Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 8 of 25
Found at i:1088806 original size:11 final size:11
Alignment explanation
Indices: 1088764--1088812 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
1088754 ATATTTTTTA
1088764 TTTTATATTTAT
1 TTTTATA-TTAT
1088776 ATTTTATA-TAT
1 -TTTTATATTAT
1088787 TTTTA-ATTAT
1 TTTTATATTAT
1088797 TTTTATATTAT
1 TTTTATATTAT
*
1088808 ATTTA
1 TTTTA
1088813 AAATTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 1 0.03
10 13 0.39
11 12 0.36
13 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:1089616 original size:23 final size:23
Alignment explanation
Indices: 1089569--1089615 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1089559 CAAATACCCC
* *
1089569 TTAATTTATTTTTTACTATTATT
1 TTAATTTAATTTTTACTATAATT
1089592 TTAATTTAATTTTTA-TATAATT
1 TTAATTTAATTTTTACTATAATT
1089614 TT
1 TT
1089616 TTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTAATTTAATTTTTACTATAATT
Found at i:1092448 original size:14 final size:15
Alignment explanation
Indices: 1092431--1092459 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1092421 TAAATATATT
1092431 TTTATTAT-ATTATA
1 TTTATTATAATTATA
1092445 TTTATTATAATTATA
1 TTTATTATAATTATA
1092460 AATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATAATTATA
Found at i:1092519 original size:26 final size:25
Alignment explanation
Indices: 1092465--1092521 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
1092455 TTATAAATAT
* * *
1092465 AATAAATATTATTATAAATAATTAT
1 AATAAATATGATTATAAATAATAAA
1092490 AATAAATATAGATTATAAAT-ATCAAA
1 AATAAATAT-GATTATAAATAAT-AAA
1092516 AATAAA
1 AATAAA
1092522 AAATTAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAATATGATTATAAATAATAAA
Found at i:1094379 original size:21 final size:21
Alignment explanation
Indices: 1094355--1094420 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1094345 CAAAGTCACA
1094355 TATAAATTAATATATTTATAT
1 TATAAATTAATATATTTATAT
**
1094376 TATATTTTAAT-TATTTTATAT
1 TATAAATTAATATA-TTTATAT
* *
1094397 TAT--ATTTATATAATTATAT
1 TATAAATTAATATATTTATAT
1094416 TATAA
1 TATAA
1094421 TATATTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 13 0.36
20 4 0.11
21 19 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATAAATTAATATATTTATAT
Found at i:1094380 original size:5 final size:5
Alignment explanation
Indices: 1094365--1094426 Score: 56
Period size: 5 Copynumber: 12.2 Consensus size: 5
1094355 TATAAATTAA
* *
1094365 TATATT TATAT TATAT TTTAAT TATTT TATAT TATAT T-TA- TATAAT
1 TATA-T TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TAT-AT
*
1094411 TATAT TATAA TATAT T
1 TATAT TATAT TATAT T
1094427 TAAAATTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
3 1 0.02
4 3 0.07
5 31 0.67
6 11 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:1094381 original size:11 final size:11
Alignment explanation
Indices: 1094365--1094428 Score: 69
Period size: 11 Copynumber: 5.7 Consensus size: 11
1094355 TATAAATTAA
1094365 TATATTTATAT
1 TATATTTATAT
1094376 TATATTT-TAAT
1 TATATTTAT-AT
1094387 TAT-TTTATAT
1 TATATTTATAT
1094397 TATATTTATAT
1 TATATTTATAT
* *
1094408 AATTATATTATAA
1 TA-TAT-TTATAT
1094421 TATATTTA
1 TATATTTA
1094429 AAATTTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 9 0.20
11 24 0.53
12 6 0.13
13 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1094389 original size:16 final size:16
Alignment explanation
Indices: 1094365--1094450 Score: 63
Period size: 16 Copynumber: 5.6 Consensus size: 16
1094355 TATAAATTAA
*
1094365 TATATTTATATTATAT
1 TATAATTATATTATAT
* *
1094381 TTTAATTATTTTATAT
1 TATAATTATATTATAT
*
1094397 TATATTTATA-TA-AT
1 TATAATTATATTATAT
*
1094411 TAT-ATTATAATATATT
1 TATAATTATATTATA-T
* *
1094427 TAAAATT-TATTAAAT
1 TATAATTATATTATAT
*
1094442 TAAAATTAT
1 TATAATTAT
1094451 CGCGTCATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
13 5 0.09
14 7 0.13
15 11 0.20
16 29 0.53
17 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAATTATATTATAT
Found at i:1094414 original size:14 final size:12
Alignment explanation
Indices: 1094364--1094416 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
1094354 ATATAAATTA
1094364 ATATATTTATATT
1 ATAT-TTTATATT
1094377 ATATTTTA-A-T
1 ATATTTTATATT
1094387 -TATTTTATATT
1 ATATTTTATATT
1094398 ATATTTATATAATT
1 ATATTT-TAT-ATT
1094412 ATATT
1 ATATT
1094417 ATAATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 2 0.06
12 9 0.26
13 7 0.20
14 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:1094634 original size:21 final size:21
Alignment explanation
Indices: 1094608--1094678 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1094598 GCACCTGAGT
1094608 TAATTTAAATAAATTTATTTA
1 TAATTTAAATAAATTTATTTA
* * *
1094629 TAATTTAAGTTAAGTTATTT-
1 TAATTTAAATAAATTTATTTA
*
1094649 TATATAATAAA-AAATTTTATTTA
1 TA-AT-TTAAATAAA-TTTATTTA
1094672 -AATTTAA
1 TAATTTAA
1094679 TTATAAATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 5 0.13
21 23 0.61
22 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAATTTAAATAAATTTATTTA
Found at i:1095377 original size:20 final size:20
Alignment explanation
Indices: 1095340--1095378 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1095330 TACAAAATAC
*
1095340 TATTAAATTCAAAAAATATA
1 TATTAAAATCAAAAAATATA
1095360 TATTAAAAT-AAAATAATAT
1 TATTAAAATCAAAA-AATAT
1095379 CAATACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTAAAATCAAAAAATATA
Found at i:1096249 original size:30 final size:31
Alignment explanation
Indices: 1096181--1096258 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
1096171 TAAAAGTAAG
1096181 TTTAAAATTT-AATTTAATTAATTTATATAA
1 TTTAAAATTTAAATTTAATTAATTTATATAA
*
1096211 -TAAAAATTTAAATTATAA-T-ATTTA-ATAAA
1 TTTAAAATTTAAATT-TAATTAATTTATAT-AA
1096240 TTTAAAATTTAAATCTTAA
1 TTTAAAATTTAAAT-TTAA
1096259 CATATTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 2 0.05
29 15 0.37
30 20 0.49
31 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTAAAATTTAAATTTAATTAATTTATATAA
Found at i:1096258 original size:23 final size:24
Alignment explanation
Indices: 1096214--1096267 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
1096204 TATATAATAA
*
1096214 AAATTT-AAATTATAATATTTAAT
1 AAATTTAAAATTATAATATTTAAC
1096237 AAATTTAAAATT-TAA-ATCTTAAC
1 AAATTTAAAATTATAATAT-TTAAC
*
1096260 ATATTTAA
1 AAATTTAA
1096268 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 20 0.74
24 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATTTAAAATTATAATATTTAAC
Found at i:1096911 original size:19 final size:20
Alignment explanation
Indices: 1096873--1096910 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1096863 AATATGATGA
*
1096873 CTTTTTTTTCTATTTATTTT
1 CTTTTTTATCTATTTATTTT
1096893 CTTTTTTAT-TATTT-TTTT
1 CTTTTTTATCTATTTATTTT
1096911 TATTTGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTTTTATCTATTTATTTT
Found at i:1097997 original size:37 final size:36
Alignment explanation
Indices: 1097950--1098132 Score: 129
Period size: 34 Copynumber: 5.2 Consensus size: 36
1097940 TTATTTTTAT
*
1097950 TAATTTTTAATATAATCTTAATTAGTATTTAG-TAAATA
1 TAATTTTTAATAT-ATATT--TTAGTATTTAGATAAATA
*
1097988 TAA-TTTTAATATATATTTTATTATTTAGTATAAATA
1 TAATTTTTAATATATATTTTAGTATTTAG-ATAAATA
* *
1098024 TAATTTTTAATA-A-ATTATT--T-TTAATATAAATA
1 TAATTTTTAATATATATT-TTAGTATTTAGATAAATA
*
1098056 TAA-TTTTAATA-AT-TTGTAGTTATTTA-ATAAAATA
1 TAATTTTTAATATATATTTTAG-TATTTAGAT-AAATA
* * * *
1098090 TCA-TTTTAATTTATATTTTATTATTTAATATAAATA
1 TAATTTTTAATATATATTTTAGTATTT-AGATAAATA
1098126 TAATTTT
1 TAATTTT
1098133 AATGATTATT
Statistics
Matches: 119, Mismatches: 11, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
30 1 0.01
31 11 0.09
32 10 0.08
33 6 0.05
34 28 0.24
35 10 0.08
36 28 0.24
37 22 0.18
38 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATTTTTAATATATATTTTAGTATTTAGATAAATA
Found at i:1098124 original size:70 final size:68
Alignment explanation
Indices: 1097982--1098135 Score: 190
Period size: 70 Copynumber: 2.2 Consensus size: 68
1097972 TAGTATTTAG
* *
1097982 TAAATATAATTTTAATATATATTTTATTATTTAGTATAAATATAATTTTTAATAAATTATTTTTA
1 TAAATATAATTTTAATATATATTGTATTATTTAATATAAATATAATTTTTAATAAATTATTTTTA
1098047 ATA
66 ATA
* *
1098050 TAAATATAATTTTAATA-AT-TTGTAGTTATTTAATA-AAATATCA-TTTTAATTTATATTTTAT
1 TAAATATAATTTTAATATATATTGTA-TTATTTAATATAAATATAATTTTTAA--TA-A-ATTAT
1098111 TATTTAATA
61 T-TTTAATA
1098120 TAAATATAATTTTAAT
1 TAAATATAATTTTAAT
1098136 GATTATTTGG
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
65 6 0.08
66 11 0.14
67 13 0.17
68 18 0.24
69 5 0.07
70 23 0.30
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (68 bp):
TAAATATAATTTTAATATATATTGTATTATTTAATATAAATATAATTTTTAATAAATTATTTTTA
ATA
Found at i:1098130 original size:30 final size:31
Alignment explanation
Indices: 1098000--1098131 Score: 115
Period size: 35 Copynumber: 4.0 Consensus size: 31
1097990 ATTTTAATAT
*
1098000 ATATTTTATTATTTAGTATAAATATAATTTTTA
1 ATATTTTATTATTTAATATAAATATAA--TTTA
**
1098033 ATAAATTATT-TTTAATATAAATATAATTTTA
1 ATATTTTATTATTTAATATAAATATAA-TTTA
*
1098064 ATAATTTGTAGTTATTTAATA-AAATATCATTTTAA
1 AT-ATTT-TA-TTATTTAATATAAATAT-AATTT-A
1098099 TTTATATTTTATTATTTAATATAAATATAATTT
1 ---ATATTTTATTATTTAATATAAATATAATTT
1098132 TAATGATTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
31 7 0.09
32 17 0.21
33 10 0.12
34 11 0.13
35 23 0.28
36 8 0.10
37 4 0.05
38 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (31 bp):
ATATTTTATTATTTAATATAAATATAATTTA
Found at i:1100476 original size:12 final size:12
Alignment explanation
Indices: 1100459--1100490 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1100449 TATTATTTTA
1100459 TAATTAAAAAAT
1 TAATTAAAAAAT
1100471 TAATT-AAAAAT
1 TAATTAAAAAAT
1100482 TAA-TAAAAA
1 TAATTAAAAA
1100491 CAAATAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 13 0.68
12 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAATTAAAAAAT
Found at i:1100843 original size:22 final size:19
Alignment explanation
Indices: 1100802--1100844 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
1100792 TTTTTTAATG
*
1100802 TATTTATAAAATTTAAAAA
1 TATTTATAAAATATAAAAA
1100821 TATTATATATAAATATATAAAA
1 TATT-TATA-AAATATA-AAAA
1100843 TA
1 TA
1100845 CGAAGTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 6 0.30
22 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTTATAAAATATAAAAA
Found at i:1101026 original size:16 final size:16
Alignment explanation
Indices: 1101002--1101041 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1100992 ATATTTTTAT
*
1101002 TAATAAAATAAAATTA
1 TAATTAAATAAAATTA
*
1101018 TAATTAAATCAAATTA
1 TAATTAAATAAAATTA
1101034 -AATTAAAT
1 TAATTAAAT
1101042 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAAATAAAATTA
Found at i:1101036 original size:21 final size:20
Alignment explanation
Indices: 1101007--1101053 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1100997 TTTATTAATA
1101007 AAATAAAATTATAA-TTAAAT
1 AAATAAAATTA-AATTTAAAT
*
1101027 CAAATTAAATTAAATTTAAAT
1 -AAATAAAATTAAATTTAAAT
1101048 AAATAA
1 AAATAA
1101054 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAATTAAATTTAAAT
Found at i:1102002 original size:22 final size:22
Alignment explanation
Indices: 1101974--1102019 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1101964 TGTACAAGCT
1101974 TTTACTCATTTACAGGATTCCA
1 TTTACTCATTTACAGGATTCCA
1101996 TTTACTCATTTACAGGATTCCA
1 TTTACTCATTTACAGGATTCCA
1102018 TT
1 TT
1102020 ATGTTTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTACTCATTTACAGGATTCCA
Found at i:1102433 original size:2 final size:2
Alignment explanation
Indices: 1102426--1102451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1102416 AATTTTAGAC
1102426 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
1102452 TTTCTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1107804 original size:33 final size:33
Alignment explanation
Indices: 1107767--1107833 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1107757 TTCAACGATT
1107767 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1107800 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1107833 T
1 T
1107834 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1107805 original size:13 final size:13
Alignment explanation
Indices: 1107787--1107811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1107777 CATAAAATGT
1107787 TGTATCGATACAA
1 TGTATCGATACAA
1107800 TGTATCGATACA
1 TGTATCGATACA
1107812 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1107890 original size:13 final size:13
Alignment explanation
Indices: 1107872--1107898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1107862 ACATTACTCA
1107872 AATGTATCGATAC
1 AATGTATCGATAC
1107885 AATGTATCGATAC
1 AATGTATCGATAC
1107898 A
1 A
1107899 CCGATCTTTG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1107948 original size:32 final size:32
Alignment explanation
Indices: 1107907--1107987 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 32
1107897 CACCGATCTT
* *
1107907 TGTATCGATACATGCAGGCAAATTTGCGCAGA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGA
1107939 TGTATCGATACATTTCATGCAGGCAAATCTGCCCAGA
1 TGTATCGAT--A---CATGCAGGCAAATCTGCCCAGA
1107976 TGTATCGATACA
1 TGTATCGATACA
1107988 CTATTAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
32 11 0.26
34 1 0.02
35 1 0.02
37 29 0.69
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (32 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGA
Found at i:1107976 original size:37 final size:37
Alignment explanation
Indices: 1107917--1107987 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1107907 TGTATCGATA
* *
1107917 CATGCAGGCAAATTTGCGCAGATGTATCGATACATTT
1 CATGCAGGCAAATCTGCCCAGATGTATCGATACATTT
1107954 CATGCAGGCAAATCTGCCCAGATGTATCGATACA
1 CATGCAGGCAAATCTGCCCAGATGTATCGATACA
1107988 CTATTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (37 bp):
CATGCAGGCAAATCTGCCCAGATGTATCGATACATTT
Found at i:1113790 original size:129 final size:129
Alignment explanation
Indices: 1113560--1113819 Score: 414
Period size: 129 Copynumber: 2.0 Consensus size: 129
1113550 CCCTGCTAAC
* *
1113560 ATTTATAATTATGCTGCAATGAGATCTATACTAGAAAAATACTGTAAAGGGCTAGGACAACTTGT
1 ATTTATAATTATGCTGCAATGAGATCTATACTAGAAAAATACTATAAAGGGCGAGGACAACTTGT
*
1113625 GAATTTGCAAAAGTCCAATATTATTTTCAGTAAGAATATGCCAAATCAAGTCAAGTAGAAAGTG
66 GAATTTGCAAAAGTCCAATATTATTTTCAGCAAGAATATGCCAAATCAAGTCAAGTAGAAAGTG
* * **
1113689 ATTTATAATTGTGCTGCAATGAGATCTATACTGGAAAAATACTATAGGGGGCCGA-GACAACTTG
1 ATTTATAATTATGCTGCAATGAGATCTATACTAGAAAAATACTATAAAGGG-CGAGGACAACTTG
* * *
1113753 TGAATTTGCAAAAGTTCAATATTGTTTTCAGCAAGAATATGCCAAATCAAGTTAAGTAGAAAGTG
65 TGAATTTGCAAAAGTCCAATATTATTTTCAGCAAGAATATGCCAAATCAAGTCAAGTAGAAAGTG
1113818 AT
1 AT
1113820 AGAACTGATG
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
129 118 0.98
130 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (129 bp):
ATTTATAATTATGCTGCAATGAGATCTATACTAGAAAAATACTATAAAGGGCGAGGACAACTTGT
GAATTTGCAAAAGTCCAATATTATTTTCAGCAAGAATATGCCAAATCAAGTCAAGTAGAAAGTG
Found at i:1117387 original size:20 final size:20
Alignment explanation
Indices: 1117362--1117408 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1117352 GTGATTTAAA
*
1117362 GCTTGAAAAGAATTTGTTGT
1 GCTTGAAAAGAATTTGTTAT
*
1117382 GCTTGAAAAGAGTTTGTTAT
1 GCTTGAAAAGAATTTGTTAT
1117402 GCTTGAA
1 GCTTGAA
1117409 CTTGATGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (20 bp):
GCTTGAAAAGAATTTGTTAT
Found at i:1125886 original size:50 final size:47
Alignment explanation
Indices: 1125794--1125887 Score: 109
Period size: 50 Copynumber: 1.9 Consensus size: 47
1125784 ATACAATGTA
* * *
1125794 ATACTATATGATATATATTATAATATATCATATTAAGTAATTATATT
1 ATACTATATCATATATATTATAATATATCATAATAAGCAATTATATT
*
1125841 ATACTATATCATATATTTATTTATAATATATGATTAATAA-CAATTAT
1 ATACTATATCATATA--TA-TTATAATATATCA-TAATAAGCAATTAT
1125888 GTTGTATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
47 14 0.36
49 2 0.05
50 18 0.46
51 5 0.13
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (47 bp):
ATACTATATCATATATATTATAATATATCATAATAAGCAATTATATT
Found at i:1125969 original size:25 final size:24
Alignment explanation
Indices: 1125934--1125987 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1125924 GACCTTATAA
* *
1125934 AATTAATATATATTTTATGTTACT
1 AATTAATATATACTTTATGCTACT
*
1125958 ATATTACTATATACTTTATGCTACT
1 A-ATTAATATATACTTTATGCTACT
1125983 AATTA
1 AATTA
1125988 TTTTTAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (24 bp):
AATTAATATATACTTTATGCTACT
Found at i:1126844 original size:16 final size:15
Alignment explanation
Indices: 1126775--1126844 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
1126765 GTGTTTCAAA
1126775 TTTTTTAAATTTGAAT
1 TTTTTTAAATTT-AAT
**
1126791 CATTTTAAATTTAAT
1 TTTTTTAAATTTAAT
* *
1126806 TTATTATAAACTTAGAT
1 TT-TTTTAAATTTA-AT
**
1126823 AATTTTAAATTTTAAT
1 TTTTTTAAA-TTTAAT
1126839 TTTTTT
1 TTTTTT
1126845 TACTTTTTGA
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.08
16 31 0.79
17 5 0.13
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTTTTAAATTTAAT
Found at i:1127584 original size:47 final size:47
Alignment explanation
Indices: 1127530--1127643 Score: 210
Period size: 47 Copynumber: 2.4 Consensus size: 47
1127520 GAAGAGTAAG
* *
1127530 TAACTAGCATTCACAAAAAGGTATAGAAATGATACTAAGATTAGGAC
1 TAACTAGCATTCACTAAAAGGTACAGAAATGATACTAAGATTAGGAC
1127577 TAACTAGCATTCACTAAAAGGTACAGAAATGATACTAAGATTAGGAC
1 TAACTAGCATTCACTAAAAGGTACAGAAATGATACTAAGATTAGGAC
1127624 TAACTAGCATTCACTAAAAG
1 TAACTAGCATTCACTAAAAG
1127644 ACTGCGTTGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.24
Consensus pattern (47 bp):
TAACTAGCATTCACTAAAAGGTACAGAAATGATACTAAGATTAGGAC
Found at i:1129609 original size:81 final size:81
Alignment explanation
Indices: 1129475--1129657 Score: 350
Period size: 81 Copynumber: 2.3 Consensus size: 81
1129465 GGAAATTGCC
1129475 CATAAAGATTCCCCATGTACCGCATGTTATCATATTACCATCCATATAGCTACTACTACATTTAT
1 CATAAAGATTCCCCATGTACCGCATGTTATCATATTACCATCCATATAGCTACTACTACATTTAT
1129540 CAAGGAAGAGAAGAAG
66 CAAGGAAGAGAAGAAG
1129556 CATAAAGATTCCCCATGTACCGCATGTTATCATATTACCATCCATATAGCTACTACTACATTTAT
1 CATAAAGATTCCCCATGTACCGCATGTTATCATATTACCATCCATATAGCTACTACTACATTTAT
1129621 CAAGGAAGAGAAGAAG
66 CAAGGAAGAGAAGAAG
1129637 CATAAAGATT-CCCAGTGTACC
1 CATAAAGATTCCCCA-TGTACC
1129658 ACATTTTTGT
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
80 4 0.04
81 97 0.96
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (81 bp):
CATAAAGATTCCCCATGTACCGCATGTTATCATATTACCATCCATATAGCTACTACTACATTTAT
CAAGGAAGAGAAGAAG
Found at i:1139287 original size:17 final size:18
Alignment explanation
Indices: 1139244--1139284 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1139234 AAAACAAGAT
1139244 AAAAAATCTTTAAAATAA
1 AAAAAATCTTTAAAATAA
*
1139262 AAAAAATCTTTAAAGTAA
1 AAAAAATCTTTAAAATAA
1139280 AAAAA
1 AAAAA
1139285 TCTGAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAATCTTTAAAATAA
Found at i:1139991 original size:18 final size:18
Alignment explanation
Indices: 1139942--1139994 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
1139932 ATAAAAATAA
*
1139942 TTTTATA-AATA-TATAT
1 TTTTATATAATATTTTAT
* *
1139958 TTTTATTTTATATTTTAT
1 TTTTATATAATATTTTAT
*
1139976 TTTTATATAATTTTTTAT
1 TTTTATATAATATTTTAT
1139994 T
1 T
1139995 AAATGTTACG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 6 0.21
17 3 0.10
18 20 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATAATATTTTAT
Found at i:1141268 original size:18 final size:19
Alignment explanation
Indices: 1141245--1141283 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
1141235 GAGATAAGAT
1141245 AATTTATTTAA-ATTTAAA
1 AATTTATTTAATATTTAAA
1141263 AATTTATTTAATATTTAAA
1 AATTTATTTAATATTTAAA
1141282 AA
1 AA
1141284 GATTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTATTTAATATTTAAA
Found at i:1141291 original size:19 final size:18
Alignment explanation
Indices: 1141248--1141283 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1141238 ATAAGATAAT
*
1141248 TTATTTAAATTTAAAAAT
1 TTATTTAAATTTAAAAAA
1141266 TTATTTAATATTTAAAAA
1 TTATTTAA-ATTTAAAAA
1141284 GATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTTAAATTTAAAAAA
Found at i:1142107 original size:17 final size:16
Alignment explanation
Indices: 1142077--1142111 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1142067 TAAAAATATA
1142077 ATATTAAATATTAAAT
1 ATATTAAATATTAAAT
*
1142093 ATATTAAAATTTTAAAT
1 ATATT-AAATATTAAAT
1142110 AT
1 AT
1142112 TAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAATATTAAAT
Found at i:1142173 original size:24 final size:24
Alignment explanation
Indices: 1142128--1142173 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1142118 AATATGTTTT
*
1142128 TATTAAATATATTATATTTAATGA
1 TATTAAATATATTATATGTAATGA
*
1142152 TATTAATTATATT-TATCGTAAT
1 TATTAAATATATTATAT-GTAAT
1142174 TAAATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
TATTAAATATATTATATGTAATGA
Found at i:1142450 original size:3 final size:3
Alignment explanation
Indices: 1142444--1142485 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1142434 AAAAAACATA
1142444 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1142486 CTGATAGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1142942 original size:49 final size:48
Alignment explanation
Indices: 1142844--1142942 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 48
1142834 ATAAGTCAAG
* ** * * * *
1142844 TTTAAGTTATTATTAGATATAAAATTATAAAATATAAATGTTATTAAA
1 TTTAAGTTATTATTAAATATAAAACAATAAAACATAAATATCACTAAA
1142892 TTTAAGTTATTATTAAATATAAAAACAATAAAACATAAATATCACTAAA
1 TTTAAGTTATTATTAAATAT-AAAACAATAAAACATAAATATCACTAAA
1142941 TT
1 TT
1142943 ATTAAGTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (48 bp):
TTTAAGTTATTATTAAATATAAAACAATAAAACATAAATATCACTAAA
Found at i:1146258 original size:21 final size:21
Alignment explanation
Indices: 1146233--1146272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1146223 TCGTTTCGTT
*
1146233 TTATTTTATCTTTTGAAATTA
1 TTATTTTATCTTTTAAAATTA
*
1146254 TTATTTTATTTTTTAAAAT
1 TTATTTTATCTTTTAAAAT
1146273 ATTTTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATTTTATCTTTTAAAATTA
Found at i:1148939 original size:25 final size:25
Alignment explanation
Indices: 1148888--1148939 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1148878 AAGAAAATTA
** *
1148888 TAATGTTTTATTAACATCATTTTTT
1 TAATGTTTTATTAACATCAACTATT
1148913 TAATGTTTTATTAACATCAACTATT
1 TAATGTTTTATTAACATCAACTATT
1148938 TA
1 TA
1148940 TAAAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.54
Consensus pattern (25 bp):
TAATGTTTTATTAACATCAACTATT
Found at i:1149143 original size:13 final size:13
Alignment explanation
Indices: 1149125--1149165 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1149115 CCTACTCATA
*
1149125 TTATTTTTTTAAT
1 TTATTTTTTAAAT
1149138 TTATTTTTTAAAT
1 TTATTTTTTAAAT
* *
1149151 ATATTTTTAAAAT
1 TTATTTTTTAAAT
1149164 TT
1 TT
1149166 TAATATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTTTTAAAT
Found at i:1149726 original size:17 final size:18
Alignment explanation
Indices: 1149706--1149742 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1149696 GATTTGCACT
1149706 TTTAATTTT-TATAGATA
1 TTTAATTTTATATAGATA
*
1149723 TTTAATTTTATTTAGATA
1 TTTAATTTTATATAGATA
1149741 TT
1 TT
1149743 ATATAAATAT
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:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTAATTTTATATAGATA
Found at i:1157621 original size:17 final size:17
Alignment explanation
Indices: 1157599--1157634 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1157589 AAGTTCTTAA
1157599 ATTTATATTAAAATTAT
1 ATTTATATTAAAATTAT
1157616 ATTTATATTAAAATTAT
1 ATTTATATTAAAATTAT
1157633 AT
1 AT
1157635 CATTTAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTAAAATTAT
Found at i:1160301 original size:12 final size:12
Alignment explanation
Indices: 1160286--1160338 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
1160276 AAATAAAAAT
1160286 TTAAATATTAAA
1 TTAAATATTAAA
* *
1160298 TT-AATAATTTAT
1 TTAAAT-ATTAAA
1160310 TTAAATATTAAA
1 TTAAATATTAAA
* *
1160322 TTAAAAATCAAA
1 TTAAATATTAAA
1160334 TTAAA
1 TTAAA
1160339 ACACACAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 3 0.09
12 27 0.82
13 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAATATTAAA
Found at i:1160337 original size:24 final size:24
Alignment explanation
Indices: 1160286--1160338 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1160276 AAATAAAAAT
* ** *
1160286 TTAAATATTAAATTAATAATTTAT
1 TTAAATATTAAATTAAAAATCAAA
1160310 TTAAATATTAAATTAAAAATCAAA
1 TTAAATATTAAATTAAAAATCAAA
1160334 TTAAA
1 TTAAA
1160339 ACACACAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAAATATTAAATTAAAAATCAAA
Found at i:1165917 original size:18 final size:17
Alignment explanation
Indices: 1165883--1165939 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1165873 ATTTAAACTT
1165883 TATATTTATCTCAATAAA
1 TATATTTATC-CAATAAA
1165901 TAATATTTATCCAATAAA
1 T-ATATTTATCCAATAAA
* * *
1165919 TATAATTATCTAATAAT
1 TATATTTATCCAATAAA
1165936 TATA
1 TATA
1165940 AAATTAGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 17 0.49
18 9 0.26
19 9 0.26
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATTTATCCAATAAA
Found at i:1177419 original size:16 final size:18
Alignment explanation
Indices: 1177390--1177428 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
1177380 AAAATTATCT
1177390 AAAATAAAATATAATAAA
1 AAAATAAAATATAATAAA
1177408 AAAAT-AAA-ATAATAAA
1 AAAATAAAATATAATAAA
1177424 AAAAT
1 AAAAT
1177429 GTAAACTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 3 0.14
18 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAATAAAATATAATAAA
Found at i:1180053 original size:22 final size:21
Alignment explanation
Indices: 1180023--1180076 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1180013 TATAATAATT
*
1180023 TCTT-TTTTTTTCTCTTTTTTCC
1 TCTTCTTTTTTT-T-TTTTTGCC
*
1180045 TCTTCTTTTTTTTTTTTTGTC
1 TCTTCTTTTTTTTTTTTTGCC
1180066 TCTCTCTTTTT
1 TCT-TCTTTTT
1180077 AAGATAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 7 0.25
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (21 bp):
TCTTCTTTTTTTTTTTTTGCC
Found at i:1180828 original size:11 final size:12
Alignment explanation
Indices: 1180814--1180854 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
1180804 TTAAAATATC
1180814 TTTA-ATTTTAA
1 TTTATATTTTAA
*
1180825 TTTATATTATAA
1 TTTATATTTTAA
*
1180837 -TTATATTTTAG
1 TTTATATTTTAA
1180848 TTTATAT
1 TTTATAT
1180855 GTAACCAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTATATTTTAA
Found at i:1182369 original size:58 final size:57
Alignment explanation
Indices: 1182300--1182474 Score: 158
Period size: 58 Copynumber: 3.0 Consensus size: 57
1182290 AAAAAAAGTC
* *
1182300 CCTAAA-ACATGGCAAATTACTTTAATGACCATAAGATGCATGAAATTACGTAATAAT
1 CCTAAATACATGG-AAATTACTTAAATGACCATAAAATGCATGAAATTACGTAATAAT
* * * * *** * *
1182357 CCTTAATGCATGGAAAATGAC-TAGATTGGTTATAAAATGCATGAAATTACATAATAGT
1 CCTAAATACATGG-AAATTACTTA-AATGACCATAAAATGCATGAAATTACGTAATAAT
* * *
1182415 CTCTAAATACATGGAAAATACCTTAAATGACC-TAAAATGCATAAAATTACGTTATAAT
1 C-CTAAATACATGGAAATTA-CTTAAATGACCATAAAATGCATGAAATTACGTAATAAT
1182473 CC
1 CC
1182475 GTATATCAAG
Statistics
Matches: 89, Mismatches: 24, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
57 7 0.08
58 66 0.74
59 14 0.16
60 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (57 bp):
CCTAAATACATGGAAATTACTTAAATGACCATAAAATGCATGAAATTACGTAATAAT
Found at i:1182515 original size:116 final size:117
Alignment explanation
Indices: 1182252--1182518 Score: 278
Period size: 116 Copynumber: 2.3 Consensus size: 117
1182242 CCCACAACAT
*
1182252 AAAAATAACTAAAATGGTCCT-AATATGCATGAAAATTTAAAAAAAGTCCCTAAAACATGGCAAA
1 AAAAATGACTAAAATGGTCCTAAATATGCATG-AAATTTAAAAAAAGTCCCTAAAACATGGCAAA
* * * * * *
1182316 TTACTTTAATGACCATAAGATGCATGAAATTACGTAATAATCCTTAATGCATG
65 ATACTTAAATGACCATAAAATGCATAAAATTACGTAATAATCCGTAATGCAAG
* * * ** * * *
1182369 GAAAATGACTAGATTGGTTATAAA-ATGCATGAAA-TTACATAATAGTCTCTAAATACATGG-AA
1 AAAAATGACTAAAATGGTCCTAAATATGCATGAAATTTA-AAAAAAGTCCCTAAA-ACATGGCAA
*
1182431 AATACCTTAAATGACC-TAAAATGCATAAAATTACGTTATAATCCGTATAT-CAAG
64 AATA-CTTAAATGACCATAAAATGCATAAAATTACGTAATAATCCGTA-ATGCAAG
* *
1182485 AAAAATGATTAAAATGCTCCTAAATA-GCATGAAA
1 AAAAATGACTAAAATGGTCCTAAATATGCATGAAA
1182519 GTCCCTAAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
115 3 0.02
116 75 0.62
117 41 0.34
118 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (117 bp):
AAAAATGACTAAAATGGTCCTAAATATGCATGAAATTTAAAAAAAGTCCCTAAAACATGGCAAAA
TACTTAAATGACCATAAAATGCATAAAATTACGTAATAATCCGTAATGCAAG
Found at i:1184747 original size:29 final size:27
Alignment explanation
Indices: 1184714--1184767 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
1184704 CGATGATTAG
1184714 AAAATAAATCGAGATTGGAGTATCCCCTC
1 AAAAT-AA-CGAGATTGGAGTATCCCCTC
*
1184743 AAAATAACGGGATTGGAGTATCCCC
1 AAAATAACGAGATTGGAGTATCCCC
1184768 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 17 0.71
28 2 0.08
29 5 0.21
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AAAATAACGAGATTGGAGTATCCCCTC
Found at i:1184843 original size:28 final size:28
Alignment explanation
Indices: 1184801--1184877 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
1184791 GGAATAAAGC
* *
1184801 CGGGGTTGGAGTATCCCC-TTGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
*
1184829 CGGGGTTGGAATATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1184857 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1184878 TATGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1185075 original size:51 final size:51
Alignment explanation
Indices: 1184860--1185082 Score: 205
Period size: 52 Copynumber: 4.3 Consensus size: 51
1184850 GAAATAACGA
* * * *
1184860 GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAA-T--TAGTGTTTTGGAAATAAAACCGG
* * * * *
1184914 AGTTGGAGTAT-CCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
1184966 GGTTAGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATG-AAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * **
1185018 GATTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAGATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
1185069 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
1185083 TTCGGAAATA
Statistics
Matches: 135, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
51 35 0.26
52 70 0.52
53 13 0.10
54 11 0.08
55 6 0.04
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1185190 original size:53 final size:50
Alignment explanation
Indices: 1185129--1185249 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 50
1185119 AACGGGGTTA
* * *
1185129 GAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGGAGCTG
1 GAGTATCCCCGATTGTGAAAA-TTAGTG--TCTTGAAAATAAAATCGGAGCTG
* *
1185182 GAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGT-GAAAATTAGTGTCTTGAAAATAAAATCGGAGCTG
*
1185233 GAATATCCCCGATTGTG
1 GAGTATCCCCGATTGTG
1185250 GAGAATTGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 1 0.02
51 34 0.57
53 20 0.33
54 5 0.08
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (50 bp):
GAGTATCCCCGATTGTGAAAATTAGTGTCTTGAAAATAAAATCGGAGCTG
Found at i:1187628 original size:33 final size:33
Alignment explanation
Indices: 1187590--1187656 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1187580 AAAATTTTCA
***
1187590 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1187623 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1187656 A
1 A
1187657 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1187629 original size:13 final size:13
Alignment explanation
Indices: 1187611--1187636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1187601 ACAAAGATCC
1187611 ATGTATCGATACA
1 ATGTATCGATACA
1187624 ATGTATCGATACA
1 ATGTATCGATACA
1187637 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1187700 original size:19 final size:19
Alignment explanation
Indices: 1187676--1187730 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1187666 CAGTAGCTAA
*
1187676 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
1187695 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1187714 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1187731 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1188420 original size:21 final size:21
Alignment explanation
Indices: 1188363--1188427 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1188353 TATTTTATTA
* * * *
1188363 ATATAATATGGCTTTGTACCA
1 ATATAATATGGCATTATATCG
*
1188384 ATAAAATA-GGCATTATATCG
1 ATATAATATGGCATTATATCG
*
1188404 ATATAATATGGCCTTATATCG
1 ATATAATATGGCATTATATCG
1188425 ATA
1 ATA
1188428 CAATGCATGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
ATATAATATGGCATTATATCG
Found at i:1194042 original size:13 final size:13
Alignment explanation
Indices: 1194024--1194065 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1194014 CACAGACACT
1194024 TTGGCA-TAGGTAC
1 TTGGCACTA-GTAC
1194037 TTGGCACTAGTAC
1 TTGGCACTAGTAC
*
1194050 TTTGACACTAGTAC
1 -TTGGCACTAGTAC
1194064 TT
1 TT
1194066 TTTGCACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (13 bp):
TTGGCACTAGTAC
Found at i:1194043 original size:27 final size:27
Alignment explanation
Indices: 1193968--1194043 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
1193958 GCATAGGTAT
* * * * *
1193968 CTTTGGCACAAGTACTTGGTACATATA
1 CTTTGGCATAGGTACTTGGCACAGACA
* *
1193995 CTTTGACATAGGTA-TCTAGCACAGACA
1 CTTTGGCATAGGTACT-TGGCACAGACA
1194022 CTTTGGCATAGGTACTTGGCAC
1 CTTTGGCATAGGTACTTGGCAC
1194044 TAGTACTTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.95
28 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (27 bp):
CTTTGGCATAGGTACTTGGCACAGACA
Found at i:1194051 original size:27 final size:27
Alignment explanation
Indices: 1193955--1194053 Score: 71
Period size: 27 Copynumber: 3.6 Consensus size: 27
1193945 AACAAGCACT
* *
1193955 TTGGCA-TAGGTATCTTTGGCACAAGTAC
1 TTGGCACTA-GTA-CTTTGGCATAGGTAC
* *
1193983 TTGGTACATA-TACTTTGACATAGGTA-
1 TTGGCAC-TAGTACTTTGGCATAGGTAC
* *
1194009 TCTAGCAC-AGACACTTTGGCATAGGTAC
1 T-TGGCACTAG-TACTTTGGCATAGGTAC
1194037 TTGGCACTAGTACTTTG
1 TTGGCACTAGTACTTTG
1194054 ACACTAGTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 40 0.74
28 10 0.19
30 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (27 bp):
TTGGCACTAGTACTTTGGCATAGGTAC
Found at i:1194117 original size:27 final size:28
Alignment explanation
Indices: 1193992--1194130 Score: 85
Period size: 27 Copynumber: 5.0 Consensus size: 28
1193982 CTTGGTACAT
* * *
1193992 ATACTTTGACATAGGTATC-TAGCACAG
1 ATACTTTGGCATAGGTAACTTAGCACAA
* * *
1194019 ACACTTTGGCATAGGT-ACTTGGCACTA
1 ATACTTTGGCATAGGTAACTTAGCACAA
* * *
1194046 GTACTTTGACACTA-GT-ACTTTTTGCACAA
1 ATACTTTGGCA-TAGGTAAC--TTAGCACAA
1194075 ATACTTTAGTGC--AGGTAAC-TAGCACAA
1 ATACTTT-G-GCATAGGTAACTTAGCACAA
*
1194102 ATACTTTGGCATAGGTACCTTTAGCACAA
1 ATACTTTGGCATAGGTAAC-TTAGCACAA
1194131 GTACCTGGCA
Statistics
Matches: 85, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
25 2 0.02
26 2 0.02
27 51 0.60
28 3 0.04
29 23 0.27
30 3 0.04
31 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (28 bp):
ATACTTTGGCATAGGTAACTTAGCACAA
Found at i:1194134 original size:15 final size:15
Alignment explanation
Indices: 1194096--1194197 Score: 77
Period size: 15 Copynumber: 7.1 Consensus size: 15
1194086 CAGGTAACTA
*
1194096 GCACAAATA-CTTTG
1 GCACAAGTACCTTTG
* * *
1194110 GCATAGGTACCTTTA
1 GCACAAGTACCTTTG
1194125 GCACAAGTACC--TG
1 GCACAAGTACCTTTG
* *
1194138 GCACAAATACATTTG
1 GCACAAGTACCTTTG
*
1194153 GCACAAGTA-CTATG
1 GCACAAGTACCTTTG
* *
1194167 GCATAAATACCTTTG
1 GCACAAGTACCTTTG
* *
1194182 GCACAGGTATCTTTG
1 GCACAAGTACCTTTG
1194197 G
1 G
1194198 TACAGGTGCT
Statistics
Matches: 65, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
13 10 0.15
14 16 0.25
15 39 0.60
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (15 bp):
GCACAAGTACCTTTG
Found at i:1194175 original size:29 final size:29
Alignment explanation
Indices: 1194096--1194186 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
1194086 CAGGTAACTA
* * ** *
1194096 GCACAAATACTTTGGCATAGGTACCTTTA
1 GCACAAGTACTATGGCATAAATACCTTTG
* * *
1194125 GCACAAGTAC-CTGGCACAAATACATTTG
1 GCACAAGTACTATGGCATAAATACCTTTG
1194153 GCACAAGTACTATGGCATAAATACCTTTG
1 GCACAAGTACTATGGCATAAATACCTTTG
1194182 GCACA
1 GCACA
1194187 GGTATCTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 22 0.43
29 29 0.57
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (29 bp):
GCACAAGTACTATGGCATAAATACCTTTG
Found at i:1194243 original size:14 final size:15
Alignment explanation
Indices: 1194218--1194259 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1194208 TAGCATAGGC
1194218 ACTTTTGATACAAAT
1 ACTTTTGATACAAAT
* *
1194233 A-TTTTGGTACATAT
1 ACTTTTGATACAAAT
*
1194247 ACTTTTGACACAA
1 ACTTTTGATACAA
1194260 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (15 bp):
ACTTTTGATACAAAT
Found at i:1194297 original size:15 final size:15
Alignment explanation
Indices: 1194227--1194300 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
1194217 CACTTTTGAT
*
1194227 ACAAATA-TTTTGGT
1 ACAAATACTTTTGGC
* *
1194241 ACATATACTTTTGAC
1 ACAAATACTTTTGGC
* *
1194256 ACAAGTA-TTTTCGC
1 ACAAATACTTTTGGC
** *
1194270 ACAAGCACCTTTGGC
1 ACAAATACTTTTGGC
1194285 ACAAATACTTTTGGC
1 ACAAATACTTTTGGC
1194300 A
1 A
1194301 AAGGTAGCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
14 17 0.38
15 28 0.62
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (15 bp):
ACAAATACTTTTGGC
Found at i:1197500 original size:20 final size:19
Alignment explanation
Indices: 1197455--1197510 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1197445 TGTATCGATA
* **
1197455 CATTGCATCGATACATGTT
1 CATTGTATCGATACATACT
1197474 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
1197493 CAATTGTATCGATACATA
1 C-ATTGTATCGATACATA
1197511 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:1207389 original size:39 final size:39
Alignment explanation
Indices: 1207335--1207428 Score: 152
Period size: 39 Copynumber: 2.4 Consensus size: 39
1207325 CAATGAGAAA
*
1207335 TGTATCGATACATTTCCTTGGCAATATATAAGATGGTTT
1 TGTATCGATACATTTCCTTGGCAATATACAAGATGGTTT
* * *
1207374 TGTATCGATACATTTCCTTGGCAGTATGCAGGATGGTTT
1 TGTATCGATACATTTCCTTGGCAATATACAAGATGGTTT
1207413 TGTATCGATACATTTC
1 TGTATCGATACATTTC
1207429 AAGCATGTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (39 bp):
TGTATCGATACATTTCCTTGGCAATATACAAGATGGTTT
Found at i:1207459 original size:20 final size:21
Alignment explanation
Indices: 1207436--1207486 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1207426 TTCAAGCATG
1207436 TATCGATACATTCACT-TATA
1 TATCGATACATTCACTATATA
* *
1207456 TATCGATACATTTACTATTTA
1 TATCGATACATTCACTATATA
1207477 TATCGATACA
1 TATCGATACA
1207487 AATTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (21 bp):
TATCGATACATTCACTATATA
Found at i:1210132 original size:3 final size:3
Alignment explanation
Indices: 1210124--1210183 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1210114 AGTACACTGC
1210124 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1210172 ATT ATT ATT ATT
1 ATT ATT ATT ATT
1210184 TATTCAAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1212113 original size:16 final size:15
Alignment explanation
Indices: 1212101--1212184 Score: 78
Period size: 16 Copynumber: 5.3 Consensus size: 15
1212091 ACCCGAACTT
1212101 GAAATGACTCGAATCC
1 GAAATGACTCGAAT-C
*
1212117 GAAATGACCCGAATC
1 GAAATGACTCGAATC
* *
1212132 CAAAGTGACTTGAATTC
1 GAAA-TGACTCGAA-TC
*
1212149 GAAATGACTCGAACCC
1 GAAATGACTCGAA-TC
*
1212165 AAAATGACTCGAATC
1 GAAATGACTCGAATC
1212180 TGAAA
1 -GAAA
1212185 ACAATGACAA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
15 5 0.09
16 44 0.81
17 5 0.09
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (15 bp):
GAAATGACTCGAATC
Found at i:1212141 original size:32 final size:32
Alignment explanation
Indices: 1212102--1212184 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
1212092 CCCGAACTTG
*
1212102 AAATGACTCGAATCCGAAATGACCCGAATCCA
1 AAATGACTCGAATCCGAAATGACCCGAACCCA
* * * *
1212134 AAGTGACTTGAATTCGAAATGACTCGAACCCA
1 AAATGACTCGAATCCGAAATGACCCGAACCCA
*
1212166 AAATGACTCGAATCTGAAA
1 AAATGACTCGAATCCGAAA
1212185 ACAATGACAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (32 bp):
AAATGACTCGAATCCGAAATGACCCGAACCCA
Found at i:1212218 original size:15 final size:15
Alignment explanation
Indices: 1212208--1212242 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1212198 TTTATAACTC
1212208 AAAATAATATAACCT
1 AAAATAATATAACCT
* *
1212223 AAAATAATTTAATCT
1 AAAATAATATAACCT
1212238 AAAAT
1 AAAAT
1212243 TAATCCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAATATAACCT
Found at i:1212291 original size:14 final size:14
Alignment explanation
Indices: 1212272--1212299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1212262 AACAGGTGTA
1212272 ATAGAGAATGGTTT
1 ATAGAGAATGGTTT
1212286 ATAGAGAATGGTTT
1 ATAGAGAATGGTTT
1212300 TGGAGGGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
ATAGAGAATGGTTT
Found at i:1215357 original size:34 final size:34
Alignment explanation
Indices: 1215295--1215511 Score: 310
Period size: 34 Copynumber: 6.4 Consensus size: 34
1215285 ATGTTATAGG
* *
1215295 TGTTGATTAAAT-GGTGATTTTGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
1215328 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
1215362 TATTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
1215396 TGTTGATTAAATGAGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
1215430 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* *
1215464 TGTTGACTAAATGGGAGATTTGGTAGGTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
1215498 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1215512 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 12 0.07
34 152 0.93
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
Found at i:1215486 original size:102 final size:101
Alignment explanation
Indices: 1215295--1215511 Score: 380
Period size: 102 Copynumber: 2.1 Consensus size: 101
1215285 ATGTTATAGG
* * *
1215295 TGTTGATTAAATGGTGATTTTGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1215360 ATTATTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTATTGACTAAATGGGAGATTTGGTAGCTTACCAT
1215396 TGTTGATTAAATGAGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTAC
1 TGTTGATTAAATG-GAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTAC
* *
1215461 CATTGTTGACTAAATGGGAGATTTGGTAGGTTACCAT
65 CATTATTGACTAAATGGGAGATTTGGTAGCTTACCAT
1215498 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1215512 TGGTTTTTAC
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 14 0.13
102 96 0.87
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
ATTATTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1223719 original size:45 final size:48
Alignment explanation
Indices: 1223618--1223723 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 48
1223608 AATGTGCCAT
* *
1223618 TTCAAGGTCAGCGACATCGGGCTAAGGGAAAAGTGGACCAATGTGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAA-GGAAAAGTGGACCAATATGCTGA
* * * *
1223667 CTCAAGGCCAGCGACATTGGGCTTA-GAAAGGT-G-CCAATATGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
1223712 TTCAAGGCCAGC
1 TTCAAGGCCAGC
1223724 AATATCGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 22 0.44
46 1 0.02
47 6 0.12
49 21 0.42
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (48 bp):
TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
Found at i:1223812 original size:32 final size:32
Alignment explanation
Indices: 1223756--1224739 Score: 1318
Period size: 32 Copynumber: 31.8 Consensus size: 32
1223746 AAAATGGTGA
* ** **
1223756 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1223788 TTTTAAATGGGTTGCCCCCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1223820 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1223852 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1223884 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1223916 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1223948 TTTGAAATGGG-TGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1223979 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1224011 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224043 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224075 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
1224107 TTTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1224135 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1224165 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224193 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224223 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224251 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224283 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1224315 TTTGGAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224347 TTTGAAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224378 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1224410 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224442 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224474 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
1224506 TTTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1224534 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1224564 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224592 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224622 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224650 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1224682 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1224714 TTTGGAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1224740 GATTTAAAAG
Statistics
Matches: 864, Mismatches: 70, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
28 126 0.15
29 6 0.01
30 130 0.15
31 76 0.09
32 526 0.61
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1224583 original size:399 final size:398
Alignment explanation
Indices: 1223845--1224730 Score: 1729
Period size: 399 Copynumber: 2.2 Consensus size: 398
1223835 CACCGACTTG
1223845 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
*
1223910 GTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTATGT
66 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTATGT
1223975 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
131 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
1224040 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
196 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT-GGTTGCCACCGACTTGTGTGG
1224105 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
260 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
1224170 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
325 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
1224235 CCACTGACT
390 CCACTGACT
1224244 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
*
1224309 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
66 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTATGT
1224374 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
131 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
1224439 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
196 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT-GGTTGCCACCGACTTGTGTGG
1224504 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
260 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
1224569 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
325 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
1224634 CCACTGACT
390 CCACTGACT
1224643 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1224708 GTGGGCTTTGGAATGGG-TGCCAC
66 GTGGGCTTTGGAATGGGTTGCCAC
1224731 AGAGTTGTGG
Statistics
Matches: 485, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
398 6 0.01
399 479 0.99
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (398 bp):
TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTATGT
GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGTTGCCACCGACTTGTGTGGG
CTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGAA
AGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATGC
CACTGACT
Found at i:1224763 original size:27 final size:27
Alignment explanation
Indices: 1224722--1225897 Score: 1884
Period size: 27 Copynumber: 43.0 Consensus size: 27
1224712 GCTTTGGAAT
* *
1224722 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1224749 GGATGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1224776 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1224803 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1224830 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1224858 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1224885 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1224912 GGGTGCCACGGAGTTGTGGACCTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1224939 GGGTGCCACGGAGTTGTGAACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1224966 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1224994 GGGTGCCACGGAGTTGTGGACTTAAACA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
*
1225022 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1225050 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225077 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1225104 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225131 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225158 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1225186 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225213 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1225241 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225268 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1225295 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225322 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225349 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225376 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
1225404 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1225431 GGGTGCCACGGAATTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1225459 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225486 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225513 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1225540 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1225568 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225595 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1225622 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1225649 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1225677 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225704 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
* *
1225732 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225759 GGGTACCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
1225787 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225814 AGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1225842 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1225869 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1225897 G
1 G
1225898 AAAATGCCAC
Statistics
Matches: 1065, Mismatches: 70, Indels: 27
0.92 0.06 0.02
Matches are distributed among these distances:
27 756 0.71
28 287 0.27
29 22 0.02
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1224881 original size:55 final size:54
Alignment explanation
Indices: 1224722--1225897 Score: 1893
Period size: 55 Copynumber: 21.5 Consensus size: 54
1224712 GCTTTGGAAT
* * * * *
1224722 GGGTGCCACAGAGTTGTGGATTTAAAAGGATGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1224776 GGGTGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1224830 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * *
1224885 GAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACCTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1224939 GGGTGCCACGGAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGAGTTGTGGACTTAAAA
1224994 GGGTGCCACGGAGTTGTGGACTTAAACAGGGATGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAA-AGGG-TGCCACAGAGTTGTGGACTTAAAA
*
1225050 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225104 AGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1225158 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * *
1225213 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225268 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
1225322 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
1225376 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
1225431 GGGTGCCACGGAATTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
*
1225486 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225540 GGGTGCCACGGAGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225595 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1225649 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* * *
1225704 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225759 GGGTACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225814 AGGTACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
* *
1225869 GGATGCCACAGAGTTGTGGACTTTAAAAG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAG
1225898 AAAATGCCAC
Statistics
Matches: 1058, Mismatches: 53, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
54 465 0.44
55 503 0.48
56 90 0.09
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (54 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
Found at i:1224892 original size:82 final size:81
Alignment explanation
Indices: 1224722--1225897 Score: 1884
Period size: 82 Copynumber: 14.3 Consensus size: 81
1224712 GCTTTGGAAT
* * * *
1224722 GGGTGCCACAGAGTTGTGGATTTAAAAGGATGCTACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1224787 AGTTATGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
1224803 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
1224868 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1224885 GAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACCTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1224950 AGTTGTGAACTTAAAA
66 AGTTGTGGACTTAAAA
1224966 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAACAGGGATGCCA
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA-AGGG-TGCCA
*
1225031 CAGAGTTGTGGACTTAAAA
63 CGGAGTTGTGGACTTAAAA
*
1225050 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1225115 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * *
1225131 GGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
1225196 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1225213 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1225278 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1225295 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1225360 AGTTGTGGACTAAAAA
66 AGTTGTGGACTTAAAA
* *
1225376 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
1225441 GAATTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
*
1225459 GGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1225524 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
1225540 GGGTGCCACGGAGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1225605 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1225622 GGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
1225687 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * * * *
1225704 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTACCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
1225769 GAGTTGTGGATTTTAAAA
65 GAGTTGTGGA-CTTAAAA
* * * *
1225787 GGGTGCCACAGAGTTGTGGACTTAAAAAGGTACCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
1225852 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1225869 GGATGCCACAGAGTTGTGGACTTTAAAAG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAG
1225898 AAAATGCCAC
Statistics
Matches: 1016, Mismatches: 65, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
81 291 0.29
82 499 0.49
83 201 0.20
84 25 0.02
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:1226967 original size:13 final size:13
Alignment explanation
Indices: 1226949--1226974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1226939 AGGGTGAAAA
1226949 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
1226962 GGTTTTTTTTTTT
1 GGTTTTTTTTTTT
1226975 TTTTAGGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
GGTTTTTTTTTTT
Found at i:1234775 original size:34 final size:34
Alignment explanation
Indices: 1234695--1234912 Score: 233
Period size: 34 Copynumber: 6.4 Consensus size: 34
1234685 AAGTGGGAGA
1234695 ATTGTTGATTAAATG-GTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
* * * * *
1234728 ATTATTGATTAAATGAGTCATTTAGTGGTTTGCC
1 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
* * * *
1234762 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACA
1 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
* * *
1234796 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
* *
1234830 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
* * * * * *
1234864 ATTGTTGACTAAATG-GAAGATTTGATAGGTTGCT
1 ATTGTTGATTAAATGAG-TGATTTGGTAGTTTACC
1234898 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
1234913 GTGGTTTTTA
Statistics
Matches: 155, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
33 15 0.10
34 140 0.90
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGAGTGATTTGGTAGTTTACC
Found at i:1234869 original size:102 final size:102
Alignment explanation
Indices: 1234694--1234913 Score: 318
Period size: 102 Copynumber: 2.2 Consensus size: 102
1234684 CAAGTGGGAG
* *
1234694 AATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTATTGATTAAATGAGTCATTTAGTGGTT
1 AATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGAGTCATTTAGTGGTT
* *
1234758 TGCCATTGTTGACTAAAT-GAGAGATTTGGTAGCTTAC
66 TACCATTGTTGACTAAATGGA-AGATTTGATAGCTTAC
* * * *
1234795 AATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGTT
1 AATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGAGTCATTTAGTGGTT
* *
1234860 TACCATTGTTGACTAAATGGAAGATTTGATAGGTTGC
66 TACCATTGTTGACTAAATGGAAGATTTGATAGCTTAC
*
1234897 TATTGTTGATTAAATGG
1 AATTGTTGATTAAATGG
1234914 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 15 0.14
102 89 0.84
103 2 0.02
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (102 bp):
AATTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGAGTCATTTAGTGGTT
TACCATTGTTGACTAAATGGAAGATTTGATAGCTTAC
Found at i:1235547 original size:15 final size:15
Alignment explanation
Indices: 1235529--1235579 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1235519 TTTTAATTAT
1235529 ATTATATTTATAATA
1 ATTATATTTATAATA
**
1235544 ATTATAAATATAATA
1 ATTATATTTATAATA
*
1235559 AATAT-TATTATAATTA
1 ATTATAT-TTATAA-TA
1235575 ATTAT
1 ATTAT
1235580 TATAAAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATTTATAATA
Found at i:1236184 original size:37 final size:36
Alignment explanation
Indices: 1236104--1236190 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 36
1236094 AGATTTAAAT
* *
1236104 AGATTTAAAATTTAAATTTTTTTAAATTTAAATATTA
1 AGATTTAAAA-TTAAATTATTTTAAATTTAAACATTA
* * *
1236141 AAATTTAATAATTGAATTATTTTAAATTTACACCA-TA
1 AGATTTAA-AATTAAATTATTTTAAATTTA-AACATTA
1236178 AGATTTAAAATTA
1 AGATTTAAAATTA
1236191 TTTTTTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
36 4 0.10
37 33 0.80
38 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (36 bp):
AGATTTAAAATTAAATTATTTTAAATTTAAACATTA
Found at i:1236255 original size:19 final size:19
Alignment explanation
Indices: 1236223--1236259 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1236213 TACTTTTAAA
1236223 AAGTTAAATCAATTTAATT
1 AAGTTAAATCAATTTAATT
* *
1236242 AAGTTCAATTAATTTAAT
1 AAGTTAAATCAATTTAAT
1236260 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (19 bp):
AAGTTAAATCAATTTAATT
Found at i:1236388 original size:20 final size:20
Alignment explanation
Indices: 1236356--1236403 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1236346 ATTGAATTAA
1236356 ATTAAATTTTAAAATAAAATT
1 ATTAAA-TTTAAAATAAAATT
* **
1236377 ATTAAATTTAAATTAATTTT
1 ATTAAATTTAAAATAAAATT
1236397 ATTAAAT
1 ATTAAAT
1236404 ATATGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAAATTTAAAATAAAATT
Found at i:1240950 original size:15 final size:15
Alignment explanation
Indices: 1240886--1240951 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
1240876 TTTTATAATT
1240886 AAATTTAAA-T-AAA
1 AAATTTAAATTAAAA
* *
1240899 AATTTTATTATTAAATA
1 AAATTTA-AATTAAA-A
**
1240916 ATAATTTAAATTAAGT
1 A-AATTTAAATTAAAA
1240932 AAATTTAAATTAAAA
1 AAATTTAAATTAAAA
1240947 AAATT
1 AAATT
1240952 ATGTTTAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 6 0.15
14 1 0.03
15 18 0.45
16 3 0.08
17 7 0.17
18 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AAATTTAAATTAAAA
Found at i:1241212 original size:23 final size:22
Alignment explanation
Indices: 1241186--1241254 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 22
1241176 TTATATATTT
1241186 TTTATTTTTAAATATGTTTTTAA
1 TTTATTTTTAAATAT-TTTTTAA
* *
1241209 TTTAATTTAATATATATTTTTATAA
1 TTT-ATTT-TTAAATATTTTT-TAA
1241234 TTT-TTTGTT-AATATTTTTTAA
1 TTTATTT-TTAAATATTTTTTAA
1241255 AAATATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 3 0.08
22 8 0.21
23 7 0.18
24 8 0.21
25 12 0.32
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTATTTTTAAATATTTTTTAA
Found at i:1241346 original size:22 final size:20
Alignment explanation
Indices: 1241313--1241372 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
1241303 CTAGTAAAAT
*
1241313 AAAATTATAATTATTTTATA
1 AAAAATATAATTATTTTATA
*
1241333 AAATATATATAATTATATTA-A
1 AAA-A-ATATAATTATTTTATA
1241354 AAAAATATAA--ATTTTATA
1 AAAAATATAATTATTTTATA
1241372 A
1 A
1241373 TTAAAAACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 5 0.15
18 2 0.06
19 6 0.18
20 4 0.12
21 5 0.15
22 12 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATATAATTATTTTATA
Found at i:1241362 original size:23 final size:23
Alignment explanation
Indices: 1241318--1241379 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1241308 AAAATAAAAT
* *
1241318 TATAATTAT-TTTATAAAATATA
1 TATAATTATATTAAAAAAATATA
1241340 TATAATTATATTAAAAAAATATA
1 TATAATTATATTAAAAAAATATA
* *
1241363 AAT-TTTATAATTAAAAA
1 TATAATTAT-ATTAAAAA
1241380 CCTTATTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATTATATTAAAAAAATATA
Found at i:1241951 original size:41 final size:43
Alignment explanation
Indices: 1241905--1241985 Score: 98
Period size: 41 Copynumber: 1.9 Consensus size: 43
1241895 AAGTTGTTAT
1241905 TAAATACAA-AAAAT-AAAAAATTAATATT-ATTA-ATTATATTG
1 TAAATA-AATAAAATCAAAAAATT-ATATTAATTATATTATATTG
* *
1241946 TAAATAAATAAATTCAAATAATTATATTAATTATATTATA
1 TAAATAAATAAAATCAAAAAATTATATTAATTATATTATA
1241986 ATGAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 2 0.06
41 15 0.44
42 11 0.32
43 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (43 bp):
TAAATAAATAAAATCAAAAAATTATATTAATTATATTATATTG
Found at i:1242882 original size:14 final size:14
Alignment explanation
Indices: 1242863--1242911 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
1242853 ATCATAATAT
1242863 TAAATATAATTATA
1 TAAATATAATTATA
1242877 TAAATATAA-TATA
1 TAAATATAATTATA
1242890 T--ATATAATTATA
1 TAAATATAATTATA
*
1242902 AAAATATAAT
1 TAAATATAAT
1242912 ATAATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 6 0.19
12 4 0.13
13 5 0.16
14 16 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1242900 original size:25 final size:25
Alignment explanation
Indices: 1242856--1242930 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
1242846 CTATATTATC
* *
1242856 ATAATATTAAATATAATTATATAAAT
1 ATAATA-TATATATAATTATAAAAAT
1242882 ATAATATATATATAATTATAAAAAT
1 ATAATATATATATAATTATAAAAAT
1242907 ATAATATA-ATATATATT-TAAAAAT
1 ATAATATATATATA-ATTATAAAAAT
1242931 TTTATAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.26
25 28 0.61
26 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATATATATAATTATAAAAAT
Found at i:1242959 original size:33 final size:33
Alignment explanation
Indices: 1242866--1242981 Score: 107
Period size: 33 Copynumber: 3.5 Consensus size: 33
1242856 ATAATATTAA
* *
1242866 ATATAATTATATAAATA-TAATATATATATAA-TT
1 ATATAAATATA-AAATATTAATATATTTA-AATTT
* * *
1242899 ATAAAAATATAATATAAT-ATATATTTAAAAATTT
1 ATATAAATATAAAATATTAATATATTT--AAATTT
*
1242933 -TAT-AATATAAACTATTAATATATTTAAATTT
1 ATATAAATATAAAATATTAATATATTTAAATTT
1242964 ATATAAATATAAAATATT
1 ATATAAATATAAAATATT
1242982 TTAAATACAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
31 6 0.09
32 24 0.36
33 34 0.51
34 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAAATATAAAATATTAATATATTTAAATTT
Found at i:1242980 original size:7 final size:8
Alignment explanation
Indices: 1242866--1243035 Score: 55
Period size: 8 Copynumber: 20.0 Consensus size: 8
1242856 ATAATATTAA
*
1242866 ATATAATT
1 ATATAAAT
1242874 ATATAAAT
1 ATATAAAT
*
1242882 ATA-ATAT
1 ATATAAAT
1242889 ATATATAAT
1 ATATA-AAT
*
1242898 -TATAAAA
1 ATATAAAT
1242905 ATAT-AAT
1 ATATAAAT
*
1242912 ATAATATAT
1 AT-ATAAAT
* *
1242921 ATTTAAAA
1 ATATAAAT
*
1242929 ATTTTATAAT
1 A-TATA-AAT
*
1242939 ATA-AACT
1 ATATAAAT
1242946 AT-TAATAT
1 ATATAA-AT
*
1242954 ATTTAAATTT
1 ATATAAA--T
1242964 ATATAAAT
1 ATATAAAT
1242972 ATA-AAAT
1 ATATAAAT
*
1242979 ATTTTAAAT
1 A-TATAAAT
*
1242988 ACAATTATAAT
1 A-TA-TA-AAT
1242999 ATGATAAAAT
1 AT-AT-AAAT
1243009 ATATAAATAT
1 ATAT-AA-AT
1243019 AATATAAAT
1 -ATATAAAT
1243028 ATATAAAT
1 ATATAAAT
1243036 GTTATGTATA
Statistics
Matches: 123, Mismatches: 19, Indels: 40
0.68 0.10 0.22
Matches are distributed among these distances:
7 23 0.19
8 42 0.34
9 26 0.21
10 22 0.18
11 10 0.08
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:1243114 original size:7 final size:6
Alignment explanation
Indices: 1243081--1243105 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1243071 TATTAGTTTC
1243081 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
1243106 TATCTTTTAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1243202 original size:14 final size:14
Alignment explanation
Indices: 1243183--1243214 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1243173 TATTCTTTTA
*
1243183 ATTAATATATAAAT
1 ATTAATATAAAAAT
1243197 ATTAATATAAAAAT
1 ATTAATATAAAAAT
1243211 ATTA
1 ATTA
1243215 GGTGGTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAATATAAAAAT
Found at i:1244351 original size:20 final size:21
Alignment explanation
Indices: 1244314--1244353 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244304 TCCTTTTTTT
* *
1244314 TTTTTAGTATTTACTTAAAAC
1 TTTTTAGAATTCACTTAAAAC
1244335 TTTTTAGAATTCA-TTAAAA
1 TTTTTAGAATTCACTTAAAA
1244354 AAATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTTAGAATTCACTTAAAAC
Found at i:1259052 original size:1 final size:1
Alignment explanation
Indices: 1259042--1259098 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1259032 CAATAAATTG
* * * * * * *
1259042 TTTTTCTTTTTTTTTTTCTTTCTTTTTTCTTCTTCTTTTTCTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1259099 CAAGATGATT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:1259077 original size:17 final size:16
Alignment explanation
Indices: 1259044--1259090 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1259034 ATAAATTGTT
*
1259044 TTTCTTTTTTTTTTTC
1 TTTCTTTTTTTTCTTC
1259060 TTTCTTTTTTCTTCTTC
1 TTTCTTTTTT-TTCTTC
1259077 TTTTTCTTTTTTTT
1 --TTTCTTTTTTTT
1259091 TTTTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 5 0.19
18 2 0.07
19 10 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTCTTTTTTTTCTTC
Found at i:1259711 original size:14 final size:14
Alignment explanation
Indices: 1259668--1259737 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 14
1259658 ATATAATTAG
*
1259668 AAATTTTATATGCA
1 AAATTTTATATGTA
*
1259682 AATATTTAAT-TG-A
1 AA-ATTTTATATGTA
1259695 AAATTTTATATGTA
1 AAATTTTATATGTA
* *
1259709 AAAGTCTA-AT-TAA
1 AAATTTTATATGT-A
1259722 AAATTTTATAT-TA
1 AAATTTTATATGTA
1259735 AAA
1 AAA
1259738 AAACTTAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
12 7 0.16
13 18 0.40
14 14 0.31
15 6 0.13
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (14 bp):
AAATTTTATATGTA
Found at i:1259738 original size:14 final size:14
Alignment explanation
Indices: 1259663--1259738 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
1259653 AAAAAATATA
*
1259663 ATTAGAAATTTTAT
1 ATTAAAAATTTTAT
**
1259677 A-TGCAAATATTTA-
1 ATTAAAAAT-TTTAT
*
1259690 ATTGAAAATTTTAT
1 ATTAAAAATTTTAT
* *
1259704 ATGT-AAAAGTCTA-
1 AT-TAAAAATTTTAT
1259717 ATTAAAAATTTTAT
1 ATTAAAAATTTTAT
1259731 ATTAAAAA
1 ATTAAAAA
1259739 AACTTAGTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
12 1 0.02
13 19 0.39
14 28 0.57
15 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42
Consensus pattern (14 bp):
ATTAAAAATTTTAT
Found at i:1259738 original size:27 final size:27
Alignment explanation
Indices: 1259654--1259738 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
1259644 CATGTATGAA
* * *
1259654 AAAAATATAATTAGAAATTTTATATGC
1 AAAAATCTAATTAAAAATTTTATATGT
* * *
1259681 AAATATTTAATTGAAAATTTTATATGT
1 AAAAATCTAATTAAAAATTTTATATGT
*
1259708 AAAAGTCTAATTAAAAATTTTATAT-T
1 AAAAATCTAATTAAAAATTTTATATGT
1259734 AAAAA
1 AAAAA
1259739 AACTTAGTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 5 0.10
27 43 0.90
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (27 bp):
AAAAATCTAATTAAAAATTTTATATGT
Found at i:1259821 original size:54 final size:52
Alignment explanation
Indices: 1259661--1259832 Score: 155
Period size: 54 Copynumber: 3.2 Consensus size: 52
1259651 GAAAAAAATA
** * * * *
1259661 TAATTAGAAATTTTATATGCAAATATTTAATTGAAAATTTTATATGTAAAAGTC
1 TAATTA-AAATTTTATATTAAAAAATTTAA-TGAAAATTTTATGTGTGAAAGTT
* * * * * *
1259715 TAATTAAAAATTTTATATTAAAAAAACTTAGTGAAAAATTCTACGCGCGAAAGTT
1 TAATT-AAAATTTTATATT-AAAAAATTTAATG-AAAATTTTATGTGTGAAAGTT
*
1259770 TAATTAAAATTTTATATTAAAAAATTTAATGGATAAATTTTATGTATGAAAGTT
1 TAATTAAAATTTTATATTAAAAAATTTAAT-GA-AAATTTTATGTGTGAAAGTT
*
1259824 CAATTAAAA
1 TAATTAAAA
1259833 ATTCTATCGA
Statistics
Matches: 93, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
53 11 0.12
54 55 0.59
55 27 0.29
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (52 bp):
TAATTAAAATTTTATATTAAAAAATTTAATGAAAATTTTATGTGTGAAAGTT
Found at i:1260272 original size:38 final size:38
Alignment explanation
Indices: 1260196--1260273 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1260186 TTGCATATGG
* *
1260196 AAGGGTTTAAAAAATTCTATAAATAAAAAGTTCGATAA
1 AAGGATTTAAAAAATTCTATAAATAAAAAGTTCAATAA
* *
1260234 AAGGATTTAAAAAATTCTATAAATGAAAAGTTTAATAA
1 AAGGATTTAAAAAATTCTATAAATAAAAAGTTCAATAA
1260272 AA
1 AA
1260274 AATTTATACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (38 bp):
AAGGATTTAAAAAATTCTATAAATAAAAAGTTCAATAA
Found at i:1260299 original size:27 final size:29
Alignment explanation
Indices: 1260240--1260300 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1260230 ATAAAAGGAT
*
1260240 TTAAAAAATTCTATAAATGAAAAGTTTAA
1 TTAAAAAATTCTATAAATGAAAAGCTTAA
**
1260269 -TAAAAAATT-TATACGTGAAAA-CTTAA
1 TTAAAAAATTCTATAAATGAAAAGCTTAA
1260295 TTAAAA
1 TTAAAA
1260301 GTTTCACACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.14
27 15 0.54
28 9 0.32
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (29 bp):
TTAAAAAATTCTATAAATGAAAAGCTTAA
Found at i:1261792 original size:2 final size:2
Alignment explanation
Indices: 1261780--1261816 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1261770 TTTTGTACAT
*
1261780 TA TA TA AA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1261817 GATGTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1261895 original size:20 final size:20
Alignment explanation
Indices: 1261865--1261917 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1261855 ATTTATTTAG
1261865 AAATATA-ATTA-TAATGAATA
1 AAATATATATTATTAA-GAA-A
1261885 AAATA-ATATTATTAAGAAA
1 AAATATATATTATTAAGAAA
1261904 AAATATATA-TATTA
1 AAATATATATTATTA
1261918 TTCGGGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.40
20 15 0.50
21 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AAATATATATTATTAAGAAA
Found at i:1263989 original size:3 final size:3
Alignment explanation
Indices: 1263981--1264019 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1263971 ATAGATAAAT
1263981 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1264020 GCTTAGAGGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1265472 original size:18 final size:17
Alignment explanation
Indices: 1265427--1265473 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1265417 TTATTATTAA
*
1265427 ATATTATATAATT-AAT
1 ATATTTTATAATTAAAT
1265443 ATA-TTTAT-ATTAAATT
1 ATATTTTATAATTAAA-T
1265459 ATATTTTATAATTAA
1 ATATTTTATAATTAA
1265474 TCCTATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.12
15 6 0.23
16 7 0.27
17 5 0.19
18 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTTATAATTAAAT
Found at i:1269831 original size:23 final size:23
Alignment explanation
Indices: 1269781--1269835 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1269771 ATTTCATTTT
* *
1269781 TTTTCTTTTTCTTTCTTTCTTCAT
1 TTTT-TTTTTCTTTCTTTCTTAAC
1269805 TTTTTTTTTCTTT-TTTACTTAAC
1 TTTTTTTTTCTTTCTTT-CTTAAC
1269828 TTTTTTTT
1 TTTTTTTT
1269836 CAGCCCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTTTTCTTTCTTTCTTAAC
Done.