Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1420868 original size:12 final size:12
Alignment explanation
Indices: 1420851--1420880 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1420841 TCTGGTACAT
1420851 AATCCAAGCTCA
1 AATCCAAGCTCA
1420863 AATCCAAGCTCA
1 AATCCAAGCTCA
*
1420875 ACTCCA
1 AATCCA
1420881 TTATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.37, G:0.07, T:0.17
Consensus pattern (12 bp):
AATCCAAGCTCA
Found at i:1422571 original size:30 final size:30
Alignment explanation
Indices: 1422493--1422584 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
1422483 ATTAAATTTT
*
1422493 AAATAAAA-TTTTAACTATTTATTT-AATA
1 AAATAAAATTTTTATCTATTTATTTAAATA
* *
1422521 TAA-AAAATTATTTATTTATTTATTTAAATA
1 AAATAAAATT-TTTATCTATTTATTTAAATA
1422551 AAATAAAATTTTTATCTATTTATTTAAAATA
1 AAATAAAATTTTTATCTATTTATTT-AAATA
1422582 AAA
1 AAA
1422585 AAATCAACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.07
28 3 0.06
29 13 0.24
30 20 0.37
31 14 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATAAAATTTTTATCTATTTATTTAAATA
Found at i:1422678 original size:17 final size:17
Alignment explanation
Indices: 1422638--1422689 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1422628 TGGGTGAAAA
* *
1422638 ATATTTTTAATAAAATTT
1 ATATATTTAA-AAAATAT
1422656 ATTATATTTAAAAAATAT
1 A-TATATTTAAAAAATAT
*
1422674 ATATAATTAAAAAATA
1 ATATATTTAAAAAATA
1422690 AAAAAGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.47
18 8 0.27
19 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATTTAAAAAATAT
Found at i:1423706 original size:14 final size:16
Alignment explanation
Indices: 1423674--1423707 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1423664 TAACCAAAAA
1423674 AAAAAATTATAAATGT
1 AAAAAATTATAAATGT
1423690 AAAAAATTA-AAAT-T
1 AAAAAATTATAAATGT
1423704 AAAA
1 AAAA
1423708 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAATTATAAATGT
Found at i:1424305 original size:14 final size:14
Alignment explanation
Indices: 1424283--1424322 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1424273 TAATTGATAA
*
1424283 AATTGATAAATTTT
1 AATTTATAAATTTT
1424297 AATTTATAAATTTT
1 AATTTATAAATTTT
1424311 ACA-TTATAAATT
1 A-ATTTATAAATT
1424323 ATATTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (14 bp):
AATTTATAAATTTT
Found at i:1424353 original size:22 final size:24
Alignment explanation
Indices: 1424324--1424378 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1424314 TTATAAATTA
*
1424324 TATTATTAAATTAAATA-TATATT
1 TATTATTAAATTAAAAATTATATT
1424347 T-TTATT-AATTAAAAATTATATT
1 TATTATTAAATTAAAAATTATATT
*
1424369 TAATATTAAA
1 TATTATTAAA
1424379 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 8 0.30
22 12 0.44
23 5 0.19
24 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTATTAAATTAAAAATTATATT
Found at i:1424388 original size:39 final size:41
Alignment explanation
Indices: 1424313--1424387 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
1424303 TAAATTTTAC
*
1424313 ATTATAAATTATATTATTAAATTAAATATATATTTTTATTA
1 ATTAAAAATTATATTATTAAATTAAATATATATTTTTATTA
1424354 ATTAAAAATTATA-T-TTAATATTAAA-AT-TATTTTT
1 ATTAAAAATTATATTATTAA-ATTAAATATATATTTTT
1424388 TAAATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
38 7 0.22
39 6 0.19
40 7 0.22
41 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
ATTAAAAATTATATTATTAAATTAAATATATATTTTTATTA
Found at i:1424395 original size:20 final size:18
Alignment explanation
Indices: 1424313--1424399 Score: 59
Period size: 20 Copynumber: 4.4 Consensus size: 18
1424303 TAAATTTTAC
1424313 ATTATAAATTATATTATTAA-
1 ATTA-AAATTATA-T-TTAAT
* *
1424333 ATTAAATATATATTTTTATT
1 ATTAAA-AT-TATATTTAAT
1424353 AATTAAAAATTATATTTAAT
1 -ATT-AAAATTATATTTAAT
*
1424373 ATTAAAATTATTTTTTAAAT
1 ATTAAAATTA-TATTT-AAT
1424393 ATTAAAA
1 ATTAAAA
1424400 AAAATTATCA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
18 7 0.13
19 12 0.22
20 25 0.45
21 8 0.15
22 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAAAATTATATTTAAT
Found at i:1425294 original size:19 final size:19
Alignment explanation
Indices: 1425266--1425305 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1425256 TTATTATTTA
1425266 TTTAATATTTAAAA-TATT
1 TTTAATATTTAAAAGTATT
1425284 TTTATATATTTAAAAGTATT
1 TTTA-ATATTTAAAAGTATT
1425304 TT
1 TT
1425306 AATTAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAATATTTAAAAGTATT
Found at i:1425798 original size:2 final size:2
Alignment explanation
Indices: 1425791--1425824 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1425781 GAAGTTCTCA
1425791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1425825 GTAAGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1427530 original size:27 final size:30
Alignment explanation
Indices: 1427496--1427564 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 30
1427486 AATTTTAAAT
* *
1427496 TAAT-TAAAAATATTT-TATTATTTAT-TA
1 TAATATAAAAATATTTCAATTATTAATATA
*
1427523 -AATATAAAAAAATTTCAATTATTAATATA
1 TAATATAAAAATATTTCAATTATTAATATA
*
1427552 TATTATAAAAATA
1 TAATATAAAAATA
1427565 ATAAACTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 3 0.09
27 10 0.30
28 8 0.24
29 2 0.06
30 10 0.30
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATATAAAAATATTTCAATTATTAATATA
Found at i:1427953 original size:2 final size:2
Alignment explanation
Indices: 1427946--1427972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1427936 ATGAACTGCA
1427946 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1427973 AATTTAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1428331 original size:20 final size:18
Alignment explanation
Indices: 1428298--1428338 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 18
1428288 ATTTAATTAA
1428298 TAAAAATATATTAATATT
1 TAAAAATATATTAATATT
1428316 TAAAAATAATTATTAATATT
1 TAAAAAT-A-TATTAATATT
1428336 TAA
1 TAA
1428339 TATTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAATATATTAATATT
Found at i:1428661 original size:21 final size:22
Alignment explanation
Indices: 1428637--1428687 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
1428627 TTTAAAAATT
1428637 TTTATTTAAATTTAATTT-T-AG
1 TTTATTT-AATTTAATTTATGAG
1428658 TTTAATTTAATTTAATTTATGAG
1 TTT-ATTTAATTTAATTTATGAG
1428681 TTTATTT
1 TTTATTT
1428688 TATTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 13 0.48
22 9 0.33
23 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTATTTAATTTAATTTATGAG
Found at i:1428664 original size:16 final size:16
Alignment explanation
Indices: 1428636--1428676 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1428626 TTTTAAAAAT
1428636 TTTTATTTAAATTTAA
1 TTTTATTTAAATTTAA
1428652 TTTTAGTTT-AATTTAA
1 TTTTA-TTTAAATTTAA
*
1428668 TTTAATTTA
1 TTTTATTTA
1428677 TGAGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTATTTAAATTTAA
Found at i:1429677 original size:2 final size:2
Alignment explanation
Indices: 1429670--1429702 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1429660 ATAAAAATTA
1429670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1429703 ATTTTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1431401 original size:22 final size:23
Alignment explanation
Indices: 1431360--1431404 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1431350 TAAACATTTT
* *
1431360 TAATTTATTTAAAATCTAATATA
1 TAATTTATGTAAAATATAATATA
1431383 TAATTTATGT-AAATATAATATA
1 TAATTTATGTAAAATATAATATA
1431405 AAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTTATGTAAAATATAATATA
Found at i:1431669 original size:2 final size:2
Alignment explanation
Indices: 1431664--1431695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1431654 ACACACACAC
1431664 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
1431696 TAATCAGTTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1434934 original size:12 final size:12
Alignment explanation
Indices: 1434912--1434962 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1434902 AACTGTGCCG
1434912 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
1434925 TCAATTTGAAAT
1 TCAATTTGAAAT
*
1434937 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
1434952 TCAATTTGAAA
1 TCAATTTGAAA
1434963 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:1434974 original size:27 final size:27
Alignment explanation
Indices: 1434918--1434974 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1434908 GCCGTCAATT
* *
1434918 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
1434945 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
1434972 TTG
1 TTG
1434975 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:1435039 original size:9 final size:9
Alignment explanation
Indices: 1435025--1435057 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1435015 AGAAGGCTCA
1435025 AGCAGAGAC
1 AGCAGAGAC
1435034 AGCAGAGAC
1 AGCAGAGAC
*
1435043 AGCAGAGAT
1 AGCAGAGAC
1435052 AGCAGA
1 AGCAGA
1435058 AAGAGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:1439714 original size:12 final size:12
Alignment explanation
Indices: 1439692--1439742 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1439682 AACTGTGCCG
1439692 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
1439705 TCAATTTGAAAT
1 TCAATTTGAAAT
*
1439717 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
1439732 TCAATTTGAAA
1 TCAATTTGAAA
1439743 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:1439754 original size:27 final size:27
Alignment explanation
Indices: 1439698--1439754 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1439688 GCCGTCAATT
* *
1439698 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
1439725 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
1439752 TTG
1 TTG
1439755 CATAGTACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:1439819 original size:9 final size:9
Alignment explanation
Indices: 1439805--1439846 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
1439795 AGAAGGCTCA
1439805 AGCAGAGAC
1 AGCAGAGAC
1439814 AGCAGAGAC
1 AGCAGAGAC
1439823 AGCAGAGAC
1 AGCAGAGAC
*
1439832 AGCAGAGAT
1 AGCAGAGAC
1439841 AGCAGA
1 AGCAGA
1439847 AAGAGAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.33, T:0.02
Consensus pattern (9 bp):
AGCAGAGAC
Found at i:1442699 original size:8 final size:8
Alignment explanation
Indices: 1442686--1442752 Score: 57
Period size: 8 Copynumber: 8.0 Consensus size: 8
1442676 GTAAAATTAA
1442686 ATTTATAT
1 ATTTATAT
1442694 ATTTATAT
1 ATTTATAT
1442702 ATTTATATT
1 ATTTATA-T
1442711 ATATTATATTT
1 AT-TTATA--T
1442722 ATTT-TAT
1 ATTTATAT
*
1442729 TTTTAT-T
1 ATTTATAT
1442736 ATTTTATAT
1 A-TTTATAT
*
1442745 AATTATAT
1 ATTTATAT
1442753 TTAATATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
7 5 0.10
8 27 0.54
9 7 0.14
10 7 0.14
11 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTTATAT
Found at i:1442710 original size:14 final size:14
Alignment explanation
Indices: 1442691--1442761 Score: 69
Period size: 14 Copynumber: 5.1 Consensus size: 14
1442681 ATTAAATTTA
1442691 TATATTTATATATT
1 TATATTTATATATT
1442705 TATATTATATTATATT
1 TATATT-TA-TATATT
1442721 TAT-TTTAT-T-TT
1 TATATTTATATATT
*
1442732 TATTATTTTATATAAT
1 TA-TA-TTTATATATT
1442748 TATATTTA-ATATT
1 TATATTTATATATT
1442761 T
1 T
1442762 TCAGGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
11 4 0.08
12 2 0.04
13 6 0.12
14 17 0.35
15 7 0.15
16 12 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATATTTATATATT
Found at i:1448221 original size:14 final size:15
Alignment explanation
Indices: 1448202--1448230 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1448192 TGTTTATAGA
1448202 TATTTTTT-AATTAT
1 TATTTTTTAAATTAT
1448216 TATTTTTTAAATTAT
1 TATTTTTTAAATTAT
1448231 ATTAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTTAAATTAT
Found at i:1454434 original size:2 final size:2
Alignment explanation
Indices: 1454417--1454457 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
1454407 AAATAAAAAC
1454417 AT AT GAT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1454458 AAATATGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1455954 original size:18 final size:19
Alignment explanation
Indices: 1455928--1455965 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1455918 ATCTCATATT
*
1455928 AAATAATAATTTAAA-TAA
1 AAATAATAATGTAAACTAA
*
1455946 AAATCATAATGTAAACTAA
1 AAATAATAATGTAAACTAA
1455965 A
1 A
1455966 CCCTCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
AAATAATAATGTAAACTAA
Found at i:1456715 original size:71 final size:68
Alignment explanation
Indices: 1456529--1456736 Score: 335
Period size: 68 Copynumber: 3.0 Consensus size: 68
1456519 ACAATGTCCT
*
1456529 TTCACACTGTTTATTAAGGGGGAGGGGTTATTATTTTGTTGTTGTTGTTGGAAGATCCTGGAGAG
1 TTCACACTGTTTATTAA-GGGGAGGGGTTATTATTTTGTTGTTGTTGTTGGAAGATCTTGGAGAG
1456594 AGAA
65 AGAA
*
1456598 TTCACACTGTTTATTAAGGGGAGGGGTTATTATTTTGCTGTTGTTGTTGGAAGATCTTGGAGAGA
1 TTCACACTGTTTATTAAGGGGAGGGGTTATTATTTTGTTGTTGTTGTTGGAAGATCTTGGAGAGA
1456663 GAA
66 GAA
* * *
1456666 TTCACACTGTTTATTAAGGGAAGGGTTTATTATTTTGTTGTGGTTGTTGTTGGAAGATCTTAGAG
1 TTCACACTGTTTATTAAGGGGAGGGGTTATTATTTTG-T-T-GTTGTTGTTGGAAGATCTTGGAG
1456731 AGAGAA
63 AGAGAA
1456737 AGTGAATGAA
Statistics
Matches: 130, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
68 84 0.65
69 17 0.13
70 1 0.01
71 28 0.22
ACGTcount: A:0.24, C:0.07, G:0.30, T:0.39
Consensus pattern (68 bp):
TTCACACTGTTTATTAAGGGGAGGGGTTATTATTTTGTTGTTGTTGTTGGAAGATCTTGGAGAGA
GAA
Found at i:1463195 original size:4 final size:4
Alignment explanation
Indices: 1463188--1463223 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1463178 AAAAAAAAAA
1463188 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAATG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAA
1463224 TGGAGAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:1480869 original size:22 final size:22
Alignment explanation
Indices: 1480826--1480875 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1480816 TATTTCATAT
1480826 AATTTT-TTAATAAAAAATTAAA
1 AATTTTATTAATAAAAAATT-AA
* *
1480848 AATTTTATTAATTATAAA-TAA
1 AATTTTATTAATAAAAAATTAA
1480869 AATTTTA
1 AATTTTA
1480876 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTATTAATAAAAAATTAA
Found at i:1481318 original size:28 final size:31
Alignment explanation
Indices: 1481286--1481356 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 31
1481276 TCAAACTTGT
*
1481286 TATAATTATA-ATTAAAATT-TAA-TATTTA
1 TATAATTATACATTAAAATTATAATTATATA
* *
1481314 TATAATTTTACATTTAAATTATAATTTATATA
1 TATAATTATACATTAAAATTATAA-TTATATA
1481346 TATAATTATAC
1 TATAATTATAC
1481357 TTATACATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.26
29 8 0.23
30 3 0.09
32 15 0.43
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
TATAATTATACATTAAAATTATAATTATATA
Found at i:1481456 original size:13 final size:13
Alignment explanation
Indices: 1481423--1481469 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1481413 ACAATAAAAA
*
1481423 TTATAATATTTAAT
1 TTATAA-ATATAAT
1481437 TTATAAATAATAAT
1 TTATAAAT-ATAAT
1481451 TT-TAAATATAAT
1 TTATAAATATAAT
*
1481463 ATATAAA
1 TTATAAA
1481470 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 6 0.21
13 11 0.38
14 12 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTATAAATATAAT
Found at i:1481475 original size:24 final size:25
Alignment explanation
Indices: 1481418--1481476 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1481408 TCGAGACAAT
* *
1481418 AAAAATTATAATATTTAATTTATAA
1 AAAAATTATAATATATAATATATAA
*
1481443 ATAATAATTTTAA-ATATAATATATAA
1 A-AA-AATTATAATATATAATATATAA
1481469 AAAAATTA
1 AAAAATTA
1481477 AAAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 4 0.14
25 3 0.11
26 14 0.50
27 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAAATTATAATATATAATATATAA
Found at i:1481981 original size:14 final size:14
Alignment explanation
Indices: 1481962--1481993 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1481952 GATTTTTTTT
1481962 AATTATTTTCAGAA
1 AATTATTTTCAGAA
*
1481976 AATTATTTTTAGAA
1 AATTATTTTCAGAA
1481990 AATT
1 AATT
1481994 TCAAAGACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (14 bp):
AATTATTTTCAGAA
Found at i:1484661 original size:16 final size:15
Alignment explanation
Indices: 1484640--1484669 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1484630 TCAAATTAGA
1484640 AGGGGGCGGGGGGGGG
1 AGGGGG-GGGGGGGGG
1484656 AGGGGGGGGGGGGG
1 AGGGGGGGGGGGGG
1484670 AGATGTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.03, G:0.90, T:0.00
Consensus pattern (15 bp):
AGGGGGGGGGGGGGG
Found at i:1484666 original size:14 final size:15
Alignment explanation
Indices: 1484642--1484671 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1484632 AAATTAGAAG
1484642 GGGGCGGGGGGGGGA
1 GGGGCGGGGGGGGGA
1484657 GGGG-GGGGGGGGGA
1 GGGGCGGGGGGGGGA
1484671 G
1 G
1484672 ATGTGAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.07, C:0.03, G:0.90, T:0.00
Consensus pattern (15 bp):
GGGGCGGGGGGGGGA
Found at i:1488189 original size:37 final size:36
Alignment explanation
Indices: 1488114--1488190 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
1488104 TTTATCAAAA
* * * *
1488114 TTAAAAATTTAATTTAATTAATTTATATATTTATTT
1 TTAAAAATTAAATTTAATAAATTTATAAATTCATTT
1488150 TTAAAAATTAATATTTAATAAATTT-TAAATTCATATT
1 TTAAAAATTAA-ATTTAATAAATTTATAAATTCAT-TT
1488187 TTAA
1 TTAA
1488191 TTTTTATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 17 0.49
37 18 0.51
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (36 bp):
TTAAAAATTAAATTTAATAAATTTATAAATTCATTT
Found at i:1488838 original size:2 final size:2
Alignment explanation
Indices: 1488825--1488866 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1488815 AGACCATCAG
*
1488825 AT AT AC AT 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 AT AT AT AT
1488867 CAAAGACGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1499235 original size:17 final size:18
Alignment explanation
Indices: 1499182--1499221 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1499172 GTTTGAGGTG
*
1499182 TTTTATTTTTATA-TTTA
1 TTTTATATTTATATTTTA
1499199 TTTTATATTTATATTTTA
1 TTTTATATTTATATTTTA
1499217 TTTTA
1 TTTTA
1499222 ATTATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATATTTATATTTTA
Found at i:1505009 original size:11 final size:12
Alignment explanation
Indices: 1504989--1505013 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1504979 ATTGGTGTCC
1504989 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1505001 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1505013 T
1 T
1505014 CATTGGTGGG
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1506240 original size:16 final size:16
Alignment explanation
Indices: 1506219--1506252 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1506209 CTGTTATTTA
1506219 CTCTTCAAATCACTTT
1 CTCTTCAAATCACTTT
1506235 CTCTTCAAATCACTTT
1 CTCTTCAAATCACTTT
1506251 CT
1 CT
1506253 GAGTGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (16 bp):
CTCTTCAAATCACTTT
Found at i:1506361 original size:93 final size:95
Alignment explanation
Indices: 1506255--1506434 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 95
1506245 CACTTTCTGA
* *
1506255 GTGAAAATGGATAATTTAATTTATGATTTAGGTTTTGATC-TTGAAAA-G-GAGAGAAGAGCAGC
1 GTGAAAATGGATAATATAATTTATGAGTTAGGTTTTGATCTTTGAAAAGGAGAGAGAAGAGCAGC
1506317 AGGGATGATTAAATTAAGCTTTCTGAGCTAC
66 AGGGATGATTAAATTAAG-TTTCTGAGCTAC
1506348 GTGAAAATGGATAATATAATTTATGAGTTAGGTTTTGATCTTTGAAAAGGAGAGAGAAGAGCAGC
1 GTGAAAATGGATAATATAATTTATGAGTTAGGTTTTGATCTTTGAAAAGGAGAGAGAAGAGCAGC
*
1506413 AGGGATTATTAAATTAAGTTTC
66 AGGGATGATTAAATTAAGTTTC
1506435 AGGGTTATTG
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
93 38 0.47
94 7 0.09
95 5 0.06
96 31 0.38
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (95 bp):
GTGAAAATGGATAATATAATTTATGAGTTAGGTTTTGATCTTTGAAAAGGAGAGAGAAGAGCAGC
AGGGATGATTAAATTAAGTTTCTGAGCTAC
Found at i:1506759 original size:5 final size:6
Alignment explanation
Indices: 1506728--1506757 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1506718 GAAGATATTC
1506728 TTAAAT TTAAAT TTAAAT TTAAA- TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
1506758 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:1509439 original size:15 final size:16
Alignment explanation
Indices: 1509419--1509449 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1509409 TTGATCATTA
1509419 TTTAT-AAACATAATT
1 TTTATAAAACATAATT
1509434 TTTATAAAACATAATT
1 TTTATAAAACATAATT
1509450 GAATCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATAAAACATAATT
Found at i:1509669 original size:2 final size:2
Alignment explanation
Indices: 1509664--1509697 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1509654 TTCAAAACAG
1509664 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
1509698 GAGTGCCAAT
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:1510015 original size:2 final size:2
Alignment explanation
Indices: 1510010--1510040 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1510000 ACACACACAC
1510010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1510041 ATAAGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1521144 original size:20 final size:20
Alignment explanation
Indices: 1521121--1521159 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1521111 ATATTACATA
1521121 ATAA-ATAAATATAAAAATAT
1 ATAATATAAATA-AAAAATAT
*
1521141 ATAATATAATTAAAAAATA
1 ATAATATAAATAAAAAATA
1521160 AATTAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAATATAAATAAAAAATAT
Found at i:1522902 original size:18 final size:17
Alignment explanation
Indices: 1522868--1522921 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1522858 TAAATAAAAT
1522868 ATTTAAAATATAATTTA
1 ATTTAAAATATAATTTA
1522885 ATTTAAAA-AT-ATTT-
1 ATTTAAAATATAATTTA
* *
1522899 -TTTAAAATTTAATATA
1 ATTTAAAATATAATTTA
*
1522915 ATATAAA
1 ATTTAAA
1522922 TTATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
15 7 0.23
16 2 0.07
17 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAAATATAATTTA
Found at i:1522941 original size:24 final size:26
Alignment explanation
Indices: 1522903--1522979 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 26
1522893 ATATTTTTTA
1522903 AAATTTA-ATATAATATA-AAT-TATT
1 AAATTTATATA-AATATATAATATATT
*
1522927 AAATTTATATAAATATATAATATTTT
1 AAATTTATATAAATATATAATATATT
* *
1522953 AAAATTATTATATATATATATATATAT
1 AAATTTA-TATAAATATATA-ATATAT
1522980 ATATATATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.30
25 6 0.14
26 9 0.20
27 11 0.25
28 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATTTATATAAATATATAATATATT
Found at i:1522941 original size:29 final size:29
Alignment explanation
Indices: 1522909--1522976 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
1522899 TTTAAAATTT
*
1522909 AATATAATATAAATTATTAAATTTA-TATA
1 AATATAATATAAATT-TTAAAATTATTATA
*
1522938 AATAT-ATA-ATATTTTAAAATTATTATA
1 AATATAATATAAATTTTAAAATTATTATA
*
1522965 TATATATATATA
1 AATATA-ATATA
1522977 TATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 8 0.25
27 12 0.38
28 3 0.09
29 8 0.25
30 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATAATATAAATTTTAAAATTATTATA
Found at i:1522968 original size:2 final size:2
Alignment explanation
Indices: 1522961--1522988 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1522951 TTAAAATTAT
1522961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1522989 CACACGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1523289 original size:2 final size:2
Alignment explanation
Indices: 1523282--1523315 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1523272 GATACTTATT
1523282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1523316 ATAAGGTGAC
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):
TA
Found at i:1529296 original size:2 final size:2
Alignment explanation
Indices: 1529289--1529324 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1529279 ATAGGGACGT
1529289 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1529325 AGAGTAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1534561 original size:18 final size:18
Alignment explanation
Indices: 1534540--1534592 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1534530 TTATAATTAA
1534540 TAATATATAAATATTTTT
1 TAATATATAAATATTTTT
* * *
1534558 TAATATTTTAATATATTT
1 TAATATATAAATATTTTT
*
1534576 TAA-ATAATAAAAATTTT
1 TAATAT-ATAAATATTTT
1534593 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATATAAATATTTTT
Found at i:1536303 original size:2 final size:2
Alignment explanation
Indices: 1536288--1536328 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1536278 GATAGTTGTC
1536288 AT AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1536328 A
1 A
1536329 CCTTGATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1537602 original size:25 final size:23
Alignment explanation
Indices: 1537561--1537628 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1537551 TATTAAGATG
*
1537561 ATATATTTTAAA-AAATAATTAAT
1 ATATATTTTAAATAAATAA-AAAT
*
1537584 ATATATTTTAAATTTAATAAAAAT
1 ATATATTTTAAA-TAAATAAAAAT
* *
1537608 A-ATATATTAAATACA-AAAAAT
1 ATATATTTTAAATAAATAAAAAT
1537629 TATCTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 6 0.16
22 2 0.05
23 21 0.55
24 4 0.11
25 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATATTTTAAATAAATAAAAAT
Found at i:1539620 original size:139 final size:139
Alignment explanation
Indices: 1539370--1539649 Score: 461
Period size: 139 Copynumber: 2.0 Consensus size: 139
1539360 TAGAGAGTGC
* * * *
1539370 AAGTTTGTTTAAGAAATGCGATTAAAATTCTGCATGGATTAAGTAAATTTTGACTATGAATTGTG
1 AAGTTTGTGTAAGAAATGCGATTAAAATTCTACATGGAATAAGTAAATTTTGACTATAAATTGTG
* *
1539435 TACTTAATCTAGGATGTTTTAGAAATGTATAAGATGCTGTAAAAGGTGAAGTTTAATGAATTTAA
66 TACTTAATCCAGGATGTTTTAGAAATGTATAAGATGCTGTAAAAGGTAAAGTTTAATGAATTTAA
*
1539500 TGCTGCCAA
131 TGCTGACAA
* * * *
1539509 AAGTTTGTGTAAGAAATGCGATTAAAATTCTACATTGAATAAGTAAATTTTGATTTTAAATTTTG
1 AAGTTTGTGTAAGAAATGCGATTAAAATTCTACATGGAATAAGTAAATTTTGACTATAAATTGTG
1539574 TACTTAATCCAGGATGTTTTAGAAATGTATAAGATGCTGTAAAAGGTAAAGTTTAATGAATTTAA
66 TACTTAATCCAGGATGTTTTAGAAATGTATAAGATGCTGTAAAAGGTAAAGTTTAATGAATTTAA
1539639 TGCTGACAA
131 TGCTGACAA
1539648 AA
1 AA
1539650 AACCTTTAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.37
Consensus pattern (139 bp):
AAGTTTGTGTAAGAAATGCGATTAAAATTCTACATGGAATAAGTAAATTTTGACTATAAATTGTG
TACTTAATCCAGGATGTTTTAGAAATGTATAAGATGCTGTAAAAGGTAAAGTTTAATGAATTTAA
TGCTGACAA
Found at i:1555435 original size:2 final size:2
Alignment explanation
Indices: 1555428--1555455 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1555418 ATCTGGCTTA
1555428 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
1555456 GGTAGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1558023 original size:23 final size:23
Alignment explanation
Indices: 1557975--1558037 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1557965 TAATAAAATA
*
1557975 TAAATTTAAACTT--AAACCTATT
1 TAAATTTAAA-TTAAAAACCTATC
*
1557997 TAAATTTAAATTAAAAATCTATC
1 TAAATTTAAATTAAAAACCTATC
*
1558020 TAAACTTAAATTAAAAAC
1 TAAATTTAAATTAAAAAC
1558038 TCAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 10 0.29
23 23 0.66
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATTTAAATTAAAAACCTATC
Found at i:1558046 original size:23 final size:22
Alignment explanation
Indices: 1557996--1558046 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1557986 TTAAACCTAT
* *
1557996 TTAAATTTAAATTAAAAATCTA
1 TTAAACTTAAATTAAAAATCAA
1558018 TCTAAACTTAAATTAAAAACTCAA
1 T-TAAACTTAAATTAAAAA-TCAA
1558042 TTAAA
1 TTAAA
1558047 ATAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 20 0.80
24 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TTAAACTTAAATTAAAAATCAA
Found at i:1558060 original size:24 final size:24
Alignment explanation
Indices: 1558032--1558106 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
1558022 AACTTAAATT
1558032 AAAAACTCAATTAAAATAAAA-AA
1 AAAAACTCAATTAAAATAAAATAA
*
1558055 ATAAAACTTAATTAAAATAAAATAA
1 A-AAAACTCAATTAAAATAAAATAA
*
1558080 AAAAA-TCTAGATT-GAATAAAATAA
1 AAAAACTC-A-ATTAAAATAAAATAA
1558104 AAA
1 AAA
1558107 TAATTCGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.04
24 37 0.82
25 6 0.13
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (24 bp):
AAAAACTCAATTAAAATAAAATAA
Found at i:1558121 original size:24 final size:24
Alignment explanation
Indices: 1558068--1558124 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1558058 AAACTTAATT
*
1558068 AAAATAAAATAAAAAAATCTAGAT
1 AAAATAAAATAAAAAAATCTAGAA
** *
1558092 TGAATAAAATAAAAATAAT-TCGAA
1 AAAATAAAATAAAAA-AATCTAGAA
1558116 AAAATAAAA
1 AAAATAAAA
1558125 AAATTGATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (24 bp):
AAAATAAAATAAAAAAATCTAGAA
Found at i:1558205 original size:31 final size:31
Alignment explanation
Indices: 1558167--1558230 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1558157 TTTGATTTGT
*
1558167 TTAATTTTAA-ATTTAAAATTGA-TAAATTTAA
1 TTAATTTTAATA-TTAAAATTAATTAAA-TTAA
1558198 TTAATTTTAATATTAAAATTAATTAAATTAA
1 TTAATTTTAATATTAAAATTAATTAAATTAA
1558229 TT
1 TT
1558231 TTTTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
TTAATTTTAATATTAAAATTAATTAAATTAA
Found at i:1558240 original size:27 final size:28
Alignment explanation
Indices: 1558166--1558249 Score: 77
Period size: 31 Copynumber: 3.0 Consensus size: 28
1558156 ATTTGATTTG
** *
1558166 TTTAATTTTAAATTTAAAATTGA-TAAA
1 TTTAATTTTTTATTTAAAATTAATTAAA
1558193 TTTAATTAATTTTAATATTAAAATTAATTAAA
1 TTTAATT--TTTT-AT-TTAAAATTAATTAAA
1558225 -TTAATTTTTTATTT-AAA-TAATTAAA
1 TTTAATTTTTTATTTAAAATTAATTAAA
1558250 AAACTGATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
25 8 0.16
26 3 0.06
27 9 0.18
28 2 0.04
29 6 0.12
30 2 0.04
31 15 0.31
32 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTAATTTTTTATTTAAAATTAATTAAA
Found at i:1558308 original size:2 final size:2
Alignment explanation
Indices: 1558301--1558327 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1558291 TATTATTTAG
1558301 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1558328 CCACCAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1558711 original size:32 final size:33
Alignment explanation
Indices: 1558648--1558758 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 33
1558638 TAGATATAAA
1558648 ATAAA-ATAATAATATAATATAAATATTAAAATTTAT
1 ATAAATATAA-AATATAA-AT--ATATTAAAATTTAT
*
1558684 TTAACAT-T-AAATATAAATATATTAAAATTTAT
1 ATAA-ATATAAAATATAAATATATTAAAATTTAT
*
1558716 ATAAATATAAAATATAAA-ATA-T-AAATATAT
1 ATAAATATAAAATATAAATATATTAAAATTTAT
1558746 A-AAATTATAAAAT
1 ATAAA-TATAAAAT
1558759 TACACATCAG
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
29 3 0.04
30 16 0.24
31 3 0.04
32 21 0.31
33 9 0.13
34 2 0.03
35 7 0.10
36 4 0.06
37 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATAAATATAAAATATAAATATATTAAAATTTAT
Found at i:1558746 original size:22 final size:22
Alignment explanation
Indices: 1558641--1558758 Score: 80
Period size: 23 Copynumber: 5.0 Consensus size: 22
1558631 AATAAATTAG
*
1558641 ATATAAA-ATAAAATAATAATAT
1 ATATAAATATAAAAT-ATAAAAT
** *
1558663 AATATAAATATTAAAATTTATTTAAC
1 -ATATAAATA-TAAAA--TATAAAAT
1558689 AT-TAAATATAAATATATTAAAATTT
1 ATATAAATATAAA-ATA-TAAAA--T
1558714 ATATAAATATAAAATATAAAAT
1 ATATAAATATAAAATATAAAAT
1558736 ATA-AATATATAAAATTATAAAAT
1 ATATAA-ATATAAAA-TATAAAAT
1558759 TACACATCAG
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
21 2 0.03
22 14 0.18
23 22 0.29
24 13 0.17
25 12 0.16
26 13 0.17
27 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAAATATAAAATATAAAAT
Found at i:1558754 original size:8 final size:8
Alignment explanation
Indices: 1558706--1558760 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
1558696 ATAAATATAT
1558706 TAAAATTTA
1 TAAAA-TTA
1558715 TATAAA-TA
1 TA-AAATTA
1558723 TAAAA-TA
1 TAAAATTA
1558730 TAAAA-TA
1 TAAAATTA
1558737 T-AAATATA
1 TAAAAT-TA
1558745 TAAAATTA
1 TAAAATTA
1558753 TAAAATTA
1 TAAAATTA
1558761 CACATCAGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.07
7 13 0.31
8 17 0.40
9 6 0.14
10 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:1563496 original size:2 final size:2
Alignment explanation
Indices: 1563489--1563527 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1563479 AGAAAAGTAC
1563489 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1563528 ATCAAAGCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1564398 original size:39 final size:37
Alignment explanation
Indices: 1564317--1564390 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
1564307 AATACATATT
** *
1564317 AAATATAATTATATTTAATTTTTTAAATATATTTAAA
1 AAATATAATTATATTTAATTTTAAAAATATATATAAA
*
1564354 AAATATAATTTTATATTAATGTTTAAAAATATATATA
1 AAATATAATTATAT-TTAAT-TTTAAAAATATATATA
1564391 GATAATATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 13 0.42
38 5 0.16
39 13 0.42
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (37 bp):
AAATATAATTATATTTAATTTTAAAAATATATATAAA
Found at i:1567889 original size:32 final size:32
Alignment explanation
Indices: 1567821--1567889 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1567811 TATTCAAATT
* **
1567821 TATATATAATAGATAAATATATTAAAAAGGTT
1 TATATATAATAGATAAATATATTAAAAACGAG
* *
1567853 TATATATAATATATAAATATATTAAAGACGAG
1 TATATATAATAGATAAATATATTAAAAACGAG
1567885 TATAT
1 TATAT
1567890 GTGAGAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (32 bp):
TATATATAATAGATAAATATATTAAAAACGAG
Found at i:1568029 original size:5 final size:5
Alignment explanation
Indices: 1568019--1568053 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
1568009 CCATCCTCCC
1568019 TCTTT TCTTT TCTTT TCTTT TCCTTT CTCTTT TCT
1 TCTTT TCTTT TCTTT TCTTT T-CTTT -TCTTT TCT
1568054 CTCTGTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.68
6 8 0.29
7 1 0.04
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (5 bp):
TCTTT
Found at i:1568039 original size:15 final size:17
Alignment explanation
Indices: 1568019--1568053 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1568009 CCATCCTCCC
1568019 TCTTTT-CTTT-TCTTT
1 TCTTTTCCTTTCTCTTT
1568034 TCTTTTCCTTTCTCTTT
1 TCTTTTCCTTTCTCTTT
1568051 TCT
1 TCT
1568054 CTCTGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 8 0.44
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TCTTTTCCTTTCTCTTT
Found at i:1569108 original size:13 final size:13
Alignment explanation
Indices: 1569073--1569118 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
1569063 ATTAAAGCAA
1569073 ATAATAT-TAAAT
1 ATAATATATAAAT
1569085 ATAATTATATAAAT
1 ATAA-TATATAAAT
*
1569099 ATTATATATAAAT
1 ATAATATATAAAT
1569112 AATAATA
1 -ATAATA
1569119 AAAGAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:1569986 original size:29 final size:29
Alignment explanation
Indices: 1569922--1569987 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
1569912 GTCATGACTC
1569922 AAATAAAATAAATTTAATTATAAAATTAT
1 AAATAAAATAAATTTAATTATAAAATTAT
1569951 AAA-AAAATAAATTTAAATTAT-AAA-TAT
1 AAATAAAATAAATTT-AATTATAAAATTAT
1569978 AAAATAAAAT
1 -AAATAAAAT
1569988 TAAAGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 3 0.09
28 17 0.50
29 14 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
AAATAAAATAAATTTAATTATAAAATTAT
Found at i:1570498 original size:25 final size:22
Alignment explanation
Indices: 1570454--1570503 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 22
1570444 TCTAGTTAAT
* *
1570454 AATAAACAATTTTTAAAACACA
1 AATAAACAATTTTAAAAACAAA
1570476 AATAAACAATCATTTAAATAACAAA
1 AATAAACAAT--TTTAAA-AACAAA
1570501 AAT
1 AAT
1570504 TAGATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
24 5 0.22
25 8 0.35
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAACAATTTTAAAAACAAA
Found at i:1571008 original size:7 final size:7
Alignment explanation
Indices: 1570996--1571041 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
1570986 TTAATGTATT
1570996 ATTTATA
1 ATTTATA
1571003 ATTTATA
1 ATTTATA
1571010 ATTTATA
1 ATTTATA
1571017 ATTTATA
1 ATTTATA
1571024 ATTTATA
1 ATTTATA
*
1571031 TTTTATA
1 ATTTATA
1571038 ATTT
1 ATTT
1571042 TTGATCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTATA
Found at i:1571011 original size:21 final size:21
Alignment explanation
Indices: 1570987--1571041 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1570977 TATTTAAAAT
*
1570987 TAATGTATTATTTATAATTTA
1 TAATGTATAATTTATAATTTA
*
1571008 TAATTTATAATTTATAATTTA
1 TAATGTATAATTTATAATTTA
* *
1571029 TATTTTATAATTT
1 TAATGTATAATTT
1571042 TTGATCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATGTATAATTTATAATTTA
Found at i:1573775 original size:2 final size:2
Alignment explanation
Indices: 1573768--1573792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1573758 AGGGCATGAC
1573768 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1573793 ACCTTGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1575146 original size:5 final size:5
Alignment explanation
Indices: 1575138--1575167 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1575128 TCAGATCATA
1575138 ATTTT ATTTT ATTTT ATTTT ATATTT ATTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTT
1575168 ATGTTCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:1575258 original size:32 final size:33
Alignment explanation
Indices: 1575208--1575270 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1575198 AAAATTTTGT
1575208 TTTATTATTTAAAATAATATTAAAAATTAAAAA
1 TTTATTATTTAAAATAATATTAAAAATTAAAAA
* * * *
1575241 TTTATT-TTTATATTAATATTTATAATTAAA
1 TTTATTATTTAAAATAATATTAAAAATTAAA
1575271 TTTTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTATTATTTAAAATAATATTAAAAATTAAAAA
Found at i:1576967 original size:25 final size:23
Alignment explanation
Indices: 1576938--1576983 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1576928 ATGGTGTATT
*
1576938 AATATATTTATATTTTTTTTTATCA
1 AATAT-TTTA-ATTATTTTTTATCA
1576963 AATATTTTAATTATTTTTTAT
1 AATATTTTAATTATTTTTTAT
1576984 ATTATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 4 0.20
25 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
AATATTTTAATTATTTTTTATCA
Found at i:1583135 original size:12 final size:11
Alignment explanation
Indices: 1583118--1583155 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1583108 TTTTTATTTG
1583118 AAATTAATTATA
1 AAATTAA-TATA
1583130 AAATT-ATATA
1 AAATTAATATA
1583140 AATATTAATATA
1 AA-ATTAATATA
1583152 AAAT
1 AAAT
1583156 ATTTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATATA
Found at i:1583148 original size:23 final size:21
Alignment explanation
Indices: 1583120--1583165 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1583110 TTTATTTGAA
1583120 ATTAATTATAAAATTATATAAAT
1 ATTAA-TATAAAA-TATATAAAT
*
1583143 ATTAATATAAAATATTTAAAT
1 ATTAATATAAAATATATAAAT
1583164 AT
1 AT
1583166 ATTTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATATAAAATATATAAAT
Found at i:1583162 original size:21 final size:23
Alignment explanation
Indices: 1583111--1583165 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1583101 TAAATTATTT
*
1583111 TTATTTGAA-ATTAATTATAAAA
1 TTATTTAAATATTAATTATAAAA
*
1583133 TTATATAAATATTAA-TATAAAA
1 TTATTTAAATATTAATTATAAAA
1583155 -TATTTAAATAT
1 TTATTTAAATAT
1583166 ATTTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.34
22 14 0.48
23 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTATTTAAATATTAATTATAAAA
Found at i:1583172 original size:21 final size:21
Alignment explanation
Indices: 1583112--1583177 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
1583102 AAATTATTTT
*
1583112 TATTTGAAAT-TAATTATAAAA
1 TATTT-AAATATATTTATAAAA
* *
1583133 TTATATAAATAT-TAATATAAAA
1 -TATTTAAATATAT-TTATAAAA
*
1583155 TATTTAAATATATTTATATAA
1 TATTTAAATATATTTATAAAA
1583176 TA
1 TA
1583178 AAATACATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATTTAAATATATTTATAAAA
Found at i:1583916 original size:16 final size:16
Alignment explanation
Indices: 1583885--1583930 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1583875 TAGTATCATT
*
1583885 TTAAAATAATATATTTA
1 TTAAATTAATA-ATTTA
*
1583902 TTAAATTAATAATTTT
1 TTAAATTAATAATTTA
1583918 TTAAATTAATAAT
1 TTAAATTAATAAT
1583931 AGTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTAATAATTTA
Found at i:1583944 original size:23 final size:24
Alignment explanation
Indices: 1583913--1583963 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
1583903 TAAATTAATA
*
1583913 ATTTTTTAAATTAATAATAGTAT-
1 ATTTATTAAATTAATAATAGTATC
1583936 ATTTATTAAATTAATAATAGTATC
1 ATTTATTAAATTAATAATAGTATC
1583960 ATTT
1 ATTT
1583964 TAAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATTTATTAAATTAATAATAGTATC
Found at i:1583969 original size:23 final size:22
Alignment explanation
Indices: 1583915--1583973 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
1583905 AATTAATAAT
1583915 TTTTTAAATTAATAATAGTATA
1 TTTTTAAATTAATAATAGTATA
1583937 TTTATTAAATTAATAATAGTATCA
1 TTT-TTAAATTAATAATAGTAT-A
*
1583961 -TTTTAAAATAATA
1 TTTTTAAATTAATA
1583974 TATCTTAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.38
23 20 0.59
24 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (22 bp):
TTTTTAAATTAATAATAGTATA
Found at i:1583976 original size:39 final size:39
Alignment explanation
Indices: 1583874--1583976 Score: 136
Period size: 39 Copynumber: 2.6 Consensus size: 39
1583864 ATCCACTTAG
1583874 ATAGTATCATTTTAAAATAATATATTTATTAAATTAATA
1 ATAGTATCATTTTAAAATAATATATTTATTAAATTAATA
* * * ** *
1583913 AT-TTTTTAAATTAATAATAGTATATTTATTAAATTAATA
1 ATAGTATCATTTTAA-AATAATATATTTATTAAATTAATA
1583952 ATAGTATCATTTTAAAATAATATAT
1 ATAGTATCATTTTAAAATAATATAT
1583977 CTTAGTATTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
38 7 0.14
39 36 0.72
40 7 0.14
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (39 bp):
ATAGTATCATTTTAAAATAATATATTTATTAAATTAATA
Found at i:1584991 original size:2 final size:2
Alignment explanation
Indices: 1584984--1585012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1584974 CATAAATCTA
1584984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1585013 CTATTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1585752 original size:2 final size:2
Alignment explanation
Indices: 1585745--1585782 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1585735 TTTAAGAGTA
1585745 AT AT 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 AT AT
1585783 TGGTGGCGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1586128 original size:25 final size:25
Alignment explanation
Indices: 1586100--1586147 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1586090 TAATGATCAC
1586100 ATATAAAAAATAAAATAATATAAAT
1 ATATAAAAAATAAAATAATATAAAT
* * * *
1586125 ATATTAAAATTTATATAATATAA
1 ATATAAAAAATAAAATAATATAA
1586148 TTTATTAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATATAAAAAATAAAATAATATAAAT
Found at i:1586142 original size:20 final size:19
Alignment explanation
Indices: 1586117--1586183 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
1586107 AAATAAAATA
1586117 ATATAAATATATTAAAATTT
1 ATAT-AATATATTAAAATTT
1586137 ATAT-A-ATA-T--AATTT
1 ATATAATATATTAAAATTT
1586151 AT-TAATGA-ATTAAAATTT
1 ATATAAT-ATATTAAAATTT
1586169 ATATAAATATATTAA
1 ATAT-AATATATTAA
1586184 TTATTAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
13 1 0.03
14 8 0.21
15 1 0.03
16 3 0.08
17 3 0.08
18 8 0.21
19 2 0.05
20 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (19 bp):
ATATAATATATTAAAATTT
Found at i:1587093 original size:2 final size:2
Alignment explanation
Indices: 1587086--1587112 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1587076 ATAATACCTT
1587086 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1587113 TATATCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1587390 original size:118 final size:118
Alignment explanation
Indices: 1587232--1587465 Score: 373
Period size: 118 Copynumber: 2.0 Consensus size: 118
1587222 AAATTTTCAA
*
1587232 CTTGGAGATAAGATAAAAAATTATAGACGTTAAGATTTAAACTACGTATCTATTAAATACAATTT
1 CTTGGAGATAAGATAAAAAATTATAGACGTTAAGATTTAAACTACGTATCCATTAAATACAATTT
* *
1587297 TTTAAAAATGATTAC-ATAAATCAATTAAACTAAATTCTAAATTGATCTTTATG
66 TTTAAAAATGATTACGA-AAATCAATTAAACTAAATTCTAAACTCATCTTTATG
* * * *
1587350 CTTGGAGATAAGATAAGAAATTAT-GTATGTTAGGATTTAAATTACGTATCCATTAAATACAATT
1 CTTGGAGATAAGATAAAAAATTATAG-ACGTTAAGATTTAAACTACGTATCCATTAAATACAATT
1587414 TTTTAAAAATGATTACGAAAATCAATTAAACTAAATTCTAAACTCATCTTTA
65 TTTTAAAAATGATTACGAAAATCAATTAAACTAAATTCTAAACTCATCTTTA
1587466 CATACACATG
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
117 1 0.01
118 105 0.98
119 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (118 bp):
CTTGGAGATAAGATAAAAAATTATAGACGTTAAGATTTAAACTACGTATCCATTAAATACAATTT
TTTAAAAATGATTACGAAAATCAATTAAACTAAATTCTAAACTCATCTTTATG
Found at i:1591512 original size:27 final size:27
Alignment explanation
Indices: 1591481--1591544 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
1591471 TTTGATATAA
*
1591481 ATATATTTAAT-ATTTTTAAAAATTTTT
1 ATATATTTAATAAATTTTAAAAA-TTTT
1591508 ATATATTTAAAATAAATTTTAAAAATTTT
1 ATATATTT--AATAAATTTTAAAAATTTT
1591537 ATAT-TTTA
1 ATATATTTA
1591545 CATTATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 1 0.03
27 8 0.24
28 3 0.09
29 11 0.33
30 10 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATATTTAATAAATTTTAAAAATTTT
Found at i:1592008 original size:18 final size:17
Alignment explanation
Indices: 1591959--1592010 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
1591949 TTTTATTGTC
1591959 AAATT-ATATATATTTTT
1 AAATTAATATA-ATTTTT
* *
1591976 AATTTAATTAAAATTTTT
1 AAATTAA-TATAATTTTT
1591994 AAAATTAATATAATTTT
1 -AAATTAATATAATTTT
1592011 AATACGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 4 0.14
18 15 0.54
19 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTAATATAATTTTT
Found at i:1592197 original size:29 final size:29
Alignment explanation
Indices: 1592164--1592221 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1592154 ACATGTTAAC
1592164 GTGATTAGAGAGATAGCTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
*
1592193 GTGATTAGAGGGATAGCTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
1592222 AATTATAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (29 bp):
GTGATTAGAGAGATAGCTGTCAATAACAA
Found at i:1592236 original size:29 final size:29
Alignment explanation
Indices: 1592167--1592236 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1592157 TGTTAACGTG
*
1592167 ATTAGA-GAGATAGCTGTCAATAACAAGTG
1 ATTAGAGGAGATAGCTGTCAATAACAAG-A
1592196 ATTAGAGG-GATAGCTGTCAATAACAA-A
1 ATTAGAGGAGATAGCTGTCAATAACAAGA
*
1592223 ATTATAGGAAGATA
1 ATTAGAGG-AGATA
1592237 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 7 0.19
29 28 0.78
30 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (29 bp):
ATTAGAGGAGATAGCTGTCAATAACAAGA
Found at i:1596830 original size:29 final size:29
Alignment explanation
Indices: 1596796--1596851 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1596786 GTGTTAACGG
1596796 GATTAGAGAGATAGCTGTCAATAACAAGT
1 GATTAGAGAGATAGCTGTCAATAACAAGT
*
1596825 GATTAGAGGGATAGCTGTCAATAACAA
1 GATTAGAGAGATAGCTGTCAATAACAA
1596852 AATTATAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (29 bp):
GATTAGAGAGATAGCTGTCAATAACAAGT
Found at i:1596866 original size:29 final size:29
Alignment explanation
Indices: 1596797--1596866 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1596787 TGTTAACGGG
*
1596797 ATTAGA-GAGATAGCTGTCAATAACAAGTG
1 ATTAGAGGAGATAGCTGTCAATAACAAG-A
1596826 ATTAGAGG-GATAGCTGTCAATAACAA-A
1 ATTAGAGGAGATAGCTGTCAATAACAAGA
*
1596853 ATTATAGGAAGATA
1 ATTAGAGG-AGATA
1596867 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 7 0.19
29 28 0.78
30 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (29 bp):
ATTAGAGGAGATAGCTGTCAATAACAAGA
Found at i:1598075 original size:18 final size:18
Alignment explanation
Indices: 1598054--1598088 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1598044 ATAAATAGAC
1598054 ATATAAATATATATGTGA
1 ATATAAATATATATGTGA
*
1598072 ATATATATATATATGTG
1 ATATAAATATATATGTG
1598089 TGTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (18 bp):
ATATAAATATATATGTGA
Found at i:1601011 original size:21 final size:20
Alignment explanation
Indices: 1600981--1601033 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1600971 GTATATTTTT
*
1600981 TATTTATAAAATAAAATTTAAA
1 TATTT-TAAAATAAAA-ATAAA
* *
1601003 T-TTTTTAAATAAAAATATA
1 TATTTTAAAATAAAAATAAA
1601022 TATTTTAAAATA
1 TATTTTAAAATA
1601034 TATACTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 3 0.12
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTTAAAATAAAAATAAA
Found at i:1601347 original size:37 final size:37
Alignment explanation
Indices: 1601304--1601393 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
1601294 ATATTAATAA
*
1601304 TTTATATTATATAAATTTTAATATATTTT-TTATTATT
1 TTTATATCATATAAATTTTAATATATTTTATTATT-TT
** * *
1601341 TTTATATCATATTATTTTTTATTTTATTTTAATTATTTT
1 TTTATATCATA-TAAATTTTAATATATTTT-ATTATTTT
1601380 TTTATATCATATAA
1 TTTATATCATATAA
1601394 TTATATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
37 10 0.23
38 16 0.36
39 13 0.30
40 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (37 bp):
TTTATATCATATAAATTTTAATATATTTTATTATTTT
Found at i:1601352 original size:23 final size:21
Alignment explanation
Indices: 1601319--1601365 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
1601309 ATTATATAAA
1601319 TTTTAATATATT-TTTTATTAT
1 TTTTAATATATTATTTT-TTAT
1601340 TTTTATATCATATTATTTTTTAT
1 TTTTA-AT-ATATTATTTTTTAT
1601363 TTT
1 TTT
1601366 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 12 0.52
24 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTAATATATTATTTTTTAT
Found at i:1601394 original size:21 final size:21
Alignment explanation
Indices: 1601333--1601404 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
1601323 AATATATTTT
*
1601333 TTATTATTTTTATATCATATTA
1 TTATT-TTTTTATATCATATAA
*
1601355 TT-TTTTATTT-TAT--TTTAA
1 TTATTTT-TTTATATCATATAA
1601373 TTATTTTTTTATATCATATAA
1 TTATTTTTTTATATCATATAA
1601394 TTATATTTTTT
1 TTAT-TTTTTT
1601405 TTAAATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 7 0.17
20 5 0.12
21 13 0.32
22 8 0.20
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTTTTATATCATATAA
Found at i:1601401 original size:37 final size:38
Alignment explanation
Indices: 1601333--1601414 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 38
1601323 AATATATTTT
* *
1601333 TTATTATTTTTATATCATATTATTTTTTATTTTATTTTAA
1 TTATT-TTTTTATATCATATTATATTATATTTT-TTTTAA
1601373 TTATTTTTTTATATCATA-TA-ATTATATTTTTTTTAA
1 TTATTTTTTTATATCATATTATATTATATTTTTTTTAA
*
1601409 ATATTT
1 TTATTT
1601415 ATATATAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
36 11 0.28
37 8 0.21
38 2 0.05
39 13 0.33
40 5 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (38 bp):
TTATTTTTTTATATCATATTATATTATATTTTTTTTAA
Found at i:1602193 original size:20 final size:20
Alignment explanation
Indices: 1602168--1602206 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1602158 AAGAATTTAA
1602168 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
1602188 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
1602207 GGAAGGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:1606767 original size:20 final size:20
Alignment explanation
Indices: 1606742--1606787 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1606732 AAGAATTGAA
*
1606742 GAGGGATACAAGAGAGAGAT
1 GAGGGATACAAGAGAGAGAG
**
1606762 GAGGGATACTTGAGAGAGAG
1 GAGGGATACAAGAGAGAGAG
1606782 GAGGGA
1 GAGGGA
1606788 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.46, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGAGAG
Found at i:1606903 original size:28 final size:27
Alignment explanation
Indices: 1606863--1606933 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
1606853 AAACAAGCCT
* *
1606863 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
* *
1606891 CTATTTTTGACAAACACAAAATAACTA
1 CCATTTTTGACAAACACAAAATAACCA
1606918 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1606934 AATGGGTGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1609466 original size:17 final size:17
Alignment explanation
Indices: 1609424--1609466 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1609414 TTAAATGTGT
*
1609424 TATAAATAATTATATAAA
1 TATAAAT-ATAATATAAA
1609442 -ATAAATATAATATAAA
1 TATAAATATAATATAAA
1609458 TATAAATAT
1 TATAAATAT
1609467 TAAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAATATAATATAAA
Found at i:1609563 original size:11 final size:11
Alignment explanation
Indices: 1609435--1609566 Score: 66
Period size: 11 Copynumber: 12.5 Consensus size: 11
1609425 ATAAATAATT
*
1609435 ATATAAAATAA
1 ATATAATATAA
1609446 ATATAATATAA
1 ATATAATATAA
1609457 ATATAAATATTAA
1 ATAT-AATA-TAA
*
1609470 A-ATATTA-AA
1 ATATAATATAA
* *
1609479 AT-TTATAAAA
1 ATATAATATAA
*
1609489 AT-TAATTATTA
1 ATATAA-TATAA
1609500 ATAT-ATA-AA
1 ATATAATATAA
*
1609509 ATATAATAT-T
1 ATATAATATAA
*
1609519 TTA-AATATAA
1 ATATAATATAA
* *
1609529 TTGTAAT-TAA
1 ATATAATATAA
* *
1609539 AAATATATAAAA
1 ATATA-ATATAA
1609551 ATATAATATAA
1 ATATAATATAA
1609562 ATATA
1 ATATA
1609567 TAAATTATTA
Statistics
Matches: 91, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
9 16 0.18
10 20 0.22
11 38 0.42
12 13 0.14
13 4 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1611982 original size:14 final size:14
Alignment explanation
Indices: 1611965--1611991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1611955 TATTTATTAA
1611965 GAGTGTATTATTTC
1 GAGTGTATTATTTC
1611979 GAGTGTATTATTT
1 GAGTGTATTATTT
1611992 AATAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (14 bp):
GAGTGTATTATTTC
Found at i:1614171 original size:30 final size:30
Alignment explanation
Indices: 1614097--1614196 Score: 91
Period size: 32 Copynumber: 3.3 Consensus size: 30
1614087 ATAAAAGATC
*
1614097 ATTTACTTTTTAAATCTTTATAAAAAT-TTT
1 ATTTACTCTTTAAAT-TTTATAAAAATATTT
* *
1614127 ATTTTATTTTTTTAATATTTTA-AAAAATATTT
1 A-TTTA-CTCTTTAA-ATTTTATAAAAATATTT
1614159 ATTTACTCTTTAAAATTTTATTAAAAATA--T
1 ATTTACTCTTT-AAATTTTA-TAAAAATATTT
1614189 ATTTACTC
1 ATTTACTC
1614197 AATAGATAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
30 20 0.33
31 16 0.27
32 22 0.37
33 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTACTCTTTAAATTTTATAAAAATATTT
Found at i:1614185 original size:32 final size:31
Alignment explanation
Indices: 1614097--1614196 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 31
1614087 ATAAAAGATC
*
1614097 ATTTACT-TTTTAAATCTTTATAAAAAT-TTT
1 ATTTACTCTTTAAAAT-TTTATAAAAATATTT
* * *
1614127 ATTTTATTTTTTTAATATTTTA-AAAAATATTT
1 A-TTTA-CTCTTTAAAATTTTATAAAAATATTT
1614159 ATTTACTCTTTAAAATTTTATTAAAAATA--T
1 ATTTACTCTTTAAAATTTTA-TAAAAATATTT
1614189 ATTTACTC
1 ATTTACTC
1614197 AATAGATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 22 0.38
31 14 0.24
32 16 0.28
33 6 0.10
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTACTCTTTAAAATTTTATAAAAATATTT
Found at i:1614267 original size:18 final size:18
Alignment explanation
Indices: 1614244--1614281 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1614234 GAGAAATAAA
1614244 TTTTTT-ATTGATTATTAT
1 TTTTTTGATT-ATTATTAT
*
1614262 TTTTTTGATTATTTTTAT
1 TTTTTTGATTATTATTAT
1614280 TT
1 TT
1614282 AAAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTTTGATTATTATTAT
Found at i:1614269 original size:15 final size:16
Alignment explanation
Indices: 1614245--1614274 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1614235 AGAAATAAAT
1614245 TTTTTATTGATTATTA
1 TTTTTATTGATTATTA
1614261 TTTTT-TTGATTATT
1 TTTTTATTGATTATT
1614275 TTTATTTAAA
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:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTATTGATTATTA
Done.