Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 163 of 167
Found at i:54138327 original size:29 final size:27
Alignment explanation
Indices: 54138289--54138365 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 27
54138279 TATTAAGAAA
* *
54138289 ATATATTTTATACTTTTTAAATAATCTT
1 ATATATTTTTTAATTTTTAAATAAT-TT
*
54138317 A-ATGTTTTTTAATTTTTAAAAATAATTT
1 ATATATTTTTTAATTTTT--AAATAATTT
54138345 ATATATTTTTTAATTTTTAAA
1 ATATATTTTTTAATTTTTAAA
54138366 GTTTTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 16 0.38
28 4 0.10
29 22 0.52
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (27 bp):
ATATATTTTTTAATTTTTAAATAATTT
Found at i:54145909 original size:15 final size:15
Alignment explanation
Indices: 54145889--54145919 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54145879 AAATTCAGAC
54145889 CACAGCCACCAAATA
1 CACAGCCACCAAATA
54145904 CACAGCCACCAAATA
1 CACAGCCACCAAATA
54145919 C
1 C
54145920 CAAGGACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.06
Consensus pattern (15 bp):
CACAGCCACCAAATA
Found at i:54146056 original size:25 final size:25
Alignment explanation
Indices: 54145997--54146109 Score: 86
Period size: 25 Copynumber: 4.5 Consensus size: 25
54145987 ATTATTTAGA
* *
54145997 TCTTATGAGCATCTCGTTATATGGC
1 TCTTATGAGCTTCTCGATATATGGC
* * *
54146022 TCTCACGAGCTTCTCGATATTTGGC
1 TCTTATGAGCTTCTCGATATATGGC
*
54146047 TCTTATGAGCTTTTCGACTA-ATGGC
1 TCTTATGAGCTTCTCGA-TATATGGC
* * * **
54146072 TCTCT-TGAGCTACCCGTTATACAGC
1 TCT-TATGAGCTTCTCGATATATGGC
*
54146097 TCATATGAGCTTC
1 TCTTATGAGCTTC
54146110 CCATTACGTG
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
24 3 0.04
25 61 0.91
26 3 0.04
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (25 bp):
TCTTATGAGCTTCTCGATATATGGC
Found at i:54150693 original size:29 final size:29
Alignment explanation
Indices: 54150658--54150716 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54150648 GAAATATGAG
54150658 ATTGTTTTAAGCAATGGTTTGTTGTTAGC
1 ATTGTTTTAAGCAATGGTTTGTTGTTAGC
54150687 ATTGTTTTAAGCAATGGTTTGTTGTTAGC
1 ATTGTTTTAAGCAATGGTTTGTTGTTAGC
54150716 A
1 A
54150717 GTGACCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (29 bp):
ATTGTTTTAAGCAATGGTTTGTTGTTAGC
Found at i:54152608 original size:22 final size:23
Alignment explanation
Indices: 54152583--54152629 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
54152573 AAAAATATTC
*
54152583 AAATCCAACT-CAAAAAACTAAA
1 AAATCCAACTGAAAAAAACTAAA
54152605 AAATCCAACTGAAAAAAACTAAA
1 AAATCCAACTGAAAAAAACTAAA
54152628 AA
1 AA
54152630 TCAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.66, C:0.19, G:0.02, T:0.13
Consensus pattern (23 bp):
AAATCCAACTGAAAAAAACTAAA
Found at i:54152642 original size:23 final size:23
Alignment explanation
Indices: 54152594--54152642 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
54152584 AATCCAACTC
* **
54152594 AAAAAACTAAAAAATCCAACTGA
1 AAAAAACTAAAAAATCAAAAAGA
54152617 AAAAAACT-AAAAATCAAAAAGA
1 AAAAAACTAAAAAATCAAAAAGA
54152639 AAAA
1 AAAA
54152643 TTTAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.73, C:0.12, G:0.04, T:0.10
Consensus pattern (23 bp):
AAAAAACTAAAAAATCAAAAAGA
Found at i:54153972 original size:11 final size:10
Alignment explanation
Indices: 54153956--54153996 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 10
54153946 TATTTTTTTA
54153956 TTTTAAATAGT
1 TTTTAAATA-T
54153967 TTTTAAATAT
1 TTTTAAATAT
54153977 TTTT-AAT-T
1 TTTTAAATAT
*
54153985 TTTAAAATAT
1 TTTTAAATAT
54153995 TT
1 TT
54153997 CAATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 4 0.15
9 6 0.22
10 8 0.30
11 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:54154004 original size:18 final size:17
Alignment explanation
Indices: 54153966--54154016 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
54153956 TTTTAAATAG
*
54153966 TTTTTAAATATTTTTAA
1 TTTTTAAATATTTTCAA
54153983 TTTTTAAA-ATATTTCAA
1 TTTTTAAATAT-TTTCAA
54154000 TTTTTAAGAT-TTTTCAA
1 TTTTTAA-ATATTTTCAA
54154017 ATGTTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTTAAATATTTTCAA
Found at i:54155851 original size:43 final size:42
Alignment explanation
Indices: 54155790--54155875 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 42
54155780 ATGTGTATGA
54155790 TAAGCGTTCCATATAGTTTAGGGAAAGAATGTTGCATGTACNT
1 TAAGCGTTCCATATAGTTTAGGGAAAGAATGTTGCATGTAC-T
*
54155833 TAAGCTTTCCATATAGTTTAGGGAAAGAATGTTGCATGTACT
1 TAAGCGTTCCATATAGTTTAGGGAAAGAATGTTGCATGTACT
54155875 T
1 T
54155876 GTCATGCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 2 0.05
43 40 0.95
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAGCGTTCCATATAGTTTAGGGAAAGAATGTTGCATGTACT
Found at i:54161558 original size:46 final size:46
Alignment explanation
Indices: 54161491--54161580 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
54161481 AAGGTAAACA
*
54161491 ACACCCGTTTAAAACCTTATTTTGACGAGATTAATAGCAGGAATCC
1 ACACCCGTTTAAAACCTTATTTTGACGAGAATAATAGCAGGAATCC
* * *
54161537 ACACCCGTTTGAAACCTTATTTTGATGAGAATGATAGCAGGAAT
1 ACACCCGTTTAAAACCTTATTTTGACGAGAATAATAGCAGGAAT
54161581 GAAGAGTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (46 bp):
ACACCCGTTTAAAACCTTATTTTGACGAGAATAATAGCAGGAATCC
Found at i:54173271 original size:105 final size:102
Alignment explanation
Indices: 54173092--54173289 Score: 249
Period size: 105 Copynumber: 1.9 Consensus size: 102
54173082 AATTGACGGA
* * *
54173092 TAAGACCATGGTTGGACCATGCCAAAGTGTTAAAAGTAAAACCATAGTTGGGCTATGGCATTTCA
1 TAAGACCATGGTTGGACCATGCCAAAGTGTTAAAAGTAAAACCATAGCTGGGCTACGGCATCTCA
*
54173157 ATGAAAAGACTATAACTAGGTTATGGCATCGTGAACG
66 ATGAAAAGACCATAACTAGGTTATGGCATCGTGAACG
* **
54173194 TAAGACCATGGTTGGACCATGGCAGTATA-TG-TAAAAGTGTATGACCATAGCTGGGCTACGGCA
1 TAAGACCATGGTTGGACCATGCCA--A-AGTGTTAAAA--GTAAAACCATAGCTGGGCTACGGCA
*
54173257 TC-CTAATGATAAGACCATAACTAGGTTATGGCA
61 TCTC-AATGAAAAGACCATAACTAGGTTATGGCA
54173290 CTACGAGTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
102 23 0.28
103 5 0.06
104 4 0.05
105 50 0.61
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (102 bp):
TAAGACCATGGTTGGACCATGCCAAAGTGTTAAAAGTAAAACCATAGCTGGGCTACGGCATCTCA
ATGAAAAGACCATAACTAGGTTATGGCATCGTGAACG
Found at i:54175081 original size:18 final size:18
Alignment explanation
Indices: 54175058--54175103 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
54175048 TTTAGATTAA
*
54175058 TGGGCCCACATACCCGTG
1 TGGGCCCACATACCCATG
54175076 TGGGCCCACATACCCATG
1 TGGGCCCACATACCCATG
*
54175094 TAGGCCCACA
1 TGGGCCCACA
54175104 CGTCGGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.24, T:0.15
Consensus pattern (18 bp):
TGGGCCCACATACCCATG
Found at i:54176411 original size:23 final size:24
Alignment explanation
Indices: 54176381--54176428 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
54176371 ATATAAAATT
*
54176381 ATTTTAGAAAATAA-ATTTTAGAA
1 ATTTTAGAAAAAAATATTTTAGAA
*
54176404 ATTTTAGAAAAAAATATTTTTGAA
1 ATTTTAGAAAAAAATATTTTAGAA
54176428 A
1 A
54176429 ATTAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
ATTTTAGAAAAAAATATTTTAGAA
Found at i:54176428 original size:15 final size:16
Alignment explanation
Indices: 54176404--54176441 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
54176394 AATTTTAGAA
*
54176404 ATTTTAGAAAA-AAAT
1 ATTTTTGAAAATAAAT
54176419 ATTTTTGAAAATTAAAT
1 ATTTTTGAAAA-TAAAT
54176436 ATTTTT
1 ATTTTT
54176442 AGGTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
ATTTTTGAAAATAAAT
Found at i:54176706 original size:21 final size:22
Alignment explanation
Indices: 54176676--54176738 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
54176666 TTTACCTTCC
54176676 ACTTG-AATTTATTTTAAAAAA
1 ACTTGAAATTTATTTTAAAAAA
* *
54176697 AC-TGAAATTTGTATTATAAAAA
1 ACTTGAAATTTATTTTA-AAAAA
**
54176719 ACTTGGTATTTATTTTAAAA
1 ACTTGAAATTTATTTTAAAA
54176739 CATGGAATCT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.06
21 11 0.33
22 10 0.30
23 10 0.30
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (22 bp):
ACTTGAAATTTATTTTAAAAAA
Found at i:54176959 original size:27 final size:29
Alignment explanation
Indices: 54176920--54176974 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
54176910 ACAAAATTTT
*
54176920 AAAATTGACAAAAAATTCTAAAATATATA
1 AAAATTGACAAAAAATTATAAAATATATA
*
54176949 AAAATT-A-AAAATATTATAAAATATAT
1 AAAATTGACAAAAAATTATAAAATATAT
54176975 GAAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 17 0.71
28 1 0.04
29 6 0.25
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATTGACAAAAAATTATAAAATATATA
Found at i:54178523 original size:16 final size:15
Alignment explanation
Indices: 54178472--54178527 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
54178462 ACAAAGCAAA
*
54178472 AGAA-AAAGAAAAAG
1 AGAAGAAAGAAACAG
54178486 A-ATAGAAAGAAACAG
1 AGA-AGAAAGAAACAG
54178501 AGAAGAAACGAAACAG
1 AGAAGAAA-GAAACAG
* *
54178517 GGGAGAAAGAA
1 AGAAGAAAGAA
54178528 GGAGAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 18 0.51
16 14 0.40
ACGTcount: A:0.66, C:0.05, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAGAAAGAAACAG
Found at i:54179173 original size:3 final size:3
Alignment explanation
Indices: 54179165--54179203 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
54179155 GAATGGTAAG
* *
54179165 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54179204 GGTATTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:54179538 original size:48 final size:48
Alignment explanation
Indices: 54179486--54179591 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
54179476 AGTGTCGCCA
** *
54179486 GACTGTGACTATTTTGGATTCGTTCCTATGAGGTACTTAGTGTAACGT
1 GACTGTGACTATTCCGGATTCGTTCCGATGAGGTACTTAGTGTAACGT
* * *
54179534 GACTGTGACTGTTCCGGATTCGTTCCGATGAGGTACTTTGTGTACCGT
1 GACTGTGACTATTCCGGATTCGTTCCGATGAGGTACTTAGTGTAACGT
*
54179582 GACTGAGACT
1 GACTGTGACT
54179592 GTTACCGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (48 bp):
GACTGTGACTATTCCGGATTCGTTCCGATGAGGTACTTAGTGTAACGT
Found at i:54179592 original size:48 final size:48
Alignment explanation
Indices: 54179501--54179594 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
54179491 TGACTATTTT
* *
54179501 GGATTCGTTCCTATGAGGTACTTAGTGTAACGTGACTGTGACTGTTCC
1 GGATTCGTTCCGATGAGGTACTTAGTGTAACGTGACTGAGACTGTTCC
* *
54179549 GGATTCGTTCCGATGAGGTACTTTGTGTACCGTGACTGAGACTGTT
1 GGATTCGTTCCGATGAGGTACTTAGTGTAACGTGACTGAGACTGTT
54179595 ACCGTTACGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (48 bp):
GGATTCGTTCCGATGAGGTACTTAGTGTAACGTGACTGAGACTGTTCC
Found at i:54179760 original size:18 final size:18
Alignment explanation
Indices: 54179739--54179782 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
54179729 ATGGATTAAT
54179739 TGACTGTTATTGAATAAA
1 TGACTGTTATTGAATAAA
* *
54179757 TGACTGTTATTGCATAAC
1 TGACTGTTATTGAATAAA
54179775 TGACTGTT
1 TGACTGTT
54179783 CTAGATTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (18 bp):
TGACTGTTATTGAATAAA
Found at i:54181173 original size:41 final size:40
Alignment explanation
Indices: 54181116--54181242 Score: 155
Period size: 41 Copynumber: 3.1 Consensus size: 40
54181106 GCGGCGCGCA
* *
54181116 AAAAATTGAACAATAGCGGCGTTTTTGGCCCAAACGCCGC
1 AAAAATTGATCAATAGCGGCGTTTTTGGTCCAAACGCCGC
* *
54181156 TAAAAACTGATCAATAGCGGCATTTTTGGTCCAAACGCCGC
1 -AAAAATTGATCAATAGCGGCGTTTTTGGTCCAAACGCCGC
* * * *
54181197 AAAAAAGTTTATCTACAACGGCGTTTTTGGTCCAAACGCCGC
1 -AAAAA-TTGATCAATAGCGGCGTTTTTGGTCCAAACGCCGC
54181239 AAAA
1 AAAA
54181243 TGTTAGGCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 45 0.61
42 29 0.39
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAATTGATCAATAGCGGCGTTTTTGGTCCAAACGCCGC
Found at i:54181544 original size:7 final size:7
Alignment explanation
Indices: 54181523--54181625 Score: 62
Period size: 7 Copynumber: 14.4 Consensus size: 7
54181513 GCATGGCTTT
54181523 CCCTAAA
1 CCCTAAA
54181530 CCCTTAAA
1 CCC-TAAA
*
54181538 TCCTAAA
1 CCCTAAA
**
54181545 CATTAAA
1 CCCTAAA
54181552 CCCTAAA
1 CCCTAAA
*
54181559 CACTAAA
1 CCCTAAA
54181566 CCCTAAA
1 CCCTAAA
**
54181573 TTCTAAA
1 CCCTAAA
***
54181580 ATATAAA
1 CCCTAAA
54181587 CCCTAAA
1 CCCTAAA
* *
54181594 CACTAAT
1 CCCTAAA
*
54181601 CCATAAA
1 CCCTAAA
**
54181608 CTTTAAAA
1 CCCT-AAA
54181616 CCCTAAA
1 CCCTAAA
54181623 CCC
1 CCC
54181626 CAAAAAATCA
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
7 59 0.84
8 11 0.16
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (7 bp):
CCCTAAA
Found at i:54181810 original size:36 final size:36
Alignment explanation
Indices: 54181735--54181811 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 36
54181725 TTTATTTTGG
*
54181735 GGTTTAGGGTTCAATGGTAGAATATATTTTAAGTTTAT
1 GGTTTAGGGTTCAATGGT--AATATATGTTAAGTTTAT
54181773 GGTTTAGGGTTCAATGGT-ATAGTATGTTAAGTTTAT
1 GGTTTAGGGTTCAATGGTAATA-TATGTTAAGTTTAT
54181809 GGT
1 GGT
54181812 ATTGGTCAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 3 0.08
36 16 0.43
38 18 0.49
ACGTcount: A:0.26, C:0.03, G:0.27, T:0.44
Consensus pattern (36 bp):
GGTTTAGGGTTCAATGGTAATATATGTTAAGTTTAT
Found at i:54182937 original size:40 final size:41
Alignment explanation
Indices: 54182875--54182977 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 41
54182865 TTAGCGGCCT
* * * *
54182875 TTTTCTAAAAATGCCACT-AAAGATTGAGAATTGGCGGAGC
1 TTTTGTAAAAACGCCGCTAAAAGATTGAGAATTAGCGGAGC
* * *
54182915 TTTTGTAAAAACGCTGC-AAAAGATTGAGATTTAGCGGCGC
1 TTTTGTAAAAACGCCGCTAAAAGATTGAGAATTAGCGGAGC
54182955 TTTTGTAAAAACGCCGCTAAAAG
1 TTTTGTAAAAACGCCGCTAAAAG
54182978 TTTAATTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 48 0.91
41 5 0.09
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (41 bp):
TTTTGTAAAAACGCCGCTAAAAGATTGAGAATTAGCGGAGC
Found at i:54186142 original size:14 final size:14
Alignment explanation
Indices: 54186123--54186167 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
54186113 ATTGTAATAT
54186123 ATATATCAATATGC
1 ATATATCAATATGC
54186137 ATATAT--ATA--C
1 ATATATCAATATGC
54186147 ATATATCAATATGC
1 ATATATCAATATGC
54186161 ATATATC
1 ATATATC
54186168 TTGGGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 7 0.26
12 6 0.22
14 14 0.52
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (14 bp):
ATATATCAATATGC
Found at i:54186352 original size:25 final size:25
Alignment explanation
Indices: 54186278--54186345 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
54186268 TTGGCATCGT
* * * *
54186278 CGTCGACAGCCCTCTGCTATATTTC
1 CGTCGGCATCCCTCTGCTACATCTC
*
54186303 CTTCGGCATCCCTCTGCTACATCTC
1 CGTCGGCATCCCTCTGCTACATCTC
54186328 CGTCGGCATCCCTCTGCT
1 CGTCGGCATCCCTCTGCT
54186346 GCTTCTCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.12, C:0.41, G:0.16, T:0.31
Consensus pattern (25 bp):
CGTCGGCATCCCTCTGCTACATCTC
Found at i:54186957 original size:23 final size:23
Alignment explanation
Indices: 54186927--54186972 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
54186917 AAAGTATTTG
*
54186927 GTTAAGAAAATTTAGTTGATAAT
1 GTTAAGAAAATTCAGTTGATAAT
*
54186950 GTTAAGAAAATTCATTTGATAAT
1 GTTAAGAAAATTCAGTTGATAAT
54186973 AATAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.39
Consensus pattern (23 bp):
GTTAAGAAAATTCAGTTGATAAT
Found at i:54189084 original size:13 final size:14
Alignment explanation
Indices: 54189066--54189097 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
54189056 TTATTATAAA
54189066 TAATTTTAAT-GTT
1 TAATTTTAATGGTT
54189079 TAATTTTAATGGTT
1 TAATTTTAATGGTT
54189093 TAATT
1 TAATT
54189098 CGTCGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
TAATTTTAATGGTT
Found at i:54189533 original size:27 final size:27
Alignment explanation
Indices: 54189503--54189560 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
54189493 ATAACTTAGA
* * *
54189503 GCAGATGCAGTAGCGAGGGAGGCAGAG
1 GCAGAGGCAGCAGCAAGGGAGGCAGAG
* * *
54189530 GCAGCGGCAGCAGTAAGGGAGGTAGAG
1 GCAGAGGCAGCAGCAAGGGAGGCAGAG
54189557 GCAG
1 GCAG
54189561 CAGCGATGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.48, T:0.07
Consensus pattern (27 bp):
GCAGAGGCAGCAGCAAGGGAGGCAGAG
Found at i:54189961 original size:43 final size:43
Alignment explanation
Indices: 54189913--54190011 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
54189903 TCTGCCAAAA
54189913 TTAGCGGCATTTGTAACAAAAACGCCGCTAAAAGCCATGA-CTT
1 TTAGCGGCATTT-TAACAAAAACGCCGCTAAAAGCCATGATCTT
* * * **
54189956 TTAGCGGCGATTTTATCACAAACGCTGCTAAAATTCATGATCTT
1 TTAGCGGC-ATTTTAACAAAAACGCCGCTAAAAGCCATGATCTT
*
54190000 TT-GTGGCATTTT
1 TTAGCGGCATTTT
54190012 TTTAAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
42 5 0.10
43 34 0.71
44 9 0.19
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (43 bp):
TTAGCGGCATTTTAACAAAAACGCCGCTAAAAGCCATGATCTT
Found at i:54191118 original size:34 final size:34
Alignment explanation
Indices: 54191068--54191183 Score: 151
Period size: 34 Copynumber: 3.4 Consensus size: 34
54191058 ACATATACAA
* *
54191068 ATATCATATCAGAATGTCACATTACCAGAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* * *
54191102 ATATCAAATCAAAATGTCATATTTCCAGAAGCAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
* * * *
54191136 ATACCAGATCAGAATGTCATATTTTCAAAAACAT
1 ATATCATATCAGAATGTCATATTTCCAGAAACAT
54191170 ATATCATATCAGAA
1 ATATCATATCAGAA
54191184 CAAATCCTAC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTTCCAGAAACAT
Found at i:54197101 original size:43 final size:42
Alignment explanation
Indices: 54197053--54197251 Score: 145
Period size: 43 Copynumber: 4.9 Consensus size: 42
54197043 ACTGAGATGA
*
54197053 GATTACATGTAAGACCATGTCTAGGACATTGGCATTGTATTGT
1 GATTACGTGTAAGACCATGTCTAGGACA-TGGCATTGTATTGT
54197096 GATTACGTGTAAGACCA----T--G--A---CATTGTATTGT
1 GATTACGTGTAAGACCATGTCTAGGACATGGCATTGTATTGT
* * * * *
54197127 GATTACGTGTAAGACCATGTCTGGGATATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTAGGACA-TGGCATTG-TATTGT
* *
54197170 GATTACGTGTAAGACCCTGTCTAGGACAGTGGCATCG-ATGTGT
1 GATTACGTGTAAGACCATGTCTAGGACA-TGGCATTGTAT-TGT
* * * * *
54197213 GATAACATGTAAGACCATATCTGGGATATGGCATTGTAT
1 GATTACGTGTAAGACCATGTCTAGGACATGGCATTGTAT
54197252 GAGCTTATGT
Statistics
Matches: 123, Mismatches: 17, Indels: 32
0.72 0.10 0.19
Matches are distributed among these distances:
31 28 0.23
35 2 0.02
37 2 0.02
39 2 0.02
41 1 0.01
42 8 0.07
43 77 0.63
44 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTAGGACATGGCATTGTATTGT
Found at i:54197123 original size:31 final size:31
Alignment explanation
Indices: 54197085--54197145 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
54197075 AGGACATTGG
54197085 CATTGTATTGTGATTACGTGTAAGACCATGA
1 CATTGTATTGTGATTACGTGTAAGACCATGA
54197116 CATTGTATTGTGATTACGTGTAAGACCATG
1 CATTGTATTGTGATTACGTGTAAGACCATG
54197146 TCTGGGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (31 bp):
CATTGTATTGTGATTACGTGTAAGACCATGA
Found at i:54206166 original size:44 final size:44
Alignment explanation
Indices: 54206097--54206185 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
54206087 CAAAAATAGA
*
54206097 TTTGAGATCGGGTTATTACTAGTTACGAGTTAGAAACTCTGATG
1 TTTGAGATCGGGTTATTACCAGTTACGAGTTAGAAACTCTGATG
* *
54206141 TTTGAGATCGGGTTATTACCGGTTACGAGTTAGAGACTCTGATG
1 TTTGAGATCGGGTTATTACCAGTTACGAGTTAGAAACTCTGATG
54206185 T
1 T
54206186 ACCAAAGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (44 bp):
TTTGAGATCGGGTTATTACCAGTTACGAGTTAGAAACTCTGATG
Found at i:54207268 original size:27 final size:27
Alignment explanation
Indices: 54207230--54207293 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
54207220 TAATGAAGGG
54207230 ACTATTTTGCAAAATGGTTGAGAGTCT
1 ACTATTTTGCAAAATGGTTGAGAGTCT
54207257 ACTATTTTGCAAAATGGTTGAGAGTCT
1 ACTATTTTGCAAAATGGTTGAGAGTCT
* *
54207284 AGTGTTTTGC
1 ACTATTTTGC
54207294 CATGAAAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (27 bp):
ACTATTTTGCAAAATGGTTGAGAGTCT
Found at i:54207952 original size:46 final size:47
Alignment explanation
Indices: 54207899--54208025 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 47
54207889 TGATATGTGT
54207899 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATG-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGA-GAAGA
* *
54207945 GCTAGTGTAAGACATGTCTAGGACATGCATC-G--ACTTTGAGACAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAG--AAGA
*
54207991 GCTAGTGTAAGACATATCTGGGACATGCATCAGCC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCC
54208026 TCGAGATATA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
43 5 0.07
44 1 0.01
45 1 0.01
46 62 0.89
47 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTGAGAAGA
Found at i:54208163 original size:49 final size:48
Alignment explanation
Indices: 54208110--54208214 Score: 113
Period size: 49 Copynumber: 2.2 Consensus size: 48
54208100 CTAAGACATG
* * *
54208110 GCATCGACAC-CGATAGATGAGAGCCAGTGTAAGACTTGTCTGGGACACA
1 GCATCGAC-CTCGATAGATGAAAGCCAGTATAAGACCTGTCTGGGAC-CA
* * * * *
54208159 GCATCGGCCTCGATATATGAAAGTCAGTATAAGCCCTGTCTGGGACTA
1 GCATCGACCTCGATAGATGAAAGCCAGTATAAGACCTGTCTGGGACCA
54208207 GCATCGAC
1 GCATCGAC
54208215 TTTTATGTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
48 9 0.20
49 37 0.80
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (48 bp):
GCATCGACCTCGATAGATGAAAGCCAGTATAAGACCTGTCTGGGACCA
Found at i:54218069 original size:22 final size:23
Alignment explanation
Indices: 54218040--54218096 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
54218030 TGCACAAACG
*
54218040 AACAGAGAGCACTA-AAGTGTTA
1 AACAGAGAGCACTAGAAGTGCTA
* * *
54218062 TACAGAGAACAC-AGATGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
54218084 AACAGAGAGCACT
1 AACAGAGAGCACT
54218097 TAACGTGCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (23 bp):
AACAGAGAGCACTAGAAGTGCTA
Found at i:54219284 original size:7 final size:7
Alignment explanation
Indices: 54219274--54219362 Score: 55
Period size: 7 Copynumber: 13.3 Consensus size: 7
54219264 ACTTTATGTT
54219274 TTATATA
1 TTATATA
54219281 -T-TATA
1 TTATATA
54219286 TTATATA
1 TTATATA
*
54219293 TAATATA
1 TTATATA
*
54219300 ATA-ATA
1 TTATATA
*
54219306 TAATATA
1 TTATATA
54219313 TTATATA
1 TTATATA
54219320 TTA-ATA
1 TTATATA
*
54219326 CTTAAATA
1 -TTATATA
54219334 TTA-AGT-
1 TTATA-TA
*
54219340 TAATATA
1 TTATATA
*
54219347 ATATATA
1 TTATATA
*
54219354 ATATATA
1 TTATATA
54219361 TT
1 TT
54219363 TTTATATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 13 0.20
7 44 0.69
8 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (7 bp):
TTATATA
Found at i:54221426 original size:43 final size:43
Alignment explanation
Indices: 54221379--54221539 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 43
54221369 TGAGATTATA
* *
54221379 TGTAAGACCATGTTTGGTACATTGGCATTGTATTGTGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACG
* *
54221422 TGTAAGACCATGTCTGGGACATTGGCATCAT-TAAT-CGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCAT--TGTATTGTGATTACG
* * * *
54221465 TGTAAGACCCTGTCTGGGAC-TGTGGCATCG-ATATGTGATAACA
1 TGTAAGACCATGTCTGGGACAT-TGGCATTGTAT-TGTGATTACG
* *
54221508 TGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTAT
54221540 GAGCTTATGT
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.01
42 9 0.09
43 82 0.85
44 3 0.03
45 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGATTACG
Found at i:54232696 original size:48 final size:48
Alignment explanation
Indices: 54232627--54233735 Score: 2137
Period size: 48 Copynumber: 23.1 Consensus size: 48
54232617 GCTGAAATTG
*
54232627 ATGTATAAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
54232675 ATGTATGAGATATGTACATGTGGTAAAGTCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54232723 ATGTATGAGATATGTATATGTGGTGAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* * *
54232771 ATGTATGAGATATGTATACGTGGTGAAGCTGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54232819 ATGTATGAGATATGTATAGGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54232867 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54232915 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54232963 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233011 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233059 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233107 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233155 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233203 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233251 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233299 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233347 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233395 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233443 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233491 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233539 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233587 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233635 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54233683 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54233731 ATGTA
1 ATGTA
54233736 GGCGATGTGT
Statistics
Matches: 1048, Mismatches: 13, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 1048 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:54233932 original size:37 final size:36
Alignment explanation
Indices: 54233882--54233990 Score: 182
Period size: 37 Copynumber: 3.0 Consensus size: 36
54233872 GGAAATATAT
54233882 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT-TG
54233919 TCCGGGTAAGACCCGATGACTACGTGTGGAGAATTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAG-ATTTG
* *
54233956 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
54233991 CATCTGAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
36 4 0.06
37 62 0.90
38 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
Found at i:54236154 original size:40 final size:40
Alignment explanation
Indices: 54236085--54236290 Score: 315
Period size: 40 Copynumber: 5.2 Consensus size: 40
54236075 AACCCAAGTA
* ** *
54236085 CCTTCGGGATTTAG-CCGGATATAACAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54236124 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54236164 CCTTCGGGACTTAGCCCGGATATAGTAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54236204 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54236244 CCTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54236284 CCTTCGG
1 CCTTCGG
54236291 ATCTTAGTCC
Statistics
Matches: 153, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 13 0.08
40 140 0.92
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54251581 original size:22 final size:23
Alignment explanation
Indices: 54251552--54251599 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
54251542 ATTAAAGGTT
54251552 ATTAAAGTCAT-T-TAATAAAAC
1 ATTAAAGTCATATATAATAAAAC
*
54251573 ATTATAAGTTATAATATAATAAAAC
1 ATTA-AAGTCAT-ATATAATAAAAC
54251598 AT
1 AT
54251600 AAAAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 6 0.27
24 1 0.05
25 11 0.50
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTAAAGTCATATATAATAAAAC
Found at i:54252797 original size:50 final size:50
Alignment explanation
Indices: 54252722--54252830 Score: 209
Period size: 50 Copynumber: 2.2 Consensus size: 50
54252712 TAAATGACCA
54252722 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
54252772 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
1 TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
*
54252822 TGTGTATTC
1 TGTATATTC
54252831 CGCTAAATGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (50 bp):
TGTATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTTGATCT
Found at i:54255559 original size:93 final size:93
Alignment explanation
Indices: 54255448--54255618 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
54255438 GCCCCTAAGT
* * *
54255448 GAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGACCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
54255513 CGAGTTCGGATGCCTAGTTACATCACAC
66 CAAGTTCGGATGCCTAGTTACATCACAC
* * *
54255541 GAACTCGGACTCAACTCAACGACCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGACCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54255606 CAAGTTCGGATGC
66 CAAGTTCGGATGC
54255619 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAAAGACCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CAAGTTCGGATGCCTAGTTACATCACAC
Found at i:54255615 original size:46 final size:46
Alignment explanation
Indices: 54255443--54255615 Score: 156
Period size: 46 Copynumber: 3.7 Consensus size: 46
54255433 AACCCGCCCC
* * *
54255443 TAAGTGAACTCGGACTCAACTCAA-AGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACA-AGCTCGGACATTTGCATCCA
* * * * *
54255489 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-CA
1 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGA---C-ATTTGCATCCA
* * * *
54255538 -CA-CGAACTCGGACTCAACTCAACGACCTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGACATTTGCATCCA
*
54255582 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACAAGCTCGGA
54255616 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
43 6 0.06
44 3 0.03
45 1 0.01
46 55 0.55
47 27 0.27
48 1 0.01
49 3 0.03
50 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACAAGCTCGGACATTTGCATCCA
Found at i:54263583 original size:63 final size:63
Alignment explanation
Indices: 54263499--54263620 Score: 208
Period size: 63 Copynumber: 1.9 Consensus size: 63
54263489 ATTATTTCTA
* * *
54263499 TCTCGGATTTGTGGTCACGAAACCATTATTCCGATTAAGCCCTAATTCAGGATATTACAACTC
1 TCTCAGATTTGTGATCACGAAACCACTATTCCGATTAAGCCCTAATTCAGGATATTACAACTC
*
54263562 TCTCAGATTTGTGATCACGAAACCACTATTCTGATTAAGCCCTAATTCAGGATATTACA
1 TCTCAGATTTGTGATCACGAAACCACTATTCCGATTAAGCCCTAATTCAGGATATTACA
54263621 TGTAAAATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (63 bp):
TCTCAGATTTGTGATCACGAAACCACTATTCCGATTAAGCCCTAATTCAGGATATTACAACTC
Found at i:54265267 original size:72 final size:72
Alignment explanation
Indices: 54265182--54265326 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
54265172 CCTCAGGAAC
*
54265182 CGGTTGAGGAGCAAGTGGGGGAGGTCGTTGAACAACAGGGTTTGTTCTCAAGTACTCTGTAAACC
1 CGGTTGAGGAGCAAGTGGGGGAGGTCATTGAACAACAGGGTTTGTTCTCAAGTACTCTGTAAACC
54265247 ATTCATT
66 ATTCATT
54265254 CGGTTGAGGAGCAAGTGGGGGAGGTCATTGAACAACAGGGTTTGTTCTCAAGTACTCTGTAAACC
1 CGGTTGAGGAGCAAGTGGGGGAGGTCATTGAACAACAGGGTTTGTTCTCAAGTACTCTGTAAACC
54265319 ATTCATT
66 ATTCATT
54265326 C
1 C
54265327 ATTATTTAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (72 bp):
CGGTTGAGGAGCAAGTGGGGGAGGTCATTGAACAACAGGGTTTGTTCTCAAGTACTCTGTAAACC
ATTCATT
Found at i:54268748 original size:42 final size:42
Alignment explanation
Indices: 54268689--54268850 Score: 168
Period size: 42 Copynumber: 3.8 Consensus size: 42
54268679 AGGGTTACTA
54268689 AGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATG
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATG
* * * * * *
54268731 AGATTTCGTTTAAGACCATATCTAGGATATGCCATCGATGTG
1 AGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATG
* * *
54268773 AGACTT-CGTGTAAAACCATAGCTGGGCTATTGGCAT-TGATACT-
1 AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCT-ATA-TG
* *
54268816 AGATTACATGTAAGACCATATATGGGATATGGCAT
1 AGATTACGTGTAAGACCATATCTGGGATATGGCAT
54268851 TGGTATAGTA
Statistics
Matches: 96, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 65 0.68
43 30 0.31
44 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATG
Found at i:54275281 original size:42 final size:42
Alignment explanation
Indices: 54275216--54275379 Score: 152
Period size: 42 Copynumber: 3.9 Consensus size: 42
54275206 TTAGGGTTAC
* * * **
54275216 TGAGATTACATGTAAAACCATATCTAGGATATGGCATTTATA
1 TGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
* *
54275258 TGAGATTTCGTGTAAGACGATATCTGGGATATGGCATCGATA
1 TGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
* * *
54275300 TGAGACTTCGTGTAAGACCATAACTAGGCGAT-TGGCATCAATA
1 TGAGATTTCGTGTAAGACCATATCTA-G-GATATGGCATCGATA
* ** * *
54275343 CGAGATCACATGTAA-AGCCATATCTGGGATATGGCAT
1 TGAGATTTCGTGTAAGA-CCATATCTAGGATATGGCAT
54275380 TGGTATAGTA
Statistics
Matches: 99, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.03
42 65 0.66
43 28 0.28
44 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
Found at i:54284214 original size:29 final size:29
Alignment explanation
Indices: 54284179--54284252 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
54284169 GTTGTGAGAT
* *
54284179 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
54284208 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
54284237 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54284253 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:54284646 original size:40 final size:41
Alignment explanation
Indices: 54284563--54284798 Score: 141
Period size: 40 Copynumber: 5.9 Consensus size: 41
54284553 TCGAATGATG
* *
54284563 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAA
* * *
54284603 TCCGGACTAAGAT-CCGAAGGCATTGGTGC-AAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTGGTGCTAAGTGACCAAA
** * ***
54284643 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGCGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTGGTGCTAAGTGACCAAA
** ***
54284683 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTA
1 TCCGGGCTAAGTCCCGAAG-GCATTGGTGCTAAGTGACCAAA
* ** * *
54284723 TCCGGGCTAAGTTCCGAAGAGCATTCATGCT-AGTGA-TATA
1 TCCGGGCTAAGTCCCGAAG-GCATTGGTGCTAAGTGACCAAA
* * *
54284763 TTCGGGCTAAGTCCCGAGGAGCATTCGTGCT-AGTGA
1 TCCGGGCTAAGTCCCGAAG-GCATTGGTGCTAAGTGA
54284799 TGTATCCGGG
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 153 0.89
41 18 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAA
Found at i:54284700 original size:80 final size:80
Alignment explanation
Indices: 54284563--54284814 Score: 296
Period size: 80 Copynumber: 3.1 Consensus size: 80
54284553 TCGAATGATG
** * * *
54284563 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAG-GC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGCGA-TATATCCGGGCTAAG-TCCCGAAGAGC
* * * **
54284624 ATTGGTGCAAGTTACTAAA
63 ATTCGTGCTAGTGA-TGTA
*
54284643 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
*
54284708 CATGCTAGTGATGTA
66 CGTGCTAGTGATGTA
* * * *
54284723 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATATTCGGGCTAAGTCCCGAGGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
54284788 CGTGCTAGTGATGTA
66 CGTGCTAGTGATGTA
54284803 TCCGGGCTAAGT
1 TCCGGGCTAAGT
54284815 TCCTGTAACA
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 125 0.83
81 18 0.12
82 6 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATATATCCGGGCTAAGTCCCGAAGAGCATT
CGTGCTAGTGATGTA
Found at i:54284776 original size:120 final size:120
Alignment explanation
Indices: 54284563--54284814 Score: 321
Period size: 120 Copynumber: 2.1 Consensus size: 120
54284553 TCGAATGATG
** *
54284563 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTG
1 TCCGGGCTAAGTCCCGAAGGCTTCATGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTC
* *
54284628 GTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
66 ATGCAAGTGACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
** * *
54284683 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAG-GC-TTCATGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
* * * * * *
54284746 TTCATGCTAGTGA-TATATTCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
63 TTCATGCAAGTGACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
54284803 TCCGGGCTAAGT
1 TCCGGGCTAAGT
54284815 TCCTGTAACA
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
120 89 0.78
121 19 0.17
122 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTCATGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTC
ATGCAAGTGACTAAATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
Found at i:54284799 original size:40 final size:40
Alignment explanation
Indices: 54284642--54284814 Score: 292
Period size: 40 Copynumber: 4.3 Consensus size: 40
54284632 AAGTTACTAA
*
54284642 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
54284682 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* *
54284722 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* * *
54284762 ATTCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
54284802 ATCCGGGCTAAGT
1 ATCCGGGCTAAGT
54284815 TCCTGTAACA
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 124 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:54286306 original size:27 final size:27
Alignment explanation
Indices: 54286276--54286454 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
54286266 TATATTGAGT
* * *
54286276 TCGCACACTCAGTGCTATATAATCATC
1 TCGCACACTTAGTGCTACATAATCAAC
* *
54286303 TCGCACACTTAGTGCTACGTAATCAAA
1 TCGCACACTTAGTGCTACATAATCAAC
*
54286330 TCGCACACTTAGTGCTACATAGTCAAAC
1 TCGCACACTTAGTGCTACATAATC-AAC
** ** *
54286358 TCGCACACTTAGTGCCGCATGGTCAAT
1 TCGCACACTTAGTGCTACATAATCAAC
* **
54286385 TCGCACACTTAGTGC-ATCATATTCATT
1 TCGCACACTTAGTGCTA-CATAATCAAC
* * *
54286412 TCGCACACTTAGTGCAACATAGTCAAA
1 TCGCACACTTAGTGCTACATAATCAAC
54286439 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
54286455 GTACAATTTA
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
TCGCACACTTAGTGCTACATAATCAAC
Found at i:54286416 original size:82 final size:81
Alignment explanation
Indices: 54286303--54286453 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
54286293 TATAATCATC
* *
54286303 TCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
54286368 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
54286385 TCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
54286449 AGTGC
65 AGTGC
54286454 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:54288160 original size:68 final size:68
Alignment explanation
Indices: 54288076--54288205 Score: 251
Period size: 68 Copynumber: 1.9 Consensus size: 68
54288066 ACATTCATGA
54288076 TTACATATTCTAGACAATAAACATCACATTCCAACCTTTCGGTGACTCGGTTTAGCGGTCCCGAA
1 TTACATATTCTAGACAATAAACATCACATTCCAACCTTTCGGTGACTCGGTTTAGCGGTCCCGAA
54288141 ACC
66 ACC
*
54288144 TTACATATTCTAGACAATAAACATCACCTTCCAACCTTTCGGTGACTCGGTTTAGCGGTCCC
1 TTACATATTCTAGACAATAAACATCACATTCCAACCTTTCGGTGACTCGGTTTAGCGGTCCC
54288206 AAAATGACTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (68 bp):
TTACATATTCTAGACAATAAACATCACATTCCAACCTTTCGGTGACTCGGTTTAGCGGTCCCGAA
ACC
Found at i:54295984 original size:40 final size:40
Alignment explanation
Indices: 54295929--54296153 Score: 362
Period size: 40 Copynumber: 5.6 Consensus size: 40
54295919 NNNNNNNNNN
54295929 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54295969 CAAATGCCTTCGGGACTTAGCTCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54296009 CAAATGCCTTCGGGACCTAGCCCGGATATAGTAACTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54296049 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54296089 CAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* *
54296129 CAAAGGCCTTCGGGACCTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54296154 TTATCATTCG
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.01
40 173 0.99
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54302117 original size:40 final size:40
Alignment explanation
Indices: 54301900--54302117 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
54301890 AAGCCAAGTA
* * * *
54301900 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
54301939 CCTTCGGGACATAGCCCGAATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
54301979 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54302019 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54302059 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
54302099 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54302118 TTATCATCCA
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 149 0.92
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54306196 original size:40 final size:40
Alignment explanation
Indices: 54306114--54306211 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
54306104 AAACCAAGTA
* * * *
54306114 CCTTTGGGATTTAG-CCGGATATAGCTACTCGCTCAAATG
1 CCTTTGGGACTTAGCCCGGATATAGCTACTAGCACAAAGG
*
54306153 CCTTCGGGACTTAGCCCGGATATAG-TCACTAGCACAAAGG
1 CCTTTGGGACTTAGCCCGGATATAGCT-ACTAGCACAAAGG
*
54306193 CCTTTGGGACCTAGCCCGG
1 CCTTTGGGACTTAGCCCGG
54306212 TTATCATTCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.26
40 37 0.74
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (40 bp):
CCTTTGGGACTTAGCCCGGATATAGCTACTAGCACAAAGG
Found at i:54306359 original size:40 final size:40
Alignment explanation
Indices: 54306306--54306890 Score: 1039
Period size: 40 Copynumber: 14.6 Consensus size: 40
54306296 ACACTTATCA
* * * *
54306306 CAAATGCGTTCGGGACCTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306346 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306386 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306426 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306466 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306506 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306546 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306586 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306626 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306666 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306706 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
54306746 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
*
54306786 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
* * *
54306826 CAAATGCCTTCGGGACTTAGCCTGGA-ATTAGTCACT-AGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CT
* * *
54306866 CAAAGGCCTTTGGGACCTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54306891 TTATCATTCG
Statistics
Matches: 530, Mismatches: 13, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
39 1 0.00
40 529 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACT
Found at i:54311641 original size:40 final size:40
Alignment explanation
Indices: 54311558--54311733 Score: 171
Period size: 40 Copynumber: 4.5 Consensus size: 40
54311548 ACCCAAGTAT
* ** * * *
54311558 CTTCGGGATTTAG-CCGGATATAACCACTCGCA-CAAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
* *
54311596 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
* *
54311636 CTTCGGGACTTAGCCCGGATATAGTAACTCGC-TCAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCAT-AAATGC
* * *
54311676 CTTCGGGACTTAGCCTGGA-ATTAGTCACTAGCACAAAGGC
1 CTTCGGGACTTAGCCCGGATA-TAGTCACTAGCATAAATGC
* *
54311716 CTTTGGGACCTAGCCCGG
1 CTTCGGGACTTAGCCCGG
54311734 TTATCATTCG
Statistics
Matches: 113, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 11 0.10
39 17 0.15
40 85 0.75
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGC
Found at i:54311689 original size:80 final size:79
Alignment explanation
Indices: 54311558--54311733 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 79
54311548 ACCCAAGTAT
* * * *
54311558 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGG-ATATGGT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
54311621 CACTAGCATAAATGC
65 CACTAGCACAAAGGC
** * * *
54311636 CTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATGCCTTCGGGACTTAGCCTGGAATTAGT
1 CTTCGGGACTTAGCCCGGATATAACAACTCGCAC-AAGGCCTTCGGGACTTAGCCCGGAATTAGT
54311701 CACTAGCACAAAGGC
65 CACTAGCACAAAGGC
* *
54311716 CTTTGGGACCTAGCCCGG
1 CTTCGGGACTTAGCCCGG
54311734 TTATCATTCG
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 12 0.15
79 16 0.20
80 52 0.63
81 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAACAACTCGCACAAGGCCTTCGGGACTTAGCCCGGAATTAGTC
ACTAGCACAAAGGC
Found at i:54313139 original size:10 final size:10
Alignment explanation
Indices: 54313106--54313156 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
54313096 ATTAAATTCT
*
54313106 TAAAGATATA
1 TAAAGATAAA
54313116 TACAA-ATAAA
1 TA-AAGATAAA
*
54313126 TAAAGATAAT
1 TAAAGATAAA
54313136 TAAAGATAAA
1 TAAAGATAAA
54313146 TGAAA-ATAAA
1 T-AAAGATAAA
54313156 T
1 T
54313157 CTTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (10 bp):
TAAAGATAAA
Found at i:54314058 original size:119 final size:119
Alignment explanation
Indices: 54313921--54314146 Score: 335
Period size: 119 Copynumber: 1.9 Consensus size: 119
54313911 CTAGTTAGCT
* * *
54313921 GAGTTTTACCCATCACGTCACACAACCTTTTGACGCGAAGTAGAATGATAACCCAAGCACCCTAC
1 GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
* * * *
54313986 CCCGGTTACTTAATCAGTCACGTTCTGAGCTGTACTTATAACCTCGGGTTAACG
66 CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAACCTCGGGTTAACG
* * * *
54314040 GAGTTTTACCTAACACGTCACAGAACTTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCTTAC
1 GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
* *
54314105 CCCGGTTACTCAGTCAGTCACGTTTTAAGCTGCACTCATAAC
66 CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAAC
54314147 TATGGAAACA
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 94 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (119 bp):
GAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAAGGACAACCCAAGCACCCTAC
CCCGGTTACTCAATCAGTCACGTTCTAAGCTGCACTCATAACCTCGGGTTAACG
Found at i:54315041 original size:8 final size:7
Alignment explanation
Indices: 54315030--54315084 Score: 58
Period size: 8 Copynumber: 7.3 Consensus size: 7
54315020 TTAATATTCA
54315030 AATAAAGT
1 AATAAA-T
54315038 AATAAAT
1 AATAAAT
54315045 AATAAAAT
1 AAT-AAAT
54315053 AAAATAAAGT
1 --AATAAA-T
54315063 AATAAAT
1 AATAAAT
54315070 AA-AAAT
1 AATAAAT
54315076 AATAAAT
1 AATAAAT
54315083 AA
1 AA
54315085 AATAAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.14
7 13 0.31
8 16 0.38
9 3 0.07
10 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:54315055 original size:5 final size:5
Alignment explanation
Indices: 54315045--54315096 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
54315035 AGTAATAAAT
* *
54315045 AATAA AATAA AATAA AGTAATA AATAA AA-AT AAT-A AATAA AATAA AATAA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AATAA AATAA
54315095 AA
1 AA
54315097 ATAGAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.15
5 28 0.72
6 2 0.05
7 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:54315060 original size:17 final size:17
Alignment explanation
Indices: 54315038--54315104 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
54315028 CAAATAAAGT
54315038 AATAAATAATAAAATAA
1 AATAAATAATAAAATAA
54315055 AATAAAGTAAT-AAATAA
1 AATAAA-TAATAAAATAA
54315072 AA-ATAATAAATAAAATAA
1 AATA-AAT-AATAAAATAA
54315090 AATAAA-AATAGAAAT
1 AATAAATAATA-AAAT
54315105 TGGGTTGCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.14
17 23 0.52
18 14 0.32
19 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AATAAATAATAAAATAA
Found at i:54315061 original size:25 final size:25
Alignment explanation
Indices: 54315029--54315099 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
54315019 ATTAATATTC
*
54315029 AAATAAAGTAATAAATAATAA-AAT
1 AAATAAAGTAATAAATAAAAATAAT
54315053 AAAATAAAGTAATAAATAAAAATAAT
1 -AAATAAAGTAATAAATAAAAATAAT
*
54315079 AAATAAAAT-A-AAATAAAAATA
1 AAATAAAGTAATAAATAAAAATA
54315100 GAAATTGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.26
24 1 0.02
25 28 0.65
26 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (25 bp):
AAATAAAGTAATAAATAAAAATAAT
Found at i:54315086 original size:12 final size:12
Alignment explanation
Indices: 54315029--54315089 Score: 70
Period size: 12 Copynumber: 4.9 Consensus size: 12
54315019 ATTAATATTC
*
54315029 AAATAAAGTAAT
1 AAATAAAATAAT
54315041 AAATAATAA-AAT
1 AAATAA-AATAAT
*
54315053 AAAATAAAGTAAT
1 -AAATAAAATAAT
54315066 AAATAAAAATAAT
1 AAAT-AAAATAAT
54315079 AAATAAAATAA
1 AAATAAAATAA
54315090 AATAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 21 0.50
13 21 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:54316829 original size:46 final size:45
Alignment explanation
Indices: 54316712--54316842 Score: 144
Period size: 45 Copynumber: 2.9 Consensus size: 45
54316702 AGTCTAGTAT
*
54316712 ATCT-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACAC
1 ATCTCATGCCGATGCCATGTCCCAGACATGATCTTACACTGACAC
* * *
54316756 ATCTCGTAGCCGATG-CATGTCCCAGACAT-ATTTTACA-TAGCACTC
1 ATCTCAT-GCCGATGCCATGTCCCAGACATGATCTTACACT-G-ACAC
* *
54316801 GTCTCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTG
1 ATCTC-ATGCCGATGCCATGTCCCAGACATGATCTTACACTG
54316843 GCTCTCATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 11 0.15
45 29 0.41
46 22 0.31
47 7 0.10
48 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
ATCTCATGCCGATGCCATGTCCCAGACATGATCTTACACTGACAC
Found at i:54321326 original size:10 final size:10
Alignment explanation
Indices: 54321299--54321358 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
54321289 TTAAATTTTA
54321299 AAAGATAAAT
1 AAAGATAAAT
54321309 ACAA-ATAAAT
1 A-AAGATAAAT
*
54321319 AAAGATAATT
1 AAAGATAAAT
*
54321329 AAAGATAATT
1 AAAGATAAAT
54321339 AAAGATAAAT
1 AAAGATAAAT
54321349 GAAA-ATAAAT
1 -AAAGATAAAT
54321359 CCAAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:54322632 original size:136 final size:136
Alignment explanation
Indices: 54322438--54322847 Score: 775
Period size: 136 Copynumber: 3.0 Consensus size: 136
54322428 GCCCATTCAA
*
54322438 GTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
54322503 AGAAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
66 AGAAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
54322568 ATTTGG
131 ATTTGG
54322574 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
54322639 AGAAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
66 AGAAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
54322704 ATTTGG
131 ATTTGG
54322710 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
1 GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
* * *
54322775 AGATAACAGTATGGCCCATAGGCTCATTTCAAAATACATGCAACATCAGTAAACAAATGCAAGCT
66 AGA-AACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCC
54322840 CATTTGG
130 CATTTGG
54322847 G
1 G
54322848 GAGACTACTC
Statistics
Matches: 269, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
136 203 0.75
137 66 0.25
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (136 bp):
GTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTC
AGAAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCC
ATTTGG
Found at i:54323124 original size:26 final size:26
Alignment explanation
Indices: 54323095--54323147 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
54323085 TCAAACATGC
*
54323095 ATTTAGGTCAATTTAACT-CTAGGGGT
1 ATTTAGAT-AATTTAACTACTAGGGGT
* *
54323121 ATTTCGATAATTTATCTACTAGGGGT
1 ATTTAGATAATTTAACTACTAGGGGT
54323147 A
1 A
54323148 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGATAATTTAACTACTAGGGGT
Found at i:54324668 original size:26 final size:26
Alignment explanation
Indices: 54324632--54324741 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
54324622 CATGAAATTC
54324632 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
54324658 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
54324684 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* * *
54324710 TTATCATGGAATATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
54324736 TTATCA
1 TTATCA
54324742 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:54327666 original size:43 final size:42
Alignment explanation
Indices: 54327604--54328049 Score: 141
Period size: 43 Copynumber: 10.2 Consensus size: 42
54327594 CTATTTAGGG
54327604 AGATAAGACCTTCAATCTTCAATCTGCTTCCTTGCTACCTCATGA
1 AGATAAGA-CTTCAATCTTCAATCTGC-TCCTTGCTACCTCA-GA
*
54327649 AGATAAGAC-TCAATCTTCAA-CTTGCTCTTTTGCTACCTCAG-
1 AGATAAGACTTCAATCTTCAATC-TGCTC-CTTGCTACCTCAGA
* **** * * *
54327690 AGATAAGGCTTGGGGCTTCAAATCTACTCCATTGC--CGATACATGG
1 AGATAAGACTTCAATCTTC-AATCTGCTCC-TTGCTAC-CT-CA-GA
* * * * *
54327735 AGATAAGA-TTCACCATCTTCGATCTACTCC--GCTACTGTTTAGGG
1 AGATAAGACTTCA--ATCTTCAATCTGCTCCTTGCTAC--CTCA-GA
* * *
54327779 AGATAAGATCTTCAATTTTCAGTCTGCTTCCTTACTACCTCAGGA
1 AGATAAGA-CTTCAATCTTCAATCTGC-TCCTTGCTACCTCA-GA
*
54327824 AGATAAGAC-TCAATCTTCAACCTGCTCTCTTGCTACCTCAGA
1 AGATAAGACTTCAATCTTCAATCTGCTC-CTTGCTACCTCAGA
* ** * * *
54327866 GAGATAAGGCTT-AGGGCTTAAATCTGCTCCATTGC--CGATACATGG
1 -AGATAAGACTTCA-ATCTTCAATCTGCTCC-TTGCTAC-CT-CA-GA
* * * * *
54327911 AGATAAGA-TTCGCCATCTTCGATCTGCTCC--GCTACTATTTAGGG
1 AGATAAGACTT--CAATCTTCAATCTGCTCCTTGCTAC--CTCA-GA
* * * *
54327955 ATATAAGATCTTCAATCTTTAGTCTGCTTTCTTGCTACCTCAAGA
1 AGATAAGA-CTTCAATCTTCAATCTGC-TCCTTGCTACCTC-AGA
* * *
54328000 AGATAAGAC-TCTATTTTCAACCTGCTCTCTTGCTACCTCAGA
1 AGATAAGACTTCAATCTTCAATCTGCTC-CTTGCTACCTCAGA
54328042 GAGATAAG
1 -AGATAAG
54328050 GCTTGGGGCT
Statistics
Matches: 296, Mismatches: 63, Indels: 86
0.67 0.14 0.19
Matches are distributed among these distances:
41 9 0.03
42 23 0.08
43 103 0.35
44 75 0.25
45 66 0.22
46 11 0.04
47 9 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (42 bp):
AGATAAGACTTCAATCTTCAATCTGCTCCTTGCTACCTCAGA
Found at i:54327963 original size:176 final size:176
Alignment explanation
Indices: 54327529--54328275 Score: 1057
Period size: 176 Copynumber: 4.3 Consensus size: 176
54327519 CAGGGCTAGT
* * * *
54327529 GGCTTAAATCTGCTCCATTGCCAATACATGGAGATAAGATTCGCCATCCTCGATCTGTTCCACTA
1 GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTA
* * * *
54327594 CTATTTAGGGAGATAAGACCTTCAATCTTCAATCTGCTTCCTTGCTACCTCATGAAGATAAGACT
66 CTATTTAGGGAGATAAGATCTTCAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
* *
54327659 CAATCTTCAACTTGCTCTTTTGCTACCTC--AGAGATAAGGCTTGG
131 CAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
* * *
54327703 GGCTTCAAATCTACTCCATTGCCGATACATGGAGATAAGATTCACCATCTTCGATCTACTCCGCT
1 GGCTT-AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCT
* *
54327768 ACTGTTTAGGGAGATAAGATCTTCAATTTTCAGTCTGCTTCCTTACTACCTCAGGAAGATAAGAC
65 ACTATTTAGGGAGATAAGATCTTCAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
*
54327833 TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTAG
130 TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
54327880 GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTA
1 GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTA
* * *
54327945 CTATTTAGGGATATAAGATCTTCAATCTTT-AGTCTGCTTTCTTGCTACCTCAAGAAGATAAGAC
66 CTATTTAGGGAGATAAGATCTTCAAT-TTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
* *
54328009 TCTATTTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
130 TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
* * ** * *
54328056 GGCTTAAATCTACTCCATTGTCGATACATGGAGATAAGATTTTCCATCTTCGATCTGCTCTGCTG
1 GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTA
* * * * *
54328121 CAACTTCAGGGAGATAAGATCTTC------CA-TCTGCTTTCTTGCTACTTCAGAAAGATAAGAC
66 CTA-TTTAGGGAGATAAGATCTTCAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGAC
*
54328179 TCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGC-TGG
130 TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
* * *
54328225 TGGCTTAAATCTGCTCTATTGCCAATATATGGAGATAAGATTCGCCATCTT
1 -GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTT
54328276 TAATCTCCAT
Statistics
Matches: 517, Mismatches: 49, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
169 3 0.01
170 112 0.22
171 1 0.00
174 5 0.01
175 139 0.27
176 217 0.42
177 40 0.08
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (176 bp):
GGCTTAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCGCCATCTTCGATCTGCTCCGCTA
CTATTTAGGGAGATAAGATCTTCAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
CAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTGG
Found at i:54328165 original size:38 final size:38
Alignment explanation
Indices: 54328101--54328219 Score: 105
Period size: 38 Copynumber: 3.0 Consensus size: 38
54328091 AAGATTTTCC
* * * *
54328101 ATCTTCGATCTGCTCTGC-TGCAACTTCAGGGAGATAAG
1 ATCTTCCATCTGCT-TTCTTGCTACTTCAGAGAGATAAG
*
54328139 ATCTTCCATCTGCTTTCTTGCTACTTCAGAAAGATAAG
1 ATCTTCCATCTGCTTTCTTGCTACTTCAGAGAGATAAG
* * *
54328177 ACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAG
1 A-TC-TTC--C-ATCTGCTTTCTTGCTACTTCAGAGAGATAAG
54328220 GCTGGTGGCT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 2 0.03
38 31 0.47
39 2 0.03
40 3 0.05
42 1 0.02
43 27 0.41
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (38 bp):
ATCTTCCATCTGCTTTCTTGCTACTTCAGAGAGATAAG
Found at i:54329388 original size:20 final size:21
Alignment explanation
Indices: 54329365--54329405 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
54329355 CCTTGGCCTC
54329365 TCCTTTTT-CCTTTTTTATTT
1 TCCTTTTTACCTTTTTTATTT
54329385 TCCTTTTTACCCTTTTTTATT
1 TCCTTTTTA-CCTTTTTTATT
54329406 GAGTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCCTTTTTACCTTTTTTATTT
Found at i:54340228 original size:71 final size:71
Alignment explanation
Indices: 54340112--54340253 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 71
54340102 CGAATTTCCA
*
54340112 AATATTGAATATTGCCCTATTTTAGAATCTTTGAATAATAAAGAGAATTGAAAATTAGCTCAAAA
1 AATATTGAATATTGCCCTATTTTAGAATCTTTAAATAATAAAGAGAATTGAAAATTAGCTCAAAA
54340177 CACATT
66 CACATT
* * *
54340183 AATATTGAATATTGTCTTATTTTAGAATCTTTAAATAATAAAGAGAATTGGAAATTAGCTCAAAA
1 AATATTGAATATTGCCCTATTTTAGAATCTTTAAATAATAAAGAGAATTGAAAATTAGCTCAAAA
54340248 CACATT
66 CACATT
54340254 TATTTGTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (71 bp):
AATATTGAATATTGCCCTATTTTAGAATCTTTAAATAATAAAGAGAATTGAAAATTAGCTCAAAA
CACATT
Found at i:54349689 original size:20 final size:21
Alignment explanation
Indices: 54349646--54349689 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
54349636 TATATTTGTT
**
54349646 TTAAATAATAAATAAATATTA
1 TTAAATAATAAATAAATAAAA
*
54349667 TTAAA-AATAAATAGATAAAA
1 TTAAATAATAAATAAATAAAA
54349687 TTA
1 TTA
54349690 TTTTCTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAATAATAAATAAATAAAA
Found at i:54349689 original size:23 final size:23
Alignment explanation
Indices: 54349648--54349691 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54349638 TATTTGTTTT
54349648 AAATAATAAATAAATATTATTAA
1 AAATAATAAATAAATATTATTAA
*
54349671 AAATAAATAGATAAA-ATTATT
1 AAAT-AATAAATAAATATTATT
54349692 TTCTTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATAATAAATAAATATTATTAA
Found at i:54350997 original size:37 final size:39
Alignment explanation
Indices: 54350924--54350997 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 39
54350914 TAATTAATAT
*
54350924 ATAATTTGTAATAGAAAGTAAGAACTGAAATAATTTATC
1 ATAATTTGTAATAGAAAGTAAGAACTGAAAAAATTTATC
* *
54350963 ATAATTT-T-ATAGAAATTAAG-ATTGAAAAATATTTA
1 ATAATTTGTAATAGAAAGTAAGAACTGAAAAA-ATTTA
54350998 AGGAACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 16 0.52
38 1 0.03
39 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (39 bp):
ATAATTTGTAATAGAAAGTAAGAACTGAAAAAATTTATC
Found at i:54355738 original size:33 final size:33
Alignment explanation
Indices: 54355701--54355797 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
54355691 CCATATGCTT
*
54355701 ATGTGGCCCCACACGCCCAACTTAGCCTAGCCC
1 ATGTGGCCCCACACGCCCAACTTGGCCTAGCCC
*
54355734 ATGTGGCCCCACATGCCCAACTTGGCCTAGCCC
1 ATGTGGCCCCACACGCCCAACTTGGCCTAGCCC
* *
54355767 GTGTGG-CCCACACGTCCAACTTGGCCTAGCC
1 ATGTGGCCCCACACGCCCAACTTGGCCTAGCC
54355798 TGTGTAGCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 23 0.39
33 36 0.61
ACGTcount: A:0.19, C:0.42, G:0.22, T:0.18
Consensus pattern (33 bp):
ATGTGGCCCCACACGCCCAACTTGGCCTAGCCC
Found at i:54355812 original size:32 final size:32
Alignment explanation
Indices: 54355711--54355821 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 32
54355701 ATGTGGCCCC
* * * * *
54355711 ACACGCCCAACTTAGCCTAGCCCATGTGGCCCC
1 ACACGGCCAACTTGGCCTAGCCCGTGTAG-CCA
* * * *
54355744 ACATGCCCAACTTGGCCTAGCCCGTGTGGCCC
1 ACACGGCCAACTTGGCCTAGCCCGTGTAGCCA
* *
54355776 ACACGTCCAACTTGGCCTAGCCTGTGTAGCCA
1 ACACGGCCAACTTGGCCTAGCCCGTGTAGCCA
54355808 ACACGGCCACACTT
1 ACACGGCCA-ACTT
54355822 AAGCCACCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 38 0.56
33 30 0.44
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.18
Consensus pattern (32 bp):
ACACGGCCAACTTGGCCTAGCCCGTGTAGCCA
Found at i:54358917 original size:33 final size:32
Alignment explanation
Indices: 54358880--54358957 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
54358870 TGGCCCTGCC
* * *
54358880 ATGGTCTTACACTTGTG-GTGCCATAATCCAGTT
1 ATGGTCTTACA-TT-TGAATGCCATAACCCAGCT
*
54358913 ATGGTCTTATCATTTGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTTGAATGCCATAACCCAGCT
54358946 ATGGTCTTACAT
1 ATGGTCTTACAT
54358958 ACAAATACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 5 0.13
33 32 0.82
34 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (32 bp):
ATGGTCTTACATTTGAATGCCATAACCCAGCT
Found at i:54358950 original size:66 final size:66
Alignment explanation
Indices: 54358831--54358956 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
54358821 CGTTTTCTTT
* * *
54358831 GTGCCATAGTCCAATTATGGTCTTATACGTGAATTCCCATGGCCCTGCCATGGTCTTACACTTGT
1 GTGCCATAATCCAATTATGGTCTTATACGTGAATTCCCATAGCCCAGCCATGGTCTTACACTTGT
54358896 G
66 G
* ** * *
54358897 GTGCCATAATCCAGTTATGGTCTTATCATTTGAA-TGCCATAGCCCAGCTATGGTCTTACA
1 GTGCCATAATCCAATTATGGTCTTAT-ACGTGAATTCCCATAGCCCAGCCATGGTCTTACA
54358957 TACAAATACT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 46 0.90
67 5 0.10
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (66 bp):
GTGCCATAATCCAATTATGGTCTTATACGTGAATTCCCATAGCCCAGCCATGGTCTTACACTTGT
G
Found at i:54361074 original size:21 final size:20
Alignment explanation
Indices: 54361050--54361089 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54361040 AGAGAATGGA
54361050 AAAGAAAAAAAAAGAAAATTT
1 AAAGAAAAAAAAA-AAAATTT
* *
54361071 AAAGAACATAAAAAAAATT
1 AAAGAAAAAAAAAAAAATT
54361090 AAATTACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAGAAAAAAAAAAAAATTT
Found at i:54369754 original size:26 final size:26
Alignment explanation
Indices: 54369674--54369757 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
54369664 CATGAAATTC
*
54369674 TTATCATGAAACATTTACCTAGCCCA
1 TTATCATGAAACATTTACCTAACCCA
*
54369700 TCATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
54369726 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
54369752 TTATCA
1 TTATCA
54369758 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:54371839 original size:22 final size:22
Alignment explanation
Indices: 54371785--54371862 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
54371775 GTTTGATTTA
54371785 TTTAT-TTATTTATTTTAAACT
1 TTTATATTATTTATTTTAAACT
* * **
54371806 ATTATTATTATTCATTTTAAGTT
1 TTTA-TATTATTTATTTTAAACT
54371829 TTTATATTATTTATTTTAAATCAT
1 TTTATATTATTTATTTTAAA-C-T
54371853 TTTATCATTA
1 TTTAT-ATTA
54371863 CTCTTTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.07
22 15 0.34
23 16 0.36
24 6 0.14
25 4 0.09
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (22 bp):
TTTATATTATTTATTTTAAACT
Found at i:54371981 original size:27 final size:25
Alignment explanation
Indices: 54371915--54372148 Score: 103
Period size: 26 Copynumber: 9.4 Consensus size: 25
54371905 AATATTTTAC
* *
54371915 ATATATTATTTATTTCAAACTA-TT
1 ATATATTATTTATTTTAAATTATTT
** *
54371939 ATACCTCATTTATTTTGAAATTATTT
1 ATATATTATTTATTTT-AAATTATTT
* *
54371965 ATATATCTTTTTATTTTAAACTATTAT
1 ATATAT-TATTTATTTTAAATTATT-T
* *
54371992 ATATATTATTCATTTTAAATTTCTTT
1 ATATATTATTTATTTTAAA-TTATTT
* * *
54372018 ATATAGTATTAATTTCAAACTGT-TTT
1 ATATATTATTTATTTTAAA-T-TATTT
* * *
54372044 A-ATA-CATATTATTCTGAATTATTTT
1 ATATATTAT-TTATTTTAAATTA-TTT
* * *
54372069 ATATATTAATTATTTTACATTA-CT
1 ATATATTATTTATTTTAAATTATTT
* *
54372093 -TAT-TTATTTAATTTAAACTCTTTTT
1 ATATATTATTTATTTTAAA-T-TATTT
*
54372118 ATATAATA-TT-TTTT-AATTATTT
1 ATATATTATTTATTTTAAATTATTT
54372140 -TATTATTAT
1 ATA-TATTAT
54372149 AAATTTATAT
Statistics
Matches: 154, Mismatches: 38, Indels: 37
0.67 0.17 0.16
Matches are distributed among these distances:
21 2 0.01
22 19 0.12
23 6 0.04
24 19 0.12
25 22 0.14
26 64 0.42
27 22 0.14
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATATTATTTATTTTAAATTATTT
Found at i:54372127 original size:74 final size:76
Alignment explanation
Indices: 54371986--54372147 Score: 178
Period size: 77 Copynumber: 2.2 Consensus size: 76
54371976 TATTTTAAAC
* *
54371986 TATTATATATATT-ATTCATTTTAAATTTCTTTATATAGTATTAATTTCAAACTGTTTTAATACA
1 TATTTTATATATTAATTCATTTTAAATTACTTTATATAGTATTAATTTCAAACTGTTTTAATACA
54372050 TATTATTCTGAAT
66 TATT-TT-TGAAT
* * *
54372063 TATTTTATATATTAATT-ATTTTACATTAC-TTATTTA-T-TTAATTT-AAACTCTTTTTATATA
1 TATTTTATATATTAATTCATTTTAAATTACTTTATATAGTATTAATTTCAAACT-GTTTTA-ATA
*
54372123 -ATATTTTTTAAT
64 CATATTTTTGAAT
54372135 TATTTTAT-TATTA
1 TATTTTATATATTA
54372148 TAAATTTATA
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
71 5 0.07
72 12 0.16
73 7 0.09
74 17 0.22
75 4 0.05
76 6 0.08
77 22 0.29
78 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (76 bp):
TATTTTATATATTAATTCATTTTAAATTACTTTATATAGTATTAATTTCAAACTGTTTTAATACA
TATTTTTGAAT
Found at i:54372235 original size:27 final size:27
Alignment explanation
Indices: 54372152--54372293 Score: 94
Period size: 28 Copynumber: 5.2 Consensus size: 27
54372142 TTATTATAAA
* * *
54372152 TTTATATACTGTTTATTCTTAAACTTCTT
1 TTTATATATTATTTA-TCTTAAA-TTATT
* *
54372181 TTTATATGGATTATTTATTTTCAA--ATT
1 TTTATAT--ATTATTTATCTTAAATTATT
*
54372208 TTTATATATTGTTTATCTTAAATTA-T
1 TTTATATATTATTTATCTTAAATTATT
* * *
54372234 TTTATACATTATTTAT-TCTATATTTTT
1 TTTATATATTATTTATCT-TAAATTATT
* * *
54372261 TTATATATATTATTTATATTAAACTGTT
1 TT-TATATATTATTTATCTTAAATTATT
54372289 TTTAT
1 TTTAT
54372294 TTCATGTATA
Statistics
Matches: 89, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
25 13 0.15
26 20 0.22
27 16 0.18
28 21 0.24
29 8 0.09
30 5 0.06
31 6 0.07
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTATATATTATTTATCTTAAATTATT
Found at i:54372248 original size:26 final size:25
Alignment explanation
Indices: 54372190--54372249 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
54372180 TTTTATATGG
* *
54372190 ATTATTTATTTTCAAATTTTTATAT
1 ATTATTTATCTTCAAATTTTTATAC
*
54372215 ATTGTTTATCTT-AAATTATTTTATAC
1 ATTATTTATCTTCAAA-T-TTTTATAC
54372241 ATTATTTAT
1 ATTATTTAT
54372250 TCTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 11 0.38
26 15 0.52
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTATTTATCTTCAAATTTTTATAC
Found at i:54372262 original size:26 final size:26
Alignment explanation
Indices: 54372206--54372280 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
54372196 TATTTTCAAA
* *
54372206 TTTTTATATATTGTTTA-TCTTAAATT
1 TTTTTATATATTATTTATTC-TATATT
* *
54372232 ATTTTATACATTATTTATTCTATATT
1 TTTTTATATATTATTTATTCTATATT
54372258 TTTTTATATA-TA-TTATT-TATATT
1 TTTTTATATATTATTTATTCTATATT
54372281 AAACTGTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 6 0.14
24 5 0.12
25 2 0.05
26 27 0.64
27 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTTATATATTATTTATTCTATATT
Found at i:54377616 original size:23 final size:23
Alignment explanation
Indices: 54377585--54377628 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54377575 ATTCTGTACA
*
54377585 TGGGTTAGGATTATTGGGTTATT
1 TGGGCTAGGATTATTGGGTTATT
*
54377608 TGGGCTAGGTTTATTGGGTTA
1 TGGGCTAGGATTATTGGGTTA
54377629 AGGATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (23 bp):
TGGGCTAGGATTATTGGGTTATT
Found at i:54378149 original size:25 final size:25
Alignment explanation
Indices: 54378115--54378165 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
54378105 AAGTTATAAC
54378115 CATTTTTTATAATAAATAAATTAAG
1 CATTTTTTATAATAAATAAATTAAG
**
54378140 CATTTTTTATAATATGTAAATTAAG
1 CATTTTTTATAATAAATAAATTAAG
54378165 C
1 C
54378166 CAAAAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (25 bp):
CATTTTTTATAATAAATAAATTAAG
Found at i:54380625 original size:3 final size:3
Alignment explanation
Indices: 54380619--54380838 Score: 133
Period size: 3 Copynumber: 72.7 Consensus size: 3
54380609 AATGAGAACG
* * * **
54380619 ATA ATA ATA ATA TTA ATA ATA ATA ATA GTA AAA ATA ATA ATA ATA CCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
54380667 ATG ACA ATA ATA ATA GTA ATA ATA AGA ATA TTA ATA TTA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
54380715 ATG ATA ATA GTA ATA GAAA ATA AAA ATA AAA ATA AT- ATA GTG ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
54380760 GTA ATA A-A AGTA A-A AGTA ATA GTA ATA ATA ATG GTA ATA ATAA ATA
1 ATA ATA ATA A-TA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* *
54380806 GTA ATA ATA ACA ATA ATA CA-A ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA -ATA ATA AT-A ATA AT
54380839 CTAAAGTTGG
Statistics
Matches: 158, Mismatches: 49, Indels: 20
0.70 0.22 0.09
Matches are distributed among these distances:
2 7 0.04
3 138 0.87
4 13 0.08
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:54380999 original size:3 final size:3
Alignment explanation
Indices: 54380991--54381306 Score: 94
Period size: 3 Copynumber: 105.0 Consensus size: 3
54380981 AAATACAAAA
* * **
54380991 AAT AAT AAT AAT AAT AAT -AT AGT AAT AAT AAT -AT ATT AAAT GGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* * * * ** * * *
54381035 AAA AAA AAT AGT AAC AAT AAT TTT AA- AAA AAT GAT AAT AGT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
54381081 AAT AA- GAT TAT AAT AAT AAT ATT AAT AAA AAT AAG AAT AAA AAG GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
54381128 AGT AAT AAT AGT AAT AAT AAT AGT AAT AGT AA- AAT GAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
** * ** ** * *
54381173 AGC AAT AAT AAG AGC GTT AAT GAT AGT AAT AAT -AT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * * * * *
54381218 -AT ATAT GTAT GAAA AAT AAT AAT AAT AGA- AGT AGT ACT AAT TAT AATT
1 AAT A-AT -AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA-T
*
54381266 AAT AGT AAT AAT AAAT GACA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT -A-AT AAT AAT AAT AAT AAT AAT AAT
54381307 TAATTTGAAA
Statistics
Matches: 221, Mismatches: 73, Indels: 38
0.67 0.22 0.11
Matches are distributed among these distances:
2 16 0.07
3 183 0.83
4 21 0.10
5 1 0.00
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54381018 original size:14 final size:13
Alignment explanation
Indices: 54380991--54381026 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
54380981 AAATACAAAA
54380991 AATAATA-ATAAT
1 AATAATATATAAT
54381003 AATAATATAGTAAT
1 AATAATATA-TAAT
54381017 AATAATATAT
1 AATAATATAT
54381027 TAAATGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:54382864 original size:44 final size:43
Alignment explanation
Indices: 54382728--54382873 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 43
54382718 TATTTATAGT
* * * * * *
54382728 TTCAATCTGTTCCACTGCAACGTCATGGAAATAAGATTTGCTATC
1 TTCAAT-TGCTCCACTGCAACTTCAAGGAGATAAGACTTG-TAAC
* * * * *
54382773 TTTAGTCTGCTCCACTGCAAGTTTAGGGAGATAAGACTTGTAAC
1 TTCAAT-TGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAAC
* * **
54382817 TTCAACTTGCTCCATTGCAACTTCAAGGAGATAAGGCTTGTGGC
1 TTCAA-TTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAAC
*
54382861 TTCAATCGCTCCA
1 TTCAATTGCTCCA
54382874 ATGCCATTTC
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 7 0.09
44 41 0.51
45 32 0.40
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (43 bp):
TTCAATTGCTCCACTGCAACTTCAAGGAGATAAGACTTGTAAC
Found at i:54382890 original size:43 final size:44
Alignment explanation
Indices: 54382781--54382890 Score: 114
Period size: 44 Copynumber: 2.5 Consensus size: 44
54382771 TCTTTAGTCT
* * * *
54382781 GCTCCACTGCAAGTTTAGGGAGATAAGACTTGTAACTTCAACTT
1 GCTCCAATGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTC
* * * **
54382825 GCTCCATTGCAACTTCAAGGAGATAAGGCTTGTGGCTTCAA-TC
1 GCTCCAATGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTC
* *
54382868 GCTCCAATGCCATTTCAGGGAGA
1 GCTCCAATGCAACTTCAGGGAGA
54382891 AGAGATTTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 20 0.37
44 34 0.63
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (44 bp):
GCTCCAATGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTC
Found at i:54382992 original size:88 final size:88
Alignment explanation
Indices: 54382869--54383112 Score: 335
Period size: 88 Copynumber: 2.8 Consensus size: 88
54382859 GCTTCAATCG
* * * * *
54382869 CTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTTGATCTACTCTGCTGAGACTTCAAGGAG
1 CTCCAGTGCCATATCAAGGAGAAGAGATTTGTAGCTTTGATCTACTCCGCTGAAACTTCAAGGAG
54382934 ATACAAAATGTGGCTTCGAGCCT
66 ATACAAAATGTGGCTTCGAGCCT
* * * **
54382957 CTCCAGTGTCATATCAAGGAGAAGATATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGTT
1 CTCCAGTGCCATATCAAGGAGAAGAGATTTGTAGCTTTGATCTACTCCGCTGAAACTTCAAGGAG
* *
54383022 ATACGAATTGTGGCTTCGAGCCT
66 ATACAAAATGTGGCTTCGAGCCT
* * ** *
54383045 CTCCAGTGCCATTTCAGGGAGAAGAGATTTGTAGCTTTGATCTACTCCATTGGAACTTCAAGGAG
1 CTCCAGTGCCATATCAAGGAGAAGAGATTTGTAGCTTTGATCTACTCCGCTGAAACTTCAAGGAG
54383110 ATA
66 ATA
54383113 GGGTTTGTTT
Statistics
Matches: 134, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 134 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (88 bp):
CTCCAGTGCCATATCAAGGAGAAGAGATTTGTAGCTTTGATCTACTCCGCTGAAACTTCAAGGAG
ATACAAAATGTGGCTTCGAGCCT
Found at i:54382994 original size:44 final size:42
Alignment explanation
Indices: 54382946--54383081 Score: 98
Period size: 44 Copynumber: 3.1 Consensus size: 42
54382936 ACAAAATGTG
*
54382946 GCTTCGAGCCTCTCCAGTGTCATATCAAGGAGAAGATATTTGTA
1 GCTTCGAGCCTCTCCAGTGACAT-TCAAGGAGAAGA-ATTTGTA
* * * * *
54382990 GCTTCGA-TCTACTCC-GCTGAAACTTCAAGGTTATACGAA-TTGTG
1 GCTTCGAGCCT-CTCCAG-TGACA-TTCAAGG--AGAAGAATTTGTA
* *
54383034 GCTTCGAGCCTCTCCAGTGCCATTTCAGGGAGAAGAGATTTGTA
1 GCTTCGAGCCTCTCCAGTGACA-TTCAAGGAGAAGA-ATTTGTA
54383078 GCTT
1 GCTT
54383082 TGATCTACTC
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
42 4 0.06
43 4 0.06
44 52 0.75
45 5 0.07
46 4 0.06
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (42 bp):
GCTTCGAGCCTCTCCAGTGACATTCAAGGAGAAGAATTTGTA
Found at i:54383143 original size:41 final size:41
Alignment explanation
Indices: 54383080--54383287 Score: 114
Period size: 41 Copynumber: 4.9 Consensus size: 41
54383070 GATTTGTAGC
* * * *
54383080 TTTGATCTACTCCATTGGAACTTCA-AGGAGATAGGGTTTGT
1 TTTGATCTACTCCACTGCAACTTCAGA-GAGATAAGATTTGT
*
54383121 TTTGATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGTTAT
1 TTTGATCTACTCCACTGCAACTTCAGAGAGATAAGATTTG---T
* * * * * * * *
54383165 TTTTAGTCTGCTTCACTACAAATTCAGGGAGATAAGACTAGTGAC
1 TTTGA-TCTACTCCACTGCAACTTCAGAGAGATAAGA-T-TTG-T
** * ** * *
54383210 TTCAACCTGTTCCACTGCAACTTCAGGGAGGTAA-AGTTTGT
1 TTTGATCTACTCCACTGCAACTTCAGAGAGATAAGA-TTTGT
* * *
54383251 TTTGATATGCTCTACTGCAACTTCAGAGAGATAAGAT
1 TTTGATCTACTCCACTGCAACTTCAGAGAGATAAGAT
54383288 CTGTGATTTA
Statistics
Matches: 126, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 60 0.48
42 4 0.03
43 2 0.02
44 28 0.22
45 29 0.23
46 1 0.01
47 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (41 bp):
TTTGATCTACTCCACTGCAACTTCAGAGAGATAAGATTTGT
Found at i:54383320 original size:92 final size:96
Alignment explanation
Indices: 54383208--54383382 Score: 234
Period size: 92 Copynumber: 1.9 Consensus size: 96
54383198 AAGACTAGTG
** * *
54383208 ACTTCAACCTGTTCCACTGCAACTTCAGGGAGGTAA-AGTTTG-T-T-TTGA-TATGCTCTACTG
1 ACTTCAACCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTTGCTATCTTCAGTATGCTCCACTG
54383268 CAACTTCAGAGAGATAAGATCTGTGATTTATA
65 CAACTTCAGAGAGATAAGATCTGTGATTTATA
** * *
54383300 ACTTCAATTTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
1 ACTTCAACCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTATGCTCCACTGC
54383365 AACTTCAGAGAGATAAGA
66 AACTTCAGAGAGATAAGA
54383383 CTTGTAACTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 35 0.50
93 2 0.03
94 1 0.01
95 3 0.04
96 29 0.41
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (96 bp):
ACTTCAACCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTATGCTCCACTGC
AACTTCAGAGAGATAAGATCTGTGATTTATA
Found at i:54383361 original size:45 final size:44
Alignment explanation
Indices: 54383298--54383415 Score: 119
Period size: 45 Copynumber: 2.7 Consensus size: 44
54383288 CTGTGATTTA
* ** * * *
54383298 TAACTTCAATTTGTTCCACTGCAACTTTAGGGAAATAAGATTTG
1 TAACTTCAATCTACTCCACTGCAACTTCAGAGAAATAAGACTTG
* * * *
54383342 CTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTG
1 -TAACTTCAATCTACTCCACTGCAACTTCAGAGAAATAAGACTTG
* *
54383387 TAACTTCAATCTACTCCGCTGAAACTTCA
1 TAACTTCAATCTACTCCACTGCAACTTCA
54383416 AGGAGATCTA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 24 0.40
45 36 0.60
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (44 bp):
TAACTTCAATCTACTCCACTGCAACTTCAGAGAAATAAGACTTG
Found at i:54383488 original size:47 final size:47
Alignment explanation
Indices: 54383418--54383522 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 47
54383408 AAACTTCAAG
* *
54383418 GAGATCTACTGTGGCTTCGAACCGCTCCAATGCCATTTCAGGGAGAA
1 GAGATCTGCTGTGGCTTCGAACCGCTCCAACGCCATTTCAGGGAGAA
*
54383465 GAGATCTGCTGTGGCTTCTAACCGCTCCAACGCCATTTCAGGGAGAA
1 GAGATCTGCTGTGGCTTCGAACCGCTCCAACGCCATTTCAGGGAGAA
*
54383512 GAGATCCGCTG
1 GAGATCTGCTG
54383523 AAACTTCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (47 bp):
GAGATCTGCTGTGGCTTCGAACCGCTCCAACGCCATTTCAGGGAGAA
Found at i:54383574 original size:68 final size:68
Alignment explanation
Indices: 54383463--54383720 Score: 356
Period size: 68 Copynumber: 3.8 Consensus size: 68
54383453 TTTCAGGGAG
54383463 AAGAGATCTGCTGTGGCTTCTAA-CCGCTCCAACGCCATTTCAGGGAGAAGAGATCCGCTGAAAC
1 AAGAGATCTGCTGTGGCTTC-AAGCCGCTCCAACGCCATTTCAGGGAGAAGAGATCCGCTGAAAC
54383527 TTCA
65 TTCA
* * * *
54383531 AGGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAAAGATCCGCTAAAAAT
1 AAGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAGATCCGCTGAAACT
54383596 TCA
66 TCA
** * * * * *
54383599 AAGAGATCTATTGTGGCTTCTAGCCGTTCCAACGCTATTTCAGAGAGAAGAGATCTGCTGAAACT
1 AAGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAGATCCGCTGAAACT
54383664 TCA
66 TCA
* * * * *
54383667 AAGAGATCTGTTGTGGCTTCTAGCCACTCCAACGCCATTTTATGGAGAAGAGAT
1 AAGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
54383721 TTGTAATTCC
Statistics
Matches: 167, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 2 0.01
68 165 0.99
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (68 bp):
AAGAGATCTGCTGTGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAGAGATCCGCTGAAACT
TCA
Found at i:54383840 original size:86 final size:86
Alignment explanation
Indices: 54383736--54384154 Score: 552
Period size: 86 Copynumber: 4.9 Consensus size: 86
54383726 ATTCCCAGCT
* * * * *
54383736 TGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGTATTTGATCTACTCCACTATTGCTTAGGGA
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGA
54383801 GACAAGATCTGTAATTCGGCC
66 GACAAGATCTGTAATTCGGCC
* * *
54383822 TATTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCTACAACTGCTTAGGGA
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGA
*
54383887 GACAAGATCTGTAATTCGACC
66 GACAAGATCTGTAATTCGGCC
** * * * *
54383908 TGTTACCCTACTGCTTAAAGGGTTAAGGCTCACTGTCTTCGATCTGCTTCACTACTACTTAGGGA
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGA
* *
54383973 GATAAGATCTATAATTCGGCC
66 GACAAGATCTGTAATTCGGCC
* * *
54383994 TGTTACCCTACTGTTTAGGGGGTTAAGGCTCACCATCTTTGATCTGCTCCACTACTGCTTGGGGA
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGA
*
54384059 GACAAGATCTGTAATTCGGCT
66 GACAAGATCTGTAATTCGGCC
* * * * * * * *
54384080 TGTTTCCCTACT-TTTAAAGGGGTTAAAGCTCACCGTATTCGGTCTGCTCCACTATTGCTTAGGG
1 TGTTACCCTACTGCTT-AGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGG
*
54384144 AGTCAAGATCT
65 AGACAAGATCT
54384155 ACGAATTCAC
Statistics
Matches: 289, Mismatches: 43, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
85 3 0.01
86 286 0.99
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (86 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGA
GACAAGATCTGTAATTCGGCC
Found at i:54389133 original size:93 final size:93
Alignment explanation
Indices: 54389025--54389195 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54389015 GCCCCTAAGT
* * *
54389025 GAACTCTGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54389090 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
54389118 GAACTCGGACTCAACTCCACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54389183 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54389196 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54389192 original size:46 final size:46
Alignment explanation
Indices: 54389020--54389192 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
54389010 AACCCGCCCC
* * * *
54389020 TAAGTGAACTCTGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
54389066 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
54389114 TCA-CGAACTCGGACTCAACTCCACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54389159 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54389193 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54391631 original size:30 final size:30
Alignment explanation
Indices: 54391587--54391675 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
54391577 CAAAGATAAC
54391587 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
54391616 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
54391646 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
54391676 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:54391635 original size:15 final size:15
Alignment explanation
Indices: 54391587--54391666 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
54391577 CAAAGATAAC
*
54391587 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54391601 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54391616 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54391631 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54391646 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54391661 AAGAAA
1 AAGAAA
54391667 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54391675 original size:15 final size:15
Alignment explanation
Indices: 54391598--54391675 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
54391588 AGAAAACCGA
54391598 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
54391613 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
54391627 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
54391642 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
54391658 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54391673 ATA
1 ATA
54391676 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:54392699 original size:47 final size:47
Alignment explanation
Indices: 54392637--54392762 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 47
54392627 CTTTACATAA
* * * *
54392637 TGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC
* * *
54392684 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
* * *
54392731 CGATGCCATATCCTAGATATGGTCTTATACAG
1 TGATGCCATATCCCAGATATGGTCTTACACAG
54392763 AAATCACTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 66 0.97
48 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
Found at i:54392778 original size:7 final size:7
Alignment explanation
Indices: 54392766--54392794 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54392756 TATACAGAAA
54392766 TCACTTG
1 TCACTTG
54392773 TCACTTG
1 TCACTTG
54392780 TCACTTG
1 TCACTTG
54392787 TCACTTG
1 TCACTTG
54392794 T
1 T
54392795 AGCTGAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Done.