Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold76
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: 2182696
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.29
Warning! 286211 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:1255998 original size:19 final size:19
Alignment explanation
Indices: 1255974--1256038 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1255964 AGCGATACAT
1255974 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1255993 TGTATCGATAC---A-TT-
1 TGTATCGATACAAAACTTA
*
1256007 T-TATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1256025 TGTATCGATACAAA
1 TGTATCGATACAAA
1256039 TCGCTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
15 2 0.05
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.56
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1256012 original size:32 final size:32
Alignment explanation
Indices: 1255966--1256036 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1255956 AGTTTCCTAG
1255966 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1255998 CGATACATTTTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1256030 CGATACA
1 CGATACA
1256037 AATCGCTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1256100 original size:21 final size:21
Alignment explanation
Indices: 1256093--1256150 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1256083 ACATTTGTAG
1256093 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
1256114 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
1256135 AATGTATCGATACATT
1 AATGTATCGATACATT
1256151 TGGATAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:1256570 original size:19 final size:18
Alignment explanation
Indices: 1256554--1256599 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1256544 TCTCTTTTTC
1256554 TTTGTTTTGTTTTTTTTGT
1 TTTGTTTT-TTTTTTTTGT
1256573 TTTG-TTTTTTTTTTTGCT
1 TTTGTTTTTTTTTTTTG-T
1256591 TTT-TTTTTT
1 TTTGTTTTTT
1256600 GAAGAGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.36
18 12 0.48
19 4 0.16
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (18 bp):
TTTGTTTTTTTTTTTTGT
Found at i:1256582 original size:12 final size:13
Alignment explanation
Indices: 1256549--1256600 Score: 63
Period size: 12 Copynumber: 4.0 Consensus size: 13
1256539 TTTTCTCTCT
1256549 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
1256563 TTTTTTTTGTTTTG
1 -TTTTTTTGTTTTG
1256577 TTTTTTT-TTTTG
1 TTTTTTTGTTTTG
*
1256589 CTTTTTT-TTTTG
1 TTTTTTTGTTTTG
1256601 AAGAGAAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 16 0.44
13 7 0.19
14 9 0.25
15 4 0.11
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:1256583 original size:17 final size:17
Alignment explanation
Indices: 1256548--1256599 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
1256538 CTTTTCTCTC
1256548 TTTTT-CTTTGTTTTGTTT
1 TTTTTGCTTT-TTTT-TTT
1256566 TTTTTG-TTTTGTTTTTT
1 TTTTTGCTTTT-TTTTTT
1256583 TTTTTGCTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
1256600 GAAGAGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.87
Consensus pattern (17 bp):
TTTTTGCTTTTTTTTTT
Found at i:1258078 original size:59 final size:56
Alignment explanation
Indices: 1257555--1258257 Score: 734
Period size: 55 Copynumber: 12.3 Consensus size: 56
1257545 ATAAAGTGTA
* * *
1257555 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT--GAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
* *
1257610 TCCTGGTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAG--AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
** * * *
1257665 TCCTGCTCTTTGAGGACTGGAAAATGCCACAAACTTATGTGGGCTTT--GAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
* * *
1257720 TCCTTCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AG-GAGGTG
1 TCCTGCTCTTTGA-GGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
** **
1257775 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--GAAAGGTT
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
* ** * * *
1257830 TCCGGCTCTTTGAGGACTGGAAAATGTCACCAATTTGTGTGGGCTTT--GAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
* * *
1257885 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT---AAG-AAAGGCG
* *
1257946 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGT-GGATTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCG
* *
1258004 TCCCGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCG
*
1258063 TCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCG
* *
1258122 TCTTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-AAAGGCG
* *
1258181 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGG-TTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AA-G-AAAGGCG
1258240 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1258258 AAAAACCGGA
Statistics
Matches: 574, Mismatches: 53, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
53 1 0.00
54 4 0.01
55 267 0.47
56 4 0.01
57 1 0.00
58 54 0.09
59 201 0.35
60 20 0.03
61 22 0.04
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAAAGGCG
Found at i:1259251 original size:5 final size:5
Alignment explanation
Indices: 1259243--1259290 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
1259233 TCTCTTTTTC
* *
1259243 TTTGT TTTGT TTT-T TTTGT TTTGT TTT-T TTTTT TTTGCT TTTTT TTTG
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTG-T TTTGT TTTG
1259291 AAGAGAAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 8 0.22
5 25 0.68
6 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (5 bp):
TTTGT
Found at i:1259255 original size:14 final size:14
Alignment explanation
Indices: 1259237--1259288 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
1259227 CTTTTCTCTC
1259237 TTTTTCTTTGTTTTG
1 TTTTT-TTTGTTTTG
1259252 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
*
1259266 TTTTTTTTTTTTTG
1 TTTTTTTTGTTTTG
1259280 CTTTTTTTT
1 -TTTTTTTT
1259289 TGAAGAGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.87
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:1259259 original size:19 final size:18
Alignment explanation
Indices: 1259237--1259289 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1259227 CTTTTCTCTC
1259237 TTTTTCTTTGTTTTGTTTT
1 TTTTTCTTTGTTTT-TTTT
1259256 TTTTGT-TTTGTTTTTTTT
1 TTTT-TCTTTGTTTTTTTT
1259274 TTTTTGCTTT-TTTTTT
1 TTTTT-CTTTGTTTTTT
1259290 GAAGAGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 15 0.48
20 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTGTTTTTTTT
Found at i:1287507 original size:10 final size:10
Alignment explanation
Indices: 1287494--1287523 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1287484 CAATGGAATA
1287494 GTGTTTTTTT
1 GTGTTTTTTT
1287504 GTGTTTTTTT
1 GTGTTTTTTT
1287514 G-GTTTTTTT
1 GTGTTTTTTT
1287523 G
1 G
1287524 CTAAAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (10 bp):
GTGTTTTTTT
Found at i:1288077 original size:20 final size:21
Alignment explanation
Indices: 1288029--1288084 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1288019 TAAACTTCCT
1288029 AGATGTATCGATACAAAGAAA
1 AGATGTATCGATACAAAGAAA
*
1288050 AGATGTATCGATACACAGAAA
1 AGATGTATCGATACAAAGAAA
1288071 A-ATGTATCGATACA
1 AGATGTATCGATACA
1288085 TTTCCTTGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (21 bp):
AGATGTATCGATACAAAGAAA
Found at i:1288126 original size:13 final size:13
Alignment explanation
Indices: 1288108--1288191 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1288098 AGCTTCCTAG
1288108 CGATACATTGTAT
1 CGATACATTGTAT
1288121 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1288140 CGATACATTGTAT
1 CGATACATTGTAT
1288153 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1288172 CGATACATTGTAT
1 CGATACATTGTAT
1288185 CGATACA
1 CGATACA
1288192 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1288140 original size:19 final size:18
Alignment explanation
Indices: 1288116--1288212 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1288106 AGCGATACAT
1288116 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1288135 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1288148 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1288167 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1288180 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1288199 TGTATCGATACAAA
1 TGTATCGATACAAA
1288213 TCGCTGAAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1288149 original size:32 final size:32
Alignment explanation
Indices: 1288108--1288210 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1288098 AGCTTCCTAG
*
1288108 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1288140 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1288172 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1288204 CGATACA
1 CGATACA
1288211 AATCGCTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1288274 original size:21 final size:22
Alignment explanation
Indices: 1288248--1288305 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1288238 GTTGAGACCC
* *
1288248 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
1288269 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
1288290 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1288306 GATAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:1288705 original size:1 final size:1
Alignment explanation
Indices: 1288701--1288762 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
1288691 CTTTTCTCTC
* * * * * ** *
1288701 TTTTTCTTTGTTTTGTTTTTTTTGTTTTGTTTTTTTTTTTTGCTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1288763 GAAGAGAAGG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (1 bp):
T
Found at i:1288719 original size:14 final size:14
Alignment explanation
Indices: 1288701--1288762 Score: 83
Period size: 14 Copynumber: 4.4 Consensus size: 14
1288691 CTTTTCTCTC
1288701 TTTTTCTTTGTTTTG
1 TTTTT-TTTGTTTTG
1288716 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
1288730 TTTTTTTT-TTTTG
1 TTTTTTTTGTTTTG
*
1288743 CTTTTTTTTCTTTT-
1 -TTTTTTTTGTTTTG
1288757 TTTTTT
1 TTTTTT
1288763 GAAGAGAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.24
14 25 0.56
15 9 0.20
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:1288723 original size:19 final size:18
Alignment explanation
Indices: 1288701--1288760 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
1288691 CTTTTCTCTC
1288701 TTTTTCTTTGTTTTGTTTT
1 TTTTTCTTTGTTTT-TTTT
1288720 TTTTGT-TTTGTTTTTTTT
1 TTTT-TCTTTGTTTTTTTT
*
1288738 TTTTGCTTT-TTTTTCTTT
1 TTTTTCTTTGTTTTT-TTT
1288756 TTTTT
1 TTTTT
1288761 TTGAAGAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.14
18 18 0.50
19 12 0.33
20 1 0.03
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTGTTTTTTTT
Found at i:1289812 original size:55 final size:55
Alignment explanation
Indices: 1289728--1290346 Score: 698
Period size: 55 Copynumber: 11.0 Consensus size: 55
1289718 ATAAAGTGTA
* * *
1289728 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1289783 TCCTGCTCTTCGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
1289838 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1289893 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AGGAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGA-AAGGCG
* * *
1289948 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGGAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1290003 TCCTGCTCTTTGAGGACTCGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1290058 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * * *
1290119 TCCTGCTCTTTGAGGACTG-GAGGTGCCACCAACTTGGGTGGGCTTTAAAAAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAGGCG
* * *
1290177 TCCCGCTCTTTGAGGACTG-AAGGTGCCACTAACTTGTATGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
*
1290236 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * *
1290295 TCCCGCTCTCTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
1290347 AAAAGGCATC
Statistics
Matches: 500, Mismatches: 43, Indels: 43
0.85 0.07 0.07
Matches are distributed among these distances:
54 16 0.03
55 272 0.54
56 14 0.03
58 50 0.10
59 99 0.20
60 26 0.05
61 19 0.04
63 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1291361 original size:1 final size:1
Alignment explanation
Indices: 1291357--1291413 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1291347 CTTTTCTCTC
* * * * * * *
1291357 TTTTTCTTTGTTTTGTTTTTTTTGTTTTGTTTTTTTTCTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1291414 GAAGAGAAGG
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:0.05, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:1291375 original size:14 final size:14
Alignment explanation
Indices: 1291358--1291410 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
1291348 TTTTCTCTCT
1291358 TTTTCTTTGTTTTG
1 TTTTCTTTGTTTTG
*
1291372 TTTTTTTTGTTTTG
1 TTTTCTTTGTTTTG
* *
1291386 TTTTTTTTCTTTT-
1 TTTTCTTTGTTTTG
1291399 TTTTCTTT-TTTT
1 TTTTCTTTGTTTT
1291411 TTTGAAGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
12 4 0.11
13 7 0.19
14 25 0.69
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.87
Consensus pattern (14 bp):
TTTTCTTTGTTTTG
Found at i:1291378 original size:32 final size:32
Alignment explanation
Indices: 1291342--1291411 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1291332 AAGCAGGTTC
*
1291342 TTTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTT
1 TTTTTCTTTTCT-TCTTTTTCTTTGTTTTCTTT
* * * *
1291375 TTTTTGTTTTGTTTTTTTTCTTTTTTTTCTTT
1 TTTTTCTTTTCTTCTTTTTCTTTGTTTTCTTT
1291407 TTTTT
1 TTTTT
1291412 TTGAAGAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (32 bp):
TTTTTCTTTTCTTCTTTTTCTTTGTTTTCTTT
Found at i:1291412 original size:14 final size:14
Alignment explanation
Indices: 1291342--1291413 Score: 58
Period size: 13 Copynumber: 5.1 Consensus size: 14
1291332 AAGCAGGTTC
* *
1291342 TTTTTCTTTTCTCTC
1 TTTTTCTTTT-TTTT
*
1291357 TTTTTCTTTGTTTTG
1 TTTTTCTTT-TTTTT
*
1291372 TTTTT-TTTGTTTT
1 TTTTTCTTTTTTTT
* *
1291385 GTTTT-TTTTCTTT
1 TTTTTCTTTTTTTT
1291398 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
1291412 TT
1 TT
1291414 GAAGAGAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 17 0.37
14 12 0.26
15 16 0.35
16 1 0.02
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:1292230 original size:31 final size:31
Alignment explanation
Indices: 1292191--1292258 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
1292181 GCGTCCTCCG
1292191 CAAAAAAAAAC-AAA-AAAACAAAAAAAACAA
1 CAAAAAAAAACAAAACAAAAC-AAAAAAACAA
1292221 CGAAAAAAAAACAAAACAAAACAAAAAAACAA
1 C-AAAAAAAAACAAAACAAAACAAAAAAACAA
1292253 CAAAAA
1 CAAAAA
1292259 GGGTCCGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 1 0.03
31 15 0.43
32 14 0.40
33 5 0.14
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (31 bp):
CAAAAAAAAACAAAACAAAACAAAAAAACAA
Found at i:1292257 original size:28 final size:28
Alignment explanation
Indices: 1292194--1292258 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
1292184 TCCTCCGCAA
* *
1292194 AAAAAAACAAAAAAACAAAAAAAACAACG
1 AAAAAAA-AACAAAACAAAAAAAAAAACG
1292223 AAAAAAAAACAAAACAAAACAAAAAAAC-
1 AAAAAAAAACAAAACAAAA-AAAAAAACG
*
1292251 AACAAAAA
1 AAAAAAAA
1292259 GGGTCCGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.85, C:0.14, G:0.02, T:0.00
Consensus pattern (28 bp):
AAAAAAAAACAAAACAAAAAAAAAAACG
Found at i:1293742 original size:8 final size:9
Alignment explanation
Indices: 1293710--1293843 Score: 52
Period size: 8 Copynumber: 15.6 Consensus size: 9
1293700 CATATTTCTC
*
1293710 AAAAGCACA
1 AAAAACACA
*
1293719 AAAAAAACA
1 AAAAACACA
*
1293728 CATAAAC-CA
1 -AAAAACACA
1293737 AAAAACACAA
1 AAAAACAC-A
*
1293747 AAAAAAACA
1 AAAAACACA
*
1293756 AAAAA-ATA
1 AAAAACACA
*
1293764 AACAA-ACA
1 AAAAACACA
1293772 AAAAA-A-A
1 AAAAACACA
**
1293779 ACCAACACA
1 AAAAACACA
1293788 AAAAA-AC-
1 AAAAACACA
1293795 AAAAACA-A
1 AAAAACACA
* *
1293803 AAAACCAAA
1 AAAAACACA
*
1293812 AAAAAAAC-
1 AAAAACACA
* *
1293820 AACAACAAA
1 AAAAACACA
*
1293829 AACAAAAACA
1 AA-AAACACA
1293839 AAAAA
1 AAAAA
1293844 AAACATTTGT
Statistics
Matches: 91, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
7 9 0.10
8 33 0.36
9 31 0.34
10 18 0.20
ACGTcount: A:0.80, C:0.18, G:0.01, T:0.01
Consensus pattern (9 bp):
AAAAACACA
Found at i:1293749 original size:1 final size:1
Alignment explanation
Indices: 1293745--1293846 Score: 51
Period size: 1 Copynumber: 102.0 Consensus size: 1
1293735 CAAAAAACAC
* * * * ** * * * * **
1293745 AAAAAAAAACAAAAAAATAAACAAACAAAAAAAAACCAACACAAAAAAACAAAAACAAAAAACCA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
1293810 AAAAAAAAACAACAACAAAAACAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1293847 CATTTGTTTT
Statistics
Matches: 71, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:1293772 original size:16 final size:15
Alignment explanation
Indices: 1293745--1293846 Score: 92
Period size: 14 Copynumber: 7.1 Consensus size: 15
1293735 CAAAAAACAC
1293745 AAAAAA-AAACAAAA
1 AAAAAACAAACAAAA
1293759 AAATAAACAAAC-AAA
1 AAA-AAACAAACAAAA
* *
1293774 AAAAAACCAAC-ACA
1 AAAAAACAAACAAAA
*
1293788 AAAAAACAAA-AACA
1 AAAAAACAAACAAAA
*
1293802 AAAAACCAAA-AAAA
1 AAAAAACAAACAAAA
*
1293816 AAACAAC-AACAAAA
1 AAAAAACAAACAAAA
1293830 ACAAAAACAAA-AAAA
1 A-AAAAACAAACAAAA
1293845 AA
1 AA
1293847 CATTTGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
13 2 0.03
14 47 0.64
15 19 0.26
16 6 0.08
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.01
Consensus pattern (15 bp):
AAAAAACAAACAAAA
Found at i:1293775 original size:53 final size:52
Alignment explanation
Indices: 1293716--1293844 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 52
1293706 TCTCAAAAGC
* *
1293716 ACAAAAAAAACACATAAACCAAAAAACACAAA-AAAAAA-CAAAAAAATAAACAA
1 ACAAAAAAAACACA-AAACAAAAAAACAAAAACAAAAAACCAAAAAAA-AAAC-A
*
1293769 ACAAAAAAAA-ACCAACACAAAAAAACAAAAACAAAAAACCAAAAAAAAAACA
1 ACAAAAAAAACA-CAAAACAAAAAAACAAAAACAAAAAACCAAAAAAAAAACA
*
1293821 ACAACAAAAACA-AAAACAAAAAAA
1 ACAAAAAAAACACAAAACAAAAAAA
1293845 AACATTTGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
51 11 0.16
52 25 0.37
53 23 0.34
54 8 0.12
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.02
Consensus pattern (52 bp):
ACAAAAAAAACACAAAACAAAAAAACAAAAACAAAAAACCAAAAAAAAAACA
Found at i:1293778 original size:38 final size:39
Alignment explanation
Indices: 1293718--1293846 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 39
1293708 TCAAAAGCAC
**
1293718 AAAAAAAACACATAAACCAAAAAAC-ACAAAAAAAAACAAA
1 AAAAAAAAC-CA-AAAAAAAAAAACAACAAAAAAAAACAAA
* *
1293758 AAAATAAA-CAAACAAAAAAAAACCAACACAAAAAAACAAA
1 AAAAAAAACCAAA-AAAAAAAAA-CAACAAAAAAAAACAAA
1293798 AACAAAAAACCAAAAAAAAAACAACAACAAAAACAAAAACAAA
1 AA-AAAAAACCAAAAAAAAAA-AACAAC-AAAA-AAAAACAAA
1293841 AAAAAA
1 AAAAAA
1293847 CATTTGTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
37 2 0.03
38 9 0.12
39 1 0.01
40 23 0.31
41 16 0.21
42 13 0.17
43 11 0.15
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (39 bp):
AAAAAAAACCAAAAAAAAAAAACAACAAAAAAAAACAAA
Found at i:1293848 original size:28 final size:26
Alignment explanation
Indices: 1293716--1293846 Score: 115
Period size: 27 Copynumber: 4.8 Consensus size: 26
1293706 TCTCAAAAGC
* *
1293716 ACAAAAAAAACACATAAACCAAAAAAC-
1 ACAAAAAAAAAACA-AAA-AAAAAAACA
*
1293743 AC-AAAAAAAAACAAAAAAATAAACAA
1 ACAAAAAAAAAACAAAAAAAAAAAC-A
* *
1293769 ACAAAAAAAAACCAACACAAAAAAACA
1 ACAAAAAAAAAACAA-AAAAAAAAACA
*
1293796 A-AAACAAAAAACCAAAAAAAAAACAACA
1 ACAAA-AAAAAAAC-AAAAAAAAA-AACA
1293824 ACAAAAACAAAAACAAAAAAAAA
1 ACAAAAA-AAAAACAAAAAAAAA
1293847 CATTTGTTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
24 6 0.07
25 3 0.03
26 15 0.17
27 29 0.33
28 26 0.30
29 8 0.09
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.02
Consensus pattern (26 bp):
ACAAAAAAAAAACAAAAAAAAAAACA
Found at i:1294020 original size:26 final size:26
Alignment explanation
Indices: 1293991--1294073 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
1293981 GGGTCTTTGG
1293991 GTGTGGTGGGGTGTTGGGTTTTGGGT
1 GTGTGGTGGGGTGTTGGGTTTTGGGT
* * *
1294017 GTGTTGGTTGGTTG-TGTGTTTTGGGT
1 GTG-TGGTGGGGTGTTGGGTTTTGGGT
*
1294043 G-G-GGTGTGTGTGTTGTGG--TTGGGT
1 GTGTGGTG-GGGTGTTG-GGTTTTGGGT
1294067 GTGTGGT
1 GTGTGGT
1294074 TTTGTGGGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
23 3 0.07
24 10 0.23
25 4 0.09
26 19 0.43
27 8 0.18
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (26 bp):
GTGTGGTGGGGTGTTGGGTTTTGGGT
Found at i:1294054 original size:20 final size:20
Alignment explanation
Indices: 1294029--1294077 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1294019 GTTGGTTGGT
1294029 TGTGTGTTTTGGGTGGGGTG
1 TGTGTGTTTTGGGTGGGGTG
* *
1294049 TGTGTGTTGT-GGTTGGGTG
1 TGTGTGTTTTGGGTGGGGTG
1294068 TGTG-GTTTTG
1 TGTGTGTTTTG
1294078 TGGGGTGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 12 0.48
20 9 0.36
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (20 bp):
TGTGTGTTTTGGGTGGGGTG
Found at i:1294078 original size:20 final size:19
Alignment explanation
Indices: 1294021--1294080 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
1294011 TTGGGTGTGT
*
1294021 TGGTTGGTTGTGTGTTTTG
1 TGGTTGGGTGTGTGTTTTG
* *
1294040 -GGTGGGGTGTGTGTGTTG
1 TGGTTGGGTGTGTGTTTTG
1294058 TGGTTGGGTGTGTGGTTTTG
1 TGGTTGGGTGTGT-GTTTTG
1294078 TGG
1 TGG
1294081 GGTGGTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 15 0.44
19 11 0.32
20 8 0.24
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (19 bp):
TGGTTGGGTGTGTGTTTTG
Found at i:1294171 original size:21 final size:20
Alignment explanation
Indices: 1294103--1294173 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 20
1294093 TTGGTTTTTG
* *
1294103 GGGTGTGGGTGGTTGTGTTTT
1 GGGTGGGGGT-GTTGTGGTTT
**
1294124 GGTGTGGGGGT-TTG-GGGGT
1 GG-GTGGGGGTGTTGTGGTTT
1294143 GTGGTGGGGGTGTTGTTGGTTT
1 G-GGTGGGGGTGTTG-TGGTTT
1294165 GGGTGGGGG
1 GGGTGGGGG
1294174 CTTTTTGGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 11 0.28
20 7 0.18
21 10 0.26
22 11 0.28
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (20 bp):
GGGTGGGGGTGTTGTGGTTT
Found at i:1294311 original size:20 final size:20
Alignment explanation
Indices: 1294274--1294311 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1294264 TGGTGTCGGT
*
1294274 TGGTGTTTGGTGTTGGGGCG
1 TGGTGTTTGGTGTGGGGGCG
1294294 TGGTG-TTGTGTGTGGGGG
1 TGGTGTTTG-GTGTGGGGG
1294312 GGTGTGGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.00, C:0.03, G:0.58, T:0.39
Consensus pattern (20 bp):
TGGTGTTTGGTGTGGGGGCG
Found at i:1294411 original size:19 final size:20
Alignment explanation
Indices: 1294374--1294411 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1294364 TTGGGTGGGG
* *
1294374 TGGGTTGTGGTGGTTGGTTT
1 TGGGTTGTGGTGCTGGGTTT
1294394 TGGGTT-TGGTGCTGGGTT
1 TGGGTTGTGGTGCTGGGTT
1294412 GGGTGGGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (20 bp):
TGGGTTGTGGTGCTGGGTTT
Found at i:1294564 original size:34 final size:33
Alignment explanation
Indices: 1294489--1294590 Score: 105
Period size: 34 Copynumber: 3.0 Consensus size: 33
1294479 TTCCAGTGGA
* * *
1294489 CCTTCTAAAGTCCCACAATCTCAGTGGCAACTTTT
1 CCTTTTAAAG-CCCACAA-CTCTGTGGCACCTTTT
** *
1294524 TTTTTTAAAGCCCGCAACTCTGTGGCACTCTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCAC-CTTTT
* *
1294558 CCTTTTACAGTCCACAACTCTGTGGCACCTTTT
1 CCTTTTAAAGCCCACAACTCTGTGGCACCTTTT
1294591 AAGCCCACAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
33 14 0.25
34 34 0.62
35 7 0.13
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (33 bp):
CCTTTTAAAGCCCACAACTCTGTGGCACCTTTT
Found at i:1294627 original size:29 final size:28
Alignment explanation
Indices: 1294579--1294684 Score: 110
Period size: 28 Copynumber: 3.8 Consensus size: 28
1294569 CCACAACTCT
1294579 GTGGCA-CCTTTT-AAGCCCACAAGTTG
1 GTGGCACCCTTTTAAAGCCCACAAGTTG
*
1294605 GTGGCACCCCTTTTAAAGCCCACAAGTTA
1 GTGGCA-CCCTTTTAAAGCCCACAAGTTG
* ** *
1294634 GTGGCAACCTTCAAAAGCACACAAGTTG
1 GTGGCACCCTTTTAAAGCCCACAAGTTG
* *
1294662 AT-GCAACCCTTTCAAAGCCCACA
1 GTGGC-ACCCTTTTAAAGCCCACA
1294685 CAAGTTGATG
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
26 6 0.09
27 2 0.03
28 38 0.58
29 19 0.29
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (28 bp):
GTGGCACCCTTTTAAAGCCCACAAGTTG
Found at i:1294629 original size:55 final size:56
Alignment explanation
Indices: 1294558--1294684 Score: 134
Period size: 56 Copynumber: 2.3 Consensus size: 56
1294548 GCACTCTTTT
* * ** * * *
1294558 CCTTTTACAGTCCACAACTCT-GTGGC-ACCTT-TTAAGCCCACAAGTTGGTGGCACC
1 CCTTTTAAAGCCCACAACT-TAGTGGCAACCTTCAAAAGCACACAAGTTGAT-GCAAC
*
1294613 CCTTTTAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCACACAAGTTGATGCAAC
1 CCTTTTAAAGCCCACAACTTAGTGGCAACCTTCAAAAGCACACAAGTTGATGCAAC
*
1294669 CCTTTCAAAGCCCACA
1 CCTTTTAAAGCCCACA
1294685 CAAGTTGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
54 1 0.02
55 21 0.35
56 24 0.40
57 14 0.23
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (56 bp):
CCTTTTAAAGCCCACAACTTAGTGGCAACCTTCAAAAGCACACAAGTTGATGCAAC
Found at i:1294644 original size:28 final size:27
Alignment explanation
Indices: 1294558--1294684 Score: 107
Period size: 28 Copynumber: 4.6 Consensus size: 27
1294548 GCACTCTTTT
* * *
1294558 CCTTTTACAGTCCACAACTCTGTGGC-A
1 CCTTTTAAAGCCCACAAGT-TGTGGCAA
*
1294585 CCTTTT-AAGCCCACAAGTTGGTGGCACC
1 CCTTTTAAAGCCCACAAGTT-GTGGCA-A
1294613 CCTTTTAAAGCCCACAAGTTAGTGGCAA
1 CCTTTTAAAGCCCACAAGTT-GTGGCAA
** *
1294641 CCTTCAAAAGCACACAAGTTGAT-GCAA
1 CCTTTTAAAGCCCACAAGTTG-TGGCAA
*
1294668 CCCTTTCAAAGCCCACA
1 -CCTTTTAAAGCCCACA
1294685 CAAGTTGATG
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
25 1 0.01
26 14 0.17
27 11 0.13
28 37 0.45
29 19 0.23
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (27 bp):
CCTTTTAAAGCCCACAAGTTGTGGCAA
Found at i:1294826 original size:49 final size:49
Alignment explanation
Indices: 1294754--1294937 Score: 217
Period size: 49 Copynumber: 3.7 Consensus size: 49
1294744 ACCTTGAAGA
* * *
1294754 CCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
1294803 CCAATGTAGCTGGCCTTGAATCAGCACACTGGCATCTTCACCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * ** *
1294852 CCAATAG-CGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTTGAGT
1 CCAAT-GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-T-TTAAGT
* *
1294903 CCAATATAGCTGGCCTTGAATCAGCACATTAGCAC
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1294938 AAGTCCAATA
Statistics
Matches: 113, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
49 76 0.67
50 2 0.02
51 35 0.31
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (49 bp):
CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:1294869 original size:98 final size:100
Alignment explanation
Indices: 1294743--1294930 Score: 265
Period size: 98 Copynumber: 1.9 Consensus size: 100
1294733 AGCATATTGA
1294743 CACCTTGAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATC-T-TTAAGTCCA
1 CACCTTGAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATCGTCTTAAGTCCA
*
1294806 ATGTAGCTGGCCTTGAATCAGCACACTGGCATCTT
66 ATATAGCTGGCCTTGAATCAGCACACTGGCATCTT
* * * * * ** *
1294841 CACCTTTAAGTCCAATAG-CGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCGTCTTGAGTCC
1 CACCTTGAAGACCAAT-GTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATCGTCTTAAGTCC
1294905 AATATAGCTGGCCTTGAATCAGCACA
65 AATATAGCTGGCCTTGAATCAGCACA
1294931 TTAGCACAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 44 0.56
99 2 0.03
100 32 0.41
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (100 bp):
CACCTTGAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATCGTCTTAAGTCCA
ATATAGCTGGCCTTGAATCAGCACACTGGCATCTT
Found at i:1295845 original size:13 final size:13
Alignment explanation
Indices: 1295827--1295851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1295817 ACATAAGTGT
1295827 TGTATCGATACAA
1 TGTATCGATACAA
1295840 TGTATCGATACA
1 TGTATCGATACA
1295852 TAAGTTTTGT
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:1295851 original size:32 final size:32
Alignment explanation
Indices: 1295808--1295875 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1295798 CATAAAGTGT
1295808 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
* *
1295840 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTGTTGTATCGATACAA
1295872 TGTA
1 TGTA
1295876 AGCTACTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTGTTGTATCGATACAA
Found at i:1295864 original size:19 final size:19
Alignment explanation
Indices: 1295787--1295870 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
1295777 TTTCAACGAT
1295787 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
*
1295807 TTGTATCAATACATAAGTG
1 TTGTATCGATACATAAGTG
1295826 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
1295840 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1295858 TTGTATCGATACA
1 TTGTATCGATACA
1295871 ATGTAAGCTA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 28 0.50
20 13 0.23
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1295989 original size:52 final size:52
Alignment explanation
Indices: 1295926--1296123 Score: 310
Period size: 52 Copynumber: 3.8 Consensus size: 52
1295916 ATTGATACAT
** * * *
1295926 TGTATCGATACACTGAT-CTTTGTATCAATACATGCAGGAAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
1295978 TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
1296030 TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
*
1296082 TGTATCGATACACTATGAAA-TGTATCGATACATGCAGGCAAA
1 TGTATCGATACACTAT-AAATTGTATCGATACATACAGGCAAA
1296124 GTTTCATATT
Statistics
Matches: 138, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
51 2 0.01
52 133 0.96
53 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
Found at i:1302298 original size:18 final size:17
Alignment explanation
Indices: 1302275--1302341 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 17
1302265 TTCTTTCACC
1302275 AAAGAGAAAAAAAGAAG
1 AAAGAGAAAAAAAGAAG
1302292 AATAGAGAAAAATAAAGAAG
1 AA-AGAG-AAAA-AAAGAAG
*
1302312 AAA-AGAAAAAAAAAAG
1 AAAGAGAAAAAAAGAAG
*
1302328 GAA-A-AAAAAAAGAA
1 AAAGAGAAAAAAAGAA
1302342 TTTCTAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
15 9 0.20
16 9 0.20
17 6 0.14
18 6 0.14
19 5 0.11
20 9 0.20
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAGAGAAAAAAAGAAG
Found at i:1302310 original size:20 final size:19
Alignment explanation
Indices: 1302275--1302327 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1302265 TTCTTTCACC
1302275 AAAGAG-AAAAAAAGAAGA
1 AAAGAGAAAAAAAAGAAGA
*
1302293 ATAGAGAAAAATAAAGAAGA
1 AAAGAGAAAAA-AAAGAAGA
*
1302313 AAAGAAAAAAAAAAG
1 AAAGAGAAAAAAAAG
1302328 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.17
19 8 0.27
20 17 0.57
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAGAGAAAAAAAAGAAGA
Found at i:1302332 original size:11 final size:11
Alignment explanation
Indices: 1302279--1302341 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 11
1302269 TTCACCAAAG
*
1302279 AGAAAAAAAGA
1 AGAAAAAAAAA
*
1302290 AGAATAGAGAAAA
1 AGAA-A-AAAAAA
* *
1302303 ATAAAGAAGAAA
1 AGAAA-AAAAAA
1302315 AGAAAAAAAAA
1 AGAAAAAAAAA
1302326 AGGAAAAAAAAA
1 A-GAAAAAAAAA
1302338 AGAA
1 AGAA
1302342 TTTCTAACTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
11 13 0.31
12 22 0.52
13 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:1303040 original size:19 final size:18
Alignment explanation
Indices: 1303002--1303038 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1302992 AATTTTTACC
* *
1303002 TAAATAGTCTAGAATTTT
1 TAAACAGTCCAGAATTTT
1303020 TAAACAGTCCAGAATTTT
1 TAAACAGTCCAGAATTTT
1303038 T
1 T
1303039 TAGCATTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TAAACAGTCCAGAATTTT
Found at i:1305802 original size:92 final size:91
Alignment explanation
Indices: 1305603--1305824 Score: 263
Period size: 91 Copynumber: 2.4 Consensus size: 91
1305593 TCAAATGTTC
* * * * *
1305603 CCTTCGTATAATTTTATCCTTAGGAAAACTCTATCTCCATTACTTCGAGGGGATACTCCAACCCC
1 CCTTTGTATAATTTTATCCTTAGGAAAACTCCATCCCCATTACTTCAAGAGGATACTCCAACCCC
*
1305668 GTTTTTCTAAAAATTTCAAAATTTTT
66 GTTTTTCTAAAAATTTCAAAATTTTA
* * * * * *
1305694 CCTTTGTATAATTTTATCTTTGAGG-ATACTCCATCCCCATTCCTTCAAGATGATACTTCACCCC
1 CCTTTGTATAATTTTATCCTT-AGGAAAACTCCATCCCCATTACTTCAAGAGGATACTCCAACCC
1305758 CGTTTTAT-TAAAAAAATTTC-AAA-TTTA
65 CGTTTT-TCT--AAAAATTTCAAAATTTTA
1305785 CCATTTGTATAATTTTATCCTTAGGAAAACTCCATCCCCA
1 CC-TTTGTATAATTTTATCCTTAGGAAAACTCCATCCCCA
1305825 CTATACCGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
91 64 0.58
92 38 0.34
93 9 0.08
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (91 bp):
CCTTTGTATAATTTTATCCTTAGGAAAACTCCATCCCCATTACTTCAAGAGGATACTCCAACCCC
GTTTTTCTAAAAATTTCAAAATTTTA
Found at i:1308474 original size:22 final size:23
Alignment explanation
Indices: 1308449--1308499 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1308439 TAATCTTGTT
*
1308449 AAATAAAACAATT-AATTAAATA
1 AAATAAAACAATTAAATAAAATA
* * *
1308471 AAATTAAATAATTAAATAAAATC
1 AAATAAAACAATTAAATAAAATA
1308494 AAATAA
1 AAATAA
1308500 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAAAACAATTAAATAAAATA
Found at i:1308484 original size:18 final size:18
Alignment explanation
Indices: 1308447--1308514 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
1308437 ATTAATCTTG
*
1308447 TTAAATAAAA-CAATTAA
1 TTAAATAAAATCAAATAA
*
1308464 TTAAATAAAATTAAATAA
1 TTAAATAAAATCAAATAA
1308482 TTAAATAAAATCAAATAA
1 TTAAATAAAATCAAATAA
*
1308500 TTAAATAAAACCAAA
1 TTAAATAAAATCAAA
1308515 ATTAAGAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 10 0.22
18 36 0.78
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAATAAAATCAAATAA
Found at i:1308486 original size:14 final size:14
Alignment explanation
Indices: 1308447--1308508 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1308437 ATTAATCTTG
*
1308447 TTAAATAAA-ACAA
1 TTAAATAAATAAAA
*
1308460 TTAATTAAATAAAA
1 TTAAATAAATAAAA
*
1308474 TTAAAT-AATTAAA
1 TTAAATAAATAAAA
*
1308487 TAAAATCAAAT--AA
1 TTAAAT-AAATAAAA
1308500 TTAAATAAA
1 TTAAATAAA
1308509 ACCAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 3 0.08
13 26 0.65
14 8 0.20
15 3 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAATAAATAAAA
Found at i:1309267 original size:23 final size:24
Alignment explanation
Indices: 1309241--1309285 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1309231 GGAATAATTT
*
1309241 AGCTATTAGTGA-CAAAATAATCG
1 AGCTATTAGAGATCAAAATAATCG
*
1309264 AGCTATTTGAGATCAAAATAAT
1 AGCTATTAGAGATCAAAATAAT
1309286 ATTTTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (24 bp):
AGCTATTAGAGATCAAAATAATCG
Found at i:1311601 original size:57 final size:57
Alignment explanation
Indices: 1311523--1311637 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
1311513 ATACAAACAA
* *
1311523 TCTACTTAGACCTATGTGCAGGGCAGTAATAGGGTCAACGGAGGTCCTATTGAAAAT
1 TCTAATTAGACCTATGAGCAGGGCAGTAATAGGGTCAACGGAGGTCCTATTGAAAAT
1311580 TCTAATTAGACCTATGAGCAGGGCAGTAATAGGGTCAACGGAGGTCCTATTGAAAAT
1 TCTAATTAGACCTATGAGCAGGGCAGTAATAGGGTCAACGGAGGTCCTATTGAAAAT
1311637 T
1 T
1311638 AAGTACAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (57 bp):
TCTAATTAGACCTATGAGCAGGGCAGTAATAGGGTCAACGGAGGTCCTATTGAAAAT
Found at i:1314994 original size:22 final size:24
Alignment explanation
Indices: 1314967--1315022 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1314957 CTATTTAAAA
* *
1314967 AAATTATTTTTATATA-TTTTTAT
1 AAATTATATTTAAATATTTTTTAT
*
1314990 -AATTAAATTTAAATATTTTTTAT
1 AAATTATATTTAAATATTTTTTAT
1315013 AAATTATATT
1 AAATTATATT
1315023 GTGGTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 12 0.44
23 7 0.26
24 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AAATTATATTTAAATATTTTTTAT
Found at i:1318343 original size:18 final size:18
Alignment explanation
Indices: 1318279--1318336 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
1318269 AAAGATAATT
1318279 TTTAAAATA-AAATATAGA
1 TTTAAAATATAAATATA-A
**
1318297 TAAAAAATATAAATATAA
1 TTTAAAATATAAATATAA
*
1318315 TTTAAAATATAAATTTAA
1 TTTAAAATATAAATATAA
1318333 TTTA
1 TTTA
1318337 TTATATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 27 0.79
19 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTTAAAATATAAATATAA
Found at i:1319289 original size:27 final size:27
Alignment explanation
Indices: 1319258--1319313 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1319248 ATGTTATGTG
* * * *
1319258 TTAAAATATAGTTTTTAACTTAGTCAT
1 TTAAAATAAAGTTGTTAACTCAATCAT
*
1319285 TTAAAGTAAAGTTGTTAACTCAATCAT
1 TTAAAATAAAGTTGTTAACTCAATCAT
1319312 TT
1 TT
1319314 TTATAGTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (27 bp):
TTAAAATAAAGTTGTTAACTCAATCAT
Found at i:1319845 original size:19 final size:19
Alignment explanation
Indices: 1319805--1319866 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
1319795 TATGACATTA
*
1319805 ATACATGAAGATATTAAA-AT
1 ATACAT-AAAATA-TAAATAT
1319825 ATACATAAAATATAAATAT
1 ATACATAAAATATAAATAT
*
1319844 ATA-ATAAAA-ATAACATAA
1 ATACATAAAATATAA-ATAT
1319862 ATACA
1 ATACA
1319867 ATTCGAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 4 0.11
18 16 0.43
19 11 0.30
20 6 0.16
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.27
Consensus pattern (19 bp):
ATACATAAAATATAAATAT
Found at i:1321149 original size:13 final size:13
Alignment explanation
Indices: 1321131--1321156 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1321121 TACAGCAAGT
1321131 ATGTATCGATACA
1 ATGTATCGATACA
1321144 ATGTATCGATACA
1 ATGTATCGATACA
1321157 CAAAAAAATT
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:1325245 original size:15 final size:15
Alignment explanation
Indices: 1325225--1325255 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1325215 TAAAAATGTC
*
1325225 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1325240 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1325255 C
1 C
1325256 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1327367 original size:13 final size:13
Alignment explanation
Indices: 1327334--1327369 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1327324 ACATTTTTCT
*
1327334 TTGTATCCATACA
1 TTGTATCGATACA
1327347 TTGTATCGATACA
1 TTGTATCGATACA
1327360 TTGTATCGAT
1 TTGTATCGAT
1327370 TTGAACAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1327504 original size:21 final size:21
Alignment explanation
Indices: 1327480--1327526 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1327470 AAATCTTTTG
1327480 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1327501 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1327521 CAAAAT
1 CAAAAT
1327527 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1327523 original size:20 final size:19
Alignment explanation
Indices: 1327482--1327524 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1327472 ATCTTTTGCA
1327482 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1327502 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1327522 AAA
1 AAA
1327525 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1329923 original size:13 final size:13
Alignment explanation
Indices: 1329905--1329930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1329895 TACAGCAAGT
1329905 ATGTATCGATACA
1 ATGTATCGATACA
1329918 ATGTATCGATACA
1 ATGTATCGATACA
1329931 CAAAAAAATT
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:1333447 original size:21 final size:21
Alignment explanation
Indices: 1333423--1333478 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1333413 CTTTTGCCAA
1333423 AATGTATCGATACATGCCCTT
1 AATGTATCGATACATGCCCTT
*
1333444 AATGTGTCGATACATGCCCTT
1 AATGTATCGATACATGCCCTT
1333465 AATGTATCGATACA
1 AATGTATCGATACA
1333479 AGGTCCCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACATGCCCTT
Found at i:1333577 original size:33 final size:33
Alignment explanation
Indices: 1333518--1333582 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1333508 TCACAATTTG
* *
1333518 TATCGATACATTGTTCATTGTGTCGATACATTA
1 TATCGATACATTGTTCAATGTATCGATACATTA
* *
1333551 TATCGATATATTTTTCAATGTATCGATACATT
1 TATCGATACATTGTTCAATGTATCGATACATT
1333583 CAGGCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (33 bp):
TATCGATACATTGTTCAATGTATCGATACATTA
Found at i:1335951 original size:50 final size:50
Alignment explanation
Indices: 1335865--1335973 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
1335855 AAATTTCTAG
* * *
1335865 ATTTTTCATCTCGGGGATACTCCAACCCCAGCTTTA-TTTCTAAAATATTA
1 ATTTTTCATCTCGGGGATACGCCAACCCCAGCTTTATTTTC-AAAACATCA
* * * *
1335915 ATTTTTCATCTCGGGGATACGCTAGCCTC-GATTTTATTTTCAAAACATCA
1 ATTTTTCATCTCGGGGATACGCCAACCCCAG-CTTTATTTTCAAAACATCA
1335965 ATTTTTCAT
1 ATTTTTCAT
1335974 AATTGAGGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.02
50 45 0.90
51 4 0.08
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (50 bp):
ATTTTTCATCTCGGGGATACGCCAACCCCAGCTTTATTTTCAAAACATCA
Found at i:1336027 original size:79 final size:79
Alignment explanation
Indices: 1335944--1336151 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 79
1335934 CGCTAGCCTC
* * ** *
1335944 GATTTTATTT-TCAAAACATCAATTTTTCATAATTGAGGATACTCCAATCCTGTTATTTCCAAGA
1 GATTTTATTTCT-AAAACATCAATTTCTCACAACCGAGGATACTCCAACCCTGTTATTTCCAAGA
1336008 GGATACTCCAACCCT
65 GGATACTCCAACCCT
* ** * * * *
1336023 GATTTTATTTCTAAAATATTGATTTCTCACAACCGGGGATACTCTAACCCTGTTATTTCCGAGGG
1 GATTTTATTTCTAAAACATCAATTTCTCACAACCGAGGATACTCCAACCCTGTTATTTCCAAGAG
*
1336088 GATACTCTAA-CCT
66 GATACTCCAACCCT
** * ** * *
1336101 CGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCC
1 -GATTTTATTTCTAAAACATCAATTTCTCACAACCGAGGATACTCCAACCC
1336152 CTATTTTATT
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.03
79 106 0.96
80 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
GATTTTATTTCTAAAACATCAATTTCTCACAACCGAGGATACTCCAACCCTGTTATTTCCAAGAG
GATACTCCAACCCT
Found at i:1336145 original size:51 final size:51
Alignment explanation
Indices: 1336085--1336204 Score: 150
Period size: 51 Copynumber: 2.4 Consensus size: 51
1336075 TTATTTCCGA
* * * * *
1336085 GGGGATACTCTAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATC
1 GGGGATACTCTAACCCCGACTTTATTTCTAAAACACTAATTTCTCACAATC
* * * * *
1336136 GGGGATACTCCAACCCCTATTTTATTTCTAAAACACTAATTTTTCATAATC
1 GGGGATACTCTAACCCCGACTTTATTTCTAAAACACTAATTTCTCACAATC
1336187 GGGGATACTCTAACCCCG
1 GGGGATACTCTAACCCCG
1336205 TTATTTTCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGACTTTATTTCTAAAACACTAATTTCTCACAATC
Found at i:1336218 original size:79 final size:79
Alignment explanation
Indices: 1336136--1336443 Score: 327
Period size: 79 Copynumber: 3.9 Consensus size: 79
1336126 TCTCACAATC
* ** *
1336136 GGGGATACTCCAACCCCTATTTTATTTCTAAAACACTAATTTTTCATAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAAC
*
1336201 CCCGTTATTTTCGC
66 CCCGTTATTTTCGA
*** * ** *
1336215 GGGGATACTCCAA-CCCGGCCTT-TTTCTAAAGCTTCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAAC
1336278 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * ** *
1336292 GGGGATACTCCAACCTCGATTTTATTT-TCAAAACGCCGATTTCTT-ATAATTAGGGATGCTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCGATTT-TTCATAATCGGGGATACTCCA
**
1336355 ACCTTGTTATTTTCGA
64 ACCCCGTTATTTTCGA
** * * *
1336371 GGGGATACTCCAACCCCGATTAAAATTTCTAGAACACCGATTTTCCATAATCAGGGGATACTCTA
1 GGGGATACTCCAACCCCGATT-TTATTTCTAAAACACCGATTTTTCATAATC-GGGGATACTCCA
*
1336436 GCCCCGTT
64 ACCCCGTT
1336444 GTCATTTCCA
Statistics
Matches: 183, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
77 60 0.33
78 11 0.06
79 75 0.41
80 22 0.12
81 15 0.08
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:1336287 original size:130 final size:131
Alignment explanation
Indices: 1336008--1336288 Score: 374
Period size: 130 Copynumber: 2.2 Consensus size: 131
1335998 ATTTCCAAGA
* * * *
1336008 GGATACTCCAA-CCCTGATTTTATTTCTAAAATATTGATTTCTCACAACCGGGGATACTCTAACC
1 GGATACTCCAACCCCTTATTTTATTTCTAAAACACTAATTTCTCACAACCGGGGATACTCTAACC
* * * *
1336072 CTGTTATTTCCGAGGGGATACTCTAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATCG
66 CCGTTATTTCCGAGGGGATACTCCAACCTCGGCCTTATTTCTAAAATATCGATTTCTCACAATCG
1336137 G
131 G
* * *
1336138 GGATACTCCAACCCC-TATTTTATTTCTAAAACACTAATTTTTCATAATCGGGGATACTCTAACC
1 GGATACTCCAACCCCTTATTTTATTTCTAAAACACTAATTTCTCACAACCGGGGATACTCTAACC
* * * *
1336202 CCGTTATTTTCGCGGGGATACTCCAACC-CGGCCTT-TTTCTAAAGCT-TCGATTTTTCACAATC
66 CCGTTATTTCCGAGGGGATACTCCAACCTCGGCCTTATTTCTAAA-ATATCGATTTCTCACAATC
1336264 GG
130 GG
1336266 GGATACTCCAACCCCGTTATTTT
1 GGATACTCCAACCCC-TTATTTT
1336289 CGAGGGGATA
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
128 39 0.30
129 7 0.05
130 83 0.63
131 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (131 bp):
GGATACTCCAACCCCTTATTTTATTTCTAAAACACTAATTTCTCACAACCGGGGATACTCTAACC
CCGTTATTTCCGAGGGGATACTCCAACCTCGGCCTTATTTCTAAAATATCGATTTCTCACAATCG
G
Found at i:1336356 original size:207 final size:209
Alignment explanation
Indices: 1335945--1336357 Score: 469
Period size: 207 Copynumber: 2.0 Consensus size: 209
1335935 GCTAGCCTCG
* * *
1335945 ATTTTATTTTCAAAACATCAATTTTTCATAATTGAGGATACTCCAATCCTGTTATTTCCAAGAGG
1 ATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCAACCCCGTTATTTCCAAGAGG
** * * *
1336010 ATACTCCAACCCTGATTTTATTTCTAAAATATTGATTTCTCACAACCGGGGATACTCTAACCCTG
66 ATACTCCAACCCTGACCTTATTTCTAAAATATCGATTTCTCACAACCGGGGATACTCCAACCCCG
* * * ** *
1336075 TTATTTCCGAGGGGATACTCTAACCTCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGG
131 TTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTCTAAAACACCGATTTCTCACAATCAGGG
1336140 ATACTCCAACCCCT
196 ATACTCCAACCCCT
* * * ** *
1336154 ATTTTA-TTTCTAAAACA-CTAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGCGG
1 ATTTTATTTTC-AAAACATC-AATTTTTCATAATCGAGGATACTCCAACCCCGTTATTTCCAAGA
* * * *
1336217 GGATACTCCAACCC-GGCCTT-TTTCTAAAGCT-TCGATTTTTCACAATCGGGGATACTCCAACC
64 GGATACTCCAACCCTGACCTTATTTCTAAA-ATATCGATTTCTCACAACCGGGGATACTCCAACC
* * * * * *
1336279 CCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTT-TCAAAACGCCGATTTCTTATAATT
128 CCGTTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTCT-AAAACACCGATTTCTCACAATC
*
1336343 AGGGATGCTCCAACC
192 AGGGATACTCCAACC
1336358 TTGTTATTTT
Statistics
Matches: 169, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
206 1 0.01
207 98 0.58
208 9 0.05
209 61 0.36
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (209 bp):
ATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCAACCCCGTTATTTCCAAGAGG
ATACTCCAACCCTGACCTTATTTCTAAAATATCGATTTCTCACAACCGGGGATACTCCAACCCCG
TTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTCTAAAACACCGATTTCTCACAATCAGGG
ATACTCCAACCCCT
Found at i:1348618 original size:1 final size:1
Alignment explanation
Indices: 1348614--1348671 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
1348604 CCTTTTTTTG
* * * * * * *
1348614 AAAAAAAACAAAAAAAAAAACAAAAAACAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1348672 TGAGAGAAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1348628 original size:7 final size:7
Alignment explanation
Indices: 1348616--1348665 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
1348606 TTTTTTTGAA
1348616 AAAAAAC
1 AAAAAAC
1348623 -AAAAA-
1 AAAAAAC
1348628 AAAAAAC
1 AAAAAAC
1348635 AAAAAAC
1 AAAAAAC
1348642 AAAAAAC
1 AAAAAAC
1348649 AAAAAA-
1 AAAAAAC
1348655 AACAAAAC
1 AA-AAAAC
1348663 AAA
1 AAA
1348666 GAAAAATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.31
7 25 0.64
8 2 0.05
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:1348628 original size:9 final size:9
Alignment explanation
Indices: 1348614--1348671 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
1348604 CCTTTTTTTG
1348614 AAAAAAAAC
1 AAAAAAAAC
1348623 AAAAAAAA-
1 AAAAAAAAC
1348631 AAACAAAAA-
1 AAA-AAAAAC
*
1348640 ACAAAAAAC
1 AAAAAAAAC
1348649 AAAAAAAAC
1 AAAAAAAAC
* *
1348658 AAAACAAAG
1 AAAAAAAAC
1348667 AAAAA
1 AAAAA
1348672 TGAGAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
8 8 0.19
9 34 0.81
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1348633 original size:14 final size:14
Alignment explanation
Indices: 1348614--1348671 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
1348604 CCTTTTTTTG
1348614 AAAAAAAAC--AAA
1 AAAAAAAACAAAAA
1348626 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
*
1348640 ACAAAAAACAAAAA
1 AAAAAAAACAAAAA
*
1348654 AAACAAAACAAAGAA
1 AAAAAAAACAAA-AA
1348669 AAA
1 AAA
1348672 TGAGAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
12 9 0.22
14 26 0.65
15 5 0.12
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAA
Found at i:1348652 original size:23 final size:21
Alignment explanation
Indices: 1348614--1348671 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
1348604 CCTTTTTTTG
1348614 AAAAAAAAC--AAAAAAAAAA
1 AAAAAAAACAAAAAAAAAAAA
* *
1348633 ACAAAAAACAAAAAACAAAAA
1 AAAAAAAACAAAAAAAAAAAA
* *
1348654 AAACAAAACAAAGAAAAA
1 AAAAAAAACAAAAAAAAA
1348672 TGAGAGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 8 0.26
21 23 0.74
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAAA
Found at i:1349842 original size:100 final size:100
Alignment explanation
Indices: 1349645--1349834 Score: 276
Period size: 100 Copynumber: 1.9 Consensus size: 100
1349635 ACCTAAACTT
* * ** *
1349645 TCTCCTTTCACTTTTCAGTTCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTG
1 TCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTGCAAAGCCCACACAAGTTC
1349710 GTGGCACTTCCCAATCCTCAAAGAGCAAGACGCTC
66 GTGGCACTTCCCAATCCTCAAAGAGCAAGACGCTC
* *
1349745 TCTCCTTTCACCCTTT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTGCAAAGCCCACACAAGTT
1 TCTCCTTTCA-CCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTGCAAAGCCCACACAAGTT
*
1349809 CGTGGCACCTT-CCAGTCCTCAAAGAG
65 CGTGGCA-CTTCCCAATCCTCAAAGAG
1349835 TAGGACGCCT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 73 0.91
101 7 0.09
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (100 bp):
TCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTGCAAAGCCCACACAAGTTC
GTGGCACTTCCCAATCCTCAAAGAGCAAGACGCTC
Found at i:1349856 original size:61 final size:61
Alignment explanation
Indices: 1349761--1349973 Score: 311
Period size: 61 Copynumber: 3.5 Consensus size: 61
1349751 TTCACCCTTT
* *
1349761 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTGCAAAGCCCACACAAGTTCGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTCC
*
1349822 AGTCCTCAAAGAGTAGGACGCCTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTCC
* * ** * * **
1349883 AGTCCTCAAAGAGCAAGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGAGGC-CCTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACC-TTCC
1349944 AGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1349974 TTCTCCTTTG
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
60 2 0.01
61 135 0.99
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTCC
Found at i:1349991 original size:38 final size:38
Alignment explanation
Indices: 1349945--1350086 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 38
1349935 GCCCTTTTTA
1349945 GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTT
* * **
1349983 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTCTATTTT
1 GTCCTCAAAGAGCAGGACGC----CTTTTCC-T-TTTCTCCTTT
* * * * *
1350027 GTCCTCAAAAAGCAAGATGCCTTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTCTCCTTT
*
1350067 GTCCTCAAAGAGCATGACGC
1 GTCCTCAAAGAGCAGGACGC
1350087 ACTTCATTTC
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
38 19 0.24
40 25 0.31
41 1 0.01
42 10 0.12
43 1 0.01
44 24 0.30
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (38 bp):
GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCTCCTTT
Found at i:1350028 original size:44 final size:43
Alignment explanation
Indices: 1349967--1350190 Score: 160
Period size: 42 Copynumber: 5.2 Consensus size: 43
1349957 CAGGACGCCT
*
1349967 TTTCC-TTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
1 TTTCCTTTTTCTCCTTTGTCCTCAAAGAGCAAGACACATTTCA
** * ** *
1350009 TTTCCTTCTTTCTATTTTGTCCTCAAAAAGCAAGATGCCTTT--
1 TTTCCTT-TTTCTCCTTTGTCCTCAAAGAGCAAGACACATTTCA
* * * *
1350051 TTTTCTTTTT-TCCTTTGTCCTCAAAGAGCATGACGCACTTCA
1 TTTCCTTTTTCTCCTTTGTCCTCAAAGAGCAAGACACATTTCA
*
1350093 TTTCCTTCTTT-TCCCTTCTAGTTCTCAAAGAGCAAGATGCAC-TTT-A
1 TTTCCTT-TTTCT-CCTT-T-GTCCTCAAAGAGCAAGA--CACATTTCA
* * * *
1350139 TTCTCC-TTTT-TCCTTTGTCTTCAAGGAGCAGGACCCATTTCA
1 TT-TCCTTTTTCTCCTTTGTCCTCAAAGAGCAAGACACATTTCA
1350181 TTCTCCTTTT
1 TT-TCCTTTT
1350191 CCTTAATCCT
Statistics
Matches: 143, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
40 25 0.17
41 6 0.04
42 37 0.26
43 9 0.06
44 35 0.24
45 5 0.03
46 19 0.13
47 5 0.03
48 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (43 bp):
TTTCCTTTTTCTCCTTTGTCCTCAAAGAGCAAGACACATTTCA
Found at i:1350093 original size:84 final size:85
Alignment explanation
Indices: 1349940--1350216 Score: 280
Period size: 84 Copynumber: 3.3 Consensus size: 85
1349930 TGGAGGCCCT
* * * *
1349940 TTTTAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACAC
1 TTTT-GTCCTCAAAGAGCAAGATGCCTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACAC
*
1350003 ATTTCATTTCCTTC-TTTCTA
65 ATTTCATTTCCTTCTTTTCCA
* * *
1350023 TTTTGTCCTCAAAAAGCAAGATGCCTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCATGACGCA
1 TTTTGTCCTCAAAGAGCAAGATGCCTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACA
* *
1350088 CTTCATTTCCTTCTTTTCCC
66 TTTCATTTCCTTCTTTTCCA
* * * * * *
1350108 TTCTAGTTCTCAAAGAGCAAGATGCACTTTATTCTCCTTTTTCCTTTGTCTTCAAGGAGCAGGAC
1 TT-TTGTCCTCAAAGAGCAAGATGC-CTTT-TTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGAC
* *
1350173 CCATTTCA-TT-CTCCTTTTCC-
63 ACATTTCATTTCCTTCTTTTCCA
** *
1350193 -TTAATCCTCAAAGAGCAGGATGCC
1 TTTTGTCCTCAAAGAGCAAGATGCC
1350217 CCTTTCCTTT
Statistics
Matches: 164, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
82 19 0.12
83 23 0.14
84 47 0.29
85 6 0.04
86 28 0.17
87 6 0.04
88 35 0.21
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (85 bp):
TTTTGTCCTCAAAGAGCAAGATGCCTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACA
TTTCATTTCCTTCTTTTCCA
Found at i:1350209 original size:41 final size:42
Alignment explanation
Indices: 1350057--1350212 Score: 111
Period size: 46 Copynumber: 3.6 Consensus size: 42
1350047 CTTTTTTTCT
** * * *
1350057 TTTTTCCTTTGTCCTCAAAGAGCATGACGCACTTCATT-TCC
1 TTTTTCCTTAATCCTCAAAGAGCAGGACCCACTTTATTCTCC
* * * **
1350098 TTCTTTTCCCTTCTAGTTCTCAAAGAGCAAGATGCACTTTATTCTCC
1 -T-TTTT-CC-T-TAATCCTCAAAGAGCAGGACCCACTTTATTCTCC
** * *
1350145 TTTTTCCTTTGTCTTCAAGGAGCAGGACCCA-TTTCATTCTCC
1 TTTTTCCTTAATCCTCAAAGAGCAGGACCCACTTT-ATTCTCC
1350187 -TTTTCCTTAATCCTCAAAGAGCAGGA
1 TTTTTCCTTAATCCTCAAAGAGCAGGA
1350213 TGCCCCTTTC
Statistics
Matches: 92, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
41 25 0.27
42 24 0.26
43 5 0.05
44 4 0.04
45 5 0.05
46 26 0.28
47 3 0.03
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (42 bp):
TTTTTCCTTAATCCTCAAAGAGCAGGACCCACTTTATTCTCC
Found at i:1350819 original size:13 final size:13
Alignment explanation
Indices: 1350803--1350832 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1350793 ATACATTGTT
1350803 CATTGTATCGATA
1 CATTGTATCGATA
*
1350816 CATTGTATCGATG
1 CATTGTATCGATA
1350829 CATT
1 CATT
1350833 CTAGGTTTAC
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:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1353385 original size:80 final size:80
Alignment explanation
Indices: 1353294--1353446 Score: 193
Period size: 80 Copynumber: 1.9 Consensus size: 80
1353284 AATCCTGTTA
** * * * * * *
1353294 TTTCTGAGGGGATAATTTAACC-CTGATTTTATTTTTAAAATATTGATTTCTCATAATTGGGGAT
1 TTTCTGAGGGGATAATCCAACCTC-GACTTTATTTCTAAAATATTAATTTCTCACAATCGAGGA-
1353358 TACTCCAACCCCTTTAT
64 TACTCCAACCCCTTTAT
*
1353375 TTTC-GAGGGGATAGTCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCACAATCGAGGATA
1 TTTCTGAGGGGATAATCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCACAATCGAGGATA
1353439 CTCCAACC
66 CTCCAACC
1353447 TCTATTTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 10 0.16
80 47 0.76
81 5 0.08
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (80 bp):
TTTCTGAGGGGATAATCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCACAATCGAGGATA
CTCCAACCCCTTTAT
Found at i:1353456 original size:51 final size:51
Alignment explanation
Indices: 1353383--1353497 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 51
1353373 ATTTTCGAGG
* * *
1353383 GGATAGTCCAACCTCGACTTTATTTCTAAAATATTAATTTCTCACAATCGA
1 GGATACTCCAACCTCGACTTTATTTCTAAAACACTAATTTCTCACAATCGA
* * * * *
1353434 GGATACTCCAACCTCTATTTTATTTCTAAAACACTAATTTTTCAGAATCGG
1 GGATACTCCAACCTCGACTTTATTTCTAAAACACTAATTTCTCACAATCGA
*
1353485 GGCTACTCCAACC
1 GGATACTCCAACC
1353498 CCGTTATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (51 bp):
GGATACTCCAACCTCGACTTTATTTCTAAAACACTAATTTCTCACAATCGA
Found at i:1353517 original size:79 final size:79
Alignment explanation
Indices: 1353434--1353730 Score: 262
Period size: 79 Copynumber: 3.7 Consensus size: 79
1353424 TCACAATCGA
* * * * *
1353434 GGATACTCCAACCTCTATTTTATTTCTAAAACACT-AATTTTTCAGAATCGGGGCTACTCCAACC
1 GGATACTCCAACCCCGATTTTATTTCTAAAAC-CTCAATTTTCCACAATCGGGGATACTCCAACC
1353498 CCGTTATTTTCGTA-G
65 CCGTTATTTTCG-AGG
*** * * *
1353513 GGATACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACCTCAATTTTCCACAATCGGGGATACTCCAACCC
*
1353578 CGTTATTTTTGAGG
66 CGTTATTTTCGAGG
** * * ** *
1353592 GGATACTCCAACCCCGATTTTATTT-TCAAAATGTCGA-TTTCCTATAATTAGGGATGCTCCAAC
1 GGATACTCCAACCCCGATTTTATTTCT-AAAACCTCAATTTTCC-ACAATCGGGGATACTCCAAC
** *
1353655 CTTGTTATTTTCAAGG
64 CCCGTTATTTTCGAGG
* * * * *
1353671 GGATACTCCAACCCTGATTTTATTTTTAGAACACT-GATTTTCCATAATCAGGGGATACTC
1 GGATACTCCAACCCCGATTTTATTTCTAAAAC-CTCAATTTTCCACAATC-GGGGATACTC
1353731 TAGCTCCAAA
Statistics
Matches: 177, Mismatches: 33, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
78 8 0.05
79 154 0.87
80 15 0.08
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACCTCAATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTTCGAGG
Found at i:1355236 original size:32 final size:34
Alignment explanation
Indices: 1355195--1355281 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 34
1355185 ACTATCTTTC
1355195 AAGGCTAAGATAGAAACCTC-C-CTATCTTTT-CA
1 AAGGCTAAGATAG-AACCTCTCTCTATCTTTTACA
**
1355227 TGGGCTAAGATAGAACCTTTCTCTCTATCTTTTACA
1 AAGGCTAAGATAGAACC--TCTCTCTATCTTTTACA
1355263 AAGGCTAAGATAGAACCTC
1 AAGGCTAAGATAGAACCTC
1355282 ACAATCACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
31 4 0.09
32 11 0.24
33 2 0.04
34 3 0.07
35 9 0.20
36 17 0.37
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (34 bp):
AAGGCTAAGATAGAACCTCTCTCTATCTTTTACA
Found at i:1355740 original size:13 final size:13
Alignment explanation
Indices: 1355722--1355746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1355712 GTTGGACTCA
1355722 ATGTATTGATACT
1 ATGTATTGATACT
1355735 ATGTATTGATAC
1 ATGTATTGATAC
1355747 ATGAATAGTG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATGTATTGATACT
Found at i:1355779 original size:32 final size:32
Alignment explanation
Indices: 1355743--1355863 Score: 206
Period size: 32 Copynumber: 3.8 Consensus size: 32
1355733 CTATGTATTG
*
1355743 ATACATGAATAGTGATGAACAGTGATGTATCC
1 ATACATGAATAGTGATGAACAGTGATGTATCA
*
1355775 ATACATGAATAGTGATGAACAGTGATGTATCG
1 ATACATGAATAGTGATGAACAGTGATGTATCA
* *
1355807 ATACATGAATAGTGATGAACATTGTTGTATCA
1 ATACATGAATAGTGATGAACAGTGATGTATCA
1355839 ATACATGAATAGTGATGAACAGTGA
1 ATACATGAATAGTGATGAACAGTGA
1355864 AAATGTGATT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (32 bp):
ATACATGAATAGTGATGAACAGTGATGTATCA
Found at i:1359217 original size:21 final size:21
Alignment explanation
Indices: 1359192--1359246 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1359182 CACTTGCAAC
*
1359192 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1359213 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
1359234 TCACTTAATTTCT
1 TCATTTATTTTCT
1359247 TTTCAAGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1359247 original size:21 final size:21
Alignment explanation
Indices: 1359207--1359250 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1359197 TCTTTTCTCC
* *
1359207 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1359228 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1359249 TC
1 TC
1359251 AAGAACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1361360 original size:13 final size:13
Alignment explanation
Indices: 1361342--1361366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1361332 GTTGGACTCA
1361342 ATGTATCGATACT
1 ATGTATCGATACT
1361355 ATGTATCGATAC
1 ATGTATCGATAC
1361367 ATGAATAGTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
ATGTATCGATACT
Found at i:1361399 original size:24 final size:24
Alignment explanation
Indices: 1361367--1361416 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1361357 GTATCGATAC
1361367 ATGAATAGTGATGAACAGTGATGT
1 ATGAATAGTGATGAACAGTGATGT
*
1361391 ATGAGTAGTGATGAACAGTGATGT
1 ATGAATAGTGATGAACAGTGATGT
1361415 AT
1 AT
1361417 CGATACATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (24 bp):
ATGAATAGTGATGAACAGTGATGT
Found at i:1362314 original size:19 final size:19
Alignment explanation
Indices: 1362290--1362326 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1362280 GGGTCATATA
1362290 ATTTGGAGCACTTACTATG
1 ATTTGGAGCACTTACTATG
1362309 ATTTGGAGCACTTACTAT
1 ATTTGGAGCACTTACTAT
1362327 TAAGGTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (19 bp):
ATTTGGAGCACTTACTATG
Found at i:1362852 original size:21 final size:21
Alignment explanation
Indices: 1362826--1362870 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1362816 TACTTGCAAC
*
1362826 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1362847 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
1362868 TCA
1 TCA
1362871 CTTAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1362883 original size:21 final size:21
Alignment explanation
Indices: 1362841--1362884 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1362831 TCTTTTCTCC
* * *
1362841 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTATTT
1362862 TCTAATTCACTTAATTTATTT
1 TCTAATTCACTTAATTTATTT
1362883 TC
1 TC
1362885 AAGAGTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTATTT
Found at i:1368040 original size:2 final size:2
Alignment explanation
Indices: 1368033--1368064 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1368023 TATCCCTTGG
1368033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368065 TATTTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1368270 original size:29 final size:27
Alignment explanation
Indices: 1368218--1368277 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1368208 TTAATAATTA
* *
1368218 TATTTATAAGATAAATTAATTTTTTAT
1 TATTTATAAGATAAATTAAATTTTAAT
*
1368245 TATTTATATGATAAATAGTAAATTTTAAT
1 TATTTATAAGATAAAT--TAAATTTTAAT
1368274 TATT
1 TATT
1368278 GAATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 15 0.54
29 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTTATAAGATAAATTAAATTTTAAT
Found at i:1369468 original size:22 final size:21
Alignment explanation
Indices: 1369428--1369475 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
1369418 GTAAATATTT
1369428 ATATAATATCATAATGTATA-
1 ATATAATATCATAATGTATAC
1369448 ATATAATAT-ATCAATAGGTATAC
1 ATATAATATCAT-AAT--GTATAC
1369471 ATATA
1 ATATA
1369476 TATGTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
22 5 0.21
23 5 0.21
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (21 bp):
ATATAATATCATAATGTATAC
Found at i:1370086 original size:20 final size:19
Alignment explanation
Indices: 1370061--1370129 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
1370051 CCTTGTATGC
*
1370061 ATCGATACATATTCAGATGT
1 ATCGATACATATTCA-TTGT
* *
1370081 ATCGATACATTATGCTTTGT
1 ATCGATACA-TATTCATTGT
*
1370101 ATCGATACATGTTCATTGT
1 ATCGATACATATTCATTGT
1370120 ATCGATACAT
1 ATCGATACAT
1370130 GCACAATTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 17 0.40
20 21 0.50
21 4 0.10
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
ATCGATACATATTCATTGT
Found at i:1370140 original size:20 final size:19
Alignment explanation
Indices: 1370097--1370149 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1370087 ACATTATGCT
**
1370097 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
1370116 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
*
1370136 TTGTAACGATACAT
1 TTGTATCGATACAT
1370150 AAAACTGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:1370222 original size:33 final size:33
Alignment explanation
Indices: 1370180--1370244 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1370170 TACCACTGTT
*
1370180 TGTATCGATACATGGC-ATATTGTATCAATACAA
1 TGTATCGATACATGACGA-ATTGTATCAATACAA
*
1370213 TGTATCGATACATGACGAATTGTATCGATACA
1 TGTATCGATACATGACGAATTGTATCAATACA
1370245 TTGTCCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGACGAATTGTATCAATACAA
Found at i:1371861 original size:15 final size:15
Alignment explanation
Indices: 1371841--1371875 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1371831 AACCATTAAA
1371841 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1371856 GATGATGATGATAAT
1 GATGATGAAGATAAT
1371871 GATGA
1 GATGA
1371876 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1373649 original size:19 final size:18
Alignment explanation
Indices: 1373624--1373688 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
1373614 ATTTCAACGA
1373624 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1373642 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1373658 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1373674 TTTTGTATTGATACA
1 -TTTGTATCGATACA
1373689 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1373662 original size:32 final size:32
Alignment explanation
Indices: 1373626--1373696 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1373616 TTCAACGATT
1373626 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1373658 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1373690 TGTATCG
1 TGTATCG
1373697 CTAGGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1373663 original size:13 final size:13
Alignment explanation
Indices: 1373645--1373669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1373635 ACATAAGTGT
1373645 TGTATCGATACAA
1 TGTATCGATACAA
1373658 TGTATCGATACA
1 TGTATCGATACA
1373670 TAAGTTTTGT
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:1376222 original size:54 final size:51
Alignment explanation
Indices: 1376109--1376232 Score: 162
Period size: 54 Copynumber: 2.4 Consensus size: 51
1376099 CAATTCTCCG
*
1376109 CAATCGGGGGTA-TCTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGGTACTC-CAACTCCGATTTTATTTCCAAAACACTAATTTTCTA
*
1376160 TAATCGGGGGTACTCCAACTCCGATTTTATTTCCAAAAAAACACTAATTTT-TCA
1 CAATCGGGGGTACTCCAACTCCGATTTTATTTCC---AAAACACTAATTTTCT-A
*
1376214 CAATCGGGGATACTCCAAC
1 CAATCGGGGGTACTCCAAC
1376233 CCCGTTAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
51 29 0.45
52 2 0.03
53 1 0.02
54 32 0.50
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (51 bp):
CAATCGGGGGTACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTCTA
Found at i:1376356 original size:52 final size:52
Alignment explanation
Indices: 1376243--1376364 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 52
1376233 CCCGTTAATC
* **
1376243 ATCAGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTA
1 ATCAGGGATACTCCAACCCCGATTTTATTTTAAAAACACCAATTTTCCTACA
* * * * *
1376295 ATCAGGGATACTCCGACTCTGATTTTATTTCTAAAAACACCAATTTTTC-ACC
1 ATCAGGGATACTCCAACCCCGATTTTATTT-TAAAAACACCAATTTTCCTACA
1376347 ATC-GAGGATACTCCAACC
1 ATCAG-GGATACTCCAACC
1376365 TCGTTATTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
51 1 0.02
52 41 0.71
53 16 0.28
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (52 bp):
ATCAGGGATACTCCAACCCCGATTTTATTTTAAAAACACCAATTTTCCTACA
Found at i:1376370 original size:131 final size:133
Alignment explanation
Indices: 1376124--1376395 Score: 388
Period size: 132 Copynumber: 2.1 Consensus size: 133
1376114 GGGGGTATCT
* * * *
1376124 CAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGGTACTCCAACTCCGATTTTA
1 CAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACTCCGATTTTA
* *
1376189 TTTCCAAAAAAACACTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA-ATCATCAGGGATA
66 TTTCCAAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCAGGGATA
1376253 CTC
131 CTC
* * *
1376256 CAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCAGGGATACTCCGACTCTGATTTT
1 CAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCAGGGATACTCCAACTCCGATTTT
* * * * *
1376321 ATTT-C-TAAAAACACCAATTTTTCACCATCGAGGATACTCCAACCTCGTTATTTCATCGGGGAT
65 ATTTCCAAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCAGGGAT
1376384 ACTC
130 ACTC
1376388 CAACCCCG
1 CAACCCCG
1376396 TTACCTCCGA
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 40 0.32
132 54 0.44
133 30 0.24
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (133 bp):
CAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACTCCGATTTTA
TTTCCAAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCAGGGATA
CTC
Found at i:1376526 original size:79 final size:79
Alignment explanation
Indices: 1376377--1376581 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
1376367 GTTATTTCAT
** *
1376377 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
1376442 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * ** *
1376456 TGGGGATACTTCAACCCCGTTATTTCCAAGGGGATACTCCAATCCCGATG-TTT-TTTTC-TAAT
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT
1376518 CATCGATTTCTCACAAC
64 -ATCGATTTCTCACAAC
* * * *
1376535 CGGGGATACTCCAGCCCCGTCATTTTCAAGGGGACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCG
1376582 TTATTATCTC
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
78 3 0.03
79 97 0.93
80 3 0.03
81 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1380605 original size:32 final size:31
Alignment explanation
Indices: 1380569--1380630 Score: 106
Period size: 32 Copynumber: 2.0 Consensus size: 31
1380559 TTCAACGATT
*
1380569 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAG-TATGTATCGATACAA
1380601 TGTATCGATACATAAGTATGTATCGATACA
1 TGTATCGATACATAAGTATGTATCGATACA
1380631 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (31 bp):
TGTATCGATACATAAGTATGTATCGATACAA
Found at i:1380606 original size:13 final size:13
Alignment explanation
Indices: 1380588--1380612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1380578 ACATAAGTTT
1380588 TGTATCGATACAA
1 TGTATCGATACAA
1380601 TGTATCGATACA
1 TGTATCGATACA
1380613 TAAGTATGTA
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:1380623 original size:18 final size:18
Alignment explanation
Indices: 1380569--1380633 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
1380559 TTCAACGATT
*
1380569 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TA
1380588 TGTATCGATAC---A--A
1 TGTATCGATACATAAGTA
1380601 TGTATCGATACATAAGTA
1 TGTATCGATACATAAGTA
1380619 TGTATCGATACATAA
1 TGTATCGATACATAA
1380634 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.28
16 2 0.05
18 16 0.40
19 11 0.28
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAAGTA
Found at i:1380691 original size:13 final size:13
Alignment explanation
Indices: 1380673--1380698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1380663 CATTTTTCTG
1380673 TGTATCGATACAT
1 TGTATCGATACAT
1380686 TGTATCGATACAT
1 TGTATCGATACAT
1380699 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1380695 original size:33 final size:33
Alignment explanation
Indices: 1380653--1380719 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1380643 GCCAAGGAAA
***
1380653 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1380686 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1380719 T
1 T
1380720 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.