13 final size:14
Alignment explanation
Indices: 40442818--40442854 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
40442808 TCTTTGATTT
40442818 ATTATTTTATTTGA
1 ATTATTTTATTTGA
40442832 ATTA-TTTATTTGA
1 ATTATTTTATTTGA
*
40442845 ATTGTTTTAT
1 ATTATTTTAT
40442855 CTGACTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (14 bp):
ATTATTTTATTTGA
Found at i:40447339 original size:41 final size:41
Alignment explanation
Indices: 40447045--40447369 Score: 248
Period size: 41 Copynumber: 7.9 Consensus size: 41
40447035 CTTTGAGTCC
* * * * * *
40447045 AGCAGGCTTCATGCCAGTGATTTACATCAGGTTTTGTGTCT
1 AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCT
* * * * * * *
40447086 AGCAGACTCCGTGTCAG-CATGTTCTATCAGGCTCTGTGCAT
1 AGCAGGCTTCGTGCCGGTGAT-TTATATCAGGCTCTGTGCCT
* * ** * *
40447127 ACCAGGTTTCGTGCCTATGATTTATATCTGGCT-TAGTGACT
1 AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCT-GTGCCT
* * * *
40447168 AGCAGTCTTCGTGCCAGTGATTTATATTAGGCTCTATGCCT
1 AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCT
* * *
40447209 AGCAAGG-TTCGTGTCGATGATTTATATCAGGCTCTATGCCT
1 AGC-AGGCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCT
* * * * * *
40447250 AGCAGGCTTAGTGTCAGTGATTTATATTAGGTTCAGTGCCT
1 AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCT
*
40447291 AGCAGGCTTGGTGCCGGTGATTTATATCAGGCTCTGTAG-CT
1 AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCTGT-GCCT
*
40447332 A-CTAGGCTTAGTAG-CGGTGATTTATATCAGGCTCTGTG
1 AGC-AGGCTTCGT-GCCGGTGATTTATATCAGGCTCTGTG
40447370 TCGGTGTAAT
Statistics
Matches: 224, Mismatches: 51, Indels: 19
0.76 0.17 0.06
Matches are distributed among these distances:
40 8 0.04
41 209 0.93
42 7 0.03
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (41 bp):
AGCAGGCTTCGTGCCGGTGATTTATATCAGGCTCTGTGCCT
Found at i:40447353 original size:123 final size:123
Alignment explanation
Indices: 40447144--40447366 Score: 285
Period size: 123 Copynumber: 1.8 Consensus size: 123
40447134 TTCGTGCCTA
* *
40447144 TGATTTATATCTGGCTTAGTGACTAGCAGTCTTCGTGCCAGTGATTTATATTAGGCTCTATGCCT
1 TGATTTATATCTGGCTTAGTGACTAGCAGGCTTCGTGCCAGTGATTTATATCAGGCTCTATGCCT
*
40447209 AGCAAGGTTCGTGTCGATGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
66 AGCAAGGTTAGTGTCGATGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
* * * *
40447267 TGATTTATAT-TAGG-TTCAGTGCCTAGCAGGCTTGGTGCCGGTGATTTATATCAGGCTCTGTAG
1 TGATTTATATCT-GGCTT-AGTGACTAGCAGGCTTCGTGCCAGTGATTTATATCAGGCTCTAT-G
* *
40447330 -CTA-CTAGGCTTAGTAG-CGGTGATTTATATCAGGCTCT
63 CCTAGCAAGG-TTAGT-GTCGATGATTTATATCAGGCTCT
40447367 GTGTCGGTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
122 7 0.08
123 77 0.90
124 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (123 bp):
TGATTTATATCTGGCTTAGTGACTAGCAGGCTTCGTGCCAGTGATTTATATCAGGCTCTATGCCT
AGCAAGGTTAGTGTCGATGATTTATATCAGGCTCTATGCCTAGCAGGCTTAGTGTCAG
Found at i:40453712 original size:30 final size:29
Alignment explanation
Indices: 40453676--40453735 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
40453666 TTCGAGCTTT
*
40453676 GGGGCAAAAGT-GTAATTATGTAAAAGTTTA
1 GGGGCAAAA-TCGTAATTATGCAAAA-TTTA
*
40453706 GGGGCAAAATCGTAATTTTGCAAAATTTA
1 GGGGCAAAATCGTAATTATGCAAAATTTA
40453735 G
1 G
40453736 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (29 bp):
GGGGCAAAATCGTAATTATGCAAAATTTA
Found at i:40454180 original size:50 final size:50
Alignment explanation
Indices: 40454125--40454316 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
40454115 CATTGAGATT
*
40454125 ATGAGAGGTCCCATGTAAGACCATATCGGGGACATGGCATTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
* * * *
40454175 ATGAGAGGTCCCCCAT-T-AGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGT--CCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
** * *
40454225 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCA--CCAAG
** * *
40454277 A--A-ACATCCCATGTAAGACCATGTCTAGGACATGGCATTGG
1 ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGG
40454317 AATATTATTA
Statistics
Matches: 118, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
48 5 0.04
49 34 0.29
50 70 0.59
51 1 0.01
52 8 0.07
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAG
Found at i:40463837 original size:14 final size:14
Alignment explanation
Indices: 40463818--40463849 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40463808 ATTTTCTCTC
*
40463818 TTTCTTTTCTTTAA
1 TTTCTTTACTTTAA
40463832 TTTCTTTACTTTAA
1 TTTCTTTACTTTAA
40463846 TTTC
1 TTTC
40463850 ATTCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCTTTACTTTAA
Found at i:40486850 original size:23 final size:23
Alignment explanation
Indices: 40486823--40486875 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40486813 ACTCAATTTA
*
40486823 TTTTCTCTCT-ATTTTTCTTTTT
1 TTTTCTCTCTCATTTTTATTTTT
* *
40486845 TCTTTCTTTTTCATTTTTATTTTT
1 T-TTTCTCTCTCATTTTTATTTTT
40486869 TTTTCTC
1 TTTTCTC
40486876 ATTTGCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 12 0.48
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTCTCTCATTTTTATTTTT
Found at i:40486854 original size:17 final size:17
Alignment explanation
Indices: 40486834--40486874 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40486824 TTTCTCTCTA
*
40486834 TTTTTCTTTTTTCTTTC
1 TTTTTCTTTTTTATTTC
* *
40486851 TTTTTCATTTTTATTTT
1 TTTTTCTTTTTTATTTC
40486868 TTTTTCT
1 TTTTTCT
40486875 CATTTGCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTTATTTC
Found at i:40489597 original size:20 final size:20
Alignment explanation
Indices: 40489572--40489610 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40489562 TACTTTCTTC
40489572 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
40489592 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
40489611 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:40489957 original size:50 final size:52
Alignment explanation
Indices: 40489873--40490000 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 52
40489863 GTGCCCATTT
* * *
40489873 CATGTCCCCGACATGGTCTTACGGGGCACTTCTCAT-CTC-AGTCCCAATGC
1 CATGTCCCAGACATGGTCTTACGGGGCACCTCTCATACTCAAATCCCAATGC
* *
40489923 CATGTCCCAGACATGGTCTTATGTGGG-ACCTCTCATAACCTCAATAATGCCAATGC
1 CATGTCCCAGACATGGTCTTACG-GGGCACCTCTCAT-A-CTC-A-AATCCCAATGC
*
40489979 CATGTCCCAGACATGGTATTAC
1 CATGTCCCAGACATGGTCTTAC
40490001 ATGGGATCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
50 29 0.45
51 3 0.05
53 3 0.05
56 29 0.45
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (52 bp):
CATGTCCCAGACATGGTCTTACGGGGCACCTCTCATACTCAAATCCCAATGC
Found at i:40493168 original size:16 final size:16
Alignment explanation
Indices: 40493128--40493171 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
40493118 AAATAACATC
40493128 AAGACAT-ATT-AATT
1 AAGACATAATTAAATT
*
40493142 AATACACTAATTAAATT
1 AAGACA-TAATTAAATT
40493159 AAGACATAATTAA
1 AAGACATAATTAA
40493172 TATAGACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 10 0.40
17 9 0.36
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (16 bp):
AAGACATAATTAAATT
Found at i:40498917 original size:11 final size:11
Alignment explanation
Indices: 40498901--40498925 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40498891 GCGATTATTG
40498901 TATTTATTGTA
1 TATTTATTGTA
40498912 TATTTATTGTA
1 TATTTATTGTA
40498923 TAT
1 TAT
40498926 AAAGGGACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATTTATTGTA
Found at i:40506387 original size:12 final size:12
Alignment explanation
Indices: 40506372--40506396 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40506362 TCACAAGCAG
40506372 CAAATATCTCAC
1 CAAATATCTCAC
40506384 CAAATATCTCAC
1 CAAATATCTCAC
40506396 C
1 C
40506397 TAGCAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (12 bp):
CAAATATCTCAC
Found at i:40507925 original size:31 final size:31
Alignment explanation
Indices: 40507890--40507949 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40507880 CAATCAAACA
*
40507890 TTTTTTCTCATATTCTTTT-TCCTTTTCTTCC
1 TTTTTT-TCATATTCTTTTCTCATTTTCTTCC
* *
40507921 TTTTTTTCTTTTTCTTTTCTCATTTTCTT
1 TTTTTTTCATATTCTTTTCTCATTTTCTT
40507950 TTATCTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTTTTTCATATTCTTTTCTCATTTTCTTCC
Found at i:40507932 original size:6 final size:6
Alignment explanation
Indices: 40507902--40508009 Score: 64
Period size: 6 Copynumber: 18.0 Consensus size: 6
40507892 TTTTCTCATA
* * *
40507902 TTCTTT TTCCTT TTCTTCC TT-TTT TTCTTT TTCTTT TCTCATT TTCTTT
1 TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT TTCTTT T-TCTTT TTCTTT
* * * * *
40507951 TATCTTT CTCTTG TT-ATT TTC-TT TTCTTT TCCTCATT TTC-AT TT-TTT
1 T-TCTTT TTCTTT TTCTTT TTCTTT TTCTTT T--TCTTT TTCTTT TTCTTT
40507998 TTCTTT TTCTTT
1 TTCTTT TTCTTT
40508010 CAATTGATCT
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
5 16 0.21
6 45 0.58
7 12 0.15
8 5 0.06
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:40507940 original size:43 final size:41
Alignment explanation
Indices: 40507892--40508001 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 41
40507882 ATCAAACATT
* *
40507892 TTTTCTCATATTCTTTTTCCTTT-TCTTCCTTTTTTTCTTTTTC
1 TTTTCTCATTTTCTTTTT-CTTTCTCTT-CTTATTTTC-TTTTC
*
40507935 TTTTCTCATTTTCTTTTATCTTTCTCTTGTTATTTTCTTTTC
1 TTTTCTCATTTTCTTTT-TCTTTCTCTTCTTATTTTCTTTTC
40507977 TTTTCCTCATTTTCATTTTT-TTTCT
1 TTTT-CTCATTTTC-TTTTTCTTTCT
40508002 TTTTCTTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
42 14 0.23
43 37 0.62
44 9 0.15
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (41 bp):
TTTTCTCATTTTCTTTTTCTTTCTCTTCTTATTTTCTTTTC
Found at i:40507951 original size:24 final size:23
Alignment explanation
Indices: 40507902--40508009 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 23
40507892 TTTTCTCATA
*
40507902 TTCTTTTTCCTTTTCTTC-CTTTTT
1 TTCTTTTT-CTTTTC-TCATTTTTT
40507926 TTCTTTTTCTTTTCTCATTTTCTT
1 TTCTTTTTCTTTTCTCATTTT-TT
* * * * *
40507950 TTATCTTTCTCTTGTTATTTTCTT
1 TTCTTTTTCTTTTCTCATTTT-TT
*
40507974 TTCTTTTCCTCATTT-TCATTTTTT
1 TTCTTTT--TCTTTTCTCATTTTTT
40507998 TTCTTTTTCTTT
1 TTCTTTTTCTTT
40508010 CAATTGATCT
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
22 6 0.09
23 9 0.13
24 43 0.63
25 6 0.09
26 4 0.06
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (23 bp):
TTCTTTTTCTTTTCTCATTTTTT
Found at i:40513132 original size:35 final size:36
Alignment explanation
Indices: 40513052--40513134 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 36
40513042 ACACCAGTCC
* *
40513052 TCTTTCAATTAACATCCTGCCACAAACACCGATACT
1 TCTTTCAATTAACATCCTGACACAAACACCAATACT
*
40513088 TCTTTCAATTAACATCCT-ACA-AGAACATCAATACT
1 TCTTTCAATTAACATCCTGACACA-AACACCAATACT
*
40513123 TCTTCCAATTAA
1 TCTTTCAATTAA
40513135 TATCAAGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.02
35 23 0.55
36 18 0.43
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (36 bp):
TCTTTCAATTAACATCCTGACACAAACACCAATACT
Found at i:40538486 original size:39 final size:39
Alignment explanation
Indices: 40538366--40538495 Score: 167
Period size: 39 Copynumber: 3.3 Consensus size: 39
40538356 GCTACTCGTT
40538366 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGAC-TAGCCCGGATT-TAGTAACTCGCA
* * *
40538406 CAATTGCCTTCGGGACTA-CCCAGATTTAGTAACTCGGA
1 CAAATGCCTTCGGGACTAGCCCGGATTTAGTAACTCGCA
* *
40538444 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGAC-TAGCCCGGATTTAGTAACTCGCA
40538483 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40538496 ATCTTAGTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
37 1 0.01
38 30 0.38
39 33 0.42
40 15 0.19
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTAGCCCGGATTTAGTAACTCGCA
Found at i:40543020 original size:11 final size:11
Alignment explanation
Indices: 40543004--40543028 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40542994 TTAGAATGTC
40543004 CCTTGAAGCTT
1 CCTTGAAGCTT
40543015 CCTTGAAGCTT
1 CCTTGAAGCTT
40543026 CCT
1 CCT
40543029 AGAATAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (11 bp):
CCTTGAAGCTT
Found at i:40543913 original size:10 final size:10
Alignment explanation
Indices: 40543898--40543964 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
40543888 AAAATAAAAA
40543898 TGAGCTAAAT
1 TGAGCTAAAT
*
40543908 TGAGCTAAGT
1 TGAGCTAAAT
*
40543918 TGAGCTGAAT
1 TGAGCTAAAT
* *
40543928 TAAGCTCAA-
1 TGAGCTAAAT
40543937 TGAGCTAGAATT
1 TGAGCTA-AA-T
*
40543949 TGAGTTAAAT
1 TGAGCTAAAT
*
40543959 TAAGCT
1 TGAGCT
40543965 TGCATAGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 5 0.11
10 31 0.70
11 2 0.05
12 6 0.14
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (10 bp):
TGAGCTAAAT
Found at i:40549075 original size:19 final size:21
Alignment explanation
Indices: 40549043--40549081 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40549033 AATAGAAATC
40549043 AGCTCAATAAAGCTA-AATTA
1 AGCTCAATAAAGCTAGAATTA
*
40549063 AGCTCAAT-TAGCTAGAATT
1 AGCTCAATAAAGCTAGAATT
40549082 CAAGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (21 bp):
AGCTCAATAAAGCTAGAATTA
Found at i:40553103 original size:47 final size:47
Alignment explanation
Indices: 40553034--40553366 Score: 549
Period size: 47 Copynumber: 7.1 Consensus size: 47
40553024 GAAAAGATAG
40553034 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40553081 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40553128 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40553175 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40553222 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40553269 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*** * * * * * * *
40553316 CGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40553363 TAAG
1 TAAG
40553367 TCCCGAAGGG
Statistics
Matches: 267, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 267 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40553541 original size:37 final size:37
Alignment explanation
Indices: 40553485--40553563 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40553475 CCGAGCTCTA
* *
40553485 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
40553522 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40553559 AAGAC
1 AAGAC
40553564 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40556115 original size:18 final size:18
Alignment explanation
Indices: 40556092--40556140 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
40556082 TCAACCTCAA
* *
40556092 AATTTTTATTTTCATTTT
1 AATTTTTATTTTAATATT
40556110 AATTTTTTATTTTTAATATT
1 AA-TTTTTA-TTTTAATATT
40556130 AA-TTTTATTTT
1 AATTTTTATTTT
40556141 TTATGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 4 0.15
18 7 0.26
19 6 0.22
20 10 0.37
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTTTATTTTAATATT
Found at i:40556123 original size:20 final size:19
Alignment explanation
Indices: 40556094--40556135 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
40556084 AACCTCAAAA
* *
40556094 TTTTTATTTTCATTTTAAT
1 TTTTTATTTTAATATTAAT
40556113 TTTTTATTTTTAATATTAAT
1 TTTTTA-TTTTAATATTAAT
40556133 TTT
1 TTT
40556136 ATTTTTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTAATATTAAT
Found at i:40556123 original size:25 final size:24
Alignment explanation
Indices: 40556093--40556149 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
40556083 CAACCTCAAA
* *
40556093 ATTTTTATTTTCATTTTAATTTTTT
1 ATTTTTATATTAATTTT-ATTTTTT
40556118 ATTTTTAATATTAATTTTATTTTTT
1 ATTTTT-ATATTAATTTTATTTTTT
*
40556143 ATGTTTA
1 ATTTTTA
40556150 ATAAGAGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 18 0.64
26 9 0.32
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTATATTAATTTTATTTTTT
Found at i:40558429 original size:47 final size:45
Alignment explanation
Indices: 40558355--40558447 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 45
40558345 GAATATAAAT
40558355 TGAAAACAAATTTGGAAAATTTCGTTACCTTATTCAAAAACCAAG
1 TGAAAACAAATTTGGAAAATTTCGTTACCTTATTCAAAAACCAAG
40558400 TGAAAACAAATTTGGGGAAAATTTCGTTACCTTATTCAAAAACCAAG
1 TGAAAACAAATTT--GGAAAATTTCGTTACCTTATTCAAAAACCAAG
40558447 T
1 T
40558448 ATCAAAACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 13 0.28
47 33 0.72
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (45 bp):
TGAAAACAAATTTGGAAAATTTCGTTACCTTATTCAAAAACCAAG
Found at i:40562568 original size:52 final size:51
Alignment explanation
Indices: 40562500--40562631 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 51
40562490 ATAAACAAAT
* * *
40562500 GAGTTACTTAATGCATGACTTAATTTAATGATGAAAATTTTAACTAACATGA
1 GAGTTACATAAAGCATGACTTAATTTAATGATGAAAA-CTTAACTAACATGA
* * * * *
40562552 GAGTTATATAAAGCATGCCATAATTT-ATTATGCAAACTTAACTAACATGA
1 GAGTTACATAAAGCATGACTTAATTTAATGATGAAAACTTAACTAACATGA
* **
40562602 GAGTTACATAATGCATGACTTTCTTTAATG
1 GAGTTACATAAAGCATGACTTAATTTAATG
40562632 CAAAACACAT
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
50 33 0.52
51 10 0.16
52 21 0.33
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (51 bp):
GAGTTACATAAAGCATGACTTAATTTAATGATGAAAACTTAACTAACATGA
Found at i:40573094 original size:27 final size:27
Alignment explanation
Indices: 40573064--40573231 Score: 171
Period size: 27 Copynumber: 6.3 Consensus size: 27
40573054 ATTCATGGGG
* * *
40573064 AAATGACCAAAATACCCTCAAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * * *
40573091 AAATGACTGAACTACCCTTGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* * *
40573118 AAATGACTGAACTACCCTCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
40573145 AAATGATTGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
40573172 AAATGATCGAAATACTCCT-GAAGGGTA
1 AAATGACCGAAATAC-CCTCGAAGGGTA
*
40573199 AAATGACCGAAATACCC-CCATAGGGT-
1 AAATGACCGAAATACCCTCGA-AGGGTA
40573225 AAATGAC
1 AAATGAC
40573232 TGTTATACTC
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
26 10 0.08
27 111 0.90
28 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:40573225 original size:81 final size:81
Alignment explanation
Indices: 40573073--40573227 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
40573063 GAAATGACCA
* * * * *
40573073 AAATACCCTCAAAAGGTAAAATGACTGAACTACCCTTGATGGGTAAAATGACTGAACTACCCTCG
1 AAATACCCTCAAAAGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTCC
40573138 ATGGGTAAAATGATTG
66 ATGGGTAAAATGATTG
* *
40573154 AAATACCCTCGAAGGGTAAAATGA-TCGAAATACTCC-TGAAGGGTAAAATGACCGAAATACCC-
1 AAATACCCTCAAAAGGTAAAATGACT-GAAATAC-CCTTGAAGGGTAAAATGACCGAAATACCCT
40573216 CCATAGGGTAAA
64 CCAT-GGGTAAA
40573228 TGACTGTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
80 4 0.06
81 58 0.91
82 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (81 bp):
AAATACCCTCAAAAGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGACCGAAATACCCTCC
ATGGGTAAAATGATTG
Found at i:40573633 original size:28 final size:28
Alignment explanation
Indices: 40573593--40573677 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
40573583 ATTGTACCGA
40573593 TTACTGTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
40573621 TTACTGTATTGGGCTAAGGCCCACACACTG
1 TTACTGTATTGGGCTAAGG-CC-CACACTG
*
40573651 TTACTGTAATGGGCTAAGGCCCACACT
1 TTACTGTATTGGGCTAAGGCCCACACT
40573678 ATACTGCTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
28 25 0.46
29 4 0.07
30 25 0.46
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.27
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:40573650 original size:30 final size:30
Alignment explanation
Indices: 40573593--40573676 Score: 145
Period size: 30 Copynumber: 2.9 Consensus size: 30
40573583 ATTGTACCGA
40573593 TTACTGTATTGGGCTAAGG-CC-CACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
40573621 TTACTGTATTGGGCTAAGGCCCACACACTG
1 TTACTGTATTGGGCTAAGGCCCACACACTG
*
40573651 TTACTGTAATGGGCTAAGGCCCACAC
1 TTACTGTATTGGGCTAAGGCCCACAC
40573677 TATACTGCTA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
28 19 0.36
29 2 0.04
30 32 0.60
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (30 bp):
TTACTGTATTGGGCTAAGGCCCACACACTG
Found at i:40577889 original size:25 final size:26
Alignment explanation
Indices: 40577861--40577912 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
40577851 AGAGGAAAGT
40577861 TTAAAGAACATAAAAT-AAAAAAATA
1 TTAAAGAACATAAAATGAAAAAAATA
** *
40577886 TTAAATTACTTAAAATGAAAAAAATA
1 TTAAAGAACATAAAATGAAAAAAATA
40577912 T
1 T
40577913 GAGGATCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (26 bp):
TTAAAGAACATAAAATGAAAAAAATA
Found at i:40580975 original size:27 final size:27
Alignment explanation
Indices: 40580944--40581216 Score: 329
Period size: 27 Copynumber: 10.1 Consensus size: 27
40580934 ATTCATGGGC
40580944 AAATGACCGAAATACCCTCAATGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
*
40580971 AAATGACCAAAATACCCTCGAA-GGGTA
1 AAATGACCGAAATACCCTC-AATGGGTA
*
40580998 AAATGACCGAAATACCCTCGATGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
* * **
40581025 AAATGATCGAAATACCGTTTATGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
* *
40581052 AAATGATCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
* * * *
40581079 AAATAATCAAAATACCGTCAATGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
* *
40581106 AAATGATCGAATTACCCTCAATGGGT-
1 AAATGACCGAAATACCCTCAATGGGTA
*
40581132 AAATGACCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCAATGGGTA
* *
40581159 AAATGATCGAAATACTCCTGAA-GGGTA
1 AAATGACCGAAATAC-CCTCAATGGGTA
*
40581186 AAATAACCGAAATACCCT-AATAGGGTA
1 AAATGACCGAAATACCCTCAAT-GGGTA
40581213 AAAT
1 AAAT
40581217 TACTATTATA
Statistics
Matches: 214, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.01
26 27 0.13
27 178 0.83
28 7 0.03
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCAATGGGTA
Found at i:40581079 original size:81 final size:81
Alignment explanation
Indices: 40580944--40581216 Score: 363
Period size: 81 Copynumber: 3.4 Consensus size: 81
40580934 ATTCATGGGC
* * *
40580944 AAATGACCGAAATACCCTCAATGGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCGAA
1 AAATGACCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGATCGAA
40581009 ATACCCTCGATGGGTA
66 ATACCCTCGATGGGTA
* * ** * * *
40581025 AAATGATCGAAATACCGTTTATGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATAATCAAA
1 AAATGACCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGATCGAA
* *
40581090 ATACCGTCAATGGGTA
66 ATACCCTCGATGGGTA
* *
40581106 AAATGATCGAATTACCCTCAATGGGT-AAATGACCGAAATACCCTCAAAGGGTAAAATGATCGAA
1 AAATGACCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGATCGAA
*
40581170 ATACTCCT-GAAGGGTA
66 ATAC-CCTCGATGGGTA
*
40581186 AAATAACCGAAATACCCT-AATAGGGTAAAAT
1 AAATGACCGAAATACCCTCAAT-GGGTAAAAT
40581217 TACTATTATA
Statistics
Matches: 164, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
79 3 0.02
80 64 0.39
81 97 0.59
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (81 bp):
AAATGACCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCAAAGGGTAAAATGATCGAA
ATACCCTCGATGGGTA
Found at i:40581245 original size:134 final size:134
Alignment explanation
Indices: 40580953--40581216 Score: 356
Period size: 134 Copynumber: 2.0 Consensus size: 134
40580943 CAAATGACCG
* * * * *
40580953 AAATACCCTCAATGGGTAAAATGACCAAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCG
1 AAATA-CCGCAATGGGTAAAATGATCGAATTACCCTCGAAGGGTAAAATGACCGAAATACCCTCA
* * * * * *
40581018 ATGGGTAAAATGATCGAAATACCGTTTATGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAAT
65 AAGGGTAAAATGATCGAAATACCGCTGAAGGGTAAAATAACCGAAATACCCTCAAAGGGTAAAAT
40581083 AATCA
130 AATCA
40581088 AAATACCGTCAATGGGTAAAATGATCGAATTACCCTC-AATGGGT-AAATGACCGAAATACCCTC
1 AAATACCG-CAATGGGTAAAATGATCGAATTACCCTCGAA-GGGTAAAATGACCGAAATACCCTC
40581151 AAAGGGTAAAATGATCGAAATACTC-CTGAAGGGTAAAATAACCGAAATACCCT-AATAGGGTAA
64 AAAGGGTAAAATGATCGAAATAC-CGCTGAAGGGTAAAATAACCGAAATACCCTCAA-AGGGTAA
40581214 AAT
127 AAT
40581217 TACTATTATA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
133 2 0.02
134 77 0.68
135 35 0.31
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (134 bp):
AAATACCGCAATGGGTAAAATGATCGAATTACCCTCGAAGGGTAAAATGACCGAAATACCCTCAA
AGGGTAAAATGATCGAAATACCGCTGAAGGGTAAAATAACCGAAATACCCTCAAAGGGTAAAATA
ATCA
Found at i:40581452 original size:26 final size:26
Alignment explanation
Indices: 40581394--40581467 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
40581384 TTGCCACATA
* * *
40581394 TACTGTTACTGGAAGCTTTGTTGTGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
40581420 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
40581446 CT-TTGTTACTGACAGCTTTGCT
1 -TACTGTTACTGGCAGCTTTGCT
40581468 ACGATATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 41 0.98
27 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:40584773 original size:55 final size:55
Alignment explanation
Indices: 40584685--40584813 Score: 177
Period size: 55 Copynumber: 2.3 Consensus size: 55
40584675 ATGGTCGACG
* * *
40584685 CCGTGTAACTCATTAACTTGGGCCACACAGCCAACCACACGTCCGTATAACTAGC
1 CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCCCATATAACTAGC
* * * * * *
40584740 CCGTGTAACTCACTGACTTGGGTCACACGGCCAACCACATGCCCATGTGACTAGC
1 CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCCCATATAACTAGC
40584795 CCGTGTAACTCATTGACTT
1 CCGTGTAACTCATTGACTT
40584814 TCTTTCATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (55 bp):
CCGTGTAACTCATTGACTTGGGCCACACAGCCAACCACACGCCCATATAACTAGC
Found at i:40591902 original size:20 final size:20
Alignment explanation
Indices: 40591874--40591911 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40591864 AATACTATGA
40591874 ACCACTCCATTTACTTTCTT
1 ACCACTCCATTTACTTTCTT
*
40591894 ACCATTCCATTTACTTTC
1 ACCACTCCATTTACTTTC
40591912 CATTGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (20 bp):
ACCACTCCATTTACTTTCTT
Found at i:40591920 original size:16 final size:16
Alignment explanation
Indices: 40591895--40591925 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40591885 TACTTTCTTA
40591895 CCATTCCATTTACTTT
1 CCATTCCATTTACTTT
*
40591911 CCATTGCATTTACTT
1 CCATTCCATTTACTT
40591926 AGCATAAACT
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:0.19, C:0.29, G:0.03, T:0.48
Consensus pattern (16 bp):
CCATTCCATTTACTTT
Found at i:40594223 original size:39 final size:40
Alignment explanation
Indices: 40594178--40594349 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
40594168 GCTCCTCGTT
* * *
40594178 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
40594218 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
40594257 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
40594297 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
40594337 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40594350 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:40594278 original size:40 final size:39
Alignment explanation
Indices: 40594180--40594402 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
40594170 TCCTCGTTCA
* * * *
40594180 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
40594219 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
40594258 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
40594298 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
40594338 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
40594379 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
40594403 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:40594362 original size:80 final size:79
Alignment explanation
Indices: 40594178--40594402 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
40594168 GCTCCTCGTT
* * * * *
40594178 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
40594242 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
40594257 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
40594322 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
40594337 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
40594401 GA
63 GA
40594403 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:40594411 original size:41 final size:41
Alignment explanation
Indices: 40594334--40594411 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40594324 TTTGTATCTC
* * *
40594334 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40594375 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40594412 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40604878 original size:14 final size:15
Alignment explanation
Indices: 40604859--40604887 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40604849 CTCTTTCGTT
40604859 CTCTTTTCC-TCTTC
1 CTCTTTTCCTTCTTC
40604873 CTCTTTTCCTTCTTC
1 CTCTTTTCCTTCTTC
40604888 TTACCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTCTTTTCCTTCTTC
Found at i:40610980 original size:40 final size:40
Alignment explanation
Indices: 40610943--40611127 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
40610933 GCTACTCGTT
*
40610943 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
40610983 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40611023 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
40611062 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40611103 CAAAT-CCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40611128 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 75 0.61
41 14 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40611054 original size:79 final size:82
Alignment explanation
Indices: 40610943--40611127 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
40610933 GCTACTCGTT
* * *
40610943 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTT-GGGATCTTAACCC
* *
40611006 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
40611023 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTTGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
* *
40611086 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40611103 CAAAT-CCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40611128 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 52 0.58
80 35 0.39
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTGGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40613473 original size:25 final size:25
Alignment explanation
Indices: 40613414--40613475 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
40613404 CAACCTGTAT
*
40613414 AAGCTTACCATTATCCAGATCAGAG
1 AAGCTTACCGTTATCCAGATCAGAG
* * *
40613439 AAGCTTACCGTTATTCAGCTTAGAG
1 AAGCTTACCGTTATCCAGATCAGAG
*
40613464 TAGCTTACCGTT
1 AAGCTTACCGTT
40613476 TACAGCTCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (25 bp):
AAGCTTACCGTTATCCAGATCAGAG
Found at i:40613496 original size:24 final size:25
Alignment explanation
Indices: 40613469--40613520 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
40613459 TAGAGTAGCT
40613469 TACCG-TTTACAGCTCGTAAGAGCA
1 TACCGATTTACAGCTCGTAAGAGCA
* *
40613493 TACCGATTTAGAGCTCGTATGAGCA
1 TACCGATTTACAGCTCGTAAGAGCA
40613518 TAC
1 TAC
40613521 GTGTATAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
TACCGATTTACAGCTCGTAAGAGCA
Found at i:40623238 original size:28 final size:28
Alignment explanation
Indices: 40623191--40623371 Score: 256
Period size: 28 Copynumber: 6.5 Consensus size: 28
40623181 CTATGCAGTA
*
40623191 ACAGT-ACAGTGTGGGCCTTAGCCCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * * *
40623218 ACAGTAACAATGCGAGCCTTAGCCCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
40623246 ACAGTAATAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
40623274 ATAGTAAAAGTGTGGGCCTTAGTCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
40623302 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
40623330 ACAGAAACAGTGTGGGCCTTAGCCTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
40623358 ACAGTAACAGTGTG
1 ACAGTAACAGTGTG
40623372 ATAATGCAAC
Statistics
Matches: 136, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 5 0.04
28 131 0.96
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:40623504 original size:26 final size:26
Alignment explanation
Indices: 40623465--40623539 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
40623455 AACACACCAA
40623465 TATCGCAGCAAAGCTACCAGTAAAAG
1 TATCGCAGCAAAGCTACCAGTAAAAG
* * *
40623491 TATCGCAGCGAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTACCAGTAAAAG
* * *
40623517 TATATGTAGCAAAGCCACCAGTA
1 TAT-CGCAGCAAAGCTACCAGTA
40623540 CAGTATACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 26 0.65
27 14 0.35
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTACCAGTAAAAG
Found at i:40623728 original size:27 final size:27
Alignment explanation
Indices: 40623695--40623828 Score: 115
Period size: 27 Copynumber: 5.0 Consensus size: 27
40623685 TTGACTCCTA
**
40623695 GGGGTATAACAATCATTTTACCCTTCG
1 GGGGTATTTCAATCATTTTACCCTTCG
* * ** * *
40623722 GGAGTATTTTAGCCATTTTATCCTTTG
1 GGGGTATTTCAATCATTTTACCCTTCG
*
40623749 GGGGTATTTCAATTATTTTACCCTTCG
1 GGGGTATTTCAATCATTTTACCCTTCG
** * **
40623776 GGGGTATTTCGGTCATCTTACTTTTCG
1 GGGGTATTTCAATCATTTTACCCTTCG
* **
40623803 AGGGTATTTCGGTCATTTTACCCTTC
1 GGGGTATTTCAATCATTTTACCCTTC
40623829 AGGTGCAAGT
Statistics
Matches: 82, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAATCATTTTACCCTTCG
Found at i:40623808 original size:54 final size:54
Alignment explanation
Indices: 40623704--40623828 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 54
40623694 AGGGGTATAA
* * *
40623704 CAATCATTTTACCCTTCGGGAGTATTTTAGCCATTTTATCCTTTGGGGGTATTT
1 CAATCATTTTACCCTTCGGGAGTATTTCAGCCATCTTATCCTTTGAGGGTATTT
* * * * *
40623758 CAATTATTTTACCCTTCGGGGGTATTTCGGTCATCTTA-CTTTTCGAGGGTATTT
1 CAATCATTTTACCCTTCGGGAGTATTTCAGCCATCTTATCCTTT-GAGGGTATTT
**
40623812 CGGTCATTTTACCCTTC
1 CAATCATTTTACCCTTC
40623829 AGGTGCAAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 4 0.07
54 55 0.93
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (54 bp):
CAATCATTTTACCCTTCGGGAGTATTTCAGCCATCTTATCCTTTGAGGGTATTT
Found at i:40625054 original size:11 final size:11
Alignment explanation
Indices: 40625038--40625062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40625028 CCCCAACAAC
40625038 TCCATTCAAAT
1 TCCATTCAAAT
40625049 TCCATTCAAAT
1 TCCATTCAAAT
40625060 TCC
1 TCC
40625063 CCTTAGCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (11 bp):
TCCATTCAAAT
Found at i:40633301 original size:20 final size:20
Alignment explanation
Indices: 40633263--40633301 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40633253 TCAAAAGACA
* *
40633263 AGAAAATATCAGTACAATTG
1 AGAAAATATCAATAAAATTG
*
40633283 AGAAAGTATCAATAAAATT
1 AGAAAATATCAATAAAATT
40633302 ATCCCAAGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AGAAAATATCAATAAAATTG
Found at i:40643796 original size:30 final size:30
Alignment explanation
Indices: 40643762--40643823 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
40643752 TTTTTAAATT
* *
40643762 CTTTTTTCAACAACCCAAGATTATCTTCTC
1 CTTTTTTCAACAACCCAAAATTATCGTCTC
40643792 CTTTTTTCAACAACCCAAAATTATCGTCTC
1 CTTTTTTCAACAACCCAAAATTATCGTCTC
40643822 CT
1 CT
40643824 CTTTCTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.31, G:0.03, T:0.39
Consensus pattern (30 bp):
CTTTTTTCAACAACCCAAAATTATCGTCTC
Found at i:40659424 original size:4 final size:4
Alignment explanation
Indices: 40659415--40659479 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
40659405 CTTTTAAAAG
40659415 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
40659463 GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT G
40659480 ACAAGGTACT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:40661378 original size:28 final size:27
Alignment explanation
Indices: 40661314--40661493 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
40661304 TTATTAAGTC
* * *
40661314 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40661341 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
40661369 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
40661396 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
40661424 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
40661452 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40661479 CGGACACTTAGTGCT
1 CGCACACTTAGTGCT
40661494 GCACAATTTA
Statistics
Matches: 146, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 65 0.45
28 81 0.55
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:40661398 original size:55 final size:54
Alignment explanation
Indices: 40661314--40661493 Score: 279
Period size: 55 Copynumber: 3.3 Consensus size: 54
40661304 TTATTAAGTC
* * * *
40661314 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCA-ACT
40661369 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTC-AACT
*
40661424 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAACT
*
40661479 CGGACACTTAGTGCT
1 CGCACACTTAGTGCT
40661494 GCACAATTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
55 89 0.76
56 28 0.24
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
Found at i:40661434 original size:83 final size:82
Alignment explanation
Indices: 40661314--40661493 Score: 288
Period size: 83 Copynumber: 2.2 Consensus size: 82
40661304 TTATTAAGTC
* * *
40661314 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
40661379 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
40661396 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
40661461 AGTGCTACATAGTCAATT
65 AGTGCTACATAGTCAACT
*
40661479 CGGACACTTAGTGCT
1 CGCACACTTAGTGCT
40661494 GCACAATTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 20 0.22
83 70 0.78
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:40669243 original size:28 final size:27
Alignment explanation
Indices: 40669179--40669357 Score: 279
Period size: 28 Copynumber: 6.6 Consensus size: 27
40669169 TTATTAAGTC
* * *
40669179 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40669206 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
40669234 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
40669261 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
40669289 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
40669317 CGCACACTTA-TGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
40669343 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40669358 GCACAATTTA
Statistics
Matches: 145, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
26 13 0.09
27 64 0.44
28 68 0.47
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:40669263 original size:55 final size:54
Alignment explanation
Indices: 40669179--40669357 Score: 279
Period size: 55 Copynumber: 3.3 Consensus size: 54
40669169 TTATTAAGTC
* * * *
40669179 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCA-ACT
40669234 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTC-AACT
*
40669289 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA-TGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAACT
40669343 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40669358 GCACAATTTA
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
54 18 0.15
55 84 0.72
56 15 0.13
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACT
Found at i:40669376 original size:55 final size:54
Alignment explanation
Indices: 40669202--40669382 Score: 222
Period size: 55 Copynumber: 3.3 Consensus size: 54
40669192 CTATATAATC
* * *
40669202 AACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTAGTGCTAC-ATAGTC
1 AACTCGCACACTTAGTGCTACATAGTCA-ACTCGCACACTTAGTGCTACAAT-TTA
* *
40669257 AACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCA
1 AACTCGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACA-ATTTA
*
40669313 AACTCGCACACTTA-TGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTA
1 AACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT--ACAATTTA
* *
40669368 AACCCGCACTCTTAG
1 AACTCGCACACTTAG
40669383 CGCCAATCTC
Statistics
Matches: 110, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
54 18 0.16
55 73 0.66
56 18 0.16
57 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (54 bp):
AACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACAATTTA
Found at i:40669382 original size:83 final size:83
Alignment explanation
Indices: 40669179--40669357 Score: 272
Period size: 82 Copynumber: 2.2 Consensus size: 83
40669169 TTATTAAGTC
* * * * *
40669179 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACATAATCATACTCGCACACTT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
40669243 AGTGCTACATAGTCAACT
66 AGTGCTACATAGTCAACT
* *
40669261 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
40669326 A-TGCTACATAGTCAATT
66 AGTGCTACATAGTCAACT
40669343 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40669358 GCACAATTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 50 0.56
83 40 0.44
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
AGTGCTACATAGTCAACT
Found at i:40684088 original size:10 final size:10
Alignment explanation
Indices: 40684073--40684099 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40684063 TTTAAATTAC
40684073 AATTACATAT
1 AATTACATAT
40684083 AATTACATAT
1 AATTACATAT
40684093 AATTACA
1 AATTACA
40684100 ATTACAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (10 bp):
AATTACATAT
Found at i:40689152 original size:255 final size:259
Alignment explanation
Indices: 40688787--40689283 Score: 654
Period size: 255 Copynumber: 1.9 Consensus size: 259
40688777 GGCATTAATA
* *
40688787 AAATATTCTTTTGTATTTAAAATAAGTTATATTATTCGAGGGCACTTTAGTATTTTCATTTAAAA
1 AAATATTCTTTTGTATTTAAAATAAGTTATATTATTCGAGAGCACTGTAGTATTTTCATTTAAAA
* * *
40688852 TATATATATAGGATTATAATTGGATTTGAACCCATACCTTGCATAAAACCTTAAATTTACCATTC
66 TATATATATA-GATTATAATGGGATTTGAACCCACACCTTGCATAAAACCTTAAATTTACCACTC
40688917 AATCAAAGTTATA-TTTAATTGTGT-ATACATTTTAATTTTATTATACACACTTTATTACCTCCA
130 AATCAAAGTTATATTTTAATT-TGTAATACATTTTAATTTTATTATACACACTTT-TTACCTCCA
*
40688980 TGAATTATATATCTATATTGTTATTTAAACCT-CTGACTGAGTTGATATCACGAGTCAGGGACAT
193 TGAATTATATATCTATATTATTATTT-AACCTCCTGACTGAGTTGATATCACGAGTCAGGGACAT
40689044 TAC
257 TAC
* * *
40689047 AAATATATCTTTTCGTATTTAAAGTAAGTTATATTATTCGAGAGTACTGTAG-ATTTTTTATTT-
1 AAATAT-TCTTTT-GTATTTAAAATAAGTTATATTATTCGAGAGCACTGTAGTA-TTTTCATTTA
* * ** *
40689110 TAA-A-A-A-AT-GTTTATAATGGGATTTGAACCCACATTTTGCATAAAACCTTAAATTTACTAC
63 AAATATATATATAGATTATAATGGGATTTGAACCCACACCTTGCATAAAACCTTAAATTTACCAC
* * * * *
40689170 TCAATCAAAGTTTTATTTTACTTTTTCAATACATTTTAGTTTTATTATGCACACTTTTTACCTCC
128 TCAATCAAAGTTATATTTTAATTTGT-AATACATTTTAATTTTATTATACACACTTTTTACCTCC
* * *
40689235 ATGAATTGTATATCTATATTATTATTTAAGCTCCTGATTGAGTTGATAT
192 ATGAATTATATATCTATATTATTATTTAACCTCCTGACTGAGTTGATAT
40689284 TACTCACAAC
Statistics
Matches: 208, Mismatches: 22, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
255 65 0.31
256 54 0.26
257 29 0.14
258 1 0.00
259 1 0.00
260 7 0.03
261 9 0.04
262 42 0.20
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (259 bp):
AAATATTCTTTTGTATTTAAAATAAGTTATATTATTCGAGAGCACTGTAGTATTTTCATTTAAAA
TATATATATAGATTATAATGGGATTTGAACCCACACCTTGCATAAAACCTTAAATTTACCACTCA
ATCAAAGTTATATTTTAATTTGTAATACATTTTAATTTTATTATACACACTTTTTACCTCCATGA
ATTATATATCTATATTATTATTTAACCTCCTGACTGAGTTGATATCACGAGTCAGGGACATTAC
Found at i:40695069 original size:13 final size:14
Alignment explanation
Indices: 40695046--40695082 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
40695036 TCTTTGATAT
40695046 ATTATTTTATTTTA
1 ATTATTTTATTTTA
40695060 ATTA-TTTATTTTA
1 ATTATTTTATTTTA
*
40695073 ATTGTTTTAT
1 ATTATTTTAT
40695083 CTAACTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
ATTATTTTATTTTA
Found at i:40699872 original size:22 final size:22
Alignment explanation
Indices: 40699844--40699891 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40699834 CTACAATCAC
*
40699844 TTCTGAATGAAGTGAAGGAATA
1 TTCTGAAGGAAGTGAAGGAATA
40699866 TTCTGAAGGAAGTGAAGGAATA
1 TTCTGAAGGAAGTGAAGGAATA
40699888 TTCT
1 TTCT
40699892 TAAGCCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (22 bp):
TTCTGAAGGAAGTGAAGGAATA
Found at i:40705627 original size:3 final size:3
Alignment explanation
Indices: 40705587--40705611 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40705577 GCTCTTCCAA
40705587 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
40705612 AATATAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:40713754 original size:23 final size:22
Alignment explanation
Indices: 40713711--40713754 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40713701 TTCTAAGTCG
40713711 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
40713734 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
40713755 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:40713868 original size:45 final size:45
Alignment explanation
Indices: 40713801--40713892 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
40713791 CAGATACTCA
* * * *
40713801 GTGGATTCAGGACATAGCAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTCCG
* * *
40713846 GTGGAATCAGCACATAGAAACCACTTTACTAATCAGTGATGTTCG
1 GTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTCCG
40713891 GT
1 GT
40713893 TCACATAGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (45 bp):
GTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTCCG
Found at i:40713958 original size:51 final size:50
Alignment explanation
Indices: 40713889--40714082 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 50
40713879 CAGTGATGTT
* * *
40713889 CGGTTCACATAGTAGCCTGTACATAGTACTACACATGTGACCGTTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCG-TACCATC
* * * * * *
40713940 CGATACACGCAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCG-TACCATC
* * * *
40713991 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCGTACCA-TC
*
40714041 CGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC
40714083 ATCACTTTCA
Statistics
Matches: 118, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 76 0.64
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCGTACCATC
Found at i:40714074 original size:101 final size:101
Alignment explanation
Indices: 40713896--40714080 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
40713886 GTTCGGTTCA
* * *
40713896 CATAGTAGCCTGTACATAGTACTACACATGTGACCGTTACCATCCGATACACGCAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCG-TACCATCCGATACACGCAGTAGCCTACA
40713961 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
40713998 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCGTACCA-TCCGATACACGCAGTAGCCTACA
*
40714062 CATAGTACTACACATGTGA
65 CATAGTACTACACACGTGA
40714081 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 33 0.44
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCGTACCATCCGATACACGCAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:40715962 original size:27 final size:27
Alignment explanation
Indices: 40715918--40715984 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40715908 ATGGAATTAG
* *
40715918 GACATATTAAAAAGGTGCAATAAGCTGA
1 GACAAATTAAAAAGGTGCAATAA-CTAA
* * *
40715946 -ACAAATTAAATATGTGCACTAACTAA
1 GACAAATTAAAAAGGTGCAATAACTAA
40715972 GACAAATTAAAAA
1 GACAAATTAAAAA
40715985 CATGCATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.22
Consensus pattern (27 bp):
GACAAATTAAAAAGGTGCAATAACTAA
Found at i:40719471 original size:17 final size:16
Alignment explanation
Indices: 40719445--40719480 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
40719435 TGAGAGCTAA
*
40719445 GAGAGTTGAGAGAGGAT
1 GAGAGATGAGA-AGGAT
40719462 GAGAGATGAGAAGGAT
1 GAGAGATGAGAAGGAT
40719478 GAG
1 GAG
40719481 GGATAAGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.47, T:0.14
Consensus pattern (16 bp):
GAGAGATGAGAAGGAT
Found at i:40725843 original size:49 final size:50
Alignment explanation
Indices: 40725737--40725918 Score: 172
Period size: 49 Copynumber: 3.7 Consensus size: 50
40725727 TAATAGGTCC
** * * * **
40725737 CATGTAAGACCATGTCTGGGACATGGTGTTGGTACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
** * *
40725787 CCCGTAAGACCATAT-TGGGACATGGCATTGGCACTGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
* * * * * *
40725836 CATGTAAGACCGTGTCTGGGATATGGCATTTGCAGT-ACAAGA-AACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAAC-TCT
*
40725885 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
40725919 TGTTATTATC
Statistics
Matches: 106, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
48 3 0.03
49 74 0.70
50 29 0.27
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACTGACATGAGAACTCT
Found at i:40727120 original size:41 final size:42
Alignment explanation
Indices: 40727064--40727166 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
40727054 TTATCTATGC
* *
40727064 GTCCCAGACAGGGTCTTACACG-AA-ACAAATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAACACAAAT-CAATGCCAAT
* *
40727105 GTCCCATACATGGTCTTACACGTAACACAAGTCAATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAACACAAATCAATGCCAAT
40727147 GTCCCAGA-ATTGGTCTTACA
1 GTCCCAGACA-TGGTCTTACA
40727167 AGATAACATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 21 0.39
42 28 0.52
43 5 0.09
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAACACAAATCAATGCCAAT
Found at i:40736034 original size:27 final size:27
Alignment explanation
Indices: 40736003--40736063 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40735993 CCCAATATTT
*
40736003 GTAAAATAACCATAATGCCCCTGTAAG
1 GTAAAATAACCATAATACCCCTGTAAG
* * * *
40736030 GTAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATAACCATAATACCCCTGTAAG
40736057 GTAAAAT
1 GTAAAAT
40736064 GATCAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (27 bp):
GTAAAATAACCATAATACCCCTGTAAG
Found at i:40736064 original size:27 final size:27
Alignment explanation
Indices: 40736015--40736180 Score: 147
Period size: 27 Copynumber: 6.1 Consensus size: 27
40736005 AAAATAACCA
* * * *
40736015 TAATGCCCCTGTAAGGTAAAATGACCG
1 TAATACCCTTGTAGGGTAAAATGATCG
*
40736042 TAATACCCTTGTAGGGTAAAATGATCA
1 TAATACCCTTGTAGGGTAAAATGATCG
* * * * * *
40736069 AAAAATCCTTATAGGGTCAAATGACCG
1 TAATACCCTTGTAGGGTAAAATGATCG
*
40736096 TAATGCCCTTGTAGGGTAAAATGATCG
1 TAATACCCTTGTAGGGTAAAATGATCG
* * *
40736123 TAATA-CCTTCATAGGGTTAAATGATTG
1 TAATACCCTT-GTAGGGTAAAATGATCG
* *
40736150 AAATACTCC-TGTAAGGTAAAATGATCG
1 TAATAC-CCTTGTAGGGTAAAATGATCG
40736177 TAAT
1 TAAT
40736181 GCCCCTAGAG
Statistics
Matches: 107, Mismatches: 29, Indels: 6
0.75 0.20 0.04
Matches are distributed among these distances:
26 4 0.04
27 100 0.93
28 1 0.01
29 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
TAATACCCTTGTAGGGTAAAATGATCG
Found at i:40736091 original size:54 final size:54
Alignment explanation
Indices: 40736033--40736175 Score: 173
Period size: 54 Copynumber: 2.6 Consensus size: 54
40736023 CTGTAAGGTA
40736033 AAATGACCGTAATACCCTTGTAGGGTAAAATGATCAAAAAATCCTT-ATAGGGTC
1 AAATGACCGTAATACCCTTGTAGGGTAAAATGATCAAAAAA-CCTTCATAGGGTC
* ** * *
40736087 AAATGACCGTAATGCCCTTGTAGGGTAAAATGATCGTAATACCTTCATAGGGTT
1 AAATGACCGTAATACCCTTGTAGGGTAAAATGATCAAAAAACCTTCATAGGGTC
** * *
40736141 AAATGATTGAAATACTCC-TGTAAGGTAAAATGATC
1 AAATGACCGTAATAC-CCTTGTAGGGTAAAATGATC
40736176 GTAATGCCCC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 4 0.05
54 71 0.92
55 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (54 bp):
AAATGACCGTAATACCCTTGTAGGGTAAAATGATCAAAAAACCTTCATAGGGTC
Found at i:40736193 original size:81 final size:81
Alignment explanation
Indices: 40736003--40736186 Score: 212
Period size: 81 Copynumber: 2.3 Consensus size: 81
40735993 CCCAATATTT
* * * *
40736003 GTAAAATAACCATAATGCCCCTGTAAGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATGATC
1 GTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGATC
40736068 AAAAAATCCTTATAGG
66 AAAAAATCCTTATAGG
* * * *
40736084 GTCAAATGACCGTAATGCCCTTGTAGGGTAAAATGATCGTAATA-CCTTCATAGGGTTAAATGAT
1 GTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTT-ATAGGGTAAAATGA-
* * *
40736148 TGAAATACTCCTGTA-A-G
64 TCAAAAAATCCT-TATAGG
*
40736165 GTAAAATGATCGTAATGCCCCT
1 GTAAAATGACCGTAATGCCCCT
40736187 AGAGGGTCAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 4 0.05
81 70 0.81
82 10 0.12
83 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (81 bp):
GTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGATC
AAAAAATCCTTATAGG
Found at i:40736297 original size:24 final size:24
Alignment explanation
Indices: 40736248--40736304 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
40736238 TGATGTAAAC
* *
40736248 GACTCATTTGTCTGTGATTGGTAT
1 GACTGATTTGTCTGTGATTGGCAT
* *
40736272 GACTGATTTGTTTGTGATTTGCAT
1 GACTGATTTGTCTGTGATTGGCAT
*
40736296 GACGGATTT
1 GACTGATTT
40736305 TAAGTATGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.18, C:0.11, G:0.26, T:0.46
Consensus pattern (24 bp):
GACTGATTTGTCTGTGATTGGCAT
Done.