Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 103 of 438
Found at i:29361710 original size:11 final size:11
Alignment explanation
Indices: 29361696--29361748 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
29361686 AATTAACCAT
29361696 ACCACCACCTC
1 ACCACCACCTC
*
29361707 ACCATCA-CTGC
1 ACCACCACCT-C
29361718 ACCACCACCTC
1 ACCACCACCTC
* *
29361729 ACCACCGCCGC
1 ACCACCACCTC
29361740 ACCACCACC
1 ACCACCACC
29361749 GTGATCATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 2 0.06
11 31 0.89
12 2 0.06
ACGTcount: A:0.26, C:0.60, G:0.06, T:0.08
Consensus pattern (11 bp):
ACCACCACCTC
Found at i:29361721 original size:22 final size:22
Alignment explanation
Indices: 29361696--29361748 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
29361686 AATTAACCAT
* *
29361696 ACCACCACCTCACCATCACTGC
1 ACCACCACCTCACCACCACCGC
*
29361718 ACCACCACCTCACCACCGCCGC
1 ACCACCACCTCACCACCACCGC
29361740 ACCACCACC
1 ACCACCACC
29361749 GTGATCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.60, G:0.06, T:0.08
Consensus pattern (22 bp):
ACCACCACCTCACCACCACCGC
Found at i:29362011 original size:2 final size:2
Alignment explanation
Indices: 29362004--29362051 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
29361994 CTGTAACCGA
*
29362004 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29362046 AT AT AT
1 AT AT AT
29362052 GTTATTGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29363641 original size:31 final size:31
Alignment explanation
Indices: 29363558--29363771 Score: 131
Period size: 30 Copynumber: 7.1 Consensus size: 31
29363548 TCGATCAATG
* * *
29363558 AAAAGGGATAGCTTCGGCTATCGAATCATGA
1 AAAAAGGATAGCTTCGGCTATCAAATTATGA
* * *
29363589 AAAGA-GATAACTTTGGCTATCAAATTATGA
1 AAAAAGGATAGCTTCGGCTATCAAATTATGA
*
29363619 AAAAAGGATAGCTTCAGCTATCAAATTATG-
1 AAAAAGGATAGCTTCGGCTATCAAATTATGA
* * * * *
29363649 AAAAGGGAT-GGTGACGACCATCAACA--ATGA
1 AAAAAGGATAGCT-TCGGCTATCAA-ATTATGA
* * * * * ** *
29363679 AAAAGGGATGGCGAT-GACCATTGAACTATG-
1 AAAAAGGATAGC-TTCGGCTATCAAATTATGA
* *
29363709 AAAAGGGATAGCTTCGGCTATCGAATTATG-
1 AAAAAGGATAGCTTCGGCTATCAAATTATGA
*
29363739 -AAAAGGATAGCTTTGGCTATCAAATTATGA
1 AAAAAGGATAGCTTCGGCTATCAAATTATGA
29363769 AAA
1 AAA
29363772 GGGATGGTGA
Statistics
Matches: 142, Mismatches: 30, Indels: 22
0.73 0.15 0.11
Matches are distributed among these distances:
29 33 0.23
30 78 0.55
31 31 0.22
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (31 bp):
AAAAAGGATAGCTTCGGCTATCAAATTATGA
Found at i:29363775 original size:119 final size:119
Alignment explanation
Indices: 29363585--29363861 Score: 351
Period size: 119 Copynumber: 2.3 Consensus size: 119
29363575 CTATCGAATC
* * * *
29363585 ATGAAAAGAGATAACTTTGGCTATCAAATTATGAAAAAAGGATAGCTTCAGCTATCAAATTATGA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATTATG--AAAAGGATAGCTTCAGCTATCAAATTATGA
* * ***
29363650 AAAGGGATGGTGACGACCATCAACAATGAAAAAGGGATGGCGATGACCA-TTGAACT
64 AAAGGGATGGTGACAACCATCAACAAT-AAAAAGGGATGGCGACGACCACCAAAACT
**
29363706 ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGATAGCTTTGGCTATCAAATTATGAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGATAGCTTCAGCTATCAAATTATGAAA
* * * *
29363771 AGGGATGGTGACAACTATCAACTATAAAAAGGGATGGTGACGACCACCAAAATT
66 AGGGATGGTGACAACCATCAACAATAAAAAGGGATGGCGACGACCACCAAAACT
* *
29363825 ATTAAAAGGGATAGCTTCGGTTATCG-ATATATGAAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT-TATGAAAA
29363862 AGGTTGGTGA
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
118 21 0.15
119 87 0.64
121 29 0.21
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.24
Consensus pattern (119 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGATAGCTTCAGCTATCAAATTATGAAA
AGGGATGGTGACAACCATCAACAATAAAAAGGGATGGCGACGACCACCAAAACT
Found at i:29363835 original size:31 final size:30
Alignment explanation
Indices: 29363759--29363836 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
29363749 CTTTGGCTAT
* * *
29363759 CAAATTATGAAAAGGGATGGTGACAACTAT
1 CAAATTATAAAAAGGGATGGTGACAACCAC
* *
29363789 C-AACTATAAAAAGGGATGGTGACGACCAC
1 CAAATTATAAAAAGGGATGGTGACAACCAC
*
29363818 CAAAATTATTAAAAGGGAT
1 C-AAATTATAAAAAGGGAT
29363837 AGCTTCGGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.62
30 1 0.03
31 14 0.36
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.21
Consensus pattern (30 bp):
CAAATTATAAAAAGGGATGGTGACAACCAC
Found at i:29365344 original size:34 final size:35
Alignment explanation
Indices: 29365300--29365380 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 35
29365290 GAACAGTCTA
* *
29365300 GGCCTAAGCCCATAT-CAGTCGCAATATCAGTGTG
1 GGCCTTAGCCCATATACAGTAGCAATATCAGTGTG
* *
29365334 GGCCTTAGCCCA-ATACAGTAGCAGTATTAGTGTG
1 GGCCTTAGCCCATATACAGTAGCAATATCAGTGTG
*
29365368 GGCCTTGGCCCAT
1 GGCCTTAGCCCAT
29365381 TTCAATTCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
33 2 0.05
34 38 0.95
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (35 bp):
GGCCTTAGCCCATATACAGTAGCAATATCAGTGTG
Found at i:29369742 original size:3 final size:3
Alignment explanation
Indices: 29369734--29369773 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29369724 ATATGTATTG
29369734 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29369774 TTAAGAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:29380341 original size:33 final size:33
Alignment explanation
Indices: 29380299--29380361 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
29380289 AAATAAAAAG
29380299 ATTGATTGTTTTCTTAGTTCTTCACAGGTTTAC
1 ATTGATTGTTTTCTTAGTTCTTCACAGGTTTAC
29380332 ATTGATTGTTTTCTTAGTTCTTCACAGGTT
1 ATTGATTGTTTTCTTAGTTCTTCACAGGTT
29380362 CACCCAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.52
Consensus pattern (33 bp):
ATTGATTGTTTTCTTAGTTCTTCACAGGTTTAC
Found at i:29386420 original size:13 final size:13
Alignment explanation
Indices: 29386402--29386426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29386392 AAGTAATCGC
29386402 ACACGGGCGTGTT
1 ACACGGGCGTGTT
29386415 ACACGGGCGTGT
1 ACACGGGCGTGT
29386427 CCCTGCCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:29390111 original size:34 final size:34
Alignment explanation
Indices: 29390060--29390153 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 34
29390050 CAGAATTGAA
* *
29390060 CAGTCTGGGCCTAAGCCCATATCAGTAGCAATAT
1 CAGTGTGGGCCTTAGCCCATATCAGTAGCAATAT
* *
29390094 CAGTGTGGGCCTTAGCCCA-ATACAGTAGTAGTAT
1 CAGTGTGGGCCTTAGCCCATAT-CAGTAGCAATAT
* * * *
29390128 TAGTGTTGGCCTTGGCCCATTTCAGT
1 CAGTGTGGGCCTTAGCCCATATCAGT
29390154 TCAGTATCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 2 0.04
34 47 0.94
35 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (34 bp):
CAGTGTGGGCCTTAGCCCATATCAGTAGCAATAT
Found at i:29403671 original size:39 final size:39
Alignment explanation
Indices: 29403589--29403778 Score: 145
Period size: 39 Copynumber: 4.8 Consensus size: 39
29403579 TTGAATGATG
* * * * *
29403589 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGC-GAGTTAATAAA
*
29403629 TCCGGACT-AGATCCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCGAAGGCATTCGTGCGAGTTAATAAA
* * * *
29403668 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
* * * *
29403707 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGTTAATA-AA
* * *
29403748 -CCGGGCT-TGTCCCGAAGGCATTTGAGCGAGT
1 TCCGGGCTAAGT-CCGAAGGCATTCGTGCGAGT
29403779 CGTTATATCC
Statistics
Matches: 124, Mismatches: 21, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
39 78 0.63
40 44 0.35
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTCGTGCGAGTTAATAAA
Found at i:29403724 original size:79 final size:81
Alignment explanation
Indices: 29403589--29403771 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
29403579 TTGAATGATG
* *
29403589 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAGATCCGAAGGCATTC
*
29403653 GTGCGAGTTAATA-AA
66 GTGCGAGTCAATATAA
* **
29403668 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTA-AGTCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAGA-T-CCGAAGGCAT
*
29403730 TCGTGCGAGTCACTATAA
64 TCGTGCGAGTCAATATAA
*
29403748 -CCGGGCT-TGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29403772 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
77 1 0.01
78 26 0.29
79 62 0.68
80 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAGATCCGAAGGCATTC
GTGCGAGTCAATATAA
Found at i:29409582 original size:40 final size:40
Alignment explanation
Indices: 29409497--29409647 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
29409487 AATTGAATGA
* * * *
29409497 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
29409537 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
29409578 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
29409617 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
29409648 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 80 0.87
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:29409661 original size:40 final size:40
Alignment explanation
Indices: 29409534--29409663 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
29409524 ATGCTGGAAA
* * *
29409534 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
29409574 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
29409614 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
29409654 TTATATCCGG
1 TTATATCCGG
29409664 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:29409662 original size:80 final size:80
Alignment explanation
Indices: 29409496--29409663 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
29409486 AAATTGAATG
* *
29409496 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
29409561 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * *
29409576 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
29409639 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
29409656 ATATCCGG
1 ATATCCGG
29409664 TTATATTCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.07
80 70 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:29417527 original size:40 final size:40
Alignment explanation
Indices: 29417461--29417611 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
29417451 AAATTGAATG
* *
29417461 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
29417500 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
29417540 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
29417580 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
29417612 ACGTGGTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 16 0.18
40 72 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:29417625 original size:40 final size:40
Alignment explanation
Indices: 29417498--29417627 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
29417488 ATGCTGGAAA
* * *
29417498 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
29417538 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
29417578 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
29417618 TTATATCCGG
1 TTATATCCGG
29417628 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:29417626 original size:80 final size:79
Alignment explanation
Indices: 29417461--29417627 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
29417451 AAATTGAATG
*
29417461 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
29417526 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * * *
29417540 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
29417603 CATTTGTGC-ACGTGGTT
63 CAATTGTGCTA-GTGGCT
29417620 ATATCCGG
1 ATATCCGG
29417628 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.24
80 57 0.76
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:29425122 original size:21 final size:21
Alignment explanation
Indices: 29425054--29425122 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
29425044 GAAAAAGTGA
29425054 TCGAATAGCCGTAAAAGCCGT
1 TCGAATAGCCGTAAAAGCCGT
* ** * * *
29425075 TCGACAACAGGGGAAAAAAG-TGA
1 TCG--AATAGCCG-TAAAAGCCGT
29425098 TCGAATAGCCGTAAAAGCCGT
1 TCGAATAGCCGTAAAAGCCGT
29425119 TCGA
1 TCGA
29425123 CAACATCCGG
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 5 0.16
21 13 0.41
23 9 0.28
24 5 0.16
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (21 bp):
TCGAATAGCCGTAAAAGCCGT
Found at i:29425431 original size:40 final size:40
Alignment explanation
Indices: 29425346--29425496 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
29425336 AATTGAATGA
* * * *
29425346 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
29425386 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
29425427 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
29425466 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
29425497 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 80 0.87
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:29425510 original size:40 final size:40
Alignment explanation
Indices: 29425383--29425512 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
29425373 ATGCTGGAAA
* * *
29425383 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
29425423 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
29425463 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
29425503 TTATATCCGG
1 TTATATCCGG
29425513 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:29425511 original size:80 final size:80
Alignment explanation
Indices: 29425345--29425512 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
29425335 AAATTGAATG
* *
29425345 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
29425410 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * *
29425425 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
29425488 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
29425505 ATATCCGG
1 ATATCCGG
29425513 TTATATTCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.07
80 70 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:29430780 original size:79 final size:82
Alignment explanation
Indices: 29430640--29430824 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
29430630 TTGAATGATG
* * *
29430640 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
29430704 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
29430720 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
29430782 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
29430800 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29430825 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:29430832 original size:40 final size:40
Alignment explanation
Indices: 29430641--29430832 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
29430631 TGAATGATGT
* * * * *
29430641 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * *
29430681 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
29430721 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
29430760 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
29430800 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
29430833 GTTATATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
39 33 0.26
40 82 0.65
41 11 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:29437754 original size:40 final size:39
Alignment explanation
Indices: 29437689--29437892 Score: 221
Period size: 40 Copynumber: 5.1 Consensus size: 39
29437679 CGGAATACAA
* *
29437689 CCGGATATAACCAC-ACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAA-CACTA-GCACAAATGCCTTCGGGTCTTAGC
* *
29437729 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
29437769 CCGGATATAACAACTTGCACAAATGCCTTCAGGTATTAGC
1 CCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
29437809 CCGGATATAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
29437849 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGC
29437889 CCGG
1 CCGG
29437893 GTATCATTCA
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 139 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29440847 original size:29 final size:29
Alignment explanation
Indices: 29440815--29440872 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
29440805 GCAAGATATA
* *
29440815 CTGA-TTTAGCTTCGGGCCATGCATATCAG
1 CTGATTTTAGCTTCAGACCATG-ATATCAG
*
29440844 CTGATTTTGGCTTCAGACCATGATATCAG
1 CTGATTTTAGCTTCAGACCATGATATCAG
29440873 AACTTCAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (29 bp):
CTGATTTTAGCTTCAGACCATGATATCAG
Found at i:29443670 original size:29 final size:29
Alignment explanation
Indices: 29443631--29443710 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
29443621 CTTAATAATC
*
29443631 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
29443661 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
29443690 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
29443711 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:29462863 original size:40 final size:40
Alignment explanation
Indices: 29462819--29462963 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
29462809 CTCACACAAG
* * *
29462819 GCCTTCGGGTCTTAGCCCGAATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
29462859 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
* * * * *
29462899 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATGGTCAC-TAGCACAAAT
*
29462940 GCCTTTGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
29462964 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.65
41 26 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
Found at i:29464918 original size:37 final size:37
Alignment explanation
Indices: 29464865--29464986 Score: 217
Period size: 37 Copynumber: 3.3 Consensus size: 37
29464855 TATAAAAGAA
*
29464865 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
29464902 GTCTTACCCAGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
29464939 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
*
29464976 GTCTCACCCGG
1 GTCTTACCCGG
29464987 AACATATTCC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 81 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:29465143 original size:49 final size:49
Alignment explanation
Indices: 29465088--29465351 Score: 447
Period size: 49 Copynumber: 5.4 Consensus size: 49
29465078 TTTTACATTA
*
29465088 GCCATTAGGCCTTATCACATATACTTACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
29465137 GCCATTAGGCCTTATCACATATGCATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
29465186 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* *
29465235 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
* * *
29465284 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCGCATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
29465333 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
29465352 CATATATGTA
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 206 1.00
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:29466962 original size:13 final size:13
Alignment explanation
Indices: 29466944--29466970 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29466934 GAGATATTGT
29466944 ATATGTCATACCA
1 ATATGTCATACCA
29466957 ATATGTCATACCA
1 ATATGTCATACCA
29466970 A
1 A
29466971 GTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ATATGTCATACCA
Found at i:29474122 original size:40 final size:40
Alignment explanation
Indices: 29474067--29474211 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
29474057 CTCGCACAAG
* * *
29474067 GCCTTCGGGTCTTAGCCCGAATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
29474107 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
* * * * *
29474147 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATGGTCAC-TAGCACAAAT
29474188 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
29474212 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAAT
Found at i:29474194 original size:41 final size:40
Alignment explanation
Indices: 29474044--29474211 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
29474034 CGGAGTTTAA
** * * *
29474044 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
* * *
29474083 CCGAATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
* *
29474123 CCGGATATGGTCACTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGA-CTTAGC
* * *
29474163 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGACTTAGC
29474204 CCGGATAT
1 CCGGATAT
29474212 CATTCGAGTA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 17 0.16
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGC
Found at i:29475975 original size:29 final size:29
Alignment explanation
Indices: 29475942--29476043 Score: 118
Period size: 29 Copynumber: 3.5 Consensus size: 29
29475932 ATATAGTGAA
*
29475942 TCGCACACTTAGTGCTATATATTTTCAGC
1 TCGCACACTTAGTGCTATATATTTTCAAC
*
29475971 TCGCACACTTAGTGCTATATA--ATCAAAC
1 TCGCACACTTAGTGCTATATATTTTC-AAC
* * *
29475999 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 TCGCACACTTAGTGCTATA-TATTTTCAAC
*
29476029 CCGCACACTTAGTGC
1 TCGCACACTTAGTGC
29476044 CAATCTTGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.32
29 22 0.35
30 17 0.27
31 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (29 bp):
TCGCACACTTAGTGCTATATATTTTCAAC
Found at i:29476036 original size:30 final size:29
Alignment explanation
Indices: 29475942--29476043 Score: 118
Period size: 28 Copynumber: 3.5 Consensus size: 29
29475932 ATATAGTGAA
* * *
29475942 TCGCACACTTAGTGCTATATATTTTCAGC
1 TCGCACACTTAGTGCTATAAATTTTAAAC
*
29475971 TCGCACACTTAGTGCTATATAA--TCAAAC
1 TCGCACACTTAGTGCTATA-AATTTTAAAC
*
29475999 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 TCGCACACTTAGTGCTATA-AATTTTAAAC
*
29476029 CCGCACACTTAGTGC
1 TCGCACACTTAGTGC
29476044 CAATCTTGTC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 23 0.37
29 19 0.31
30 20 0.32
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (29 bp):
TCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:29478029 original size:2 final size:2
Alignment explanation
Indices: 29478022--29478049 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29478012 ATGTGCAAAC
29478022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29478050 GTGCAAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29481438 original size:23 final size:23
Alignment explanation
Indices: 29481412--29481467 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
29481402 CAAGAAAACT
29481412 AAACAAAACAAAAAC-AAAGAT-AA
1 AAACAAAA-AAAAACTAAA-ATGAA
*
29481435 AAACAGAAAATAAACTAAAATGAA
1 AAACA-AAAAAAAACTAAAATGAA
29481459 AAACAAAAA
1 AAACAAAAA
29481468 CTAAAGTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (23 bp):
AAACAAAAAAAAACTAAAATGAA
Found at i:29484458 original size:18 final size:18
Alignment explanation
Indices: 29484432--29484466 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29484422 GTAGGGGTCT
29484432 CCTCCTCATCATCATCAA
1 CCTCCTCATCATCATCAA
*
29484450 CCTCGTCATCATCATCA
1 CCTCCTCATCATCATCA
29484467 TCGGCACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.43, G:0.03, T:0.29
Consensus pattern (18 bp):
CCTCCTCATCATCATCAA
Found at i:29494245 original size:2 final size:2
Alignment explanation
Indices: 29494238--29494288 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
29494228 AGCTTATGTT
29494238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29494280 TA TA TA TA T
1 TA TA TA TA T
29494289 TTGATTTGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29497146 original size:30 final size:30
Alignment explanation
Indices: 29497111--29497168 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29497101 CTTTAATACG
*
29497111 AACTTTGGCAAAACTACATTTTTGCCCCTA
1 AACTTTGGCAAAACTACACTTTTGCCCCTA
* * *
29497141 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGCAAAACTACACTTTTGCCCC
29497169 AGGCTCGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (30 bp):
AACTTTGGCAAAACTACACTTTTGCCCCTA
Found at i:29505273 original size:29 final size:29
Alignment explanation
Indices: 29505231--29505350 Score: 170
Period size: 29 Copynumber: 4.2 Consensus size: 29
29505221 GAAAACATGT
*
29505231 ATATGAATGTGATTTGGGCCTAATGGGAC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
29505260 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
29505289 ATACGAATGTTATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
29505318 ATATGAATGAGA-TTGGGCTTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
29505346 ATATG
1 ATATG
29505351 CTTTTATGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 18 0.22
29 63 0.78
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:29508654 original size:42 final size:41
Alignment explanation
Indices: 29508608--29508749 Score: 135
Period size: 42 Copynumber: 3.3 Consensus size: 41
29508598 CCCTGATAGG
29508608 GTCTTACACGATATCAGATACGATGCCAATGTCCCAGACAT
1 GTCTTACACGATATCAGATACGATGCCAATGTCCCAGACAT
* * *
29508649 AGTCTTACATG-TAATCAGATACGATACCAATGCCCCAGACAT
1 -GTCTTACACGAT-ATCAGATACGATGCCAATGTCCCAGACAT
* * * * *
29508691 GGTCTTACACGTAAATCTCAAAT-CGAGGCCTATGTCCTAGACACT
1 -GTCTTACACG---ATATCAGATACGATGCCAATGTCCCAGACA-T
29508736 GTCTTACACGATAT
1 GTCTTACACGATAT
29508750 ATCTGATCAA
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
41 4 0.05
42 45 0.56
44 25 0.31
45 6 0.07
46 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (41 bp):
GTCTTACACGATATCAGATACGATGCCAATGTCCCAGACAT
Found at i:29512352 original size:28 final size:29
Alignment explanation
Indices: 29512269--29512364 Score: 131
Period size: 29 Copynumber: 3.3 Consensus size: 29
29512259 GAAAGCATGT
29512269 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
29512298 ATACGAATGTTATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
29512327 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
29512355 AAATGCATGT
1 ATATGAATGT
29512365 ATGTAGACTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 22 0.38
29 36 0.62
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:29516404 original size:12 final size:12
Alignment explanation
Indices: 29516386--29516419 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29516376 AGCGAATGAG
29516386 TGAATGAATGGA
1 TGAATGAATGGA
29516398 TTG-ATGAATGGA
1 -TGAATGAATGGA
29516410 TGAATGAATG
1 TGAATGAATG
29516420 AATAATTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (12 bp):
TGAATGAATGGA
Found at i:29517340 original size:33 final size:33
Alignment explanation
Indices: 29517303--29517370 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
29517293 TTAATTGCAA
29517303 TGACATAGAGATTTTGCTTCTTTTAGGTGCCAC
1 TGACATAGAGATTTTGCTTCTTTTAGGTGCCAC
29517336 TGACATAGAGATTTTGCTTCTTTTAGGTGCCAC
1 TGACATAGAGATTTTGCTTCTTTTAGGTGCCAC
29517369 TG
1 TG
29517371 GATATACGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (33 bp):
TGACATAGAGATTTTGCTTCTTTTAGGTGCCAC
Found at i:29523926 original size:100 final size:100
Alignment explanation
Indices: 29523812--29523999 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
29523802 GAAGCTATCT
**
29523812 GGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAATAATTTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAATAATCCGGTACACGTAGTAGCC
*
29523877 TGCACTTAGTACTACACGCGTGATCACAGTTTTCA
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCA
* *
29523912 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAATAATCCGGTACACGTAGTAGCC
29523977 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
29524000 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAATAATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCA
Found at i:29523936 original size:51 final size:48
Alignment explanation
Indices: 29523812--29524001 Score: 211
Period size: 49 Copynumber: 3.9 Consensus size: 48
29523802 GAAGCTATCT
* * *
29523812 GGTACGCATAGTAGCCTGCACTTAGTAATACACATGCGACCAATAATTT-
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT--TTTC
* * * *
29523861 GGTACACGTAGTAGCCTGCACTTAGTACTACACGCGTGATCACAGTTTTC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAATTTTC
* * *
29523911 AGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCC
1 -GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATT-TTC
* *
29523961 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
29524002 TCACAATAGT
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 77 0.65
50 4 0.03
51 37 0.31
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (48 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTTTC
Found at i:29526879 original size:45 final size:45
Alignment explanation
Indices: 29526829--29526914 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
29526819 CCAAAACATG
*
29526829 TGTCACATACATCATGAACTCAGACCACGACTCAATGAGTTTGGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTGGA
*
29526874 TGTCACATATATCATGAACTCAGACCACAACTCAATGAGTT
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTT
29526915 CAGATCACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTTGGA
Found at i:29527421 original size:3 final size:3
Alignment explanation
Indices: 29527413--29527452 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29527403 ACAAAAATAT
29527413 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29527453 ATATGTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29532851 original size:146 final size:147
Alignment explanation
Indices: 29532549--29532855 Score: 469
Period size: 146 Copynumber: 2.1 Consensus size: 147
29532539 TCAAAGTTTC
*
29532549 TTTAAAAAGAATCACTACTTTTCTTAAAAATCAAAACTTTATTTAGAAATAGTTGAAAAAGATCA
1 TTTAAAAA-AATCACTACTTTTCTTAAAAATCAAAACTTTATTTAGAAATAATTGAAAAAGATCA
* * *
29532614 AAATTTTATTTTAAAAAATTTAAACTTTTCCTTTAAAATGACGAAAAATCATATTTTTATTTTAA
65 AAACTTTATTTTAAAAAATTTAAACATTTCCTTTAAAATGACGAAAAAACATATTTTTATTTTAA
29532679 AAATCTAAACCTTTTCTT
130 AAATCTAAACCTTTTCTT
* *
29532697 TTTAAAAAAATCACTATTTTTCTTAAAAATC-AAACTTTATTTCGAAATAATTGAAAAAGATCAA
1 TTTAAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTAGAAATAATTGAAAAAGATCAA
* * *
29532761 AACTTTGTTTT-AAAAATTTAAACATTTCCTTTAATATGACTAAAAAAC-TATTTTTATTTTAAA
66 AACTTTATTTTAAAAAATTTAAACATTTCCTTTAAAATGACGAAAAAACATATTTTTATTTTAAA
29532824 AATCTAAA-CTTTATCTTT
131 AATCTAAACCTTT-TC-TT
29532842 TTTAGAAAAAATCA
1 TTTA-AAAAAATCA
29532856 ACATGTTTCC
Statistics
Matches: 147, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
143 4 0.03
144 25 0.17
145 39 0.27
146 49 0.33
147 22 0.15
148 8 0.05
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (147 bp):
TTTAAAAAAATCACTACTTTTCTTAAAAATCAAAACTTTATTTAGAAATAATTGAAAAAGATCAA
AACTTTATTTTAAAAAATTTAAACATTTCCTTTAAAATGACGAAAAAACATATTTTTATTTTAAA
AATCTAAACCTTTTCTT
Found at i:29534446 original size:18 final size:17
Alignment explanation
Indices: 29534419--29534452 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29534409 TGCCAATACA
29534419 ATATCAACATCTATCAT
1 ATATCAACATCTATCAT
*
29534436 ATATGCAACATTTATCA
1 ATAT-CAACATCTATCA
29534453 AACCACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (17 bp):
ATATCAACATCTATCAT
Found at i:29536292 original size:46 final size:45
Alignment explanation
Indices: 29536206--29536422 Score: 201
Period size: 46 Copynumber: 4.7 Consensus size: 45
29536196 GGGGTAAGGT
* *
29536206 GCCGATGCCATGTCCCAGACATGGTCTTACACAGACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACTCATCTCGTAG
*
29536252 GCCGATGCATGTCCCAGACATGTCTTACACTGACTTACATCTTG-AG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGAC-T-CATCTCGTAG
* * * *
29536298 GCCGATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTC-AAT
1 GCCGATGCATGTCCCAGACATGTCTTACACT-G-ACTCATCTCGTAG
* *
29536344 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGT-G
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGACTCATC-T--CGTAG
* *
29536392 ACCGATGCATGTCCCAAACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
29536423 AGCTCACAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
44 12 0.08
45 17 0.12
46 69 0.48
47 29 0.20
48 18 0.12
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGACTCATCTCGTAG
Found at i:29536397 original size:94 final size:92
Alignment explanation
Indices: 29536207--29536430 Score: 276
Period size: 94 Copynumber: 2.4 Consensus size: 92
29536197 GGGTAAGGTG
* *
29536207 CCGATGCCATGTCCCAGACATGGTCTTACAC-AG-ACACATCTCGTAGCCGATGCATGTCCCAGA
1 CCGATG-CATGTCCCAAACAT-GTCTTACACTAGCACACATCTCATAGCCGATGCATGTCCCAGA
** *
29536270 CATGTCTTACACTGACTTACATCTTGAGG
64 CATGTCTTACACTGACTTACATAATGAGA
* *
29536299 CCGATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCA-ATGCCGATGCCATGTCCCAGA
1 CCGATGCATGTCCCAAACATGTCTTACACTAGCACACATCTCATA-GCCGATG-CATGTCCCAGA
* *
29536363 CATGGTCTTACACTGGCTCT-CATAATGTGA
64 CAT-GTCTTACACTGACT-TACATAATGAGA
*
29536393 CCGATGCATGTCCCAAACATGTCTTACACTAGCTCACA
1 CCGATGCATGTCCCAAACATGTCTTACACTAGCACACA
29536431 ATAGCCCATA
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
90 9 0.08
91 16 0.14
92 20 0.18
93 14 0.12
94 54 0.47
95 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (92 bp):
CCGATGCATGTCCCAAACATGTCTTACACTAGCACACATCTCATAGCCGATGCATGTCCCAGACA
TGTCTTACACTGACTTACATAATGAGA
Found at i:29540052 original size:49 final size:49
Alignment explanation
Indices: 29539995--29540092 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
29539985 TCAACTGGGA
*
29539995 CTCAATATCCGTCTATTCATCATAGCTTTGATACTTTTATATTTTTGAT
1 CTCAATATCCGTCAATTCATCATAGCTTTGATACTTTTATATTTTTGAT
29540044 CTCAATATCCGTCAATTCATCATAGCTTTGATACTTTTATATTTTTGAT
1 CTCAATATCCGTCAATTCATCATAGCTTTGATACTTTTATATTTTTGAT
29540093 TCATTTACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (49 bp):
CTCAATATCCGTCAATTCATCATAGCTTTGATACTTTTATATTTTTGAT
Found at i:29540316 original size:23 final size:23
Alignment explanation
Indices: 29540290--29540337 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29540280 TCTAACAGAA
29540290 AAATCAATTCATTTTATGCAATT
1 AAATCAATTCATTTTATGCAATT
29540313 AAATCAATTCATTTTATGCAATT
1 AAATCAATTCATTTTATGCAATT
29540336 AA
1 AA
29540338 GTCATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (23 bp):
AAATCAATTCATTTTATGCAATT
Found at i:29547049 original size:27 final size:25
Alignment explanation
Indices: 29547019--29547071 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
29547009 CTCTTTTGCG
*
29547019 TTAATAAATTCTCTTTGAGTTTTCTTT
1 TTAAGAAATTCTC-TTGAG-TTTCTTT
*
29547046 TTAAGAATTTCTCTTGAGTTTCTTT
1 TTAAGAAATTCTCTTGAGTTTCTTT
29547071 T
1 T
29547072 AGAAGAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.58
Consensus pattern (25 bp):
TTAAGAAATTCTCTTGAGTTTCTTT
Found at i:29547077 original size:26 final size:27
Alignment explanation
Indices: 29547027--29547077 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
29547017 CGTTAATAAA
*
29547027 TTCTCTTTGAGTTTTCTTTTTAAGAAT
1 TTCTCTTTGAGTTTTCTTTTGAAGAAT
29547054 TTCTC-TTGAG-TTTCTTTTAGAAGA
1 TTCTCTTTGAGTTTTCTTTT-GAAGA
29547078 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 9 0.41
27 5 0.23
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.55
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTCTTTTGAAGAAT
Found at i:29550079 original size:82 final size:83
Alignment explanation
Indices: 29549941--29550131 Score: 258
Period size: 82 Copynumber: 2.3 Consensus size: 83
29549931 TAGCCAAGCC
* * *
29549941 ACATGCCCATGTGCCAAGCCGTGTGATCAATTTTGAGCATTCTATTTTGACATTTTAAAGATAAA
1 ACATGCCCATGTGCTAGGCCGTGTGATCAATTCTGAGCATTCTATTTTGACATTTTAAAGATAAA
*
29550006 GGAGACACACGGCCAGAT
66 GGAGACACACGGCCAAAT
* * * **
29550024 -CATGCCCATGTGCTAGGCCGTGTGATCAATTCTGAGCATTCTGTTTTGACGTTTTAGAGATGTA
1 ACATGCCCATGTGCTAGGCCGTGTGATCAATTCTGAGCATTCTATTTTGACATTTTAAAGATAAA
*
29550088 GGGGACACACGGCCAAAT
66 GGAGACACACGGCCAAAT
* *
29550106 CACACGCCTATGTGCTAGGCCGTGTG
1 -ACATGCCCATGTGCTAGGCCGTGTG
29550132 TCACACACGG
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
82 72 0.77
84 22 0.23
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (83 bp):
ACATGCCCATGTGCTAGGCCGTGTGATCAATTCTGAGCATTCTATTTTGACATTTTAAAGATAAA
GGAGACACACGGCCAAAT
Found at i:29557433 original size:40 final size:40
Alignment explanation
Indices: 29557306--29557456 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
29557296 ATAACCACGT
* * *
29557306 GCACAAATGCCTTCGGGTCTTAGCCC-GATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
29557345 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
29557385 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* * *
29557425 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
29557457 CATTCAATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 25 0.28
40 65 0.72
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:29560374 original size:40 final size:40
Alignment explanation
Indices: 29560329--29560496 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
29560319 CGGAATATAA
29560329 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* *** * *
29560369 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
29560409 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
29560449 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
29560489 CCGGATAT
1 CCGGATAT
29560497 CATTCAATTT
Statistics
Matches: 102, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 101 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29560479 original size:80 final size:80
Alignment explanation
Indices: 29560345--29560494 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
29560335 ATAACCACGT
* *
29560345 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
29560410 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * * * *
29560425 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG
29560488 CCCGGAT
64 CCCGGAT
29560495 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 3 0.05
80 58 0.95
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:29562417 original size:43 final size:43
Alignment explanation
Indices: 29562281--29562450 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 43
29562271 CATAAGCTCG
* * * * *
29562281 TACAATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-A
1 TACAATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAA
* ** * * * * *
29562322 TATCGATGCCTCTGTCCCAAATAGGGTCTTACACGAAATC-GAT
1 TA-CAATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAA
* *
29562365 TAACGATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAA
1 T-ACAATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAA
* *
29562409 TACAATGCCAATGTCCCAAACATTGTCTTACATGTAATCACA
1 TACAATGCCAATGTCCCAAACATGGTCTTACACGTAATCACA
29562451 TCTCGGTAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.02
42 6 0.06
43 91 0.89
44 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
TACAATGCCAATGTCCCAAACATGGTCTTACACGTAATCACAA
Found at i:29565463 original size:40 final size:40
Alignment explanation
Indices: 29565404--29565588 Score: 318
Period size: 40 Copynumber: 4.6 Consensus size: 40
29565394 CGGATGATAA
* *
29565404 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
29565444 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
29565484 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29565524 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
29565564 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29565589 AGCAAGTAGT
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
40 138 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29565603 original size:80 final size:79
Alignment explanation
Indices: 29565400--29565620 Score: 311
Period size: 80 Copynumber: 2.8 Consensus size: 79
29565390 TATTCGGATG
* * *
29565400 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCAAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCCGGGCTAAGTCCCGAAGGC
29565464 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* * *
29565480 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGGCTAAGTCCCGAAGGCA
29565545 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
* * *
29565560 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-GGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGGCTAAGTCCCGAAG
29565621 ATGCTTGGGT
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
79 16 0.12
80 111 0.86
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:29569201 original size:47 final size:47
Alignment explanation
Indices: 29569126--29569344 Score: 195
Period size: 46 Copynumber: 4.7 Consensus size: 47
29569116 GCCCATAAGC
*
29569126 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAT
* * * * * *
29569173 GCACTCGGACTCAACTTAATGAGTTCGGA---C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-TCA-T
29569219 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAT
* * * * *
29569266 GAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT-C-TCA-T
*
29569312 GAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCC
29569345 CAAATATCCG
Statistics
Matches: 138, Mismatches: 19, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.01
43 10 0.07
44 5 0.04
45 5 0.04
46 52 0.38
47 51 0.37
48 3 0.02
49 4 0.03
50 4 0.03
51 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAT
Found at i:29569233 original size:93 final size:93
Alignment explanation
Indices: 29569118--29569344 Score: 382
Period size: 93 Copynumber: 2.4 Consensus size: 93
29569108 TGTAACCCGC
* *
29569118 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGCACTCGGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
* * *
29569183 TCAACTTAATGAGTTCGGACATTCGCAT
66 TCAACTCAACGAGTTCAGACATTCGCAT
*
29569211 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCATGAACTCGGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
*
29569276 TCAACTCAACGAGTTCAGACATTTGCAT
66 TCAACTCAACGAGTTCAGACATTCGCAT
*
29569304 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCC
29569345 CAAATATCCG
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 126 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
TCAACTCAACGAGTTCAGACATTCGCAT
Found at i:29574339 original size:28 final size:29
Alignment explanation
Indices: 29574308--29574379 Score: 112
Period size: 28 Copynumber: 2.5 Consensus size: 29
29574298 AAAATTGTAC
*
29574308 AGCACTAAGTGTGCGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGCGAG-TTGAATACATAT
29574336 AGCACTAAGTGTGCGAGTTGAATACATAT
1 AGCACTAAGTGTGCGAGTTGAATACATAT
29574365 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
29574380 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 3 0.07
28 19 0.46
29 19 0.46
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGTTGAATACATAT
Found at i:29578152 original size:17 final size:19
Alignment explanation
Indices: 29578110--29578153 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29578100 ATGAAATTTT
*
29578110 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
29578129 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
29578147 AA-TATTA
1 AATTATTA
29578154 CTGTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:29579980 original size:28 final size:28
Alignment explanation
Indices: 29579947--29580015 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
29579937 GCGTAGATCA
29579947 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29579975 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29580003 CGATA-TACCCCTA
1 CGAAATTACCCCTA
29580016 GAGTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:29582029 original size:40 final size:40
Alignment explanation
Indices: 29581969--29582108 Score: 212
Period size: 40 Copynumber: 3.5 Consensus size: 40
29581959 TTCGGATGAC
*
29581969 ATCCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
* *
29582009 ATCCAGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29582049 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
*
29582089 ATCC-GGCTAAATCCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
29582109 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 15 0.16
40 75 0.82
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:29590455 original size:39 final size:40
Alignment explanation
Indices: 29590377--29590594 Score: 354
Period size: 40 Copynumber: 5.5 Consensus size: 40
29590367 ATTCGGTGAC
29590377 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
29590417 ATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29590456 ATCCGGGCTAAG-CCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29590495 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
*
29590535 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTAT
* *
29590575 ATCC-GGCTAAATCTCGAAGG
1 ATCCGGGCTAAGTCCCGAAGG
29590595 TACTTGGGTT
Statistics
Matches: 170, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
38 10 0.06
39 69 0.41
40 89 0.52
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
Found at i:29593376 original size:93 final size:93
Alignment explanation
Indices: 29593260--29593525 Score: 399
Period size: 93 Copynumber: 2.9 Consensus size: 93
29593250 CGCCCATAAG
* * * *
29593260 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTAGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
29593325 ACGAGCTCGGATGCCTAGTTACATCTC-
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
29593352 CTGCACTAGGACTCAACTCAACGAGTTTGGATGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 C-GAACTAGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
29593417 AACGAGCTCGGATGCCTAGTTACATCTCA
65 AACGAGCTCGGATGCCTAGTTACATCTCA
* * * * *
29593446 CGAACTCGGAGTCAACTCAATGAGTTCGGACGTTTGTATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTAGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
29593511 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
29593526 CAAATATTCG
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
92 1 0.01
93 154 0.99
94 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTAGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:29593521 original size:46 final size:46
Alignment explanation
Indices: 29593253--29593523 Score: 233
Period size: 46 Copynumber: 5.8 Consensus size: 46
29593243 TGTAACCCGC
* ** * *
29593253 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTAGTAT
* *
29593299 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTAGTAT
* *** * * * * * *
29593345 ACATCTCCTGCACTAGGACTCAACTCAACGAGTTTGGATGTTCGCAT
1 CCAT-AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTAGTAT
*
29593392 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-TTAGTAT
* * * * * * * *
29593438 ACATCTCA-CGAACTCGGAGTCAACTCAATGAGTTCGGACGTTTGTAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTAGTAT
*
29593485 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG
29593524 CCCAAATATT
Statistics
Matches: 172, Mismatches: 45, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
45 2 0.01
46 103 0.60
47 65 0.38
48 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGTTAGTAT
Found at i:29595555 original size:43 final size:42
Alignment explanation
Indices: 29595489--29595617 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 42
29595479 ATATCGTACA
* * *
29595489 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCATATATCG
1 ATGCCAATGTCCCAAACAG-GGTCTTACATG-AATCACATATCG
* * *
29595532 ATGCCACTGTCCTAAACAGGGTCTTACACGAATCACATATACG
1 ATGCCAATGTCCCAAACAGGGTCTTACATGAATCACATAT-CG
* *
29595575 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCG
1 ATGCCAATGTCCCAAACAGGGTCTTACATG-AATCACATATCG
29595618 TAAATCCTAT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 9 0.12
43 52 0.72
44 11 0.15
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAAACAGGGTCTTACATGAATCACATATCG
Found at i:29596154 original size:29 final size:28
Alignment explanation
Indices: 29596117--29596176 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
29596107 AAGTCCATAC
*
29596117 ATTTCATTTATTTCACATTTTAGTCCCTCA
1 ATTTCATTTATTTCACAATTTAG-CCCT-A
* *
29596147 ATTT-ATTTTTTTTACAATTTAGCCCTA
1 ATTTCATTTATTTCACAATTTAGCCCTA
29596174 ATT
1 ATT
29596177 ACTCGAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 15 0.56
30 4 0.15
ACGTcount: A:0.25, C:0.18, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTTCATTTATTTCACAATTTAGCCCTA
Found at i:29599585 original size:30 final size:30
Alignment explanation
Indices: 29599549--29599608 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
29599539 ATTTGTACAC
29599549 TCAAGGTGTACAAATATACAATCATAGATG
1 TCAAGGTGTACAAATATACAATCATAGATG
29599579 TCAAGGTGTACAAATATACAATCATAGATG
1 TCAAGGTGTACAAATATACAATCATAGATG
29599609 AACATATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (30 bp):
TCAAGGTGTACAAATATACAATCATAGATG
Found at i:29600032 original size:26 final size:26
Alignment explanation
Indices: 29599963--29600046 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 26
29599953 ATATAGAAGA
* * *
29599963 AAGCTCA-TAAGAGCC-ATAATTAGG
1 AAGCTCACAAAGAGCCTTTAATCAGG
* *
29599987 AAGTTCACAAA-AACCTTTTAATCAGG
1 AAGCTCACAAAGAGCC-TTTAATCAGG
* *
29600013 AAGCTCACAAAGAGCCTTTAAACGGG
1 AAGCTCACAAAGAGCCTTTAATCAGG
29600039 AAGCTCAC
1 AAGCTCAC
29600047 GAAGCCATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
24 9 0.19
25 2 0.04
26 33 0.70
27 3 0.06
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (26 bp):
AAGCTCACAAAGAGCCTTTAATCAGG
Found at i:29603974 original size:40 final size:40
Alignment explanation
Indices: 29603919--29604128 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
29603909 AACATTGGAA
29603919 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29603959 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29603999 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29604039 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29604078 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29604119 CTATATCCGG
1 ATATATCCGG
29604129 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29612110 original size:40 final size:40
Alignment explanation
Indices: 29612055--29612264 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
29612045 AACATTGGAA
29612055 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29612095 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29612135 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29612175 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29612214 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29612255 CTATATCCGG
1 ATATATCCGG
29612265 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29614572 original size:29 final size:29
Alignment explanation
Indices: 29614536--29614595 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
29614526 ATTAATTAAA
29614536 TTAATTAACCTAA-ATTAACCTAATGGAAT
1 TTAATTAACCTAATA-TAACCTAATGGAAT
**
29614565 TTAATTAACCTAATATATTCTAATGGAAT
1 TTAATTAACCTAATATAACCTAATGGAAT
29614594 TT
1 TT
29614596 CATATTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (29 bp):
TTAATTAACCTAATATAACCTAATGGAAT
Found at i:29616300 original size:27 final size:27
Alignment explanation
Indices: 29616243--29616307 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
29616233 ACCTCATTAT
*
29616243 CCCCGTGTTTACTATCCTGGCGATCTG
1 CCCCGTGTTTACTATCCTGGCGATCTA
*
29616270 CCCCGTGTTTATTATCTCTGTG-GA-CTA
1 CCCCGTGTTTACTATC-CTG-GCGATCTA
*
29616297 CCCCATGTTTA
1 CCCCGTGTTTA
29616308 GTGTCTAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 27 0.82
28 5 0.15
29 1 0.03
ACGTcount: A:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (27 bp):
CCCCGTGTTTACTATCCTGGCGATCTA
Found at i:29617873 original size:25 final size:24
Alignment explanation
Indices: 29617826--29617878 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
29617816 ACATACCACA
* *
29617826 GCTCTTTATGAGCGTCTTGATATAG
1 GCTCTTTATGAGCGTCCTAATAT-G
* *
29617851 GCTCTTTGTGAGCTTCCTAATATG
1 GCTCTTTATGAGCGTCCTAATATG
29617875 GCTC
1 GCTC
29617879 GCTTGAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTAATATG
Found at i:29646621 original size:18 final size:19
Alignment explanation
Indices: 29646598--29646633 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29646588 ATTGTTTTCA
29646598 TACCTT-TAGGTATATCAC
1 TACCTTGTAGGTATATCAC
29646616 TACCTTGTAGGTATATCA
1 TACCTTGTAGGTATATCA
29646634 TTAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (19 bp):
TACCTTGTAGGTATATCAC
Found at i:29647037 original size:32 final size:32
Alignment explanation
Indices: 29646996--29647060 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
29646986 TAAACATGTT
29646996 AGCCTTTTCGGTTCATAACATAAATAAATTTA
1 AGCCTTTTCGGTTCATAACATAAATAAATTTA
*
29647028 AGCCTTTTCGGTTCATAACGTAAATAAATTTA
1 AGCCTTTTCGGTTCATAACATAAATAAATTTA
29647060 A
1 A
29647061 ATATGATTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (32 bp):
AGCCTTTTCGGTTCATAACATAAATAAATTTA
Found at i:29647728 original size:18 final size:18
Alignment explanation
Indices: 29647705--29647740 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29647695 CCTATTGTAT
29647705 TACTGATTTATGCTTACA
1 TACTGATTTATGCTTACA
29647723 TACTGATTTATGCTTACA
1 TACTGATTTATGCTTACA
29647741 CTTGTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
TACTGATTTATGCTTACA
Found at i:29648988 original size:32 final size:32
Alignment explanation
Indices: 29648952--29649072 Score: 179
Period size: 32 Copynumber: 3.8 Consensus size: 32
29648942 ACTATGCTAG
29648952 TTTTTTATATGTAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATCTAC
* * * *
29648984 TTTTTTCTATGTGAACCTAATGTATTATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATCTAC
*
29649016 TTTTTTATATGCAAAACTAATGTATGATCTAC
1 TTTTTTATATGTAAAACTAATGTATGATCTAC
* *
29649048 TTTTTTATACGTAAACCTAATGTAT
1 TTTTTTATATGTAAAACTAATGTAT
29649073 CATATTTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (32 bp):
TTTTTTATATGTAAAACTAATGTATGATCTAC
Found at i:29649053 original size:64 final size:64
Alignment explanation
Indices: 29648952--29649072 Score: 206
Period size: 64 Copynumber: 1.9 Consensus size: 64
29648942 ACTATGCTAG
* * * *
29648952 TTTTTTATATGTAAAACTAATGTATGATCTACTTTTTTCTATGTGAACCTAATGTATTATCTAC
1 TTTTTTATATGCAAAACTAATGTATGATCTACTTTTTTATACGTAAACCTAATGTATTATCTAC
29649016 TTTTTTATATGCAAAACTAATGTATGATCTACTTTTTTATACGTAAACCTAATGTAT
1 TTTTTTATATGCAAAACTAATGTATGATCTACTTTTTTATACGTAAACCTAATGTAT
29649073 CATATTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (64 bp):
TTTTTTATATGCAAAACTAATGTATGATCTACTTTTTTATACGTAAACCTAATGTATTATCTAC
Found at i:29652202 original size:2 final size:2
Alignment explanation
Indices: 29652195--29652223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29652185 TGTCTTATGT
29652195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29652224 TTTATTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29652632 original size:21 final size:21
Alignment explanation
Indices: 29652607--29652659 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
29652597 CGTTGTTTCT
*
29652607 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
29652628 AATCTCACCGCTACTGTAACT
1 AATCTCACCGCTACAGTAACC
29652649 AATCTCACCGC
1 AATCTCACCGC
29652660 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:29653125 original size:25 final size:25
Alignment explanation
Indices: 29653091--29653141 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29653081 TATATTCTCG
29653091 AAGATAGATCTTCGTTCTGGTTATT
1 AAGATAGATCTTCGTTCTGGTTATT
29653116 AAGATAGATCTTCGTTCTGGTTATT
1 AAGATAGATCTTCGTTCTGGTTATT
29653141 A
1 A
29653142 TCAACTACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (25 bp):
AAGATAGATCTTCGTTCTGGTTATT
Found at i:29658557 original size:25 final size:24
Alignment explanation
Indices: 29658515--29658567 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
29658505 ACATACAGCA
*
29658515 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAACGTCCTGATAT-G
* *
29658540 GCTCTTTGTGAACTTCCTGATATG
1 GCTCTTTATGAACGTCCTGATATG
29658564 GCTC
1 GCTC
29658568 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAACGTCCTGATATG
Found at i:29658578 original size:23 final size:25
Alignment explanation
Indices: 29658529--29658578 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29658519 TTTATGAGCG
**
29658529 TCCTGATATAGGCTCTTTGTGAACT
1 TCCTGATATAGGCTCGCTGTGAACT
29658554 TCCTGATAT-GGCTCGCT-TGAACT
1 TCCTGATATAGGCTCGCTGTGAACT
29658577 TC
1 TC
29658579 TTGTTATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 8 0.35
24 6 0.26
25 9 0.39
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (25 bp):
TCCTGATATAGGCTCGCTGTGAACT
Found at i:29659502 original size:19 final size:19
Alignment explanation
Indices: 29659475--29659540 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
29659465 AAGATTGGTT
*
29659475 TTGGCTTGGTTTTAATGTC
1 TTGGATTGGTTTTAATGTC
* * *
29659494 TTGGATTGGTATT--GGTT
1 TTGGATTGGTTTTAATGTC
*
29659511 TTGGTTTGGTTTTAATGTC
1 TTGGATTGGTTTTAATGTC
29659530 TTGGATTGGTT
1 TTGGATTGGTT
29659541 AGTGCATGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 13 0.36
19 23 0.64
ACGTcount: A:0.11, C:0.05, G:0.30, T:0.55
Consensus pattern (19 bp):
TTGGATTGGTTTTAATGTC
Found at i:29659520 original size:36 final size:36
Alignment explanation
Indices: 29659468--29659539 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
29659458 CATGAATAAG
29659468 ATTGGTTTTGGCTTGGTTTTAATGTCTTGGATTGGT
1 ATTGGTTTTGGCTTGGTTTTAATGTCTTGGATTGGT
*
29659504 ATTGGTTTTGGTTTGGTTTTAATGTCTTGGATTGGT
1 ATTGGTTTTGGCTTGGTTTTAATGTCTTGGATTGGT
29659540 TAGTGCATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.11, C:0.04, G:0.31, T:0.54
Consensus pattern (36 bp):
ATTGGTTTTGGCTTGGTTTTAATGTCTTGGATTGGT
Found at i:29661223 original size:40 final size:40
Alignment explanation
Indices: 29661178--29661345 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
29661168 CGGAATATAA
29661178 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
29661218 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
29661258 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
29661298 CCGGATATAATTTCCAGCATAATTGTCC-TCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATG-CCTTCGGGTCTTAGC
29661338 CCGGATAT
1 CCGGATAT
29661346 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 104 0.97
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29664054 original size:22 final size:22
Alignment explanation
Indices: 29664012--29664054 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
29664002 CACCCTGAAT
**
29664012 TTTGGGGTTAGGTGTTTTGAGC
1 TTTGGGGTTAGGTGTAGTGAGC
29664034 TTTGGGGTTAGG-GTCAGTGAG
1 TTTGGGGTTAGGTGT-AGTGAG
29664055 TAGGTTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.12, C:0.05, G:0.44, T:0.40
Consensus pattern (22 bp):
TTTGGGGTTAGGTGTAGTGAGC
Found at i:29666777 original size:21 final size:20
Alignment explanation
Indices: 29666748--29666799 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
29666738 GGAAACTCAG
* *
29666748 AAAAGTTTTCGCAAAATTTTA
1 AAAATTTTTCACAAAA-TTTA
*
29666769 AAATATTTTCCACAAAATTTA
1 AAA-ATTTTTCACAAAATTTA
29666790 AAAATTTTTC
1 AAAATTTTTC
29666800 TTAGGTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATTTTTCACAAAATTTA
Found at i:29666785 original size:22 final size:21
Alignment explanation
Indices: 29666759--29666799 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29666749 AAAGTTTTCG
*
29666759 CAAAATTTTAAAATATTTTCCA
1 CAAAATTTAAAAAT-TTTTCCA
29666781 CAAAATTTAAAAATTTTTC
1 CAAAATTTAAAAATTTTTC
29666800 TTAGGTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
CAAAATTTAAAAATTTTTCCA
Found at i:29666981 original size:21 final size:21
Alignment explanation
Indices: 29666952--29666993 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29666942 TGACTTGGGT
*
29666952 AAGACGGCCAGCCACACACTC
1 AAGACGGCCAACCACACACTC
*
29666973 AAGATGGCCAACCACACACTC
1 AAGACGGCCAACCACACACTC
29666994 GTGTGCTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.40, G:0.17, T:0.07
Consensus pattern (21 bp):
AAGACGGCCAACCACACACTC
Found at i:29668283 original size:23 final size:25
Alignment explanation
Indices: 29668263--29668315 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29668253 AAGTTCAAGT
29668263 GAGCC-ATATCAGGAAGCTCAAAAA
1 GAGCCTATATCAGGAAGCTCAAAAA
*
29668287 GAGCCTATATCAGGACA-CTCATAAA
1 GAGCCTATATCAGGA-AGCTCAAAAA
29668312 GAGC
1 GAGC
29668316 TGCGTTTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (25 bp):
GAGCCTATATCAGGAAGCTCAAAAA
Found at i:29668835 original size:21 final size:21
Alignment explanation
Indices: 29668795--29668835 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29668785 ATGAATTTAA
*
29668795 TATCAATTTAATCCATTTCAT
1 TATCAATTTAATCCAATTCAT
*
29668816 TATCAATTTAATTCAATTCA
1 TATCAATTTAATCCAATTCA
29668836 AATCCTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (21 bp):
TATCAATTTAATCCAATTCAT
Found at i:29677883 original size:15 final size:15
Alignment explanation
Indices: 29677863--29677892 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29677853 CAACACTTGT
29677863 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
29677878 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
29677893 ATACATTAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:29682251 original size:40 final size:40
Alignment explanation
Indices: 29682163--29682255 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
29682153 TGCAATCAAG
* * **
29682163 CTGCCAGTATTGTGGACAAGCTACCAGTTATGCAAATAAA
1 CTGCTAGTATTGTGGACAAGCCACCAGAAATGCAAATAAA
29682203 CTGCTAGTATTGTGGACAAGCCACCAGAAATGCAAATAAA
1 CTGCTAGTATTGTGGACAAGCCACCAGAAATGCAAATAAA
* *
29682243 TTGTTAGTATTGT
1 CTGCTAGTATTGT
29682256 AGGCAAGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (40 bp):
CTGCTAGTATTGTGGACAAGCCACCAGAAATGCAAATAAA
Found at i:29682370 original size:20 final size:20
Alignment explanation
Indices: 29682304--29682361 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
29682294 GCTGATAAAG
29682304 TGCCAGTATTGCAGACAAGC
1 TGCCAGTATTGCAGACAAGC
*
29682324 TGCCAGTATTG-TGACAAGC
1 TGCCAGTATTGCAGACAAGC
**
29682343 CACCAGTATTGCAGACAAG
1 TGCCAGTATTGCAGACAAG
29682362 TTGTCAGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
TGCCAGTATTGCAGACAAGC
Found at i:29682510 original size:38 final size:38
Alignment explanation
Indices: 29682436--29682515 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
29682426 AACAATACAA
* * * *
29682436 TAGGCATGATTAAAGTATGCAATCATTAGTAGAAATAC
1 TAGGCATGATTAAAGCATGCAATCAGTAATAAAAATAC
* *
29682474 TAGGCATGATTTAAA-CATGCGATCAGTAATAAAAATAG
1 TAGGCATGA-TTAAAGCATGCAATCAGTAATAAAAATAC
29682512 TAGG
1 TAGG
29682516 TGCATTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (38 bp):
TAGGCATGATTAAAGCATGCAATCAGTAATAAAAATAC
Found at i:29685512 original size:18 final size:18
Alignment explanation
Indices: 29685489--29685525 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29685479 TTAGGAATAC
*
29685489 TTTTGTCTCAAAAGTGCT
1 TTTTGTCCCAAAAGTGCT
29685507 TTTTGTCCCAAAAGTGCT
1 TTTTGTCCCAAAAGTGCT
29685525 T
1 T
29685526 CTTAGAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (18 bp):
TTTTGTCCCAAAAGTGCT
Found at i:29690740 original size:3 final size:3
Alignment explanation
Indices: 29690732--29690764 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29690722 AATATATGAA
29690732 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29690765 GGTGGTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29691182 original size:17 final size:18
Alignment explanation
Indices: 29691160--29691193 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29691150 AACGAACAAA
29691160 AAAAATTAAAAC-CTAAT
1 AAAAATTAAAACTCTAAT
*
29691177 AAAAATTGAAACTCTAA
1 AAAAATTAAAACTCTAA
29691194 AGTTTCTCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAATTAAAACTCTAAT
Found at i:29695138 original size:29 final size:29
Alignment explanation
Indices: 29695105--29695265 Score: 187
Period size: 29 Copynumber: 5.6 Consensus size: 29
29695095 GTGACGAGAT
*
29695105 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29695134 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29695163 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
29695192 TGGCACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
29695221 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29695250 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
29695266 GGCTTAAATT
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 117 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:29702953 original size:29 final size:29
Alignment explanation
Indices: 29702920--29703078 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 29
29702910 GTGACGAGAT
29702920 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
29702949 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
29702978 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * **
29703007 TGACACTATGTGTGCAAGCTGGAAA-ATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * * ***
29703035 CGGCACT-GGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
29703063 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
29703079 GGCTTAAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 13 0.11
28 16 0.14
29 85 0.75
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:29704519 original size:83 final size:83
Alignment explanation
Indices: 29704380--29704545 Score: 323
Period size: 83 Copynumber: 2.0 Consensus size: 83
29704370 CGGTGACGCA
29704380 GTTTTCCAGCCTGACTGGAAATGTCAAATTGGTTGGTACCTTGAGAGGATTTGGCCGTTAACCCC
1 GTTTTCCAGCCTGACTGGAAATGTCAAATTGGTTGGTACCTTGAGAGGATTTGGCCGTTAACCCC
29704445 TCGTGTCCGACACCGGCG
66 TCGTGTCCGACACCGGCG
*
29704463 GTTTTCCAGCCTGACTGGTAATGTCAAATTGGTTGGTACCTTGAGAGGATTTGGCCGTTAACCCC
1 GTTTTCCAGCCTGACTGGAAATGTCAAATTGGTTGGTACCTTGAGAGGATTTGGCCGTTAACCCC
29704528 TCGTGTCCGACACCGGCG
66 TCGTGTCCGACACCGGCG
29704546 ACGGTCACGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (83 bp):
GTTTTCCAGCCTGACTGGAAATGTCAAATTGGTTGGTACCTTGAGAGGATTTGGCCGTTAACCCC
TCGTGTCCGACACCGGCG
Found at i:29709903 original size:84 final size:82
Alignment explanation
Indices: 29709763--29709929 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 82
29709753 TAGGGATATG
*
29709763 ATGAAAACAAAAGAAAAAAAAAAGTGTTCATTCTCTCATTTTCTCCTTGCTTGGCCGAATATACT
1 ATGAAAACAAAAAAAAAAAAAAAGTGTTCATTCTCTCATTTTCTCCTTGCTTGGCCGAATATACT
29709828 AAGAAGAAAGGGGGGAAA
66 AAGAA-AAAGGGGGGAAA
29709846 ATGAAAACAAAAAAAAAAAAAAAAGTGTTCATTCTCTCATTTTCTCCTTGCTTGGCCGAATATAC
1 ATGAAAAC-AAAAAAAAAAAAAAAGTGTTCATTCTCTCATTTTCTCCTTGCTTGGCCGAATATAC
29709911 TAAGAAAAAGGGGGGAAA
65 TAAGAAAAAGGGGGGAAA
29709929 A
1 A
29709930 AGCTTGAGAA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
83 21 0.26
84 61 0.74
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (82 bp):
ATGAAAACAAAAAAAAAAAAAAAGTGTTCATTCTCTCATTTTCTCCTTGCTTGGCCGAATATACT
AAGAAAAAGGGGGGAAA
Found at i:29710981 original size:28 final size:29
Alignment explanation
Indices: 29710881--29711002 Score: 174
Period size: 29 Copynumber: 4.2 Consensus size: 29
29710871 GTGACGAGAT
* *
29710881 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* *
29710910 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
29710939 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* *
29710968 T-GCACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
29710996 CGGCACT
1 TGGCACT
29711003 GGGTGTGCGA
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 25 0.29
29 62 0.71
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:29711010 original size:57 final size:58
Alignment explanation
Indices: 29710882--29711002 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 58
29710872 TGACGAGATT
* * ** * *
29710882 GGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTGCAAGCTGGAAAAATAC
*
29710940 GGCACTAAGTGTGCATGCTGGAAAAATAT-GCACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTGCAAGCTGGAAAAATAC
29710997 GGCACT
1 GGCACT
29711003 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 29 0.52
58 27 0.48
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (58 bp):
GGCACTAAGTGTGCATGCTGGAAAAATATGGCACTAAGTGTGCAAGCTGGAAAAATAC
Found at i:29718723 original size:29 final size:29
Alignment explanation
Indices: 29718690--29718850 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 29
29718680 GTGACGAGAT
*
29718690 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29718719 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29718748 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
29718777 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
29718806 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
29718835 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
29718851 GGCTTAAATT
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:29721390 original size:47 final size:44
Alignment explanation
Indices: 29721272--29721404 Score: 133
Period size: 47 Copynumber: 2.9 Consensus size: 44
29721262 ATGTGTGTGT
* * *
29721272 GCTATTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTATGAGA
1 GCTAGTGTAAAACATGTCTGGGACATGGCATCGG---CATTACGAGA
* * * *
29721318 GCCAGTGTAAGACCATGTATAGGACATGGCATCGGCATTGAGACGAGA
1 GCTAGTGTAA-AACATGTCTGGGACATGGCATCGGCATT---ACGAGA
29721366 GCTAGTGTAAAACATGTCTGGGACATGGCATCGGCATTA
1 GCTAGTGTAAAACATGTCTGGGACATGGCATCGGCATTA
29721405 TACCCTATGT
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 4 0.06
46 8 0.11
47 37 0.52
48 21 0.30
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (44 bp):
GCTAGTGTAAAACATGTCTGGGACATGGCATCGGCATTACGAGA
Found at i:29729019 original size:16 final size:17
Alignment explanation
Indices: 29728988--29729019 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29728978 AAATTCTGAT
29728988 ATGAGTTATGAATTGAA
1 ATGAGTTATGAATTGAA
29729005 ATGAGTTAT-AATTGA
1 ATGAGTTATGAATTGA
29729020 TTTATTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATGAGTTATGAATTGAA
Found at i:29733169 original size:78 final size:81
Alignment explanation
Indices: 29733034--29733215 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 81
29733024 TCGAATGATG
* * *
29733034 ACCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
29733098 TGTGTGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
29733113 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACCAAATCCGGGTTAAG-TCCCGAAGGCAT
1 ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
29733175 TTGTGCGAGTTACTATA
65 TTGTGCGAGTTACTATA
*
29733192 ACCGGGCTATGTCCCGAAGGCATT
1 ACCGGGCTAAGTCCCGAAGGCATT
29733216 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 49 0.56
79 26 0.30
80 12 0.14
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:29733224 original size:40 final size:39
Alignment explanation
Indices: 29733034--29733217 Score: 212
Period size: 40 Copynumber: 4.7 Consensus size: 39
29733024 TCGAATGATG
* *
29733034 ACCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* * *
29733074 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTAA
1 ACCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* * *
29733113 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACCAA
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
29733151 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 A-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
29733192 ACCGGGCTATGTCCCGAAGGCATTTG
1 ACCGGGCTAAGTCCCGAAGGCATTTG
29733218 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 23 0.19
39 20 0.16
40 71 0.58
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Done.