Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 8 of 26
Found at i:1403475 original size:11 final size:11
Alignment explanation
Indices: 1403459--1403504 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
1403449 TATAAAATCG
1403459 TATATTTATAT
1 TATATTTATAT
1403470 TATATTTACATAT
1 TATATTT--ATAT
1403483 TATA-TTATAT
1 TATATTTATAT
*
1403493 TATAATTATAT
1 TATATTTATAT
1403504 T
1 T
1403505 TAAAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 2 0.06
13 8 0.25
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1403500 original size:29 final size:30
Alignment explanation
Indices: 1403459--1403516 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1403449 TATAAAATCG
*
1403459 TATATTTATATTATATTT-ACATATTATAT
1 TATATTTATATTATATTTAAAATATTATAT
1403488 TATA-TTATAATTATATTTAAAATATTATA
1 TATATTTAT-ATTATATTTAAAATATTATA
1403517 AATCTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 13 0.50
30 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TATATTTATATTATATTTAAAATATTATAT
Found at i:1403920 original size:18 final size:18
Alignment explanation
Indices: 1403897--1403960 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 18
1403887 GTGGATAATT
1403897 TTATTTAAAAATTTATAA
1 TTATTTAAAAATTTATAA
* *
1403915 TTATTTTAAAAATATATAT
1 TTA-TTTAAAAATTTATAA
*
1403934 TTATGT--AAATTTA-AA
1 TTATTTAAAAATTTATAA
*
1403949 TTTTTTAAAAAT
1 TTATTTAAAAAT
1403961 ATAAATATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.14
16 6 0.17
17 4 0.11
18 5 0.14
19 16 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTTAAAAATTTATAA
Found at i:1404137 original size:2 final size:2
Alignment explanation
Indices: 1404132--1404164 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1404122 ATATATATAT
1404132 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 A
1404165 TCCTACTTGC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1404239 original size:3 final size:3
Alignment explanation
Indices: 1404231--1404280 Score: 64
Period size: 3 Copynumber: 15.3 Consensus size: 3
1404221 CTTACAGCAC
1404231 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATAA ATAA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A ATA ATA
1404280 A
1 A
1404281 AAGCTCTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 31 0.67
4 15 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1404834 original size:18 final size:16
Alignment explanation
Indices: 1404787--1404837 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 16
1404777 CAAAAATAAA
1404787 AAATATAA-TATATTT
1 AAATATAATTATATTT
1404802 AAATATAATTAATATTT
1 AAATATAATT-ATATTT
1404819 AATATATACATTATATTT
1 AA-ATATA-ATTATATTT
1404837 A
1 A
1404838 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.25
16 1 0.03
17 8 0.25
18 12 0.38
19 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATAATTATATTT
Found at i:1405240 original size:31 final size:32
Alignment explanation
Indices: 1405194--1405263 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
1405184 ATTTTTTAAT
*
1405194 TAAATAATTTAATTTAAATTATTATT-TAAAAA
1 TAAATAATTTAATTTAAATT-TAATTATAAAAA
*
1405226 TAAA-AATTTTATTTAAATTTAATTATAAAAA
1 TAAATAATTTAATTTAAATTTAATTATAAAAA
*
1405257 TATATAA
1 TAAATAA
1405264 ATATTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.12
31 23 0.70
32 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAATAATTTAATTTAAATTTAATTATAAAAA
Found at i:1405274 original size:22 final size:22
Alignment explanation
Indices: 1405239--1405281 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1405229 AAATTTTATT
1405239 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1405261 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
1405282 TTATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1406653 original size:2 final size:2
Alignment explanation
Indices: 1406646--1406672 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1406636 TATTGTAAAC
1406646 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
1406673 ATAAGAATAT
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:1409526 original size:12 final size:12
Alignment explanation
Indices: 1409470--1409538 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 12
1409460 TAAATTAAAT
1409470 TATAA-AAAT-A
1 TATAATAAATAA
*
1409480 TATAAAAAATTAA
1 TATAATAAA-TAA
1409493 TATAA-AAATAA
1 TATAATAAATAA
** *
1409504 TATTTTTAATAA
1 TATAATAAATAA
1409516 TATAATAAATAA
1 TATAATAAATAA
*
1409528 TAAAATAAATA
1 TATAATAAATA
1409539 TTTAATTAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 5 0.10
11 9 0.19
12 28 0.58
13 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:1410104 original size:17 final size:19
Alignment explanation
Indices: 1410049--1410105 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
1410039 TTTAAATTAT
*
1410049 AATTAAAATATTAAATTTTAA
1 AATTAAAA-A-TAAACTTTAA
1410070 AATTAAAAATAAAC-TTAA
1 AATTAAAAATAAACTTTAA
*
1410088 AA-TATAAAT-AACTTTAA
1 AATTAAAAATAAACTTTAA
1410105 A
1 A
1410106 GCTACTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 6 0.18
19 4 0.12
20 1 0.03
21 8 0.24
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAAAAATAAACTTTAA
Found at i:1415294 original size:15 final size:17
Alignment explanation
Indices: 1415262--1415297 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
1415252 AAAATTTATA
1415262 AAATTAACAATAAATTT
1 AAATTAACAATAAATTT
1415279 AAATTAA-AAT-AATTT
1 AAATTAACAATAAATTT
1415294 AAAT
1 AAAT
1415298 CATTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAACAATAAATTT
Found at i:1415685 original size:15 final size:15
Alignment explanation
Indices: 1415667--1415716 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1415657 GCAGAATATA
*
1415667 TATTAATACATAAAT
1 TATTAATATATAAAT
*
1415682 TATT-ATATATACA-
1 TATTAATATATAAAT
1415695 TATATAATATATAAATT
1 TAT-TAATATATAAA-T
1415712 TATTA
1 TATTA
1415717 CATAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 12 0.43
16 2 0.07
17 3 0.11
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTAATATATAAAT
Found at i:1415816 original size:25 final size:25
Alignment explanation
Indices: 1415787--1415842 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1415777 AATGTTTAAG
*
1415787 TTAAATAAAATATTTTATTTAAATT
1 TTAAATAAAATATTTAATTTAAATT
* *
1415812 TTAAAATTAATTATTTAATTTAAATT
1 TT-AAATAAAATATTTAATTTAAATT
1415838 TTAAA
1 TTAAA
1415843 ATTATCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAATAAAATATTTAATTTAAATT
Found at i:1415826 original size:26 final size:26
Alignment explanation
Indices: 1415797--1415879 Score: 96
Period size: 26 Copynumber: 3.1 Consensus size: 26
1415787 TTAAATAAAA
*
1415797 TATTTTATTTAAATTTTAAAATTAAT
1 TATTTAATTTAAATTTTAAAATTAAT
1415823 TATTTAATTTAAATTTTAAAATT-AT
1 TATTTAATTTAAATTTTAAAATTAAT
* * *
1415848 CATTAGACATTTAAATTTTAAATTTAAAT
1 TATT-TA-ATTTAAATTTTAAAATT-AAT
1415877 TAT
1 TAT
1415880 GATTTTATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.10
26 23 0.48
27 16 0.33
29 4 0.08
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (26 bp):
TATTTAATTTAAATTTTAAAATTAAT
Found at i:1415874 original size:13 final size:13
Alignment explanation
Indices: 1415803--1415877 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 13
1415793 AAAATATTTT
1415803 ATTTAAATTTTAA
1 ATTTAAATTTTAA
* *
1415816 AATT-AATTATTTA
1 ATTTAAATT-TTAA
1415829 ATTTAAATTTTAA
1 ATTTAAATTTTAA
* * ** *
1415842 AATTATCATTAGAC
1 ATTTA-AATTTTAA
1415856 ATTTAAATTTTAA
1 ATTTAAATTTTAA
1415869 ATTTAAATT
1 ATTTAAATT
1415878 ATGATTTTAT
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
12 4 0.09
13 29 0.64
14 12 0.27
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (13 bp):
ATTTAAATTTTAA
Found at i:1415916 original size:15 final size:15
Alignment explanation
Indices: 1415893--1415924 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1415883 TTTATCAAGG
*
1415893 ATTTCAAAATTTAAA
1 ATTTAAAAATTTAAA
1415908 ATTTAAAAATTTAAA
1 ATTTAAAAATTTAAA
1415923 AT
1 AT
1415925 AATTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTAAAAATTTAAA
Found at i:1416254 original size:23 final size:24
Alignment explanation
Indices: 1416200--1416264 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
1416190 AATATTGTTT
* *
1416200 TAAAATAAAAATTTTAAATTTTAA
1 TAAAATTAATATTTTAAATTTTAA
***
1416224 TTCGATTAATATTTTAAA-TTTAA
1 TAAAATTAATATTTTAAATTTTAA
*
1416247 TAAAATTAATTTTTTAAA
1 TAAAATTAATATTTTAAA
1416265 ATATTTATTA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TAAAATTAATATTTTAAATTTTAA
Found at i:1416829 original size:18 final size:19
Alignment explanation
Indices: 1416818--1416888 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 19
1416808 ATATTTTTAT
1416818 TATTATTTATATTATTAAA
1 TATTATTTATATTATTAAA
*
1416837 TATTATTT-T-TTA-TAAT
1 TATTATTTATATTATTAAA
* * *
1416853 TA-AATTTA-AATA-AAAA
1 TATTATTTATATTATTAAA
1416869 TATTATTT-TATTATTAAA
1 TATTATTTATATTATTAAA
1416887 TA
1 TA
1416889 GATAAGTCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
15 4 0.10
16 11 0.28
17 10 0.26
18 6 0.15
19 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATTTATATTATTAAA
Found at i:1416856 original size:20 final size:22
Alignment explanation
Indices: 1416815--1416857 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1416805 ATTATATTTT
*
1416815 TATTATTATTTATATTATTAAA
1 TATTATTATTTATATAATTAAA
1416837 TATTATT-TTT-TATAATTAAA
1 TATTATTATTTATATAATTAAA
1416857 T
1 T
1416858 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTATTATTTATATAATTAAA
Found at i:1424906 original size:55 final size:55
Alignment explanation
Indices: 1424822--1424975 Score: 283
Period size: 54 Copynumber: 2.8 Consensus size: 55
1424812 AAAACAATGT
*
1424822 GCAGAGCAGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTTTCCTTGTATC
1 GCAGAACAGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTTTCCTTGTATC
1424877 GCAGAACAGTTAAAACAAGCATCTAAAACTACCAGTAGA-TTTTTTCCTTGTATC
1 GCAGAACAGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTTTCCTTGTATC
*
1424931 GCAGAACGGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTT
1 GCAGAACAGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTT
1424976 ACTAAGAACA
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
54 53 0.55
55 43 0.45
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (55 bp):
GCAGAACAGTTAAAACAAGCATCTAAAACTACCAGTAGATTTTTTTCCTTGTATC
Found at i:1427621 original size:15 final size:14
Alignment explanation
Indices: 1427589--1427628 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
1427579 ATATATTTAA
1427589 TATATTTTAATGAT
1 TATATTTTAATGAT
1427603 TATATTTTATTAT-AT
1 TATATTTTA--ATGAT
1427618 TATATTTTAAT
1 TATATTTTAAT
1427629 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TATATTTTAATGAT
Found at i:1428926 original size:40 final size:39
Alignment explanation
Indices: 1428866--1428944 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
1428856 GCAATCATAC
** *
1428866 TATTAAACATTTAATTATAATGCAAATTTCGATACTTAA
1 TATTAAACATTTAAGCATAATGCAAATCTCGATACTTAA
* *
1428905 TATTAAACACTTTAAGCATAATGTAAATCTCGATATTTAA
1 TATTAAACA-TTTAAGCATAATGCAAATCTCGATACTTAA
1428945 AACTTAAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 9 0.26
40 25 0.74
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.39
Consensus pattern (39 bp):
TATTAAACATTTAAGCATAATGCAAATCTCGATACTTAA
Found at i:1429404 original size:17 final size:17
Alignment explanation
Indices: 1429355--1429405 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1429345 AAAAATTTTA
*
1429355 AAATTATATATAA-AAAT
1 AAATT-TATATAATATAT
*
1429372 AAATTCATTAATAATATAT
1 AAATTTA-T-ATAATATAT
1429391 AAATTTATATAATAT
1 AAATTTATATAATAT
1429406 CAATGTATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 5 0.18
19 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTATATAATATAT
Found at i:1430512 original size:16 final size:17
Alignment explanation
Indices: 1430472--1430512 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1430462 TTTTTAAAAA
*
1430472 ATAATATTTAATAATTT
1 ATAATTTTTAATAATTT
*
1430489 -TAAATTTTAAT-ATTT
1 ATAATTTTTAATAATTT
1430504 ATAATTTTT
1 ATAATTTTT
1430513 TTAATCCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTTAATAATTT
Found at i:1430566 original size:2 final size:2
Alignment explanation
Indices: 1430561--1430592 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1430551 ATTATGATTG
1430561 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
1430593 GAAACAAAGC
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:1431226 original size:11 final size:11
Alignment explanation
Indices: 1431210--1431238 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1431200 AAAAAAATTA
1431210 AAATATAATAT
1 AAATATAATAT
1431221 AAATATAATAT
1 AAATATAATAT
1431232 AAATATA
1 AAATATA
1431239 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1431258 original size:29 final size:30
Alignment explanation
Indices: 1431223--1431283 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
1431213 TATAATATAA
* *
1431223 ATATAATATA-AATATATAAATTAA-AAAAT
1 ATATAATATATAA-AAATAAATGAATAAAAT
1431252 ATATAATATATAAAAATAAATGAATAAAAT
1 ATATAATATATAAAAATAAATGAATAAAAT
1431282 AT
1 AT
1431284 GAATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
ATATAATATATAAAAATAAATGAATAAAAT
Found at i:1431271 original size:24 final size:23
Alignment explanation
Indices: 1431197--1431271 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
1431187 AAAATAATTT
*
1431197 AATAAAAAA-AT-TAAAATATAA
1 AATAAAAAATATATAATATATAA
*
1431218 TATAAATATAATATA-AATATATAA
1 AATAAA-A-AATATATAATATATAA
*
1431242 ATTAAAAAATATATAATATATAAA
1 AATAAAAAATATATAATATAT-AA
1431266 AATAAA
1 AATAAA
1431272 TGAATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.12
22 7 0.16
23 10 0.23
24 21 0.49
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AATAAAAAATATATAATATATAA
Found at i:1431288 original size:29 final size:28
Alignment explanation
Indices: 1431216--1431289 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
1431206 ATTAAAATAT
* *
1431216 AATATAAATATAATATAAATATATAAATT
1 AATA-AAATATAATATAAATAAATAAATG
*
1431245 AAAAAATATATAATATATAA-AAATAAATG
1 AATAAA-ATATAATATA-AATAAATAAATG
1431274 AATAAAATATGAATAT
1 AATAAAATAT-AATAT
1431290 TTATAGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 6 0.16
29 30 0.79
30 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
AATAAAATATAATATAAATAAATAAATG
Found at i:1434263 original size:3 final size:3
Alignment explanation
Indices: 1434255--1434279 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1434245 ACTCAAATTT
1434255 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1434280 ATGGGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1434557 original size:20 final size:18
Alignment explanation
Indices: 1434525--1434565 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1434515 TCTTTTTGAT
1434525 AAAAATTTGAATAAATTTA
1 AAAAATTTGAATAAA-TTA
*
1434544 AAAATATTTTAATAAATTA
1 AAAA-ATTTGAATAAATTA
1434563 AAA
1 AAA
1434566 TCATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAATTTGAATAAATTA
Found at i:1434664 original size:24 final size:26
Alignment explanation
Indices: 1434620--1434667 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1434610 ATTATTTAAT
*
1434620 AAATAGATTTATAATTTTATATTTTA
1 AAATAGATTTATAATTATATATTTTA
1434646 AAATA-ATTTA-AATTATATATTT
1 AAATAGATTTATAATTATATATTT
1434668 AAATTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 5 0.24
26 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATAGATTTATAATTATATATTTTA
Found at i:1434713 original size:28 final size:27
Alignment explanation
Indices: 1434669--1434738 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
1434659 TATATATTTA
* *
1434669 AATTTATAATTTT--AAAATAATTTTGT
1 AATTTTTAATTTTAAAAAATAAGTTT-T
1434695 AATTTTTAATTTTAAAAAATAAGTTTT
1 AATTTTTAATTTTAAAAAATAAGTTTT
*
1434722 -ATTTTTAAAATTTAAAA
1 AATTTTT-AATTTTAAAA
1434739 TTTTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 18 0.47
27 10 0.26
28 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
AATTTTTAATTTTAAAAAATAAGTTTT
Found at i:1435116 original size:20 final size:22
Alignment explanation
Indices: 1435093--1435133 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1435083 ATTTTTTGTT
1435093 TTAAATTT-TT-AAAATATTTA
1 TTAAATTTATTAAAAATATTTA
1435113 TTAAATTTATTAAAAATATTT
1 TTAAATTTATTAAAAATATTT
1435134 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATTTATTAAAAATATTTA
Found at i:1437978 original size:23 final size:23
Alignment explanation
Indices: 1437942--1437988 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1437932 GAATTATGAA
** * *
1437942 TTTTAAAATTTAATTTTTTAAAT
1 TTTTAAAAAATAATTATATAAAT
1437965 TTTTAAAAAATAATTATATAAAT
1 TTTTAAAAAATAATTATATAAAT
1437988 T
1 T
1437989 AATTAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAAAATAATTATATAAAT
Found at i:1444667 original size:2 final size:2
Alignment explanation
Indices: 1444656--1444692 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1444646 AGTATTCTTC
*
1444656 TA TA -A TA TA TA TA TA TA TA TA TA TA TA AA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1444693 TTCTATGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1446647 original size:2 final size:2
Alignment explanation
Indices: 1446640--1446673 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1446630 AGAACTGTAG
1446640 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
1446674 GGCGAGTAGA
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:1452696 original size:17 final size:17
Alignment explanation
Indices: 1452674--1452723 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1452664 TGAAAAAAAT
*
1452674 TAAAATATAATATAATA
1 TAAAATATAATATAACA
1452691 TAAAATAATAATATTAACA
1 TAAAAT-ATAATA-TAACA
*
1452710 TAATA-ATAATATAA
1 TAAAATATAATATAA
1452724 ACAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
18 6 0.21
19 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATATAATATAACA
Found at i:1452714 original size:14 final size:13
Alignment explanation
Indices: 1452685--1452748 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 13
1452675 AAAATATAAT
1452685 ATAATATAAAATA
1 ATAATATAAAATA
1452698 ATAATATTAACATAATA
1 ATAATA-T-A-A-AATA
1452715 ATAATATAAACA-A
1 ATAATATAAA-ATA
*
1452728 ATTAT-TAAAATA
1 ATAATATAAAATA
1452740 TATAATATA
1 -ATAATATA
1452749 TATTTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
11 1 0.02
12 5 0.12
13 16 0.39
14 5 0.12
15 2 0.05
16 2 0.05
17 10 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATAAAATA
Found at i:1452726 original size:17 final size:17
Alignment explanation
Indices: 1452680--1452726 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 17
1452670 AAATTAAAAT
1452680 ATAAT-ATAATATAAA-
1 ATAATAATAATATAAAC
1452695 ATAATAAT-AT-T-AAC
1 ATAATAATAATATAAAC
1452709 ATAATAATAATATAAAC
1 ATAATAATAATATAAAC
1452726 A
1 A
1452727 AATTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 9 0.33
16 3 0.11
17 4 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATAATATAAAC
Found at i:1453480 original size:26 final size:26
Alignment explanation
Indices: 1453444--1453495 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1453434 CAATGAGCGT
* *
1453444 AGCAGGACTTGCTTCACTACACTGCA
1 AGCAGGACTTGCATCACTAAACTGCA
1453470 AGCAGGACTTGCATCACTAAACTGCA
1 AGCAGGACTTGCATCACTAAACTGCA
1453496 GGCGGCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (26 bp):
AGCAGGACTTGCATCACTAAACTGCA
Found at i:1454452 original size:22 final size:21
Alignment explanation
Indices: 1454409--1454448 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1454399 AATGTTTATT
1454409 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1454430 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
1454449 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1461743 original size:9 final size:9
Alignment explanation
Indices: 1461731--1461757 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1461721 TAAAATAAAA
1461731 AATTAAATT
1 AATTAAATT
1461740 AATTAAATT
1 AATTAAATT
1461749 AATTAAATT
1 AATTAAATT
1461758 TTTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAAATT
Found at i:1462308 original size:18 final size:18
Alignment explanation
Indices: 1462282--1462324 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1462272 TTTTATAGAA
1462282 AAATATATAATAATTT-TT
1 AAATATAT-ATAATTTATT
*
1462300 AAATTTATATAATTTATT
1 AAATATATATAATTTATT
1462318 -AATATAT
1 AAATATAT
1462325 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATATAATTTATT
Found at i:1463181 original size:20 final size:22
Alignment explanation
Indices: 1463158--1463206 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1463148 AGTCAAAATT
1463158 TATATAATAAAAATTAT-T-AA
1 TATATAATAAAAATTATATAAA
*
1463178 TATAT--TAAAATTTATATAAA
1 TATATAATAAAAATTATATAAA
1463198 TATATAATA
1 TATATAATA
1463207 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 9 0.38
19 1 0.04
20 12 0.50
22 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATAAAAATTATATAAA
Found at i:1463186 original size:18 final size:20
Alignment explanation
Indices: 1463159--1463202 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1463149 GTCAAAATTT
*
1463159 ATATAATAAAAATTAT-T-A
1 ATATATTAAAAATTATATAA
*
1463177 ATATATTAAAATTTATATAA
1 ATATATTAAAAATTATATAA
1463197 ATATAT
1 ATATAT
1463203 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 1 0.05
20 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATTAAAAATTATATAA
Found at i:1463856 original size:27 final size:27
Alignment explanation
Indices: 1463826--1463901 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 27
1463816 TTGTAATTAT
1463826 TTTTAAAATATTTTATATTTATATAAA
1 TTTTAAAATATTTTATATTTATATAAA
*
1463853 TTTTAATATATTGATTATTTATTTATATAAA
1 TTTTAAAATATT--TTA--TATTTATATAAA
1463884 TTTTAAAATATTTATATA
1 TTTTAAAATATTT-TATA
1463902 ATAATATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 11 0.26
28 2 0.05
29 4 0.10
30 2 0.05
31 23 0.55
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTAAAATATTTTATATTTATATAAA
Found at i:1463898 original size:24 final size:24
Alignment explanation
Indices: 1463868--1463939 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 24
1463858 ATATATTGAT
1463868 TATTTATTTATATAAATTTTAAAA
1 TATTTATTTATATAAATTTTAAAA
* * *
1463892 TATTTATATA-AT-AATATTAAAT
1 TATTTATTTATATAAATTTTAAAA
1463914 TATATTATTTTAATATAATATTTTAA
1 TAT-TTA-TTT-ATATAA-ATTTTAA
1463940 TTATTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
22 11 0.30
23 5 0.14
24 11 0.30
25 1 0.03
26 2 0.05
27 1 0.03
28 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTATTTATATAAATTTTAAAA
Found at i:1463911 original size:22 final size:20
Alignment explanation
Indices: 1463872--1463912 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1463862 ATTGATTATT
*
1463872 TATTTATATAAATTTTAAAA
1 TATTTATATAAATATTAAAA
1463892 TATTTATATAATAATATTAAA
1 TATTTATAT-A-AATATTAAA
1463913 TTATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTATATAAATATTAAAA
Found at i:1463951 original size:23 final size:23
Alignment explanation
Indices: 1463856--1463958 Score: 68
Period size: 23 Copynumber: 4.3 Consensus size: 23
1463846 ATATAAATTT
* * *
1463856 TAATATATTGATTATTTATTTATA
1 TAATATTTTAATTATTT-TTAATA
* *
1463880 TAA-ATTTTAA-AATATTTATATAA
1 TAATATTTTAATTATTTTTA-AT-A
1463903 TAATATTAAATTATATTA-TTTTAATA
1 TAATATT---TTA-ATTATTTTTAATA
1463929 TAATATTTTAATTATTTTTAATA
1 TAATATTTTAATTATTTTTAATA
*
1463952 TCATATT
1 TAATATT
1463959 AAATATTATG
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.03
22 9 0.15
23 26 0.42
24 6 0.10
26 8 0.13
27 5 0.08
28 5 0.08
29 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
TAATATTTTAATTATTTTTAATA
Found at i:1463965 original size:21 final size:22
Alignment explanation
Indices: 1463921--1463965 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1463911 AATTATATTA
*
1463921 TTTTAATATAATATTTTAATTAT
1 TTTTAATATAATA-TTTAAATAT
*
1463944 TTTTAATATCATA-TTAAATAT
1 TTTTAATATAATATTTAAATAT
1463965 T
1 T
1463966 ATGTTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAATATAATATTTAAATAT
Found at i:1464195 original size:16 final size:14
Alignment explanation
Indices: 1464163--1464204 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1464153 TTTAAATATT
1464163 AATATAAT-TATAA
1 AATATAATATATAA
1464176 AATATAATATATAA
1 AATATAATATATAA
* *
1464190 AAAATATTATATAA
1 AATATAATATATAA
1464204 A
1 A
1464205 TTTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAATATATAA
Found at i:1469162 original size:16 final size:16
Alignment explanation
Indices: 1469143--1469197 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1469133 ATTTTATTAT
1469143 TTTTATATTTTTAAAA
1 TTTTATATTTTTAAAA
1469159 TTTTAT-TATTTT-AAA
1 TTTTATAT-TTTTAAAA
* *
1469174 -TATATATTTTTAATA
1 TTTTATATTTTTAAAA
1469189 TTTTA-ATTT
1 TTTTATATTT
1469198 CTTGTCCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
16 13 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATATTTTTAAAA
Found at i:1477242 original size:1 final size:1
Alignment explanation
Indices: 1477238--1477263 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1477228 AAATATTAAA
1477238 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1477264 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1478196 original size:30 final size:30
Alignment explanation
Indices: 1478162--1478221 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1478152 CATGGCAATT
1478162 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1478192 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1478222 AGTGAAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAAA
Found at i:1481524 original size:2 final size:2
Alignment explanation
Indices: 1481512--1481551 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1481502 AGTAAGAAGA
*
1481512 AT AT CT 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
1481552 GAGAATTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1484397 original size:20 final size:20
Alignment explanation
Indices: 1484364--1484403 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1484354 TCTACTTTTG
*
1484364 TAAAAATTTCATTTTTTAAT
1 TAAAAATTTAATTTTTTAAT
*
1484384 TAAAATTTTAATTTTTTAAT
1 TAAAAATTTAATTTTTTAAT
1484404 ATATTATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TAAAAATTTAATTTTTTAAT
Found at i:1484856 original size:19 final size:19
Alignment explanation
Indices: 1484832--1484883 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 19
1484822 TATAAAATAT
1484832 AATTTATAATTAATAAAAA
1 AATTTATAATTAATAAAAA
*
1484851 AATTTATTTAATTTAATAATAA
1 AATTTA--TAA-TTAATAAAAA
*
1484873 AATTTTTAATT
1 AATTTATAATT
1484884 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 3 0.11
22 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTATAATTAATAAAAA
Found at i:1484884 original size:25 final size:23
Alignment explanation
Indices: 1484825--1484892 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 23
1484815 AAATAAATAT
*
1484825 AAAATATAATTTATAATTAATAAA
1 AAAATTTAATTTA-AATTAATAAA
*
1484849 AAAATTT-ATTTAATTTAATAATA
1 AAAATTTAATTTAAATTAATAA-A
*
1484872 AAATTTTTAATTTAAAATTAA
1 AAA-ATTTAATTT-AAATTAA
1484893 AAATTAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
24 9 0.25
25 4 0.11
26 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTTAATTTAAATTAATAAA
Found at i:1484894 original size:20 final size:20
Alignment explanation
Indices: 1484827--1484886 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1484817 ATAAATATAA
* *
1484827 AATATAATTTATAA-TTAAT
1 AATAAAATTTTTAATTTAAT
*
1484846 AAAAAAATTTATTTAATTTAAT
1 AATAAAA-TT-TTTAATTTAAT
1484868 AATAAAATTTTTAATTTAA
1 AATAAAATTTTTAATTTAA
1484887 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.15
20 12 0.35
21 6 0.18
22 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAAATTTTTAATTTAAT
Found at i:1485161 original size:33 final size:32
Alignment explanation
Indices: 1485124--1485189 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
1485114 AGATAAATTT
1485124 ATAATATATATTTATATT-TTGTTTTTAAATAAA
1 ATAATAT-TATTT-TATTATTGTTTTTAAATAAA
*
1485157 ATAATATTATTTTATTAATTTTTTTTAAATAAA
1 ATAATATTATTTTATT-ATTGTTTTTAAATAAA
1485190 TACGAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 4 0.13
32 5 0.17
33 21 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
ATAATATTATTTTATTATTGTTTTTAAATAAA
Found at i:1485449 original size:2 final size:2
Alignment explanation
Indices: 1485444--1485468 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1485434 AAATATTTAC
1485444 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
1485469 AAGTATAGTA
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:1485592 original size:15 final size:15
Alignment explanation
Indices: 1485574--1485623 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1485564 ATTAATACGA
1485574 TATATTTTTAATATT
1 TATATTTTTAATATT
**
1485589 TATATTTAAAAT-TT
1 TATATTTTTAATATT
*
1485603 TAATATTTTTTATATT
1 T-ATATTTTTAATATT
1485619 TATAT
1 TATAT
1485624 AATTAATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTTAATATT
Found at i:1496087 original size:20 final size:21
Alignment explanation
Indices: 1496064--1496106 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1496054 ATACGTTGAT
1496064 AAAA-ATATATTTATATTTAA
1 AAAATATATATTTATATTTAA
1496084 AAAATTATATATTTATATTTAA
1 AAAA-TATATATTTATATTTAA
1496106 A
1 A
1496107 TATATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.19
22 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATATATATTTATATTTAA
Found at i:1496122 original size:17 final size:18
Alignment explanation
Indices: 1496089--1496137 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1496079 TTTAAAAAAT
*
1496089 TATATATTTATATTTAAA
1 TATATATTTAAATTTAAA
1496107 TATATA-TTAAATTTAAA
1 TATATATTTAAATTTAAA
*
1496124 TATTAAATTTAAAT
1 TA-TATATTTAAAT
1496138 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 12 0.44
18 9 0.33
19 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATTTAAATTTAAA
Found at i:1496128 original size:13 final size:13
Alignment explanation
Indices: 1496110--1496140 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1496100 ATTTAAATAT
1496110 ATATTAAATTTAA
1 ATATTAAATTTAA
1496123 ATATTAAATTTAA
1 ATATTAAATTTAA
1496136 ATATT
1 ATATT
1496141 TAAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTAAATTTAA
Found at i:1502545 original size:2 final size:2
Alignment explanation
Indices: 1502538--1502576 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1502528 GCAGAAAAGC
* *
1502538 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TC TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1502577 TCCAGTGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.03, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1509416 original size:3 final size:3
Alignment explanation
Indices: 1509408--1509446 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1509398 GTAGTTTGCC
1509408 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1509447 ACCTTTTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1510238 original size:39 final size:39
Alignment explanation
Indices: 1510193--1510271 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1510183 TATAGATGGG
1510193 TGCCTTTTTAGAAAATAATATTATAGAAGAATAGAATTT
1 TGCCTTTTTAGAAAATAATATTATAGAAGAATAGAATTT
1510232 TGCCTTTTTAGAAAATAATATTATAGAAGAATAGAATTT
1 TGCCTTTTTAGAAAATAATATTATAGAAGAATAGAATTT
1510271 T
1 T
1510272 CTTATAAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (39 bp):
TGCCTTTTTAGAAAATAATATTATAGAAGAATAGAATTT
Found at i:1510512 original size:18 final size:19
Alignment explanation
Indices: 1510491--1510528 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1510481 TAACCTAAAG
*
1510491 TTAA-TTGAAGCTTTTACT
1 TTAATTTGAAGCTTGTACT
1510509 TTAATTTGAAGCTTGTACT
1 TTAATTTGAAGCTTGTACT
1510528 T
1 T
1510529 CTCATCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (19 bp):
TTAATTTGAAGCTTGTACT
Found at i:1513944 original size:2 final size:2
Alignment explanation
Indices: 1513937--1513968 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1513927 TCTACTTTCC
1513937 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
1513969 GAGAGAGAGA
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):
TA
Found at i:1513973 original size:2 final size:2
Alignment explanation
Indices: 1513968--1513994 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1513958 ATATATATAT
1513968 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 A
1513995 CATATATAGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1514117 original size:2 final size:2
Alignment explanation
Indices: 1514105--1514147 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1514095 GCCATTTCTT
* *
1514105 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1514147 T
1 T
1514148 TTTTTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1514156 original size:10 final size:10
Alignment explanation
Indices: 1514112--1514157 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1514102 CTTTATATAC
*
1514112 ATATATATAT
1 ATATATATTT
*
1514122 ATATATATAT
1 ATATATATTT
1514132 ATATATATTT
1 ATATATATTT
*
1514142 ATATATTTTT
1 ATATATATTT
*
1514152 TTATAT
1 ATATAT
1514158 GGGTCAGACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATATTT
Found at i:1516863 original size:2 final size:2
Alignment explanation
Indices: 1516856--1516901 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1516846 CATGCATTGG
1516856 AT AT 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 AT AT
1516898 AT AT
1 AT AT
1516902 GTTTTAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1519545 original size:31 final size:31
Alignment explanation
Indices: 1519507--1519565 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1519497 ATGCACAATC
1519507 TGAAAATGGTATGTTAATATTGCTATATACA
1 TGAAAATGGTATGTTAATATTGCTATATACA
* *
1519538 TGAAAATGGTATTTTAATGTTGCTATAT
1 TGAAAATGGTATGTTAATATTGCTATAT
1519566 TTCCAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
TGAAAATGGTATGTTAATATTGCTATATACA
Found at i:1529290 original size:5 final size:5
Alignment explanation
Indices: 1529282--1529334 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
1529272 CAATCTATTA
* * *
1529282 AATTT AATTT ATTTT ATTTT AAAATT AA-TT AATTT AATTT AATTT -ATTT
1 AATTT AATTT AATTT AATTT -AATTT AATTT AATTT AATTT AATTT AATTT
1529331 AATT
1 AATT
1529335 AGTTAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 8 0.19
5 31 0.74
6 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:1529309 original size:21 final size:21
Alignment explanation
Indices: 1529279--1529321 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1529269 ATTCAATCTA
* * *
1529279 TTAAATTTAATTTATTTTATT
1 TTAAAATTAATTAATTTAATT
1529300 TTAAAATTAATTAATTTAATT
1 TTAAAATTAATTAATTTAATT
1529321 T
1 T
1529322 AATTTATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAAAATTAATTAATTTAATT
Found at i:1529459 original size:20 final size:21
Alignment explanation
Indices: 1529408--1529461 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1529398 TAAAGATTTA
*
1529408 TATATAATATAAATAAAACAT
1 TATATAATATAATTAAAACAT
* * *
1529429 TTTATAGTATAATTTAAA-AT
1 TATATAATATAATTAAAACAT
1529449 TATATAATATAAT
1 TATATAATATAAT
1529462 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TATATAATATAATTAAAACAT
Found at i:1529469 original size:26 final size:28
Alignment explanation
Indices: 1529440--1529497 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
1529430 TTATAGTATA
1529440 ATTTAAAATTAT-ATAATAT-AAT-ATTT
1 ATTT-AAATTATAATAATATAAATAATTT
* *
1529466 ATTTATATTGTAATAATATAAATAATTT
1 ATTTAAATTATAATAATATAAATAATTT
1529494 ATTT
1 ATTT
1529498 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.19
26 11 0.41
27 3 0.11
28 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATTTAAATTATAATAATATAAATAATTT
Found at i:1529507 original size:28 final size:26
Alignment explanation
Indices: 1529441--1529507 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 26
1529431 TATAGTATAA
1529441 TTTAAAATTATATAATATAATATTTATT
1 TTTAAAA-TA-ATAATATAATATTTATT
* ***
1529469 TATATTGTAATAATATAAATAATTTATT
1 TTTAAAATAATAATAT-AAT-ATTTATT
1529497 TTTAAAATAAT
1 TTTAAAATAAT
1529508 TAAAACTAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
26 7 0.24
27 5 0.17
28 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
TTTAAAATAATAATATAATATTTATT
Found at i:1532873 original size:40 final size:40
Alignment explanation
Indices: 1532818--1532897 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1532808 GAAAAAAAGA
1532818 AAGTTTGATTGATTAAATATTTGAGAATCCAATAATTCCT
1 AAGTTTGATTGATTAAATATTTGAGAATCCAATAATTCCT
1532858 AAGTTTGATTGATTAAATATTTGAGAATCCAATAATTCCT
1 AAGTTTGATTGATTAAATATTTGAGAATCCAATAATTCCT
1532898 TTCTTGTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (40 bp):
AAGTTTGATTGATTAAATATTTGAGAATCCAATAATTCCT
Found at i:1533536 original size:2 final size:2
Alignment explanation
Indices: 1533529--1533555 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1533519 ATAACATAAC
1533529 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
1533556 GATCACATAC
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:1537814 original size:25 final size:25
Alignment explanation
Indices: 1537786--1537840 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1537776 TTTGTTTATT
*
1537786 AATTTTATTAT-TAAATTTAAATAAA
1 AATTATATTATAT-AATTTAAATAAA
* *
1537811 AATTATATTATATTATTTAAATAAT
1 AATTATATTATATAATTTAAATAAA
1537836 AATTA
1 AATTA
1537841 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTATATTATATAATTTAAATAAA
Found at i:1538733 original size:27 final size:27
Alignment explanation
Indices: 1538673--1538768 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 27
1538663 TAAAAATTAG
* *
1538673 TCACCAATTTTGACAAAC-AACA--AA
1 TCACCATTTTTGACAAACAAAAAGGAA
*
1538697 TCATCATTTTTGACAAACAAAAAGGAA
1 TCACCATTTTTGACAAACAAAAAGGAA
* *
1538724 TCACCATTTTTTACAAACACAAAGGAA
1 TCACCATTTTTGACAAACAAAAAGGAA
* * *
1538751 CCGCCATTTGTGACAAAC
1 TCACCATTTTTGACAAAC
1538769 GCAAAGGGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 16 0.27
25 3 0.05
27 40 0.68
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (27 bp):
TCACCATTTTTGACAAACAAAAAGGAA
Found at i:1543261 original size:28 final size:27
Alignment explanation
Indices: 1543229--1543292 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1543219 ACTAATTTTG
* *
1543229 ATAAAAAATAAGCCACTATTTTTTACAA
1 ATAAAAAAGAA-CCACTATTTTTAACAA
* *
1543257 ATAAAAAGGAATCACTATTTTTAACAA
1 ATAAAAAAGAACCACTATTTTTAACAA
1543284 ATACAAAAA
1 ATA-AAAAA
1543293 ATATTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (27 bp):
ATAAAAAAGAACCACTATTTTTAACAA
Found at i:1552850 original size:27 final size:25
Alignment explanation
Indices: 1552784--1552853 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
1552774 TTTAAAATTT
* *
1552784 TAAAAAATGAAATAAATTAATTTAA
1 TAAAAAATTAAATCAATTAATTTAA
1552809 TAAAAAATATCAAATCAATTAATTTTTAA
1 TAAAAAAT-T-AAATCAATTAA--TTTAA
*
1552838 TTAAAAATTAAATCAA
1 TAAAAAATTAAATCAA
1552854 AATTAATAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 8 0.21
27 17 0.45
28 1 0.03
29 12 0.32
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAAAAATTAAATCAATTAATTTAA
Found at i:1552857 original size:29 final size:29
Alignment explanation
Indices: 1552785--1552860 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
1552775 TTAAAATTTT
*
1552785 AAAAA-ATGAAAT-AAATTAA-TTTAATA
1 AAAAATATCAAATCAAATTAATTTTAATA
*
1552811 AAAAATATCAAATC-AATTAATTTTTAATT
1 AAAAATATCAAATCAAATTAA-TTTTAATA
1552840 AAAAAT-T-AAATCAAAATTAAT
1 AAAAATATCAAATC-AAATTAAT
1552861 AACTTTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
26 5 0.12
27 17 0.40
28 2 0.05
29 18 0.43
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAAATATCAAATCAAATTAATTTTAATA
Found at i:1553435 original size:11 final size:11
Alignment explanation
Indices: 1553421--1553521 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 11
1553411 ATTTAATACG
1553421 ATATAAATAAA
1 ATATAAATAAA
*
1553432 ATATAATTAAA
1 ATATAAATAAA
* *
1553443 ATAAAAAAATAA
1 ATATAAATA-AA
1553455 ATAT-AATATAA
1 ATATAAATA-AA
1553466 ATAT--ATAATA
1 ATATAAATAA-A
*
1553476 ATTTAAATATAA
1 ATATAAATA-AA
*
1553488 TTATAATATAAA
1 ATATAA-ATAAA
*
1553500 ATATATTATAAA
1 ATATA-AATAAA
1553512 TATATAAATA
1 -ATATAAATA
1553522 GTTACAACTA
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
9 1 0.01
10 7 0.10
11 26 0.37
12 27 0.39
13 9 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:1553482 original size:27 final size:29
Alignment explanation
Indices: 1553430--1553515 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 29
1553420 GATATAAATA
1553430 AAATATAATTA-AA-ATAAAA-A-A--AT
1 AAATATAATTATAATATAAAATATATTAT
*
1553453 AAATATAA-TATAAATATATAATA-ATT-T
1 AAATATAATTAT-AATATAAAATATATTAT
1553480 AAATATAATTATAATATAAAATATATTAT
1 AAATATAATTATAATATAAAATATATTAT
1553509 AAATATA
1 AAATATA
1553516 TAAATAGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.04
23 8 0.15
24 2 0.04
25 5 0.10
26 2 0.04
27 19 0.37
28 6 0.12
29 8 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAATATAATTATAATATAAAATATATTAT
Found at i:1553509 original size:12 final size:11
Alignment explanation
Indices: 1553451--1553516 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
1553441 AAATAAAAAA
*
1553451 ATAAATATAAT
1 ATAAATATATT
*
1553462 ATAAATATATA
1 ATAAATATATT
* *
1553473 AT-AATTTAAAT
1 ATAAATAT-ATT
* *
1553484 ATAATTATAAT
1 ATAAATATATT
1553495 ATAAAATATATT
1 AT-AAATATATT
1553507 ATAAATATAT
1 ATAAATATAT
1553517 AAATAGTTAC
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
10 4 0.09
11 27 0.63
12 12 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAATATATT
Found at i:1553774 original size:18 final size:19
Alignment explanation
Indices: 1553730--1553778 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1553720 GGGTTGATAT
1553730 AATTATTTT-TAATATTTAA
1 AATTATTTTAT-ATATTTAA
1553749 AATTTATTTTATATATTTAA
1 AA-TTATTTTATATATTTAA
1553769 AA-TATTTTAT
1 AATTATTTTAT
1553779 TTTATTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.29
19 2 0.07
20 17 0.61
21 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTATTTTATATATTTAA
Found at i:1553801 original size:27 final size:23
Alignment explanation
Indices: 1553736--1553783 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1553726 ATATAATTAT
1553736 TTTTA-ATATTT-AAA-A-TTTA
1 TTTTATATATTTAAAATATTTTA
1553755 TTTTATATATTTAAAATATTTTA
1 TTTTATATATTTAAAATATTTTA
1553778 TTTTAT
1 TTTTAT
1553784 TTATATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 3 0.12
22 1 0.04
23 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATATATTTAAAATATTTTA
Found at i:1557470 original size:34 final size:34
Alignment explanation
Indices: 1557432--1557503 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
1557422 CTGATCAAGT
*
1557432 TATTCAAATGAATTGCTCAAGTTATGCATTAAAA
1 TATTCAAATGAATTGCTCAAATTATGCATTAAAA
*
1557466 TATTCAAATGAATTGCTCAAATTATTCATTAAAA
1 TATTCAAATGAATTGCTCAAATTATGCATTAAAA
1557500 TATT
1 TATT
1557504 TGAATTTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (34 bp):
TATTCAAATGAATTGCTCAAATTATGCATTAAAA
Found at i:1557968 original size:2 final size:2
Alignment explanation
Indices: 1557917--1557948 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1557907 ATTGAAATAA
1557917 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
1557949 TAAGAAAAAA
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:1562055 original size:27 final size:28
Alignment explanation
Indices: 1562008--1562064 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1561998 TATTATAAAA
* * *
1562008 ATAAAAATTAATTTCATTTAAATA-ATT
1 ATAAAAATTAAATTAAATTAAATATATT
1562035 ATAAAAATTAAATTAAATTAAATATATT
1 ATAAAAATTAAATTAAATTAAATATATT
1562063 AT
1 AT
1562065 TCCTTCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAAAAATTAAATTAAATTAAATATATT
Found at i:1567100 original size:24 final size:24
Alignment explanation
Indices: 1567043--1567117 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 24
1567033 TTTTAATAAA
1567043 TTTAAATATTTATTTTTATTTGATATTT
1 TTTAAAT-TTTATTTTT-TTT-AT-TTT
1567071 TTTAAATTTTATTTTTTTTATTTT
1 TTTAAATTTTATTTTTTTTATTTT
* *
1567095 TTTAAATATTATTAATTTTTATT
1 TTTAAATTTTATT-TTTTTTATT
1567118 CATTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 15 0.34
25 10 0.23
26 3 0.07
27 9 0.20
28 7 0.16
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (24 bp):
TTTAAATTTTATTTTTTTTATTTT
Found at i:1567943 original size:15 final size:15
Alignment explanation
Indices: 1567900--1567945 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1567890 TTCGTCTTAA
1567900 AATTTATA-TGATTT
1 AATTTATATTGATTT
* **
1567914 -ATTTTTATTTTTTT
1 AATTTATATTGATTT
1567928 AATTTATATTGATTT
1 AATTTATATTGATTT
1567943 AAT
1 AAT
1567946 GTATTGATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
13 6 0.25
14 4 0.17
15 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
AATTTATATTGATTT
Found at i:1567955 original size:23 final size:23
Alignment explanation
Indices: 1567929--1567983 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1567919 TATTTTTTTA
* *
1567929 ATTTATATTGATTTAA-TGTATTG
1 ATTTATATTGATTAAATTG-ATCG
1567952 ATTT-TAATTGATTAAATTGATCG
1 ATTTAT-ATTGATTAAATTGATCG
1567975 ATTTATATT
1 ATTTATATT
1567984 TTTATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 23 0.85
24 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.55
Consensus pattern (23 bp):
ATTTATATTGATTAAATTGATCG
Found at i:1569548 original size:22 final size:20
Alignment explanation
Indices: 1569509--1569549 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1569499 CAATTCTTTT
1569509 TATTTTTTAAAAAATATTTA
1 TATTTTTTAAAAAATATTTA
*
1569529 TATTTATTATAAAAAGTATTT
1 TATTT-TT-TAAAAAATATTT
1569550 TATAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTTTTTAAAAAATATTTA
Found at i:1576155 original size:2 final size:2
Alignment explanation
Indices: 1576148--1576173 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1576138 AGACATGTTT
1576148 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
1576174 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1576501 original size:21 final size:20
Alignment explanation
Indices: 1576467--1576506 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1576457 ATTTTTATTT
1576467 AAAATATTATATATAAATAA
1 AAAATATTATATATAAATAA
* *
1576487 AAAATTTTAATATATTAATA
1 AAAATATT-ATATATAAATA
1576507 TTTTATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATTATATATAAATAA
Found at i:1576507 original size:34 final size:32
Alignment explanation
Indices: 1576469--1576539 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1576459 TTTTATTTAA
1576469 AATATTATATATAAATAAAAAATTTTAATATATT
1 AATATTATATAT-AAT-AAAAATTTTAATATATT
* * * *
1576503 AATATTTTATATTATATAAATTTTTATATATT
1 AATATTATATATAATAAAAATTTTAATATATT
*
1576535 TATAT
1 AATAT
1576540 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 19 0.59
33 2 0.06
34 11 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATATTATATATAATAAAAATTTTAATATATT
Found at i:1576524 original size:32 final size:33
Alignment explanation
Indices: 1576488--1576638 Score: 103
Period size: 32 Copynumber: 4.9 Consensus size: 33
1576478 TATAAATAAA
1576488 AAATTTTAATATA-TTA-ATATTTTATATTATAT
1 AAATTTTAATATATTTATATATTTT-TATTATAT
* *
1576520 AAATTTTTATATATTTATATATTTTTATTATGT
1 AAATTTTAATATATTTATATATTTTTATTATAT
* *
1576553 -TATTATT-AT-TATTT-TATA-TGTTA--ATAT
1 AAATT-TTAATATATTTATATATTTTTATTATAT
* * *
1576580 --TTTTTAATATA-TGAT-TAATTTATATTATAT
1 AAATTTTAATATATTTATAT-ATTTTTATTATAT
* *
1576610 AAATTATAATATTTTTATATATTTTTATT
1 AAATTTTAATATATTTATATATTTTTATT
1576639 CTATTATATT
Statistics
Matches: 91, Mismatches: 14, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
25 2 0.02
26 6 0.07
27 7 0.08
28 3 0.03
29 4 0.04
30 8 0.09
31 5 0.05
32 25 0.27
33 23 0.25
34 8 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (33 bp):
AAATTTTAATATATTTATATATTTTTATTATAT
Found at i:1576555 original size:18 final size:19
Alignment explanation
Indices: 1576517--1576631 Score: 80
Period size: 20 Copynumber: 5.9 Consensus size: 19
1576507 TTTTATATTA
*
1576517 TATAAATTTTTATATAT-T
1 TATATATTTTTATATATGT
1576535 TATATATTTTTAT-TATGT
1 TATATATTTTTATATATGT
1576553 TATTATTATTATTT-TATATGT
1 TA-TA-TATT-TTTATATATGT
1576574 TA-ATATTTTTTAATATATGAT
1 TATATA-TTTTT-ATATATG-T
**
1576595 TA-AT-TTATATTATATAAAT
1 TATATATT-T-TTATATATGT
1576614 TATAATATTTTTATATAT
1 TAT-ATATTTTTATATAT
1576632 TTTTATTCTA
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
17 3 0.04
18 20 0.25
19 10 0.13
20 24 0.30
21 20 0.25
22 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TATATATTTTTATATATGT
Found at i:1576568 original size:40 final size:39
Alignment explanation
Indices: 1576524--1576631 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 39
1576514 TTATATAAAT
* * *
1576524 TTTTATATATTTATATATTTTTATTATGTTATTATTATTA
1 TTTTATATATTTATATATTTTTATTATATGATTAAT-TTA
* * *
1576564 TTTTATATGTTAATAT-TTTTTAATATATGATTAATTTA
1 TTTTATATATTTATATATTTTTATTATATGATTAATTTA
* *
1576602 TATTATATAAATTATAATATTTTTA-TATAT
1 TTTTATAT-ATTTAT-ATATTTTTATTATAT
1576632 TTTTATTCTA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
38 10 0.18
39 18 0.33
40 21 0.38
41 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (39 bp):
TTTTATATATTTATATATTTTTATTATATGATTAATTTA
Found at i:1576602 original size:90 final size:89
Alignment explanation
Indices: 1576491--1576656 Score: 242
Period size: 90 Copynumber: 1.9 Consensus size: 89
1576481 AAATAAAAAA
* * * * *
1576491 TTTTAATATATTAATATTTTATATTATATAAATTTTTATATATTTATATATTTTTATTATGTTAT
1 TTTTAATATATGAATAATTTATATTATATAAATTATAATATATTTATATATTTTTATTATATTA-
1576556 TATTATTATTTTATATGTTAATATT
65 TATTATTATTTTATATGTTAATATT
* * *
1576581 TTTTAATATATGATTAATTTATATTATATAAATTATAATATTTTTATATATTTTTATTCTATTAT
1 TTTTAATATATGAATAATTTATATTATATAAATTATAATATATTTATATATTTTTATTATATTAT
*
1576646 ATTATTTTTTT
66 ATTATTATTTT
1576657 CAAAGATCTA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 11 0.16
90 56 0.84
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (89 bp):
TTTTAATATATGAATAATTTATATTATATAAATTATAATATATTTATATATTTTTATTATATTAT
ATTATTATTTTATATGTTAATATT
Found at i:1576643 original size:11 final size:10
Alignment explanation
Indices: 1576517--1576637 Score: 53
Period size: 10 Copynumber: 12.3 Consensus size: 10
1576507 TTTTATATTA
*
1576517 TATAAATTTT
1 TATATATTTT
1576527 TATATA--TT
1 TATATATTTT
1576535 TATATATTTT
1 TATATATTTT
1576545 TAT-TATGTTAT
1 TATATAT-TT-T
1576556 TAT-TATTATT
1 TATATATT-TT
*
1576566 T-TATATGTT
1 TATATATTTT
*
1576575 AATAT-TTTT
1 TATATATTTT
**
1576584 TAATATATGAT
1 T-ATATATTTT
1576595 TA-AT-TTATAT
1 TATATATT-T-T
**
1576605 TATATA-AAT
1 TATATATTTT
1576614 TATAATATTTT
1 TAT-ATATTTT
1576625 TATATATTTT
1 TATATATTTT
1576635 TAT
1 TAT
1576638 TCTATTATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
8 9 0.11
9 15 0.18
10 42 0.51
11 17 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TATATATTTT
Found at i:1577077 original size:21 final size:21
Alignment explanation
Indices: 1577051--1577090 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1577041 ATAAGAATAT
1577051 AATATA-AATTATTAATTATTA
1 AATATATAATT-TTAATTATTA
*
1577072 AATATATTATTTTAATTAT
1 AATATATAATTTTAATTAT
1577091 ATTTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATATAATTTTAATTATTA
Found at i:1577377 original size:37 final size:37
Alignment explanation
Indices: 1577314--1577388 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
1577304 GAAATTTTTA
* * *
1577314 ATTTTTTTTTTAAATTTTTTATATATTTAAAAAATAT
1 ATTTTTTTTATAAATTATTTAAATATTTAAAAAATAT
**
1577351 ATTTTTTTATATAAA-TATTTAAATATTTATTAAATAT
1 ATTTTTTT-TATAAATTATTTAAATATTTAAAAAATAT
1577388 A
1 A
1577389 AAATATCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
ATTTTTTTTATAAATTATTTAAATATTTAAAAAATAT
Found at i:1584684 original size:19 final size:19
Alignment explanation
Indices: 1584660--1584700 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1584650 TATTTTTATA
1584660 AAAATAA-ATATTTAAAAAT
1 AAAATAATA-ATTTAAAAAT
*
1584679 AAAATAATAATTTTAAAAT
1 AAAATAATAATTTAAAAAT
1584698 AAA
1 AAA
1584701 TGAGATGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATAATAATTTAAAAAT
Found at i:1585345 original size:3 final size:3
Alignment explanation
Indices: 1585337--1585364 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1585327 AATAAAAGAA
1585337 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1585365 CAAGAGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1588116 original size:3 final size:3
Alignment explanation
Indices: 1588108--1588136 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1588098 CATGGAAGAA
1588108 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1588137 AATGAAGGTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1588458 original size:19 final size:21
Alignment explanation
Indices: 1588421--1588459 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1588411 GATAATATAA
1588421 TATATTATTTGTAAATAAAAT
1 TATATTATTTGTAAATAAAAT
1588442 TATATTATTT-T-AATAAAA
1 TATATTATTTGTAAATAAAA
1588460 GTATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TATATTATTTGTAAATAAAAT
Found at i:1590418 original size:36 final size:36
Alignment explanation
Indices: 1590378--1590450 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1590368 AATTCGACGT
1590378 ATTAAATTAAATTTTAATATAATATTT-AATAAATAA
1 ATTAAATTAAATTTTAAT-TAATATTTAAATAAATAA
* * * *
1590414 ATTAAATTTAGTTTTAATTACTATTTAAATAATTAA
1 ATTAAATTAAATTTTAATTAATATTTAAATAAATAA
1590450 A
1 A
1590451 AATATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 7 0.22
36 25 0.78
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTAAATTAAATTTTAATTAATATTTAAATAAATAA
Found at i:1591852 original size:21 final size:20
Alignment explanation
Indices: 1591819--1591859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1591809 ATCATGTTTA
* *
1591819 AAATTTTATATATTTATAAT
1 AAATTTTAAATATTAATAAT
1591839 AAATTTTAAAATATTAATAAT
1 AAATTTT-AAATATTAATAAT
1591860 TCGTATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTTTAAATATTAATAAT
Found at i:1592585 original size:16 final size:17
Alignment explanation
Indices: 1592554--1592586 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1592544 GCTTGATATC
1592554 TTTATATTTGTATTATA
1 TTTATATTTGTATTATA
*
1592571 TTTAT-TTTTTATTATA
1 TTTATATTTGTATTATA
1592587 ATATTATGTT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATATTTGTATTATA
Found at i:1592935 original size:30 final size:32
Alignment explanation
Indices: 1592849--1592935 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 32
1592839 TATTAATAAA
* *
1592849 AAATATATTATTTAAATTTAATTATAAAATATAT
1 AAATATA-AATTTTAATTTAATT-TAAAATATAT
* * *
1592883 AAATATTATTTTTAA--TATTTTAAAATA-AT
1 AAATATAAATTTTAATTTAATTTAAAATATAT
1592912 AAA-ATAAATTTTAATTTAATTTAA
1 AAATATAAATTTTAATTTAATTTAA
1592936 TTTAATCTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
28 9 0.21
29 5 0.12
30 14 0.33
31 4 0.09
33 5 0.12
34 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
AAATATAAATTTTAATTTAATTTAAAATATAT
Found at i:1593524 original size:30 final size:31
Alignment explanation
Indices: 1593490--1593547 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1593480 TTTTATATTT
1593490 AAAATA-ATAATTTAAA-TAAATTAAATTATA
1 AAAATATAT-ATTTAAATTAAATTAAATTATA
*
1593520 AAAATTTATATTTAAATTAAATTAAATT
1 AAAATATATATTTAAATTAAATTAAATT
1593548 TATTAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATATATATTTAAATTAAATTAAATTATA
Done.