Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 149 of 182
Found at i:45877959 original size:27 final size:28
Alignment explanation
Indices: 45877929--45877981 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
45877919 AACGATCAAA
*
45877929 GTCAACGGTTAACGGTCAA-AGTCAACG
1 GTCAACGGTCAACGGTCAACAGTCAACG
45877956 GTCAACGGTCAACGGTCAACAGTCAA
1 GTCAACGGTCAACGGTCAACAGTCAA
45877982 TCAACACCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.17
Consensus pattern (28 bp):
GTCAACGGTCAACGGTCAACAGTCAACG
Found at i:45878083 original size:15 final size:15
Alignment explanation
Indices: 45878063--45878092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45878053 TGGTTCATTT
45878063 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
45878078 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
45878093 AATTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:45878102 original size:21 final size:22
Alignment explanation
Indices: 45878076--45878122 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
45878066 TTGGTTCAAA
*
45878076 TGGGTTTGGTTTAAATGA-ATT
1 TGGGTTTGGTTTAAATAAGATT
45878097 TGGGTTTGGTTTAAATAAGATT
1 TGGGTTTGGTTTAAATAAGATT
45878119 TGGG
1 TGGG
45878123 CTTAATGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (22 bp):
TGGGTTTGGTTTAAATAAGATT
Found at i:45878526 original size:11 final size:11
Alignment explanation
Indices: 45878493--45878567 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
45878483 AAGTGTGATT
*
45878493 AAAAGAGCAAG
1 AAAAGAGAAAG
*
45878504 AAAATAGAAAAG
1 AAAAGAG-AAAG
45878516 AAAAGAGAAAG
1 AAAAGAGAAAG
45878527 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
45878539 AATGAGAAAAAG
1 AA-AAGAGAAAG
45878551 AAAAGAGAAAG
1 AAAAGAGAAAG
*
45878562 GAAAGA
1 AAAAGA
45878568 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.01, G:0.24, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:45878535 original size:23 final size:23
Alignment explanation
Indices: 45878493--45878565 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
45878483 AAGTGTGATT
*
45878493 AAAAGAGCAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
45878516 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
45878539 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
45878563 AAA
1 AAA
45878566 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.23, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:45879594 original size:25 final size:23
Alignment explanation
Indices: 45879566--45879613 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
45879556 TTTACACTAA
45879566 TTATAGTAATTAAAATAGAATATTT
1 TTATAGTAA--AAAATAGAATATTT
*
45879591 TTATATTAAAAAATAGAATATTT
1 TTATAGTAAAAAATAGAATATTT
45879614 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
TTATAGTAAAAAATAGAATATTT
Found at i:45887453 original size:13 final size:13
Alignment explanation
Indices: 45887415--45887460 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
45887405 TATATAGTGT
*
45887415 TAATATATGATACA
1 TAATATATTATA-A
45887429 TAATAGTATTATAA
1 TAATA-TATTATAA
45887443 TAATATATTATAA
1 TAATATATTATAA
45887456 TAATA
1 TAATA
45887461 AAAAAATAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.43
14 11 0.37
15 6 0.20
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:45906030 original size:24 final size:24
Alignment explanation
Indices: 45906003--45906050 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
45905993 TTTTTATGAC
*
45906003 AATAAAATATAGTTTTATCATTTT
1 AATAAAATATAGTTTTATAATTTT
** *
45906027 AATAATTTATATTTTTATAATTTT
1 AATAAAATATAGTTTTATAATTTT
45906051 TAATGGATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
AATAAAATATAGTTTTATAATTTT
Found at i:45906046 original size:15 final size:16
Alignment explanation
Indices: 45906016--45906049 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45906006 AAAATATAGT
45906016 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
45906032 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
45906047 TTT
1 TTT
45906050 TTAATGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Found at i:45908582 original size:100 final size:99
Alignment explanation
Indices: 45908407--45908595 Score: 274
Period size: 100 Copynumber: 1.9 Consensus size: 99
45908397 ACCATTCATT
* * *
45908407 CAATTTAAAAAGTGAAAATCCAGCAAAAGCAAAAACTCCGGAGTTGCAGACTCACAGTGGTTTTC
1 CAATTTAAAAAGTGAAAAACCAGCAAAACCAAAAACTCCGGAGTTGCAGACTCACAG-GATTTTC
*
45908472 ACAGTCGACTTGTCTCAATGACAACCCCGTTCCCA
65 ACAGTCGACTTGTCTCAATAACAACCCCGTTCCCA
*
45908507 CAATTTAAAAAGTGAAAAACCAGTAAAACCAAAAACT-CGAGAGTTGCAGACTTGCACA-GATTT
1 CAATTTAAAAAGTGAAAAACCAGCAAAACCAAAAACTCCG-GAGTTGCAGAC-T-CACAGGATTT
*
45908570 TCACAGTGGACTTGTCTCAATAACAA
63 TCACAGTCGACTTGTCTCAATAACAA
45908596 TTTTGAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
99 2 0.03
100 73 0.91
101 1 0.01
102 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (99 bp):
CAATTTAAAAAGTGAAAAACCAGCAAAACCAAAAACTCCGGAGTTGCAGACTCACAGGATTTTCA
CAGTCGACTTGTCTCAATAACAACCCCGTTCCCA
Found at i:45913653 original size:10 final size:10
Alignment explanation
Indices: 45913638--45913664 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
45913628 AAACAAAAGA
45913638 TGAGCCAAAT
1 TGAGCCAAAT
45913648 TGAGCCAAAT
1 TGAGCCAAAT
45913658 TGAGCCA
1 TGAGCCA
45913665 TTGTGATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (10 bp):
TGAGCCAAAT
Found at i:45923780 original size:13 final size:13
Alignment explanation
Indices: 45923762--45923786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45923752 GAGAATTTTT
45923762 CATTTTAAAGAGA
1 CATTTTAAAGAGA
45923775 CATTTTAAAGAG
1 CATTTTAAAGAG
45923787 GTGAAAAATT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
CATTTTAAAGAGA
Found at i:45925118 original size:19 final size:18
Alignment explanation
Indices: 45925096--45925138 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
45925086 TAAAATTAAA
* *
45925096 AAAAATCAAATTAATTTTT
1 AAAAATCAAAAT-ATTTAT
*
45925115 AAAATTCAAAATATTTAT
1 AAAAATCAAAATATTTAT
45925133 AAAAAT
1 AAAAAT
45925139 TTCAATATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:45930029 original size:17 final size:18
Alignment explanation
Indices: 45930003--45930037 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
45929993 TAATTTAGGT
45930003 TTAGTCATTT-TATTTCC
1 TTAGTCATTTCTATTTCC
*
45930020 TTAGTTATTTCTATTTCC
1 TTAGTCATTTCTATTTCC
45930038 ATTTTATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (18 bp):
TTAGTCATTTCTATTTCC
Found at i:45932113 original size:43 final size:43
Alignment explanation
Indices: 45932045--45932202 Score: 237
Period size: 43 Copynumber: 3.7 Consensus size: 43
45932035 GCCGCAAAAA
* *
45932045 TAGCGGCG-TTTATGCGAAAAAGCGCCGCTGAATGCCATGTTCTT
1 TAGCGGCGCTTTAT-C-CAAAAGCGCCGCTGAAGGCCATGTTCTT
* * *
45932089 CAGCGGCGCTTTCTCCAGAAGCGCCGCTGAAGGCCATGTTCTT
1 TAGCGGCGCTTTATCCAAAAGCGCCGCTGAAGGCCATGTTCTT
*
45932132 TAGCGGCGCTTTATCCACAAGCGCCGCTGAAGGCCATGTTCTT
1 TAGCGGCGCTTTATCCAAAAGCGCCGCTGAAGGCCATGTTCTT
45932175 TAGCGGCGCTTTATCCAAAAGCGCCGCT
1 TAGCGGCGCTTTATCCAAAAGCGCCGCT
45932203 AATATAACAG
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
43 92 0.88
44 8 0.08
45 4 0.04
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.25
Consensus pattern (43 bp):
TAGCGGCGCTTTATCCAAAAGCGCCGCTGAAGGCCATGTTCTT
Found at i:45932657 original size:66 final size:66
Alignment explanation
Indices: 45932551--45932698 Score: 217
Period size: 66 Copynumber: 2.2 Consensus size: 66
45932541 CTCGCTGTTG
* * *
45932551 CCTCCACTTTAAGTTGTATGTGGAGTTCTTCATATTTTTTTTGAGACTCTGTTTCTCTCATTGCA
1 CCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCATTGCA
45932616 A
66 A
* * *
45932617 CCTCCTCTTTAAGTTTTA-GATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGTTGC
1 CCTCCTCTTTAAGTTGTATG-TGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCATTGC
*
45932681 AG
65 AA
45932683 CCTCCTCTTTAAGTTG
1 CCTCCTCTTTAAGTTG
45932699 AGCAATTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 1 0.01
66 72 0.99
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (66 bp):
CCTCCTCTTTAAGTTGTATGTGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCATTGCA
A
Found at i:45935915 original size:8 final size:8
Alignment explanation
Indices: 45935902--45935995 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
45935892 CTGTTTTTAT
45935902 TAATTAAA
1 TAATTAAA
45935910 TAATTAAA
1 TAATTAAA
*
45935918 T-ATTTAA
1 TAATTAAA
45935925 T--TTAATA
1 TAATTAA-A
45935932 TAATTAAA
1 TAATTAAA
45935940 TAATTAAA
1 TAATTAAA
* *
45935948 T-CTT--T
1 TAATTAAA
45935953 TCAATTAAA
1 T-AATTAAA
45935962 TAATTAAA
1 TAATTAAA
45935970 TAAGCTTAAA
1 TAA--TTAAA
45935980 TAATTATATA
1 TAATTA-A-A
45935990 TAATTA
1 TAATTA
45935996 TTTACGACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 12 0.17
8 32 0.46
9 6 0.09
10 15 0.22
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATTAAA
Found at i:45935936 original size:30 final size:29
Alignment explanation
Indices: 45935902--45935981 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 29
45935892 CTGTTTTTAT
45935902 TAATTAAATAATTAAATATTT-AATTTAATA
1 TAATTAAATAATTAAATATTTCAA-TTAA-A
*
45935932 TAATTAAATAATTAAATCTTTTCAATTAAA
1 TAATTAAATAATTAAAT-ATTTCAATTAAA
45935962 TAATTAAATAAGCTTAAATA
1 TAATTAAATAA--TTAAATA
45935982 ATTATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 29 0.66
31 7 0.16
32 8 0.18
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TAATTAAATAATTAAATATTTCAATTAAA
Found at i:45935937 original size:22 final size:20
Alignment explanation
Indices: 45935900--45935946 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
45935890 GCCTGTTTTT
45935900 ATTAATTAAATAATTAAATA
1 ATTAATTAAATAATTAAATA
*
45935920 TTTAATTTAATATAATTAAATA
1 ATTAA-TTAA-ATAATTAAATA
45935942 ATTAA
1 ATTAA
45935947 ATCTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATTAAATAATTAAATA
Found at i:45936044 original size:8 final size:8
Alignment explanation
Indices: 45936033--45936134 Score: 59
Period size: 8 Copynumber: 12.2 Consensus size: 8
45936023 TTAATTAAAT
45936033 ATAATTAA
1 ATAATTAA
45936041 ATAATTTAA
1 ATAA-TTAA
*
45936050 TATAATTAT
1 -ATAATTAA
* *
45936059 TTACCTTAA
1 ATA-ATTAA
45936068 TATAATTAA
1 -ATAATTAA
45936077 ATAATTAA
1 ATAATTAA
45936085 ATAATT-A
1 ATAATTAA
45936092 AT--TTAA
1 ATAATTAA
*
45936098 TATACTT-A
1 -ATAATTAA
*
45936106 TTAACTTTAA
1 ATAA--TTAA
45936116 TATAATTAA
1 -ATAATTAA
45936125 ATAATTAA
1 ATAATTAA
45936133 AT
1 AT
45936135 CTTTTAACTT
Statistics
Matches: 73, Mismatches: 9, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
5 2 0.03
6 1 0.01
7 7 0.10
8 31 0.42
9 22 0.30
10 7 0.10
11 3 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (8 bp):
ATAATTAA
Found at i:45936051 original size:18 final size:18
Alignment explanation
Indices: 45936024--45936742 Score: 126
Period size: 18 Copynumber: 42.3 Consensus size: 18
45936014 GTTAAATAGT
*
45936024 TAATTAAATATAATTAAA
1 TAATTTAATATAATTAAA
**
45936042 TAATTTAATATAATTATT
1 TAATTTAATATAATTAAA
**
45936060 TACCTTAATATAATTAAA
1 TAATTTAATATAATTAAA
45936078 TAA-TTAA-ATAA-T---
1 TAATTTAATATAATTAAA
* *
45936090 TAATTTAATATACTT-AT
1 TAATTTAATATAATTAAA
45936107 TAACTTTAATATAATTAAA
1 TAA-TTTAATATAATTAAA
* *
45936126 TAA-TTAA-AT-CTT--T
1 TAATTTAATATAATTAAA
*
45936139 TAACTTAATATAA--AAGGA
1 TAATTTAATATAATTAA--A
*
45936157 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
*
45936175 TAA-TTAA-AT-CTT---
1 TAATTTAATATAATTAAA
* * **
45936187 TCAACTTGATATAATTAGT
1 T-AATTTAATATAATTAAA
*
45936206 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
* *
45936224 TAATTAAATCTTTTAACTTAAA
1 TAATTTAA---TATAA-TTAAA
****
45936246 T-ATTTAAT-TAA-GCGG
1 TAATTTAATATAATTAAA
*
45936261 TAGTGTT--TATAATTAAA
1 TAAT-TTAATATAATTAAA
* *
45936278 TATATAATTAAACATGATTAAA
1 TA-AT--TT-AATATAATTAAA
**
45936300 TAATTTAATATAATTATT
1 TAATTTAATATAATTAAA
* *
45936318 TAGTTTAATACAATTAAA
1 TAATTTAATATAATTAAA
* *
45936336 TAA-TT-ATAT-CTT--T
1 TAATTTAATATAATTAAA
* * **
45936349 TAAATTAATATACTTATT
1 TAATTTAATATAATTAAA
*
45936367 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
45936385 TAA-TT-A-AT-ATT---
1 TAATTTAATATAATTAAA
* **
45936396 TAATTTAATATACTTATT
1 TAATTTAATATAATTAAA
*
45936414 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
* *
45936432 TAA-TTAA-AT-CTT--T
1 TAATTTAATATAATTAAA
**
45936445 TAATTTAATATAATTAGT
1 TAATTTAATATAATTAAA
*
45936463 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
* *
45936481 TAA-TTAA-AT-CTT--T
1 TAATTTAATATAATTAAA
* **
45936494 TAACTTAATATAATTATT
1 TAATTTAATATAATTAAA
*
45936512 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
* *
45936530 TAATTAAATCTTTTAACTTAAA
1 TAATTTAA---TATAA-TTAAA
**
45936552 T-ATTTAAT-TAA-TCGA
1 TAATTTAATATAATTAAA
*
45936567 TAGTGTT--TATAATTAAA
1 TAAT-TTAATATAATTAAA
* *
45936584 TACATAATTAAACATGATTAAA
1 TA-AT--TT-AATATAATTAAA
**
45936606 TAATTTAATATAATTATT
1 TAATTTAATATAATTAAA
* *
45936624 TAGTTTAATACAA-TAAA
1 TAATTTAATATAATTAAA
* *
45936641 TAA-TT-ATAT-CTT--T
1 TAATTTAATATAATTAAA
* * **
45936654 TAAATTAATATACTTATT
1 TAATTTAATATAATTAAA
*
45936672 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
45936690 TAA-TTAA-AT-ATT---
1 TAATTTAATATAATTAAA
* **
45936702 TAATTTAATATACTTATT
1 TAATTTAATATAATTAAA
*
45936720 TACTTTAATATAATTAAA
1 TAATTTAATATAATTAAA
45936738 TAATT
1 TAATT
45936743 AAATCTTTTA
Statistics
Matches: 500, Mismatches: 118, Indels: 166
0.64 0.15 0.21
Matches are distributed among these distances:
11 3 0.01
12 9 0.02
13 26 0.05
14 29 0.06
15 47 0.09
16 40 0.08
17 51 0.10
18 226 0.45
19 13 0.03
20 2 0.00
21 22 0.04
22 32 0.06
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TAATTTAATATAATTAAA
Found at i:45936166 original size:49 final size:49
Alignment explanation
Indices: 45936046--45936244 Score: 267
Period size: 49 Copynumber: 4.1 Consensus size: 49
45936036 ATTAAATAAT
* ** *
45936046 TTAATATAATTATTTACCTTAATATAATTAAATAATTAAAT-AATTAAT
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
* *
45936094 TTAATATACTTATTAACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
* ** *
45936143 TTAATATAA-AAGGATACTTTAATATAATTAAATAATTAAATCTTTCAAC
1 TTAATATAATTA-TTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
* *
45936192 TTGATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
45936241 TTAA
1 TTAA
45936245 ATATTTAATT
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 39 0.30
49 91 0.69
50 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (49 bp):
TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
Found at i:45936359 original size:49 final size:49
Alignment explanation
Indices: 45936300--45936763 Score: 551
Period size: 49 Copynumber: 9.3 Consensus size: 49
45936290 CATGATTAAA
* * *
45936300 TAATTTAATATAATTATTTAGTTTAATACAATTAAATAATTATATCTTT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
* * *
45936349 TAAATTAATATACTTATTTACTTTAATATAATTAAATAATT-AAT-ATT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
*
45936396 TAATTTAATATACTTATTTACTTTAATATAATTAAATAATTAAATCTTT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
*
45936445 TAATTTAATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
*
45936494 TAACTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
* * * * * *
45936543 TAACTTAAATATTTAATTAATCGATAGTGTTTATAATTAAATACATAATTAAA-CATGATT
1 TAA-TTTAATA--TAATT-AT--TTACT-TTAAT-A-TAATTAAATAATTAAATC-T--TT
* * *
45936603 AAATAATTTAATATAATTATTTAGTTTAATACAA-TAAATAATTATATCTTT
1 ---TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
* * *
45936654 TAAATTAATATACTTATTTACTTTAATATAATTAAATAATTAAAT-ATT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
*
45936702 TAATTTAATATACTTATTTACTTTAATATAATTAAATAATTAAATCTTT
1 TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
*
45936751 TAACTTAATATAA
1 TAATTTAATATAA
45936764 AAGGATACTT
Statistics
Matches: 360, Mismatches: 35, Indels: 40
0.83 0.08 0.09
Matches are distributed among these distances:
47 42 0.12
48 78 0.22
49 161 0.45
50 5 0.01
51 2 0.01
52 5 0.01
53 13 0.04
54 3 0.01
55 4 0.01
56 8 0.02
57 6 0.02
58 15 0.04
59 2 0.01
60 7 0.02
62 6 0.02
63 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (49 bp):
TAATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTT
Found at i:45936387 original size:8 final size:9
Alignment explanation
Indices: 45936371--45936536 Score: 60
Period size: 8 Copynumber: 19.4 Consensus size: 9
45936361 CTTATTTACT
45936371 TTAATATAA
1 TTAATATAA
45936380 TTAA-ATAA
1 TTAATATAA
45936388 TTAATATTTAA
1 TTAATA--TAA
*
45936399 TTTAATATAC
1 -TTAATATAA
* *
45936409 TT-ATTTACT
1 TTAATATA-A
45936418 TTAATATAA
1 TTAATATAA
45936427 TTAA-ATAA
1 TTAATATAA
*
45936435 TTAA-AT-C
1 TTAATATAA
45936442 TT--T-TAA
1 TTAATATAA
45936448 TTTAATATAA
1 -TTAATATAA
* *
45936458 TTAGT-TACT
1 TTAATATA-A
45936467 TTAATATAA
1 TTAATATAA
45936476 TTAA-ATAA
1 TTAATATAA
*
45936484 TTAA-AT-C
1 TTAATATAA
45936491 TT--T-TAA
1 TTAATATAA
45936497 CTTAATATAA
1 -TTAATATAA
* *
45936507 TT-ATTTACT
1 TTAATATA-A
45936516 TTAATATAA
1 TTAATATAA
45936525 TTAA-ATAA
1 TTAATATAA
45936533 TTAA
1 TTAA
45936537 ATCTTTTAAC
Statistics
Matches: 118, Mismatches: 17, Indels: 45
0.66 0.09 0.25
Matches are distributed among these distances:
5 2 0.02
7 8 0.07
8 46 0.39
9 35 0.30
10 18 0.15
11 3 0.03
12 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (9 bp):
TTAATATAA
Found at i:45936413 original size:306 final size:306
Alignment explanation
Indices: 45936046--45936773 Score: 1307
Period size: 306 Copynumber: 2.4 Consensus size: 306
45936036 ATTAAATAAT
* * * *
45936046 TTAATATAATTATTTACCTTAATATAATTAAATAATTAAATAATTAATTTAATATACTTATTAAC
1 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATACTTATTTAC
45936111 TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAAAAGGATACTTTAATATAATTAAAT
66 TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAAAAGGATACTTTAATATAATTAAAT
*
45936176 AATTAAATCTTTCAACTTGATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
131 AATTAAATCTTTCAACTTAATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
* *
45936241 TTAAATATTTAATTAAGCGGTAGTGTTTATAATTAAATATATAATTAAACATGATTAAATAATTT
196 TTAAATATTTAATTAAGCGATAGTGTTTATAATTAAATACATAATTAAACATGATTAAATAATTT
45936306 AATATAATTATTTAGTTTAATACAATTAAATAATTATATCTTTTAAA
261 AATATAATTATTTAGTTTAATACAA-TAAATAATTATATCTTTTAAA
45936353 TTAATATACTTATTTACTTTAATATAATTAAATAATT-AATATTTAATTTAATATACTTATTTAC
1 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATACTTATTTAC
* * *
45936417 TTTAATATAATTAAATAATTAAATCTTTTAATTTAATATAATTA-GTTACTTTAATATAATTAAA
66 TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAA-AAGGATACTTTAATATAATTAAA
* *
45936481 TAATTAAATCTTTTAACTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAA
130 TAATTAAATCTTTCAACTTAATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAA
*
45936546 CTTAAATATTTAATTAATCGATAGTGTTTATAATTAAATACATAATTAAACATGATTAAATAATT
195 CTTAAATATTTAATTAAGCGATAGTGTTTATAATTAAATACATAATTAAACATGATTAAATAATT
45936611 TAATATAATTATTTAGTTTAATACAATAAATAATTATATCTTTTAAA
260 TAATATAATTATTTAGTTTAATACAATAAATAATTATATCTTTTAAA
45936658 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATACTTATTTAC
1 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATACTTATTTAC
45936723 TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAAAAGGATACTT
66 TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAAAAGGATACTT
45936774 ATTTAAGTTT
Statistics
Matches: 402, Mismatches: 16, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
305 59 0.15
306 307 0.76
307 36 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (306 bp):
TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATACTTATTTAC
TTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAAAAGGATACTTTAATATAATTAAAT
AATTAAATCTTTCAACTTAATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
TTAAATATTTAATTAAGCGATAGTGTTTATAATTAAATACATAATTAAACATGATTAAATAATTT
AATATAATTATTTAGTTTAATACAATAAATAATTATATCTTTTAAA
Found at i:45936562 original size:26 final size:24
Alignment explanation
Indices: 45936431--45936554 Score: 71
Period size: 26 Copynumber: 5.1 Consensus size: 24
45936421 ATATAATTAA
*
45936431 ATAATTAAATCTTTTAA-TTTAAT
1 ATAATTAAATCTTTTAACTTAAAT
** *
45936454 ATAATTAGTTAC-TTTAA-TATAATTAA
1 ATAATTAAAT-CTTTTAACT-TAA--AT
45936480 ATAATTAAATCTTTTAACTT-AAT
1 ATAATTAAATCTTTTAACTTAAAT
** *
45936503 ATAATTATTTAC-TTTAA-TATAATTAA
1 ATAATTAAAT-CTTTTAACT-TAA--AT
45936529 ATAATTAAATCTTTTAACTTAAAT
1 ATAATTAAATCTTTTAACTTAAAT
45936553 AT
1 AT
45936555 TTAATTAATC
Statistics
Matches: 75, Mismatches: 13, Indels: 25
0.66 0.12 0.22
Matches are distributed among these distances:
22 1 0.01
23 29 0.39
24 8 0.11
25 3 0.04
26 32 0.43
27 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (24 bp):
ATAATTAAATCTTTTAACTTAAAT
Found at i:45936662 original size:48 final size:49
Alignment explanation
Indices: 45936610--45936763 Score: 222
Period size: 48 Copynumber: 3.2 Consensus size: 49
45936600 ATTAAATAAT
* * *
45936610 TTAATATAATTATTTAGTTTAATACAA-TAAATAATTATATCTTTTAAA
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAA
* * *
45936658 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAAT-ATTTAAT
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAA
* *
45936706 TTAATATACTTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAA
45936755 TTAATATAA
1 TTAATATAA
45936764 AAGGATACTT
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
48 70 0.74
49 25 0.26
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (49 bp):
TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAA
Found at i:45936759 original size:257 final size:253
Alignment explanation
Indices: 45936015--45936763 Score: 810
Period size: 257 Copynumber: 2.9 Consensus size: 253
45936005 ACATTTTAAG
** * * * ** *
45936015 TTAAATAGTTAATTAAATATAATTAAATAATTTAATATAATTATTTACCTTAATATAATTAAATA
1 TTAAATAAATAATTAAACATAATTAAATAATTTAATATAATGATGTAGTTTAATACAATTAAATA
* * *
45936080 ATTA-AA-TAATTAATTTAATATACTTATTAACTTTAATATAATTAAATAATTAAATCTTTTAAC
66 ATTATAACT-TTTAATTTAATATACTTATTTACTTTAATATAATTAAATAATT-AATCTTTTAAA
** ** * * *
45936143 TTAATATA-AAAGGATACTTTAATATAATTAAATAATTAAATCTTTCAACTTGATATAATTAGTT
129 TTAATATACTTA-TTTACTTTAATATAATTAAATAATTAAATATTT-AATTTAATATAATTAGTT
* *
45936207 ACTTTAATATAATTAAATAATTAAATCTTTTAACTTAAATATTTAATTAAGCGGTAGTGTTTATA
192 ACTTTAATATAATTAAATAATTAAATCTTTTAACTT-AATA--TAATTAA-CGGTACTGTTAATA
45936272 A
253 A
* * * *
45936273 TTAAATATATAATTAAACATGATTAAATAATTTAATATAATTATTTAGTTTAATACAATTAAATA
1 TTAAATAAATAATTAAACATAATTAAATAATTTAATATAATGATGTAGTTTAATACAATTAAATA
* * * *
45936338 ATTATATCTTTTAAATTAATATACTTATTTACTTTAATATAATTAAATAATTAAT-ATTTAATTT
66 ATTATAACTTTTAATTTAATATACTTATTTACTTTAATATAATTAAATAATTAATCTTTTAAATT
*
45936402 AATATACTTATTTACTTTAATATAATTAAATAATTAAATCTTTTAATTTAATATAATTAGTTACT
131 AATATACTTATTTACTTTAATATAATTAAATAATTAAAT-ATTTAATTTAATATAATTAGTTACT
**
45936467 TTAATATAATTAAATAATTAAATCTTTTAACTTAATATAATT-A-TTTACT-TTAAT-A
195 TTAATATAATTAAATAATTAAATCTTTTAACTTAATATAATTAACGGTACTGTTAATAA
* *
45936522 -TAATTAAATAATTAAATCTTTTAACTTAAAT-ATTTAAT-TAATCGATAGT-GTTT-AT--AAT
1 TTAAATAAATAATTAAA-C--ATAA-TTAAATAATTTAATATAAT-GAT-GTAGTTTAATACAAT
* * * *
45936580 TAAATACATAATTAAACATGATTAAATAATTTAATATAATTATTTAGTTTAATACAA-TAAATAA
60 TAAATA-ATTA-T-AAC-T--TT---TAATTTAATATACTTATTTACTTTAATATAATTAAATAA
45936644 TTATATCTTTTAAATTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTA
116 TTA-ATCTTTTAAATTAATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTA
* *
45936709 ATATACTTATTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAA
180 ATATAATTAGTTACTTTAATATAATTAAATAATTAAATCTTTTAACTTAATATAA
45936764 AAGGATACTT
Statistics
Matches: 429, Mismatches: 41, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
248 23 0.05
249 5 0.01
250 11 0.03
251 20 0.05
252 8 0.02
253 1 0.00
254 7 0.02
256 14 0.03
257 183 0.43
258 115 0.27
259 41 0.10
260 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (253 bp):
TTAAATAAATAATTAAACATAATTAAATAATTTAATATAATGATGTAGTTTAATACAATTAAATA
ATTATAACTTTTAATTTAATATACTTATTTACTTTAATATAATTAAATAATTAATCTTTTAAATT
AATATACTTATTTACTTTAATATAATTAAATAATTAAATATTTAATTTAATATAATTAGTTACTT
TAATATAATTAAATAATTAAATCTTTTAACTTAATATAATTAACGGTACTGTTAATAA
Found at i:45939099 original size:41 final size:41
Alignment explanation
Indices: 45938947--45939310 Score: 325
Period size: 41 Copynumber: 8.9 Consensus size: 41
45938937 GCTTATTATA
* * **
45938947 AAAGCGCCGCTAATGACCTGACCTTTAGCGACGCTTTATAT
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGT
* **
45938988 ATAAGCGCCGCTAATGACCCGAA-CTTTAGCGGCGC-TTAAAT
1 A-AAGCGCCGCTAATGA-CCTAACCTTTAGCGGCGCTTTAGGT
*
45939029 GAAAGCGCCGCTAAATGATCCT-ACCTTTAGCGGCGCTTTAGGG
1 -AAAGCGCCGCT-AATGA-CCTAACCTTTAGCGGCGCTTTAGGT
*
45939072 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGG
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGT
*
45939113 AAAGCGCCGCTAAT-ACCCT-ACCTTTAGCGGCGCTTGT-GAT
1 AAAGCGCCGCTAATGA-CCTAACCTTTAGCGGCGCTT-TAGGT
* * *
45939153 AAAGCGCCGCTAATTACATAACCTTTAGCGGCGCTTGT-GAT
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTT-TAGGT
* * * *
45939194 AAAGCGCCGCGAATTACCTGACCTTTAGCGGCGCTTT-TGT
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGT
* * * * * * * *
45939234 TAAGCGCCGCTAATG-CTTTACATTTTGCGGCGCATTAAGC
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGT
* * * *
45939274 AAAACGCCGCTAATG-CTTTACCTTTTGCGGCGCTTTA
1 AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTA
45939311 TTTCCAAACG
Statistics
Matches: 280, Mismatches: 31, Indels: 25
0.83 0.09 0.07
Matches are distributed among these distances:
39 16 0.06
40 85 0.30
41 116 0.41
42 57 0.20
43 6 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (41 bp):
AAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGT
Found at i:45939175 original size:81 final size:81
Alignment explanation
Indices: 45938890--45939309 Score: 335
Period size: 81 Copynumber: 5.2 Consensus size: 81
45938880 TTTAAATACA
** * * * * *
45938890 TTAGCGGCGCTTATGGGAAAGCGCCGCTAAT-TCA-CACCTTTAGTGACGCTTATTA-TAAAAGC
1 TTAGCGGCGCTT-TGATAAAGCGCCGCTAATGACATAACCTTTAGCGGCGC-T-TTAGTGAAAGC
45938952 GCCGCTAATGACCTGACCT
63 GCCGCTAATGACCTGACCT
* * ** * *
45938971 TTAGCGACGCTTTATATATAAGCGCCGCTAATGACCCGAA-CTTTAGCGGCGCTTAAATGAAAGC
1 TTAGCGGCGCTTT-GATA-AAGCGCCGCTAATGA-CATAACCTTTAGCGGCGCTTTAGTGAAAGC
45939035 GCCGCTAAATGATCCT-ACCT
63 GCCGCT-AATGA-CCTGACCT
** * *
45939055 TTAGCGGCGCTTTAGGGAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTTAGGGAAAGCGC
1 TTAGCGGCGCTTT-GATAAAGCGCCGCTAATGACATAACCTTTAGCGGCGCTTTAGTGAAAGCGC
45939120 CGCTAAT-ACCCT-ACCT
65 CGCTAATGA-CCTGACCT
*
45939136 TTAGCGGCGCTTGTGATAAAGCGCCGCTAATTACATAACCTTTAGCGGCGC-TT-GTGATAAAGC
1 TTAGCGGCGCTT-TGATAAAGCGCCGCTAATGACATAACCTTTAGCGGCGCTTTAGTG--AAAGC
* *
45939199 GCCGCGAATTACCTGACCT
63 GCCGCTAATGACCTGACCT
* * * * * * * *
45939218 TTAGCGGCGCTTTTG-TTAAGCGCCGCTAATG-CTTTACATTTTGCGGCGCATTAAG-CAAAACG
1 TTAGCGGCGC-TTTGATAAAGCGCCGCTAATGACATAACCTTTAGCGGCGC-TTTAGTGAAAGCG
* *
45939280 CCGCTAATG-CTTTACCT
64 CCGCTAATGACCTGACCT
*
45939297 TTTGCGGCGCTTT
1 TTAGCGGCGCTTT
45939310 ATTTCCAAAC
Statistics
Matches: 281, Mismatches: 40, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
78 3 0.01
79 17 0.06
80 29 0.10
81 95 0.34
82 41 0.15
83 58 0.21
84 34 0.12
85 4 0.01
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (81 bp):
TTAGCGGCGCTTTGATAAAGCGCCGCTAATGACATAACCTTTAGCGGCGCTTTAGTGAAAGCGCC
GCTAATGACCTGACCT
Found at i:45941686 original size:19 final size:19
Alignment explanation
Indices: 45941659--45941699 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
45941649 AATATAGGGA
45941659 TAAAAATGAGC-ATGCAAAT
1 TAAAAATGAGCTATGC-AAT
*
45941678 TAAATATGAGCTATGCAAT
1 TAAAAATGAGCTATGCAAT
45941697 TAA
1 TAA
45941700 TGATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
TAAAAATGAGCTATGCAAT
Found at i:45941928 original size:30 final size:29
Alignment explanation
Indices: 45941866--45942275 Score: 335
Period size: 30 Copynumber: 13.9 Consensus size: 29
45941856 AAAAGGGTTG
*
45941866 AAAATG-AAGTTTT-AGAGAGTTT-GGGGTT
1 AAAATGTAA-TTTTGAGA-AGTTTAGGGGTA
* * *
45941894 AAAATATAATTTTAAAAAGTTTAAGGGGTA
1 AAAATGTAATTTTGAGAAGTTT-AGGGGTA
* ** * *
45941924 AAAATGTCATTTT-AGGAAAATTCGAGGTA
1 AAAATGTAATTTTGA-GAAGTTTAGGGGTA
* * * *
45941953 AAAACGTGATTTTCGA-AAG-TTCGAGGGCA
1 AAAATGTAATTTT-GAGAAGTTTAG-GGGTA
*
45941982 AAAATGTAATTTTG-GAAGTTT-GGATGTA
1 AAAATGTAATTTTGAGAAGTTTAGG-GGTA
45942010 AAAATGTAATTTTTGAGAAGTTTGAGGGGTA
1 AAAATGTAA-TTTTGAGAAGTTT-AGGGGTA
*
45942041 AAAACGTGAATTTTTG-GAAGTTT-GAGGGTA
1 AAAATGT-AA-TTTTGAGAAGTTTAG-GGGTA
*
45942071 AAAATGTAATTTTTAGAA-TTTAGGGGGTA
1 AAAATGTAATTTTGAGAAGTTTA-GGGGTA
45942100 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
1 AAAATGTAA-TTTTGAGAAGTTTAGGGGTA
*
45942130 AAAATGTAAATTTTGA-AAGTTTAGGGGCA
1 AAAATGT-AATTTTGAGAAGTTTAGGGGTA
45942159 AAAATGTAATTTTTGAGAAGTTTAGGGGTA
1 AAAATGTAA-TTTTGAGAAGTTTAGGGGTA
* *
45942189 AAAATATAATTTTTGAGAAGTTTAGGGTTA
1 AAAATGTAA-TTTTGAGAAGTTTAGGGGTA
* *
45942219 AAAATGTAATTTTGGAAAAGTTTAGAGGTTA
1 AAAATGTAATTTT-GAGAAGTTTAG-GGGTA
*
45942250 AAATATG-ATTTTTG-GATAGTTTAGGG
1 AAA-ATGTAATTTTGAGA-AGTTTAGGG
45942276 ACCTTTTGGG
Statistics
Matches: 321, Mismatches: 32, Indels: 57
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.00
28 43 0.13
29 96 0.30
30 132 0.41
31 36 0.11
32 13 0.04
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGAGAAGTTTAGGGGTA
Found at i:45941952 original size:29 final size:28
Alignment explanation
Indices: 45941920--45942237 Score: 113
Period size: 29 Copynumber: 10.8 Consensus size: 28
45941910 AAGTTTAAGG
*
45941920 GGTAAAAATGTCATTTTAGGAAAATTCGA
1 GGTAAAAATGTAATTTT-GGAAAATTCGA
* * * *
45941949 GGTAAAAACGTGATTTTCGAAAGTTCGA
1 GGTAAAAATGTAATTTTGGAAAATTCGA
* ** *
45941977 GGGCAAAAATGTAATTTTGGAAGTTTGGA
1 -GGTAAAAATGTAATTTTGGAAAATTCGA
* * * *
45942006 TGTAAAAATGTAATTTTTGAGAAGTTTGA
1 GGTAAAAATGTAATTTTGGA-AAATTCGA
* * *
45942035 GGGGTAAAAACGTGAATTTTTGG-AAGTTTGA
1 --GGTAAAAATGT-AA-TTTTGGAAAATTCGA
* * * *
45942066 GGGTAAAAATGTAATTTT-TAGAATTTAGGG
1 -GGTAAAAATGTAATTTTGGA-AAATT-CGA
** * *
45942096 GGTAAAAATGTAATTTTTGAGAAGTTTAGG
1 GGTAAAAATGTAA-TTTTG-GAAAATTCGA
* * *
45942126 GGTAAAAATGTAAATTTT-GAAAGTTTAGG
1 GGTAAAAATGT-AATTTTGGAAA-ATTCGA
* ** * *
45942155 GGCAAAAATGTAATTTTTGAGAAGTTTAGG
1 GGTAAAAATGTAA-TTTTG-GAAAATTCGA
* * * *
45942185 GGTAAAAATATAATTTTTGAGAAGTT-TA
1 GGTAAAAATGTAATTTTGGA-AAATTCGA
45942213 GGGTTAAAAATGTAATTTTGGAAAA
1 -GG-TAAAAATGTAATTTTGGAAAA
45942238 GTTTAGAGGT
Statistics
Matches: 228, Mismatches: 41, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
28 37 0.16
29 91 0.40
30 66 0.29
31 26 0.11
32 3 0.01
33 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
GGTAAAAATGTAATTTTGGAAAATTCGA
Found at i:45942074 original size:89 final size:88
Alignment explanation
Indices: 45941910--45942275 Score: 395
Period size: 89 Copynumber: 4.1 Consensus size: 88
45941900 TAATTTTAAA
* * ** * * * *
45941910 AAGTTTAAGGGGTAAAAATGTCATTTTAG-GAAAATTCGAGGTAAAAACGTGATTTTCGAAAGTT
1 AAGTTT-AGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAACGTAATTTTTGAAAGTT
*
45941974 CGAGGGCAAAAATGTAA-TTTTGG
65 TGAGGGCAAAAATGTAATTTTTGG
* *
45941997 AAGTTT-GGATGTAAAAATGTAATTTTTGAGAAGTTTGAGGGGTAAAAACGTGAATTTTTGGAAG
1 AAGTTTAGG-GGTAAAAATGTAATTTTTGAGAAGTTT-AGGGGTAAAAACGT-AATTTTTGAAAG
* *
45942061 TTTGAGGGTAAAAATGTAATTTTTAG
63 TTTGAGGGCAAAAATGTAATTTTTGG
* *
45942087 AA-TTTAGGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAAATTTTGAAAGTT
1 AAGTTTA-GGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAACGTAATTTTTGAAAGTT
45942151 T-AGGGGCAAAAATGTAATTTTTGAG
65 TGA-GGGCAAAAATGTAATTTTTG-G
* * * *
45942176 AAGTTTAGGGGTAAAAATATAATTTTTGAGAAGTTTAGGGTTAAAAATGTAATTTTGGAAAAGTT
1 AAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAACGTAATTTTTG-AAAGTT
**
45942241 TAGAGGTTAAAATATG--ATTTTTGG
65 T-GAGGGCAAAA-ATGTAATTTTTGG
45942265 ATAGTTTAGGG
1 A-AGTTTAGGG
45942276 ACCTTTTGGG
Statistics
Matches: 239, Mismatches: 25, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
85 2 0.01
86 16 0.07
87 12 0.05
88 43 0.18
89 94 0.39
90 60 0.25
91 8 0.03
92 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (88 bp):
AAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAACGTAATTTTTGAAAGTTT
GAGGGCAAAAATGTAATTTTTGG
Found at i:45942129 original size:59 final size:60
Alignment explanation
Indices: 45941866--45942275 Score: 375
Period size: 59 Copynumber: 7.0 Consensus size: 60
45941856 AAAAGGGTTG
* * * * *
45941866 AAAATG-AAGTTTT-AGAGAGTTT-GGGGTTAAAATATAA-TTTTAAAAAGTTTAAGGGGTA
1 AAAATGTAATTTTTGAGA-AGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTT-AGGGGTA
* * ** * * * * * * *
45941924 AAAATGTCATTTTAG-GAAAATTCGAGGTAAAAACGTGATTTTCGA-AAG-TTCGAGGGCA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAG-GGGTA
*
45941982 AAAATGTAA-TTTTG-GAAGTTT-GGATGTAAAAATGTAATTTTTGAGAAGTTTGAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTAGG-GGTAAAAATGTAATTTTTGAGAAGTTT-AGGGGTA
*
45942041 AAAACGTGAATTTTTG-GAAGTTT-GAGGGTAAAAATGTAATTTTT-AGAA-TTTAGGGGGTA
1 AAAATGT-AATTTTTGAGAAGTTTAG-GGGTAAAAATGTAATTTTTGAGAAGTTTA-GGGGTA
* *
45942100 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAAATTTTGA-AAGTTTAGGGGCA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTA
* *
45942159 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATATAATTTTTGAGAAGTTTAGGGTTA
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTA
* * * * * *
45942219 AAAATGTAATTTTGGAAAAGTTTAGAGGTTAAAATATGATTTTTG-GATAGTTTAGGG
1 AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGA-AGTTTAGGG
45942276 ACCTTTTGGG
Statistics
Matches: 294, Mismatches: 39, Indels: 36
0.80 0.11 0.10
Matches are distributed among these distances:
56 1 0.00
57 26 0.09
58 35 0.12
59 124 0.42
60 77 0.26
61 30 0.10
62 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTTGAGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTTAGGGGTA
Found at i:45943456 original size:30 final size:32
Alignment explanation
Indices: 45943395--45943454 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 32
45943385 GTAGAAAATG
45943395 ATAAATAAGTAATTAATGAATATGTTTATATA
1 ATAAATAAGTAATTAATGAATATGTTTATATA
*
45943427 ATAAATAA-T-ATTAAT--ATATATTTATATA
1 ATAAATAAGTAATTAATGAATATGTTTATATA
45943455 TATTAAAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 12 0.44
30 6 0.22
31 1 0.04
32 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (32 bp):
ATAAATAAGTAATTAATGAATATGTTTATATA
Found at i:45944144 original size:17 final size:16
Alignment explanation
Indices: 45944093--45944190 Score: 88
Period size: 17 Copynumber: 5.8 Consensus size: 16
45944083 ACTCTCTCTT
*
45944093 TTTAAATTAAATTAAA
1 TTTAAATTAAAATAAA
* *
45944109 TTTAAATATAGAATGAA
1 TTTAAAT-TAAAATAAA
45944126 TTTAAATTCAAAATAAA
1 TTTAAATT-AAAATAAA
*
45944143 TTTAAATTTAAACTAAA
1 TTTAAA-TTAAAATAAA
* *
45944160 TATAAACCTAAAATAAA
1 TTTAAA-TTAAAATAAA
*
45944177 TTAAAATTTAAAAT
1 TTTAAA-TTAAAAT
45944191 TGGGTTCAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
16 8 0.12
17 55 0.85
18 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
TTTAAATTAAAATAAA
Found at i:45946047 original size:51 final size:51
Alignment explanation
Indices: 45945970--45946208 Score: 311
Period size: 51 Copynumber: 4.6 Consensus size: 51
45945960 GCTATAAACG
45945970 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACT-GATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTA-TGGATT
45946022 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * *
45946073 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * * * * * * *
45946124 AAAGGTCTGATGACTCAGTGTTATCGTGAGTATATAAATTCCTATACGAAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATT
45946176 AAGAGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
45946209 TTAAATGAAA
Statistics
Matches: 165, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.01
51 124 0.75
52 14 0.08
53 25 0.15
54 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:45948892 original size:23 final size:20
Alignment explanation
Indices: 45948833--45948878 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
45948823 AACATTTATC
45948833 GTTTAAAAATATCATTTACT
1 GTTTAAAAATATCATTTACT
45948853 GTTTAAAAATATCATTTACT
1 GTTTAAAAATATCATTTACT
45948873 GTTTAA
1 GTTTAA
45948879 TAAAGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (20 bp):
GTTTAAAAATATCATTTACT
Found at i:45949156 original size:21 final size:21
Alignment explanation
Indices: 45949130--45949172 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
45949120 CTTAACGAGA
*
45949130 TAGCTGACGTTGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
*
45949151 TAGCTGATGTGGCCAGTTAAC
1 TAGCTGACGTGGCCAGTTAAC
45949172 T
1 T
45949173 TGCCACGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
TAGCTGACGTGGCCAGTTAAC
Found at i:45949977 original size:3 final size:3
Alignment explanation
Indices: 45949951--45950018 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
45949941 CCAATTTTTC
* *
45949951 TCT TC- TCT TC- TCT TC- TCTT TCT TCT TCT TCT TC- TCC TCC TCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
*
45949993 TCT TCT TCT TTT TC- TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
45950019 ACAGGCTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
2 10 0.18
3 44 0.79
4 2 0.04
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:45949978 original size:17 final size:16
Alignment explanation
Indices: 45949948--45950018 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
45949938 TCTCCAATTT
45949948 TTCTCTTCTCTTC-TC
1 TTCTCTTCTCTTCTTC
45949963 TTCTCTTTCTTCTTCTTC
1 TTCTC-TTC-TCTTCTTC
*
45949981 TTCTCCTCCTCTTCTTC
1 TTCT-CTTCTCTTCTTC
*
45949998 TTCTTTTTCTCTTCTTC
1 TTC-TCTTCTCTTCTTC
45950015 TTCT
1 TTCT
45950019 ACAGGCTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.10
16 4 0.08
17 29 0.60
18 9 0.19
19 1 0.02
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCTCTTCTCTTCTTC
Found at i:45949981 original size:20 final size:20
Alignment explanation
Indices: 45949951--45950018 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 20
45949941 CCAATTTTTC
45949951 TCTTC-TCTTCTCTTCTCTT
1 TCTTCTTCTTCTCTTCTCTT
*
45949970 TCTTCTTCTTCTTCTCCTCCTCT
1 TCTTCTTCTTC-TCTTCT-CT-T
45949993 TCTTCTTCTT-T-TTCTC-T
1 TCTTCTTCTTCTCTTCTCTT
45950010 TCTTCTTCT
1 TCTTCTTCT
45950019 ACAGGCTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 10 0.23
19 6 0.14
20 8 0.19
21 6 0.14
22 2 0.05
23 11 0.26
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
TCTTCTTCTTCTCTTCTCTT
Found at i:45951260 original size:22 final size:23
Alignment explanation
Indices: 45951229--45951271 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
45951219 AAACTATATT
45951229 TCATGCTT-AATT-AGTTAAAAA
1 TCATGCTTAAATTAAGTTAAAAA
45951250 TCATGTCTTAAATTAAGTTAAA
1 TCATG-CTTAAATTAAGTTAAA
45951272 TGGCATGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 4 0.21
24 7 0.37
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
TCATGCTTAAATTAAGTTAAAAA
Found at i:45959207 original size:96 final size:96
Alignment explanation
Indices: 45959041--45959228 Score: 331
Period size: 96 Copynumber: 2.0 Consensus size: 96
45959031 AAAGAAGAAT
* * *
45959041 GGAGGAAAAGGAAGGAGGTGTGTTTGAAATTTAAAATTCTGAATTTTTTAAACCTGTTCTTTGCC
1 GGAGGAAAAGGAAGGAGGTGTGTTTGAAATTTAAAACTCTAAATTTTTTAAACCTATTCTTTGCC
*
45959106 CCCAAATGAACCCATTTATCTACACCTATTA
66 CCCAAATGAACCCATTTATCCACACCTATTA
45959137 GGAGGAAAAGGAAGGAGGTGTGTTTGAAATTTAAAACTCTAAATTTTTTAAACCTATTCTTTGCC
1 GGAGGAAAAGGAAGGAGGTGTGTTTGAAATTTAAAACTCTAAATTTTTTAAACCTATTCTTTGCC
*
45959202 TCCAAATGAACCCATTTATCCACACCT
66 CCCAAATGAACCCATTTATCCACACCT
45959229 GTTATTGTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (96 bp):
GGAGGAAAAGGAAGGAGGTGTGTTTGAAATTTAAAACTCTAAATTTTTTAAACCTATTCTTTGCC
CCCAAATGAACCCATTTATCCACACCTATTA
Found at i:45959813 original size:29 final size:31
Alignment explanation
Indices: 45959750--45959816 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
45959740 GATGATGAGA
*
45959750 AGAAGAAGTGGTGTTAGATAAAAAAATAGTG
1 AGAAGAAGTGGTGTTAAATAAAAAAATAGTG
45959781 AGAAGAAGTGGTGTTAAATAAAAAAAT-G-G
1 AGAAGAAGTGGTGTTAAATAAAAAAATAGTG
45959810 AGAAGAA
1 AGAAGAA
45959817 TATGAAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 8 0.23
30 1 0.03
31 26 0.74
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.19
Consensus pattern (31 bp):
AGAAGAAGTGGTGTTAAATAAAAAAATAGTG
Found at i:45959919 original size:19 final size:17
Alignment explanation
Indices: 45959879--45959911 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
45959869 TTTTTTAATA
45959879 ATTTTATATTTAAAAAG
1 ATTTTATATTTAAAAAG
45959896 ATTTTATATTTAAAAA
1 ATTTTATATTTAAAAA
45959912 AATATTTTTA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATTTTATATTTAAAAAG
Found at i:45961362 original size:5 final size:5
Alignment explanation
Indices: 45961352--45961400 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
45961342 TTGCAACAAG
* * *
45961352 ATTTT ATTTT ACTTT A-TTT ATTTC ATTTT ATTTT GTTTT ATTTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT ATTT
45961401 AAGACTCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:45962869 original size:21 final size:19
Alignment explanation
Indices: 45962840--45962879 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
45962830 TTGTAAATAT
*
45962840 TTTGTATTTTTTATATATTTA
1 TTTGCATTTTTT-TAT-TTTA
45962861 TTTGCATTTTTTTATTTTA
1 TTTGCATTTTTTTATTTTA
45962880 ATATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 11 0.61
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTGCATTTTTTTATTTTA
Found at i:45963317 original size:15 final size:17
Alignment explanation
Indices: 45963274--45963311 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
45963264 CTCCACCTTG
*
45963274 ACAAGAATTCTCTACGA
1 ACAAGAATTCTCAACGA
*
45963291 ACAAGAACTCTCAACGA
1 ACAAGAATTCTCAACGA
45963308 ACAA
1 ACAA
45963312 ATTCTCCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (17 bp):
ACAAGAATTCTCAACGA
Found at i:45971739 original size:27 final size:28
Alignment explanation
Indices: 45971683--45971739 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
45971673 TTAAAATATC
45971683 TTTTAAAAGTAATAATAAAAAATGTTCAT
1 TTTTAAAAGTAATAAT-AAAAATGTTCAT
* * *
45971712 TTTTTAAAGTAATAGT-AAAATTTTCAT
1 TTTTAAAAGTAATAATAAAAATGTTCAT
45971739 T
1 T
45971740 AGGTCCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
29 14 0.56
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTAAAAGTAATAATAAAAATGTTCAT
Found at i:45973742 original size:24 final size:24
Alignment explanation
Indices: 45973715--45973771 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
45973705 AATCTTTTAG
45973715 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
*
45973739 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
45973763 TTAAACTCT
1 TTAAACTCT
45973772 TATTAATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:45982322 original size:19 final size:19
Alignment explanation
Indices: 45982298--45982335 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
45982288 ACATTGGTCT
*
45982298 TTATTATTATATTTGTTTA
1 TTATTATTATAGTTGTTTA
*
45982317 TTATTATTTTAGTTGTTTA
1 TTATTATTATAGTTGTTTA
45982336 ATAAGAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (19 bp):
TTATTATTATAGTTGTTTA
Found at i:45985672 original size:22 final size:23
Alignment explanation
Indices: 45985641--45985691 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
45985631 GCCACATTGT
45985641 GACGTCGTGT-TCAGC-TCGTCGG
1 GACGTCGTGTGTC-GCGTCGTCGG
* *
45985663 GACGTGGTGTGTCGCGTTGTCGG
1 GACGTCGTGTGTCGCGTCGTCGG
45985686 GACGTC
1 GACGTC
45985692 AGCTCTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.08, C:0.24, G:0.41, T:0.27
Consensus pattern (23 bp):
GACGTCGTGTGTCGCGTCGTCGG
Found at i:45989983 original size:18 final size:19
Alignment explanation
Indices: 45989939--45989991 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
45989929 ATTTTCCATG
*
45989939 ATGAAAAATATTAAAAACTA
1 ATGAAAAATAAT-AAAACTA
45989959 ATGAAAAATAATAAAA-TA
1 ATGAAAAATAATAAAACTA
* *
45989977 ATTAAAAATTATAAA
1 ATGAAAAATAATAAA
45989992 GTTCCCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 15 0.50
19 4 0.13
20 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
ATGAAAAATAATAAAACTA
Found at i:45993488 original size:15 final size:16
Alignment explanation
Indices: 45993462--45993491 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45993452 TACCCAACTG
45993462 ATTTATATATAATAAC
1 ATTTATATATAATAAC
45993478 ATTTA-ATATAATAA
1 ATTTATATATAATAA
45993492 TTAGAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTATATATAATAAC
Found at i:46001264 original size:3 final size:3
Alignment explanation
Indices: 46001256--46001284 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46001246 GGAGAAACAG
46001256 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
46001285 ACAGCAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:46002147 original size:31 final size:31
Alignment explanation
Indices: 46002112--46002171 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
46002102 TTTTTTTTTG
* * *
46002112 TTAAATTTAACCCTCAACCTTTTAAAAATGA
1 TTAAATTTAACCATCAACATTTCAAAAATGA
*
46002143 TTAAATTTGACCATCAACATTTCAAAAAT
1 TTAAATTTAACCATCAACATTTCAAAAAT
46002172 AGTAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (31 bp):
TTAAATTTAACCATCAACATTTCAAAAATGA
Found at i:46007384 original size:18 final size:19
Alignment explanation
Indices: 46007358--46007395 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
46007348 CTATAACTTT
*
46007358 TAAAGTAAAAATT-AAAAA
1 TAAAATAAAAATTGAAAAA
*
46007376 TAAAATAAAACTTGAAAAA
1 TAAAATAAAAATTGAAAAA
46007395 T
1 T
46007396 GAGTGAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
TAAAATAAAAATTGAAAAA
Found at i:46008100 original size:6 final size:6
Alignment explanation
Indices: 46008089--46008122 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
46008079 AAAATTCATC
* *
46008089 ATTTTT ATTTTT ATTTTT ATTTTC ATTTTC ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
46008123 AATGACAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:46016509 original size:29 final size:29
Alignment explanation
Indices: 46016454--46016509 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
46016444 TATCGTCTAA
* *
46016454 ATTTTAAATTAATAATTAAATTTTAAAAC
1 ATTTTAAATTAATAATTAAAATATAAAAC
*
46016483 ATTTT-AATTAAGTACTTAAAATATAAA
1 ATTTTAAATTAA-TAATTAAAATATAAA
46016510 TATTATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
ATTTTAAATTAATAATTAAAATATAAAAC
Found at i:46016745 original size:26 final size:26
Alignment explanation
Indices: 46016715--46016765 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
46016705 TTGTAATGGT
* *
46016715 TGATTTGATCAATTTATTCTATTAAC
1 TGATTTGAGCAATTGATTCTATTAAC
46016741 TGATTTGAGCAATTGATTCTATTAA
1 TGATTTGAGCAATTGATTCTATTAA
46016766 TTGTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (26 bp):
TGATTTGAGCAATTGATTCTATTAAC
Found at i:46023468 original size:35 final size:35
Alignment explanation
Indices: 46023429--46023504 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
46023419 TTGCATGTTT
*
46023429 TAATTTAAAT-TATTTTATAATTCAATAT-TTTTATA
1 TAATTTAAATGTATTTT-TAATTCAATATCATTTA-A
**
46023464 TAATTTTCATGTATTTTTAATTCAATATCATTTAA
1 TAATTTAAATGTATTTTTAATTCAATATCATTTAA
46023499 TAATTT
1 TAATTT
46023505 TTTAACTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 26 0.72
36 10 0.28
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (35 bp):
TAATTTAAATGTATTTTTAATTCAATATCATTTAA
Found at i:46023593 original size:19 final size:19
Alignment explanation
Indices: 46023566--46023602 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46023556 TTACTTGGAT
*
46023566 AATATAAAAATAATATTTA
1 AATACAAAAATAATATTTA
*
46023585 AATACAAAAATGATATTT
1 AATACAAAAATAATATTT
46023603 TAGTCCCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AATACAAAAATAATATTTA
Found at i:46035066 original size:82 final size:82
Alignment explanation
Indices: 46034929--46035087 Score: 309
Period size: 82 Copynumber: 1.9 Consensus size: 82
46034919 CGGATGCCTC
46034929 CAGATAACTCTGCCATCACTTCATTTTGTTGAAGTCTGACACCTGGCAATGCTTTTCTTTGCTGA
1 CAGATAACTCTGCCATCACTTCATTTTGTTGAAGTCTGACACCTGGCAATGCTTTTCTTTGCTGA
46034994 TAAGCATGAATTTTTAT
66 TAAGCATGAATTTTTAT
*
46035011 CAGATAACTCTGCCATCACTTCATTTTGTTGAAGTCTGACACCTGGCAATGCTTTTCTTTGTTGA
1 CAGATAACTCTGCCATCACTTCATTTTGTTGAAGTCTGACACCTGGCAATGCTTTTCTTTGCTGA
46035076 TAAGCATGAATT
66 TAAGCATGAATT
46035088 CTTCCGGATT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (82 bp):
CAGATAACTCTGCCATCACTTCATTTTGTTGAAGTCTGACACCTGGCAATGCTTTTCTTTGCTGA
TAAGCATGAATTTTTAT
Found at i:46036512 original size:19 final size:21
Alignment explanation
Indices: 46036488--46036527 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46036478 TTCCATTTGA
46036488 ATACAGTA-T-ATATACGAGT
1 ATACAGTATTAATATACGAGT
46036507 ATACAGTATTAATATACGAGT
1 ATACAGTATTAATATACGAGT
46036528 TTTGGACAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
ATACAGTATTAATATACGAGT
Found at i:46037599 original size:32 final size:32
Alignment explanation
Indices: 46037537--46037600 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
46037527 ATTCGATCCG
**
46037537 TTTTTAAATTTATAATAATTTATATTATATTA
1 TTTTTAAATTTATAATAATTTATAACATATTA
* *
46037569 TTTTTATATATTAT-ATAATTTGTAACATATTA
1 TTTTTAAAT-TTATAATAATTTATAACATATTA
46037601 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTTTAAATTTATAATAATTTATAACATATTA
Found at i:46045916 original size:123 final size:123
Alignment explanation
Indices: 46045688--46045930 Score: 292
Period size: 123 Copynumber: 2.0 Consensus size: 123
46045678 TTATGCATAT
* * * *
46045688 TAAAATATATCAAAATAAAGCTTTGGTTGAATAATAAATTTAAAGTTTTACTAATTCAATTAGTA
1 TAAAATACATCAAAATAAAGCTTTCGTTAAATAATAAATTTAAAGTTTTACTAATCCAATTAG-A
* * *
46045753 TAGGTTCAAATCTTGTGATATGCATATTTTTATTATTTTTTGTTAAAAT-AAAAATCTA
65 TAGGTTCAAATCTTATGATATGCATATTTTAATTAGTTTTTGTTAAAATGAAAAATCTA
* ** * * *
46045811 TAAAATACATCAAAATGAAGCTTTCGTTAAATGGTGAATTTAAGGTTTTATTAATCCAATTA-AT
1 TAAAATACATCAAAATAAAGCTTTCGTTAAATAATAAATTTAAAGTTTTACTAATCCAATTAGAT
* * * *
46045875 GCGAGTTCAAATCTTATTATATGGATATTTTAATTGGTTTTTGTTAAAATGAAAAA
66 -AG-GTTCAAATCTTATGATATGCATATTTTAATTAGTTTTTGTTAAAATGAAAAA
46045931 ACTAAAATAC
Statistics
Matches: 100, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
121 2 0.02
122 1 0.01
123 92 0.92
124 5 0.05
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (123 bp):
TAAAATACATCAAAATAAAGCTTTCGTTAAATAATAAATTTAAAGTTTTACTAATCCAATTAGAT
AGGTTCAAATCTTATGATATGCATATTTTAATTAGTTTTTGTTAAAATGAAAAATCTA
Found at i:46048839 original size:13 final size:13
Alignment explanation
Indices: 46048821--46048846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46048811 TTTCGTCTTA
46048821 CTCATAATTTAAT
1 CTCATAATTTAAT
46048834 CTCATAATTTAAT
1 CTCATAATTTAAT
46048847 TTGTTTTTCT
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:0.00, T:0.46
Consensus pattern (13 bp):
CTCATAATTTAAT
Found at i:46051571 original size:16 final size:16
Alignment explanation
Indices: 46051552--46051586 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46051542 CATCAACTCT
46051552 TTCTTTCTT-TCTTTCA
1 TTCTTTCTTAT-TTTCA
46051568 TTCTTTCTTATTTTCA
1 TTCTTTCTTATTTTCA
46051584 TTC
1 TTC
46051587 ACTACACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTCTTATTTTCA
Found at i:46054068 original size:17 final size:17
Alignment explanation
Indices: 46054038--46054075 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
46054028 GGTCGGGTTG
46054038 TCGG-TTGGTATGAGAA
1 TCGGATTGGTATGAGAA
*
46054054 TCGGATTGGTTTGAGAA
1 TCGGATTGGTATGAGAA
46054071 TCGGA
1 TCGGA
46054076 CCTACCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.24, C:0.08, G:0.37, T:0.32
Consensus pattern (17 bp):
TCGGATTGGTATGAGAA
Found at i:46061347 original size:2 final size:2
Alignment explanation
Indices: 46061340--46061371 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46061330 ATTAAAAGAT
46061340 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
46061372 AATGGTCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46068301 original size:18 final size:20
Alignment explanation
Indices: 46068266--46068305 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
46068256 ACTTTCACAT
*
46068266 ATTTTTATTTTGATTTTTCA
1 ATTTTTATTTTGAATTTTCA
46068286 ATTTTT-TTTT-AATTTTCA
1 ATTTTTATTTTGAATTTTCA
46068304 AT
1 AT
46068306 CAATGGACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTTTATTTTGAATTTTCA
Found at i:46084131 original size:12 final size:12
Alignment explanation
Indices: 46084111--46084161 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
46084101 AACCGATGGA
*
46084111 AAACCAGAAACT
1 AAACAAGAAACT
*
46084123 AAACAAGAATCT
1 AAACAAGAAACT
* *
46084135 AAACCAGAAACC
1 AAACAAGAAACT
*
46084147 AAACAAGAACCT
1 AAACAAGAAACT
46084159 AAA
1 AAA
46084162 GAAGTTGAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.61, C:0.24, G:0.08, T:0.08
Consensus pattern (12 bp):
AAACAAGAAACT
Found at i:46084138 original size:24 final size:24
Alignment explanation
Indices: 46084111--46084161 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
46084101 AACCGATGGA
* *
46084111 AAACCAGAAACTAAACAAGAATCT
1 AAACCAGAAACCAAACAAGAACCT
46084135 AAACCAGAAACCAAACAAGAACCT
1 AAACCAGAAACCAAACAAGAACCT
46084159 AAA
1 AAA
46084162 GAAGTTGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.61, C:0.24, G:0.08, T:0.08
Consensus pattern (24 bp):
AAACCAGAAACCAAACAAGAACCT
Found at i:46091211 original size:59 final size:60
Alignment explanation
Indices: 46091119--46091251 Score: 180
Period size: 59 Copynumber: 2.2 Consensus size: 60
46091109 TTACTATAAC
* * *
46091119 ATTTGGTATCTAAACTTGACACTTTTTTTTAATTTGGTACTTAAAC-TTTTTTGGGCTCA
1 ATTTGGTACCTAAACTTGACACTTTTTTTTAATTTGGTACCTAAACGTTTTTTAGGCTCA
* *
46091178 ATTTGGTACCTAAACTTGAC-TTTTTTTTCTAATTTGGTACCTAAACGTTTTTTTAGGTTCA
1 ATTTGGTACCTAAACTTGACACTTTTTTT-TAATTTGGTACCTAAACG-TTTTTTAGGCTCA
*
46091239 AATTGGTACCTAA
1 ATTTGGTACCTAA
46091252 TTTATTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 7 0.11
59 35 0.54
61 23 0.35
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTTAATTTGGTACCTAAACGTTTTTTAGGCTCA
Found at i:46091665 original size:60 final size:60
Alignment explanation
Indices: 46091601--46091713 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
46091591 ATCAAACAAA
* *
46091601 AAAAAAGATTAAG-AGTCAAATTAGGAA-AAAGAGTCAAGTTCAGGTACCAAATTGGACCCC
1 AAAAAAGATTAAGCA-TCAAATTAAGAACAAA-AGTCAAGTTCAGATACCAAATTGGACCCC
* * *
46091661 AAAAAAGATTAAGCATCAACTTAAGAACAAATGTCAAGTTTAGATACCAAATT
1 AAAAAAGATTAAGCATCAAATTAAGAACAAAAGTCAAGTTCAGATACCAAATT
46091714 AAGAAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 42 0.91
61 4 0.09
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (60 bp):
AAAAAAGATTAAGCATCAAATTAAGAACAAAAGTCAAGTTCAGATACCAAATTGGACCCC
Found at i:46092990 original size:29 final size:27
Alignment explanation
Indices: 46092944--46092999 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
46092934 AAAATTATAA
46092944 AAATAATTAAAAATAATTTTTAAAATTTT
1 AAATAATTAAAAATAA--TTTAAAATTTT
*
46092973 AAATATTTATAAAA-AATTTAAAATTTT
1 AAATAATTA-AAAATAATTTAAAATTTT
46093000 CTAAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATAATTAAAAATAATTTAAAATTTT
Found at i:46093004 original size:19 final size:20
Alignment explanation
Indices: 46092965--46093005 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
46092955 AATAATTTTT
*
46092965 AAAATTTTAAATATTTATAA
1 AAAATTTAAAATATTTATAA
*
46092985 AAAATTTAAAAT-TTTCTAA
1 AAAATTTAAAATATTTATAA
46093004 AA
1 AA
46093006 TAATAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTAAAATATTTATAA
Found at i:46093005 original size:18 final size:17
Alignment explanation
Indices: 46092958--46093005 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
46092948 AATTAAAAAT
*
46092958 AATTTTTAAAATTTTAA
1 AATTTTTAAAAATTTAA
*
46092975 ATATTTATAAAAAATTTAA
1 A-ATTT-TTAAAAATTTAA
46092994 AATTTTCTAAAA
1 AATTTT-TAAAA
46093006 TAATAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.08
18 12 0.48
19 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTAAAAATTTAA
Found at i:46100798 original size:22 final size:23
Alignment explanation
Indices: 46100772--46100870 Score: 62
Period size: 23 Copynumber: 4.3 Consensus size: 23
46100762 GCTGGGGAAA
*
46100772 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGCGCAAAT
* * * *
46100794 TAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGCGCAAAT
*
46100817 CAGTAAGCACACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGCGC-AAAT
* * *
46100840 CAATAAGCACACAAAGTGCGAAA-
1 CAGTAAGCACACACAGCGC-AAAT
46100863 CAGTAAGC
1 CAGTAAGC
46100871 GTGCTAGCGT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
22 15 0.24
23 43 0.69
24 4 0.06
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACACAGCGCAAAT
Found at i:46100847 original size:23 final size:23
Alignment explanation
Indices: 46100820--46100870 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
46100810 CGCAAATCAG
*
46100820 TAAGCACACGAAGTGCGAAACAA
1 TAAGCACACAAAGTGCGAAACAA
*
46100843 TAAGCACACAAAGTGCGAAACAG
1 TAAGCACACAAAGTGCGAAACAA
46100866 TAAGC
1 TAAGC
46100871 GTGCTAGCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (23 bp):
TAAGCACACAAAGTGCGAAACAA
Found at i:46105848 original size:79 final size:79
Alignment explanation
Indices: 46105717--46105862 Score: 240
Period size: 79 Copynumber: 1.8 Consensus size: 79
46105707 GCGTAAAACC
* * *
46105717 GTTGGTTAATCCAACTAGAGCTGGGCTCATTTTTGCGATTTATCCACTAGGCATTGGGTGCCAAG
1 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTTTGCGATTTATCCACTAGGCACTGGGTGCCAAG
46105782 ATTTGACGGAAATT
66 ATTTGACGGAAATT
*
46105796 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTTTGC-AGTTTATCCGCTAGGCACTGGGTGCCAA
1 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTTTGCGA-TTTATCCACTAGGCACTGGGTGCCAA
46105860 GAT
65 GAT
46105863 CGTCGGTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 1 0.02
79 61 0.98
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (79 bp):
GTTGGTTAATCCAACTAGAGCTAGGCTCACTTTTGCGATTTATCCACTAGGCACTGGGTGCCAAG
ATTTGACGGAAATT
Found at i:46106037 original size:82 final size:77
Alignment explanation
Indices: 46105897--46106055 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 77
46105887 GGCGCAAAAC
*
46105897 CGTTGGTTAATCCAACTAGAGCTCACTTATTGCGGTTTATACGCTAAGCACTAGGTGCCAGGAAT
1 CGTTGGTTAATCCAACTAGAGCTCACTTATTGCGGTTTATACGCTAAGCACGAGGTGCCAGGAAT
*
46105962 TGACGGAATTAT
66 AGACGGAATTAT
* * *
46105974 CGTTGGTTAATCCAACTAGAGCTGGGCTCACTTATTGTGGTTTATCCGCTAGGCACCGA-GTGCC
1 CGTTGGTTAATCCAACTAGA-----GCTCACTTATTGCGGTTTATACGCTAAGCA-CGAGGTGCC
* *
46106038 ATGAATAGACGGATTTAT
60 AGGAATAGACGGAATTAT
46106056 ACGATGATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
77 20 0.29
82 47 0.68
83 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (77 bp):
CGTTGGTTAATCCAACTAGAGCTCACTTATTGCGGTTTATACGCTAAGCACGAGGTGCCAGGAAT
AGACGGAATTAT
Found at i:46106111 original size:16 final size:16
Alignment explanation
Indices: 46106090--46106129 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
46106080 CGTTTGGTTC
46106090 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
46106106 GCTGTAATGGAATAGG
1 GCTGTAATGGAATAGA
46106122 GCTGTAAT
1 GCTGTAAT
46106130 CAGCAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:46106361 original size:57 final size:58
Alignment explanation
Indices: 46106300--46106455 Score: 194
Period size: 57 Copynumber: 2.7 Consensus size: 58
46106290 TTTTAATAAG
* *
46106300 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAAT-TATATTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATACATATTTAACATA
* * *
46106357 ATTATTATTAAATATAATTTAAT-AAAATAGTATATAA-TTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAAT-ACATATTTAACATA
46106414 ATTATTATTAAAATATGAA-TTAATAAAATCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAAA--ATAATATATAAT
46106456 ATTAGAAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
55 5 0.06
56 12 0.14
57 42 0.49
58 11 0.13
59 5 0.06
61 10 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATACATATTTAACATA
Found at i:46106375 original size:31 final size:27
Alignment explanation
Indices: 46106291--46106383 Score: 82
Period size: 26 Copynumber: 3.4 Consensus size: 27
46106281 GTTATTAAAT
*
46106291 TTTAAT-AAGATTATTATTAAATATAA
1 TTTAATAAAAATTATTATTAAATATAA
* * * *
46106317 TTTAATAAAAATAATAAAT-AATTTAA
1 TTTAATAAAAATTATTATTAAATATAA
*
46106343 TTATATTTAACATAATTATTATTAAATATAA
1 TT-TA-ATAA-A-AATTATTATTAAATATAA
46106374 TTTAATAAAA
1 TTTAATAAAA
46106384 TAGTATATAA
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
26 14 0.28
27 11 0.22
28 4 0.08
29 4 0.08
30 9 0.18
31 8 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
TTTAATAAAAATTATTATTAAATATAA
Found at i:46115677 original size:3 final size:3
Alignment explanation
Indices: 46115669--46115697 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46115659 AGACGCAAAT
46115669 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
46115698 TGGGGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:46117403 original size:16 final size:16
Alignment explanation
Indices: 46117374--46117406 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46117364 TTAAAAGTTT
46117374 TGATTATTTATGAAAA
1 TGATTATTTATGAAAA
46117390 TGATCTATTT-TGAAAA
1 TGAT-TATTTATGAAAA
46117406 T
1 T
46117407 CATACATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (16 bp):
TGATTATTTATGAAAA
Found at i:46118307 original size:24 final size:23
Alignment explanation
Indices: 46118273--46118346 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
46118263 TGATTTATTT
46118273 TTTTAAAAATAATAAAAATATAAA
1 TTTT-AAAATAATAAAAATATAAA
* *
46118297 TTATTAAAATAATAAAATTAT-AC
1 TT-TTAAAATAATAAAAATATAAA
*
46118320 TTTTATAATAATAAAAATATATAA
1 TTTTAAAATAATAAAAATATA-AA
46118344 TTT
1 TTT
46118347 AATTTTAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 16 0.38
23 3 0.07
24 21 0.50
25 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTAAAATAATAAAAATATAAA
Found at i:46120258 original size:6 final size:6
Alignment explanation
Indices: 46120247--46120275 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
46120237 AAAGGGATGA
46120247 AGGAAT AGGAAT AGGAAT AGGAAT AGGAA
1 AGGAAT AGGAAT AGGAAT AGGAAT AGGAA
46120276 ACAGAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
AGGAAT
Found at i:46125219 original size:17 final size:17
Alignment explanation
Indices: 46125185--46125217 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
46125175 AATTTAATTT
*
46125185 TTTTATAATTTATAAAA
1 TTTTATAATTAATAAAA
46125202 TTTTA-AATTAATAAAA
1 TTTTATAATTAATAAAA
46125218 ATAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTATAATTAATAAAA
Found at i:46132813 original size:99 final size:99
Alignment explanation
Indices: 46132701--46132888 Score: 367
Period size: 99 Copynumber: 1.9 Consensus size: 99
46132691 CTTGAGAAGC
46132701 ATTATAACGCACTTCTATTGATAAATAAAATACGCTTTCTCTTTTGCTCTCTTATTCTCTTTGTT
1 ATTATAACGCACTTCTATTGATAAATAAAATACGCTTTCTCTTTTGCTCTCTTATTCTCTTTGTT
*
46132766 ATTTACCCTCTGTCTCTTTATTTTGAGAAGCATT
66 ATTTACCCCCTGTCTCTTTATTTTGAGAAGCATT
46132800 ATTATAACGCACTTCTATTGATAAATAAAATACGCTTTCTCTTTTGCTCTCTTATTCTCTTTGTT
1 ATTATAACGCACTTCTATTGATAAATAAAATACGCTTTCTCTTTTGCTCTCTTATTCTCTTTGTT
46132865 ATTTACCCCCTGTCTCTTTATTTT
66 ATTTACCCCCTGTCTCTTTATTTT
46132889 ATAACACGTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.48
Consensus pattern (99 bp):
ATTATAACGCACTTCTATTGATAAATAAAATACGCTTTCTCTTTTGCTCTCTTATTCTCTTTGTT
ATTTACCCCCTGTCTCTTTATTTTGAGAAGCATT
Found at i:46150392 original size:16 final size:17
Alignment explanation
Indices: 46150358--46150391 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
46150348 AGGAAATTGC
46150358 AAAAAAAAAATGGAGAG
1 AAAAAAAAAATGGAGAG
46150375 AAAAAGAAAAATGGAGA
1 AAAAA-AAAAATGGAGA
46150392 ATATAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAATGGAGAG
Found at i:46150673 original size:17 final size:16
Alignment explanation
Indices: 46150628--46150673 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
46150618 AAAAAATGTA
46150628 AAAAT-AAAAAAGAAT
1 AAAATAAAAAAAGAAT
46150643 AAAATAAAATAAAGAA-
1 AAAATAAAA-AAAGAAT
46150659 AAAATGCAAAAAAAG
1 AAAAT--AAAAAAAG
46150674 GAAGTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
17 10 0.37
18 4 0.15
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAATAAAAAAAGAAT
Found at i:46150815 original size:110 final size:108
Alignment explanation
Indices: 46150603--46150815 Score: 256
Period size: 111 Copynumber: 1.9 Consensus size: 108
46150593 TAATTCAGTT
* *
46150603 ATAGAATAAAGATTTAAAAAATGTAAAAATAAAAAAGAATAAAATAAAATAAAGAAAAAATGCAA
1 ATAGAATAAAGATTTAAAAAATGTAAAAATAAAAAACAATAAAATAAAAAAAAGAAAAAATGCAA
*
46150668 AAAAAGGAAGTAGGAAATAAAATAAGGGAAATGAAAAAAATGGAGA
66 AAAAAAGAAGTAGGAAATAAAATAA--GAAA-GAAAAAAATGGAGA
* *
46150714 ATAGAAT-AAGATTTAAAAAATGTAAAAAATTAAAAACAATGGAAATAAAAGAAAAG-AAAAATG
1 ATAGAATAAAGATTTAAAAAATGT-AAAAATAAAAAACAAT-AAAATAAAA-AAAAGAAAAAATG
*
46150777 CAAATGAAAAA-AGAGTAGGAAATAAAGT-A-AAAGAAAAAA
63 CAAA--AAAAAGA-AGTAGGAAATAAAATAAGAAAGAAAAAA
46150816 TTCAAAAAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
109 7 0.08
110 19 0.21
111 21 0.23
112 19 0.21
113 6 0.07
114 18 0.20
ACGTcount: A:0.68, C:0.01, G:0.15, T:0.15
Consensus pattern (108 bp):
ATAGAATAAAGATTTAAAAAATGTAAAAATAAAAAACAATAAAATAAAAAAAAGAAAAAATGCAA
AAAAAAGAAGTAGGAAATAAAATAAGAAAGAAAAAAATGGAGA
Found at i:46150925 original size:150 final size:147
Alignment explanation
Indices: 46150629--46150901 Score: 354
Period size: 150 Copynumber: 1.8 Consensus size: 147
46150619 AAAAATGTAA
46150629 AAATAAAAAAGAATAAAATAAAATAAAGAAAAAATGCAAAAAAAGGAAGTAGGAAATAAAATAAG
1 AAATAAAAAAGAATAAAATAAAATAAAGAAAAAATGCAAAAAAAGGAAGTAGGAAATAAAATAAG
* *
46150694 GGAAATGAAAAAAATGGAGAATAGAATAAGATTTAAAAAATGTAAAAAATTAAAAACAATGGAAA
66 GGAAATGAAAAAAATGGAGAATAGAATAAGATTTAAAAAAAGTAAAAAAATAAAAACAA-GGAAA
46150759 TAAAAGAAAAGAAAAATGC
130 TAAAAG-AAAGAAAAATGC
* * * * *
46150778 AAATGAAAAAAGAGTAGGAAATAAAGTAAAAGAAAAAATTC-AAAAAA-GTA-TAGGAAATGAAA
1 AAAT-AAAAAAGAATA--AAATAAAAT-AAAGAAAAAATGCAAAAAAAGGAAGTAGGAAATAAAA
* *
46150840 TAAGGGAAATGTAAAAGATGGAGAAGTAGAATAATGATTTAAAAAAAAAGTAAAAAAATAAA
62 TAAGGGAAATGAAAAAAATGGAGAA-TAGAATAA-GATTT--AAAAAAAGTAAAAAAATAAA
46150902 TTAAAGAAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
149 4 0.04
150 44 0.41
151 10 0.09
152 19 0.18
153 12 0.11
154 18 0.17
ACGTcount: A:0.66, C:0.01, G:0.17, T:0.16
Consensus pattern (147 bp):
AAATAAAAAAGAATAAAATAAAATAAAGAAAAAATGCAAAAAAAGGAAGTAGGAAATAAAATAAG
GGAAATGAAAAAAATGGAGAATAGAATAAGATTTAAAAAAAGTAAAAAAATAAAAACAAGGAAAT
AAAAGAAAGAAAAATGC
Found at i:46154027 original size:26 final size:26
Alignment explanation
Indices: 46153986--46154047 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
46153976 TAAAAAGTTA
46153986 AAAAATTAATATTTTTACTTTTCAATTT
1 AAAAATT--TATTTTTACTTTTCAATTT
46154014 AAAAATTTATTTTTACTTTTCAATTT
1 AAAAATTTATTTTTACTTTTCAATTT
46154040 AAAAATTT
1 AAAAATTT
46154048 TAGTCCAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 27 0.79
28 7 0.21
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (26 bp):
AAAAATTTATTTTTACTTTTCAATTT
Found at i:46157016 original size:13 final size:13
Alignment explanation
Indices: 46156998--46157024 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46156988 ACTAACATGA
46156998 CTTGAACATAGGT
1 CTTGAACATAGGT
46157011 CTTGAACATAGGT
1 CTTGAACATAGGT
46157024 C
1 C
46157025 ACACGTTAAA
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:0.19, G:0.22, T:0.30
Consensus pattern (13 bp):
CTTGAACATAGGT
Found at i:46161449 original size:28 final size:28
Alignment explanation
Indices: 46161417--46161498 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
46161407 AGACCCACAC
*
46161417 GGCCAACCTCCTCATTTATTGAACAAGT
1 GGCCAACCTCCTCAATTATTGAACAAGT
* *
46161445 GGCCAACCTCTTGAATTATTGAACAAGT
1 GGCCAACCTCCTCAATTATTGAACAAGT
* * **
46161473 TGCCAAGCTCCTCGGTTATTGAACAA
1 GGCCAACCTCCTCAATTATTGAACAA
46161499 TGTATTACGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (28 bp):
GGCCAACCTCCTCAATTATTGAACAAGT
Found at i:46162422 original size:21 final size:19
Alignment explanation
Indices: 46162396--46162437 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
46162386 AGCTTTCAAA
*
46162396 TGTAACTATGTTAATTTAGTT
1 TGTAACT-TGTTAACTTA-TT
46162417 TGTAACTTGTTAACTTATT
1 TGTAACTTGTTAACTTATT
46162436 TG
1 TG
46162438 GTTATGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (19 bp):
TGTAACTTGTTAACTTATT
Found at i:46164145 original size:3 final size:3
Alignment explanation
Indices: 46164137--46164174 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
46164127 CAAAATCCAA
46164137 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
46164175 AGTATTCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:46169644 original size:63 final size:63
Alignment explanation
Indices: 46169553--46169784 Score: 187
Period size: 63 Copynumber: 3.8 Consensus size: 63
46169543 AATTTTTCAT
* * * * *
46169553 AAATGGCCAACA-CCCATTTTTTTC-GAGAAAAAAAATTCAAATTTTTTTGATGTTGACTATC
1 AAATGGTCAACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTTGATGTTGACCATC
* * * * * * *
46169614 AAATGGTCAATACCTCCTATTTC-TCTGAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATG
1 AAATGGTCAACACCCCCT-TTTCTTCTGAGAAAAAAAATTAAAATTTTTTTGATGTTGACCATC
* ** * *
46169677 TAATGGTTGACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTCG-TGTTGGCCATGC
1 AAATGGTCAACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTTGATGTTGACCAT-C
* * * *
46169740 -AATGGCCGACACCCCATTTTC-TC---G-AAAAAAATTCAAATTTTTTTG
1 AAATGGTCAACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTTG
46169785 GCTGACACCC
Statistics
Matches: 141, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
57 19 0.13
58 1 0.01
61 12 0.09
62 37 0.26
63 72 0.51
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (63 bp):
AAATGGTCAACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTTGATGTTGACCATC
Found at i:46169699 original size:62 final size:61
Alignment explanation
Indices: 46169581--46169785 Score: 211
Period size: 62 Copynumber: 3.4 Consensus size: 61
46169571 TTTTTCGAGA
* * * * * * *
46169581 AAAAAAATTCAAATTTTTTTGATGTTGACTATCAAATGGTCAATACCTCCTATTTCTCTGAG
1 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATGAAATGGTCGACACCCCCT-TTTCTCTGAG
* * *
46169643 AAAAAAATTTTAAATTTTTTTGGTGTTGGCCATGTAATGGTTGACACCCCCTTTTCTTCTGAG
1 AAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATGAAATGGTCGACACCCCCTTTTC-TCTGAG
* * * * *
46169706 AAAAAAAATT-AAAATTTTTTCGTGTTGGCCATGCAATGGCCGACACCCCATTTTCTC---G
1 -AAAAAAATTCAAATTTTTTTGGTGTTGGCCATGAAATGGTCGACACCCCCTTTTCTCTGAG
46169764 AAAAAAATTCAAATTTTTTTGG
1 AAAAAAATTCAAATTTTTTTGG
46169786 CTGACACCCC
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
57 9 0.07
58 11 0.09
61 2 0.02
62 50 0.41
63 42 0.35
64 7 0.06
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (61 bp):
AAAAAAATTCAAATTTTTTTGGTGTTGGCCATGAAATGGTCGACACCCCCTTTTCTCTGAG
Found at i:46169810 original size:41 final size:41
Alignment explanation
Indices: 46169742--46169826 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
46169732 GGCCATGCAA
46169742 TGGCCGACACCCCATTTTCTCG-AAAAAAATTCAAATTTTTT
1 TGGCCGACACCCCATTTTCTCGAAAAAAAATT-AAATTTTTT
* *
46169783 TGGCTGACACCCC-TTTTTTCGAGAAAAAAATTAAATTTTTT
1 TGGCCGACACCCCATTTTCTCGA-AAAAAAATTAAATTTTTT
46169824 TGG
1 TGG
46169827 TGTTGATCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 7 0.17
41 24 0.60
42 9 0.22
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (41 bp):
TGGCCGACACCCCATTTTCTCGAAAAAAAATTAAATTTTTT
Found at i:46169830 original size:99 final size:104
Alignment explanation
Indices: 46169684--46169872 Score: 271
Period size: 99 Copynumber: 1.9 Consensus size: 104
46169674 ATGTAATGGT
* *
46169684 TGACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTCGTGTTGGCCATGCAATGGCCGA
1 TGACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTCGTGTTGACCATGCAATGACCGA
46169749 CACCCCATTTTCTCGA-AAAAAATTCAAATTTTTTTGGC
66 CACCCCATTTTCTCGAGAAAAAATTCAAATTTTTTTGGC
* * *
46169787 TGACA-CCCCTTTT-TTC-GAG-AAAAAAATTAAATTTTTTTGGTGTTGATCATGCAATGACCGA
1 TGACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTCGTGTTGACCATGCAATGACCGA
* * *
46169848 CACCCCCTTTTTTTGAGAAAAAATT
66 CACCCCATTTTCTCGAGAAAAAATT
46169873 TTCAACACCA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
99 50 0.65
100 11 0.14
101 3 0.04
102 8 0.10
103 5 0.06
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (104 bp):
TGACACCCCCTTTTCTTCTGAGAAAAAAAATTAAAATTTTTTCGTGTTGACCATGCAATGACCGA
CACCCCATTTTCTCGAGAAAAAATTCAAATTTTTTTGGC
Found at i:46180337 original size:19 final size:21
Alignment explanation
Indices: 46180294--46180337 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
46180284 TTTTTAACTC
**
46180294 AATTCAATTTAATTAAAATTG
1 AATTCAATTTAATTAAAATAA
46180315 AATTCAA-TT-ATTAAAATAA
1 AATTCAATTTAATTAAAATAA
46180334 AATT
1 AATT
46180338 TATTAACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 2 0.10
21 7 0.33
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTCAATTTAATTAAAATAA
Found at i:46189671 original size:29 final size:30
Alignment explanation
Indices: 46189639--46189699 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
46189629 TAAAATGTTA
* *
46189639 TTTT-AAAATTTTTATTACTATTTT-TATTT
1 TTTTAAAAATTTATAATA-TATTTTATATTT
46189668 TTTTAAAAATTTATAATATATTTTATATTT
1 TTTTAAAAATTTATAATATATTTTATATTT
46189698 TT
1 TT
46189700 ATTGTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTTAAAAATTTATAATATATTTTATATTT
Found at i:46189681 original size:28 final size:29
Alignment explanation
Indices: 46189639--46189700 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
46189629 TAAAATGTTA
* * *
46189639 TTTTAAAATTTTTATTACTAT-TTTTATTT
1 TTTTAAAATATTTA-TAATATATTTTATAT
46189668 TTTTAAAA-ATTTATAATATATTTTATAT
1 TTTTAAAATATTTATAATATATTTTATAT
46189696 TTTTA
1 TTTTA
46189701 TTGTAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 16 0.55
29 8 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAAATATTTATAATATATTTTATAT
Found at i:46190651 original size:41 final size:41
Alignment explanation
Indices: 46190606--46190696 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
46190596 CTTCCATAAT
46190606 CAAATCCTAATCTAAATGCGGGTTCTTGATCGGTTAGTAGC
1 CAAATCCTAATCTAAATGCGGGTTCTTGATCGGTTAGTAGC
*
46190647 CAAATCCTAATCTAAGTGCGGGTTCTTGATCGGTTAGTAGC
1 CAAATCCTAATCTAAATGCGGGTTCTTGATCGGTTAGTAGC
46190688 CAAATCCTA
1 CAAATCCTA
46190697 CCATTGTGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
CAAATCCTAATCTAAATGCGGGTTCTTGATCGGTTAGTAGC
Found at i:46192634 original size:30 final size:31
Alignment explanation
Indices: 46192600--46192669 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
46192590 GTTACATTTA
*
46192600 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
*
46192630 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
*
46192661 ATAAAACAG
1 ACAAAACAG
46192670 CCCTATTGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 18 0.51
31 12 0.34
32 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:46194198 original size:22 final size:22
Alignment explanation
Indices: 46194156--46194198 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46194146 AATAATAATA
*
46194156 ATATATTTTTAATTGATATTTT
1 ATATATTTTTAATTGAGATTTT
46194178 ATATATTTTATAATT-AGATTT
1 ATATATTTT-TAATTGAGATTT
46194199 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATATATTTTTAATTGAGATTTT
Found at i:46195667 original size:41 final size:40
Alignment explanation
Indices: 46195619--46195719 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
46195609 TCGACCTTGA
** *
46195619 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
46195659 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
46195697 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
46195720 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:46200230 original size:11 final size:11
Alignment explanation
Indices: 46200214--46200243 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
46200204 TACTTTTACA
46200214 AATATAAATAC
1 AATATAAATAC
46200225 AATATAAATAC
1 AATATAAATAC
46200236 AAGTATAA
1 AA-TATAA
46200244 TGTAATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (11 bp):
AATATAAATAC
Found at i:46201295 original size:12 final size:12
Alignment explanation
Indices: 46201278--46201302 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46201268 TTTTTTTGTT
46201278 TTTTTAATTTTA
1 TTTTTAATTTTA
46201290 TTTTTAATTTTA
1 TTTTTAATTTTA
46201302 T
1 T
46201303 CCAATTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:46207361 original size:20 final size:20
Alignment explanation
Indices: 46207317--46207355 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46207307 TATTCAGTTT
46207317 TTTTAATAATTTTATTATAA
1 TTTTAATAATTTTATTATAA
*
46207337 TTTTAATTATATTTATTAT
1 TTTTAATAAT-TTTATTAT
46207356 CTTTTACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAATAATTTTATTATAA
Found at i:46212011 original size:10 final size:10
Alignment explanation
Indices: 46211986--46212037 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
46211976 AAATTTGTTG
46211986 AATTTTTAACAT
1 AATTTTT-A-AT
46211998 AATTTTTAAT
1 AATTTTTAAT
* *
46212008 AATTTATATT
1 AATTTTTAAT
*
46212018 TATTTTTAAT
1 AATTTTTAAT
46212028 ATATTTTTAA
1 A-ATTTTTAA
46212038 ATTTTTTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 17 0.52
11 9 0.27
12 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:46216509 original size:20 final size:20
Alignment explanation
Indices: 46216473--46216510 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46216463 GTTTTGTTTT
*
46216473 TTGTTTTTTTTCTTTTTTCA
1 TTGTTTTTTTTCATTTTTCA
46216493 TTGTTCTTTTTT-ATTTTT
1 TTGTT-TTTTTTCATTTTT
46216511 TAACTTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (20 bp):
TTGTTTTTTTTCATTTTTCA
Found at i:46216518 original size:22 final size:20
Alignment explanation
Indices: 46216473--46216518 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
46216463 GTTTTGTTTT
* *
46216473 TTGTTTTTTTTCTTTTTTCA
1 TTGTTTTTTTTATTTTTTAA
46216493 TTGTTCTTTTTTATTTTTTAA
1 TTGTT-TTTTTTATTTTTTAA
46216514 CTTGT
1 -TTGT
46216519 GTTAAGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (20 bp):
TTGTTTTTTTTATTTTTTAA
Found at i:46220876 original size:16 final size:16
Alignment explanation
Indices: 46220855--46220887 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46220845 AAACTAAATA
*
46220855 AATAAAATAAATAAAC
1 AATAAAATAAACAAAC
46220871 AATAAAATAAACAAAC
1 AATAAAATAAACAAAC
46220887 A
1 A
46220888 TCTAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAATAAACAAAC
Done.