Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold38
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: 2073527
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 9 of 15
Found at i:1245293 original size:21 final size:21
Alignment explanation
Indices: 1245240--1245295 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1245230 ATAACTAAGT
* * *
1245240 AATTTAAACATAAATAACTAA
1 AATTTAAATAAAAATAAATAA
*
1245261 AA-TTAATTTAAAAATAAATAA
1 AATTTAA-ATAAAAATAAATAA
1245282 AATTTAAATAAAAA
1 AATTTAAATAAAAA
1245296 CTTTAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTTAAATAAAAATAAATAA
Found at i:1245516 original size:36 final size:36
Alignment explanation
Indices: 1245449--1245522 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
1245439 TATTTTTTAA
* * *
1245449 TATAAATTAATAAAATATAAATATTATTAATTATAT
1 TATAAATAAATAAAACAGAAATATTATTAATTATAT
* *
1245485 TATAAATAAATAATACAGAAATGATTA-TAATTTTAT
1 TATAAATAAATAAAACAGAAAT-ATTATTAATTATAT
1245521 TA
1 TA
1245523 AATATATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (36 bp):
TATAAATAAATAAAACAGAAATATTATTAATTATAT
Found at i:1245563 original size:15 final size:16
Alignment explanation
Indices: 1245545--1245590 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1245535 TTGAATAATA
*
1245545 AATAAATTTAAAAAT-
1 AATAATTTTAAAAATG
*
1245560 AATATTTTTAAAAAATG
1 AATAATTTT-AAAAATG
1245577 AATAATTTTAAAAA
1 AATAATTTTAAAAA
1245591 GTTTTTAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 7 0.27
16 11 0.42
17 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATAATTTTAAAAATG
Found at i:1245580 original size:17 final size:16
Alignment explanation
Indices: 1245545--1245590 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1245535 TTGAATAATA
*
1245545 AATAAATTT-AAAAAT
1 AATAATTTTAAAAAAT
*
1245560 AATATTTTTAAAAAAT
1 AATAATTTTAAAAAAT
1245576 GAATAATTTTAAAAA
1 -AATAATTTTAAAAA
1245591 GTTTTTAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 13 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATAATTTTAAAAAAT
Found at i:1246584 original size:24 final size:23
Alignment explanation
Indices: 1246557--1246608 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1246547 TTTTCAGACT
*
1246557 TTAAATTTATATTATTATTATATA
1 TTAAATTTATATTATAATTATA-A
* *
1246581 TTAATTTTTTATTATAATTATAA
1 TTAAATTTATATTATAATTATAA
1246604 TTAAA
1 TTAAA
1246609 ATATTACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAATTTATATTATAATTATAA
Found at i:1246614 original size:41 final size:41
Alignment explanation
Indices: 1246569--1246678 Score: 95
Period size: 42 Copynumber: 2.6 Consensus size: 41
1246559 AAATTTATAT
1246569 TATTATTATATATTAATTTTTTATTAT-AATTATAATTAAA-A
1 TATTATTATATATTAATTTTTTATTATGAA-TA-AATTAAATA
* * *
1246610 TATTACATATTTATATAA-TTTTTATATATGAATAATTTAAATA
1 TATTA-TTATATAT-TAATTTTTTAT-TATGAATAAATTAAATA
1246653 TATATATT-TATATT-ATATTTTTATTA
1 TAT-TATTATATATTAAT-TTTTTATTA
1246679 ATTTTTTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
40 1 0.02
41 8 0.14
42 30 0.54
43 13 0.23
44 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (41 bp):
TATTATTATATATTAATTTTTTATTATGAATAAATTAAATA
Found at i:1246637 original size:13 final size:14
Alignment explanation
Indices: 1246616--1246676 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1246606 AAAATATTAC
1246616 ATATTTATATA-AT
1 ATATTTATATATAT
1246629 -T-TTTATATATGA-
1 ATATTTATATAT-AT
*
1246641 ATAATTTAAATATAT
1 AT-ATTTATATATAT
1246656 ATATTTATAT-TAT
1 ATATTTATATATAT
*
1246669 ATTTTTAT
1 ATATTTAT
1246677 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
11 8 0.21
12 1 0.03
13 12 0.31
14 8 0.21
15 10 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATATTTATATATAT
Found at i:1248007 original size:94 final size:94
Alignment explanation
Indices: 1247846--1248034 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
1247836 TTATCATTTG
1247846 GTCTAGCTTTTCAAAAGCTACATATACGTAATGTTAAATAAGTAAAAAAATTAATTTTTTTATTT
1 GTCTAGCTTTTCAAAAGCTACATATACGTAATGTTAAATAAGTAAAAAAATTAATTTTTTTATTT
1247911 AAAACTCTAATTTTGTAACTCTAATTAAA
66 AAAACTCTAATTTTGTAACTCTAATTAAA
1247940 GTCTAGCTTTTCAAAAGCTACATATACGTAATGTTAAATAAGTAAAAAAATTAATTTTTTTATTT
1 GTCTAGCTTTTCAAAAGCTACATATACGTAATGTTAAATAAGTAAAAAAATTAATTTTTTTATTT
1248005 AAAACTCTAATTTTGTAACTCTAATTAAA
66 AAAACTCTAATTTTGTAACTCTAATTAAA
1248034 G
1 G
1248035 GATTAAAAAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (94 bp):
GTCTAGCTTTTCAAAAGCTACATATACGTAATGTTAAATAAGTAAAAAAATTAATTTTTTTATTT
AAAACTCTAATTTTGTAACTCTAATTAAA
Found at i:1248620 original size:20 final size:21
Alignment explanation
Indices: 1248581--1248621 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1248571 GAATACTTTT
1248581 AAAATATAATAAAAATTAAAA
1 AAAATATAATAAAAATTAAAA
1248602 AAAATA-AATAAAGAA-TAAAA
1 AAAATATAATAAA-AATTAAAA
1248622 TATGGGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATATAATAAAAATTAAAA
Found at i:1248679 original size:85 final size:84
Alignment explanation
Indices: 1248565--1248724 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 84
1248555 AATTGATGAA
*
1248565 AATAATGAATACTTTTAAAATATAATAAAA-ATTAAAAAAAATAAATAAAGAATAAAATATGGGA
1 AATAATGAATACCTTTAAAATATAATAAAATATTAAAAAAAATAAATAAA-AATAAAATATGGGA
*
1248629 TACTTTTTTAATTTCACAAAG
65 -ACTTGTTTAATTTCACAAAG
** * * * *
1248650 AATAAT-ACATACCTTTAAAATATGGTAAAATTTTTAAAAAAACTAAATAAAAATAGAATATGTG
1 AATAATGA-ATACCTTTAAAATATAATAAAA-TATTAAAAAAAATAAATAAAAATAAAATATGGG
1248714 AACTTGTTTAA
64 AACTTGTTTAA
1248725 ATTTACTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
84 1 0.02
85 34 0.53
86 12 0.19
87 17 0.27
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (84 bp):
AATAATGAATACCTTTAAAATATAATAAAATATTAAAAAAAATAAATAAAAATAAAATATGGGAA
CTTGTTTAATTTCACAAAG
Found at i:1249497 original size:21 final size:22
Alignment explanation
Indices: 1249473--1249518 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1249463 TGAAGTAATG
1249473 TTTTTA-T-TTTAAAAATATTTA
1 TTTTTAGTATTTAAAAAT-TTTA
*
1249494 -TTTTAGTATTTACAAATTTTA
1 TTTTTAGTATTTAAAAATTTTA
1249515 TTTT
1 TTTT
1249519 GTGTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 11 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTAGTATTTAAAAATTTTA
Found at i:1250062 original size:16 final size:15
Alignment explanation
Indices: 1250035--1250065 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1250025 TTCAATTAAG
1250035 TATTTTTATTTTTTA
1 TATTTTTATTTTTTA
1250050 TATTTTATATTTTTTA
1 TATTTT-TATTTTTTA
1250066 AAATATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTATTTTTTA
Found at i:1250790 original size:13 final size:14
Alignment explanation
Indices: 1250734--1250784 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
1250724 TATAAAAATA
*
1250734 ATAAAATTATAA-T
1 ATAAAAATATAATT
1250747 ATAAAATATGATATATT
1 ATAAAA-AT-ATA-ATT
1250764 ATAAAAATATAATT
1 ATAAAAATATAATT
1250778 A-AAAAAT
1 ATAAAAAT
1250785 TAAATTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 12 0.36
14 5 0.15
15 6 0.18
16 3 0.09
17 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAAAATATAATT
Found at i:1250807 original size:18 final size:18
Alignment explanation
Indices: 1250786--1250856 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
1250776 TTAAAAAATT
1250786 AAATTTATAAATATTTTA
1 AAATTTATAAATATTTTA
1250804 AAATTTATTAAATA---T-
1 AAATTTA-TAAATATTTTA
* *
1250819 AAA-TTATTAATATATTA
1 AAATTTATAAATATTTTA
*
1250836 AAATTTATAAAATAATTTA
1 AAATTTAT-AAATATTTTA
1250855 AA
1 AA
1250857 TAATTTTCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 5 0.12
14 3 0.07
15 3 0.07
16 2 0.05
17 3 0.07
18 11 0.26
19 15 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTATAAATATTTTA
Found at i:1250837 original size:32 final size:33
Alignment explanation
Indices: 1250780--1250849 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
1250770 ATATAATTAA
*
1250780 AAAAT-TAAATTTATAAATATTTTAAAATTTAT
1 AAAATATAAATTTATAAATATATTAAAATTTAT
* *
1250812 TAAATATAAA-TTATTAATATATTAAAATTTAT
1 AAAATATAAATTTATAAATATATTAAAATTTAT
1250844 AAAATA
1 AAAATA
1250850 ATTTAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AAAATATAAATTTATAAATATATTAAAATTTAT
Found at i:1250857 original size:18 final size:17
Alignment explanation
Indices: 1250784--1250857 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
1250774 AATTAAAAAA
*
1250784 TTAAATTTATAAATATT
1 TTAAATTTATAAATAAT
1250801 TTAAAATTTATTAAAT-A-
1 TT-AAATTTA-TAAATAAT
*
1250818 -TAAA-TTATTAATATAT
1 TTAAATTTATAAATA-AT
*
1250834 TAAAATTTATAAAATAAT
1 TTAAATTTAT-AAATAAT
1250852 TTAAAT
1 TTAAAT
1250858 AATTTTCAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
13 4 0.09
14 3 0.07
15 4 0.09
16 1 0.02
17 5 0.11
18 18 0.41
19 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTTATAAATAAT
Found at i:1254172 original size:22 final size:21
Alignment explanation
Indices: 1254147--1254189 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1254137 GCATTGTTTC
1254147 ATCTAGGCCTTTATTTGTGATT
1 ATCTAGGCCTTTA-TTGTGATT
* **
1254169 ATCTTGTTCTTTATTGTGATT
1 ATCTAGGCCTTTATTGTGATT
1254190 TATGCGGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (21 bp):
ATCTAGGCCTTTATTGTGATT
Found at i:1256332 original size:16 final size:16
Alignment explanation
Indices: 1256290--1256353 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 16
1256280 GAGAGAGTTT
1256290 AATTTAATTAATTTATATA
1 AATTTAA-T-ATTTA-ATA
*
1256309 ATTATTAATATTTAATA
1 AAT-TTAATATTTAATA
1256326 AATTTAATATTT-A-A
1 AATTTAATATTTAATA
1256340 AATTGTAATATTTA
1 AATT-TAATATTTA
1256354 TAATATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 9 0.22
17 5 0.12
18 5 0.12
19 3 0.08
20 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTAATATTTAATA
Found at i:1258451 original size:18 final size:19
Alignment explanation
Indices: 1258430--1258481 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
1258420 ATATTTTAAA
1258430 ATTAATATAATATAAA-TT
1 ATTAATATAATATAAATTT
*
1258448 ATTAATATATTA-AAATTT
1 ATTAATATAATATAAATTT
1258466 ATATAATTATAATATA
1 AT-TAA-TATAATATA
1258482 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 15 0.54
19 3 0.11
20 6 0.21
21 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATATAATATAAATTT
Found at i:1258461 original size:32 final size:32
Alignment explanation
Indices: 1258393--1258500 Score: 96
Period size: 32 Copynumber: 3.3 Consensus size: 32
1258383 TATATAAAAT
* *
1258393 TATTAAAATATAATATGATA-AAA--ATAAATA
1 TATTAAAAT-TAATATAATATAAATTATTAATA
*
1258423 TTTTAAAATTAATATAATATAAATTATTAATA
1 TATTAAAATTAATATAATATAAATTATTAATA
* *
1258455 TATTAAAATTTATATAATTATAATATATTTTAAATA
1 TATTAAAATTAATATAA-TATAA-AT-TATT-AATA
*
1258491 TATTATAATT
1 TATTAAAATT
1258501 TTTAGAACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
29 9 0.14
30 11 0.17
32 21 0.33
33 5 0.08
34 2 0.03
35 3 0.05
36 13 0.20
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
TATTAAAATTAATATAATATAAATTATTAATA
Found at i:1258498 original size:27 final size:26
Alignment explanation
Indices: 1258433--1258500 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
1258423 TTTTAAAATT
1258433 AATATAATATAAATTATTAATATATTAA
1 AATAT-ATAT-AATTATTAATATATTAA
* *
1258461 AATTTATATAATTA-TAATATATTTTA
1 AATATATATAATTATTAATATA-TTAA
1258487 AATATATTATAATT
1 AATATA-TATAATT
1258501 TTTAGAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.20
26 13 0.37
27 11 0.31
28 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATATATAATTATTAATATATTAA
Found at i:1258773 original size:15 final size:15
Alignment explanation
Indices: 1258749--1258781 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1258739 GATAAATATA
*
1258749 AATATGAATATATTT
1 AATATAAATATATTT
1258764 AATATAAATATATTT
1 AATATAAATATATTT
1258779 AAT
1 AAT
1258782 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AATATAAATATATTT
Found at i:1258805 original size:22 final size:22
Alignment explanation
Indices: 1258772--1258820 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1258762 TTAATATAAA
* *
1258772 TATATTTA-ATTTTTTAAAATT
1 TATATTTATAATTTTAAAAATT
1258793 T-TATTTATAATTTTAAAAATT
1 TATATTTATAATTTTAAAAATT
1258814 TATATTT
1 TATATTT
1258821 TATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 13 0.54
22 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATATTTATAATTTTAAAAATT
Found at i:1258828 original size:20 final size:21
Alignment explanation
Indices: 1258787--1258828 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1258777 TTAATTTTTT
*
1258787 AAAATTTTATTTATAATTTTA
1 AAAATTTTATTTATAATATTA
1258808 AAAATTTATATTT-T-ATATTA
1 AAAATTT-TATTTATAATATTA
1258828 A
1 A
1258829 TATTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATTTTATTTATAATATTA
Found at i:1258859 original size:13 final size:13
Alignment explanation
Indices: 1258841--1258870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1258831 TTTAAATATG
*
1258841 TATTAAATATAAA
1 TATTAAATAAAAA
1258854 TATTAAATAAAAA
1 TATTAAATAAAAA
1258867 TATT
1 TATT
1258871 TTATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTAAATAAAAA
Found at i:1260215 original size:13 final size:13
Alignment explanation
Indices: 1260197--1260221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1260187 AAAAAAAGAA
1260197 TTAAATTAATTAG
1 TTAAATTAATTAG
1260210 TTAAATTAATTA
1 TTAAATTAATTA
1260222 AATTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTAAATTAATTAG
Found at i:1260660 original size:26 final size:26
Alignment explanation
Indices: 1260617--1260669 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1260607 TACAATAAAA
* *
1260617 ATTTTAAAATT-TATTAAATATATAAT
1 ATTTTAAAATTAAATAAAAT-TATAAT
*
1260643 ATTTTGAAATTAAATAAAATTATAAT
1 ATTTTAAAATTAAATAAAATTATAAT
1260669 A
1 A
1260670 ACATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTTTAAAATTAAATAAAATTATAAT
Found at i:1261949 original size:25 final size:25
Alignment explanation
Indices: 1261921--1261989 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
1261911 TCATGATTAA
1261921 ATATAATATATTTAATAA-ATATATT
1 ATAT-ATATATTTAATAATATATATT
*
1261946 ATAT-TAATATTTAATAATTTATATT
1 ATATAT-ATATTTAATAATATATATT
*
1261971 ATATTTATATTTATATAAT
1 ATATATATATTTA-ATAAT
1261990 GTAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 21 0.54
26 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATATATATTTAATAATATATATT
Found at i:1261961 original size:20 final size:19
Alignment explanation
Indices: 1261920--1261986 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 19
1261910 GTCATGATTA
* * *
1261920 AATATAATATATT-TAATA
1 AATATATTATATTATATTT
1261938 AATATATTATATTAATATTT
1 AATATATTATATT-ATATTT
1261958 AATA-ATTTATATTATATTT
1 AATATA-TTATATTATATTT
1261977 -ATAT-TTATAT
1 AATATATTATAT
1261987 AATGTAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
17 6 0.14
18 15 0.36
19 7 0.17
20 14 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATATTATATTATATTT
Found at i:1261980 original size:6 final size:6
Alignment explanation
Indices: 1261939--1261986 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
1261929 TATTTAATAA
*
1261939 ATATATT ATATTA ATATTT AATAATTT ATA-TT ATATTT ATATTT ATAT
1 ATAT-TT ATATTT ATATTT -AT-ATTT ATATTT ATATTT ATATTT ATAT
1261987 AATGTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 8 0.22
8 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:1262180 original size:22 final size:22
Alignment explanation
Indices: 1262142--1262209 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1262132 TAATTTTATT
1262142 TAAAT-TTAAT-TAAAAATAAA
1 TAAATATTAATATAAAAATAAA
*
1262162 TAAATATTAATATAAAAATAAT
1 TAAATATTAATATAAAAATAAA
***
1262184 TTTTTATTAATTATAAATAATAAA
1 TAAATATTAA-TATAAA-AATAAA
1262208 TA
1 TA
1262210 TGAGTAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 5 0.13
21 5 0.13
22 16 0.42
23 6 0.16
24 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTAATATAAAAATAAA
Found at i:1262402 original size:20 final size:20
Alignment explanation
Indices: 1262379--1262417 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1262369 ATTATATGAA
1262379 TTAAAA-AATTAAAATATAAT
1 TTAAAATAA-TAAAATATAAT
*
1262399 TTAAAATAATATAATATAA
1 TTAAAATAATAAAATATAA
1262418 ATATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAATAATAAAATATAAT
Found at i:1262463 original size:31 final size:33
Alignment explanation
Indices: 1262390--1262544 Score: 118
Period size: 31 Copynumber: 4.5 Consensus size: 33
1262380 TAAAAAATTA
*
1262390 AAATATAATTTAAAA-TAATATAATATAAATATAT
1 AAATAT-A-TTAAAATTTATATAATATAAATATAT
*
1262424 AAATATATTAAAATTTA-ATAATATGAAT-TAT
1 AAATATATTAAAATTTATATAATATAAATATAT
* *
1262455 TAATATATTAAAATTTATATAAATATATAATATTT
1 AAATATATTAAAATTTATAT-AATATA-AATATAT
* * *
1262490 AAAATATAATTATAATATATAAAAATATATGAATATAT
1 -AAATAT-ATTAAAATTTAT-ATAATATA--AATATAT
*
1262528 ATAATTATATAAAAATT
1 A-AA-TATATTAAAATT
1262545 CAAATCTAAC
Statistics
Matches: 96, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
31 19 0.20
32 18 0.19
33 8 0.08
34 9 0.09
35 2 0.02
36 5 0.05
37 17 0.18
38 15 0.16
39 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
AAATATATTAAAATTTATATAATATAAATATAT
Found at i:1262505 original size:6 final size:7
Alignment explanation
Indices: 1262392--1262511 Score: 70
Period size: 7 Copynumber: 16.9 Consensus size: 7
1262382 AAAAATTAAA
1262392 ATATAAT
1 ATATAAT
* *
1262399 TTAAAAT
1 ATATAAT
1262406 AATATAAT
1 -ATATAAT
1262414 ATA-AAT
1 ATATAAT
1262420 ATATAAAT
1 ATAT-AAT
*
1262428 ATATTAAA
1 ATA-TAAT
*
1262436 ATTTAAT
1 ATATAAT
1262443 AATATGAAT
1 -ATAT-AAT
1262452 -TATTAAT
1 ATA-TAAT
*
1262459 ATATTAAA
1 ATA-TAAT
*
1262467 AT-TTAT
1 ATATAAT
1262473 ATA-AAT
1 ATATAAT
1262479 ATATAAT
1 ATATAAT
* *
1262486 ATTTAAA
1 ATATAAT
1262493 ATATAAT
1 ATATAAT
1262500 -TATAAT
1 ATATAAT
1262506 ATATAA
1 ATATAA
1262512 AAATATATGA
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
6 21 0.24
7 34 0.40
8 27 0.31
9 4 0.05
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:1262515 original size:47 final size:45
Alignment explanation
Indices: 1262404--1262533 Score: 152
Period size: 50 Copynumber: 2.7 Consensus size: 45
1262394 ATAATTTAAA
*
1262404 ATAATATAATATAAATATATAAATATATTAAAATTTAATAATATGAATT
1 ATAATAT-ATAAAAATATATAAATATA-TAAAATTTAA-AATAT-AATT
* *
1262453 ATTAATATATTAAAATTTATATAAATATATAATATTTAAAATATAATT
1 A-TAATATA-TAAAA-ATATATAAATATATAAAATTTAAAATATAATT
* *
1262501 ATAATATATAAAAATATATGAATATATATAATT
1 ATAATATATAAAAATATATAAATATATAAAATT
1262534 ATATAAAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
45 16 0.23
46 5 0.07
47 7 0.10
48 5 0.07
49 7 0.10
50 19 0.27
51 12 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (45 bp):
ATAATATATAAAAATATATAAATATATAAAATTTAAAATATAATT
Found at i:1262536 original size:10 final size:9
Alignment explanation
Indices: 1262404--1262539 Score: 85
Period size: 8 Copynumber: 15.4 Consensus size: 9
1262394 ATAATTTAAA
1262404 ATAATATAAT
1 ATAATAT-AT
1262414 ATAA-ATAT
1 ATAATATAT
1262422 ATAA-ATAT
1 ATAATATAT
1262430 ATTAA-A-AT
1 A-TAATATAT
*
1262438 TTAATA-AT
1 ATAATATAT
1262446 ATGAAT-TAT
1 AT-AATATAT
1262455 -TAATATATT
1 ATAATATA-T
* *
1262464 AAAATTTAT
1 ATAATATAT
1262473 ATAA-ATAT
1 ATAATATAT
*
1262481 ATAATATTT
1 ATAATATAT
*
1262490 AAAATATAATT
1 ATAATAT-A-T
1262501 ATAATATAT
1 ATAATATAT
*
1262510 A-AAAATAT
1 ATAATATAT
1262518 ATGAATATAT
1 AT-AATATAT
1262528 ATAAT-TAT
1 ATAATATAT
1262536 ATAA
1 ATAA
1262540 AAATTCAAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 26
0.73 0.09 0.19
Matches are distributed among these distances:
7 6 0.06
8 41 0.40
9 30 0.29
10 18 0.18
11 7 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAATATAT
Found at i:1262720 original size:6 final size:6
Alignment explanation
Indices: 1262709--1262733 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1262699 ATTAAATATT
1262709 TAAATA TAAATA TAAATA TAAATA T
1 TAAATA TAAATA TAAATA TAAATA T
1262734 TAAAGCAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:1269910 original size:2 final size:2
Alignment explanation
Indices: 1269905--1269935 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1269895 TGTGTGTATC
1269905 TA TA 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 TA TA T
1269936 CTGCATGCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1270672 original size:2 final size:2
Alignment explanation
Indices: 1270665--1270689 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1270655 ACTTATATTC
1270665 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
1270690 AAAGATAAAA
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:1271305 original size:21 final size:21
Alignment explanation
Indices: 1271264--1271306 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1271254 TTAAATTAAA
* *
1271264 TTTATTTATTTATATATTATT
1 TTTATGTATTTATATAATATT
1271285 TTTATGTA-TTATAATAATATT
1 TTTATGTATTTAT-ATAATATT
1271306 T
1 T
1271307 AAAATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATGTATTTATATAATATT
Found at i:1278464 original size:17 final size:17
Alignment explanation
Indices: 1278434--1278467 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1278424 ATAATTTAAA
1278434 TTTATTAAATATTATAT
1 TTTATTAAATATTATAT
1278451 TTTA-TAAATAATTATAT
1 TTTATTAAAT-ATTATAT
1278468 AAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTATTAAATATTATAT
Found at i:1282487 original size:31 final size:32
Alignment explanation
Indices: 1282422--1282531 Score: 99
Period size: 35 Copynumber: 3.5 Consensus size: 32
1282412 AATTACAATT
*
1282422 ATATAAATATAATATATATTAAATATTAAATATATA
1 ATAT-AATATAATATATTTTAAATATT---TATATA
1282458 ATATAATATAATATATTTTAAA-ATTTATATA
1 ATATAATATAATATATTTTAAATATTTATATA
*
1282489 A-ATAA-A-AA-ATATTTTAAATACTTT-TTTA
1 ATATAATATAATATATTTTAAATA-TTTATATA
*
1282517 ATA-AATAAAATATAT
1 ATATAATATAATATAT
1282532 AAATATAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
27 10 0.15
28 9 0.14
29 6 0.09
30 6 0.09
31 11 0.17
34 3 0.05
35 17 0.26
36 4 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAATATATTTTAAATATTTATATA
Found at i:1283576 original size:15 final size:15
Alignment explanation
Indices: 1283556--1283597 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1283546 TCGATAATTT
1283556 AAATTATTATTTAAA
1 AAATTATTATTTAAA
* **
1283571 AAATTATAAAATAAA
1 AAATTATTATTTAAA
1283586 AAATTATT-TTTA
1 AAATTATTATTTA
1283598 TATTAATATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATTATTATTTAAA
Found at i:1283640 original size:21 final size:22
Alignment explanation
Indices: 1283616--1283660 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1283606 TTTATATATT
1283616 TTATAAAAATAAATAAA-AATA
1 TTATAAAAATAAATAAATAATA
** *
1283637 TTATTTAATTAAATAAATAATA
1 TTATAAAAATAAATAAATAATA
1283659 TT
1 TT
1283661 CAAATCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATAAAAATAAATAAATAATA
Found at i:1284965 original size:16 final size:16
Alignment explanation
Indices: 1284913--1284967 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1284903 TATTTAATTT
1284913 ATTTTATATTTATATAA
1 ATTTTATATTT-TATAA
**
1284930 ATTTTAATACATTA-AA
1 ATTTT-ATATTTTATAA
*
1284946 ATTTTATATTTTATAT
1 ATTTTATATTTTATAA
1284962 ATTTTA
1 ATTTTA
1284968 AAATATTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.19
16 14 0.45
17 7 0.23
18 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTTTATAA
Found at i:1285489 original size:26 final size:27
Alignment explanation
Indices: 1285426--1285491 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1285416 TACAATTAAA
*
1285426 AAAT-TATTTTTATTAAATAATACAAT
1 AAATATATTTTTATAAAATAATACAAT
* *
1285452 AAATATAATTTTATAAAATTAATA-ATT
1 AAATATATTTTTATAAAA-TAATACAAT
1285479 AAATAT-TTTTTAT
1 AAATATATTTTTAT
1285492 TAATACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 10 0.29
27 19 0.56
28 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATATATTTTTATAAAATAATACAAT
Found at i:1286529 original size:22 final size:21
Alignment explanation
Indices: 1286491--1286539 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
1286481 CAAATTTAAA
1286491 AAATCATTTTTACATTAATATTT
1 AAAT-ATTTTTACATTAA-ATTT
1286514 AAATATTTTATA-ATTAAATTT
1 AAATATTTT-TACATTAAATTT
1286535 AAATA
1 AAATA
1286540 AAAAACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTTTTACATTAAATTT
Found at i:1287218 original size:50 final size:47
Alignment explanation
Indices: 1287151--1287247 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 47
1287141 CATATTGATC
*
1287151 ATATTTATTATTTATAATT-AATAAAAAATAAAAATTATTTTTATATTA
1 ATATTTATTATTTATAATTAAAT-AAAAATAAAAATAATTTTTA-ATTA
**
1287199 ATATTTATGTATTTTATAATTAAATTTAAATAAAAATAATTTTTAATTA
1 ATATTTAT-TA-TTTATAATTAAATAAAAATAAAAATAATTTTTAATTA
1287248 TTAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 8 0.19
49 6 0.14
50 26 0.60
51 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (47 bp):
ATATTTATTATTTATAATTAAATAAAAATAAAAATAATTTTTAATTA
Found at i:1287457 original size:17 final size:16
Alignment explanation
Indices: 1287435--1287468 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1287425 ATAAATAATT
1287435 AAAATATAATACAACAC
1 AAAATATAATA-AACAC
*
1287452 AAAATATTATAAACAC
1 AAAATATAATAAACAC
1287468 A
1 A
1287469 TTATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATATAATAAACAC
Found at i:1287535 original size:13 final size:13
Alignment explanation
Indices: 1287506--1287539 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1287496 TATATAAAAT
*
1287506 AAATTATTAATTAA
1 AAATTA-TAACTAA
1287520 AAATTATAACTAA
1 AAATTATAACTAA
1287533 AAATTAT
1 AAATTAT
1287540 TTAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTATAACTAA
Found at i:1289631 original size:17 final size:17
Alignment explanation
Indices: 1289620--1289653 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1289610 TTATATTAAT
1289620 ATAAAAATTATAAAATA
1 ATAAAAATTATAAAATA
*
1289637 ATAAAAA-TATAATATA
1 ATAAAAATTATAAAATA
1289653 A
1 A
1289654 CATGATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATTATAAAATA
Found at i:1289729 original size:16 final size:16
Alignment explanation
Indices: 1289683--1289759 Score: 54
Period size: 16 Copynumber: 4.8 Consensus size: 16
1289673 ATTTTTAAAT
1289683 TTATATAATATAAAA-TA
1 TTATAT-ATA-AAAATTA
*
1289700 TTAATATATTAAAATTA
1 TT-ATATATAAAAATTA
*
1289717 TTATATATAAAAAATA
1 TTATATATAAAAATTA
1289733 TT-T-TA-AAATAATTA
1 TTATATATAAA-AATTA
*
1289747 TAATATAATAAAA
1 TTATAT-ATAAAA
1289760 TATATAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
13 3 0.06
14 7 0.15
15 2 0.04
16 19 0.40
17 10 0.21
18 7 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATATATAAAAATTA
Found at i:1289732 original size:27 final size:29
Alignment explanation
Indices: 1289702--1289764 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 29
1289692 ATAAAATATT
*
1289702 AATATATTAAAATTATTAT-ATATAA-AA
1 AATATATTAAAATAATTATAATATAATAA
*
1289729 AATATTTTAAAATAATTATAATATAATAA
1 AATATATTAAAATAATTATAATATAATAA
1289758 AATATAT
1 AATATAT
1289765 AAATATATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 17 0.55
28 6 0.19
29 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AATATATTAAAATAATTATAATATAATAA
Found at i:1289765 original size:58 final size:58
Alignment explanation
Indices: 1289625--1289765 Score: 132
Period size: 59 Copynumber: 2.4 Consensus size: 58
1289615 TTAATATAAA
* * * *
1289625 AATTATAAAATAATAAAA-ATATAATATAACATGATTTGATATAAATATATTTTTAAAT
1 AATTATAATATAATAAAATATAT-ATATAAAATGATTTGATATAAAAATATTTTAAAAT
*
1289683 --TTAT-ATA-ATATAAAATATTAATATATTAAAATTATTAT-ATATAAAAAATATTTTAAAAT
1 AATTATAATATA-ATAAAATA-T-ATATA-TAAAATGATT-TGATAT-AAAAATATTTTAAAAT
1289742 AATTATAATATAATAAAATATATA
1 AATTATAATATAATAAAATATATA
1289766 AATATATGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
54 1 0.01
55 8 0.12
56 5 0.07
57 4 0.06
58 14 0.21
59 15 0.22
60 3 0.04
61 5 0.07
62 11 0.16
63 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (58 bp):
AATTATAATATAATAAAATATATATATAAAATGATTTGATATAAAAATATTTTAAAAT
Found at i:1289768 original size:27 final size:28
Alignment explanation
Indices: 1289702--1289769 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
1289692 ATAAAATATT
*
1289702 AATATATTAA-AATTATTATATATAAAA
1 AATATATAAATAATTATTATATATAAAA
*
1289729 AATATTTTAAAATAATTA-TA-ATATAATAA
1 AATA-TAT-AAATAATTATTATATATAA-AA
1289758 AATATATAAATA
1 AATATATAAATA
1289770 TATGAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 9 0.26
28 10 0.29
29 10 0.29
30 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATATAAATAATTATTATATATAAAA
Found at i:1290053 original size:34 final size:36
Alignment explanation
Indices: 1289987--1290055 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
1289977 ATCAATTATA
1289987 TTAA-AATAAAAAATTTTAAATATTAAATATATAAAT
1 TTAATAATAAAAAATTTTAAATA-TAAATATATAAAT
*
1290023 TTAATAATAAAAAATATTT-AATAAAAATATATA
1 TTAATAATAAAAAAT-TTTAAATATAAATATATA
1290056 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 13 0.43
37 14 0.47
38 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (36 bp):
TTAATAATAAAAAATTTTAAATATAAATATATAAAT
Found at i:1290059 original size:34 final size:36
Alignment explanation
Indices: 1289983--1290061 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 36
1289973 ATCGATCAAT
1289983 TATA-TTAA-AATAAAAAATTTTAAATATTAAATATA
1 TATATTTAATAATAAAAAATTTTAAATA-TAAATATA
*
1290018 TAAATTTAATAATAAAAAATATTT-AATA-AAA-ATA
1 TATATTTAATAATAAAAAAT-TTTAAATATAAATATA
1290052 TATATTTAAT
1 TATATTTAAT
1290062 TAAATAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 12 0.31
35 6 0.15
36 4 0.10
37 14 0.36
38 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
TATATTTAATAATAAAAAATTTTAAATATAAATATA
Found at i:1290071 original size:17 final size:18
Alignment explanation
Indices: 1290008--1290071 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
1289998 AATTTTAAAT
*
1290008 ATTAAATATATAAATTTA
1 ATTAAATATATATATTTA
1290026 ATAATAAA-A-A-ATATTTA
1 AT--TAAATATATATATTTA
*
1290043 A-TAAAAATATATATTTA
1 ATTAAATATATATATTTA
1290060 ATTAAATA-ATAT
1 ATTAAATATATAT
1290072 GATCTTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 1 0.03
17 19 0.50
18 8 0.21
19 1 0.03
20 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAAATATATATATTTA
Found at i:1290956 original size:25 final size:23
Alignment explanation
Indices: 1290925--1290977 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
1290915 TAAATTTAAT
*
1290925 ATATTAAATATAAGATT-TTAAAGTA
1 ATATTAAA-A-AAAATTCTTAAA-TA
1290950 ATATTAAAAAAAATTCTTAAATA
1 ATATTAAAAAAAATTCTTAAATA
1290973 ATATT
1 ATATT
1290978 TACAACTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 12 0.46
24 6 0.23
25 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATTAAAAAAAATTCTTAAATA
Found at i:1291960 original size:21 final size:22
Alignment explanation
Indices: 1291936--1291983 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1291926 TTTTACTTCG
*
1291936 AATTAATTT-AAAAATTAATAT
1 AATTAATTTAAAAAATTAAAAT
*
1291957 AATTATTTTAAAAAATTAAAAT
1 AATTAATTTAAAAAATTAAAAT
1291979 -ATTAA
1 AATTAA
1291984 AAAATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTAATTTAAAAAATTAAAAT
Found at i:1292800 original size:49 final size:48
Alignment explanation
Indices: 1292747--1292839 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
1292737 GGTTCGATAA
*
1292747 TTTATATATATACATAAAAACTTTGTTGGATTCAATAAGAAAAGAATAG
1 TTTATATATATACATAAAAAC-TTGTTGGATTCAACAAGAAAAGAATAG
* * * *
1292796 TTTATGTATGTACATACAAGCTTGTTGGATTCAACAAGAAAAGA
1 TTTATATATATACATAAAAACTTGTTGGATTCAACAAGAAAAGA
1292840 TTATCGAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 22 0.56
49 17 0.44
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (48 bp):
TTTATATATATACATAAAAACTTGTTGGATTCAACAAGAAAAGAATAG
Found at i:1293695 original size:3 final size:3
Alignment explanation
Indices: 1293687--1293712 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1293677 GGATGTTTTC
1293687 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1293713 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1294958 original size:17 final size:16
Alignment explanation
Indices: 1294896--1294992 Score: 57
Period size: 17 Copynumber: 6.2 Consensus size: 16
1294886 AATATTCATA
*
1294896 TTATATTAATAT-ATT
1 TTATATTTATATAATT
*
1294911 TTAT-TGTATCAT-A-T
1 TTATATTTAT-ATAATT
*
1294925 TTATATTTA-ATGTATT
1 TTATATTTATAT-AATT
1294941 TTATAATTTATATAATT
1 TTAT-ATTTATATAATT
1294958 TTAGTATATTA-ATAA-T
1 TTA-TAT-TTATATAATT
1294974 TTAT-TTTATATAAATT
1 TTATATTTATAT-AATT
1294990 TTA
1 TTA
1294993 ATATATATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
13 5 0.08
14 11 0.17
15 14 0.21
16 13 0.20
17 17 0.26
18 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (16 bp):
TTATATTTATATAATT
Found at i:1295174 original size:16 final size:17
Alignment explanation
Indices: 1295145--1295182 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1295135 AATGAAATTA
*
1295145 TAAAATAAATATTTATT
1 TAAATTAAATATTTATT
*
1295162 TAAATTAAA-ATTTTTT
1 TAAATTAAATATTTATT
1295178 TAAAT
1 TAAAT
1295183 ACTTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAAATATTTATT
Found at i:1295611 original size:19 final size:20
Alignment explanation
Indices: 1295578--1295615 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1295568 AAAAATAATT
*
1295578 AAAAGATGAACATAAATATA
1 AAAAGATGAAAATAAATATA
1295598 AAAAGAT-AAAATAAATAT
1 AAAAGATGAAAATAAATAT
1295616 CTCAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAAGATGAAAATAAATATA
Found at i:1295903 original size:18 final size:17
Alignment explanation
Indices: 1295882--1295932 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
1295872 TAAATTTTTT
1295882 ATATAAATTTAATTATAA
1 ATATAAATTTAA-TATAA
*
1295900 ATATATA-TTAATATAA
1 ATATAAATTTAATATAA
*
1295916 AAATAATATTTTAATAT
1 ATATAA-A-TTTAATAT
1295933 TATCATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 9 0.33
17 5 0.19
18 6 0.22
19 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAAATTTAATATAA
Found at i:1295929 original size:19 final size:18
Alignment explanation
Indices: 1295889--1295932 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1295879 TTTATATAAA
*
1295889 TTTAAT-TATAAATATAT
1 TTTAATATAAAAATATAT
*
1295906 ATTAATATAAAAATAATAT
1 TTTAATATAAAAAT-ATAT
1295925 TTTAATAT
1 TTTAATAT
1295933 TATCATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATATAAAAATATAT
Found at i:1302701 original size:78 final size:78
Alignment explanation
Indices: 1302571--1302726 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 78
1302561 TGGTGTAACT
* *
1302571 CCTGATGCCAAGGCATCTATGGCAAGGATTAGGAGATTATCGGAGCCGAAAACAAGCAGCAGCCC
1 CCTGATGCAAAGGCATCTATGGCAAGGATTAGGAGATTATCGGAGCCAAAAACAAGCAGCAGCCC
1302636 ACATGTTTCTTCA
66 ACATGTTTCTTCA
*
1302649 CCTGATGCAAAGGCATC-AGTGGCAAGGATTAGGAGATTATCGGAGCCAAAAACAAGTAGCAGCC
1 CCTGATGCAAAGGCATCTA-TGGCAAGGATTAGGAGATTATCGGAGCCAAAAACAAGCAGCAGCC
1302713 CACATGTTTCTTCA
65 CACATGTTTCTTCA
1302727 GTGAAGTCTC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 1 0.01
78 73 0.99
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (78 bp):
CCTGATGCAAAGGCATCTATGGCAAGGATTAGGAGATTATCGGAGCCAAAAACAAGCAGCAGCCC
ACATGTTTCTTCA
Found at i:1305859 original size:2 final size:2
Alignment explanation
Indices: 1305852--1305878 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1305842 CCATACATAC
1305852 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
1305879 ATGCATATAC
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:1306276 original size:23 final size:22
Alignment explanation
Indices: 1306244--1306287 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1306234 ATATTTTTAT
*
1306244 TTAAATTTAATTATTAAAATATA
1 TTAAAATTAATT-TTAAAATATA
*
1306267 TTAAAATTAATTTTAATATAT
1 TTAAAATTAATTTTAAAATAT
1306288 TTTTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATTAATTTTAAAATATA
Found at i:1306911 original size:31 final size:32
Alignment explanation
Indices: 1306876--1306948 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
1306866 ATTTAAATGA
1306876 ATTTATATTT-AT-AGAATAAAATAATAA-TTTT
1 ATTTATATTTAATCAGAA-AAAAT-ATAATTTTT
* *
1306907 ATTTAAATTTAATCATAAAAAATATAATTTTT
1 ATTTATATTTAATCAGAAAAAATATAATTTTT
*
1306939 ATTAATATTT
1 ATTTATATTT
1306949 TAATATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 13 0.37
32 19 0.54
33 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTTATATTTAATCAGAAAAAATATAATTTTT
Found at i:1309000 original size:24 final size:25
Alignment explanation
Indices: 1308959--1309015 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
1308949 GATATTGATG
1308959 ATTTCTAA-ATTATTAATTAAGACATT
1 ATTT-TAATATTATTAATT-AGACATT
*
1308985 -TTTTAATATTA-TAATTATACATT
1 ATTTTAATATTATTAATTAGACATT
1309008 ATTTTAAT
1 ATTTTAAT
1309016 TTTTTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 6 0.21
24 15 0.54
25 7 0.25
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (25 bp):
ATTTTAATATTATTAATTAGACATT
Found at i:1312549 original size:19 final size:19
Alignment explanation
Indices: 1312517--1312560 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1312507 TACTATTATT
1312517 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
1312536 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
1312555 -AAATTT
1 TAAATTT
1312561 TGATATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 4 0.17
19 14 0.58
20 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:1313000 original size:2 final size:2
Alignment explanation
Indices: 1312993--1313022 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1312983 TTTTCAAATC
1312993 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
1313023 AATACAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1316004 original size:39 final size:37
Alignment explanation
Indices: 1315941--1316047 Score: 101
Period size: 39 Copynumber: 2.8 Consensus size: 37
1315931 ATTTAAAAAA
1315941 ATTAATA-AAAAAT-AAAAATATTAAATAAATAAATTT
1 ATTAATATAAAAATAAAAAAT-TTAAATAAATAAATTT
** *
1315977 ATTAACTATAAAAATAAAATAATTTAAATATTTACATTT
1 ATTAA-TATAAAAATAAAA-AATTTAAATAAATAAATTT
* * *
1316016 ATTATTATATAAATAACAAAAATTTAACTAAA
1 ATTAATATAAAAAT-A-AAAAATTTAAATAAA
1316048 ATATATATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
36 5 0.09
37 2 0.04
38 14 0.25
39 30 0.53
40 6 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (37 bp):
ATTAATATAAAAATAAAAAATTTAAATAAATAAATTT
Found at i:1318028 original size:2 final size:2
Alignment explanation
Indices: 1318021--1318062 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1318011 TGAAGAAATT
1318021 TC TC TC 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 TC TC TC
1318063 ATGTCTCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1319187 original size:13 final size:13
Alignment explanation
Indices: 1319169--1319195 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1319159 AAATAATAAC
1319169 TTAAACAATCATA
1 TTAAACAATCATA
1319182 TTAAACAATCATA
1 TTAAACAATCATA
1319195 T
1 T
1319196 CTTCTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAACAATCATA
Found at i:1320430 original size:20 final size:21
Alignment explanation
Indices: 1320401--1320440 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1320391 CTAATTGAAG
*
1320401 TTTTCTTTAA-TTTTTAAACA
1 TTTTCATTAATTTTTTAAACA
1320421 TTTTCATTAATTTTTTAAAC
1 TTTTCATTAATTTTTTAAAC
1320441 TACTTTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTCATTAATTTTTTAAACA
Found at i:1321911 original size:133 final size:133
Alignment explanation
Indices: 1321647--1321897 Score: 403
Period size: 133 Copynumber: 1.9 Consensus size: 133
1321637 GATGCCAAAG
* * *
1321647 TATGTTTAAGTAATGTACATTTGAAGTTCAAAGACAATATTATGCTATGTTCCTCAAACTCAGGT
1 TATGTTTAAGTAATGTACATTTGAAGTTCAAAGACAATATTATACTATATTCCTCAAACTCAAGT
* * *
1321712 ATGCGTATTAAGTGATACAAGTATGTGTATGATATGAGTATGCTCAATTTTTTTCAGATATATTA
66 ATGAGTATCAAGTGATACAAGTATGTGTATGATATGACTATGCTCAATTTTTTTCAGATATATTA
1321777 TGC
131 TGC
* * *
1321780 TATGTTTAATTAATGTACGTTTGAAGTTCAAAGACAATTTTATACTATATTCCTCAAACTCAAGT
1 TATGTTTAAGTAATGTACATTTGAAGTTCAAAGACAATATTATACTATATTCCTCAAACTCAAGT
* *
1321845 ATGAGTGTCAGGTGATACAAGTATGTGTATGATATGACTATGCTCAATTTTTT
66 ATGAGTATCAAGTGATACAAGTATGTGTATGATATGACTATGCTCAATTTTTT
1321898 CAAGTTTTTT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 107 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (133 bp):
TATGTTTAAGTAATGTACATTTGAAGTTCAAAGACAATATTATACTATATTCCTCAAACTCAAGT
ATGAGTATCAAGTGATACAAGTATGTGTATGATATGACTATGCTCAATTTTTTTCAGATATATTA
TGC
Found at i:1321959 original size:150 final size:150
Alignment explanation
Indices: 1321780--1322070 Score: 404
Period size: 150 Copynumber: 1.9 Consensus size: 150
1321770 TATATTATGC
* *
1321780 TATGTTTAATTAATGTACGTTTGAAGTTCAAAGACAATTTTATACTATATTC-CTCAAACTCAAG
1 TATGTTTAAGTAATGTACGTTTGAAGTTCAAAGACAATTTTATACTAT-GTCACTCAAACTCAAG
* * * ** * *
1321844 TATGAGTGTCAGGTGATACAAGTATGTGTATGATATGACTATGCTCAATTTTTTCAAGTTTTTTT
65 TACGAGTATCAGGTGACACAAGTACATGTACGATATGACTATGCTCAATTTTTTCAAGTTTTTTA
*
1321909 ATGTATTTGCATCAGATAAAG
130 ATGTATATGCATCAGATAAAG
* * * *
1321930 TATGTTTAAGTAATGTACGTTTGAGGTTCAAAGACAGTTTTATGCTATGTCACTCAAACTCAGGT
1 TATGTTTAAGTAATGTACGTTTGAAGTTCAAAGACAATTTTATACTATGTCACTCAAACTCAAGT
* * * *
1321995 ACGAGTATTATGTGACACAAGTACATGTACGATATGAGTATGCTCACTTTTTTCAAGTTTTTTAA
66 ACGAGTATCAGGTGACACAAGTACATGTACGATATGACTATGCTCAATTTTTTCAAGTTTTTTAA
1322060 TGTATATGCAT
131 TGTATATGCAT
1322071 AAGACATATG
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
149 2 0.02
150 120 0.98
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (150 bp):
TATGTTTAAGTAATGTACGTTTGAAGTTCAAAGACAATTTTATACTATGTCACTCAAACTCAAGT
ACGAGTATCAGGTGACACAAGTACATGTACGATATGACTATGCTCAATTTTTTCAAGTTTTTTAA
TGTATATGCATCAGATAAAG
Found at i:1326354 original size:29 final size:28
Alignment explanation
Indices: 1326317--1326381 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
1326307 TGATTATGGT
*
1326317 TTAAAATTTTTTATTAA-ATTTAAATTAA
1 TTAAAATTTATT-TTAATATTTAAATTAA
1326345 TTAATAATTTATTTTAATATTTAAATTTATA
1 TTAA-AATTTATTTTAATATTTAAA-TTA-A
1326376 TTAAAA
1 TTAAAA
1326382 ATATATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.25
29 14 0.44
30 5 0.16
31 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAAATTTATTTTAATATTTAAATTAA
Found at i:1326369 original size:35 final size:35
Alignment explanation
Indices: 1326330--1326402 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1326320 AAATTTTTTA
* *
1326330 TTAAATTTAAATTAATTAATA-ATTTATTTTAATAT
1 TTAAATTTAAATTAA-AAATATATTTATATTAATAT
* *
1326365 TTAAATTTATATTAAAAATATATTTATATTAGTAT
1 TTAAATTTAAATTAAAAATATATTTATATTAATAT
1326400 TTA
1 TTA
1326403 TTATTAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (35 bp):
TTAAATTTAAATTAAAAATATATTTATATTAATAT
Found at i:1326658 original size:18 final size:18
Alignment explanation
Indices: 1326637--1326673 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1326627 CTTTTTTTAA
1326637 TATTTTATTTTAA-AAAAT
1 TATTTTA-TTTAATAAAAT
1326655 TATTTTATTTAATAAAAT
1 TATTTTATTTAATAAAAT
1326673 T
1 T
1326674 TAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTATTTAATAAAAT
Found at i:1326727 original size:19 final size:18
Alignment explanation
Indices: 1326703--1326741 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1326693 TCTCTCTCAA
1326703 ATATATCATTTAATTAAAT
1 ATATATCATTT-ATTAAAT
* *
1326722 ATATATTATTTTTTAAAT
1 ATATATCATTTATTAAAT
1326740 AT
1 AT
1326742 TTATTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATCATTTATTAAAT
Found at i:1329026 original size:26 final size:25
Alignment explanation
Indices: 1328973--1329027 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1328963 TTTCTATGAT
* * *
1328973 TTAAAATTTTATATTTTATTTTAAA
1 TTAAAATTTTAAAATTAATTTTAAA
*
1328998 TTAAAATTTTAAAAATTAATTTTTAA
1 TTAAAATTTT-AAAATTAATTTTAAA
1329024 TTAA
1 TTAA
1329028 GTGTTCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAAAATTTTAAAATTAATTTTAAA
Found at i:1329753 original size:27 final size:25
Alignment explanation
Indices: 1329717--1329766 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
1329707 TAATATTTAT
*
1329717 ATATTTTATAATTAAAATTAAATAAAA
1 ATATTATATAATT-AAA-TAAATAAAA
1329744 ATATTATATAATTAAATAAATAA
1 ATATTATATAATTAAATAAATAA
1329767 TAATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATTATATAATTAAATAAATAAAA
Found at i:1329756 original size:21 final size:21
Alignment explanation
Indices: 1329724--1329781 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1329714 TATATATTTT
*
1329724 ATAATTAAAATTAAATAAA-A
1 ATAATTTAAATTAAATAAATA
1329744 AT-ATTATATAATTAAATAAATA
1 ATAATT-TA-AATTAAATAAATA
1329766 ATAATTTAAATTAAAT
1 ATAATTTAAATTAAAT
1329782 TAATTCGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 19 0.58
22 5 0.15
23 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTTAAATTAAATAAATA
Found at i:1334194 original size:2 final size:2
Alignment explanation
Indices: 1334189--1334213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1334179 ATATATGCAC
1334189 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
1334214 ATAAGTTTAA
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:1334968 original size:23 final size:25
Alignment explanation
Indices: 1334928--1334974 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
1334918 AAAATTTAAA
1334928 TTTTAATATTTATAATTTTTTTTAT
1 TTTTAATATTTATAATTTTTTTTAT
*
1334953 TTTTAA-A-TTATTATTTTTTTTA
1 TTTTAATATTTATAATTTTTTTTA
1334975 AAAAAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTAATATTTATAATTTTTTTTAT
Found at i:1339784 original size:26 final size:28
Alignment explanation
Indices: 1339755--1339807 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1339745 TAATGAAGAT
*
1339755 ATATT-TA-ATTTTTATATATATTTTAA
1 ATATTATATATTTATATATATATTTTAA
*
1339781 ATATTATATATTTATATTTATATTTTA
1 ATATTATATATTTATATATATATTTTA
1339808 TTATATGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 2 0.09
28 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTATATATTTATATATATATTTTAA
Found at i:1339787 original size:18 final size:17
Alignment explanation
Indices: 1339753--1339791 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1339743 TTTAATGAAG
* *
1339753 ATATATTTAATTTTTAT
1 ATATATTTAAATATTAT
1339770 ATATATTTTAAATATTAT
1 ATATA-TTTAAATATTAT
1339788 ATAT
1 ATAT
1339792 TTATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTAAATATTAT
Found at i:1340455 original size:34 final size:33
Alignment explanation
Indices: 1340392--1340455 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
1340382 TAATGAGCAA
* * **
1340392 TTTAAATTTAATAAAATTTTTAAGGTTTAACTT
1 TTTAAATTCAAAAAAATTTTTAAAATTTAACTT
1340425 TTTAAATTCAAAAATAATTTTTAAAATTTAA
1 TTTAAATTCAAAAA-AATTTTTAAAATTTAA
1340456 AAAATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 12 0.46
34 14 0.54
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTAAATTCAAAAAAATTTTTAAAATTTAACTT
Found at i:1340955 original size:29 final size:29
Alignment explanation
Indices: 1340914--1340987 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
1340904 AGTTTATTAA
* *
1340914 TAATTTTTATATTA-T--AGTGATTTTTT
1 TAATTTTTATATTATTAAAGTGAATATTT
* *
1340940 TAATTTTTATATTATTAAATTTAATATTT
1 TAATTTTTATATTATTAAAGTGAATATTT
*
1340969 TAATTTTTATATTTTTAAA
1 TAATTTTTATATTATTAAA
1340988 ATTATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 14 0.35
27 1 0.03
29 25 0.62
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (29 bp):
TAATTTTTATATTATTAAAGTGAATATTT
Found at i:1340984 original size:8 final size:7
Alignment explanation
Indices: 1340936--1340986 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
1340926 TATAGTGATT
1340936 TTTTTAA
1 TTTTTAA
1340943 TTTTTATA
1 TTTTTA-A
*
1340951 TTATTAA
1 TTTTTAA
*
1340958 -ATTTAA
1 TTTTTAA
1340964 TATTTTAA
1 T-TTTTAA
1340972 TTTTTATA
1 TTTTTA-A
1340980 TTTTTAA
1 TTTTTAA
1340987 AATTATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 4 0.11
7 13 0.36
8 19 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTTTAA
Found at i:1340984 original size:15 final size:15
Alignment explanation
Indices: 1340936--1340986 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1340926 TATAGTGATT
1340936 TTTTTAATTTTTATA
1 TTTTTAATTTTTATA
* * *
1340951 TTATTAAATTTAATA
1 TTTTTAATTTTTATA
1340966 -TTTTAATTTTTATA
1 TTTTTAATTTTTATA
1340980 TTTTTAA
1 TTTTTAA
1340987 AATTATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTAATTTTTATA
Found at i:1341716 original size:20 final size:19
Alignment explanation
Indices: 1341670--1341717 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1341660 TAAAAACAAT
1341670 AATAACATAATATAATATGA
1 AATAA-ATAATATAATATGA
*
1341690 AAAAAATAATATAAATATGA
1 AATAAATAATAT-AATATGA
*
1341710 TATAAATA
1 AATAAATA
1341718 TCGATTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAAATAATATAATATGA
Found at i:1343852 original size:19 final size:21
Alignment explanation
Indices: 1343808--1343860 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 21
1343798 TATTTTTACT
1343808 TAAA-TTTAATTATAAAAAATA
1 TAAATTTTAA-TATAAAAAATA
1343829 TAAATTTTAATAT-AAAAATA
1 TAAATTTTAATATAAAAAATA
1343849 -AAATTTTAATAT
1 TAAATTTTAATAT
1343861 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.39
20 7 0.23
21 7 0.23
22 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTTAATATAAAAAATA
Found at i:1345462 original size:9 final size:9
Alignment explanation
Indices: 1345445--1345478 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1345435 ATGATTAATA
*
1345445 ATAAAAAAT
1 ATAATAAAT
1345454 ATAATAAAT
1 ATAATAAAT
1345463 ATAATATAAT
1 ATAATA-AAT
1345473 ATAATA
1 ATAATA
1345479 TATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAATAAAT
Found at i:1345467 original size:24 final size:24
Alignment explanation
Indices: 1345423--1345468 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1345413 AAATTATATA
* *
1345423 AAAAAATATGATATGATTAATAAT
1 AAAAAATATAATATAATTAATAAT
1345447 AAAAAATATAATA-AATATAATA
1 AAAAAATATAATATAAT-TAATA
1345469 TAATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAAATATAATATAATTAATAAT
Found at i:1345468 original size:5 final size:5
Alignment explanation
Indices: 1345451--1345480 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1345441 AATAATAAAA
1345451 AATAT AATA- AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A
1345481 TTTAAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:1346534 original size:12 final size:13
Alignment explanation
Indices: 1346517--1346552 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1346507 ATATAATTAT
1346517 TATATAATAA-AA
1 TATATAATAATAA
1346529 TATATAA-AATAA
1 TATATAATAATAA
1346541 TATA-AATAATAA
1 TATATAATAATAA
1346553 ATTAGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATATAATAATAA
Found at i:1346542 original size:17 final size:17
Alignment explanation
Indices: 1346520--1346553 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1346510 TAATTATTAT
1346520 ATAATA-AAATATATAAA
1 ATAATATAAATA-ATAAA
1346537 ATAATATAAATAATAAA
1 ATAATATAAATAATAAA
1346554 TTAGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAATATAAATAATAAA
Found at i:1346660 original size:15 final size:16
Alignment explanation
Indices: 1346630--1346662 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1346620 AAAAATTTTA
1346630 TTAAATAAATAATAAT
1 TTAAATAAATAATAAT
*
1346646 TTAAATCAA-AATAAT
1 TTAAATAAATAATAAT
1346661 TT
1 TT
1346663 GTATTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATAAATAATAAT
Found at i:1347576 original size:24 final size:22
Alignment explanation
Indices: 1347549--1347596 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1347539 TATAAATTTT
*
1347549 TATGTATTAATAATTTGTTATATA
1 TATGTATTAAT-ATTT-TCATATA
*
1347573 TATGTATTGATATTTTCATATA
1 TATGTATTAATATTTTCATATA
1347595 TA
1 TA
1347597 GAGAAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 4 0.18
24 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (22 bp):
TATGTATTAATATTTTCATATA
Found at i:1348694 original size:17 final size:18
Alignment explanation
Indices: 1348674--1348707 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1348664 TTTATTTTAA
1348674 AATT-TTTTTATCAAATC
1 AATTATTTTTATCAAATC
*
1348691 AATTATTTTTATGAAAT
1 AATTATTTTTATCAAAT
1348708 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTATTTTTATCAAATC
Found at i:1350503 original size:12 final size:12
Alignment explanation
Indices: 1350486--1350512 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1350476 GACAGGCACA
1350486 TATGAAATTAGG
1 TATGAAATTAGG
1350498 TATGAAATTAGG
1 TATGAAATTAGG
1350510 TAT
1 TAT
1350513 AACAACTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (12 bp):
TATGAAATTAGG
Found at i:1354364 original size:28 final size:27
Alignment explanation
Indices: 1354323--1354376 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1354313 TTAAATTATA
1354323 TTAATATAAAATTATATTATTTT-ATAAT
1 TTAATATAAAATTA-A-TATTTTGATAAT
**
1354351 TTAATATATGATTAATATTTTGATAA
1 TTAATATAAAATTAATATTTTGATAA
1354377 ATTGATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 5 0.22
28 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTAATATAAAATTAATATTTTGATAAT
Found at i:1354893 original size:13 final size:13
Alignment explanation
Indices: 1354865--1354907 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1354855 TAAAAAAATT
1354865 ATTAAATTACTAAAA
1 ATTAAATT--TAAAA
1354880 ATTAAATTTAAAA
1 ATTAAATTTAAAA
*
1354893 AATAAATTTAAAA
1 ATTAAATTTAAAA
1354906 AT
1 AT
1354908 ATAATATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 18 0.69
15 8 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTAAATTTAAAA
Found at i:1354895 original size:14 final size:13
Alignment explanation
Indices: 1354875--1354911 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1354865 ATTAAATTAC
*
1354875 TAAAAATTAAATT
1 TAAAAAATAAATT
1354888 TAAAAAATAAATT
1 TAAAAAATAAATT
1354901 TAAAAATATAA
1 TAAAAA-ATAA
1354912 TATGAGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAATAAATT
Found at i:1355298 original size:18 final size:18
Alignment explanation
Indices: 1355277--1355315 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1355267 CCTATATATA
* *
1355277 TATATATATATATACATT
1 TATATATATACATAAATT
*
1355295 TATATGTATACATAAATT
1 TATATATATACATAAATT
1355313 TAT
1 TAT
1355316 TTATTAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
TATATATATACATAAATT
Found at i:1355305 original size:14 final size:14
Alignment explanation
Indices: 1355269--1355307 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1355259 ATCAAACACC
* *
1355269 TATATATATATATA
1 TATATATACATTTA
1355283 TATATATACATTTA
1 TATATATACATTTA
*
1355297 TATGTATACAT
1 TATATATACAT
1355308 AAATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATATACATTTA
Found at i:1356645 original size:2 final size:2
Alignment explanation
Indices: 1356638--1356669 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1356628 AATTGTTAGA
1356638 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 A
1356670 GTGTTATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1357581 original size:17 final size:18
Alignment explanation
Indices: 1357559--1357595 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1357549 CTATCGAACT
*
1357559 AACCTAAAC-TAATTTTA
1 AACCTAAACTTAAATTTA
1357576 AACCTAAACTTAAATTTA
1 AACCTAAACTTAAATTTA
1357594 AA
1 AA
1357596 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (18 bp):
AACCTAAACTTAAATTTA
Found at i:1358116 original size:27 final size:27
Alignment explanation
Indices: 1358086--1358168 Score: 76
Period size: 32 Copynumber: 2.9 Consensus size: 27
1358076 TATAATTATA
*
1358086 TTTAAAATATTATATATTTATATAATT
1 TTTAAAATATTATATATTTATATAAAT
** *
1358113 TTTAATATAATAACAATTTATATTATATAAAT
1 TTT-A-A-AAT-ATTATATAT-TTATATAAAT
1358145 TTTAAAATATTTATATATTTATAT
1 TTTAAAATA-TTATATATTTATAT
1358169 TATATTAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
27 3 0.07
28 8 0.19
29 9 0.21
30 4 0.09
31 7 0.16
32 12 0.28
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAAAATATTATATATTTATATAAAT
Found at i:1358146 original size:33 final size:34
Alignment explanation
Indices: 1358092--1358177 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
1358082 TATATTTAAA
*
1358092 ATATTATATATT-TATATAATTTTTAATATAATAAC
1 ATATT-TATATTATATATAA-TTTTAAAATAATAAC
* * *
1358127 A-ATTTATATTATATA-AATTTTAAAATATTTAT
1 ATATTTATATTATATATAATTTTAAAATAATAAC
1358159 ATATTTATATTATAT-TAAT
1 ATATTTATATTATATATAAT
1358178 ACTTTATTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 12 0.27
33 24 0.55
34 7 0.16
35 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (34 bp):
ATATTTATATTATATATAATTTTAAAATAATAAC
Found at i:1358176 original size:27 final size:26
Alignment explanation
Indices: 1358082--1358176 Score: 63
Period size: 27 Copynumber: 3.7 Consensus size: 26
1358072 GCGTTATAAT
* *
1358082 TATATTTA-AAATATT-ATATATTTA
1 TATATTTATATATATTAAAATATTTA
* * *
1358106 TATAATTTTTAATATAATAACA-ATTTA
1 TAT-ATTTAT-ATATATTAAAATATTTA
* * *
1358133 TAT-TATATAAATTTTAAAATATTTA
1 TATATTTATATATATTAAAATATTTA
1358158 TATATTTATATTATATTAA
1 TATATTTATA-TATATTAA
1358177 TACTTTATTC
Statistics
Matches: 51, Mismatches: 13, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
24 10 0.20
25 15 0.29
26 5 0.10
27 19 0.37
28 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATTTATATATATTAAAATATTTA
Found at i:1359193 original size:19 final size:18
Alignment explanation
Indices: 1359171--1359226 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1359161 ATAATCATTT
1359171 ATATTATATATATTTTAAA
1 ATATTATATATA-TTTAAA
*
1359190 ATATT-T-TATATTTATA
1 ATATTATATATATTTAAA
*
1359206 TTATTATATCATATTTAAA
1 ATATTATAT-ATATTTAAA
1359225 AT
1 AT
1359227 TAACTAACAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 2 0.07
19 14 0.47
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTATATATATTTAAA
Found at i:1359199 original size:36 final size:35
Alignment explanation
Indices: 1359153--1359226 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
1359143 ATAAAATATT
*
1359153 AATATATTATAATCATTTATATTATAT-ATATTTTAA
1 AATATATTATAATCATAT-TATTATATCATA-TTTAA
* * *
1359189 AATATTTTATATTTATATTATTATATCATATTTAA
1 AATATATTATAATCATATTATTATATCATATTTAA
1359224 AAT
1 AAT
1359227 TAACTAACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 16 0.48
36 17 0.52
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (35 bp):
AATATATTATAATCATATTATTATATCATATTTAA
Found at i:1359221 original size:26 final size:26
Alignment explanation
Indices: 1359098--1359213 Score: 75
Period size: 26 Copynumber: 4.6 Consensus size: 26
1359088 TAGACACCCA
* * *
1359098 ATTAAATAAATTATAAAATATTTTAAA
1 ATTATATATATTATAAAATATTTT-AT
* * **
1359125 AATATATTTATTTATAAAATA--AAAT
1 ATTATATATA-TTATAAAATATTTTAT
1359150 ATTA-ATATATTAT--AATCA-TTTAT
1 ATTATATATATTATAAAAT-ATTTTAT
*
1359173 ATTATATATATTTTAAAATATTTTAT
1 ATTATATATATTATAAAATATTTTAT
1359199 ATT-TATATTATTATA
1 ATTATATA-TATTATA
1359214 TCATATTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
21 3 0.04
22 1 0.01
23 10 0.15
24 12 0.18
25 9 0.13
26 17 0.25
27 6 0.09
28 10 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATATATATTATAAAATATTTTAT
Found at i:1359393 original size:18 final size:18
Alignment explanation
Indices: 1359370--1359447 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 18
1359360 TATGTAATTA
1359370 TATTATATTTATATATTT
1 TATTATATTTATATATTT
1359388 TATTATA-TTATA-ATTT
1 TATTATATTTATATATTT
1359404 TATTTAAAATATTATATATATTT
1 TA-TT---ATATT-TATATATTT
*
1359427 T-TTATATATTA-ATAATT
1 TATTATAT-TTATATATTT
1359444 TATT
1 TATT
1359448 TTAAATAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
16 6 0.12
17 13 0.26
18 15 0.30
19 1 0.02
20 3 0.06
21 3 0.06
22 4 0.08
23 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATATTTATATATTT
Done.