Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold331
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: 1394875
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 7 of 8
Found at i:1188392 original size:100 final size:97
Alignment explanation
Indices: 1188272--1188655 Score: 401
Period size: 100 Copynumber: 4.0 Consensus size: 97
1188262 TGGTGAAAGA
*
1188272 TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCGACGAAGTTGTGGACTTTAAAAGGGAAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAA-GGAAAA
*
1188337 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
65 AG-GTGCCACGGAGTTGTGGACTTT-AAAAGAAGG
* ** *
1188372 TGCCACGAAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAA-GGAAAA
*
1188437 AGAGTGCCACGGAGTTGTGGGCTTTAAAAG--GG
65 AG-GTGCCACGGAGTTGTGGACTTTAAAAGAAGG
* * * * * * * *
1188469 TGCCACGGAGTTGTGGATTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGAAAA
* * * *
1188534 AGGTGTCACAGAGTTGTGGACTTAGAAGGAAAAAGAG
65 AGGTGCCACGGAGTTGTGGACTT-TAA--AAGAAG-G
* * *
1188571 TGCCACGGAGTTGTGGGCTTAAAA-G-----GGTGCCACGAAGTTATGGAC-TTAAAA-GAAAAA
1 TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAAGGAAAAA
*
1188628 GGTGCCACGAAGTTGTGGACTTTAAAAG
66 GGTGCCACGGAGTTGTGGACTTTAAAAG
1188656 GAAAAAGATG
Statistics
Matches: 245, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
90 2 0.01
92 2 0.01
93 25 0.10
94 6 0.02
95 15 0.06
96 19 0.08
97 37 0.15
98 23 0.09
99 7 0.03
100 85 0.35
101 2 0.01
102 22 0.09
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (97 bp):
TGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAAGGAAAAA
GGTGCCACGGAGTTGTGGACTTTAAAAGAAGG
Found at i:1188602 original size:27 final size:27
Alignment explanation
Indices: 1188564--1188655 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 27
1188554 CTTAGAAGGA
* * *
1188564 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGAAGTTATGGACTT
*
1188591 AAAAGGGTGCCACGAAGTTATGGACTT
1 AAAAGAGTGCCACGAAGTTATGGACTT
*
1188618 AAAAGAAAAAGGTGCCACGAAGTTGTGGACTTT
1 AAAAG----A-GTGCCACGAAGTTATGGAC-TT
1188651 AAAAG
1 AAAAG
1188656 GAAAAAGATG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 28 0.53
32 18 0.34
33 7 0.13
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (27 bp):
AAAAGAGTGCCACGAAGTTATGGACTT
Found at i:1188688 original size:23 final size:23
Alignment explanation
Indices: 1188662--1188709 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1188652 AAAGGAAAAA
1188662 GATGCCA-TGGAGTCGTGGACTTT
1 GATGCCACT-GAGTCGTGGACTTT
*
1188685 GATGCGACTGAGTCGTGGACTTT
1 GATGCCACTGAGTCGTGGACTTT
1188708 GA
1 GA
1188710 GACAAGATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (23 bp):
GATGCCACTGAGTCGTGGACTTT
Found at i:1188729 original size:30 final size:28
Alignment explanation
Indices: 1188685--1188966 Score: 136
Period size: 28 Copynumber: 9.8 Consensus size: 28
1188675 CGTGGACTTT
* * *
1188685 GATGCGACTGAGTCGTGGACTTTGAGACAA
1 GATGCCACTAAGTTGTGGACTTTGA-A-AA
*
1188715 GATGCCACTAAGTCGTGGACTTTGAAGAAAA
1 GATGCCACTAAGTTGTGGACTTT---GAAAA
* * *
1188746 GGATGCCACTGATTTGTGGACTTTGAAAG
1 -GATGCCACTAAGTTGTGGACTTTGAAAA
* * *
1188775 GTTGCCACTAACTTGTGGGCTTTGAAAA
1 GATGCCACTAAGTTGTGGACTTTGAAAA
* *
1188803 GAGTGCCACTAATTTGTGGGCTTTGAAAA
1 GA-TGCCACTAAGTTGTGGACTTTGAAAA
* ** * * * *
1188832 GTTGCCACCGACTCGTGGGCTTT-AAAG
1 GATGCCACTAAGTTGTGGACTTTGAAAA
* * * *
1188859 GATGCCACTGATTTGTGGGCTTTGAAAG
1 GATGCCACTAAGTTGTGGACTTTGAAAA
* * * ** *
1188887 GCTACCACTAACTCATGGGCTTT-AAAA
1 GATGCCACTAAGTTGTGGACTTTGAAAA
* * * * *
1188914 GGATGCCACTGACTTATGGGCTTCGGAAAA
1 -GATGCCACTAAGTTGTGGACTT-TGAAAA
* * *
1188944 GATGCCACTGACTTGTGGGCTTT
1 GATGCCACTAAGTTGTGGACTTT
1188967 TGAAGGATGA
Statistics
Matches: 206, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
27 25 0.12
28 80 0.39
29 51 0.25
30 25 0.12
31 2 0.01
32 21 0.10
33 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (28 bp):
GATGCCACTAAGTTGTGGACTTTGAAAA
Found at i:1188782 original size:28 final size:28
Alignment explanation
Indices: 1188743--1188975 Score: 218
Period size: 28 Copynumber: 8.3 Consensus size: 28
1188733 ACTTTGAAGA
*
1188743 AAAGGATGCCACTGATTTGTGGACTTTG
1 AAAGGATGCCACTGATTTGTGGGCTTTG
* * *
1188771 AAAGGTTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGATTTGTGGGCTTTG
* *
1188799 AAAAGAGTGCCACTAATTTGTGGGCTTTG
1 AAAGGA-TGCCACTGATTTGTGGGCTTTG
* * * * *
1188828 AAAAGTTGCCACCGACTCGTGGGCTTT-
1 AAAGGATGCCACTGATTTGTGGGCTTTG
1188855 AAAGGATGCCACTGATTTGTGGGCTTTG
1 AAAGGATGCCACTGATTTGTGGGCTTTG
* * * * ** *
1188883 AAAGGCTACCACTAACTCATGGGCTTTA
1 AAAGGATGCCACTGATTTGTGGGCTTTG
* * *
1188911 AAAGGATGCCACTGACTTATGGGCTTCGG
1 AAAGGATGCCACTGATTTGTGGGCTT-TG
* *
1188940 AAAAGATGCCACTGACTTGTGGGCTTTTG
1 AAAGGATGCCACTGATTTGTGGGC-TTTG
1188969 -AAGGATG
1 AAAGGATG
1188976 AGGAATATCT
Statistics
Matches: 167, Mismatches: 34, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.13
28 94 0.56
29 49 0.29
30 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (28 bp):
AAAGGATGCCACTGATTTGTGGGCTTTG
Found at i:1188818 original size:57 final size:57
Alignment explanation
Indices: 1188685--1188966 Score: 257
Period size: 57 Copynumber: 4.9 Consensus size: 57
1188675 CGTGGACTTT
* * * * * * *
1188685 GATGCGACTGAGTCGTGGACTTTGAGACAAGATGCCACTAAGTCGTGGACTTTGAAGAAAA
1 GATGCCACTGATTTGTGGGCTTTGA-A-AAGATGCCACTAACTCGTGGGCTTT-AA-AAGA
* * * *
1188746 GGATGCCACTGATTTGTGGACTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGA
1 -GATGCCACTGATTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTT-AAAAGA
* * **
1188805 G-TGCCACTAATTTGTGGGCTTTGAAAAGTTGCCACCGACTCGTGGGCTTT-AAAG-
1 GATGCCACTGATTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTAAAAGA
* * * *
1188859 GATGCCACTGATTTGTGGGCTTTGAAAGGCTACCACTAACTCATGGGCTTTAAAAG-
1 GATGCCACTGATTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTAAAAGA
* * * * *
1188915 GATGCCACTGACTTATGGGCTTCGGAAAAGATGCCACTGACTTGTGGGCTTT
1 GATGCCACTGATTTGTGGGCTT-TGAAAAGATGCCACTAACTCGTGGGCTTT
1188967 TGAAGGATGA
Statistics
Matches: 186, Mismatches: 31, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
54 1 0.01
55 46 0.25
56 24 0.13
57 65 0.35
58 1 0.01
59 3 0.02
60 23 0.12
61 1 0.01
62 22 0.12
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (57 bp):
GATGCCACTGATTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTAAAAGA
Found at i:1188876 original size:112 final size:113
Alignment explanation
Indices: 1188743--1188975 Score: 310
Period size: 112 Copynumber: 2.1 Consensus size: 113
1188733 ACTTTGAAGA
* * **
1188743 AAAGGATGCCACTGATTTGTGGACTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAA-GAGT
1 AAAGGATGCCACTGATTTGTGGACTTTGAAAGGCTACCACTAACTCATGGGCTTT-AAAAGGA-T
* * * *
1188807 GCCACTAATTTGTGGGCTT-TGAAAAGTTGCCACCGACTCGTGGGC-TTT
64 GCCACTAACTTATGGGCTTCGGAAAAGATGCCACCGACTCGTGGGCTTTT
*
1188855 AAAGGATGCCACTGATTTGTGGGCTTTGAAAGGCTACCACTAACTCATGGGCTTTAAAAGGATGC
1 AAAGGATGCCACTGATTTGTGGACTTTGAAAGGCTACCACTAACTCATGGGCTTTAAAAGGATGC
* * *
1188920 CACTGACTTATGGGCTTCGGAAAAGATGCCACTGACTTGTGGGCTTTT
66 CACTAACTTATGGGCTTCGGAAAAGATGCCACCGACTCGTGGGCTTTT
*
1188968 GAAGGATG
1 AAAGGATG
1188976 AGGAATATCT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
111 21 0.20
112 74 0.70
113 10 0.10
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (113 bp):
AAAGGATGCCACTGATTTGTGGACTTTGAAAGGCTACCACTAACTCATGGGCTTTAAAAGGATGC
CACTAACTTATGGGCTTCGGAAAAGATGCCACCGACTCGTGGGCTTTT
Found at i:1190433 original size:6 final size:6
Alignment explanation
Indices: 1190405--1190472 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
1190395 ATTCGGACCC
* *
1190405 TTTTTG TTGTTG TTGTTTT TTTTTG TTTTTG -TTTT- TTTTTG TTTTT-
1 TTTTTG TTTTTG TT-TTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
* * *
1190451 TTCTTC TTCTTTT TTTTTG TTT
1 TTTTTG TT-TTTG TTTTTG TTT
1190473 ATTTGGTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 12 0.24
6 29 0.59
7 8 0.16
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:1190448 original size:16 final size:16
Alignment explanation
Indices: 1190405--1190472 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
1190395 ATTCGGACCC
* *
1190405 TTTTTGTTGTTGTTGT
1 TTTTTTTTGTTTTTGT
1190421 TTTTTTTTGTTTTTGT
1 TTTTTTTTGTTTTTGT
1190437 TTTTTTTTGTTTTT-T
1 TTTTTTTTGTTTTTGT
*
1190452 TCTTCTTCTTTTTTTTTGT
1 T-TT-TT-TTTGTTTTTGT
1190471 TT
1 TT
1190473 ATTTGGTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 2 0.04
16 30 0.67
17 2 0.04
18 9 0.20
19 2 0.04
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (16 bp):
TTTTTTTTGTTTTTGT
Found at i:1190487 original size:24 final size:24
Alignment explanation
Indices: 1190436--1190489 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1190426 TTTGTTTTTG
* *
1190436 TTTTTTTTTGTTTTTTTCTTCTTC
1 TTTTTTTTTGTTTATTTCGTCTTC
*
1190460 TTTTTTTTTGTTTATTTGGT-TTC
1 TTTTTTTTTGTTTATTTCGTCTTC
1190483 TTTTTTT
1 TTTTTTT
1190490 GTGGAGGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTGTTTATTTCGTCTTC
Found at i:1200387 original size:20 final size:19
Alignment explanation
Indices: 1200333--1200387 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1200323 AAAACCCTTA
*
1200333 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
1200353 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
1200373 AATGTATCGATACAT
1 AAAGTATCGATACAT
1200388 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:1200476 original size:13 final size:13
Alignment explanation
Indices: 1200458--1200483 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1200448 TACACAAAGT
1200458 ATGTATCGATACA
1 ATGTATCGATACA
1200471 ATGTATCGATACA
1 ATGTATCGATACA
1200484 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1200481 original size:32 final size:34
Alignment explanation
Indices: 1200440--1200504 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1200430 TAGCCAAACT
**
1200440 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAAATGTATCGATACAA
1200472 TGTATCGATACACCAAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAAATGTATCGATACA
1200505 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 1 0.03
34 16 0.55
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAAATGTATCGATACAA
Found at i:1206015 original size:13 final size:13
Alignment explanation
Indices: 1205997--1206021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205987 CATAAAATGT
1205997 TGTATCGATACAA
1 TGTATCGATACAA
1206010 TGTATCGATACA
1 TGTATCGATACA
1206022 TATTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1206037 original size:32 final size:33
Alignment explanation
Indices: 1205977--1206042 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1205967 TTCAATGATT
1205977 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
1206010 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1206042 T
1 T
1206043 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1206103 original size:13 final size:13
Alignment explanation
Indices: 1206085--1206109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1206075 ATTACTCACA
1206085 TGTATCGATACAT
1 TGTATCGATACAT
1206098 TGTATCGATACA
1 TGTATCGATACA
1206110 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1206246 original size:52 final size:52
Alignment explanation
Indices: 1206118--1206238 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1206108 CACTGATCTT
*
1206118 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1206170 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1206222 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1206239 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1210305 original size:13 final size:13
Alignment explanation
Indices: 1210287--1210312 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1210277 ACATTATTCT
1210287 TTGTATCGATACA
1 TTGTATCGATACA
1210300 TTGTATCGATACA
1 TTGTATCGATACA
1210313 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1210792 original size:21 final size:20
Alignment explanation
Indices: 1210755--1210797 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1210745 GCAGCACCCA
* *
1210755 CCAGGTCGCGACTGGCACTC
1 CCAGGTCGCAACGGGCACTC
*
1210775 CCAGGTCGCAACCGGGCAGTC
1 CCAGGTCGCAA-CGGGCACTC
1210796 CC
1 CC
1210798 CACACTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.16, C:0.42, G:0.30, T:0.12
Consensus pattern (20 bp):
CCAGGTCGCAACGGGCACTC
Found at i:1212758 original size:20 final size:19
Alignment explanation
Indices: 1212704--1212758 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1212694 AAAACCCTTA
*
1212704 AAAGTATCGATACACAATTG
1 AAAGTATCGATACA-TATTG
1212724 AAAGTATCGATACATATTG
1 AAAGTATCGATACATATTG
*
1212743 CAATGTATCGATACAT
1 -AAAGTATCGATACAT
1212759 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTG
Found at i:1212928 original size:20 final size:22
Alignment explanation
Indices: 1212897--1212940 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1212887 GCTATATTTT
1212897 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1212918 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1212939 CA
1 CA
1212941 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1218141 original size:31 final size:33
Alignment explanation
Indices: 1218086--1218147 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
1218076 GTTATTTCCA
* *
1218086 TATTCGAATTTATTTTAGGCTTAGATTATTTAG
1 TATTCGAATTTATTTTAAGCTTAGATAATTTAG
*
1218119 TATTCG-ATTT-TTTTAAGTTTAGATAATTT
1 TATTCGAATTTATTTTAAGCTTAGATAATTT
1218148 TGGATTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 16 0.62
32 4 0.15
33 6 0.23
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.55
Consensus pattern (33 bp):
TATTCGAATTTATTTTAAGCTTAGATAATTTAG
Found at i:1218993 original size:20 final size:20
Alignment explanation
Indices: 1218970--1219008 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1218960 GTCTTTTTGG
1218970 TTTTTT-TTTTACTTTTTAC
1 TTTTTTGTTTTACTTTTTAC
*
1218989 TTTTTTGTTTTATTTTTTAC
1 TTTTTTGTTTTACTTTTTAC
1219009 AAGGGATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTTGTTTTACTTTTTAC
Found at i:1220294 original size:20 final size:20
Alignment explanation
Indices: 1220250--1220323 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
1220240 TTTTACAATT
* * *
1220250 TGTATCGATATAAACAGTAAA
1 TGTATCGATACATA-AGTGAA
1220271 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
***
1220291 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAAGTG-AA
1220312 TGTATCGATACA
1 TGTATCGATACA
1220324 AAATCACCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 20 0.43
21 26 0.57
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1220399 original size:20 final size:21
Alignment explanation
Indices: 1220351--1220401 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1220341 GCCAAGGAAA
1220351 TGTATCGATACATTTACTATT
1 TGTATCGATACATTTACTATT
* *
1220372 TATATCGATACA-TTATTCA-T
1 TGTATCGATACATTTACT-ATT
1220392 TGTATCGATA
1 TGTATCGATA
1220402 AATTCTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTACTATT
Found at i:1235229 original size:20 final size:20
Alignment explanation
Indices: 1235204--1235368 Score: 177
Period size: 20 Copynumber: 7.7 Consensus size: 20
1235194 TTTTACCCAG
* *
1235204 ATGTATCAATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * *
1235224 ATGTATCGATACATATATGA
1 ATGTATCGATACATTTTTCA
*
1235244 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1235264 ATGTATCGATACATTATGTCTTTTTTTCCA
1 ATGTATCGATAC---A------TTTTT-CA
1235294 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1235315 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1235335 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1235355 ATGTATCGATACAT
1 ATGTATCGATACAT
1235369 CTAGTTAAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
20 98 0.78
21 2 0.02
22 5 0.04
23 1 0.01
28 1 0.01
29 4 0.03
30 2 0.02
31 12 0.10
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1235348 original size:91 final size:91
Alignment explanation
Indices: 1235200--1235368 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 91
1235190 ACATTTTTAC
* *
1235200 CCAGATGTATCAATACATTTTTTAATGTATCGATACATATATGAATGTATCGATACATTCTTCAA
1 CCAGATGTATCAATACATTTTTCAATGTATCGATACATATATCAATGTATCGATACATTCTTCAA
1235265 TGTATCGATACATTATGTCTTTTTTT
66 TGTATCGATACATTATGTCTTTTTTT
* * * *
1235291 CCAGATGTATCGATACATTTTTCAATGTATCGATACATTTTTCAATGTATCGATACATTTTTCAA
1 CCAGATGTATCAATACATTTTTCAATGTATCGATACATATATCAATGTATCGATACATTCTTCAA
1235356 TGTATCGATACAT
66 TGTATCGATACAT
1235369 CTAGTTAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (91 bp):
CCAGATGTATCAATACATTTTTCAATGTATCGATACATATATCAATGTATCGATACATTCTTCAA
TGTATCGATACATTATGTCTTTTTTT
Found at i:1239490 original size:19 final size:20
Alignment explanation
Indices: 1239466--1239520 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1239456 GTATCTATAC
*
1239466 ATTGTATCGATACATGCT-T
1 ATTGTATCGATACATGCTCA
* *
1239485 ATTGTATCGTTACATACTCA
1 ATTGTATCGATACATGCTCA
*
1239505 ATTATATCGATACATG
1 ATTGTATCGATACATG
1239521 GAACTGATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (20 bp):
ATTGTATCGATACATGCTCA
Found at i:1239518 original size:20 final size:19
Alignment explanation
Indices: 1239470--1239519 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1239460 CTATACATTG
* * *
1239470 TATCGATACATGCTTATTG
1 TATCGATACATACTAATTA
*
1239489 TATCGTTACATACTCAATTA
1 TATCGATACATACT-AATTA
1239509 TATCGATACAT
1 TATCGATACAT
1239520 GGAACTGATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (19 bp):
TATCGATACATACTAATTA
Found at i:1239578 original size:20 final size:20
Alignment explanation
Indices: 1239549--1239598 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1239539 CTAAGTGAAA
* *
1239549 TGTATTGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
1239569 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
1239589 TGTATCGATA
1 TGTATCGATA
1239599 TATTATGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:1245650 original size:52 final size:52
Alignment explanation
Indices: 1245572--1245720 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 52
1245562 CCCGAAATAT
*
1245572 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGA
1 GAAAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGA
** * *
1245624 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGA
* *
1245676 GCAAATTTGCCTGCATGTATCGATACA-AAAATCAGTGTATCGATA
1 GAAAATTTGCCTGCATGTATCGATACATTAAAT-AGTGTATCGATA
1245721 TAATGTATCG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGA
Found at i:1245817 original size:13 final size:13
Alignment explanation
Indices: 1245799--1245823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1245789 AAAAAAAAAA
1245799 TGTATCGATACAT
1 TGTATCGATACAT
1245812 TGTATCGATACA
1 TGTATCGATACA
1245824 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1249372 original size:21 final size:21
Alignment explanation
Indices: 1249346--1249401 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1249336 TTTTTGTTTA
1249346 AATGTATCGATACATTTCTTG
1 AATGTATCGATACATTTCTTG
* *
1249367 AATGTATTGATACCTTTCTTG
1 AATGTATCGATACATTTCTTG
*
1249388 AATGTATCAATACA
1 AATGTATCGATACA
1249402 AGGTAACAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (21 bp):
AATGTATCGATACATTTCTTG
Found at i:1249535 original size:20 final size:20
Alignment explanation
Indices: 1249510--1249581 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1249500 ACCCAGATGC
1249510 ATCGATACATGATTCAATGT
1 ATCGATACATGATTCAATGT
**
1249530 ATCGATACATTG-CCCAGATGT
1 ATCGATACA-TGATTCA-ATGT
*
1249551 ATCGATACATTATTCAATGT
1 ATCGATACATGATTCAATGT
1249571 ATCGATACATG
1 ATCGATACATG
1249582 CAGGCAAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATCGATACATGATTCAATGT
Found at i:1249546 original size:41 final size:41
Alignment explanation
Indices: 1249501--1249580 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
1249491 TGGGTATTTA
1249501 CCCAGATGCATCGATACATGATTCAATGTATCGATACATTG
1 CCCAGATGCATCGATACATGATTCAATGTATCGATACATTG
* *
1249542 CCCAGATGTATCGATACATTATTCAATGTATCGATACAT
1 CCCAGATGCATCGATACATGATTCAATGTATCGATACAT
1249581 GCAGGCAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (41 bp):
CCCAGATGCATCGATACATGATTCAATGTATCGATACATTG
Found at i:1249552 original size:21 final size:20
Alignment explanation
Indices: 1249524--1249580 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
1249514 ATACATGATT
1249524 CAATGTATCGATACATTGCC
1 CAATGTATCGATACATTGCC
***
1249544 CAGATGTATCGATACATTATT
1 CA-ATGTATCGATACATTGCC
1249565 CAATGTATCGATACAT
1 CAATGTATCGATACAT
1249581 GCAGGCAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
CAATGTATCGATACATTGCC
Found at i:1251550 original size:19 final size:19
Alignment explanation
Indices: 1251528--1251564 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1251518 TCCTCTGTAA
*
1251528 AAAAAATAAAAAAACAAAC
1 AAAAAACAAAAAAACAAAC
1251547 AAAAAACAAAAAAACAAA
1 AAAAAACAAAAAAACAAA
1251565 AAAGGGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (19 bp):
AAAAAACAAAAAAACAAAC
Found at i:1252928 original size:32 final size:32
Alignment explanation
Indices: 1252884--1253072 Score: 267
Period size: 32 Copynumber: 5.9 Consensus size: 32
1252874 ACACGAATCC
*
1252884 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCT
1 CTTCT-AAAGCCCACACAAGTTGGTGGCAACCT
* *
1252917 CTTCAAAAGCCCACATAAGTTGGTGGCAACC-
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
1252948 CTTTCTAAAGCCCACACAAGTTGGTGGCAACCTT
1 C-TTCTAAAGCCCACACAAGTTGGTGGCAACC-T
1252982 CTT-TAAAGCCCACACAAGTTGGTGGCAACCTT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACC-T
1253014 CTT-TAAAGCCCACACAAGTTGGTGGCAACCT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
* * *
1253045 TTTCAAAAGCCCACACAAGTTGGGGGCA
1 CTTCTAAAGCCCACACAAGTTGGTGGCA
1253073 TTTCCTTCTA
Statistics
Matches: 144, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
31 4 0.03
32 133 0.92
33 6 0.04
34 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (32 bp):
CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
Found at i:1253054 original size:96 final size:96
Alignment explanation
Indices: 1252890--1253072 Score: 296
Period size: 96 Copynumber: 1.9 Consensus size: 96
1252880 ATCCCTTCTC
* *
1252890 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACATAAGTTGGTGGCAACCCTTTCTA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCAA
*
1252955 AAGCCCACACAAGTTGGTGGCAACCTTCTTT
66 AAGCCCACACAAGTTGGGGGCAACCTTCTTT
* * *
1252986 AAAGCCCACACAAGTTGGTGGCAACCTTCTT-TAAAGCCCACACAAGTTGGTGGCAACCTTTTCA
1 AAAGCCCACACAAGTCGGTGGCAACC-TCTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCA
1253050 AAAGCCCACACAAGTTGGGGGCA
65 AAAGCCCACACAAGTTGGGGGCA
1253073 TTTCCTTCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 76 0.95
97 4 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (96 bp):
AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCAA
AAGCCCACACAAGTTGGGGGCAACCTTCTTT
Found at i:1253199 original size:52 final size:50
Alignment explanation
Indices: 1253121--1253478 Score: 287
Period size: 52 Copynumber: 7.0 Consensus size: 50
1253111 ACATTGGCAC
* * *
1253121 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGAACATTGGCACCTTTGCCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT--CAT
*
1253173 CTTTAAGTCCAATGTCGCTGGCCTTGAAT-TGCCACATTGGCA-CTTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAG-CACATTGGCACCTTTCAT
* * * *
1253222 TTTTAAGTCCAATGTCGTTGGCCTTGAATTAGCACATTGGCACC-ATCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTCAT
* * ** * * *
1253271 CTTTAAGTCCGATATTACTGGCCTTGAATCAACATATTGGCATCTTTAACAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT--CAT
* * * *
1253323 -TCCTAAG-CCCATGTCGCTGGCCTTGAACCAGCACATTGGCATTCTTCTCAT
1 CT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTT-TCAT
* * * * * ** *
1253374 CTTCAAGTCTAATGTCGCTGGTCGTGAATCAGCACATTGACATTTTTTGTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTT-CAT
* * *
1253426 CTTTAAG-CACAATATCGTTGGCCTTGAATCAGCATATTGGCACCATTCTCAT
1 CTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-TCAT
1253478 C
1 C
1253479 CTTATAATCT
Statistics
Matches: 243, Mismatches: 48, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
49 78 0.32
50 3 0.01
51 41 0.17
52 119 0.49
53 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (50 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTCAT
Found at i:1253244 original size:49 final size:48
Alignment explanation
Indices: 1253121--1253280 Score: 203
Period size: 49 Copynumber: 3.2 Consensus size: 48
1253111 ACATTGGCAC
* * *
1253121 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGAACATTGGCACCTTTGCCAT
1 CTTTAAGTCCAATGTCGTTGGCCTTGAAT-TGCACATTGGCA-CTTT--CAT
*
1253173 CTTTAAGTCCAATGTCGCTGGCCTTGAATTGCCACATTGGCACTTTCAT
1 CTTTAAGTCCAATGTCGTTGGCCTTGAATTG-CACATTGGCACTTTCAT
* **
1253222 TTTTAAGTCCAATGTCGTTGGCCTTGAATTAGCACATTGGCACCATCAT
1 CTTTAAGTCCAATGTCGTTGGCCTTGAATT-GCACATTGGCACTTTCAT
1253271 CTTTAAGTCC
1 CTTTAAGTCC
1253281 GATATTACTG
Statistics
Matches: 97, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
49 55 0.57
50 1 0.01
51 5 0.05
52 36 0.37
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (48 bp):
CTTTAAGTCCAATGTCGTTGGCCTTGAATTGCACATTGGCACTTTCAT
Found at i:1253293 original size:49 final size:49
Alignment explanation
Indices: 1253098--1253299 Score: 202
Period size: 49 Copynumber: 4.2 Consensus size: 49
1253088 AATGTCACTA
*
1253098 GCCTTGAATTAGCACATTGG---CA-C--CTTTAAGTCCAATATCGTTG
1 GCCTTGAATTAGCACATTGGCACCATCATCTTTAAGTCCAATATCGCTG
* * * *
1253141 GCCTTGAATCAGAACATTGGCACCTTTGCCATCTTTAAGTCCAATGTCGCTG
1 GCCTTGAATTAGCACATTGGCACC-AT--CATCTTTAAGTCCAATATCGCTG
** * * *
1253193 GCCTTGAATT-GCCACATTGGCACTTTCATTTTTAAGTCCAATGTCGTTG
1 GCCTTGAATTAG-CACATTGGCACCATCATCTTTAAGTCCAATATCGCTG
* **
1253242 GCCTTGAATTAGCACATTGGCACCATCATCTTTAAGTCCGATATTACTG
1 GCCTTGAATTAGCACATTGGCACCATCATCTTTAAGTCCAATATCGCTG
1253291 GCCTTGAAT
1 GCCTTGAAT
1253300 CAACATATTG
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
43 18 0.14
46 1 0.01
49 69 0.53
50 2 0.02
51 3 0.02
52 37 0.28
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (49 bp):
GCCTTGAATTAGCACATTGGCACCATCATCTTTAAGTCCAATATCGCTG
Found at i:1256360 original size:13 final size:12
Alignment explanation
Indices: 1256328--1256365 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1256318 TGTCCTTTGC
*
1256328 AACAAACAAA-A
1 AACAAAAAAATA
1256339 AACAAAAAAATA
1 AACAAAAAAATA
1256351 AACAAAAAAAATA
1 AAC-AAAAAAATA
1256364 AA
1 AA
1256366 AAAGGGGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (12 bp):
AACAAAAAAATA
Found at i:1257743 original size:32 final size:32
Alignment explanation
Indices: 1257699--1257881 Score: 219
Period size: 32 Copynumber: 5.7 Consensus size: 32
1257689 ACACGAATCC
*
1257699 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCT
1 CTTCT-AAAGCCCACACAAGTTGGTGGCAACCT
* *
1257732 CTTCAAAAGCCCACATAAGTTGGTGGCAACCT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
*
1257764 TTTCTAAAGCCCACACAAGTTGGTGGCAACCTT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACC-T
*
1257797 CTT-TAAAGCCCACACAAGTTAGTGGCAACCTT
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACC-T
* *
1257829 CTT-TAAAGCCCACACAAGTCGATGGCAACC-
1 CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
* * *
1257859 CTTTCAAAAACCCACATAAGTTG
1 C-TTCTAAAGCCCACACAAGTTG
1257882 AGAGCATTTC
Statistics
Matches: 132, Mismatches: 15, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
32 122 0.92
33 7 0.05
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (32 bp):
CTTCTAAAGCCCACACAAGTTGGTGGCAACCT
Found at i:1257806 original size:64 final size:64
Alignment explanation
Indices: 1257699--1257881 Score: 246
Period size: 64 Copynumber: 2.8 Consensus size: 64
1257689 ACACGAATCC
*
1257699 CTTCTCAAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACATAAGTTGGTGGCAACCT
1 CTTCT-AAAGCCCACACAAGTCGGTGGCAACCTCTT-TAAAGCCCACATAAGTTGGTGGCAACCT
1257764 T
64 T
* * *
1257765 -TTCTAAAGCCCACACAAGTTGGTGGCAACCTTCTTTAAAGCCCACACAAGTTAGTGGCAACCTT
1 CTTCTAAAGCCCACACAAGTCGGTGGCAACC-TCTTTAAAGCCCACATAAGTTGGTGGCAACCTT
* *
1257829 CTT-TAAAGCCCACACAAGTCGATGGCAACC-CTTTCAAAAACCCACATAAGTTG
1 CTTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTT--AAAGCCCACATAAGTTG
1257882 AGAGCATTTC
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
62 4 0.04
64 90 0.87
65 10 0.10
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (64 bp):
CTTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTTAAAGCCCACATAAGTTGGTGGCAACCTT
Found at i:1257873 original size:96 final size:96
Alignment explanation
Indices: 1257705--1257881 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 96
1257695 ATCCCTTCTC
* * * * * *
1257705 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACATAAGTTGGTGGCAACCTTTTCTA
1 AAAGCCCACACAAGTCAGTGGCAACCTCTTCAAAAGCCCACACAAGTCGATGGCAACCCTTTCAA
*
1257770 AAGCCCACACAAGTTGGTGGCAACCTTCTTT
66 AAACCCACACAAGTTGGTGGCAACCTTCTTT
* *
1257801 AAAGCCCACACAAGTTAGTGGCAACCTTCTT-TAAAGCCCACACAAGTCGATGGCAACCCTTTCA
1 AAAGCCCACACAAGTCAGTGGCAACC-TCTTCAAAAGCCCACACAAGTCGATGGCAACCCTTTCA
*
1257865 AAAACCCACATAAGTTG
65 AAAACCCACACAAGTTG
1257882 AGAGCATTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 66 0.94
97 4 0.06
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (96 bp):
AAAGCCCACACAAGTCAGTGGCAACCTCTTCAAAAGCCCACACAAGTCGATGGCAACCCTTTCAA
AAACCCACACAAGTTGGTGGCAACCTTCTTT
Found at i:1258014 original size:52 final size:50
Alignment explanation
Indices: 1257936--1258193 Score: 232
Period size: 52 Copynumber: 5.0 Consensus size: 50
1257926 ACATTGGCAC
*
1257936 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGCCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTT-CCAT
* *
1257988 CTTTAAGTCCAATGTCGGTAGCCTTGAATC-GCCACATTGGCACTTT-CAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAG-CACATTGGCACTTTCCAT
* * * *
1258037 TTTTAAGTCCAATGTCGCTGGCTTTGAATTAGCACATTGGCATTCTTCTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACT-TTC-CAT
* * ** * * **
1258089 CTTCAAGTCTAATGTCGCTGGCCGGGAATCAGCACATTGACATTTTTTGTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--CTTTCCAT
* * ** * *
1258141 CTTTAAGCCCAATATCATTGGCCTTGAATCAGCATATTAGCACATTTCTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-TTTC-CAT
1258193 C
1 C
1258194 CTTATCATCT
Statistics
Matches: 164, Mismatches: 33, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
49 39 0.24
50 3 0.02
51 8 0.05
52 110 0.67
53 2 0.01
54 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (50 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTCCAT
Found at i:1258118 original size:101 final size:100
Alignment explanation
Indices: 1257937--1258193 Score: 248
Period size: 101 Copynumber: 2.5 Consensus size: 100
1257927 CATTGGCACC
*
1257937 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGCCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-CCATCTTCAAGTCCAATG
* **
1258002 TCGGTAGCCTTGAATC-GCCACATTGGCACTTTCATT
65 TCGCTAGCCGGGAATCAG-CACATTGGCACTTTCATT
* * * * *
1258038 TTTAAGTCCAATGTCGCTGGCTTTGAATTAGCACATTGGCA-TTCTTCTCATCTTCAAGTCTAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT-TTC-CATCTTCAAGTCCAAT
* * * * *
1258102 GTCGCTGGCCGGGAATCAGCACATTGACATTTTTTGTATC
64 GTCGCTAGCCGGGAATCAGCACATTGGCA--CTTT-CATT
* ** * * *
1258142 TTTAAGCCCAATATCATTGGCCTTGAATCAGCATATTAGCACATTTCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTC-CATC
1258194 CTTATCATCT
Statistics
Matches: 126, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
100 2 0.02
101 76 0.60
102 1 0.01
103 3 0.02
104 43 0.34
105 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (100 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTCCATCTTCAAGTCCAATGT
CGCTAGCCGGGAATCAGCACATTGGCACTTTCATT
Found at i:1258227 original size:61 final size:61
Alignment explanation
Indices: 1258162--1258297 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
1258152 ATATCATTGG
*
1258162 CCTTGAATCAGCA-TATTAGCACAT-TTCTCATCCTTATCATCTTTAAATCCAGCGTTGTTGA
1 CCTTGAATCAGCACT-TTAGCAC-TCTTCTCATCCTTATCATCTTTAAATCCAGCGTTGTAGA
* * * * * * * *
1258223 CCTTGAATTAGCACTTTGGCACTCTTTTCATCTTTATCTTCTTTAAGTCCAGTGTTGTAGG
1 CCTTGAATCAGCACTTTAGCACTCTTCTCATCCTTATCATCTTTAAATCCAGCGTTGTAGA
*
1258284 CCTTGAATCTGCAC
1 CCTTGAATCAGCAC
1258298 ACTGAACATA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 1 0.02
61 60 0.97
62 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (61 bp):
CCTTGAATCAGCACTTTAGCACTCTTCTCATCCTTATCATCTTTAAATCCAGCGTTGTAGA
Found at i:1262527 original size:57 final size:60
Alignment explanation
Indices: 1262458--1262575 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
1262448 TTATAATTAG
* *
1262458 TGTTGTTCATCATCCAT-AAAGAAA-AC-AAAAAAAAAGTGTTCTAGTATCCTAACCTTT
1 TGTTGTTCATCATCCATAAAAGAAAGACAAAAAAAAAAGTGTTATAGTATCATAACCTTT
* * *
1262515 TGTTGTTCATCATCTATAAAAGAAAGCCAAAAAAAAAAGTGTTATAGTGTCATAACCTTT
1 TGTTGTTCATCATCCATAAAAGAAAGACAAAAAAAAAAGTGTTATAGTATCATAACCTTT
1262575 T
1 T
1262576 CCATCTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 16 0.30
58 7 0.13
59 1 0.02
60 29 0.55
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (60 bp):
TGTTGTTCATCATCCATAAAAGAAAGACAAAAAAAAAAGTGTTATAGTATCATAACCTTT
Found at i:1262699 original size:27 final size:27
Alignment explanation
Indices: 1262630--1262704 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
1262620 TTATAAAGAA
* *
1262630 TTCTTTGATCAGTTT-TCATTGATTTCTC
1 TTCTTTGATC--TTTCTTATTGATTTCAC
*
1262658 TTCCTTTGATATTTCTTATTGATTTCAC
1 TT-CTTTGATCTTTCTTATTGATTTCAC
1262686 TTCTTTGATCTTTCTTATT
1 TTCTTTGATCTTTCTTATT
1262705 TATTAATCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 19 0.46
28 15 0.37
29 7 0.17
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (27 bp):
TTCTTTGATCTTTCTTATTGATTTCAC
Found at i:1264201 original size:53 final size:53
Alignment explanation
Indices: 1264133--1264340 Score: 224
Period size: 53 Copynumber: 3.9 Consensus size: 53
1264123 GGAGATAATG
* * *
1264133 GGGTTGGAGTATCCTCGTAAATGAAAATTTTGATTTTTTTTGAAGTAAAAACA
1 GGGTTGGAGTATCCTCGTAGATGAAAATTTTGATATTTTTAGAAGTAAAAACA
* * **
1264186 GGGTCGGAGTATCCTCGTAGATAGAAAA-TTTAATATTTTTAGAAGTAAAAAGG
1 GGGTTGGAGTATCCTCGTAGAT-GAAAATTTTGATATTTTTAGAAGTAAAAACA
* **
1264239 GGGTTGGAGTATCC-CTGTAGATGAAAATTTTGATATTTTTAGAAATAAAAATT
1 GGGTTGGAGTATCCTC-GTAGATGAAAATTTTGATATTTTTAGAAGTAAAAACA
* * * * * *
1264292 GAGTTAGAGTATCCCCGAAGATGGAAAA-TTTGATGTTTTTGGAAGTAAA
1 GGGTTGGAGTATCCTCGTAGAT-GAAAATTTTGATATTTTTAGAAGTAAA
1264341 GACGTGGTTC
Statistics
Matches: 132, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
52 6 0.05
53 115 0.87
54 11 0.08
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (53 bp):
GGGTTGGAGTATCCTCGTAGATGAAAATTTTGATATTTTTAGAAGTAAAAACA
Found at i:1264319 original size:106 final size:106
Alignment explanation
Indices: 1264132--1264340 Score: 267
Period size: 106 Copynumber: 2.0 Consensus size: 106
1264122 TGGAGATAAT
* * * * *
1264132 GGGGTTGGAGTATCCTCGTAAATGAAAATTTTGATTTTTTTTGAAGTAAAAACAGGGTCGGAGTA
1 GGGGTTGGAGTATCCTCGTAAATGAAAATTTTGATATTTTTAGAAATAAAAACAGAGTCAGAGTA
* *
1264197 TCCTCGTAGATAGAAAATTTAATATTTTTAGAAGTAAAAAG
66 TCCCCGAAGATAGAAAATTTAATATTTTTAGAAGTAAAAAG
* ** *
1264238 GGGGTTGGAGTATCC-CTGTAGATGAAAATTTTGATATTTTTAGAAATAAAAATTGAGTTAGAGT
1 GGGGTTGGAGTATCCTC-GTAAATGAAAATTTTGATATTTTTAGAAATAAAAACAGAGTCAGAGT
* * * *
1264302 ATCCCCGAAGATGGAAAATTTGATGTTTTTGGAAGTAAA
65 ATCCCCGAAGATAGAAAATTTAATATTTTTAGAAGTAAA
1264341 GACGTGGTTC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
105 1 0.01
106 86 0.99
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.34
Consensus pattern (106 bp):
GGGGTTGGAGTATCCTCGTAAATGAAAATTTTGATATTTTTAGAAATAAAAACAGAGTCAGAGTA
TCCCCGAAGATAGAAAATTTAATATTTTTAGAAGTAAAAAG
Found at i:1264495 original size:119 final size:119
Alignment explanation
Indices: 1264346--1264572 Score: 350
Period size: 119 Copynumber: 1.9 Consensus size: 119
1264336 GTAAAGACGT
* *
1264346 GGTTCGAGTTTCCCCATAAATGACGACTTTGGTGAGTCTCAAAATTTGAATGAGATTTGCAAAAA
1 GGTTAGAGTATCCCCATAAATGACGACTTTGGTGAGTCTCAAAATTTGAATGAGATTTGCAAAAA
* * *
1264411 C-AGGATTAGAGTATCCCCTCGGAGGATGGGGTTAGAGTATCCCTCGAAATACAA
66 CGAAG-TTAGAGTATCCCCTCGGAGGACGAGGTTAGAGTATCCCTCGAAATACAA
*
1264465 GGTTAGAGTATCCCCATAAATGAC-AGCTTTGGTGAGTTTCAAAATTTGAATGAGATTTGCAAAA
1 GGTTAGAGTATCCCCATAAATGACGA-CTTTGGTGAGTCTCAAAATTTGAATGAGATTTGCAAAA
* *
1264529 GCGAAGTTAGAGTATCCCTTCGGAGGACGAGGTTAGAGTATCCC
65 ACGAAGTTAGAGTATCCCCTCGGAGGACGAGGTTAGAGTATCCC
1264573 CTAAAAAGCT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
118 1 0.01
119 95 0.97
120 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (119 bp):
GGTTAGAGTATCCCCATAAATGACGACTTTGGTGAGTCTCAAAATTTGAATGAGATTTGCAAAAA
CGAAGTTAGAGTATCCCCTCGGAGGACGAGGTTAGAGTATCCCTCGAAATACAA
Found at i:1266318 original size:20 final size:20
Alignment explanation
Indices: 1266281--1266318 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1266271 AAATTTAGAG
*
1266281 TCAAATTTTTCTAAATCTTT
1 TCAAATTTTCCTAAATCTTT
*
1266301 TCAAATTTTCCTAGATCT
1 TCAAATTTTCCTAAATCT
1266319 ACAGTAAAAG
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:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (20 bp):
TCAAATTTTCCTAAATCTTT
Found at i:1276564 original size:17 final size:17
Alignment explanation
Indices: 1276544--1276576 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1276534 CTCGGAATTA
1276544 GTATGGTTGGAGTATTT
1 GTATGGTTGGAGTATTT
1276561 GTATGGTTGGAGTATT
1 GTATGGTTGGAGTATT
1276577 CCCATAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (17 bp):
GTATGGTTGGAGTATTT
Found at i:1276680 original size:53 final size:51
Alignment explanation
Indices: 1276584--1276736 Score: 146
Period size: 53 Copynumber: 2.9 Consensus size: 51
1276574 ATTCCCATAG
* * * * **
1276584 ATGGAAATTTTTATTTTTTTAAAGTAAAAATAGGGTTAGAGTATCGTCGCAA
1 ATGGAAATTTTGATATTTTTAAAGT-AAAAGAGGGTTAAAGTATCCCCGCAA
* * *
1276636 ATGGAAATTTTGATATTTTTAGAAGTAAAAGCGGAGTTAAAGTATCCCCGTAG
1 ATGGAAATTTTGATATTTTTA-AAGTAAAAGAGG-GTTAAAGTATCCCCGCAA
* *
1276689 ATGGAAAATTTGATATTTTTAAAAGTAAAA-ATGGGGTTAGAGTATCCC
1 ATGGAAATTTTGATATTTTT-AAAGTAAAAGA--GGGTTAAAGTATCCC
1276737 TTTGGAAATA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
52 25 0.30
53 56 0.67
54 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (51 bp):
ATGGAAATTTTGATATTTTTAAAGTAAAAGAGGGTTAAAGTATCCCCGCAA
Found at i:1285492 original size:19 final size:18
Alignment explanation
Indices: 1285468--1285528 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
1285458 CGATACATTA
1285468 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
1285487 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
1285500 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
1285519 TATCGATACA
1 TATCGATACA
1285529 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:1285504 original size:32 final size:32
Alignment explanation
Indices: 1285458--1285543 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
1285448 AGCTTCATAG
*
1285458 CGATACATTATATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1285490 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1285522 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
1285544 TTGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1286152 original size:20 final size:20
Alignment explanation
Indices: 1286123--1286194 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1286113 ACCCTAGAAA
1286123 GTATCAATACATATCTAGAT
1 GTATCAATACATATCTAGAT
* *
1286143 GTATCGATACATTATGCT--TT
1 GTATCAATACA-TAT-CTAGAT
*
1286163 GTATCGATACATATCTAGAT
1 GTATCAATACATATCTAGAT
1286183 GTATCAATACAT
1 GTATCAATACAT
1286195 TATGCTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 34 0.77
21 3 0.07
22 2 0.05
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCAATACATATCTAGAT
Found at i:1286178 original size:40 final size:40
Alignment explanation
Indices: 1286123--1286214 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
1286113 ACCCTAGAAA
* *
1286123 GTATCAATACATATCTAGATGTATCGATACATTATGCTTT
1 GTATCGATACATATCTAGATGTATCAATACATTATGCTTT
1286163 GTATCGATACATATCTAGATGTATCAATACATTATGCTTT
1 GTATCGATACATATCTAGATGTATCAATACATTATGCTTT
1286203 GTATCGATACAT
1 GTATCGATACAT
1286215 TGTATCGATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (40 bp):
GTATCGATACATATCTAGATGTATCAATACATTATGCTTT
Found at i:1286205 original size:20 final size:20
Alignment explanation
Indices: 1286142--1286215 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
1286132 CATATCTAGA
1286142 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
1286162 TGTATCGATACA-TAT-CTAGA
1 TGTATCGATACATTATGCT--T
*
1286182 TGTATCAATACATTATGCTT
1 TGTATCGATACATTATGCTT
1286202 TGTATCGATACATT
1 TGTATCGATACATT
1286216 GTATCGATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 36 0.78
21 3 0.07
22 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:1286219 original size:13 final size:13
Alignment explanation
Indices: 1286201--1286227 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1286191 ACATTATGCT
1286201 TTGTATCGATACA
1 TTGTATCGATACA
1286214 TTGTATCGATACA
1 TTGTATCGATACA
1286227 T
1 T
1286228 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1286236 original size:19 final size:19
Alignment explanation
Indices: 1286212--1286267 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1286202 TGTATCGATA
*
1286212 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGCT
*
1286231 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
*
1286250 CAATTGTATTGATACATG
1 C-ATTGTATCGATACATG
1286268 AAAGTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1286339 original size:20 final size:19
Alignment explanation
Indices: 1286292--1286345 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1286282 TACCCTAAGT
*
1286292 GAAATGTATCGATACATGG
1 GAAATGTATCGATACATGA
*
1286311 GACATTGTATCGATACATGAA
1 GA-AATGTATCGATACATG-A
1286332 GAAATGTATCGATA
1 GAAATGTATCGATA
1286346 AAATATGCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (19 bp):
GAAATGTATCGATACATGA
Found at i:1289820 original size:51 final size:51
Alignment explanation
Indices: 1289742--1289857 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
1289732 AAATAACGGG
* * * *
1289742 GTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTT-GAAAATAAAACCTGA
1 GTTGGAATATCCCCAATTGTGAGAAATTAGTATTTTAGAAAA-AAAACCTGA
* *
1289793 GTTGGAATATCTCCAATTGTG-GAAAATTAGTATTTTAGAAAAAAAATC-GA
1 GTTGGAATATCCCCAATTGTGAG-AAATTAGTATTTTAGAAAAAAAACCTGA
*
1289843 GGTTGGAGTATCCCC
1 -GTTGGAATATCCCC
1289858 TCGAAAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
50 3 0.06
51 46 0.85
52 5 0.09
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (51 bp):
GTTGGAATATCCCCAATTGTGAGAAATTAGTATTTTAGAAAAAAAACCTGA
Found at i:1289881 original size:130 final size:124
Alignment explanation
Indices: 1289575--1289935 Score: 381
Period size: 122 Copynumber: 2.9 Consensus size: 124
1289565 ATCGGTGTTC
* * *
1289575 TAGAAATAAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCCTGATTAT
1 TAGAAA-AAAAATCGAGGTTGGAGTATCCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTGT
* * * * * *
1289640 AAAAAATCGGTATTTTGAAAATAAAATCGGAGTTGGAGTATCCCTGATTGTGAAAAATTAA
64 GAAAAATTGGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCTAATTGTGAAAAATTAA
* * * *
1289701 T---AATAAAGTCGGGGTTGGTGTATCCCCTC-AGAAATAACGGGGTTGGAGTATCCCCGATTGT
1 TAGAAAAAAAATCGAGGTTGGAGTATCCCCTCGA-AAATAAC-GGGTTGGAGTATCCCCGATTGT
* * *
1289762 GAGAAATTGGTGTTTTGAAAATAAAACCTGAGTTGGAATATCTCC-AATTGTGGAAAATTAGTA
64 GAAAAATTGGTGTTTTGAAAATAAAACCGGAGTTGGAATATC-CCTAATTGTGAAAAATTA--A
1289825 TTTTAGAAAAAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATT
1 ---TAGAAAAAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGG-TTGGAGTATCCCCGATT
* * ** * * *
1289890 GTGAAAAACTGCTGTTTTGGGAATAAAATCGGGGTTGGAGTATCCC
62 GTGAAAAATTGGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCC
1289936 CTCGGAAATA
Statistics
Matches: 193, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
121 1 0.01
122 96 0.50
123 4 0.02
124 1 0.01
126 1 0.01
127 1 0.01
129 5 0.03
130 83 0.43
131 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (124 bp):
TAGAAAAAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGTTGGAGTATCCCCGATTGTGA
AAAATTGGTGTTTTGAAAATAAAACCGGAGTTGGAATATCCCTAATTGTGAAAAATTAA
Found at i:1289955 original size:28 final size:28
Alignment explanation
Indices: 1289919--1289993 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
1289909 GGAATAAAAT
**
1289919 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* * *
1289947 CGGGATTGGAGTATCCCCGATGACATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
1289975 CGGGGTTGGAGTA-CCCCGA
1 CGGGGTTGGAGTATCCCCGA
1289994 TTATGAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 6 0.15
28 35 0.85
ACGTcount: A:0.24, C:0.23, G:0.33, T:0.20
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1290079 original size:134 final size:135
Alignment explanation
Indices: 1289919--1290178 Score: 416
Period size: 134 Copynumber: 1.9 Consensus size: 135
1289909 GGAATAAAAT
* * * * *
1289919 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGATTGGAGTATCCCCGATGACATAACGGGGTTGG
1 CGGGGTTAGAGTATCCCCTAGAAAATAACGAGATTGAAGTATCCCCGATGACATAACGGGGTTGG
*
1289984 AGTA-CCCCGATTATGAAAAATCAATATTTTAAATATAAAGC-CGGGATTGGAGTATCCCCTCGA
66 AGTACCCCCGATTATGAAAAATCAATATTTTAAATATAAAGCTAGGG-TTGGAGTATCCCCTCGA
1290047 AAATAA
130 AAATAA
*
1290053 CGGGGTTAGAGTATCCCCTAGAAAATAACGAGATTGAAGTATCCGCGATGACATAACGGGGTTGG
1 CGGGGTTAGAGTATCCCCTAGAAAATAACGAGATTGAAGTATCCCCGATGACATAACGGGGTTGG
* *
1290118 AGTACCCCCGATTATGAAAAATCCATATTTTAGATATAAAGCTAGGGTTGGAGTATCCCCT
66 AGTACCCCCGATTATGAAAAATCAATATTTTAAATATAAAGCTAGGGTTGGAGTATCCCCT
1290179 AGGAAAAATG
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
134 63 0.55
135 49 0.43
136 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (135 bp):
CGGGGTTAGAGTATCCCCTAGAAAATAACGAGATTGAAGTATCCCCGATGACATAACGGGGTTGG
AGTACCCCCGATTATGAAAAATCAATATTTTAAATATAAAGCTAGGGTTGGAGTATCCCCTCGAA
AATAA
Found at i:1290081 original size:106 final size:106
Alignment explanation
Indices: 1289843--1290101 Score: 294
Period size: 106 Copynumber: 2.4 Consensus size: 106
1289833 AAAAAATCGA
* * *
1289843 GGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTGTGAAAAACTGCTGTTTT
1 GGTTGGAGTATCCCCTAGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAACTGCTATTTT
* * * *
1289908 GGGAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGG
66 -GAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACGG
* * * *
1289950 GATTGGAGTATCCCCGATG-ACATAACGGGGTTGGAGTA-CCCCGATTATGAAAAA-T-CAATAT
1 GGTTGGAGTATCCCCTA-GAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAACTGC--TAT
1290011 TTT-AAATATAAAGCCGGGATTGGAGTATCCCCTCGAAAATAACGG
63 TTTGAAATA-AAA-CCGGGATTGGAGTATCCCCTCGAAAATAACGG
* * * *
1290056 GGTTAGAGTATCCCCTAGAAAATAACGAGATTGAAGTATCCGCGAT
1 GGTTGGAGTATCCCCTAGAAAATAACGGGATTGGAGTATCCCCGAT
1290102 GACATAACGG
Statistics
Matches: 126, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
104 5 0.04
105 5 0.04
106 78 0.62
107 37 0.29
108 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (106 bp):
GGTTGGAGTATCCCCTAGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAACTGCTATTTT
GAAATAAAACCGGGATTGGAGTATCCCCTCGAAAATAACGG
Found at i:1290121 original size:28 final size:28
Alignment explanation
Indices: 1290025--1290128 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
1290015 AATATAAAGC
* **
1290025 CGGGATTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCCGAGAAAATAA
* *
1290053 CGGGGTTAGAGTATCCCCTAGAAAATAA
1 CGGGGTTGGAGTATCCCCGAGAAAATAA
* * * * *
1290081 CGAGATTGAAGTATCCGCGATG-ACATAA
1 CGGGGTTGGAGTATCCCCGA-GAAAATAA
*
1290109 CGGGGTTGGAGTACCCCCGA
1 CGGGGTTGGAGTATCCCCGA
1290129 TTATGAAAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 59 0.98
29 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGAAAATAA
Found at i:1291795 original size:20 final size:19
Alignment explanation
Indices: 1291770--1291843 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
1291760 AAAATGCCTG
*
1291770 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
1291790 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
1291810 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
1291830 AATGTATCGATACA
1 AATGTATCGATACA
1291844 TCTGGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:1297211 original size:29 final size:28
Alignment explanation
Indices: 1297169--1297224 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
1297159 ATTTTTGAAA
1297169 ATAAATTTTGGCATTTGATAAAAGGGAG
1 ATAAATTTTGGCATTTGATAAAAGGGAG
1297197 ATAAATTTTTGGCATTTGATAAAAGGGA
1 ATAAA-TTTTGGCATTTGATAAAAGGGA
1297225 AGAAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (28 bp):
ATAAATTTTGGCATTTGATAAAAGGGAG
Found at i:1297925 original size:19 final size:19
Alignment explanation
Indices: 1297901--1297951 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1297891 CGATACATTA
*
1297901 TATCGATACATGTTCAGTG
1 TATCGATACATGTTAAGTG
* *
1297920 TATCGATACATACTTAATTG
1 TATCGATACAT-GTTAAGTG
1297940 TATCGATACATG
1 TATCGATACATG
1297952 AAAGTGGCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
TATCGATACATGTTAAGTG
Found at i:1300845 original size:20 final size:20
Alignment explanation
Indices: 1300820--1300872 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1300810 TTCAAATGCA
1300820 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1300840 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1300860 TGTATCGATACAT
1 TGTATCGATACAT
1300873 AGCAACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTATGAAT
Found at i:1302275 original size:129 final size:128
Alignment explanation
Indices: 1302064--1302390 Score: 349
Period size: 127 Copynumber: 2.5 Consensus size: 128
1302054 TTGTTTTGTC
* * * * * *
1302064 ATTTTATGACTAAAATTTAGCTTTGATGTGTGGGTCACAAGTAACCCTTTCCATAAATGTGACCT
1 ATTTTATGACTAAAATTTAGCTTTGGTGTAT-GGTCACAAATGACCCTTTCCATAAAGGTGGCCT
* * * *
1302129 -AGATTTGAAACCTAGGCCA-TTCATTCATTCATTCTTTTTTTTTTCTTTTTGACAATTCTTTTA
65 GGGTTTTGAAACCCAGGCCACTT-ATT--TTCATTCTTCTTTTTTTCTTTTTGACAATTCTTTTA
1302192 CT
127 CT
* * *
1302194 ATTTTATGA-TCAAAATTTAGTTTTGGTGTATGGTCACAAATGACCCTTTCTATAAAGGTGGCTT
1 ATTTTATGACT-AAAATTTAGCTTTGGTGTATGGTCACAAATGACCCTTTCCATAAAGGTGGCCT
** * * *
1302258 GGGTTTTG-AACCCAGGCCACTTATTTTTTTTCTTCTTTTTTTCTTTTTGATAATTTTTTTGCT
65 GGGTTTTGAAACCCAGGCCACTTATTTTCATTCTTCTTTTTTTCTTTTTGACAATTCTTTTACT
* * * * *
1302321 CTTTTATGACTAAAGTATAGCTTTGGCATGTA-GGTCACTAATGACCCTTTCCATAAAGATGGCC
1 ATTTTATGACTAAAATTTAGCTTTGG--TGTATGGTCACAAATGACCCTTTCCATAAAGGTGGCC
1302385 TGGGTT
64 TGGGTT
1302391 CAAAAGCCAA
Statistics
Matches: 165, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
127 52 0.32
128 35 0.21
129 45 0.27
130 33 0.20
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.44
Consensus pattern (128 bp):
ATTTTATGACTAAAATTTAGCTTTGGTGTATGGTCACAAATGACCCTTTCCATAAAGGTGGCCTG
GGTTTTGAAACCCAGGCCACTTATTTTCATTCTTCTTTTTTTCTTTTTGACAATTCTTTTACT
Found at i:1302896 original size:209 final size:209
Alignment explanation
Indices: 1302536--1302953 Score: 755
Period size: 209 Copynumber: 2.0 Consensus size: 209
1302526 TATTTTTTTG
*
1302536 TATTTTTTCAAACAAGCCTAAATTAAAATGAATTAAGCCCAATTAATCAGAATCCAGCAAACCTA
1 TATTTTTTCAAACAAGCCTAAATTAAAATGAATTAAGCCCAATTAATCAAAATCCAGCAAACCTA
* * * *
1302601 GATTAAAGATGACCTAATTAATTGAATTATTCTAAATAGTGAGTGTTTTTAAAATTACTCGGATA
66 AATTAAAGATGACCTAATTAATTGAATTATTCTAAATAATGAGTGTTTTTAAAATTACACAGATA
1302666 AAATTTGGTGTCTACAGGTTTATTAAGATGAAAATCCCTAACTTTCAAGTGAAAAATGACCTTGA
131 AAATTTGGTGTCTACAGGTTTATTAAGATGAAAATCCCTAACTTTCAAGTGAAAAATGACCTTGA
1302731 ATTATACTTGGAGT
196 ATTATACTTGGAGT
*
1302745 TATTTTTTCAAATAAGCCTAAATTAAAATGAATTAAGCCCAATTAATCAAAATCCAGCAAACCTA
1 TATTTTTTCAAACAAGCCTAAATTAAAATGAATTAAGCCCAATTAATCAAAATCCAGCAAACCTA
*
1302810 AATTAAAGATGACCTAATTAATTGAATTATTCTAAATAATGATTGTTTTTAAAATTACACAGATA
66 AATTAAAGATGACCTAATTAATTGAATTATTCTAAATAATGAGTGTTTTTAAAATTACACAGATA
* *
1302875 AAATTTGGTGTCTACAGGTTTATTAAGATGAAAATCCCTAACTTTTACGTGAAAAATGACCTTGA
131 AAATTTGGTGTCTACAGGTTTATTAAGATGAAAATCCCTAACTTTCAAGTGAAAAATGACCTTGA
1302940 ATTATACTTGGAGT
196 ATTATACTTGGAGT
1302954 AGGAGAGGAA
Statistics
Matches: 200, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
209 200 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (209 bp):
TATTTTTTCAAACAAGCCTAAATTAAAATGAATTAAGCCCAATTAATCAAAATCCAGCAAACCTA
AATTAAAGATGACCTAATTAATTGAATTATTCTAAATAATGAGTGTTTTTAAAATTACACAGATA
AAATTTGGTGTCTACAGGTTTATTAAGATGAAAATCCCTAACTTTCAAGTGAAAAATGACCTTGA
ATTATACTTGGAGT
Found at i:1305755 original size:13 final size:12
Alignment explanation
Indices: 1305734--1305777 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 12
1305724 CCAACGGGGT
1305734 TAAAAAATAAAA
1 TAAAAAATAAAA
1305746 TAATAAAATAAAA
1 TAA-AAAATAAAA
1305759 TAAAAAATTAAAA
1 TAAAAAA-TAAAA
1305772 TTAAAA
1 -TAAAA
1305778 GATGGGGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.24
13 17 0.59
14 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:1305758 original size:18 final size:19
Alignment explanation
Indices: 1305737--1305777 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
1305727 ACGGGGTTAA
1305737 AAAATAAAATAA-TAAAA-T
1 AAAATAAAA-AATTAAAATT
1305755 AAAATAAAAAATTAAAATT
1 AAAATAAAAAATTAAAATT
1305774 AAAA
1 AAAA
1305778 GATGGGGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATAAAAAATTAAAATT
Found at i:1309125 original size:33 final size:33
Alignment explanation
Indices: 1309088--1309150 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1309078 TCCAAATGTA
*
1309088 TCGATACAATGATAAATGTATCGATACATTGTG
1 TCGATACAATGATAAATGTATCGACACATTGTG
* * *
1309121 TCGATACATTTATTAATGTATCGACACATT
1 TCGATACAATGATAAATGTATCGACACATT
1309151 TCCTTGGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (33 bp):
TCGATACAATGATAAATGTATCGACACATTGTG
Found at i:1312312 original size:98 final size:97
Alignment explanation
Indices: 1312099--1312335 Score: 302
Period size: 98 Copynumber: 2.4 Consensus size: 97
1312089 TATTCATCGA
* * *
1312099 GGATACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCCCATTTTTTAAAACTTGTGAAGATT
1 GGATACTCCAACCCCATTCCTCCTAGGGGATACTCCAACCCCATTTTTTAAAACTTGTCAAGATT
* *
1312164 TAAATCTTATTTTCACTTAAATTATCATTGTCAG
66 TAAATCTTATTTGCACTAAAATTATCATTG--AG
* *
1312198 GGATACTCCAATCCCATTCCTCCTAAGGGATACTCCAACCCCA-TTTTTAAAACTTGTCAAGATT
1 GGATACTCCAACCCCATTCCTCCTAGGGGATACTCCAACCCCATTTTTTAAAACTTGTCAAGATT
1312262 TAAATCTTATCATTGC-CTAAAATGTCATCATTG-G
66 TAAATCTTAT--TTGCACTAAAAT-T-ATCATTGAG
* *
1312296 GGATATTCTAACCCCATTCCT-CTGAGGGGATACTCCAACC
1 GGATACTCCAACCCCATTCCTCCT-AGGGGATACTCCAACC
1312336 TTATTTTTCA
Statistics
Matches: 122, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
97 2 0.02
98 64 0.52
99 45 0.37
100 4 0.03
101 7 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (97 bp):
GGATACTCCAACCCCATTCCTCCTAGGGGATACTCCAACCCCATTTTTTAAAACTTGTCAAGATT
TAAATCTTATTTGCACTAAAATTATCATTGAG
Found at i:1312752 original size:20 final size:20
Alignment explanation
Indices: 1312724--1312798 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1312714 TTTTACCCAG
1312724 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1312744 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1312764 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
1312784 ATGTATCGATACATT
1 ATGTATCGATACATT
1312799 CTGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1322908 original size:9 final size:9
Alignment explanation
Indices: 1322894--1322948 Score: 65
Period size: 9 Copynumber: 5.8 Consensus size: 9
1322884 TGTGGGGACG
1322894 AATTTTTAT
1 AATTTTTAT
1322903 AATTTTTAT
1 AATTTTTAT
1322912 AATTTTTAT
1 AATTTTTAT
* *
1322921 AATGGTGTTCT
1 AAT--TTTTAT
1322932 AGATTTTTAT
1 A-ATTTTTAT
1322942 AATTTTT
1 AATTTTT
1322949 TGTTAAGCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 27 0.69
10 5 0.13
11 5 0.13
12 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:1323147 original size:13 final size:13
Alignment explanation
Indices: 1323129--1323153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1323119 CATAAAGTGT
1323129 TGTATCGATACAA
1 TGTATCGATACAA
1323142 TGTATCGATACA
1 TGTATCGATACA
1323154 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1323151 original size:33 final size:33
Alignment explanation
Indices: 1323109--1323175 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1323099 TTCAACGATT
1323109 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1323142 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1323175 T
1 T
1323176 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1323288 original size:52 final size:52
Alignment explanation
Indices: 1323249--1323429 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
1323239 CACTGATCTT
1323249 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1323301 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* * **
1323353 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1323405 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1323430 TCATATTTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1330247 original size:10 final size:10
Alignment explanation
Indices: 1330232--1330304 Score: 74
Period size: 10 Copynumber: 6.6 Consensus size: 10
1330222 CTTTACACCC
1330232 AAAAAAAACA
1 AAAAAAAACA
1330242 AAAAAAAACA
1 AAAAAAAACA
1330252 AAAAAAAACAAA
1 AAAAAAAAC--A
*
1330264 ACAAAAAAATA
1 A-AAAAAAACA
1330275 AAAAAAAACCA
1 AAAAAAAA-CA
1330286 AGAAAAAATAGCA
1 A-AAAAAA-A-CA
1330299 AAAAAA
1 AAAAAA
1330305 GAGAAGGGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 26 0.48
11 4 0.07
12 13 0.24
13 11 0.20
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1330258 original size:23 final size:23
Alignment explanation
Indices: 1330232--1330304 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
1330222 CTTTACACCC
1330232 AAAAAAAACAAAAAAAAACAAAA
1 AAAAAAAACAAAAAAAAACAAAA
* * *
1330255 AAAAACAA-AACAAAAAA-ATAA
1 AAAAAAAACAAAAAAAAACAAAA
*
1330276 AAAAAAACCAAGAAAAAATAGCAAAA
1 AAAAAAAACAA-AAAAAA-A-CAAAA
1330302 AAA
1 AAA
1330305 GAGAAGGGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
21 9 0.24
22 10 0.26
23 12 0.32
24 1 0.03
26 6 0.16
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAAACAAAA
Found at i:1330302 original size:1 final size:1
Alignment explanation
Indices: 1330232--1330282 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
1330222 CTTTACACCC
* * * * *
1330232 AAAAAAAACAAAAAAAAACAAAAAAAAACAAAACAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1330283 CCAAGAAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:1331638 original size:57 final size:57
Alignment explanation
Indices: 1331519--1332437 Score: 1258
Period size: 57 Copynumber: 15.9 Consensus size: 57
1331509 TGTTCATCCC
1331519 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTT-AGTGGCACTCT
* * * *
1331576 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCGC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* *
1331633 CTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * * *
1331690 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
*
1331747 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCCAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * *
1331805 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGACACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * * * *
1331862 TTTCCAAGCCCACAAGTCACTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * * * * *
1331920 TTTCAAAGCCCACAAGTCACTGCCACCCTTTCAAAGCCCACAAGTCACTAGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * * *
1331977 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAACCCACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACTCT
1332035 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTT-AGTGGCACTCT
1332092 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA-TTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTT-AGTGGCACTCT
* * *
1332149 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCATGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTTAGTGGCACTCT
* * *
1332207 TTTCAAAGCCCACAAATCAGTGGCACTCTGTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCCT-TTCAAAGCCCACAAGTTAGTGGCACTCT
*
1332264 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACCAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * *
1332321 TTTCAAAGCTCACAAGTCAGTGGCACCCTTTCAAACCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
** *
1332378 TTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTTAGTGGCAC
1332438 CATTTTTTTT
Statistics
Matches: 772, Mismatches: 70, Indels: 34
0.88 0.08 0.04
Matches are distributed among these distances:
56 50 0.06
57 458 0.59
58 204 0.26
59 32 0.04
60 3 0.00
61 8 0.01
62 2 0.00
63 15 0.02
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.22
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
Found at i:1331727 original size:86 final size:86
Alignment explanation
Indices: 1331517--1332438 Score: 1282
Period size: 86 Copynumber: 10.7 Consensus size: 86
1331507 AATGTTCATC
* * *
1331517 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
*
1331581 AAGCCCACAAATCAGTGGCACT
65 AAGCCCACAAGTCAGTGGCACT
* * * **
1331603 CTTTTCAAAGCCCACAAGTTAGTGGCGC-CCCTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1331667 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* *
1331688 CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1331753 AGCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* *
1331774 CCTTTCCAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
*
1331839 AGCCCACAAGTCAGTGACACT
66 AGCCCACAAGTCAGTGGCACT
* * * *
1331860 CCTTTCCAAGCCCACAAGTCACTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
* *
1331925 AAGCCCACAAGTCACTGCCAC-
65 AAGCCCACAAGTCAGTGGCACT
* * * * *
1331946 CCTTTCAAAGCCCACAAGTCACTAGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
* * *
1332011 AAACCCACAAATTAGTGGCACT
65 AAGCCCACAAGTCAGTGGCACT
* * * *
1332033 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
1332097 AAGCCCACAAGTCAGTGGCAC-
65 AAGCCCACAAGTCAGTGGCACT
* *
1332118 CCTTTCAAAGCCCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1332183 AGCCCATGCAAGTCAGTGGCAC-
66 AGCCCA--CAAGTCAGTGGCACT
* * * *
1332205 CCTTTCAAAGCCCACAAATCAGTGGCACTCTGTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
1332270 AGCCCACAAGTCAGTGGCAC-
66 AGCCCACAAGTCAGTGGCACT
* * *
1332290 CCTTTCAAAGCCCACCAGTTAGTGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCACCCTTTCAA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
*
1332355 ACCCCACAAGTCAGTGGCACT
66 AGCCCACAAGTCAGTGGCACT
* ** *
1332376 CTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGCACC
1332439 ATTTTTTTTT
Statistics
Matches: 761, Mismatches: 63, Indels: 19
0.90 0.07 0.02
Matches are distributed among these distances:
85 183 0.24
86 409 0.54
87 130 0.17
88 9 0.01
89 13 0.02
90 1 0.00
91 16 0.02
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.22
Consensus pattern (86 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACT
Found at i:1333030 original size:20 final size:20
Alignment explanation
Indices: 1333005--1333076 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1332995 TACCTAGATG
1333005 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
1333025 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATA
* *
1333045 TATCGATATATTCTTCAATA
1 TATCGATACATTTTTCAATA
1333065 TATCGATACATT
1 TATCGATACATT
1333077 CTGTCTTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:1335454 original size:25 final size:24
Alignment explanation
Indices: 1335421--1335470 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1335411 CAATCAAAAA
1335421 TTGAATCAT-TTTCTCTCTTTGAATT
1 TTGAATCATGTTTCT-T-TTTGAATT
* *
1335446 TTGAGTCATGTTTGTTTTTGAATT
1 TTGAATCATGTTTCTTTTTGAATT
1335470 T
1 T
1335471 CACTCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.18, C:0.10, G:0.14, T:0.58
Consensus pattern (24 bp):
TTGAATCATGTTTCTTTTTGAATT
Found at i:1343042 original size:26 final size:26
Alignment explanation
Indices: 1343008--1343059 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1342998 TTTATATATT
1343008 TTATAATTA-AATTTAAATAAAAATTA
1 TTATAATTATAA-TTAAATAAAAATTA
* *
1343034 TTATTATTATAATTAAATAAGAATTA
1 TTATAATTATAATTAAATAAAAATTA
1343060 GAATAGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATAATTATAATTAAATAAAAATTA
Found at i:1346390 original size:14 final size:14
Alignment explanation
Indices: 1346371--1346402 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1346361 AGCTCCACAA
1346371 AAATCAATATATTT
1 AAATCAATATATTT
1346385 AAATCAATATATTT
1 AAATCAATATATTT
1346399 AAAT
1 AAAT
1346403 ACAGCTCCAC
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATCAATATATTT
Found at i:1347388 original size:16 final size:15
Alignment explanation
Indices: 1347363--1347392 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1347353 ATTTTAATTT
1347363 ATAAAAAATATAATA
1 ATAAAAAATATAATA
1347378 ATAAAATAATATAAT
1 ATAAAA-AATATAAT
1347393 TTTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAAATATAATA
Found at i:1348073 original size:28 final size:28
Alignment explanation
Indices: 1348014--1348071 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1348004 TATTTTATAT
* *
1348014 TTATATTTAATTATATAAATATAAAAATA
1 TTAT-TTTAATAATATAAAAATAAAAATA
1348043 TTATTTTAATAATATAATAAATAATAAAT
1 TTATTTTAATAATATAA-AAATAA-AAAT
1348072 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 9 0.36
30 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTATTTTAATAATATAAAAATAAAAATA
Found at i:1348074 original size:23 final size:23
Alignment explanation
Indices: 1348022--1348075 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1348012 ATTTATATTT
*
1348022 AATTATATAAATATAAAAATATTA
1 AATTA-ATAAATATAAAAATAATA
**
1348046 TTTTAAT-AATATAATAAATAATA
1 AATTAATAAATATAA-AAATAATA
1348069 AATTAAT
1 AATTAAT
1348076 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTAATAAATATAAAAATAATA
Found at i:1348392 original size:7 final size:7
Alignment explanation
Indices: 1348343--1348398 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
1348333 TTGTTTCTAA
1348343 TGCCATT
1 TGCCATT
*
1348350 TACCATT
1 TGCCATT
*
1348357 TGCCATA
1 TGCCATT
* *
1348364 TGCTA-A
1 TGCCATT
1348370 TGCCATT
1 TGCCATT
*
1348377 TACCATT
1 TGCCATT
1348384 TGCCATT
1 TGCCATT
*
1348391 TGTCATT
1 TGCCATT
1348398 T
1 T
1348399 CTGAGTCCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (7 bp):
TGCCATT
Found at i:1348528 original size:18 final size:18
Alignment explanation
Indices: 1348492--1348547 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
1348482 GCATTATAAA
1348492 ATTTTTATATT-TA-TAT
1 ATTTTTATATTATATTAT
1348508 ATTTTTATATTATATTAT
1 ATTTTTATATTATATTAT
*
1348526 ATTTTTTTATTATATTTAT
1 ATTTTTATATTATA-TTAT
1348545 ATT
1 ATT
1348548 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
18 16 0.44
19 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTATATTATATTAT
Found at i:1348723 original size:33 final size:34
Alignment explanation
Indices: 1348639--1348723 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 34
1348629 AATATATTTA
*
1348639 AAGTAT-TTTATATTTATATAAATTTTGATAAATT
1 AAGTATATTTATA-TTATATAAATTATGATAAATT
1348673 AA-TA-ATTTATATTATATAAATTAT-A-AAATAT
1 AAGTATATTTATATTATATAAATTATGATAAAT-T
*
1348704 AAGTATATTAATATTATATA
1 AAGTATATTTATATTATATA
1348724 TATTGTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 14 0.31
33 21 0.47
34 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (34 bp):
AAGTATATTTATATTATATAAATTATGATAAATT
Found at i:1348757 original size:11 final size:12
Alignment explanation
Indices: 1348722--1348759 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1348712 TAATATTATA
*
1348722 TATATTGTTTTT
1 TATATTATTTTT
*
1348734 TATATTATATTT
1 TATATTATTTTT
1348746 TA-ATTATTTTT
1 TATATTATTTTT
1348757 TAT
1 TAT
1348760 TTCATATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
TATATTATTTTT
Found at i:1349291 original size:24 final size:22
Alignment explanation
Indices: 1349245--1349299 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
1349235 GTTTTAGATC
* *
1349245 AAATTTTATTTATTTAAATTTA
1 AAATTTTATTTATATAAAATTA
1349267 AAATTTTATTTAATAATAAAATTA
1 AAATTTTATTT-AT-ATAAAATTA
*
1349291 ATATTTTAT
1 AAATTTTAT
1349300 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 11 0.39
23 2 0.07
24 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATTTTATTTATATAAAATTA
Found at i:1349833 original size:21 final size:20
Alignment explanation
Indices: 1349804--1349845 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1349794 ACTTTTAATA
*
1349804 AAATAATAAATTATATTATAT
1 AAATAATAAAATAT-TTATAT
*
1349825 AAATTATAAAATATTTATAT
1 AAATAATAAAATATTTATAT
1349845 A
1 A
1349846 TTAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAATAAAATATTTATAT
Found at i:1349860 original size:15 final size:14
Alignment explanation
Indices: 1349834--1349872 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1349824 TAAATTATAA
1349834 AATATTTATATATT
1 AATATTTATATATT
1349848 AATATTATATATATT
1 AATATT-TATATATT
*
1349863 -ATTTTTATAT
1 AATATTTATAT
1349873 TTTATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 10 0.43
15 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:1350199 original size:2 final size:2
Alignment explanation
Indices: 1350192--1350217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1350182 GCAATGTTAC
1350192 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1350218 GTAAACCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351206 original size:13 final size:13
Alignment explanation
Indices: 1351164--1351207 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1351154 TTAATATATT
*
1351164 ATATTAATATTTAC
1 ATATT-ATATTTAA
*
1351178 ATATTATTTTTAAA
1 ATATTATATTT-AA
1351192 ATATTATATTTAA
1 ATATTATATTTAA
1351205 ATA
1 ATA
1351208 ACATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTATATTTAA
Found at i:1351379 original size:18 final size:18
Alignment explanation
Indices: 1351337--1351378 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1351327 TTTCCTATCA
1351337 CTCTCTCTAAACACCTCT
1 CTCTCTCTAAACACCTCT
1351355 CTCTCTC-AAA-ACCTCT
1 CTCTCTCTAAACACCTCT
*
1351371 CCCTCTCT
1 CTCTCTCT
1351379 CTCTAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 12 0.55
17 3 0.14
18 7 0.32
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCTCTCTAAACACCTCT
Found at i:1352039 original size:2 final size:2
Alignment explanation
Indices: 1352032--1352065 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1352022 CATGCGAGTG
1352032 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1352066 TTGAAACGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1353190 original size:20 final size:20
Alignment explanation
Indices: 1353165--1353219 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1353155 TTTTACTTAG
*
1353165 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
1353185 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
1353205 ATGTATCGATACATT
1 ATGTATCGATACATT
1353220 CTGTCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1353250 original size:51 final size:51
Alignment explanation
Indices: 1353185--1353317 Score: 230
Period size: 51 Copynumber: 2.6 Consensus size: 51
1353175 ACATTTTTCA
*
1353185 ATGTATCGATACATTTTTTAATGTATCGATACATTCTGTCTTTTTACCTAG
1 ATGTATCGATACATTTTTTAATGTATCGATACATTCTGTCTTTTTACCCAG
* *
1353236 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATTTTTTAATGTATCGATACATTCTGTCTTTTTACCCAG
*
1353287 ATATATCGATACATTTTTTAATGTATCGATA
1 ATGTATCGATACATTTTTTAATGTATCGATA
1353318 GATCTAGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (51 bp):
ATGTATCGATACATTTTTTAATGTATCGATACATTCTGTCTTTTTACCCAG
Found at i:1353277 original size:24 final size:20
Alignment explanation
Indices: 1353165--1353272 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
1353155 TTTTACTTAG
* *
1353165 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *
1353185 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTCTTCA
1353205 ATGTATCGATACATTCTGTCTTTTTACCTA
1 ATGTATCGATACA---T-TC---TT--C-A
1353235 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTCTTCA
1353256 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1353273 GTCTTTTTAC
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
20 48 0.66
21 1 0.01
22 1 0.01
23 1 0.01
24 3 0.04
27 4 0.05
28 1 0.01
30 1 0.01
31 13 0.18
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1354214 original size:321 final size:322
Alignment explanation
Indices: 1353631--1354254 Score: 898
Period size: 321 Copynumber: 1.9 Consensus size: 322
1353621 AAATAACCTA
**
1353631 AAACACCTCACATTTCACTTTAAAATTTTGGCTATAAATAGGCCAATGCAATCCTAGCAAAGGAT
1 AAACACCTCACATTTCACCCTAAAATTTTGGCTATAAATAGGCCAATGCAATCCTAGCAAAGGAT
** * * *
1353696 CCATTTTTCAACCACATTTTCTAGCCTCATTTCCATCCATATCTCGGCAAAAACATCAACACAAA
66 CCATCCTTCAACCACATTTTCCAGCCTCATTACCATCCATATCTCAGCAAAAACATCAACACAAA
* *
1353761 AACAAATCAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGAAACACCTTCAAACACTT
131 AACAAATCAAAAAGTCCATTCCCGTAGCTCCCTACAACTCCCAAAAGAAACACCTCCAAACACTT
1353826 CTTCCTTGATCACTACACAACTCCAATCCATCTCTACCCATACTATAACCTAAACATCCACTTTT
196 CTTCCTTGATCACTACACAACTCCAATCCATCTCTACCCATACTATAACCTAAACATCCACTTTT
* *
1353891 TCATCATTTT-TCAGTTTGTTTGT-AGCCTCACAAAGGTGTTAAATAAGCTGTATTACTTGTCC
261 TCATCATTTTCCCA-TTTGTTT-TCAGCCACACAAAGGTGTTAAATAAGCTGTATTACTTGTCC
* * * *
1353953 AAACACCTCACCTTTTACCCTAAAATTTTGGTTATAAATAGGCCGATGCAATCCTAGCAAAGGAT
1 AAACACCTCACATTTCACCCTAAAATTTTGGCTATAAATAGGCCAATGCAATCCTAGCAAAGGAT
* * * * *
1354018 CCCTCCTTCAACCACATTTTCCAGCCTCATTACTATTCATATCTTAG-AAAAACATCAACATAAA
66 CCATCCTTCAACCACATTTTCCAGCCTCATTACCATCCATATCTCAGCAAAAACATCAACACAAA
** ** * *
1354082 AACTCCAT-AAAAAGTTTATTCCCGTAGCTCCCTATAACTCCCAAAAGAAACACCTCCAAACATT
131 AAC-AAATCAAAAAGTCCATTCCCGTAGCTCCCTACAACTCCCAAAAGAAACACCTCCAAACACT
* * * * *
1354146 TCCTT-CTTGGTCACTACACAACTCCAATCCATCTCTACCTATATTATAACCTAAACATCTATTT
195 T-CTTCCTTGATCACTACACAACTCCAATCCATCTCTACCCATACTATAACCTAAACATCCACTT
1354210 TTTCATCATTTTCCCATTTGTTTTCAGCCACACAAAGGTGTTAAA
259 TTTCATCATTTTCCCATTTGTTTTCAGCCACACAAAGGTGTTAAA
1354255 CAAGTTACAT
Statistics
Matches: 267, Mismatches: 31, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
320 1 0.00
321 162 0.61
322 104 0.39
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (322 bp):
AAACACCTCACATTTCACCCTAAAATTTTGGCTATAAATAGGCCAATGCAATCCTAGCAAAGGAT
CCATCCTTCAACCACATTTTCCAGCCTCATTACCATCCATATCTCAGCAAAAACATCAACACAAA
AACAAATCAAAAAGTCCATTCCCGTAGCTCCCTACAACTCCCAAAAGAAACACCTCCAAACACTT
CTTCCTTGATCACTACACAACTCCAATCCATCTCTACCCATACTATAACCTAAACATCCACTTTT
TCATCATTTTCCCATTTGTTTTCAGCCACACAAAGGTGTTAAATAAGCTGTATTACTTGTCC
Found at i:1367458 original size:10 final size:10
Alignment explanation
Indices: 1367444--1367509 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
1367434 CTTCATACCC
1367444 AAAAAAA-AA
1 AAAAAAACAA
*
1367453 CAAAAAACAA
1 AAAAAAACAA
1367463 AAAAAAACCAGA
1 AAAAAAA-CA-A
*
1367475 AAAAAACCAA
1 AAAAAAACAA
**
1367485 AAAAAAAGTA
1 AAAAAAACAA
*
1367495 AAAAAAATAA
1 AAAAAAACAA
1367505 AAAAA
1 AAAAA
1367510 CCAAATAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
9 6 0.13
10 29 0.63
11 4 0.09
12 7 0.15
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1367468 original size:11 final size:11
Alignment explanation
Indices: 1367444--1367526 Score: 62
Period size: 11 Copynumber: 7.4 Consensus size: 11
1367434 CTTCATACCC
*
1367444 AAAAAA-AAAC
1 AAAAAACAAAA
1367454 AAAAAACAAAA
1 AAAAAACAAAA
* *
1367465 AAAAACCAGAA
1 AAAAAACAAAA
*
1367476 AAAAACCAAAA
1 AAAAAACAAAA
**
1367487 AAAAAGTAAAA
1 AAAAAACAAAA
1367498 AAAATAA-AAAA
1 AAAA-AACAAAA
1367509 ACCAAATAACAAAA
1 A--AAA-AACAAAA
1367523 AAAA
1 AAAA
1367527 TAGAAAGGCA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
10 6 0.10
11 40 0.66
12 4 0.07
13 6 0.10
14 5 0.08
ACGTcount: A:0.83, C:0.11, G:0.02, T:0.04
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:1367478 original size:21 final size:22
Alignment explanation
Indices: 1367454--1367512 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
1367444 AAAAAAAAAC
1367454 AAAAAACAAAAAAAAACCAG-A
1 AAAAAACAAAAAAAAACCAGTA
*
1367475 AAAAAACCAAAAAAAA--AGTA
1 AAAAAACAAAAAAAAACCAGTA
*
1367495 AAAAAA-ATAAAAAAACCA
1 AAAAAACAAAAAAAAACCA
1367513 AATAACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 9 0.28
20 7 0.22
21 16 0.50
ACGTcount: A:0.81, C:0.12, G:0.03, T:0.03
Consensus pattern (22 bp):
AAAAAACAAAAAAAAACCAGTA
Found at i:1367487 original size:29 final size:28
Alignment explanation
Indices: 1367445--1367526 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
1367435 TTCATACCCA
* *
1367445 AAAAAAAACAAAAAACAAAAAAAAACCAG
1 AAAAAAACCAAAAAACAAAAAAAAA-AAG
*
1367474 AAAAAAACCAAAAAA-AAAGTAAAAAAAAT
1 AAAAAAACCAAAAAACAAA--AAAAAAAAG
*
1367503 AAAAAAACCAAATAACAAAAAAAA
1 AAAAAAACCAAAAAACAAAAAAAA
1367527 TAGAAAGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.17
29 29 0.63
30 9 0.20
ACGTcount: A:0.83, C:0.11, G:0.02, T:0.04
Consensus pattern (28 bp):
AAAAAAACCAAAAAACAAAAAAAAAAAG
Found at i:1368735 original size:13 final size:13
Alignment explanation
Indices: 1368698--1368736 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1368688 CCTTTTGCCA
*
1368698 TTTGTCAAGAAAT
1 TTTGTCAAGAACT
1368711 TATTGTCAAGAACT
1 T-TTGTCAAGAACT
*
1368725 TTTGTCCAGAAC
1 TTTGTCAAGAAC
1368737 GTTCATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TTTGTCAAGAACT
Found at i:1368812 original size:28 final size:28
Alignment explanation
Indices: 1368745--1369349 Score: 640
Period size: 28 Copynumber: 21.0 Consensus size: 28
1368735 ACGTTCATCT
1368745 CTTT-AAAGCCCACAAGTCAGT-GCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1368771 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1368799 CTTTCAAGGTCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1368827 ATTTCAAAGACCACAAG-CTAGTGGTAACTC
1 CTTTCAAAGCCCACAAGTC-AGTGG-CAC-C
*
1368857 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1368885 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1368913 TTTTCAAAGCTCACAAGTCAGTGACACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1368942 TTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1368970 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1368998 CTTTCATAGCTCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
1369027 TTTTCAAAGCCCACACGACTCGGTGGCAACTC
1 CTTTCAAAGCCCACA--AGTCAGTGGC-AC-C
* * *
1369059 TTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1369087 CTTTCAAAGCCCACGAGTCAGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * * *
1369117 TTTTCAAAGCCCACAACTGAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1369145 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1369173 CTTTCAAAGCCCACAAGTCAGTGGCATTC
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * *
1369202 TTTTCAAAGCCCATAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1369230 CTTTCAAAACCCATAAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1369258 CTTTCAAAGCCCACAAGTTAATGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * *
1369287 TTTTTCAAAGCCTACACGAGTCGGTGGCAACTA
1 -CTTTCAAAGCC--CACAAGTCAGTGGC-AC-C
* *
1369320 TTTTCAAAGCCCACACAAGTTAGTGGCACC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACC
1369350 ATTTTTTTTT
Statistics
Matches: 492, Mismatches: 67, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.01
27 18 0.04
28 274 0.56
29 71 0.14
30 59 0.12
31 11 0.02
32 50 0.10
33 5 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1368977 original size:85 final size:85
Alignment explanation
Indices: 1368745--1369349 Score: 741
Period size: 85 Copynumber: 7.0 Consensus size: 85
1368735 ACGTTCATCT
* * *
1368745 CTTT-AAAGCCCACAAGTCAGT-GCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAG
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
* *
1368807 GTCCACAAGTCAGTGGCACT
66 GCCCACAAGTCAGTGGCACC
* * * *
1368827 ATTTCAAAGACCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
1 CTTTCAAAGCCCACAAGTC-AGTGG-CACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
1368891 AAGCCCACAAGTCAGTGGCACC
64 AAGCCCACAAGTCAGTGGCACC
* * *
1368913 TTTTCAAAGCTCACAAGTCAGTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
1368978 GCCCACAAGTCAGTGGCACC
66 GCCCACAAGTCAGTGGCACC
* * * * * *
1368998 CTTTCATAGCTCACAAATCAGTGGCACTCTTTTCAAAGCCCACACGACTCGGTGGCAACTCTTTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-A-TCCTTT
* *
1369063 CAAAGCCCACAAGTTAGTGGCATC
62 CAAAGCCCACAAGTCAGTGGCACC
* * *
1369087 CTTTCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAACTGAGTGGCATCCTTTCAA
1 CTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAA
1369152 AGCCCACAAGTCAGTGGCACC
65 AGCCCACAAGTCAGTGGCACC
* *
1369173 CTTTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAA
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
* * *
1369238 ACCCATAAGTCAGTGGTACC
66 GCCCACAAGTCAGTGGCACC
* * * * **
1369258 CTTTCAAAGCCCACAAGTTAATGGCACTCTTTTTCAAAGCCTACACGAGTCGGTGGCAACTATTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTTCAAAGCC--CACAAGTCAGTGGC-A-TCCTT
*
1369323 TCAAAGCCCACACAAGTTAGTGGCACC
61 TCAAAG-CC-CACAAGTCAGTGGCACC
1369350 ATTTTTTTTT
Statistics
Matches: 454, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
82 4 0.01
83 14 0.03
84 1 0.00
85 180 0.40
86 133 0.29
87 10 0.02
88 20 0.04
89 49 0.11
90 27 0.06
91 2 0.00
92 14 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (85 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAA
GCCCACAAGTCAGTGGCACC
Done.