Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 138 of 292
Found at i:40924609 original size:20 final size:19
Alignment explanation
Indices: 40924563--40924614 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
40924553 CGACGTTCTC
40924563 TTTCTTTCTT-TTTTTGTTT
1 TTTCTTT-TTCTTTTTGTTT
*
40924582 TTT-GTTTTCTTTTTGTTT
1 TTTCTTTTTCTTTTTGTTT
40924600 ATTTCTTTTTCTTTT
1 -TTTCTTTTTCTTTT
40924615 CTGAAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 6 0.21
20 9 0.32
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTCTTTTTCTTTTTGTTT
Found at i:40935809 original size:13 final size:13
Alignment explanation
Indices: 40935791--40935815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40935781 ACAAACAATA
40935791 AAATTTTCACACG
1 AAATTTTCACACG
40935804 AAATTTTCACAC
1 AAATTTTCACAC
40935816 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:40941671 original size:43 final size:42
Alignment explanation
Indices: 40941624--40941739 Score: 103
Period size: 42 Copynumber: 2.7 Consensus size: 42
40941614 TCCTAGACAT
*
40941624 GGTCTTACATGTAATCACATATCGATGCCACTGTCCAAAATAG
1 GGTCTTACATGTAATCACATATCGATGCCA-TGTCCAAAACAG
* * * *
40941667 GGTCTTACAAG-AA-CTCATATACGATGCCGATGTCCCAAACAT
1 GGTCTTACATGTAATCACATAT-CGATGCC-ATGTCCAAAACAG
* *
40941709 GGTCTTACACT-TAAATCACAAATCAATGCCA
1 GGTCTTACA-TGT-AATCACATATCGATGCCA
40941740 ACATCCCAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
41 6 0.10
42 27 0.47
43 12 0.21
44 8 0.14
45 5 0.09
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (42 bp):
GGTCTTACATGTAATCACATATCGATGCCATGTCCAAAACAG
Found at i:40942904 original size:13 final size:13
Alignment explanation
Indices: 40942886--40942912 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40942876 CACAAACGAT
40942886 AAAATTTTCACAC
1 AAAATTTTCACAC
40942899 AAAATTTTCACAC
1 AAAATTTTCACAC
40942912 A
1 A
40942913 TATAAATTAA
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:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:40944703 original size:18 final size:18
Alignment explanation
Indices: 40944680--40944715 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40944670 TCCAAAGAGG
*
40944680 AGTGTTATAATTTCTTAT
1 AGTGTTATAATATCTTAT
40944698 AGTGTTATAATATCTTAT
1 AGTGTTATAATATCTTAT
40944716 TAAGTAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
AGTGTTATAATATCTTAT
Found at i:40947260 original size:24 final size:24
Alignment explanation
Indices: 40947228--40947312 Score: 118
Period size: 24 Copynumber: 3.5 Consensus size: 24
40947218 AATCTCAAAT
*
40947228 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTAATATG
40947252 GCACTATGTGTGCGATTTAATATG
1 GCACTATGTGTGCGATTTAATATG
** *
40947276 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCG-ATTTAATATG
40947300 GCACTATGTGTGC
1 GCACTATGTGTGC
40947313 AACATTCGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
24 50 0.89
25 6 0.11
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTAATATG
Found at i:40951627 original size:28 final size:28
Alignment explanation
Indices: 40951558--40951658 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40951548 GACAAGATTG
* * * *
40951558 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
40951588 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40951616 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
40951645 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40951659 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40959588 original size:28 final size:28
Alignment explanation
Indices: 40959519--40959619 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40959509 GACAAGATTG
* * * *
40959519 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
40959549 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40959577 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
40959606 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40959620 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40961137 original size:15 final size:16
Alignment explanation
Indices: 40961112--40961153 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
40961102 TGGCAAACGA
40961112 AGGATTTTTTA-GGTTT
1 AGGA-TTTTTAGGGTTT
40961128 AAGG-TTTTTAGGGTTT
1 -AGGATTTTTAGGGTTT
40961144 AGGATTTTTA
1 AGGATTTTTA
40961154 AGATCGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.39
16 11 0.48
17 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (16 bp):
AGGATTTTTAGGGTTT
Found at i:40967139 original size:40 final size:40
Alignment explanation
Indices: 40967037--40967376 Score: 488
Period size: 40 Copynumber: 8.6 Consensus size: 40
40967027 CATTTGAATG
* *
40967037 ATATCCGGGCTAAGCCCCAAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * *
40967077 ATATCC-GGTTAAGACCCAAAGGCATTTGTGTGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
40967116 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
40967156 ATATCCGGGCTAAGAACCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* *
40967196 ATATCCGGGTTAAGGCCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
40967236 ATAACCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
40967276 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * * *
40967316 ATGTCCGGGTTAAGACCTGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
40967356 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
40967377 AAACTTGGGT
Statistics
Matches: 272, Mismatches: 26, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
38 1 0.00
39 47 0.17
40 224 0.82
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:40968884 original size:17 final size:17
Alignment explanation
Indices: 40968847--40968882 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40968837 AGGATAATGC
*
40968847 GGCCACATGTCCGTGTG
1 GGCCACATGCCCGTGTG
40968864 GGCCTACATGCCCGTGTG
1 GGCC-ACATGCCCGTGTG
40968882 G
1 G
40968883 CCCATACGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.31, G:0.36, T:0.22
Consensus pattern (17 bp):
GGCCACATGCCCGTGTG
Found at i:40970773 original size:12 final size:11
Alignment explanation
Indices: 40970751--40970789 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
40970741 AGATTTTGGG
40970751 AAAAGAAAAAAT
1 AAAA-AAAAAAT
40970763 AAAAAATAAAAT
1 AAAAAA-AAAAT
40970775 AAAATAAAAAAT
1 AAAA-AAAAAAT
40970787 AAA
1 AAA
40970790 TTATATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:40975474 original size:20 final size:20
Alignment explanation
Indices: 40975449--40975486 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40975439 GTTTATTCGT
*
40975449 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
40975469 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
40975487 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:40977147 original size:28 final size:28
Alignment explanation
Indices: 40977115--40977183 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
40977105 GCGTAGATCA
40977115 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
40977143 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
40977171 CGATA-TACCCCTA
1 CGAAATTACCCCTA
40977184 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:40981676 original size:4 final size:4
Alignment explanation
Indices: 40981667--40981747 Score: 162
Period size: 4 Copynumber: 20.2 Consensus size: 4
40981657 TTACTACTAA
40981667 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40981715 TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
40981748 TTTTTTTAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:40984986 original size:20 final size:20
Alignment explanation
Indices: 40984926--40984977 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
40984916 CTCACTTCTC
*
40984926 CCACGCCCGTGTATGTATGT
1 CCACGCCCGTGTATATATGT
*
40984946 CCACGCCCGTGTATAAATGT
1 CCACGCCCGTGTATATATGT
40984966 CCACGCCCGTGT
1 CCACGCCCGTGT
40984978 TTTTTTGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (20 bp):
CCACGCCCGTGTATATATGT
Found at i:40988234 original size:28 final size:28
Alignment explanation
Indices: 40988202--40988285 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
40988192 AACTGTGATC
40988202 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
40988230 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
40988252 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
40988280 ACGTGT
1 ACGTGT
40988286 ATCGAATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:40988327 original size:49 final size:49
Alignment explanation
Indices: 40988148--40988429 Score: 300
Period size: 49 Copynumber: 5.7 Consensus size: 49
40988138 TCTATTGTGA
* * *
40988148 GGTCGCATG-GTAGTACTAAGTGCAGGCTACTATGCGTACCCGAA-AACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGAATAA-T-T
* * * **
40988198 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGA-ATAATT
* *
40988247 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGAATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
* * * * *
40988297 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAA-T-T
* * * *
40988348 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
*
40988397 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40988430 TGCGTACTAG
Statistics
Matches: 196, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
49 73 0.37
50 55 0.28
51 68 0.35
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATT
Found at i:40988375 original size:100 final size:100
Alignment explanation
Indices: 40988157--40988436 Score: 359
Period size: 100 Copynumber: 2.8 Consensus size: 100
40988147 AGGTCGCATG
* * * * *
40988157 GTAGTACTAAGTGCAGGCTACTATGCGTACCCGAA-AACTGTGATCACGTGTGTAGTACTAAGTG
1 GTAGTACTAAGTGCAGGCTACTACGTGTA-CCGAATAA-T-TGGTCGCATGTGTAGTACTAAGTG
* * * * *** *
40988221 CAGGCTACTACGTGTA-TCAGATGGTTAGGTCACGTGT
63 CAGGCTACTATGCGTACCCAAAAACTTAGATCACGTGT
*
40988258 GTAGTACTAAGTGCAGGCTACTACGTGTATCGAATAATTGGTCGCATGTGTAGTACTAAGTGCAG
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGCAG
40988323 GCTACTATGCGTACCCAAAAACTGT-GATCACGTGT
66 GCTACTATGCGTACCCAAAAACT-TAGATCACGTGT
* *
40988358 GTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTATTGGTCGCATGTGTAGTACTAAGTGCAG
1 GTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGCAG
40988423 GCTACTATGCGTAC
66 GCTACTATGCGTAC
40988437 TAGATAGCTT
Statistics
Matches: 159, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
99 35 0.22
100 94 0.59
101 30 0.19
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (100 bp):
GTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACTAAGTGCAG
GCTACTATGCGTACCCAAAAACTTAGATCACGTGT
Found at i:40991433 original size:15 final size:15
Alignment explanation
Indices: 40991413--40991477 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
40991403 GTATCTTAGG
40991413 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
40991428 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
40991443 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
40991458 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
40991472 TTTCTT
1 TTTCTT
40991478 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40993684 original size:28 final size:28
Alignment explanation
Indices: 40993653--40993736 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
40993643 AACTGTGATC
40993653 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
40993681 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
40993703 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
40993731 ACGTGT
1 ACGTGT
40993737 ACCGATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:40993726 original size:50 final size:46
Alignment explanation
Indices: 40993600--40993865 Score: 244
Period size: 48 Copynumber: 5.7 Consensus size: 46
40993590 TCTATTGTGA
* *
40993600 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA--TGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA--C--AGA-TGT
* *
40993649 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGAT-G-T
* * *
40993698 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGAT--GT
* * *
40993747 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC---TGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGATGT
* *
40993790 GAT--C-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-A
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGATGT
*
40993833 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40993866 TGCGTACCAG
Statistics
Matches: 185, Mismatches: 19, Indels: 29
0.79 0.08 0.12
Matches are distributed among these distances:
40 30 0.16
41 2 0.01
43 5 0.03
44 1 0.01
45 2 0.01
46 26 0.14
47 1 0.01
48 39 0.21
49 36 0.19
50 39 0.21
51 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (46 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGATGT
Found at i:40993809 original size:40 final size:44
Alignment explanation
Indices: 40993656--40993879 Score: 195
Period size: 46 Copynumber: 4.9 Consensus size: 44
40993646 TGTGATCACG
* * * *
40993656 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CAGA----TAGATC-CA
* * * *
40993706 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACAGAT-A--GATC-CA
*
40993754 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTG-T-GAT-C-
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACAGATAGATCCA
* * *
40993794 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CAGATAGATC-CA
40993840 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CAGATAG
40993880 CTTCGGCTAC
Statistics
Matches: 152, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
40 30 0.20
41 3 0.02
42 1 0.01
43 4 0.03
45 2 0.01
46 39 0.26
47 1 0.01
48 37 0.24
49 3 0.02
50 32 0.21
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (44 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACAGATAGATCCA
Found at i:40993866 original size:86 final size:87
Alignment explanation
Indices: 40993706--40993872 Score: 302
Period size: 86 Copynumber: 1.9 Consensus size: 87
40993696 TTAGGTCACG
40993706 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCATGTGTAGTACTAAGTGC
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAA-TGGTCGCATGTGTAGTACTAAGTGC
40993771 AGGCTACTATGCGTACTGTGATC
65 AGGCTACTATGCGTACTGTGATC
40993794 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-A-GGTCGCATGTGTAGTACTAAGTGC
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATGGTCGCATGTGTAGTACTAAGTGC
40993857 AGGCTACTATGCGTAC
65 AGGCTACTATGCGTAC
40993873 CAGATAGCTT
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
86 40 0.51
88 35 0.45
89 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (87 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATGGTCGCATGTGTAGTACTAAGTGCA
GGCTACTATGCGTACTGTGATC
Found at i:40996918 original size:14 final size:15
Alignment explanation
Indices: 40996856--40996920 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
40996846 GTATCTTAGG
40996856 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
40996871 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
40996886 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
40996901 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
40996915 TTTCTT
1 TTTCTT
40996921 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.30
15 27 0.63
16 3 0.07
ACGTcount: A:0.09, C:0.12, G:0.14, T:0.65
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:40999168 original size:93 final size:93
Alignment explanation
Indices: 40999056--40999226 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40999046 GCCCATAAGT
* *
40999056 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40999121 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40999149 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40999214 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40999227 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40999223 original size:46 final size:46
Alignment explanation
Indices: 40999048--40999223 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
40999038 TGTAACCCGC
* * *
40999048 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40999094 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
40999144 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40999187 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40999224 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41001632 original size:30 final size:30
Alignment explanation
Indices: 41001588--41001676 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
41001578 CAAAGATAAC
*
41001588 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
41001617 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
41001647 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
41001677 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:41001636 original size:15 final size:14
Alignment explanation
Indices: 41001588--41001670 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
41001578 CAAAGATAAC
*
41001588 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
41001602 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
41001617 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
41001632 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
41001647 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
41001662 AAGAAACCC
1 AAGAAACCC
41001671 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:41001676 original size:15 final size:15
Alignment explanation
Indices: 41001599--41001676 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
41001589 AGAAAACCGA
41001599 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
41001614 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
41001628 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
41001643 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
41001659 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
41001674 ATA
1 ATA
41001677 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:41004736 original size:93 final size:93
Alignment explanation
Indices: 41004624--41004794 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41004614 GCCCATAAGT
* *
41004624 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41004689 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
41004717 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41004782 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41004795 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41004791 original size:46 final size:46
Alignment explanation
Indices: 41004616--41004791 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
41004606 TGTAACCCGC
* * *
41004616 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41004662 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
41004712 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
41004755 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41004792 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41007459 original size:51 final size:50
Alignment explanation
Indices: 41007393--41007665 Score: 282
Period size: 51 Copynumber: 5.5 Consensus size: 50
41007383 TGAGGTCGCA
* *
41007393 TGTGTAGTACTAAGTGTAGGCTACTACAAGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACT-TGATCACG
* * *** *
41007444 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCAG-ATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACTT-GATCACG
* * * * * *
41007494 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACTTGATCACG
***
41007543 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACT-TGATCACG
* * ** * * *
41007594 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTA-TTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACTTGATCACG
41007643 TGTGTAGTACTAAGTGCAGGCTA
1 TGTGTAGTACTAAGTGCAGGCTA
41007666 TTATGCGTAC
Statistics
Matches: 187, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
49 70 0.37
50 45 0.24
51 72 0.39
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTACCCGAAAACTTGATCACG
Found at i:41007614 original size:100 final size:100
Alignment explanation
Indices: 41007489--41007676 Score: 349
Period size: 100 Copynumber: 1.9 Consensus size: 100
41007479 GATGGTTAGG
*
41007489 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
41007554 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
*
41007589 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
*
41007654 AAGTGCAGGCTATTATGCGTACC
66 AAGTGCAGGCTACTATGCGTACC
41007677 AGATAGCTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:41007676 original size:49 final size:49
Alignment explanation
Indices: 41007386--41007681 Score: 313
Period size: 49 Copynumber: 5.9 Consensus size: 49
41007376 TCTATTGTGA
* * ** * *
41007386 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTACAAGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * * * **
41007437 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
41007486 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
41007536 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * *
41007587 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
41007636 GGTCGCATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41007682 GCTTCGGCTA
Statistics
Matches: 205, Mismatches: 37, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
49 82 0.40
50 46 0.22
51 77 0.38
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:41011719 original size:21 final size:20
Alignment explanation
Indices: 41011680--41011719 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41011670 CCCATGTTGA
* *
41011680 CCCATTTTCTCTGTTTTTAG
1 CCCATTTTCGCTCTTTTTAG
41011700 CCCATTTCTCGCTCTTTTTA
1 CCCATTT-TCGCTCTTTTTA
41011720 CTCTCCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (20 bp):
CCCATTTTCGCTCTTTTTAG
Found at i:41019848 original size:93 final size:93
Alignment explanation
Indices: 41019735--41019905 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
41019725 GCCCATAAGT
*
41019735 GAACTCGGACTCAACTCAATGA-TCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAATGAGT-TCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41019799 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
*
41019828 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41019893 CGAGTTCGGATGC
66 CGAGCTCGGATGC
41019906 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
93 73 0.99
94 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:41019898 original size:46 final size:46
Alignment explanation
Indices: 41019727--41019902 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
41019717 TGTAACCCGC
* *
41019727 CCATAAGTGAACTCGGACTCAACTCAATGA-TCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGT-TCGGACATTCGCAT
* *
41019773 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* *** *
41019819 ACATCTCTCGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41019866 CCATAAGTGAACTTGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41019903 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 65 0.61
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41023253 original size:28 final size:28
Alignment explanation
Indices: 41023207--41023275 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
41023197 TTTAAAACCC
*
41023207 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41023234 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41023262 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
41023276 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:41024927 original size:20 final size:20
Alignment explanation
Indices: 41024904--41024941 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41024894 CACATCCAAA
*
41024904 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
41024924 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
41024942 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:41031264 original size:28 final size:28
Alignment explanation
Indices: 41031218--41031286 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
41031208 TTTAAAACCC
*
41031218 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41031245 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
41031273 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
41031287 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:41032936 original size:20 final size:20
Alignment explanation
Indices: 41032913--41032950 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41032903 CACATCCAAA
*
41032913 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
41032933 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
41032951 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:41033712 original size:15 final size:15
Alignment explanation
Indices: 41033686--41033734 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
41033676 CAAAGATAAC
41033686 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
41033699 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
41033714 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
41033729 AAGAAA
1 AAGAAA
41033735 CCAAAGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 6 0.19
14 2 0.06
15 23 0.74
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:41036771 original size:93 final size:93
Alignment explanation
Indices: 41036659--41036829 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41036649 GCCCATAAGT
*
41036659 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41036724 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
41036752 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41036817 CGAGTTCGGATGC
66 CGAGCTCGGATGC
41036830 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:41036826 original size:46 final size:46
Alignment explanation
Indices: 41036651--41036826 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
41036641 TGTAACCTGC
*
41036651 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
41036697 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
41036743 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
41036790 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
41036827 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 70 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:41039810 original size:12 final size:12
Alignment explanation
Indices: 41039793--41039826 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
41039783 GTCGCACCCC
41039793 GCCTACCACATG
1 GCCTACCACATG
41039805 GCCTACCACATG
1 GCCTACCACATG
41039817 GCCTACCACA
1 GCCTACCACA
41039827 CACTCGTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.15
Consensus pattern (12 bp):
GCCTACCACATG
Found at i:41048119 original size:10 final size:10
Alignment explanation
Indices: 41048104--41048139 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
41048094 TTTTACTTTA
41048104 TTCAATTGTG
1 TTCAATTGTG
*
41048114 TTCAA-TATG
1 TTCAATTGTG
41048123 TTCAATTGTG
1 TTCAATTGTG
41048133 TTCAATT
1 TTCAATT
41048140 CATCAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (10 bp):
TTCAATTGTG
Found at i:41050257 original size:8 final size:8
Alignment explanation
Indices: 41050244--41050280 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
41050234 CGACAGCCCA
*
41050244 CTTTTCGG
1 CTTTTCAG
41050252 CTTTTCAG
1 CTTTTCAG
*
41050260 CTTTTCGG
1 CTTTTCAG
41050268 CTTTTCAG
1 CTTTTCAG
41050276 CTTTT
1 CTTTT
41050281 TCCGTTTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.05, C:0.24, G:0.16, T:0.54
Consensus pattern (8 bp):
CTTTTCAG
Found at i:41050265 original size:16 final size:16
Alignment explanation
Indices: 41050244--41050280 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
41050234 CGACAGCCCA
41050244 CTTTTCGGCTTTTCAG
1 CTTTTCGGCTTTTCAG
41050260 CTTTTCGGCTTTTCAG
1 CTTTTCGGCTTTTCAG
41050276 CTTTT
1 CTTTT
41050281 TCCGTTTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.24, G:0.16, T:0.54
Consensus pattern (16 bp):
CTTTTCGGCTTTTCAG
Found at i:41053595 original size:40 final size:40
Alignment explanation
Indices: 41053529--41053695 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
41053519 AAATTGAATG
* * *
41053529 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41053568 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41053608 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41053648 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41053688 ATATCCGG
1 ATATCCGG
41053696 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41063359 original size:20 final size:22
Alignment explanation
Indices: 41063330--41063369 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
41063320 ATTGATTTAT
*
41063330 GGAAATTATA-AT-TATTATTA
1 GGAAAATATATATATATTATTA
41063350 GGAAAATATATATATATTAT
1 GGAAAATATATATATATTAT
41063370 CGTATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (22 bp):
GGAAAATATATATATATTATTA
Found at i:41065341 original size:25 final size:25
Alignment explanation
Indices: 41065313--41065360 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41065303 TTATACCATG
* * *
41065313 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
41065338 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41065361 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41065429 original size:20 final size:20
Alignment explanation
Indices: 41065404--41065462 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
41065394 TAAATATGGT
41065404 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
41065424 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
41065444 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
41065463 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:41065444 original size:11 final size:11
Alignment explanation
Indices: 41065408--41065462 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
41065398 TATGGTATGT
41065408 ATGATATGCAC
1 ATGATATGCAC
* *
41065419 ATGAAATG--T
1 ATGATATGCAC
41065428 ATGATATGCAC
1 ATGATATGCAC
*
41065439 ATGATATG--T
1 ATGATATGCAC
41065448 ATGATATGCAC
1 ATGATATGCAC
41065459 ATGA
1 ATGA
41065463 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41065540 original size:24 final size:24
Alignment explanation
Indices: 41065513--41065631 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
41065503 GAGGAAGTGA
*
41065513 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
41065537 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
41065560 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
41065584 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41065608 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41065632 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:41065582 original size:47 final size:48
Alignment explanation
Indices: 41065513--41065631 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
41065503 GAGGAAGTGA
41065513 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
41065560 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
41065608 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41065632 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:41065858 original size:31 final size:31
Alignment explanation
Indices: 41065823--41065886 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
41065813 CGTTTACAGT
41065823 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
41065854 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41065885 AA
1 AA
41065887 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41067921 original size:20 final size:22
Alignment explanation
Indices: 41067892--41067931 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
41067882 ATTGATTTAT
*
41067892 GGAAATTATA-AT-TATTATTA
1 GGAAAATATATATATATTATTA
41067912 GGAAAATATATATATATTAT
1 GGAAAATATATATATATTAT
41067932 CGTATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (22 bp):
GGAAAATATATATATATTATTA
Found at i:41070622 original size:30 final size:28
Alignment explanation
Indices: 41070582--41070682 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
41070572 GACAAGATTG
* * *
41070582 GCACTGAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--AATTATACA
* *
41070612 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATACA
* * *
41070640 GCACTAAGTGTGCGAGCTGAATATATATA
1 GCACTAAGTGTGCGAGTTTAAT-TATACA
41070669 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41070683 GATTCACTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 25 0.40
29 20 0.32
30 17 0.27
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATACA
Found at i:41070646 original size:28 final size:29
Alignment explanation
Indices: 41070611--41070682 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
41070601 AAAATTGTAC
*
41070611 AGCACTAAGTGTGCGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGCGAG-CTGAATATATAT
41070639 AGCACTAAGTGTGCGAGCTGAATATATAT
1 AGCACTAAGTGTGCGAGCTGAATATATAT
41070668 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
41070683 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAATATATAT
Found at i:41073107 original size:11 final size:11
Alignment explanation
Indices: 41073074--41073127 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
41073064 TATGGTATGT
41073074 ATGATATGCAC
1 ATGATATGCAC
*
41073085 ATGA-ATG--T
1 ATGATATGCAC
41073093 ATGATATGCAC
1 ATGATATGCAC
*
41073104 ATGATATG--T
1 ATGATATGCAC
41073113 ATGATATGCAC
1 ATGATATGCAC
41073124 ATGA
1 ATGA
41073128 GGTAATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.12
9 11 0.32
10 3 0.09
11 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41073114 original size:20 final size:20
Alignment explanation
Indices: 41073069--41073127 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
41073059 ATAAATATGG
41073069 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
41073089 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
41073108 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
41073128 GGTAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:41073205 original size:24 final size:24
Alignment explanation
Indices: 41073178--41073296 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
41073168 GAGGAAGTGA
*
41073178 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
41073202 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
41073225 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
41073249 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
41073273 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41073297 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:41073247 original size:47 final size:48
Alignment explanation
Indices: 41073178--41073296 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
41073168 GAGGAAGTGA
41073178 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
41073225 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
41073273 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41073297 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:41073523 original size:31 final size:31
Alignment explanation
Indices: 41073488--41073551 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
41073478 CGTTTACAGT
41073488 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
41073519 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41073550 AA
1 AA
41073552 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41082721 original size:40 final size:40
Alignment explanation
Indices: 41082655--41082821 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41082645 AAATTGAATG
* * *
41082655 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41082694 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41082734 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41082774 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41082814 ATATCCGG
1 ATATCCGG
41082822 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41090709 original size:40 final size:40
Alignment explanation
Indices: 41090650--41090791 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
41090640 AAATTGAATG
* * *
41090650 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
41090690 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
41090730 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
41090770 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
41090792 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:41090792 original size:40 final size:39
Alignment explanation
Indices: 41090689--41090817 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
41090679 TGCTGGAAAT
* * *
41090689 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
41090729 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
41090769 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
41090809 TATATCCGG
1 TATATCCGG
41090818 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:41098949 original size:45 final size:45
Alignment explanation
Indices: 41098898--41098988 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
41098888 AATCCGAGAG
* *
41098898 TAAGTTCATAAATATTATTAGTTAATATTTATGAGTTAAATATGT
1 TAAGTTCATAAATATTATTAGTTAATATTTACGAGTCAAATATGT
41098943 TAAGTTCATAAATATTATTAGTTAATATTTACGAGTCAAATATGT
1 TAAGTTCATAAATATTATTAGTTAATATTTACGAGTCAAATATGT
41098988 T
1 T
41098989 TTTAAAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (45 bp):
TAAGTTCATAAATATTATTAGTTAATATTTACGAGTCAAATATGT
Found at i:41107005 original size:57 final size:57
Alignment explanation
Indices: 41106943--41107091 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 57
41106933 TTGACCTCAT
* * *
41106943 TTATGAAAGGATTTAGCCTGGACGGGTAATCCTGATATAAATC-CTCTCGAGCATATG
1 TTATGAAAGGATTTAGCCTGGACGGGTAATCCT-AGATAAAGCTCTCTAGAGCATATG
* ** * *
41107000 TTATGAATTGGATTTAGCCCAGACGGGTAATCC-AGATCAAGCTCTTTAGAGCATATG
1 TTATGAA-AGGATTTAGCCTGGACGGGTAATCCTAGATAAAGCTCTCTAGAGCATATG
* * * *
41107057 TCATAAAAAAGATTTAGCCTGGACTGGTAATCCTA
1 TTAT-GAAAGGATTTAGCCTGGACGGGTAATCCTA
41107092 TTGTATACAT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
56 6 0.08
57 42 0.58
58 25 0.34
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (57 bp):
TTATGAAAGGATTTAGCCTGGACGGGTAATCCTAGATAAAGCTCTCTAGAGCATATG
Found at i:41121539 original size:39 final size:40
Alignment explanation
Indices: 41121468--41121647 Score: 188
Period size: 40 Copynumber: 4.5 Consensus size: 40
41121458 GCTCGATTGT
* * *
41121468 CTTCGGGACA-TAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGA-ATTAGCCCGGATT-TAGTAACTCGCACAAATGC
41121508 CTTC-GGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41121547 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
41121587 CTTCGGGAATT-GACCCGAATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGAATTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
*
41121628 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGAATTAGCCCGGAT
41121648 ACCATTCGAA
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 31 0.26
40 58 0.50
41 26 0.22
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:41121564 original size:79 final size:81
Alignment explanation
Indices: 41121468--41121645 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 81
41121458 GCTCGATTGT
* * * * *
41121468 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTC-GGAATT-AGCCCGGATTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGA-CCCGAATTTAG
* *
41121531 TAAC-TCGCACAAATGC
65 TAACTTAGCACAAAAGC
* * *
41121547 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGACCCGAATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGAATTTAGT
*
41121612 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
41121628 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
41121646 ATACCATTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 37 0.44
80 19 0.23
81 28 0.33
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGAATTTAGT
AACTTAGCACAAAAGC
Found at i:41129651 original size:773 final size:767
Alignment explanation
Indices: 41128223--41129651 Score: 2223
Period size: 773 Copynumber: 1.9 Consensus size: 767
41128213 CTGCGTCACT
* *
41128223 GTCGCCTTAAAAATCATATCTTGAGTTTCAAAGCTCGAAAATCAGTTTTGTAATTTTTCCTGAAA
1 GTCGCCTTAAAAATCATAACTTGAGTTTCAAAGCTCGAAAATCAGTTTCGTAATTTTTCCTGAAA
41128288 CTAGACTCATATGTCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGCCAATTAGTACATTTA
66 CTAGACTCATATGTCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGCCAATTAGTACATTTA
* * * *
41128353 TTAGTTAAAGTCTCCCCTGTTACAGGGTCGACTACACTGACCTTCGCGCATTACAACTTGGATAT
131 TTAGTTAAAGTCTCCCATGTTACAGGGTCGACTACACTGACCTTCGCGCATTACAACTCGAATAA
41128418 CTCCCTGTACAGGGCTTCAATACTGATCCGTTTGTTTCTATAGAAACTAGACTCAAATAGGAATC
196 CTCCCTGTACAGGGCTTCAATACTGATCCGTTTGTTTCTATAGAAACTAGACTCAAATAGGAATC
41128483 TATAATATATGGCATGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAAGTCGGAAC
261 TATAATATATGGCATGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAAGTCGGAAC
* *
41128548 AGGGATCCAGAAACCGTTCTGGCCCTGTTCCGAAAACCTAAATATCTCTTAACATATAACTCATA
326 AGGGATCCAGAAACCGTTCTGGCCCTGTTCCGAAAACCCAAATATCTCTTAACATACAACTCATA
41128613 TGACCGTTTCGTTTCTTCCATATGAAATAGATTCATCAAGGTTCATTTACATAATTTATTCACTA
391 TGACCGTTTCGTTTCTTCCATATGAAATAGATTCATCAAGGTTCATTTACATAATTTATTCACTA
*
41128678 TTTAATTCCATCCTACTATTTTTAGTGATTTTTCACATCCACATCACTGCTGCTGTCAGCATCTG
456 TTTAATTCCATCCTACTATTTTTAGTGATTTTTCACATCCACATCACTGCTGCTGCCAGCATCTG
* *** ** * *
41128743 CCTTTGTGGTAGACTTTACCTATTTCATAATTTCCATGATTCAATTAGCCCTTTTTGCATACATG
521 ACTTTGTGGTAGACTTTACCTAACACATAATTTCCATGATTCAACCAGCCCTCTTTACATACATG
* * * * *
41128808 GCACAAAGTATGATCATGATTAACCATTCCAATGGCTAATCGTTTCCAAACATTTCCATACCTCT
586 GCACAAAATATAATCATGATGAACCATTCCAATGGCTAATCATTGCCAAACATTTCCATACCTCT
41128873 TAATGATCAATGTAACACCCCGAACCCGAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACAGA
651 TAATGATCAATGTAACACCCCGAACCCGAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACAGA
41128938 CTTCAAACCACTTATTGAGAATTTCCCAGACAAGCTGCCAATCTGTGTACTA
716 CTTCAAACCACTTATTGAGAATTTCCCAGACAAGCTGCCAATCTGTGTACTA
*
41128990 GTCG-CTTCAAAAATCATAACTTGAGTTTTACAA-CTCGAAAATCAGTTTCGTAATTTTTCCCTG
1 GTCGCCTT-AAAAATCATAACTTGAGTTTCA-AAGCTCGAAAATCAGTTTCGTAATTTTT-CCTG
41129053 AAACTAGACTCATAT-TCCATCTACATATTTTTTTCTAGAATTTTTGGTCGAG-CAATTAGTACA
63 AAACTAGACTCATATGTCCATCTACATATTTTTTTCTAGAATTTTTGGTCG-GCCAATTAGTACA
* *
41129116 GTTTATTAGTTAAAGTCTCCCATGTTACAGGGGTCGACTACACTGACCTTCGTGCGTTACAACTC
127 -TTTATTAGTTAAAGTCTCCCATGTTACA-GGGTCGACTACACTGACCTTCGCGCATTACAACTC
*
41129181 GAATAACTCCCTGTGCAGGGCTTCAATACTGATGCCGTTTGTTTCTATAGAAACTAGACTCAAA-
190 GAATAACTCCCTGTACAGGGCTTCAATACTGAT-CCGTTTGTTTCTATAGAAACTAGACTCAAAT
* * *
41129245 AGGAATTTATAAATATATGGTATGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTTCAAA
254 AGGAATCTAT-AATATATGGCATGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAA
*
41129310 GTCGGAACAGGGAATCCAGAAACCGTTCTGGCCCTGTTTCACGAAAACCCAAATATCTTTTAACA
318 GTCGGAACAGGG-ATCCAGAAACCGTTCTGGCCCTG-TTC-CGAAAACCCAAATATCTCTTAACA
*
41129375 TACAACTCATATGACCGTTTCGTTTCTTCCATATGAAAATGGATTCATCAAGGTTCATTTACATA
380 TACAACTCATATGACCGTTTCGTTTCTTCCATATG-AAATAGATTCATCAAGGTTCATTTACATA
* *
41129440 ATTTATTCACTATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCACATCCACGTCACTGTTG
444 ATTTATTCACTATTTAATTCCA-TCCTACTATTTTTAGTGATTTTTCACATCCACATCACTGCTG
* * *
41129505 CTGCCAGCATCT-A-TTTCTAGGGTAGACTTT-CTCTAACACATAGTTTCTATGATTCAACCA-C
508 CTGCCAGCATCTGACTTTGT--GGTAGACTTTAC-CTAACACATAATTTCCATGATTCAACCAGC
* * * * **
41129566 CC-CTTTACATATATAGTC-CAAAATATAATCATGATGACCCATTCTAATGGCTGGTCATTGCCA
570 CCTCTTTACATACAT-GGCACAAAATATAATCATGATGAACCATTCCAATGGCTAATCATTGCCA
* * *
41129629 AACATTTCCGTGCTTCTTAATGA
634 AACATTTCCATACCTCTTAATGA
41129652 GCATATACAT
Statistics
Matches: 600, Mismatches: 45, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
766 3 0.00
767 94 0.16
768 49 0.08
769 71 0.12
770 94 0.16
771 23 0.04
772 3 0.00
773 125 0.21
774 56 0.09
775 82 0.14
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (767 bp):
GTCGCCTTAAAAATCATAACTTGAGTTTCAAAGCTCGAAAATCAGTTTCGTAATTTTTCCTGAAA
CTAGACTCATATGTCCATCTACATATTTTTTTCTAGAATTTTTGGTCGGCCAATTAGTACATTTA
TTAGTTAAAGTCTCCCATGTTACAGGGTCGACTACACTGACCTTCGCGCATTACAACTCGAATAA
CTCCCTGTACAGGGCTTCAATACTGATCCGTTTGTTTCTATAGAAACTAGACTCAAATAGGAATC
TATAATATATGGCATGACTCCTAATTATCTCTGGTTAATTTATAATGAATTTCCAAAGTCGGAAC
AGGGATCCAGAAACCGTTCTGGCCCTGTTCCGAAAACCCAAATATCTCTTAACATACAACTCATA
TGACCGTTTCGTTTCTTCCATATGAAATAGATTCATCAAGGTTCATTTACATAATTTATTCACTA
TTTAATTCCATCCTACTATTTTTAGTGATTTTTCACATCCACATCACTGCTGCTGCCAGCATCTG
ACTTTGTGGTAGACTTTACCTAACACATAATTTCCATGATTCAACCAGCCCTCTTTACATACATG
GCACAAAATATAATCATGATGAACCATTCCAATGGCTAATCATTGCCAAACATTTCCATACCTCT
TAATGATCAATGTAACACCCCGAACCCGAGACCGTCGCCGGAGTCGAACACGAGGTGTTAACAGA
CTTCAAACCACTTATTGAGAATTTCCCAGACAAGCTGCCAATCTGTGTACTA
Found at i:41130329 original size:28 final size:27
Alignment explanation
Indices: 41130266--41130335 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41130256 ATAGTGAGTC
*
41130266 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
41130293 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
41130321 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41130336 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41132665 original size:40 final size:40
Alignment explanation
Indices: 41132621--41132879 Score: 295
Period size: 40 Copynumber: 6.5 Consensus size: 40
41132611 GCTCGATTGT
* * * * *
41132621 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* *
41132661 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * *
41132701 CTTCGGGACTTAACCCGGTTTTGGTAACTCTCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * *
41132741 CTTCGGGGCTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * * *
41132781 CTTCGGGGCTTAACCCGGTTTTGGTAACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
* * * * *
41132821 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGTTTTAGTAAC-TCGCACAAATGC
41132862 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
41132880 ATACCATTCA
Statistics
Matches: 193, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
40 166 0.86
41 26 0.13
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGTTTTAGTAACTCGCACAAATGC
Found at i:41135274 original size:20 final size:20
Alignment explanation
Indices: 41135249--41135311 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
41135239 TTAAAAATTC
41135249 AAAAATATTATAAAGATTAT
1 AAAAATATTATAAAGATTAT
41135269 AAAAATTATT-T-AA-ATTATT
1 AAAAA-TATTATAAAGATTA-T
* *
41135288 TAAAA-AGTATAAAGATTAT
1 AAAAATATTATAAAGATTAT
41135307 AAAAA
1 AAAAA
41135312 ATATATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 14 0.40
20 10 0.29
21 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAAATATTATAAAGATTAT
Found at i:41135276 original size:9 final size:9
Alignment explanation
Indices: 41135234--41135316 Score: 60
Period size: 9 Copynumber: 8.9 Consensus size: 9
41135224 TTAATTTTTT
*
41135234 AAATTTTAA
1 AAATTATAA
41135243 AAATTCA-AA
1 AAATT-ATAA
41135252 AATATTATAA
1 AA-ATTATAA
*
41135262 AGATTATAA
1 AAATTATAA
**
41135271 AAATTATTT
1 AAATTATAA
41135280 AAATTATTTAA
1 AAATTA--TAA
*
41135291 AAAGTATAA
1 AAATTATAA
*
41135300 AGATTATAA
1 AAATTATAA
*
41135309 AAAATATA
1 AAATTATA
41135317 TTATTTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
9 45 0.79
10 6 0.11
11 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:41135494 original size:3 final size:3
Alignment explanation
Indices: 41135486--41135517 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41135476 AAAACATGCA
41135486 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41135518 ATGAAAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41135669 original size:15 final size:15
Alignment explanation
Indices: 41135651--41135681 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41135641 CAATTTTGTG
41135651 TTAGTTTATTTTTCA
1 TTAGTTTATTTTTCA
41135666 TTAGTTTATTTTTCA
1 TTAGTTTATTTTTCA
41135681 T
1 T
41135682 ATCTTGCTTT
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:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (15 bp):
TTAGTTTATTTTTCA
Found at i:41138702 original size:14 final size:13
Alignment explanation
Indices: 41138670--41138701 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41138660 ATTTCTGGGA
41138670 TTTTTTAGCCAGT
1 TTTTTTAGCCAGT
*
41138683 TTTTTTAGCCTGT
1 TTTTTTAGCCAGT
41138696 TTTTTT
1 TTTTTT
41138702 TTTTGACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.66
Consensus pattern (13 bp):
TTTTTTAGCCAGT
Found at i:41141300 original size:21 final size:21
Alignment explanation
Indices: 41141276--41141317 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41141266 TCCAACAACC
*
41141276 AAACACTCTCATTCCAGCTCT
1 AAACACTCCCATTCCAGCTCT
*
41141297 AAACACTCCCATTCCGGCTCT
1 AAACACTCCCATTCCAGCTCT
41141318 TGTCCAGCAA
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:0.26, C:0.40, G:0.07, T:0.26
Consensus pattern (21 bp):
AAACACTCCCATTCCAGCTCT
Found at i:41156437 original size:31 final size:32
Alignment explanation
Indices: 41156373--41156460 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 32
41156363 TCTGTTTCAA
41156373 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGT-AGTGTTTG
*
41156406 GTTGCTGGACGGGAGCTGGAATGT-GTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGTAGTGTTTG
*
41156437 GTTGCTGGACAGTAGCTGGAATGT
1 GTTGCTGGACAGGAGCTGGAATGT
41156461 CAAGAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
31 29 0.56
33 23 0.44
ACGTcount: A:0.17, C:0.10, G:0.42, T:0.31
Consensus pattern (32 bp):
GTTGCTGGACAGGAGCTGGAATGTAGTGTTTG
Found at i:41157929 original size:30 final size:30
Alignment explanation
Indices: 41157895--41157951 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
41157885 TGAGAATTCC
41157895 CTTCTCCAGTGTTGCTGGTTTTGACAGTTT
1 CTTCTCCAGTGTTGCTGGTTTTGACAGTTT
41157925 CTTCTCCAGTGTTGCTGGTTTTGACAG
1 CTTCTCCAGTGTTGCTGGTTTTGACAG
41157952 ATTCAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.44
Consensus pattern (30 bp):
CTTCTCCAGTGTTGCTGGTTTTGACAGTTT
Found at i:41162850 original size:25 final size:26
Alignment explanation
Indices: 41162822--41162871 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
41162812 ATTTTATTTT
*
41162822 ATATTTTAAAATAATTCCC-ATCATA
1 ATATTTTAAAACAATTCCCAATCATA
41162847 ATATTTTAAAACAATTCCCAATCAT
1 ATATTTTAAAACAATTCCCAATCAT
41162872 TTTAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATTTTAAAACAATTCCCAATCATA
Found at i:41163809 original size:20 final size:20
Alignment explanation
Indices: 41163786--41163824 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41163776 TTATGTTTTA
* *
41163786 TTTTAACTTTTTATAACAAT
1 TTTTAACTTATAATAACAAT
*
41163806 TTTTCACTTATAATAACAA
1 TTTTAACTTATAATAACAA
41163825 CATTCATAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAACTTATAATAACAAT
Found at i:41175297 original size:40 final size:40
Alignment explanation
Indices: 41175253--41175445 Score: 189
Period size: 40 Copynumber: 4.8 Consensus size: 40
41175243 TCGAATGATG
*
41175253 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTGA-TTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTT-ACCAAA
* *
41175293 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACCAAA
* *
41175333 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACCAAA
* * * **
41175373 TCCGGGTTAACTCCCGAAGGCATTTGTGCGAGCTATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AA
* * *
41175414 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
41175446 CGCTATATCC
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 119 0.90
41 12 0.09
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAA
Found at i:41178298 original size:23 final size:23
Alignment explanation
Indices: 41178272--41178318 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41178262 ATACGAGATC
41178272 GGGTAACACTGCAGCTCGAGGTA
1 GGGTAACACTGCAGCTCGAGGTA
41178295 GGGTAACACTGCAGCTCGAGGTA
1 GGGTAACACTGCAGCTCGAGGTA
41178318 G
1 G
41178319 ACCACCCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.36, T:0.17
Consensus pattern (23 bp):
GGGTAACACTGCAGCTCGAGGTA
Found at i:41188404 original size:40 final size:40
Alignment explanation
Indices: 41188360--41188526 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
41188350 TCGAATATAA
41188360 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41188400 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41188440 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41188480 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41188519 CCGGATAT
1 CCGGATAT
41188527 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41188510 original size:80 final size:79
Alignment explanation
Indices: 41188376--41188526 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41188366 ATAATCACGT
*
41188376 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
41188441 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41188456 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
41188519 CCGGATAT
64 CCGGATAT
41188527 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41196419 original size:40 final size:40
Alignment explanation
Indices: 41196374--41196540 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
41196364 CGGAATATAA
41196374 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41196414 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41196454 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41196494 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41196533 CCGGATAT
1 CCGGATAT
41196541 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41196524 original size:80 final size:79
Alignment explanation
Indices: 41196390--41196540 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41196380 ATAATCACGT
*
41196390 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
41196455 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41196470 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
41196533 CCGGATAT
64 CCGGATAT
41196541 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41207024 original size:33 final size:33
Alignment explanation
Indices: 41206977--41207276 Score: 235
Period size: 33 Copynumber: 9.1 Consensus size: 33
41206967 TCCCAACAAA
* * *
41206977 CTCTA-TATATGTTTATTGTCCCAACAGACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* *
41207009 CTCTATTTTGTGTTTACTGTCCCAACAGACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* *
41207042 CTCTATTATGTGTTTACTGTCCTAGCGGACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* * * * * ** *
41207075 CTCTGTCATGTGTTTATTATCCTAGTGGGCTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* * *
41207108 CTTTGTGT-TGTGTTTATTGTCCCAACGGACTAT
1 CTCTAT-TATGTGTTTACTGTCCCAACGGACTAT
* * *
41207141 CTCTATTGTGTGTTTACTGTCCCAATGAACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
** * *
41207174 CTCTGCTATGTGTTTACTATCCCAGCGGACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* * * ***
41207207 CTCTATTCTATGTTTATTGTCCCAATAAACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
* * * * * * *
41207240 CTTTGTTCTATGTTTACTATCCTAATGGACTAT
1 CTCTATTATGTGTTTACTGTCCCAACGGACTAT
41207273 CTCT
1 CTCT
41207277 GTGGATGCCA
Statistics
Matches: 215, Mismatches: 50, Indels: 5
0.80 0.19 0.02
Matches are distributed among these distances:
32 6 0.03
33 209 0.97
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (33 bp):
CTCTATTATGTGTTTACTGTCCCAACGGACTAT
Found at i:41207073 original size:66 final size:66
Alignment explanation
Indices: 41206986--41207276 Score: 271
Period size: 66 Copynumber: 4.4 Consensus size: 66
41206976 ACTCTATATA
* * * * *
41206986 TGTTTATTGTCCCAACAGACTATCTCTATTTTGTGTTTACTGTCCCAACAGACTATCTCTATTAT
1 TGTTTACTGTCCCAACGGACTATCTCTATTATGTGTTTACTGTCCCAATAGACTATCTCTGTTAT
41207051 G
66 G
* * * * * * * * * * *
41207052 TGTTTACTGTCCTAGCGGACTATCTCTGTCATGTGTTTATTATCCTAGTGGGCTATCTTTGTGT-
1 TGTTTACTGTCCCAACGGACTATCTCTATTATGTGTTTACTGTCCCAATAGACTATCTCTGT-TA
41207116 TG
65 TG
* * *
41207118 TGTTTATTGTCCCAACGGACTATCTCTATTGTGTGTTTACTGTCCCAAT-GAACTATCTCTGCTA
1 TGTTTACTGTCCCAACGGACTATCTCTATTATGTGTTTACTGTCCCAATAG-ACTATCTCTGTTA
41207182 TG
65 TG
* * * * * * * *
41207184 TGTTTACTATCCCAGCGGACTATCTCTATTCTATGTTTATTGTCCCAATAAACTATCTTTGTTCT
1 TGTTTACTGTCCCAACGGACTATCTCTATTATGTGTTTACTGTCCCAATAGACTATCTCTGTTAT
*
41207249 A
66 G
* * *
41207250 TGTTTACTATCCTAATGGACTATCTCT
1 TGTTTACTGTCCCAACGGACTATCTCT
41207277 GTGGATGCCA
Statistics
Matches: 178, Mismatches: 43, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
65 2 0.01
66 175 0.98
67 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (66 bp):
TGTTTACTGTCCCAACGGACTATCTCTATTATGTGTTTACTGTCCCAATAGACTATCTCTGTTAT
G
Found at i:41207123 original size:99 final size:99
Alignment explanation
Indices: 41207003--41207278 Score: 322
Period size: 99 Copynumber: 2.8 Consensus size: 99
41206993 TGTCCCAACA
* **
41207003 GACTATCTCTATTTTGTGTTTACTGTCCCAACAGACTATCTCTATTATGTGTTTACTGTCCTAGC
1 GACTATCTCTA-TTTGTGTTTATTGTCCCAACAGACTATCTCTATTATGTGTTTACTGTCCTAAT
* * *
41207068 GGACTATCTCTGTC-ATGTGTTTATTATCCTAGTG
65 GGACTATCTCTGTCTATGTGTTTACTATCCCAGCG
* * * * * *
41207102 GGCTATCTTTGTGTTGTGTTTATTGTCCCAACGGACTATCTCTATTGTGTGTTTACTGTCCCAAT
1 GACTATCTCTAT-TTGTGTTTATTGTCCCAACAGACTATCTCTATTATGTGTTTACTGTCCTAAT
*
41207167 GAACTATCTCTG-CTATGTGTTTACTATCCCAGCG
65 GGACTATCTCTGTCTATGTGTTTACTATCCCAGCG
* * * * * * * *
41207201 GACTATCTCTATTCTATGTTTATTGTCCCAATAAACTATCTTTGTTCTATGTTTACTATCCTAAT
1 GACTATCTCTATT-TGTGTTTATTGTCCCAACAGACTATCTCTATTATGTGTTTACTGTCCTAAT
41207266 GGACTATCTCTGT
65 GGACTATCTCTGT
41207279 GGATGCCATG
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
98 3 0.02
99 143 0.98
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (99 bp):
GACTATCTCTATTTGTGTTTATTGTCCCAACAGACTATCTCTATTATGTGTTTACTGTCCTAATG
GACTATCTCTGTCTATGTGTTTACTATCCCAGCG
Found at i:41210218 original size:49 final size:50
Alignment explanation
Indices: 41209942--41210217 Score: 377
Period size: 49 Copynumber: 5.6 Consensus size: 50
41209932 AACATGTGAC
* *
41209942 TATGTGATTATGTTATCCTGTATAAGACCATATCTGGGATATGGCATCGG
1 TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGCATCGG
* * *
41209992 --TGTGATTATATGTTTCTGTATAAGACCATATCTAGGATATGGCATCGG
1 TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGCATCGG
41210040 TATGTGA-TATGTGATTCTGTATAAGACCATATCTGGGATAT-GCAATCGG
1 TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGC-ATCGG
* * *
41210089 TATGT-AATATGTGATTCTGTATAAGACCATATCTGGGATATGGCATTGA
1 TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGCATCGG
* * *
41210138 TATGTGA-TATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGG
1 TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGCATCGG
* *
41210187 T-TGTGATTATGTGACTCTGTTTAAGACCATA
1 TATGTGATTATGTGATTCTGTATAAGACCATA
41210218 GTTTTACTAT
Statistics
Matches: 201, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
48 51 0.25
49 142 0.71
50 8 0.04
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (50 bp):
TATGTGATTATGTGATTCTGTATAAGACCATATCTGGGATATGGCATCGG
Found at i:41214335 original size:79 final size:80
Alignment explanation
Indices: 41214234--41214416 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 80
41214224 ATGACTCGCT
** ** *
41214234 CAAATGCCTTCGGGACGAAGCCCGATTATAGTGGCTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCCG
* *
41214298 GGTTTAGTAACTT-GCA
64 GATATAGTAACTTAGCA
* **
41214314 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
41214378 ATATAGTCACTTAGCA
65 ATATAGTAACTTAGCA
41214394 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
41214417 GACATCATTC
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 52 0.59
80 33 0.38
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGGA
TATAGTAACTTAGCA
Found at i:41214348 original size:39 final size:40
Alignment explanation
Indices: 41214234--41214418 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
41214224 ATGACTCGCT
** ** *
41214234 CAAATGCCTTCGGGACGAAGCCC-GATTATAGTGGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTGCA
* * *
41214274 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* *
41214314 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* * * * *
41214353 CGAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTT-GCA
41214394 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41214419 CATCATTCGA
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 72 0.62
41 12 0.10
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
Found at i:41232278 original size:24 final size:24
Alignment explanation
Indices: 41232246--41232332 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
41232236 AATCTCAAAT
41232246 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
41232270 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
41232294 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
41232318 GCACTAGGTGTGCGA
1 GCACTATGTGTGCGA
41232333 ACATAATAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:41232298 original size:48 final size:48
Alignment explanation
Indices: 41232246--41232354 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 48
41232236 AATCTCAAAT
* ** *
41232246 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTAGGTGTGCGAACATAATA-A
41232294 GCACTATGTGTGCGATTTACTATGGCACTAGGTGTGCGAACATAATAA
1 GCACTATGTGTGCGATTTACTATGGCACTAGGTGTGCGAACATAATAA
41232342 GCACTATGTGTGC
1 GCACTATGTGTGC
41232355 AACGTTTGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
48 51 0.91
49 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTAGGTGTGCGAACATAATAA
Found at i:41234466 original size:33 final size:33
Alignment explanation
Indices: 41234425--41234491 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41234415 TTCTCATGAA
41234425 AACCAACTTAGAAAATATGTTTAACACACATTC
1 AACCAACTTAGAAAATATGTTTAACACACATTC
41234458 AACCAACTTAGAAAATATGTTTAACACACATTC
1 AACCAACTTAGAAAATATGTTTAACACACATTC
41234491 A
1 A
41234492 TCTTTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (33 bp):
AACCAACTTAGAAAATATGTTTAACACACATTC
Found at i:41241574 original size:40 final size:40
Alignment explanation
Indices: 41241529--41241695 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41241519 CGGAATATAA
41241529 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41241569 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41241609 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41241649 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41241688 CCGGATAT
1 CCGGATAT
41241696 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41249558 original size:40 final size:40
Alignment explanation
Indices: 41249513--41249679 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41249503 CGGAATATAA
41249513 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41249553 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41249593 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41249633 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41249672 CCGGATAT
1 CCGGATAT
41249680 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41255815 original size:24 final size:24
Alignment explanation
Indices: 41255783--41255831 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
41255773 ATATGTTCAT
41255783 AATCATGAA-TTCAGACCACAACTC
1 AATCATGAACTT-AGACCACAACTC
*
41255807 AATCATGAACTTAGACCATAACTC
1 AATCATGAACTTAGACCACAACTC
41255831 A
1 A
41255832 TGAGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (24 bp):
AATCATGAACTTAGACCACAACTC
Found at i:41259513 original size:29 final size:29
Alignment explanation
Indices: 41259481--41259610 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
41259471 ATAGTGAATC
*
41259481 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
41259510 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
41259539 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * *
41259567 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
41259597 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41259611 CAATCTTGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 20 0.22
29 50 0.56
30 17 0.19
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:41267269 original size:29 final size:29
Alignment explanation
Indices: 41267237--41267366 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
41267227 ATAGTGAATC
*
41267237 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
41267266 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
41267295 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * *
41267323 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
41267353 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41267367 CAATCTTGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 20 0.22
29 50 0.56
30 17 0.19
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:41272429 original size:29 final size:28
Alignment explanation
Indices: 41272396--41272498 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 28
41272386 GTGACGAGAT
* *
41272396 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACT-AGTGTGCGAGCTTGGAATATA
* *
41272425 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACT-AGTGTGCGAGCTTGGAATATA
* **
41272454 TGGCACTATGTGTGCGGGCTT-GAATCACG
1 TGGCACTA-GTGTGCGAGCTTGGAAT-ATA
41272483 TGGCACTAAGTGTGCG
1 TGGCACT-AGTGTGCG
41272499 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.07
29 56 0.92
30 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (28 bp):
TGGCACTAGTGTGCGAGCTTGGAATATA
Found at i:41277066 original size:28 final size:28
Alignment explanation
Indices: 41277001--41277101 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41276991 ATAGTGAATC
*
41277001 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
41277030 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41277058 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
41277088 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41277102 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41283562 original size:29 final size:29
Alignment explanation
Indices: 41283530--41283602 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
41283520 CTTCGAGCTC
*
41283530 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
41283559 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
41283588 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
41283603 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:41295851 original size:29 final size:29
Alignment explanation
Indices: 41295819--41295891 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
41295809 CTTCGAGCTC
*
41295819 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
41295848 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
41295877 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
41295892 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:41300647 original size:28 final size:28
Alignment explanation
Indices: 41300582--41300682 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
41300572 ATAGTGAATC
*
41300582 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
41300611 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41300639 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
41300669 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41300683 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41302884 original size:24 final size:23
Alignment explanation
Indices: 41302857--41302927 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
41302847 ATCATAGAAA
41302857 GTGTACATTGGCACTATGTGTGCG
1 GTGTA-ATTGGCACTATGTGTGCG
*
41302881 GTGTAGTATGGCACTATGTGTGCG
1 GTGTAAT-TGGCACTATGTGTGCG
* * *
41302905 GAGTTGATTAGCACTATGTGTGC
1 GTG-TAATTGGCACTATGTGTGC
41302928 TGATTTGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (23 bp):
GTGTAATTGGCACTATGTGTGCG
Found at i:41310777 original size:24 final size:23
Alignment explanation
Indices: 41310750--41310862 Score: 76
Period size: 24 Copynumber: 5.0 Consensus size: 23
41310740 ATCATAGAAA
41310750 GTGTACATTGGCACTATGTGTGCG
1 GTGTA-ATTGGCACTATGTGTGCG
* * *
41310774 GTGTAGTATGGCACTAAAGTGTAC-
1 GTGTAAT-TGGCACT-ATGTGTGCG
41310798 ----A-TTGGCACTATGTGTGCG
1 GTGTAATTGGCACTATGTGTGCG
*
41310816 GTGTAGTATGGCACTATGTGTGCG
1 GTGTAAT-TGGCACTATGTGTGCG
* * *
41310840 GAGTTGATTAGCACTATGTGTGC
1 GTG-TAATTGGCACTATGTGTGC
41310863 TGATTTGAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.09
18 7 0.10
19 1 0.01
20 1 0.01
22 1 0.01
23 2 0.03
24 44 0.63
25 8 0.11
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (23 bp):
GTGTAATTGGCACTATGTGTGCG
Found at i:41310806 original size:42 final size:42
Alignment explanation
Indices: 41310747--41310831 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
41310737 TTTATCATAG
41310747 AAAGTGTACATTGGCACTATGTGTGCGGTGTAGTATGGCACT
1 AAAGTGTACATTGGCACTATGTGTGCGGTGTAGTATGGCACT
41310789 AAAGTGTACATTGGCACTATGTGTGCGGTGTAGTATGGCACT
1 AAAGTGTACATTGGCACTATGTGTGCGGTGTAGTATGGCACT
41310831 A
1 A
41310832 TGTGTGCGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.31
Consensus pattern (42 bp):
AAAGTGTACATTGGCACTATGTGTGCGGTGTAGTATGGCACT
Found at i:41314207 original size:46 final size:46
Alignment explanation
Indices: 41314150--41314326 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
41314140 ATATTTGAGC
* * *
41314150 ATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAAT
1 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
* * * * *
41314196 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGGC
1 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--T
* *
41314243 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCAAAC
1 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
** * *
41314289 GCCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41314327 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 61 0.58
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
Found at i:41314259 original size:93 final size:93
Alignment explanation
Indices: 41314148--41314319 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
41314138 AGATATTTGA
* * * *
41314148 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATATCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACACCCGAGCTCATTGAGT
*
41314213 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
41314241 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCAAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACACCCGAGCTCATTGAGT
41314306 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
41314320 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACACCCGAGCTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41318173 original size:27 final size:27
Alignment explanation
Indices: 41317731--41318172 Score: 578
Period size: 27 Copynumber: 16.6 Consensus size: 27
41317721 AAAGTACTCC
41317731 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
41317758 CG-TTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
41317784 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
41317811 C-AGTTTACAGAATTATTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
41317838 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
41317865 C-ATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
41317891 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
41317918 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
41317945 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
41317972 CGATTTATAGAATTA-CGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
41317997 CTAATTTACATAATTACCATTTTACCC-
1 C-GATTTACAGAATTACCGTTTTACCCT
* *
41318024 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
41318051 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
41318078 CGATTTACA-AATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
41318104 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
41318131 -GATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
41318157 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
41318173 TAAAATACCC
Statistics
Matches: 366, Mismatches: 38, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.00
26 140 0.38
27 223 0.61
28 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:41318183 original size:53 final size:54
Alignment explanation
Indices: 41317731--41318172 Score: 571
Period size: 53 Copynumber: 8.3 Consensus size: 54
41317721 AAAGTACTCC
*
41317731 CGATTTACAGAATTACCGTTTTACCCTCG-TTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
*
41317784 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTACAGAATTATTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACTGTTTTACCCT
* * * *
41317838 TGATTTACAGAATTACTGTTTTACCCTC-ATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
** * *
41317891 CGATTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
** *
41317945 C-AGTTTACAGAATTACTATTTTACCCTCGATTTATAGAATTAC-GTTTTACCC-
1 CGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
* * * *
41317997 CTAATTTACATAATTACCATTTTACCC-CGATTTACATAATTA-TCGTTTTACCCT
1 C-GATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACT-GTTTTACCCT
* **
41318051 CGATTTATAGAATTACCGTTTTACCCTCGATTTACA-AATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
* *
41318104 CGATTTATAGAATTACTGTTTTACCCT-GATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
*
41318157 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
41318173 TAAAATACCC
Statistics
Matches: 343, Mismatches: 34, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
52 22 0.06
53 202 0.59
54 119 0.35
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (54 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
Found at i:41318199 original size:80 final size:81
Alignment explanation
Indices: 41317731--41318172 Score: 580
Period size: 80 Copynumber: 5.5 Consensus size: 81
41317721 AAAGTACTCC
*
41317731 CGATTTACAGAATTACCGTTTTACCCTCG-TTTACAGAATTACTATTTTACCCTCGATTTACAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGA
*
41317795 ATTACCGTTTTACCCT
66 ATTACTGTTTTACCCT
** * ** *
41317811 C-AGTTTACAGAATTATTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTC-ATTTATAG
1 CGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAG
*
41317874 AATTACCGTTTTACCCT
65 AATTACTGTTTTACCCT
** * *
41317891 CGATTTGTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTC-AGTTTACAG
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGA-TTTACAG
*
41317955 AATTACTATTTTACCCT
65 AATTACTGTTTTACCCT
* * * *
41317972 CGATTTATAGAATTA-CGTTTTACCC-CTAATTTACATAATTACCATTTTACCC-CGATTTACAT
1 CGATTTACAGAATTACCGTTTTACCCTC-GATTTACAGAATTACCATTTTACCCTCGATTTACAG
41318034 AATTA-TCGTTTTACCCT
65 AATTACT-GTTTTACCCT
* *
41318051 CGATTTATAGAATTACCGTTTTACCCTCGATTTACA-AATTACCATTTTACCCTCGATTTATAGA
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGA
41318115 ATTACTGTTTTACCCT
66 ATTACTGTTTTACCCT
* *
41318131 -GATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTAC
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTAC
41318173 TAAAATACCC
Statistics
Matches: 323, Mismatches: 27, Indels: 24
0.86 0.07 0.06
Matches are distributed among these distances:
78 1 0.00
79 87 0.27
80 174 0.54
81 61 0.19
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (81 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAGA
ATTACTGTTTTACCCT
Found at i:41319505 original size:9 final size:9
Alignment explanation
Indices: 41319491--41319567 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
41319481 ATTTTGATAC
41319491 ATGATATGT
1 ATGATATGT
*
41319500 ATGATATGCAC
1 ATGATATG--T
41319511 ATGATATGT
1 ATGATATGT
*
41319520 ATGATATGCAC
1 ATGATATG--T
*
41319531 ATGACATGT
1 ATGATATGT
*
41319540 ATGATATGCAC
1 ATGATATG--T
41319551 ATGATATGT
1 ATGATATGT
41319560 ATGATATG
1 ATGATATG
41319568 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:41319516 original size:11 final size:11
Alignment explanation
Indices: 41319500--41319571 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
41319490 CATGATATGT
41319500 ATGATATGCAC
1 ATGATATGCAC
*
41319511 ATGATATG--T
1 ATGATATGCAC
41319520 ATGATATGCAC
1 ATGATATGCAC
* *
41319531 ATGACATG--T
1 ATGATATGCAC
41319540 ATGATATGCAC
1 ATGATATGCAC
*
41319551 ATGATATG--T
1 ATGATATGCAC
41319560 ATGATATGCAC
1 ATGATATGCAC
41319571 A
1 A
41319572 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Done.