Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 126 of 250
Found at i:40614278 original size:28 final size:28
Alignment explanation
Indices: 40614209--40614283 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
40614199 ATAATACACA
* * * *
40614209 AATTAAAAATATAATAAAAAGTGATTAT
1 AATTAAAAATAAAATAAAATGTAAATAT
*
40614237 -ATTAAAATTGAAAATAAAATGTAAATAT
1 AATTAAAAAT-AAAATAAAATGTAAATAT
40614265 AATTAAAAATAAAA-AAAAT
1 AATTAAAAATAAAATAAAAT
40614284 ATATATTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 13 0.33
28 18 0.46
29 8 0.21
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (28 bp):
AATTAAAAATAAAATAAAATGTAAATAT
Found at i:40625466 original size:18 final size:18
Alignment explanation
Indices: 40625443--40625483 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40625433 TTTTAAAAGG
* *
40625443 AAAACAAATAAATTTTAA
1 AAAACAAATAAATCTAAA
*
40625461 AAAACAAATGAATCTAAA
1 AAAACAAATAAATCTAAA
40625479 AAAAC
1 AAAAC
40625484 TTAATGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAACAAATAAATCTAAA
Found at i:40627473 original size:17 final size:18
Alignment explanation
Indices: 40627441--40627475 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40627431 ATAATTTTTA
40627441 AATGTGTCTAAATTAATT
1 AATGTGTCTAAATTAATT
*
40627459 AATGTG-CTGAATTAATT
1 AATGTGTCTAAATTAATT
40627476 TGTGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (18 bp):
AATGTGTCTAAATTAATT
Found at i:40640513 original size:16 final size:16
Alignment explanation
Indices: 40640492--40640524 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40640482 AGGGAAAGAG
40640492 AGAAAAA-AAAAGAGAA
1 AGAAAAAGAAAAG-GAA
40640508 AGAAAAAGAAAAGGAA
1 AGAAAAAGAAAAGGAA
40640524 A
1 A
40640525 ATTTAGGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAGGAA
Found at i:40644700 original size:15 final size:15
Alignment explanation
Indices: 40644680--40644709 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40644670 TTTAATTCTT
*
40644680 TATAAATTATAAAAA
1 TATAAACTATAAAAA
40644695 TATAAACTATAAAAA
1 TATAAACTATAAAAA
40644710 ATTCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:40655649 original size:47 final size:47
Alignment explanation
Indices: 40655584--40655729 Score: 152
Period size: 47 Copynumber: 3.1 Consensus size: 47
40655574 TTCCGTATAA
*
40655584 CATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGTATAAGAC
1 CATATCTGGGATATGGCATCGGTGTGATATGTGCTACTGTATAAGAC
* * *
40655631 CATATCTGGGATATGGCATCAGTGTGATATGTGAT-CCGTATAAGAC
1 CATATCTGGGATATGGCATCGGTGTGATATGTGCTACTGTATAAGAC
** ** * **
40655677 CATGGCTGGTCTATGGCCTCGGTATGTGATATGTGACTA-TGTGCAAGAC
1 CATATCTGGGATATGGCATCGG--TGTGATATGTG-CTACTGTATAAGAC
40655726 CATA
1 CATA
40655730 ATTTTACTAT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
46 26 0.32
47 32 0.40
48 11 0.14
49 11 0.14
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (47 bp):
CATATCTGGGATATGGCATCGGTGTGATATGTGCTACTGTATAAGAC
Found at i:40655692 original size:46 final size:47
Alignment explanation
Indices: 40655509--40655712 Score: 155
Period size: 47 Copynumber: 4.3 Consensus size: 47
40655499 CATGGCAGCA
* * * *
40655509 TGTGAAATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAG
1 TGTGATATGTGA-TACCGTATAAGACCATAGCTGGGATATGGCATC-G-G
* * * * *
40655559 AAATGTGATTTGTGCTTCCGTAT-A-A-CATATCCGGGATATGGCATCGG
1 ---TGTGATATGTGATACCGTATAAGACCATAGCTGGGATATGGCATCGG
* * * *
40655606 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 TGTGATATGTGATACCGTATAAGACCATAGCTGGGATATGGCATCGG
* ** *
40655653 TGTGATATGTGAT-CCGTATAAGACCATGGCTGGTCTATGGCCTCGG
1 TGTGATATGTGATACCGTATAAGACCATAGCTGGGATATGGCATCGG
40655699 TATGTGATATGTGA
1 --TGTGATATGTGA
40655713 CTATGTGCAA
Statistics
Matches: 126, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
44 17 0.13
45 1 0.01
46 27 0.21
47 33 0.26
48 13 0.10
49 16 0.13
50 1 0.01
51 1 0.01
52 8 0.06
53 9 0.07
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (47 bp):
TGTGATATGTGATACCGTATAAGACCATAGCTGGGATATGGCATCGG
Found at i:40661080 original size:60 final size:60
Alignment explanation
Indices: 40661002--40661154 Score: 204
Period size: 59 Copynumber: 2.6 Consensus size: 60
40660992 AATTGAACCT
* *
40661002 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGGTACCAAATTGGGCT-
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGG-TA
* ** *
40661062 TAAAAAAGTTTAGGTACCAAATTAAG-AAAAAATGTCAAGTTCAGATACCAAATTAGGTA
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGTA
* *
40661121 AAAAAAAGTTTAGGTACTAAATT-AGAACAAAATA
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATA
40661155 GTAAGTTGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
58 3 0.04
59 53 0.65
60 25 0.31
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.24
Consensus pattern (60 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATACCAAGTTAAGATACCAAATTAGGTA
Found at i:40661142 original size:28 final size:28
Alignment explanation
Indices: 40661002--40661145 Score: 112
Period size: 28 Copynumber: 4.9 Consensus size: 28
40660992 AATTGAACCT
**
40661002 AAAAAAAGTTTAGGTACCAAATTAAGAAA
1 AAAAAAAGTTTAGGTACCAAATT-AGGTA
* *
40661031 AAAATACCAAGTTAAGGTACCAAATTGGGCT-
1 AAAA-A--AAGTTTAGGTACCAAATTAGG-TA
* *
40661062 TAAAAAAGTTTAGGTACCAAATTAAG-A
1 AAAAAAAGTTTAGGTACCAAATTAGGTA
* *
40661089 AAAAATGTCAAGTTCAGATACCAAATTAGGTA
1 AAAAA----AAGTTTAGGTACCAAATTAGGTA
*
40661121 AAAAAAAGTTTAGGTACTAAATTAG
1 AAAAAAAGTTTAGGTACCAAATTAG
40661146 AACAAAATAG
Statistics
Matches: 90, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
27 4 0.04
28 35 0.39
29 4 0.04
30 2 0.02
31 22 0.24
32 23 0.26
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAAAAAGTTTAGGTACCAAATTAGGTA
Found at i:40664274 original size:22 final size:22
Alignment explanation
Indices: 40664246--40664290 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
40664236 TTCAAATGAC
40664246 TATTTTAATGTATTGCTAAGCA
1 TATTTTAATGTATTGCTAAGCA
40664268 TATTTTAATGTATTGCTAAGCA
1 TATTTTAATGTATTGCTAAGCA
40664290 T
1 T
40664291 TTATACCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (22 bp):
TATTTTAATGTATTGCTAAGCA
Found at i:40671788 original size:16 final size:17
Alignment explanation
Indices: 40671755--40671789 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40671745 AGAAATAATA
*
40671755 ATATGTAAAATTTAAAT
1 ATATGTAAAATATAAAT
40671772 ATATGTAAAA-ATAAAT
1 ATATGTAAAATATAAAT
40671788 AT
1 AT
40671790 TAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
ATATGTAAAATATAAAT
Found at i:40675514 original size:21 final size:21
Alignment explanation
Indices: 40675480--40675557 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
40675470 ATGTGAAGGG
**
40675480 GGCACACGGTCGTGTGGCTGA
1 GGCACACGCCCGTGTGGCTGA
*
40675501 GGCACACGCCCGTGTGAGC-CA
1 GGCACACGCCCGTGTG-GCTGA
* ** *
40675522 GGGACACATCTGTGTGGCTGA
1 GGCACACGCCCGTGTGGCTGA
* *
40675543 GACACATGCCCGTGT
1 GGCACACGCCCGTGT
40675558 AAGCTAGGGA
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.18, C:0.28, G:0.36, T:0.18
Consensus pattern (21 bp):
GGCACACGCCCGTGTGGCTGA
Found at i:40675538 original size:42 final size:42
Alignment explanation
Indices: 40675491--40675570 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
40675481 GCACACGGTC
* *
40675491 GTGTGGCTGAGGCACACGCCCGTGTGAGCCAGGGACACATCT
1 GTGTGGCTGAGACACACGCCCGTGTAAGCCAGGGACACATCT
* *
40675533 GTGTGGCTGAGACACATGCCCGTGTAAGCTAGGGACAC
1 GTGTGGCTGAGACACACGCCCGTGTAAGCCAGGGACAC
40675571 GGCCTTGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.17
Consensus pattern (42 bp):
GTGTGGCTGAGACACACGCCCGTGTAAGCCAGGGACACATCT
Found at i:40676271 original size:15 final size:15
Alignment explanation
Indices: 40676246--40676278 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
40676236 AATTGTTTTC
40676246 AAAAATAAAAATAATA
1 AAAAATAAAAATAA-A
40676262 AAAAAT-AAAATAAA
1 AAAAATAAAAATAAA
40676276 AAA
1 AAA
40676279 CAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAATAAAAATAAA
Found at i:40679080 original size:56 final size:56
Alignment explanation
Indices: 40679010--40679122 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
40679000 GAAGAATCCC
* * *
40679010 TATAATCAAGGATTGACTCAATCCTAAAGAAAGAAAGAAATAAAATCTCATCAAAT
1 TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
* *
40679066 TATAATTAAAGATTGACCCCATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
1 TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
40679122 T
1 T
40679123 TGTCTCAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (56 bp):
TATAATCAAAGATTGACCCAATCCTAAAGAAAAAAAGAAATAAAATCTCATCAAAT
Found at i:40680489 original size:13 final size:15
Alignment explanation
Indices: 40680471--40680502 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40680461 TTATATACTA
40680471 TTTTATTA-A-TAGT
1 TTTTATTATATTAGT
40680484 TTTTATTATATTAGT
1 TTTTATTATATTAGT
40680499 TTTT
1 TTTT
40680503 GAATTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTATTATATTAGT
Found at i:40688626 original size:94 final size:94
Alignment explanation
Indices: 40688477--40688780 Score: 287
Period size: 94 Copynumber: 3.2 Consensus size: 94
40688467 TATGTGTGCT
*
40688477 AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCATGAGAGCCAGTGTAAGACATGTTTGGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCACGAGAGCCAGTGTAAGACATGTTTGGG
* * * **
40688542 GCAAGCATGGGCCTCGAGATATTTAAGCC
66 ACAAGCATCGGCCTCGACATATACAAGCC
*
40688571 AGTGTAAGACATGTCTGGGACATGCATCT-G-CATTGAG-ACGAGAGCTAGTGTAAGACATGTTT
1 AGTGTAAGACATGTCTGGGACATGCAT-TAGCCA-T-AGCACGAGAGCCAGTGTAAGACATGTTT
* * *
40688633 GGGACATGCATCGGCCTCGTCATATACAAGCT
63 GGGACAAGCATCGGCCTCGACATATACAAGCC
* * * * * * * * *
40688665 AGTGTAAGACCTGTTTGAGTCATGGCATCAACACCAATAG-ATGAGAGCCAGTGTAAGACCTGTC
1 AGTGTAAGACATGTCTGGGACAT-GCAT-TA-GCC-ATAGCACGAGAGCCAGTGTAAGACATGTT
*
40688729 TGGGACATGGCATCGGCCTCG-CTATATGA-AAGCC
62 TGGGACA-AGCATCGGCCTCGAC-ATAT-ACAAGCC
40688763 AGTGTAAGATCATGTCTG
1 AGTGTAAGA-CATGTCTG
40688781 AGGCATGGCG
Statistics
Matches: 174, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
93 2 0.01
94 95 0.55
95 8 0.05
97 30 0.17
98 31 0.18
99 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATTAGCCATAGCACGAGAGCCAGTGTAAGACATGTTTGGG
ACAAGCATCGGCCTCGACATATACAAGCC
Found at i:40688638 original size:46 final size:45
Alignment explanation
Indices: 40688477--40688644 Score: 144
Period size: 46 Copynumber: 3.6 Consensus size: 45
40688467 TATGTGTGCT
40688477 AGTGTAAGACATGTCTGGGACATGCAT-TAGCCA-T-AGCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCT-G-CATTGAG-A-GAGAGCC
* * * ** * * * *
40688523 AGTGTAAGACATGTTTGGGGCAAGCATGGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCTGCATTGAGAGA---GAGCC
*
40688571 AGTGTAAGACATGTCTGGGACATGCATCTGCATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCTGCATTGAGA-GAGAGCC
*
40688617 AGTGTAAGACATGTTTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
40688645 GGCCTCGTCA
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
45 2 0.02
46 56 0.58
47 2 0.02
48 35 0.36
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCTGCATTGAGAGAGAGCC
Found at i:40690453 original size:14 final size:14
Alignment explanation
Indices: 40690434--40690465 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40690424 GGCTCCCGCT
40690434 GACCTCATCTAAGA
1 GACCTCATCTAAGA
40690448 GACCTCATCTAAGA
1 GACCTCATCTAAGA
40690462 GACC
1 GACC
40690466 GAGAGAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (14 bp):
GACCTCATCTAAGA
Found at i:40695132 original size:30 final size:30
Alignment explanation
Indices: 40695093--40695149 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40695083 ATCGATTTTC
**
40695093 AAGTATAGGGTTAAAATGGTCATTTTGTGA
1 AAGTATAGGGGCAAAATGGTCATTTTGTGA
*
40695123 AAGTCTAGGGGCAAAATGGTCATTTTG
1 AAGTATAGGGGCAAAATGGTCATTTTG
40695150 CCCAATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (30 bp):
AAGTATAGGGGCAAAATGGTCATTTTGTGA
Found at i:40695544 original size:48 final size:45
Alignment explanation
Indices: 40695487--40695655 Score: 144
Period size: 48 Copynumber: 3.6 Consensus size: 45
40695477 TGATATGTGT
* *
40695487 GCTAATGTAAGACATGTCTGGGACATGCATGGGACTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCAT-CGACTCGAGATA--TAA
* * * * * * *
40695535 GCCAGTGTAAGACATATCTAGGAAATGCATCTG-CATTGAGACGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GAC-TCGAGA-TATAA
* *
40695581 GCTAGTGTAAGACATGTCTGGGACATGCATCAACCTCGTGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGA-CTCGAGATAT--AA
40695629 GCTAGTGTAAGACATGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
40695656 GCGTTAGCTT
Statistics
Matches: 95, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
45 1 0.01
46 32 0.34
47 2 0.02
48 59 0.62
49 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATATAA
Found at i:40695609 original size:46 final size:46
Alignment explanation
Indices: 40695533--40695655 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 46
40695523 CGAGATATTT
* * * * **
40695533 AAGCCAGTGTAAGACATATCTAGGAAATGCATCTGCAT-TG-AGAC
1 AAGCTAGTGTAAGACATGTCTGGGACATGCATCAACATCTGAAGAC
* *
40695577 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAACCTCGTGATATAC
1 -A-AGCTAGTGTAAGACATGTCTGGGACATGCATCAACATC-TGA-AGAC
40695627 AAGCTAGTGTAAGACATGTCTGGGACATG
1 AAGCTAGTGTAAGACATGTCTGGGACATG
40695656 GCGTTAGCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
45 1 0.02
46 30 0.46
48 30 0.46
49 1 0.02
50 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (46 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCAACATCTGAAGAC
Found at i:40700099 original size:24 final size:21
Alignment explanation
Indices: 40700053--40700093 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40700043 CTGCTCTGCT
40700053 CTGCCTCCCTCGCTGCTGCCG
1 CTGCCTCCCTCGCTGCTGCCG
*
40700074 CTGCCTCCCTCTCTGCTGCC
1 CTGCCTCCCTCGCTGCTGCC
40700094 TCCGCTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.54, G:0.20, T:0.27
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCTGCCG
Found at i:40705541 original size:9 final size:9
Alignment explanation
Indices: 40705527--40705598 Score: 69
Period size: 9 Copynumber: 8.2 Consensus size: 9
40705517 TAAGTACAAT
40705527 TAAGTTATG
1 TAAGTTATG
40705536 TAAGTTATG
1 TAAGTTATG
* * *
40705545 ATATGATATA
1 -TAAGTTATG
*
40705555 T-ATTTATG
1 TAAGTTATG
40705563 T-A-TTATG
1 TAAGTTATG
40705570 TAAGTTATG
1 TAAGTTATG
*
40705579 TAAATTATG
1 TAAGTTATG
40705588 TAAGTTATG
1 TAAGTTATG
40705597 TA
1 TA
40705599 TTATGTACGA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 33 0.65
10 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:40705569 original size:34 final size:34
Alignment explanation
Indices: 40705531--40705605 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
40705521 TACAATTAAG
* *
40705531 TTATGTAAGTTATG-ATATGATATATATTTATGTA
1 TTATGTAAGTTATGTAAATGATATA-AGTTATGTA
* *
40705565 TTATGTAAGTTATGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAATGATATAAGTTATGTA
40705599 TTATGTA
1 TTATGTA
40705606 CGACATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 29 0.81
35 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAATGATATAAGTTATGTA
Found at i:40705745 original size:9 final size:9
Alignment explanation
Indices: 40705731--40705871 Score: 66
Period size: 9 Copynumber: 15.7 Consensus size: 9
40705721 TGTGTTAATT
40705731 TTATGTAAA
1 TTATGTAAA
*
40705740 TTATGTAAG
1 TTATGTAAA
40705749 TTATG-AAA
1 TTATGTAAA
*
40705757 TTTGATCTTTAAA
1 -TT-A--TGTAAA
*
40705770 TTATGTAAG
1 TTATGTAAA
*
40705779 TCATGT--A
1 TTATGTAAA
40705786 TTATGTAAGA
1 TTATGTAA-A
40705796 -TATGT--A
1 TTATGTAAA
*
40705802 TTATGTAAG
1 TTATGTAAA
40705811 TTATG-AAA
1 TTATGTAAA
*
40705819 TTCAAACTTTAAA
1 TT---A-TGTAAA
*
40705832 TTATGTAAG
1 TTATGTAAA
40705841 TTATGT--A
1 TTATGTAAA
40705848 TTATGTAAA
1 TTATGTAAA
*
40705857 TTAAGTAAA
1 TTATGTAAA
40705866 TTATGT
1 TTATGT
40705872 GAGTTGCTGG
Statistics
Matches: 98, Mismatches: 16, Indels: 36
0.65 0.11 0.24
Matches are distributed among these distances:
6 1 0.01
7 16 0.16
8 6 0.06
9 58 0.59
10 3 0.03
11 2 0.02
12 4 0.04
13 8 0.08
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (9 bp):
TTATGTAAA
Found at i:40705770 original size:30 final size:30
Alignment explanation
Indices: 40705736--40705845 Score: 100
Period size: 30 Copynumber: 3.6 Consensus size: 30
40705726 TAATTTTATG
*
40705736 TAAATTATGTAAGTTATGAAATTTGATCTT
1 TAAATTATGTAAGTTATGAAATTAGATCTT
* * * *
40705766 TAAATTATGTAAGTCATGTATTATGTAAGATATG
1 TAAATTATGTAAGTTATG-A-AAT-T-AGATCTT
*
40705800 T--ATTATGTAAGTTATGAAATTCA-AACTT
1 TAAATTATGTAAGTTATGAAATT-AGATCTT
40705828 TAAATTATGTAAGTTATG
1 TAAATTATGTAAGTTATG
40705846 TATTATGTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.05
29 2 0.03
30 34 0.54
31 2 0.03
32 16 0.25
33 1 0.02
34 5 0.08
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTAGATCTT
Found at i:40705815 original size:16 final size:16
Alignment explanation
Indices: 40705769--40705855 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
40705759 TGATCTTTAA
*
40705769 ATTATGTAAGTCATGT
1 ATTATGTAAGTTATGT
*
40705785 ATTATGTAAGATATGT
1 ATTATGTAAGTTATGT
*
40705801 ATTATGTAAGTTATGA
1 ATTATGTAAGTTATGT
* ** * **
40705817 AAT-TCAAACTT-TAA
1 ATTATGTAAGTTATGT
40705831 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
40705847 ATTATGTAA
1 ATTATGTAA
40705856 ATTAAGTAAA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
14 4 0.07
15 10 0.19
16 40 0.74
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:40705815 original size:62 final size:62
Alignment explanation
Indices: 40705739--40705855 Score: 198
Period size: 62 Copynumber: 1.9 Consensus size: 62
40705729 TTTTATGTAA
** *
40705739 ATTATGTAAGTTATGAAATTTGATCTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
1 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
*
40705801 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAA
40705856 ATTAAGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (62 bp):
ATTATGTAAGTTATGAAATTCAAACTTTAAATTATGTAAGTCATGTATTATGTAAGATATGT
Found at i:40706247 original size:99 final size:99
Alignment explanation
Indices: 40705981--40706344 Score: 642
Period size: 99 Copynumber: 3.7 Consensus size: 99
40705971 AATAAAATAG
40705981 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
1 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
* *
40706046 ATTGAAAATATTTTTCGTGATTCAAA-AAAATGA
66 ATTGAAATTATTTTTCGTGATTCAAATTAAATGA
* *
40706079 AATATTTACAATAAAACTTTGAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
1 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
40706144 ATTGAAATTATTTTTCGTGATTCAAATTAAATGA
66 ATTGAAATTATTTTTCGTGATTCAAATTAAATGA
* *
40706178 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAAATAGGTAATGTTAAAATAAAATAAAAC
1 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
40706243 ATTGAAATTATCTTTT-GTGATTCAAATTAAATGA
66 ATTGAAATTAT-TTTTCGTGATTCAAATTAAATGA
*
40706277 AATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
1 AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
40706342 ATT
66 ATT
40706345 TAAAATAAAA
Statistics
Matches: 253, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
98 88 0.35
99 161 0.64
100 4 0.02
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (99 bp):
AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAAT
ATTGAAATTATTTTTCGTGATTCAAATTAAATGA
Found at i:40706292 original size:56 final size:55
Alignment explanation
Indices: 40706226--40706406 Score: 166
Period size: 56 Copynumber: 3.1 Consensus size: 55
40706216 ATAGGTAATG
* * *
40706226 TTAAAATAAAATAAAACATTGAAATTATCTTTTGTGATTCAAATTAAATGAAATAT
1 TTAAAATAAAATAAAACATT-AAATTATATTTTGTGATTCAAATAAAATAAAATAT
* ** * *
40706282 TTAAAATAAAACTTTAAATACGATTTAATT-TAATTAGGTAATGTTAAAATAAAATAAAATAT
1 TTAAAATAAAA---TAAA-AC-ATTAAATTAT-ATTTTGTGA--TTCAAATAAAATAAAATAT
* * *
40706344 TTAAAATAAAATAAAATATTAACATTATTTTTTGTGATTCAAAAAAAATAAAATAT
1 TTAAAATAAAATAAAACATTAA-ATTATATTTTGTGATTCAAATAAAATAAAATAT
40706400 TTAAAAT
1 TTAAAAT
40706407 GAAACTTTAA
Statistics
Matches: 99, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
56 35 0.35
57 4 0.04
58 9 0.09
59 10 0.10
60 11 0.11
61 3 0.03
62 27 0.27
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (55 bp):
TTAAAATAAAATAAAACATTAAATTATATTTTGTGATTCAAATAAAATAAAATAT
Found at i:40706342 original size:62 final size:60
Alignment explanation
Indices: 40706266--40706458 Score: 193
Period size: 62 Copynumber: 3.2 Consensus size: 60
40706256 TTTGTGATTC
* *
40706266 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATAC-ATTTAATTTAATTAGGTAAT-TTA
** * * *
40706328 AAATAAAATAAAATATTTAAAATAAAA-TAAAATATTAACA-TT-ATTT--TT-TGTGATTCA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAA-A-T-ACATTTAATTTAATTAGGTAATTTA
* *
40706385 AAA-AAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAATTTGA
1 AAATAAAATAAAATATTTAAAATAAAACTTTAAATA-CATTTAATTTAATTAGGTAATTT-A
40706446 AAATAAAATAAAA
1 AAATAAAATAAAA
40706459 GATAACAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
54 1 0.01
55 2 0.02
56 25 0.24
57 12 0.11
58 4 0.04
59 4 0.04
60 5 0.05
61 11 0.10
62 37 0.35
63 2 0.02
64 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.37
Consensus pattern (60 bp):
AAATAAAATAAAATATTTAAAATAAAACTTTAAATACATTTAATTTAATTAGGTAATTTA
Found at i:40706347 original size:19 final size:19
Alignment explanation
Indices: 40706325--40706363 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40706315 TTAGGTAATG
40706325 TTAAAATAAAATAAAATAT
1 TTAAAATAAAATAAAATAT
40706344 TTAAAATAAAATAAAATAT
1 TTAAAATAAAATAAAATAT
40706363 T
1 T
40706364 AACATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAATAAAATAAAATAT
Found at i:40706356 original size:118 final size:118
Alignment explanation
Indices: 40706226--40706458 Score: 362
Period size: 118 Copynumber: 2.0 Consensus size: 118
40706216 ATAGGTAATG
** *
40706226 TTAAAATAAAATAAAACATTGAA-ATTATCTTTTGTGATTCAAATTAAATGAAATATTTAAAATA
1 TTAAAATAAAATAAAACATT-AACATTATCTTTTGTGATTCAAAAAAAATAAAATATTTAAAATA
*
40706290 AAACTTTAAATACGATTTAATTTAATTAGGTAATGTT-AAAATAAAATAAAATAT
65 AAACTTTAAATACAATTTAATTTAATTAGGTAAT-TTGAAAATAAAATAAAATAT
* * *
40706344 TTAAAATAAAATAAAATATTAACATTATTTTTTGTGATTCAAAAAAAATAAAATATTTAAAATGA
1 TTAAAATAAAATAAAACATTAACATTATCTTTTGTGATTCAAAAAAAATAAAATATTTAAAATAA
*
40706409 AACTTTAAATATAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAA
66 AACTTTAAATACAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAA
40706459 GATAACAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
117 4 0.04
118 101 0.96
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.37
Consensus pattern (118 bp):
TTAAAATAAAATAAAACATTAACATTATCTTTTGTGATTCAAAAAAAATAAAATATTTAAAATAA
AACTTTAAATACAATTTAATTTAATTAGGTAATTTGAAAATAAAATAAAATAT
Found at i:40709410 original size:12 final size:12
Alignment explanation
Indices: 40709393--40709418 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40709383 CAAGTTAAAT
40709393 TAAGTCACCAAA
1 TAAGTCACCAAA
40709405 TAAGTCACCAAA
1 TAAGTCACCAAA
40709417 TA
1 TA
40709419 TGCAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAGTCACCAAA
Found at i:40712388 original size:40 final size:40
Alignment explanation
Indices: 40712303--40712388 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
40712293 CTTTTGAGGT
* * * *
40712303 GATCTTTAGCGGCGTTTTTCAGAAAGCGCTGCTAATGCTC
1 GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
*
40712343 TATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
1 GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
40712383 GATCTT
1 GATCTT
40712389 CTAAATAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (40 bp):
GATCTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAAAGATC
Found at i:40712581 original size:40 final size:40
Alignment explanation
Indices: 40712523--40712646 Score: 176
Period size: 40 Copynumber: 3.1 Consensus size: 40
40712513 AACTTTTATT
** * *
40712523 GCGGTGCTTTTTAAAAAACGCCACTAATGCTTGATCTTTA
1 GCGGTGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
* *
40712563 GCGGTGCTTTTGGGAAAACGCCGCTACTGCTTTATCTTTA
1 GCGGTGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
* *
40712603 GCGGCGCTTTTGGTAAAACGCCGCTAATGCTTTATCTTTA
1 GCGGTGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
40712643 GCGG
1 GCGG
40712647 CATTTTCGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (40 bp):
GCGGTGCTTTTGGAAAAACGCCGCTAATGCTTTATCTTTA
Found at i:40712647 original size:40 final size:40
Alignment explanation
Indices: 40712537--40712647 Score: 177
Period size: 40 Copynumber: 2.8 Consensus size: 40
40712527 TGCTTTTTAA
* * *
40712537 AAAACGCCACTAATGCTTGATCTTTAGCGGTGCTTTTGGG
1 AAAACGCCGCTAATGCTTTATCTTTAGCGGCGCTTTTGGG
* *
40712577 AAAACGCCGCTACTGCTTTATCTTTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAATGCTTTATCTTTAGCGGCGCTTTTGGG
40712617 AAAACGCCGCTAATGCTTTATCTTTAGCGGC
1 AAAACGCCGCTAATGCTTTATCTTTAGCGGC
40712648 ATTTTCGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (40 bp):
AAAACGCCGCTAATGCTTTATCTTTAGCGGCGCTTTTGGG
Found at i:40712669 original size:40 final size:38
Alignment explanation
Indices: 40712536--40712670 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 38
40712526 GTGCTTTTTA
* *
40712536 AAAAACGCCACTAATGCTTGATCTTTAGCGGTGCTTTTGG
1 AAAAACGCCGCTAATGCTTTATCTTTAGC-G-GCTTTTGG
* *
40712576 GAAAACGCCGCTACTGCTTTATCTTTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAATGCTTTATCTTTAGC-G-GCTTTTGG
* *
40712616 TAAAACGCCGCTAATGCTTTATCTTTAGCGGCATTTTCG
1 AAAAACGCCGCTAATGCTTTATCTTTAGCGGC-TTTTGG
*
40712655 AAAAAGCGCTGCTAAT
1 AAAAA-CGCCGCTAAT
40712671 TCTCGATCTA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 2 0.02
39 10 0.12
40 71 0.86
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (38 bp):
AAAAACGCCGCTAATGCTTTATCTTTAGCGGCTTTTGG
Found at i:40712687 original size:80 final size:80
Alignment explanation
Indices: 40712519--40712688 Score: 175
Period size: 80 Copynumber: 2.1 Consensus size: 80
40712509 GTTCAACTTT
* * * *
40712519 TATTGCGGTGCTTTTTAAAAAACGCCACTAATGCTTGATCTTTAGCGGTGCTTTTGGGAAAACGC
1 TATTGCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCGGTGCTTTTCGAAAAACGC
* **
40712584 CGCTACTGCTTTATC
66 CGCTAATGCTCGATC
** * *
40712599 T-TTAGCGGCGCTTTTGGTAAAACGCCGCTAATGCTTTATCTTTAGC-G-GCATTTTCGAAAAAG
1 TATT-GCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCGGTGC-TTTTCGAAAAA-
* *
40712661 CGCTGCTAATTCTCGATC
63 CGCCGCTAATGCTCGATC
40712679 TATTGCGGCG
1 TATTGCGGCG
40712689 TTTGTTTCAT
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
78 2 0.03
79 12 0.16
80 57 0.78
81 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (80 bp):
TATTGCGGCGCTTTTGAAAAAACGCCACTAATGCTTGATCTTTAGCGGTGCTTTTCGAAAAACGC
CGCTAATGCTCGATC
Found at i:40716367 original size:20 final size:20
Alignment explanation
Indices: 40716319--40716369 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
40716309 TATCAAAATA
* *
40716319 ACACGGGCATGTACCTGTAT
1 ACACGGGCGTGAACCTGTAT
40716339 ACACGGGCGTGAACCTGTAT
1 ACACGGGCGTGAACCTGTAT
40716359 ACACGGGCGTG
1 ACACGGGCGTG
40716370 GGAGGAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (20 bp):
ACACGGGCGTGAACCTGTAT
Found at i:40722528 original size:22 final size:22
Alignment explanation
Indices: 40722475--40722529 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
40722465 GAATAGTACC
40722475 ACACGCCCGTGTGGCTTGTGTG
1 ACACGCCCGTGTGGCTTGTGTG
**
40722497 ACACATCCGTGTGGC-TGATGTG
1 ACACGCCCGTGTGGCTTG-TGTG
40722519 ACACGCCCGTG
1 ACACGCCCGTG
40722530 AAGGGCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.24
Consensus pattern (22 bp):
ACACGCCCGTGTGGCTTGTGTG
Found at i:40734364 original size:27 final size:27
Alignment explanation
Indices: 40734334--40734385 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
40734324 TACCCTCAAC
40734334 TTGTAAAATTACCAAAATACCCCTGGT
1 TTGTAAAATTACCAAAATACCCCTGGT
40734361 TTGTAAAATTACCAAAATACCCCTG
1 TTGTAAAATTACCAAAATACCCCTG
40734386 TAGGGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCCTGGT
Found at i:40734397 original size:27 final size:27
Alignment explanation
Indices: 40734340--40734544 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
40734330 CAACTTGTAA
* ** *
40734340 AATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
*
40734367 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
40734394 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
40734421 AGTTAGCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
40734448 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
40734475 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
40734502 AAATACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
40734529 AATTACCGAGATACCC
1 AATTACCGAAATACCC
40734545 TTGTGGGCAA
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 2 0.01
27 152 0.99
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:40734671 original size:16 final size:16
Alignment explanation
Indices: 40734650--40734680 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40734640 CAAATATGGG
*
40734650 CATGACATTTTGCATA
1 CATGACATGTTGCATA
40734666 CATGACATGTTGCAT
1 CATGACATGTTGCAT
40734681 GGGTGGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:40738754 original size:19 final size:20
Alignment explanation
Indices: 40738720--40738757 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40738710 AGTCCTTACA
40738720 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
40738740 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
40738758 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:40746144 original size:20 final size:21
Alignment explanation
Indices: 40746119--40746169 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
40746109 GTCCTTACAT
40746119 TAAATTAACCTTAATT-AATC
1 TAAATTAACCTTAATTAAATC
*
40746139 TAAATTTA-CTTAATTAAAATC
1 TAAATTAACCTTAATT-AAATC
40746160 T-AATTAACCT
1 TAAATTAACCT
40746170 CTCACTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.27
20 12 0.46
21 7 0.27
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTAACCTTAATTAAATC
Found at i:40750300 original size:47 final size:46
Alignment explanation
Indices: 40750214--40750313 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
40750204 TATCTTAATC
* *
40750214 TAAGACACATTAAAAAGCTGTACTTATTATAACATATTAATTAAACT
1 TAAGACACATTAAAAAGCTGTACATAATATAACATATTAA-TAAACT
* * *
40750261 TAAGACACATTAAAATGTTGTA-ATAAT-TAACATCCATTAATAGACT
1 TAAGACACATTAAAAAGCTGTACATAATATAACAT--ATTAATAAACT
40750307 TAAGACA
1 TAAGACA
40750314 TATTTAAGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 6 0.13
46 15 0.33
47 25 0.54
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (46 bp):
TAAGACACATTAAAAAGCTGTACATAATATAACATATTAATAAACT
Found at i:40754240 original size:10 final size:10
Alignment explanation
Indices: 40754141--40754407 Score: 79
Period size: 10 Copynumber: 27.8 Consensus size: 10
40754131 TATAAAAGTC
40754141 ATAAAAAA-T
1 ATAAAAAATT
*
40754150 AT-AAAAATC
1 ATAAAAAATT
*
40754159 ATAAAATATT
1 ATAAAAAATT
*
40754169 AGTAAAATATT
1 A-TAAAAAATT
* **
40754180 TTAAAAAAAA
1 ATAAAAAATT
**
40754190 ATTAAAAAGCT
1 A-TAAAAAATT
*
40754201 ATAAAATA-T
1 ATAAAAAATT
* *
40754210 ATTAAAGATT
1 ATAAAAAATT
40754220 -TAGATAAAATT
1 ATA-A-AAAATT
40754231 ATAAAAAATT
1 ATAAAAAATT
* *
40754241 CATAGAAACTT
1 -ATAAAAAATT
* **
40754252 AT-TAATTTT
1 ATAAAAAATT
*
40754261 ATAAAAACTT
1 ATAAAAAATT
40754271 AT-AAAAATT
1 ATAAAAAATT
*
40754280 ATAAACAA-T
1 ATAAAAAATT
* *
40754289 CTAATAAATT
1 ATAAAAAATT
40754299 ATAAAAAAAATT
1 AT--AAAAAATT
40754311 -T-AAAAATT
1 ATAAAAAATT
40754319 CAT-AAAAATT
1 -ATAAAAAATT
* *
40754329 GT-AAATATT
1 ATAAAAAATT
*
40754338 ATAATAAATT
1 ATAAAAAATT
*
40754348 AT-AAAAGTT
1 ATAAAAAATT
*
40754357 ATAATAAATT
1 ATAAAAAATT
40754367 AT-----ATT
1 ATAAAAAATT
*
40754372 ATGAAAAATT
1 ATAAAAAATT
40754382 -T-AAAAA-T
1 ATAAAAAATT
40754389 ATATAAAAATT
1 ATA-AAAAATT
40754400 ATAAAAAA
1 ATAAAAAA
40754408 AGTCATTTAT
Statistics
Matches: 190, Mismatches: 41, Indels: 53
0.67 0.14 0.19
Matches are distributed among these distances:
5 5 0.03
7 1 0.01
8 18 0.09
9 48 0.25
10 74 0.39
11 35 0.18
12 9 0.05
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:40754276 original size:9 final size:9
Alignment explanation
Indices: 40754225--40754406 Score: 117
Period size: 10 Copynumber: 19.4 Consensus size: 9
40754215 AGATTTAGAT
40754225 AAAATTATAA
1 AAAATTAT-A
40754235 AAAATTCATA
1 AAAATT-ATA
* *
40754245 GAAACTTATT
1 -AAAATTATA
**
40754255 AATTTTATA
1 AAAATTATA
40754264 AAAACTTATA
1 AAAA-TTATA
40754274 AAAATTATA
1 AAAATTATA
40754283 AACAATCTA-A
1 AA-AAT-TATA
*
40754293 TAAATTATAAAA
1 AAAATTAT---A
40754305 AAAATT-TA
1 AAAATTATA
40754313 AAAATTCATA
1 AAAATT-ATA
*
40754323 AAAATTGTA
1 AAAATTATA
*
40754332 AATATTATA
1 AAAATTATA
40754341 ATAAATTATA
1 A-AAATTATA
*
40754351 AAAGTTATA
1 AAAATTATA
40754360 ATAAATTAT-
1 A-AAATTATA
40754369 ---ATTATGA
1 AAAATTAT-A
40754376 AAAATT-TA
1 AAAATTATA
40754384 AAAATATATA
1 AAAAT-TATA
40754394 AAAATTATA
1 AAAATTATA
40754403 AAAA
1 AAAA
40754407 AAGTCATTTA
Statistics
Matches: 137, Mismatches: 15, Indels: 41
0.71 0.08 0.21
Matches are distributed among these distances:
5 5 0.04
8 15 0.11
9 46 0.34
10 55 0.40
11 10 0.07
12 6 0.04
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:40754281 original size:19 final size:18
Alignment explanation
Indices: 40754130--40754406 Score: 120
Period size: 19 Copynumber: 14.5 Consensus size: 18
40754120 TTCATTTTTC
* *
40754130 TTATAAAAGTCATAAAAA
1 TTATAAAAATTATAAAAA
* *
40754148 ATATAAAAATCATAAAATA
1 TTATAAAAATTATAAAA-A
*
40754167 TTAGTAAAATATTTTAAAAAA
1 TTA-TAAAA-ATTAT-AAAAA
** *
40754188 AAATTAAAAAGCTAT-AAAA
1 TTA-TAAAAA-TTATAAAAA
* *
40754207 TATATTAAAGATTTAGATAAAA
1 T-TA-TAAA-AATTATA-AAAA
*
40754229 TTATAAAAAATTCATAGAAAC
1 TTAT-AAAAATT-ATA-AAAA
* **
40754250 TTATTAATTTTATAAAAA
1 TTATAAAAATTATAAAAA
40754268 CTTATAAAAATTATAAACAA
1 -TTATAAAAATTATAAA-AA
*
40754288 TCTA-ATAAATTATAAAAAAAA
1 T-TATAAAAATTAT---AAAAA
40754309 TT-TAAAAATTCATAAAAA
1 TTATAAAAATT-ATAAAAA
* *
40754327 TTGTAAATATTATAATAAA
1 TTATAAAAATTATAA-AAA
*
40754346 TTATAAAAGTTATAATAAA
1 TTATAAAAATTATAA-AAA
40754365 TTAT----ATTATGAAAAA
1 TTATAAAAATTAT-AAAAA
40754380 TT-TAAAAATATATAAAAA
1 TTATAAAAAT-TATAAAAA
40754398 TTATAAAAA
1 TTATAAAAA
40754407 AAGTCATTTA
Statistics
Matches: 198, Mismatches: 33, Indels: 55
0.69 0.12 0.19
Matches are distributed among these distances:
14 1 0.01
15 9 0.05
16 2 0.01
18 38 0.19
19 71 0.36
20 33 0.17
21 32 0.16
22 12 0.06
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
TTATAAAAATTATAAAAA
Found at i:40754381 original size:34 final size:33
Alignment explanation
Indices: 40754306--40754402 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 33
40754296 ATTATAAAAA
40754306 AAATTTAAAAAT-TCATAAAAATTGTAAATATTATAAT
1 AAATTTAAAAATAT-ATAAAAA-T-T--ATATTATAAT
*
40754343 AAATTATAAAAGT-TATAATAAATTATATTATGAA-
1 AAATT-TAAAAATATATAA-AAATTATATTAT-AAT
40754377 AAATTTAAAAATATATAAAAATTATA
1 AAATTTAAAAATATATAAAAATTATA
40754403 AAAAAAGTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
33 14 0.26
34 17 0.31
35 2 0.04
36 1 0.02
37 10 0.19
38 10 0.19
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (33 bp):
AAATTTAAAAATATATAAAAATTATATTATAAT
Found at i:40754393 original size:24 final size:24
Alignment explanation
Indices: 40754345--40754403 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 24
40754335 ATTATAATAA
*
40754345 ATTATAAAAGTTATAATAAATTAT
1 ATTATAAAAATTATAATAAATTAT
40754369 ATTATGAAAAATT-T-A-AAA--AT
1 ATTAT-AAAAATTATAATAAATTAT
40754389 A-TATAAAAATTATAA
1 ATTATAAAAATTATAA
40754404 AAAAAGTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 4 0.13
22 3 0.10
23 1 0.03
24 6 0.19
25 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
ATTATAAAAATTATAATAAATTAT
Found at i:40762876 original size:38 final size:38
Alignment explanation
Indices: 40762834--40762913 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
40762824 CAAGTGTTTT
40762834 TCATGTTCAACAATATGAACACACATTATTATAATCTA
1 TCATGTTCAACAATATGAACACACATTATTATAATCTA
40762872 TCATGTTCAACAATATGAACACACATTATTATAATCTA
1 TCATGTTCAACAATATGAACACACATTATTATAATCTA
40762910 TCAT
1 TCAT
40762914 AATTTCATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (38 bp):
TCATGTTCAACAATATGAACACACATTATTATAATCTA
Found at i:40763651 original size:42 final size:42
Alignment explanation
Indices: 40763534--40763689 Score: 215
Period size: 42 Copynumber: 3.7 Consensus size: 42
40763524 TACCAAACCA
* * *
40763534 ATGCCATATCCCAGATATGGTCTTACATGTAAATCTCGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATATCG
* *
40763577 ATGCCAATAGCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
40763620 ATGCCATATCTCAGATATTGTCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
40763662 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
40763690 ATAGTCTCGA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
42 56 0.56
43 23 0.23
44 21 0.21
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:40774505 original size:25 final size:24
Alignment explanation
Indices: 40774477--40774528 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
40774467 ATTCTAACAT
40774477 TATATTAAATT-GATAATAATTAATA
1 TATATTAAATTGGAT-ATAATT-ATA
*
40774502 TATATTATATTGGATATAATTATA
1 TATATTAAATTGGATATAATTATA
40774526 TAT
1 TAT
40774529 TAATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 16 0.64
26 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (24 bp):
TATATTAAATTGGATATAATTATA
Found at i:40774645 original size:31 final size:30
Alignment explanation
Indices: 40774584--40774646 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
40774574 AATGCCTGAA
* * * *
40774584 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAAAGGCAACCAAATTTT
40774614 AATATTTACAAAAAAAGAGCAACCAAATTTT
1 AATATTTACAAAAAAAG-GCAACCAAATTTT
40774645 AA
1 AA
40774647 AAATTGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (30 bp):
AATATTTACAAAAAAAGGCAACCAAATTTT
Found at i:40777495 original size:46 final size:46
Alignment explanation
Indices: 40777445--40777618 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
40777435 GTTGAGCATT
40777445 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
* * *
40777491 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGT-AACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G--TC
* * *
40777538 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
* *
40777584 CGAGCTCGTTGATTTGAGTCCGAGTTCACTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40777619 GTGGGTTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTC
Found at i:40777604 original size:93 final size:93
Alignment explanation
Indices: 40777440--40777610 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40777430 GGATGGTTGA
* * * *
40777440 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40777505 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
40777533 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGATT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40777598 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40777611 ACTTATGGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:40786480 original size:25 final size:28
Alignment explanation
Indices: 40786443--40786500 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
40786433 TAAATCACAA
*
40786443 AAAAAAATCTAAA-ACTTAAT-AAAAGAG
1 AAAAAAA-CTAAAGACTAAATCAAAAGAG
*
40786470 AAAAAAA-TAAAGACTAAATCCAAAGAG
1 AAAAAAACTAAAGACTAAATCAAAAGAG
40786497 AAAA
1 AAAA
40786501 TTATACAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (28 bp):
AAAAAAACTAAAGACTAAATCAAAAGAG
Found at i:40788806 original size:36 final size:37
Alignment explanation
Indices: 40788765--40788845 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
40788755 CTATGTGTCT
40788765 AACACTCATC-ATTACATGA-CCAAATAATATACGCCC
1 AACACTCATCGA-TACATGATCCAAATAATATACGCCC
* * **
40788801 AACACTCATCGATACATGATCGAAGTAATATGTGCCC
1 AACACTCATCGATACATGATCCAAATAATATACGCCC
40788838 AACACTCA
1 AACACTCA
40788846 CCGAAATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 17 0.44
37 22 0.56
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (37 bp):
AACACTCATCGATACATGATCCAAATAATATACGCCC
Found at i:40788839 original size:37 final size:36
Alignment explanation
Indices: 40788749--40788845 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 36
40788739 CGGTATGTCT
* * *
40788749 GAAGTACTATGTGTCTAACACTCATCATTACATGAC
1 GAAGTAATATGTGCCCAACACTCATCATTACATGAC
* * **
40788785 CAAATAATATACGCCCAACACTCATCGA-TACATGATC
1 GAAGTAATATGTGCCCAACACTCATC-ATTACATGA-C
40788822 GAAGTAATATGTGCCCAACACTCA
1 GAAGTAATATGTGCCCAACACTCA
40788846 CCGAAATGTA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 26 0.54
37 22 0.46
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (36 bp):
GAAGTAATATGTGCCCAACACTCATCATTACATGAC
Found at i:40788867 original size:37 final size:37
Alignment explanation
Indices: 40788777--40788871 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
40788767 CACTCATCAT
* ** *
40788777 TACATG-ACCAAATAATATACGCCCAACACTCATCGA
1 TACATGAACGAAATAATATGTGCCCAACACTCACCGA
* *
40788813 TACATGATCGAAGTAATATGTGCCCAACACTCACCGA
1 TACATGAACGAAATAATATGTGCCCAACACTCACCGA
40788850 -A-ATGTAACTGAAATAATATGTG
1 TACATG-AAC-GAAATAATATGTG
40788872 ACCTATACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
35 3 0.06
36 9 0.19
37 36 0.75
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (37 bp):
TACATGAACGAAATAATATGTGCCCAACACTCACCGA
Found at i:40795148 original size:29 final size:29
Alignment explanation
Indices: 40795113--40795245 Score: 151
Period size: 29 Copynumber: 4.6 Consensus size: 29
40795103 TAGCATAAAG
*
40795113 ACTTGGTGGACTCATACATGTC-GATTCAT
1 ACTTGGTGAACTCATACATG-CGGATTCAT
* * *
40795142 GCTTGGTGAAATCACACATGCGGATTCAT
1 ACTTGGTGAACTCATACATGCGGATTCAT
* *
40795171 ACTTGGTGAACTCATACATGAGGATCCAT
1 ACTTGGTGAACTCATACATGCGGATTCAT
** *
40795200 ACTTGGTGGGCTCATACTTGCGGATTCAT
1 ACTTGGTGAACTCATACATGCGGATTCAT
* *
40795229 ACTTGGTTAACTTATAC
1 ACTTGGTGAACTCATAC
40795246 TTAGTGAACC
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 1 0.01
29 84 0.99
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (29 bp):
ACTTGGTGAACTCATACATGCGGATTCAT
Found at i:40795230 original size:14 final size:14
Alignment explanation
Indices: 40795160--40795233 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
40795150 AAATCACACA
40795160 TGCGGATTCATACT
1 TGCGGATTCATACT
* *
40795174 TG-GTGAACTCATACA
1 TGCG-G-ATTCATACT
* *
40795189 TGAGGATCCATACT
1 TGCGGATTCATACT
* **
40795203 TGGTGGGCTCATACT
1 T-GCGGATTCATACT
40795218 TGCGGATTCATACT
1 TGCGGATTCATACT
40795232 TG
1 TG
40795234 GTTAACTTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
13 1 0.02
14 22 0.50
15 20 0.45
16 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (14 bp):
TGCGGATTCATACT
Found at i:40795246 original size:44 final size:43
Alignment explanation
Indices: 40795198--40795306 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
40795188 ATGAGGATCC
* * *
40795198 ATACTTGGTGGGCTCATACTTGCGGATTCATACTTGGTTAACTT
1 ATACTT-GTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
* * * *
40795242 ATACTTAGTGAACCCATACATGAGGATTCATACTTGGTGGACTT
1 ATACTT-GTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
* *
40795286 GTACTTGTGGATTCATACTTG
1 ATACTTGTGGACTCATACTTG
40795307 GTGAACTATA
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
43 11 0.21
44 41 0.79
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
ATACTTGTGGACTCATACTTGAGGATTCATACTTGGTGAACTT
Found at i:40795274 original size:29 final size:29
Alignment explanation
Indices: 40795242--40795312 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
40795232 TGGTTAACTT
*
40795242 ATACTTAGTGAACCCATACATGAGGATTC
1 ATACTTGGTGAACCCATACATGAGGATTC
* *** * *
40795271 ATACTTGGTGGACTTGTACTTGTGGATTC
1 ATACTTGGTGAACCCATACATGAGGATTC
40795300 ATACTTGGTGAAC
1 ATACTTGGTGAAC
40795313 TATACTGTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (29 bp):
ATACTTGGTGAACCCATACATGAGGATTC
Found at i:40795291 original size:73 final size:72
Alignment explanation
Indices: 40795169--40795318 Score: 219
Period size: 73 Copynumber: 2.1 Consensus size: 72
40795159 ATGCGGATTC
* * *
40795169 ATACTTGGTGAACTCATACATGAGGATCCATACTTGGTGGGCTCATACTTGCGGATTCATACTTG
1 ATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACTTG
*
40795234 GTTAACTT
66 GTGAAC-T
* ** *
40795242 ATACTTAGTGAACCCATACATGAGGATTCATACTTGGTGGACTTGTACTTGTGGATTCATACTTG
1 ATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACTTG
40795307 GTGAACT
66 GTGAACT
40795314 ATACT
1 ATACT
40795319 GTAGGATTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 6 0.09
73 63 0.91
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (72 bp):
ATACTTAGTGAACCCATACATGAGGATCCATACTTGGTGGACTCATACTTGCGGATTCATACTTG
GTGAACT
Found at i:40795505 original size:37 final size:37
Alignment explanation
Indices: 40795463--40795552 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
40795453 TTTGAAAATT
* *
40795463 TGAGGACACGTCCAACAGAATGGCATAACTTGAAACA
1 TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
* * * **
40795500 TGAGGACAAGTCCAGCGGACTTTCATAACCTGAAACA
1 TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
*
40795537 TGAGGCCAAGTCCAAC
1 TGAGGACAAGTCCAAC
40795553 GAACTATCGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (37 bp):
TGAGGACAAGTCCAACAGAATGGCATAACCTGAAACA
Found at i:40802444 original size:51 final size:51
Alignment explanation
Indices: 40802354--40802552 Score: 310
Period size: 51 Copynumber: 3.9 Consensus size: 51
40802344 AGGATACATG
* *
40802354 GTGGCCTTCACATAGTACCACCCTAGTAGT-CAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAA
* *
40802405 GTGGCCTTCACATAGTACCACACATGTGTCCAAAACTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
* * *
40802456 GTGACCTTCACATAGTACCACACTTTTGTCCAAAGCTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
*
40802507 GTAGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTC
40802553 GTAAGGTTTA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 2 0.01
51 132 0.99
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAA
Found at i:40808851 original size:51 final size:51
Alignment explanation
Indices: 40808775--40809018 Score: 375
Period size: 51 Copynumber: 4.8 Consensus size: 51
40808765 GGATACACGA
* *
40808775 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAGGCTATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTTTATTCACAAAG
**
40808826 TGGCCTTCACATAGTACCACACTTGTGTCTGAAGCTATTTTATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* *
40808877 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAA
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
* * * *
40808928 TGTCC-TCACATAGTGCCACACTTGTGTTCAAAGCTATTATATTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
40808978 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTT
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTT
40809019 TTTCCTAACG
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 47 0.27
51 128 0.73
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTTTATTCACAAAG
Found at i:40808978 original size:101 final size:102
Alignment explanation
Indices: 40808775--40809016 Score: 373
Period size: 101 Copynumber: 2.4 Consensus size: 102
40808765 GGATACACGA
* * * *
40808775 TGGCCTTCACATAGTACCACCCTTGTAG-CCAAGGCTATTTTATTCACAAAGTGGCCTTCACATA
1 TGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAAATGGCCTTCACATA
* *
40808839 GTACCACACTTGTGTCTGAAGCTATTTTATTCACAAAG
65 GTACCACACTTGTGTCTAAAGCTATTATATTCACAAAG
*
40808877 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGTCC-TCACATAG
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGGCCTTCACATAG
*
40808941 TGCCACACTTGTGT-TCAAAGCTATTATATTCACAAAG
66 TACCACACTTGTGTCT-AAAGCTATTATATTCACAAAG
40808978 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT
1 TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATT
40809017 TTTTTCCTAA
Statistics
Matches: 130, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 80 0.62
102 49 0.38
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (102 bp):
TGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAATGGCCTTCACATAG
TACCACACTTGTGTCTAAAGCTATTATATTCACAAAG
Found at i:40809085 original size:24 final size:24
Alignment explanation
Indices: 40809058--40809103 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40809048 ACTTAACACA
40809058 ATGCCATGGACTTATTTCACTTGG
1 ATGCCATGGACTTATTTCACTTGG
*
40809082 ATGCCGTGGACTTATTTCACTT
1 ATGCCATGGACTTATTTCACTT
40809104 AGCACATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTGG
Found at i:40811127 original size:20 final size:20
Alignment explanation
Indices: 40811102--40811153 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
40811092 GAGACAATGC
40811102 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGGG
40811122 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGGG
*
40811142 ACACGCCTGTGT
1 ACACGCCCGTGT
40811154 CCTCTACCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.31, G:0.33, T:0.25
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGGG
Found at i:40818533 original size:20 final size:21
Alignment explanation
Indices: 40818499--40818553 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
40818489 GATACGTGGG
40818499 ATATGATAT--ACATGAATA-
1 ATATGATATGCACATGAATAT
40818517 ATATGATATGCACATG-ATAT
1 ATATGATATGCACATGAATAT
* *
40818537 GTATGAAATGCACATGA
1 ATATGATATGCACATGA
40818554 TGTAATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 9 0.29
19 3 0.10
20 19 0.61
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (21 bp):
ATATGATATGCACATGAATAT
Found at i:40818646 original size:26 final size:26
Alignment explanation
Indices: 40818604--40818765 Score: 242
Period size: 26 Copynumber: 6.3 Consensus size: 26
40818594 GAGGAAGTGC
40818604 AAAAGGGC-TATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
40818629 AAAAGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40818655 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40818681 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
40818707 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
40818733 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
40818756 AAAAGAGGCT
1 AAAAG-GGCT
40818766 AGGCCTCCAG
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.04
24 8 0.06
25 16 0.13
26 96 0.77
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:40821949 original size:24 final size:24
Alignment explanation
Indices: 40821922--40821984 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
40821912 ATTGTTCAGA
*
40821922 TCAATAGAGCTTACCATTTTCATC
1 TCAATAGAGCTTACCATTATCATC
*
40821946 TCAATAGAGCTTACTATTATCATC
1 TCAATAGAGCTTACCATTATCATC
*
40821970 TCATAAAGAGCTTAC
1 TCA-ATAGAGCTTAC
40821985 TGACCATGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 25 0.71
25 10 0.29
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (24 bp):
TCAATAGAGCTTACCATTATCATC
Found at i:40829083 original size:24 final size:24
Alignment explanation
Indices: 40829056--40829119 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
40829046 ATTGTTCAGA
*
40829056 TCAATAGAGCTTACCATTTTCATC
1 TCAATAGAGCTTACCATTATCATC
*
40829080 TCAATAGAGCTTACTATTATCATC
1 TCAATAGAGCTTACCATTATCATC
*
40829104 TCATAAAGAGCTTACC
1 TCA-ATAGAGCTTACC
40829120 GACCATGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
24 25 0.71
25 10 0.29
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (24 bp):
TCAATAGAGCTTACCATTATCATC
Found at i:40830365 original size:19 final size:19
Alignment explanation
Indices: 40830341--40830377 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40830331 ACTTGAAAAG
*
40830341 TTAAAAATTTTCTATGTTT
1 TTAAAAATTTTATATGTTT
*
40830360 TTAAAATTTTTATATGTT
1 TTAAAAATTTTATATGTT
40830378 ATCAATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTAAAAATTTTATATGTTT
Found at i:40833536 original size:67 final size:67
Alignment explanation
Indices: 40833450--40833576 Score: 191
Period size: 67 Copynumber: 1.9 Consensus size: 67
40833440 GTTTCTAGGT
* * * *
40833450 CGTGGTAAAATAGGGCATACATACTAATTTGTCCACACAGCCACAAGACATGCCCGTGTGTCTAA
1 CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTGTCTAA
40833515 GC
66 GC
* * *
40833517 CGTGGCAAAACAGGGCATACATACTGACTTGTCCACATAGCCACAAGACACGCCTGTGTG
1 CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTG
40833577 CTAGGTCGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (67 bp):
CGTGGCAAAACAGGGCATACATACTAACTTGTCCACACAGCCACAAGACACGCCCGTGTGTCTAA
GC
Found at i:40834686 original size:9 final size:9
Alignment explanation
Indices: 40834642--40834717 Score: 54
Period size: 9 Copynumber: 8.9 Consensus size: 9
40834632 ATTACTCACA
*
40834642 TAATTTATG
1 TAATTCATG
*
40834651 TAATTCATA
1 TAATTCATG
*
40834660 T-A-TCATA
1 TAATTCATG
* *
40834667 AAATCCATG
1 TAATTCATG
40834676 TAATTCATG
1 TAATTCATG
40834685 TAATTCATG
1 TAATTCATG
40834694 TAACTT-A--
1 TAA-TTCATG
40834701 TAATTCATG
1 TAATTCATG
*
40834710 TAAATCAT
1 TAATTCAT
40834718 ATAGCTCTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.04
7 9 0.17
8 2 0.04
9 38 0.72
10 2 0.04
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (9 bp):
TAATTCATG
Found at i:40834710 original size:34 final size:34
Alignment explanation
Indices: 40834642--40834717 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
40834632 ATTACTCACA
* *
40834642 TAATTTATGTAATTCATATATCATAAAATCCATG
1 TAATTCATGTAATTCATATAACATAAAATCCATG
* * * *
40834676 TAATTCATGTAATTCATGTAACTTATAATTCATG
1 TAATTCATGTAATTCATATAACATAAAATCCATG
*
40834710 TAAATCAT
1 TAATTCAT
40834718 ATAGCTCTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (34 bp):
TAATTCATGTAATTCATATAACATAAAATCCATG
Found at i:40835131 original size:20 final size:20
Alignment explanation
Indices: 40835090--40835131 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40835080 ATTACATATA
* *
40835090 TTCAATATATATACATTCAT
1 TTCAATATACATACATTAAT
40835110 TTCAA-ATACATACAATTAAT
1 TTCAATATACATAC-ATTAAT
40835130 TT
1 TT
40835132 AAAGTTCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (20 bp):
TTCAATATACATACATTAAT
Found at i:40836832 original size:46 final size:47
Alignment explanation
Indices: 40836691--40836952 Score: 229
Period size: 47 Copynumber: 5.6 Consensus size: 47
40836681 TGAGCTAGCA
* *
40836691 TAAGA-CATGTCTGGGACATGCATCGGCCAC-A-TTATGAGAGCCAGTG
1 TAAGACCATGTCTGGGACATGCATCGGCCTCGAGATAT-A-AGCCAGTG
* * * * * *
40836737 TAAGACCATGTCTGCGACATGTCATCGGCATTGAGAT-GAGGTCTAGTG
1 TAAGACCATGTCTGGGACATG-CATCGGCCTCGAGATATAAG-CCAGTG
*
40836785 TAAGA-CATGTCTGGGACATGCATCGGCCTCGAGACATAAGCCAGTG
1 TAAGACCATGTCTGGGACATGCATCGGCCTCGAGATATAAGCCAGTG
40836831 TAAGA-CATGTCTGGGACATGCATCGG-CTACGAGATGAT-A-CTCAGTG
1 TAAGACCATGTCTGGGACATGCATCGGCCT-CGAGAT-ATAAGC-CAGTG
* * * * *
40836877 TAAGACCATGTCTGGGACATGGCAT-TGACTTGAGATATGAGCCAGTA
1 TAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATATAAGCCAGTG
* *
40836924 TAAGACCGTGTCTAGGACATGGCATCGGC
1 TAAGACCATGTCTGGGACAT-GCATCGGC
40836953 ACCTTACCCT
Statistics
Matches: 178, Mismatches: 23, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
45 3 0.02
46 66 0.37
47 81 0.46
48 26 0.15
49 1 0.01
50 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGCATCGGCCTCGAGATATAAGCCAGTG
Found at i:40836920 original size:93 final size:92
Alignment explanation
Indices: 40836691--40836953 Score: 270
Period size: 94 Copynumber: 2.8 Consensus size: 92
40836681 TGAGCTAGCA
* * *
40836691 TAAGACATGTCTGGGACATGCATCGG-C-C-ACATTATGAGAGCCAGTGTAAGACCATGTCTGCG
1 TAAGACATGTCTGGGACATGCATCGGACTCGAGA-CAT--GAGCCAGTGTAAGACCATGTCTGGG
*
40836753 ACATGTCATCGGCATTGAGATGAGGTCTAGTG
63 ACATG-CATCGGCATCGAGATGA-GTCTAGTG
* *
40836785 TAAGACATGTCTGGGACATGCATCGGCCTCGAGACATAAGCCAGTGTAAGA-CATGTCTGGGACA
1 TAAGACATGTCTGGGACATGCATCGGACTCGAGACATGAGCCAGTGTAAGACCATGTCTGGGACA
40836849 TGCATCGGC-TACGAGATGA-TACTCAGTG
66 TGCATCGGCAT-CGAGATGAGT-CT-AGTG
* * * * * *
40836877 TAAGACCATGTCTGGGACATGGCAT-TGACTTGAGATATGAGCCAGTATAAGACCGTGTCTAGGA
1 TAAGA-CATGTCTGGGACAT-GCATCGGACTCGAGACATGAGCCAGTGTAAGACCATGTCTGGGA
40836941 CATGGCATCGGCA
64 CAT-GCATCGGCA
40836954 CCTTACCCTA
Statistics
Matches: 145, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
90 1 0.01
91 3 0.02
92 23 0.16
93 49 0.34
94 55 0.38
95 9 0.06
96 3 0.02
97 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (92 bp):
TAAGACATGTCTGGGACATGCATCGGACTCGAGACATGAGCCAGTGTAAGACCATGTCTGGGACA
TGCATCGGCATCGAGATGAGTCTAGTG
Found at i:40836943 original size:140 final size:141
Alignment explanation
Indices: 40836691--40836952 Score: 338
Period size: 140 Copynumber: 1.9 Consensus size: 141
40836681 TGAGCTAGCA
*
40836691 TAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGCGACA
1 TAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
* * * * *
40836756 TGTCATCGGCATTGAGATGAGGTCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGAC
66 TGGCATCGACATTGAGATGAGGTCCAGTATAAGACATGTCTAGGACATGGCATCGGCCTCGAGAC
40836820 ATAAGCCAGTG
131 ATAAGCCAGTG
* * *
40836831 TAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATA-CTCAGTGTAAGACCATGTCTGGGA
1 TAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAGC-CAGTGTAAGACCATGTCTGCGA
* *
40836894 CATGGCATTGAC-TTGAGAT-ATGAG-CCAGTATAAGACCGTGTCTAGGACATGGCATCGGC
64 CATGGCATCGACATTGAGATGA-G-GTCCAGTATAAGA-CATGTCTAGGACATGGCATCGGC
40836953 ACCTTACCCT
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
138 1 0.01
139 18 0.17
140 77 0.73
141 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (141 bp):
TAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGCGACA
TGGCATCGACATTGAGATGAGGTCCAGTATAAGACATGTCTAGGACATGGCATCGGCCTCGAGAC
ATAAGCCAGTG
Found at i:40844399 original size:47 final size:46
Alignment explanation
Indices: 40844286--40844557 Score: 198
Period size: 47 Copynumber: 5.8 Consensus size: 46
40844276 ATTCGAGTGT
* *
40844286 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATT-ATG---A
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGA-GACAA
40844332 GAGCCAGTGTAAGACAATGTCTGGGACATGGCATCGGCATTGAGACAA
1 GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCATTGAGACAA
* * * * * *
40844380 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC-AA
* * * **
40844427 -AGCCAGTGTAAGACACGTCTGGGACATGCATAGGC-TACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGACAA
* * * * *
40844472 TAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATAT
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACAA
* * *
40844519 GAGCCAGTATAAGACCGTGTCTAGGACATGGCATCGGCA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
40844558 CCTTAACCTA
Statistics
Matches: 186, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
45 7 0.04
46 75 0.40
47 76 0.41
48 28 0.15
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACAA
Found at i:40844546 original size:140 final size:141
Alignment explanation
Indices: 40844291--40844554 Score: 345
Period size: 140 Copynumber: 1.9 Consensus size: 141
40844281 AGTGTGAGCT
* * * *
40844291 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACAATGTCTGG
1 AGTGTAAGACACGTCTGGGACATGCATAGGCCACATGATGAGAGCCAGTGTAAGACAATGTCTGG
* * * * *
40844356 GACATGGCATCGGCATTGAGACAAGGGCTAGTGTAAGACATGTCTGGGACAT-GCATCGACCTCG
66 GACATGGCATCGACATTGAGACAAGAGCCAGTATAAGACATGTCTAGGACATGGCATCGACCTCG
40844420 AGACGTAAGCC
131 AGACGTAAGCC
* * * *
40844431 AGTGTAAGACACGTCTGGGACATGCATAGGCTACGA-GATGATAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACACGTCTGGGACATGCATAGGCCAC-ATGATGAGAGCCAGTGTAAGACAATGTCTG
* * *
40844495 GGACATGGCATCGAC-TTGAGATATGAGCCAGTATAAGACCGTGTCTAGGACATGGCATCG
65 GGACATGGCATCGACATTGAGACAAGAGCCAGTATAAGA-CATGTCTAGGACATGGCATCG
40844555 GCACCTTAAC
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
139 18 0.17
140 80 0.76
141 7 0.07
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (141 bp):
AGTGTAAGACACGTCTGGGACATGCATAGGCCACATGATGAGAGCCAGTGTAAGACAATGTCTGG
GACATGGCATCGACATTGAGACAAGAGCCAGTATAAGACATGTCTAGGACATGGCATCGACCTCG
AGACGTAAGCC
Found at i:40845432 original size:42 final size:42
Alignment explanation
Indices: 40845386--40845487 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
40845376 GACACAGCCA
*
40845386 TGTGTCTCAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
1 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
40845428 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
1 TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
*
40845470 TGTGTCTTGGCCGTGTGA
1 TGTGTCTTAGCCGTGTGA
40845488 CATTTTGGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.24
Consensus pattern (42 bp):
TGTGTCTTAGCCGTGTGAAGGGCACGGCCTAGCACACGGGTG
Found at i:40847116 original size:27 final size:27
Alignment explanation
Indices: 40847081--40847132 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40847071 CCACTGAATC
* *
40847081 GGGGAATCATCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
40847108 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
40847133 TTTTCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:40847234 original size:71 final size:72
Alignment explanation
Indices: 40847091--40847242 Score: 227
Period size: 71 Copynumber: 2.1 Consensus size: 72
40847081 GGGGAATCAT
** *
40847091 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTTTCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATACAATGG
40847156 ATAATCG
66 ATAATCG
***
40847163 CACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATACAATG
40847227 GAT-ATCG
65 GATAATCG
40847234 CACTTAGCA
1 CACTTAGCA
40847243 CCACCAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 39 0.53
72 34 0.47
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATACAATGG
ATAATCG
Found at i:40847277 original size:76 final size:72
Alignment explanation
Indices: 40847091--40847278 Score: 211
Period size: 71 Copynumber: 2.6 Consensus size: 72
40847081 GGGGAATCAT
* ** *
40847091 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTTTCATTTCAAATATACAATG
1 CACTTAGCAA-CCATCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
40847155 GATAATCG
65 GATAATCG
* ***
40847163 CACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGG
1 CACTTAGCAACCATCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
40847228 AT-ATCG
66 ATAATCG
*
40847234 CACTTAGCACCACCAAT-GAACGGGGAATCAGCACTTAGCAACCCC
1 CACTTAGCA--ACC-ATCG---GGGGAATCAGCACATAGCAACCCC
40847279 TCGGGGGAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
71 39 0.39
72 34 0.34
73 4 0.04
74 1 0.01
76 23 0.23
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (72 bp):
CACTTAGCAACCATCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
ATAATCG
Found at i:40847289 original size:103 final size:104
Alignment explanation
Indices: 40847158--40847383 Score: 370
Period size: 103 Copynumber: 2.2 Consensus size: 104
40847148 TACAATGGAT
40847158 AATC-GCACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGAT
1 AATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGAT
* *
40847221 ATGGTGGAT-ATCGCACTTAGCACCACCAATGAA-CGGGG
66 ATGGTGGATCA-CGCACATAGCACCACCAATAAATCGGGG
40847259 AATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGAT
1 AATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGAT
*
40847324 ATGGTGGATCACGCACATAGCACCACCCATAAATCGGGG
66 ATGGTGGATCACGCACATAGCACCACCAATAAATCGGGG
**
40847363 AATCAGCACACAGCAACCCCT
1 AATCAGCACTTAGCAACCCCT
40847384 TTTATATACA
Statistics
Matches: 116, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
101 4 0.03
102 11 0.09
103 76 0.66
104 25 0.22
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (104 bp):
AATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGAT
ATGGTGGATCACGCACATAGCACCACCAATAAATCGGGG
Found at i:40847745 original size:29 final size:29
Alignment explanation
Indices: 40847712--40847775 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
40847702 TAATCCACCA
40847712 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
40847741 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
40847771 CCCAA
1 CCCAA
40847776 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:40847749 original size:30 final size:30
Alignment explanation
Indices: 40847719--40847775 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40847709 CCACCCAACT
40847719 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
40847748 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
40847776 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:40854836 original size:104 final size:104
Alignment explanation
Indices: 40854714--40854937 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
40854704 AATGGATATC
40854714 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
40854779 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
40854818 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
40854883 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
40854922 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
40854938 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:40855299 original size:29 final size:29
Alignment explanation
Indices: 40855266--40855329 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
40855256 TAATCCACCA
40855266 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
40855295 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
40855325 CCCAA
1 CCCAA
40855330 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:40855303 original size:30 final size:30
Alignment explanation
Indices: 40855273--40855329 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40855263 CCACCCAACT
40855273 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
40855302 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
40855330 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:40858759 original size:20 final size:20
Alignment explanation
Indices: 40858726--40858766 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40858716 AGCACATGTA
40858726 TTCATAAAAATTCAAAATTT
1 TTCATAAAAATTCAAAATTT
* * *
40858746 TTCATCAAATTTCACAATTT
1 TTCATAAAAATTCAAAATTT
40858766 T
1 T
40858767 ACATTTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCATAAAAATTCAAAATTT
Found at i:40860462 original size:32 final size:32
Alignment explanation
Indices: 40860421--40860484 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40860411 ATCCGAGTCA
40860421 GAAAAATTATTTTAAAATTAATGCATGATTTG
1 GAAAAATTATTTTAAAATTAATGCATGATTTG
*
40860453 GAAAAATTATTTTAAAATTAATGCATGGTTTG
1 GAAAAATTATTTTAAAATTAATGCATGATTTG
40860485 CATTATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (32 bp):
GAAAAATTATTTTAAAATTAATGCATGATTTG
Found at i:40866881 original size:25 final size:25
Alignment explanation
Indices: 40866852--40866901 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40866842 TTGTAACACA
40866852 TCTTATTATATAATTATCTATATTG
1 TCTTATTATATAATTATCTATATTG
40866877 TCTTATTATATAATTATCTATATTG
1 TCTTATTATATAATTATCTATATTG
40866902 AGGAATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (25 bp):
TCTTATTATATAATTATCTATATTG
Found at i:40866909 original size:25 final size:25
Alignment explanation
Indices: 40866856--40866912 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
40866846 AACACATCTT
* **
40866856 ATTATATAATTATCTATATTGTCTT
1 ATTATATAATTATCTATATTGACGA
*
40866881 ATTATATAATTATCTATATTGAGGA
1 ATTATATAATTATCTATATTGACGA
40866906 ATTATAT
1 ATTATAT
40866913 TTAATTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (25 bp):
ATTATATAATTATCTATATTGACGA
Found at i:40872530 original size:6 final size:6
Alignment explanation
Indices: 40872519--40872550 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
40872509 CTAAAAAAAA
*
40872519 TTATTT TTATTT TTATTT TAATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
40872551 TAAGTCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:40872593 original size:20 final size:20
Alignment explanation
Indices: 40872555--40872596 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40872545 ATTTTTTAAG
40872555 TCCTTAAATTCGTTTTTTTA
1 TCCTTAAATTCGTTTTTTTA
40872575 TCCTTAAATTCGTTTTTTTA
1 TCCTTAAATTCGTTTTTTTA
40872595 TC
1 TC
40872597 ACATGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.60
Consensus pattern (20 bp):
TCCTTAAATTCGTTTTTTTA
Found at i:40872593 original size:21 final size:21
Alignment explanation
Indices: 40872546--40872592 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
40872536 TTAATTTTTA
40872546 TTTTTTAAGTCCTTAAATTCG
1 TTTTTTAAGTCCTTAAATTCG
*
40872567 TTTTTTTA-TCCTTAAATTCG
1 TTTTTTAAGTCCTTAAATTCG
40872587 TTTTTT
1 TTTTTT
40872593 TATCACATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (21 bp):
TTTTTTAAGTCCTTAAATTCG
Found at i:40872793 original size:31 final size:31
Alignment explanation
Indices: 40872735--40872794 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40872725 GTAAAAACTA
*
40872735 TTTTTAAAAGTTAAAAATTTTAAAAATATAT
1 TTTTTAAAAGTTAAAAATATTAAAAATATAT
**
40872766 TTTTTAAATTTTAAAAA-ATTAATAAATAT
1 TTTTTAAAAGTTAAAAATATTAA-AAATAT
40872795 TGACATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
TTTTTAAAAGTTAAAAATATTAAAAATATAT
Found at i:40877005 original size:15 final size:15
Alignment explanation
Indices: 40876985--40877045 Score: 77
Period size: 15 Copynumber: 4.1 Consensus size: 15
40876975 TTAAATTAAG
*
40876985 TACTTAAATTTTCAA
1 TACTTAATTTTTCAA
40877000 TACTTAATTTTTCAA
1 TACTTAATTTTTCAA
* * *
40877015 CACTTATTTTTTTAA
1 TACTTAATTTTTCAA
*
40877030 TACTTACTTTTTCAA
1 TACTTAATTTTTCAA
40877045 T
1 T
40877046 TTATCAAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (15 bp):
TACTTAATTTTTCAA
Found at i:40890884 original size:4 final size:4
Alignment explanation
Indices: 40890875--40890919 Score: 54
Period size: 4 Copynumber: 10.5 Consensus size: 4
40890865 ATATTAGGGT
*
40890875 AATA AATA AATA GATA TAATA AGATAA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA -AATA A-AT-A AATA AATA AATA AATA AA
40890920 ATATGTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 27 0.75
5 7 0.19
6 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:40891342 original size:37 final size:37
Alignment explanation
Indices: 40891292--40891365 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
40891282 AATCATAAAG
40891292 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
1 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
40891329 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
1 GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
40891366 CGAGGACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (37 bp):
GACTAAATTAAAATGCAATGCAAAAGCTTAAGGACTC
Found at i:40891769 original size:10 final size:10
Alignment explanation
Indices: 40891751--40891783 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
40891741 GGCTATAGGG
*
40891751 CCACTGTGGT
1 CCACCGTGGT
40891761 CCACCGTGGT
1 CCACCGTGGT
40891771 CCACCGTGG-
1 CCACCGTGGT
40891780 CCAC
1 CCAC
40891784 TATTCATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.12, C:0.42, G:0.27, T:0.18
Consensus pattern (10 bp):
CCACCGTGGT
Found at i:40893051 original size:44 final size:44
Alignment explanation
Indices: 40892757--40893190 Score: 236
Period size: 44 Copynumber: 9.6 Consensus size: 44
40892747 TTCAATCCAA
* * * * *
40892757 TCCACTGCAACTTCAA-G-GATAGGATTTGTAAC-CTCATCTTGC
1 TCCACTGCAACTTTAAGGAGATAAGATTTGTAGCTTTAATC-TGC
* * * * *
40892799 TCCACTGTAACTTCAAGGAGATAAGATTTGTGACCGTAAATTCATTCTAC
1 TCCACTGCAACTTTAAGGAGATAAGATTTGT-AGC-T---TT-AATCTGC
* * * * * * *
40892849 ACCACTACAACTTT-AGGGGCATAGGATTAGTAGC-TTCATCTTGT
1 TCCACTGCAACTTTAAGGAG-ATAAGATTTGTAGCTTTAATC-TGC
* * * *
40892893 TCCACTGCAACTTTAGGGAGATAAGACTTATAGCTTCAATCTGC
1 TCCACTGCAACTTTAAGGAGATAAGATTTGTAGCTTTAATCTGC
* * *
40892937 TCCACTGCAACTTCACGGAGATAAGATTTATAGCTTTAATCTGC
1 TCCACTGCAACTTTAAGGAGATAAGATTTGTAGCTTTAATCTGC
* * * *
40892981 TCCACTACAA-TTTCAGGAAGATAAGATTTGTAGCTTTAATTTGT
1 TCCACTGCAACTTTAAGG-AGATAAGATTTGTAGCTTTAATCTGC
* *
40893025 TCCACTGCAACTTTAAGGAGATAAGATTTGCTATGGTAGATTCAATCCG-
1 TCCACTGCAACTTTAAGGAGATAAGATTTG-TA-GCT---TT-AATCTGC
* * * * * ** * * *
40893074 TCTTACTACGACTTCAAGG-GTGTTGGATCTGTAGCTTAAATCTTC
1 TC-CACTGCAACTTTAAGGAG-ATAAGATTTGTAGCTTTAATCTGC
* * *
40893119 TCCACTGAAACTTCAAGGAGATAAAATTTGTAGCTTTAATCTGC
1 TCCACTGCAACTTTAAGGAGATAAGATTTGTAGCTTTAATCTGC
* * *
40893163 TCCACTACAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTTAAGGAGATAAGATT
40893191 CGCTATGGTA
Statistics
Matches: 294, Mismatches: 73, Indels: 48
0.71 0.18 0.12
Matches are distributed among these distances:
42 15 0.05
43 7 0.02
44 188 0.64
45 21 0.07
46 2 0.01
48 2 0.01
49 13 0.04
50 44 0.15
51 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTTAAGGAGATAAGATTTGTAGCTTTAATCTGC
Found at i:40904401 original size:20 final size:19
Alignment explanation
Indices: 40904373--40904482 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 19
40904363 TTATATATAT
*
40904373 TTTTTATAATTCTTTATAAA
1 TTTTAATAATT-TTTATAAA
*
40904393 TTTTAATAATTTGTATGGAAA
1 TTTTAATAATTTTTAT--AAA
*
40904414 TGTTTTAATAA-TTTT-TAGA
1 --TTTTAATAATTTTTATAAA
* * *
40904433 TTCTT-TTAA-TATTATATA
1 TT-TTAATAATTTTTATAAA
40904451 TTTT-ATAATTCTTTATAAA
1 TTTTAATAATT-TTTATAAA
40904470 TTTTAATAATTTT
1 TTTTAATAATTTT
40904483 ATGAAAACGT
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
17 13 0.18
18 8 0.11
19 18 0.25
20 16 0.23
21 4 0.06
22 3 0.04
23 9 0.13
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTAATAATTTTTATAAA
Found at i:40904473 original size:77 final size:79
Alignment explanation
Indices: 40904343--40904494 Score: 247
Period size: 77 Copynumber: 1.9 Consensus size: 79
40904333 GAAACTTTAG
40904343 ATTTTTAGATTCTTTTAATATTATATATATTTTTTATAATTCTTTATAAATTTTAATAATTTGTA
1 ATTTTTAGATTCTTTTAATATTATATATA-TTTTTATAATTCTTTATAAATTTTAATAATTT-TA
* *
40904408 TGGAAATGTTTTAATA
64 TGAAAACGTTTTAATA
40904424 ATTTTTAGATTCTTTTAATA-T-TATATA-TTTTATAATTCTTTATAAATTTTAATAATTTTATG
1 ATTTTTAGATTCTTTTAATATTATATATATTTTTATAATTCTTTATAAATTTTAATAATTTTATG
40904486 AAAACGTTT
66 AAAACGTTT
40904495 GTTAATATTG
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
76 11 0.16
77 31 0.45
79 6 0.09
80 1 0.01
81 20 0.29
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (79 bp):
ATTTTTAGATTCTTTTAATATTATATATATTTTTATAATTCTTTATAAATTTTAATAATTTTATG
AAAACGTTTTAATA
Found at i:40911008 original size:17 final size:17
Alignment explanation
Indices: 40910983--40911023 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40910973 TTACAATTTT
*
40910983 TTTTCTTTTTTGCTTGC
1 TTTTGTTTTTTGCTTGC
*
40911000 TTTTGTTTTTTGTTTGC
1 TTTTGTTTTTTGCTTGC
*
40911017 TATTGTT
1 TTTTGTT
40911024 CTTGCTGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.02, C:0.10, G:0.15, T:0.73
Consensus pattern (17 bp):
TTTTGTTTTTTGCTTGC
Found at i:40911721 original size:44 final size:44
Alignment explanation
Indices: 40911604--40911845 Score: 234
Period size: 44 Copynumber: 5.5 Consensus size: 44
40911594 TTGTGACTTA
* * * * *
40911604 TAGCTTTAATATGCCCCACTGCAATTTCAGAGAAATAAGATTCG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG
* * * * * *
40911648 CTATCTTCAATCTACTCCACTGCACCTTCAGAGAGATAAGGTTTA
1 -TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG
* *
40911693 TAGTTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTT-G
** * * * * * * *
40911738 TTTCTTCAGTCTGCTCTACTGCAACTTCAGGGAGGTAAAACTTG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG
*
40911782 TGGCTTTAATCTGCTCCACTGCAACTTCA-AGGAGATAAGATTTG
1 TAGCTTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATTTG
*
40911826 TAGCTTTAATCTACTCCACT
1 TAGCTTTAATCTGCTCCACT
40911846 AAGATCCAAA
Statistics
Matches: 156, Mismatches: 39, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
44 89 0.57
45 67 0.43
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (44 bp):
TAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG
Found at i:40911759 original size:89 final size:89
Alignment explanation
Indices: 40911599--40911845 Score: 273
Period size: 89 Copynumber: 2.8 Consensus size: 89
40911589 AGGATTTGTG
* * * * *
40911599 ACTTATAGCTTTAATATGCCCCACTGCAATTTCAGAGAAATAAGATTCGCTATCTTCAATCTACT
1 ACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACT
* *
40911664 CCACTGCACCTTCAGAGAGATAAG
66 CCACTGCAACTTCAGAGAGATAAA
** * * * * * *
40911688 GTTTATAGTTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGGTTTCTTCAGTCTGCT
1 ACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACT
* * *
40911753 CTACTGCAACTTCAGGGAGGTAAA
66 CCACTGCAACTTCAGAGAGATAAA
* * * *
40911777 ACTTGTGGCTTTAATCTGCTCCACTGCAACTTCA-AGGAGATAAGATTTG-TAGCTTTAATCTAC
1 ACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATTTGCTATCTTCAATCTAC
40911840 TCCACT
65 TCCACT
40911846 AAGATCCAAA
Statistics
Matches: 127, Mismatches: 30, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
88 15 0.12
89 112 0.88
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (89 bp):
ACTTATAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTACT
CCACTGCAACTTCAGAGAGATAAA
Found at i:40919473 original size:17 final size:17
Alignment explanation
Indices: 40919453--40919487 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40919443 AAAATGGAAT
40919453 AAAAAATATGA-ATATAA
1 AAAAAATAT-ATATATAA
40919470 AAAAAATATATATATAA
1 AAAAAATATATATATAA
40919487 A
1 A
40919488 GAATACACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAAATATATATATAA
Found at i:40922867 original size:20 final size:20
Alignment explanation
Indices: 40922844--40922905 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
40922834 TCCAAATCAA
40922844 ATAACCATTTTCCATTTCAT
1 ATAACCATTTTCCATTTCAT
* *
40922864 ATAACAACTTGT-CATTTCAT
1 ATAACCA-TTTTCCATTTCAT
* *
40922884 ACATCCA-TTTCCATTTCAT
1 ATAACCATTTTCCATTTCAT
40922903 ATA
1 ATA
40922906 TTCGGTTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.06
19 10 0.30
20 18 0.55
21 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAACCATTTTCCATTTCAT
Found at i:40932127 original size:15 final size:15
Alignment explanation
Indices: 40932107--40932141 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40932097 GTGGTCTCAA
*
40932107 ACCACCGTTTTCGAC
1 ACCACCATTTTCGAC
*
40932122 ACCACCATTTTTGAC
1 ACCACCATTTTCGAC
40932137 ACCAC
1 ACCAC
40932142 TAAAAATAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.26
Consensus pattern (15 bp):
ACCACCATTTTCGAC
Found at i:40933620 original size:20 final size:20
Alignment explanation
Indices: 40933597--40933644 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
40933587 AAATCCAAAT
*
40933597 TAAAATACTGAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
*
40933617 TAAAATCCTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
40933637 TAAGAATA
1 TAA-AATA
40933645 TTGATGTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Done.