Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 11 of 21
Found at i:1548856 original size:13 final size:13
Alignment explanation
Indices: 1548838--1548889 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1548828 AGCTTCGTAG
1548838 CGATACATTGTAT
1 CGATACATTGTAT
1548851 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1548870 CGATACATTGTAT
1 CGATACATTGTAT
1548883 CGATACA
1 CGATACA
1548890 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1548870 original size:19 final size:19
Alignment explanation
Indices: 1548846--1548910 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1548836 AGCGATACAT
1548846 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1548865 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1548878 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
1548897 TGTATCAATACAAA
1 TGTATCGATACAAA
1548911 TCATTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1548879 original size:32 final size:32
Alignment explanation
Indices: 1548838--1548908 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1548828 AGCTTCGTAG
1548838 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1548870 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1548902 CAATACA
1 CGATACA
1548909 AATCATTGAA
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:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1551178 original size:21 final size:21
Alignment explanation
Indices: 1551137--1551180 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1551127 CTCTCCTATA
* *
1551137 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1551158 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1551179 TC
1 TC
1551181 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1558114 original size:15 final size:15
Alignment explanation
Indices: 1558094--1558124 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1558084 ATTTCGTTTG
*
1558094 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1558109 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1558124 G
1 G
1558125 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1559956 original size:21 final size:22
Alignment explanation
Indices: 1559923--1559971 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
1559913 ATGCAAGTTT
** *
1559923 TTATTTTTTTTAGCTAAC-TCA
1 TTATTTTCATTAGCCAACTTCA
*
1559944 TTATTTTCATTAGCCAACTTCT
1 TTATTTTCATTAGCCAACTTCA
1559966 TTATTT
1 TTATTT
1559972 CAACTTGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.57
Consensus pattern (22 bp):
TTATTTTCATTAGCCAACTTCA
Found at i:1562211 original size:13 final size:13
Alignment explanation
Indices: 1562193--1562218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1562183 CAATTTTTGG
1562193 TGTATCGATACAT
1 TGTATCGATACAT
1562206 TGTATCGATACAT
1 TGTATCGATACAT
1562219 ACTTGGTGTA
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:1562230 original size:32 final size:33
Alignment explanation
Indices: 1562173--1562236 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1562163 TACAAGCCAA
**
1562173 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1562206 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1562237 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1562243 original size:19 final size:18
Alignment explanation
Indices: 1562173--1562243 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
1562163 TACAAGCCAA
1562173 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
1562193 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
1562206 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1562225 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1562244 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1563442 original size:33 final size:33
Alignment explanation
Indices: 1563398--1563460 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1563388 TTTGAAGCAA
*
1563398 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCAATACAATGT-ATCATGTATCGATACAT
*
1563431 TGTATCAATACAATGTGTCATGTATCGATA
1 TGTATCAATACAATGTATCATGTATCGATA
1563461 TAAACAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCAATACAATGTATCATGTATCGATACAT
Found at i:1563517 original size:20 final size:19
Alignment explanation
Indices: 1563492--1563545 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1563482 CTGCCAGTTT
**
1563492 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
1563512 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
1563531 CATGTATCGATACAA
1 CATGTATCGATACAA
1563546 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1565068 original size:20 final size:20
Alignment explanation
Indices: 1565043--1565199 Score: 96
Period size: 20 Copynumber: 7.8 Consensus size: 20
1565033 TTTTTGCAAT
1565043 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1565063 TTGTATCGATACATTCTAGATTTACCCA
1 TTGTATCGATACA-T-T-G--TT---CA
*
1565091 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
* **
1565112 TTGTATTGATACATTACTCA
1 TTGTATCGATACATTGTTCA
1565132 TTGTATCGATACATTG-T-A
1 TTGTATCGATACATTGTTCA
*
1565150 ---T-T-GATACATTGCTCA
1 TTGTATCGATACATTGTTCA
**
1565165 TTGTATCGATACATTGTAAA
1 TTGTATCGATACATTGTTCA
*
1565185 ATGTATCGATACATT
1 TTGTATCGATACATT
1565200 CAGCCATTTT
Statistics
Matches: 109, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
13 9 0.08
14 2 0.02
15 2 0.02
18 2 0.02
19 2 0.02
20 66 0.61
21 4 0.04
22 1 0.01
23 3 0.03
25 2 0.02
27 1 0.01
28 3 0.03
29 12 0.11
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1565148 original size:13 final size:13
Alignment explanation
Indices: 1565130--1565182 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1565120 ATACATTACT
1565130 CATTGTATCGATA
1 CATTGTATCGATA
*
1565143 CATTGTATTGATA
1 CATTGTATCGATA
1565156 CATTG---C--T-
1 CATTGTATCGATA
1565163 CATTGTATCGATA
1 CATTGTATCGATA
1565176 CATTGTA
1 CATTGTA
1565183 AAATGTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 5 0.16
8 1 0.03
10 1 0.03
12 1 0.03
13 24 0.75
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1565152 original size:33 final size:33
Alignment explanation
Indices: 1565110--1565182 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
1565100 ATACATTTTG
1565110 CATTGTATTGATACATTACTCATTGTATCGATA
1 CATTGTATTGATACATTACTCATTGTATCGATA
*
1565143 CATTGTATTGATACATTGCTCATTGTATCGATA
1 CATTGTATTGATACATTACTCATTGTATCGATA
1565176 CATTGTA
1 CATTGTA
1565183 AAATGTATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
CATTGTATTGATACATTACTCATTGTATCGATA
Found at i:1567625 original size:79 final size:79
Alignment explanation
Indices: 1567475--1567915 Score: 500
Period size: 79 Copynumber: 5.6 Consensus size: 79
1567465 TTTTCATCTC
* * * * * *
1567475 GGGGATACTCCAATCCC-AGTTTCATTTCTAAAACATCAATTT-T--TCATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
*
1567536 CCCCATTATTTTCGA
65 CCCCGTTATTTTCGA
** * *
1567551 GGGGATAC-CCTAACCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATAATCTAA
1 GGGGATACTCC-AACCCCGATTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
1567615 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * * *
1567630 TGGGATGCTCCAACCCCGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGAATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
*
1567695 CCCATTATTTTCGA
66 CCCGTTATTTTCGA
* * * * * *
1567709 GGGGATACTCCAACCCCAGTTTTTTTTTCTAAAACATCAATTTTTCATAGTCGGGGATACTCCAA
1 GGGGATACTCCAACCCC-GATTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
1567774 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * * * *
1567789 GGGGATACTCCAATCTCGATTTTATTTCT-AAATCATTGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAAT-ATTAATTTCTCATAATCGGGGATACTCCAA
1567853 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * * *
1567868 AGGGATAATCCAACCCCG-TTATTATCTCCAAAATATTAAATTTCTCAT
1 GGGGATACTCCAACCCCGATT-TTATTTCTAAAATATT-AATTTCTCAT
1567916 CGGGAGATGT
Statistics
Matches: 307, Mismatches: 47, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
75 2 0.01
76 32 0.10
77 1 0.00
78 5 0.02
79 186 0.61
80 81 0.26
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:1567781 original size:159 final size:157
Alignment explanation
Indices: 1567475--1567885 Score: 517
Period size: 159 Copynumber: 2.6 Consensus size: 157
1567465 TTTTCATCTC
* * * *
1567475 GGGGATACTCCAATCCC-AGTTTCATTTCTAAAACATCAATTTTTCATCA--GGGATACTCCAAC
1 GGGGATACTCCAATCCCGACTTT-ATTTCTAAAATATTAATTTTTCATAATCGGGATACTCCAAC
* *
1567537 CCCATTATTTTCGAGGGGATAC-CCTAACCCCGGCTTTATTTCTAAAATATTAATTTCTCATAAT
65 CCCATTATTTTCGAGGGGATACTCC-AACCCCGGCTTTATTTCTAAAACATCAATTTCTCATAAT
*
1567601 CGGGGATAATCTAACCCCGTTATTTTCGA
129 CGGGGATAATCCAACCCCGTTATTTTCGA
* * * *
1567630 TGGGATGCTCCAACCCCGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGAATACTCCAAC
1 GGGGATACTCCAATCCCGACTTTATTTCTAAAATATTAATTTTTCATAATCGGG-ATACTCCAAC
** * * *
1567695 CCCATTATTTTCGAGGGGATACTCCAACCCCAGTTTTTTTTTCTAAAACATCAATTTTTCATAGT
65 CCCATTATTTTCGAGGGGATACTCCAACCCC-GGCTTTATTTCTAAAACATCAATTTCTCATAAT
*
1567760 CGGGGATACTCCAACCCCGTTATTTTCGA
129 CGGGGATAATCCAACCCCGTTATTTTCGA
* * * *
1567789 GGGGATACTCCAATCTCGATTTTATTTCT-AAATCATTGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAATCCCGACTTTATTTCTAAAAT-ATTAATTTTTCATAATC-GGGATACTCCAA
* * *
1567853 CCCCGTTATTTTCGAAGGGATAATCCAACCCCG
64 CCCCATTATTTTCGAGGGGATACTCCAACCCCG
1567886 TTATTATCTC
Statistics
Matches: 220, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
155 36 0.16
156 4 0.02
157 3 0.01
158 43 0.20
159 131 0.60
160 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (157 bp):
GGGGATACTCCAATCCCGACTTTATTTCTAAAATATTAATTTTTCATAATCGGGATACTCCAACC
CCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTCTCATAATCG
GGGATAATCCAACCCCGTTATTTTCGA
Found at i:1571751 original size:20 final size:19
Alignment explanation
Indices: 1571722--1571793 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1571712 AAAAAGACAT
1571722 AATGTATCGATATATTGAA
1 AATGTATCGATATATTGAA
* * *
1571741 GAATATATCGATACATTCATA
1 -AATGTATCGATATATTGA-A
*
1571762 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-AA
1571782 AATGTATCGATA
1 AATGTATCGATA
1571794 CATTTGGGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (19 bp):
AATGTATCGATATATTGAA
Found at i:1571778 original size:40 final size:39
Alignment explanation
Indices: 1571719--1571797 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
1571709 GGTAAAAAGA
*
1571719 CATAATGTATCGATATATTGAAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
1571758 CATACATGTATCGATATATTGAAAAATGTATCGATACATT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACATT
1571798 TGGGTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 33 0.89
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:1573580 original size:13 final size:13
Alignment explanation
Indices: 1573562--1573621 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
1573552 ATAGTAACCC
1573562 ATGTATCGATACA
1 ATGTATCGATACA
1573575 ATGTATCGATACA
1 ATGTATCGATACA
*
1573588 A---A---AAACA
1 ATGTATCGATACA
*
1573595 TTGTATCGATACA
1 ATGTATCGATACA
1573608 ATGTATCGATACA
1 ATGTATCGATACA
1573621 A
1 A
1573622 AGAACATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 4 0.11
10 2 0.05
13 31 0.84
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1573601 original size:20 final size:19
Alignment explanation
Indices: 1573576--1573640 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1573566 ATCGATACAA
1573576 TGTATCGATACAAAAAACAT
1 TGTATCGATAC-AAAAACAT
1573596 TGTATCGATAC----A-A-
1 TGTATCGATACAAAAACAT
1573609 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAA-AACAT
1573629 TGTATCGATACA
1 TGTATCGATACA
1573641 TTTGAGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 23 0.61
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (19 bp):
TGTATCGATACAAAAACAT
Found at i:1573605 original size:33 final size:33
Alignment explanation
Indices: 1573563--1573640 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1573553 TAGTAACCCA
1573563 TGTATCGATACAATGTATCGATACAAAAAACAT
1 TGTATCGATACAATGTATCGATACAAAAAACAT
*
1573596 TGTATCGATACAATGTATCGATACAAAGAACAT
1 TGTATCGATACAATGTATCGATACAAAAAACAT
1573629 TGTATCGATACA
1 TGTATCGATACA
1573641 TTTGAGTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAAAAAACAT
Found at i:1574188 original size:14 final size:14
Alignment explanation
Indices: 1574169--1574198 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1574159 TTCTTGAATA
1574169 TAACCTTTTGCTAC
1 TAACCTTTTGCTAC
1574183 TAACCTTTTGCTAC
1 TAACCTTTTGCTAC
1574197 TA
1 TA
1574199 GCCTAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (14 bp):
TAACCTTTTGCTAC
Found at i:1577009 original size:3 final size:3
Alignment explanation
Indices: 1577001--1577025 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1576991 TCTGAGTCAA
1577001 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
1577026 TTGATCGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1579215 original size:27 final size:28
Alignment explanation
Indices: 1579168--1579279 Score: 101
Period size: 27 Copynumber: 4.1 Consensus size: 28
1579158 ATCAAAATTT
*
1579168 ATATAATATAAAT-TATTAATATATTAA
1 ATATAATATAAATATATAAATATATTAA
*
1579195 A-ATTAATATAAATATA-AAATATTTTAA
1 ATA-TAATATAAATATATAAATATATTAA
* *
1579222 ATATAAT-TATGATATAATAAA-ATAAATAA
1 ATATAATATA-AATAT-ATAAATAT-ATTAA
*
1579251 ATATAATATAAATATATAAAT-TATCAA
1 ATATAATATAAATATATAAATATATTAA
1579278 AT
1 AT
1579280 TTATTACGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 3 0.04
27 34 0.50
28 12 0.18
29 17 0.25
30 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
ATATAATATAAATATATAAATATATTAA
Found at i:1579263 original size:11 final size:11
Alignment explanation
Indices: 1579168--1579266 Score: 54
Period size: 11 Copynumber: 9.5 Consensus size: 11
1579158 ATCAAAATTT
1579168 ATATAATATAA
1 ATATAATATAA
1579179 AT-T-AT-T-A
1 ATATAATATAA
*
1579186 ATATATTA-AA
1 ATATAATATAA
1579196 AT-TAATATAA
1 ATATAATATAA
*
1579206 ATATAAAAT-A
1 ATATAATATAA
* *
1579216 TTTTAAATATAA
1 ATAT-AATATAA
*
1579228 TTATGATATAATAA
1 ATAT-A-AT-ATAA
1579242 A-ATAA-ATAA
1 ATATAATATAA
1579251 ATATAATATAA
1 ATATAATATAA
1579262 ATATA
1 ATATA
1579267 TAAATTATCA
Statistics
Matches: 67, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
7 3 0.04
8 2 0.03
9 12 0.18
10 15 0.22
11 21 0.31
12 6 0.09
13 4 0.06
14 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1580668 original size:17 final size:16
Alignment explanation
Indices: 1580646--1580718 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 16
1580636 ATCTCCTTCA
1580646 ATTTTTAAATAGTATTT
1 ATTTTTAAATA-TATTT
*
1580663 ATTTTTAAA-AT-TTA
1 ATTTTTAAATATATTT
* *
1580677 ATTTTTATATTTATTT
1 ATTTTTAAATATATTT
1580693 ATTTTT--ATCA-ATTT
1 ATTTTTAAAT-ATATTT
1580707 ATTTTT-AATATA
1 ATTTTTAAATATA
1580719 AATAGAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 23 0.50
15 5 0.11
16 9 0.20
17 9 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
ATTTTTAAATATATTT
Found at i:1580680 original size:31 final size:31
Alignment explanation
Indices: 1580645--1580714 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
1580635 TATCTCCTTC
1580645 AATTTTTAAATAGTATTTATTTTTA-AAATTT
1 AATTTTTAAAT-GTATTTATTTTTATAAATTT
* * *
1580676 AATTTTTATATTTATTTATTTTTATCAATTT
1 AATTTTTAAATGTATTTATTTTTATAAATTT
1580707 -ATTTTTAA
1 AATTTTTAA
1580715 TATAAATAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (31 bp):
AATTTTTAAATGTATTTATTTTTATAAATTT
Found at i:1580708 original size:18 final size:17
Alignment explanation
Indices: 1580672--1580710 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
1580662 TATTTTTAAA
1580672 ATTTAATTTTTATATTT
1 ATTTAATTTTTATATTT
1580689 ATTT-ATTTTTATCAATTT
1 ATTTAATTTTTAT--ATTT
1580707 ATTT
1 ATTT
1580711 TTAATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTAATTTTTATATTT
Found at i:1581650 original size:33 final size:36
Alignment explanation
Indices: 1581586--1581656 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 36
1581576 AATTTTTGTT
1581586 ATTAAATATAATTATAATAAAAAATTAAAA-TTAAA
1 ATTAAATATAATTATAATAAAAAATTAAAATTTAAA
**
1581621 ATTAAAT-T-ATTATAATAAATTA-TATAAATTTAAA
1 ATTAAATATAATTATAATAAAAAATTA-AAATTTAAA
1581655 AT
1 AT
1581657 AAAAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 2 0.06
33 15 0.47
34 8 0.25
35 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (36 bp):
ATTAAATATAATTATAATAAAAAATTAAAATTTAAA
Found at i:1581670 original size:16 final size:18
Alignment explanation
Indices: 1581637--1581684 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
1581627 TTATTATAAT
*
1581637 AAATTATATAAAT-T-TA
1 AAATAATATAAATATATA
1581653 AAATAA-A-AAATATATA
1 AAATAATATAAATATATA
1581669 AAATAATATAAATATA
1 AAATAATATAAATATA
1581685 CATAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 2 0.07
16 13 0.48
17 1 0.04
18 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATATAAATATATA
Found at i:1582065 original size:15 final size:15
Alignment explanation
Indices: 1582045--1582074 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1582035 TATTATAAAT
1582045 TTTTTTAAAAATTTA
1 TTTTTTAAAAATTTA
1582060 TTTTTTAAAAATTTA
1 TTTTTTAAAAATTTA
1582075 AAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTAAAAATTTA
Found at i:1582511 original size:16 final size:16
Alignment explanation
Indices: 1582470--1582513 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1582460 TAATAAAAAA
*
1582470 ATAATTAAAATATAAT
1 ATAATAAAAATATAAT
1582486 ATAA-AAAAATATGAAT
1 ATAATAAAAATAT-AAT
1582502 -TAATAAAAATAT
1 ATAATAAAAATAT
1582514 CAAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAATAAAAATATAAT
Found at i:1582518 original size:27 final size:24
Alignment explanation
Indices: 1582454--1582518 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
1582444 ATATCATATG
1582454 AAAATATAATAAAAAAATAATTAAA
1 AAAATATAA-AAAAAAATAATTAAA
*
1582479 ATATAATATAAAAAAATATGAATTAATA
1 A-A-AATATAAAAAAAAAT-AATTAA-A
*
1582507 AAAATATCAAAA
1 AAAATATAAAAA
1582519 TTTTTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 17 0.50
27 14 0.41
28 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATATAAAAAAAAATAATTAAA
Found at i:1582728 original size:11 final size:11
Alignment explanation
Indices: 1582702--1582735 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1582692 AAAATATTAT
1582702 TATAATATAAA
1 TATAATATAAA
1582713 T-TAATATAAA
1 TATAATATAAA
1582723 TATAATATAAA
1 TATAATATAAA
1582734 TA
1 TA
1582736 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1582960 original size:36 final size:38
Alignment explanation
Indices: 1582913--1582992 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 38
1582903 GGGCCAAGGT
1582913 TTTTTTTTTTTTTATTTAT-TTC-ATAGGCCAAC-TTTG
1 TTTTTTTTTTTTT-TTTATGTTCAATAGGCCAACTTTTG
*
1582949 TTTTTTTTTTTTTTTTTTGTTCATAATAGGCCAACTTTTG
1 TTTTTTTTTTTTTTTTATGTTC--AATAGGCCAACTTTTG
1582989 TTTT
1 TTTT
1582993 GAAACTATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
35 4 0.11
36 16 0.42
39 10 0.26
40 8 0.21
ACGTcount: A:0.15, C:0.10, G:0.09, T:0.66
Consensus pattern (38 bp):
TTTTTTTTTTTTTTTTATGTTCAATAGGCCAACTTTTG
Found at i:1582978 original size:39 final size:38
Alignment explanation
Indices: 1582911--1582992 Score: 112
Period size: 37 Copynumber: 2.1 Consensus size: 38
1582901 CTGGGCCAAG
*
1582911 GTTTTTTTTTTTTTTATTTATTTCATAGGCCAAC-TTT
1 GTTTTTTTTTTTTTTATTTATTTAATAGGCCAACTTTT
* *
1582948 GTTTTTTTTTTTTTTTTTTGTTCATAATAGGCCAACTTTT
1 GTTTTTTTTTTTTTTATTTATT--TAATAGGCCAACTTTT
1582988 GTTTT
1 GTTTT
1582993 GAAACTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 20 0.51
39 11 0.28
40 8 0.21
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (38 bp):
GTTTTTTTTTTTTTTATTTATTTAATAGGCCAACTTTT
Found at i:1583681 original size:15 final size:15
Alignment explanation
Indices: 1583663--1583694 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1583653 AAAAGATCTT
1583663 TTATTAAAATTAAAA
1 TTATTAAAATTAAAA
*
1583678 TTATTAAATTTAAAA
1 TTATTAAAATTAAAA
1583693 TT
1 TT
1583695 GGATAAGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTAAAATTAAAA
Found at i:1585743 original size:6 final size:6
Alignment explanation
Indices: 1585728--1585785 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
1585718 AAAAGTTTAC
1585728 TTAT-T TTATAT TTATA- -TAT-T TTATATTT TTATAT TTATA- TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATA--T TTATAT TTATAT TTATAT
1585773 TTATAT TTATAT T
1 TTATAT TTATAT T
1585786 ATTTTTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
4 3 0.07
5 12 0.26
6 25 0.54
8 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:1585759 original size:23 final size:25
Alignment explanation
Indices: 1585731--1585789 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 25
1585721 AGTTTACTTA
1585731 TTTTATATTTATA-TAT-TTTATAT
1 TTTTATATTTATATTATATTTATAT
1585754 TTTTATATTTATATTATATTTATAT
1 TTTTATATTTATATTATATTTATAT
*
1585779 TTATATTATTT
1 TTTTA-TATTT
1585790 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 13 0.41
24 3 0.09
25 11 0.34
26 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATATTTATATTATATTTATAT
Found at i:1585760 original size:17 final size:17
Alignment explanation
Indices: 1585729--1585804 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 17
1585719 AAAGTTTACT
1585729 TATTTTATA--TTTATA
1 TATTTTATATTTTTATA
1585744 TATTTTATATTTTTATA
1 TATTTTATATTTTTATA
* * *
1585761 TTTATATTATATTTATATT
1 --TATTTTATATTTTTATA
*
1585780 TATATTAT-TTTTTA-A
1 TATTTTATATTTTTATA
*
1585795 TTTTTTATAT
1 TATTTTATAT
1585805 CGTGTTTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 15 0.31
16 6 0.12
17 14 0.29
19 14 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTATATTTTTATA
Found at i:1585928 original size:23 final size:23
Alignment explanation
Indices: 1585902--1585952 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1585892 ACAAGTTTAC
* *
1585902 TTTTTTGTGTTATGTTTGT-ATTA
1 TTTTTTATGTTATATTT-TAATTA
*
1585925 TTTTTTATGTTGTATTTTAATTA
1 TTTTTTATGTTATATTTTAATTA
1585948 TTTTT
1 TTTTT
1585953 ATTTTTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.73
Consensus pattern (23 bp):
TTTTTTATGTTATATTTTAATTA
Found at i:1586354 original size:16 final size:16
Alignment explanation
Indices: 1586333--1586375 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1586323 GAGAGGATTA
1586333 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
* *
1586349 AAAAAGATAGAGAAAG
1 AAAAAGAAAAAGAAAG
**
1586365 GGAAAGAAAAA
1 AAAAAGAAAAA
1586376 TTTTTATGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:1587463 original size:13 final size:13
Alignment explanation
Indices: 1587445--1587470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1587435 TACACAAAGT
1587445 ATGTATCGATACA
1 ATGTATCGATACA
1587458 ATGTATCGATACA
1 ATGTATCGATACA
1587471 CCAAAAAATG
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:1587468 original size:32 final size:33
Alignment explanation
Indices: 1587427--1587490 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1587417 TAGCCAAACT
**
1587427 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
1587459 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
1587491 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:1587555 original size:20 final size:22
Alignment explanation
Indices: 1587524--1587567 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1587514 GCTATATTTT
1587524 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1587545 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1587566 CA
1 CA
1587568 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1593672 original size:13 final size:13
Alignment explanation
Indices: 1593654--1593680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1593644 ATACATCTTC
1593654 TTGTATCGATACA
1 TTGTATCGATACA
1593667 TTGTATCGATACA
1 TTGTATCGATACA
1593680 T
1 T
1593681 CTTTCTTTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1593675 original size:31 final size:33
Alignment explanation
Indices: 1593637--1593705 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1593627 GAAAATTCAA
1593637 TGTATCGATACATC-TTC-TTGTATCGATACAT
1 TGTATCGATACATCTTTCTTTGTATCGATACAT
1593668 TGTATCGATACATCTTTCTTTGTATCGATACAT
1 TGTATCGATACATCTTTCTTTGTATCGATACAT
1593701 TGTAT
1 TGTAT
1593706 ACACTGTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 14 0.39
32 3 0.08
33 19 0.53
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATCTTTCTTTGTATCGATACAT
Found at i:1596201 original size:20 final size:19
Alignment explanation
Indices: 1596147--1596201 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1596137 AAAACCCTTA
*
1596147 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
1596167 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
1596187 AATGTATCGATACAT
1 AAAGTATCGATACAT
1596202 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:1596278 original size:19 final size:20
Alignment explanation
Indices: 1596254--1596304 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1596244 TAGCCAAACT
**
1596254 TGTATCGATACAC-AAAGTA
1 TGTATCGATACACTAAAAAA
1596273 TGTATCGATACACTAAAAAA
1 TGTATCGATACACTAAAAAA
1596293 TGTATCGATACA
1 TGTATCGATACA
1596305 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACTAAAAAA
Found at i:1596369 original size:20 final size:22
Alignment explanation
Indices: 1596338--1596381 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1596328 GCTATATTTT
1596338 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1596359 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1596380 CA
1 CA
1596382 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1597641 original size:22 final size:22
Alignment explanation
Indices: 1597601--1597661 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1597591 AATATAAATA
* *
1597601 TAAATATAAATTTATAATTATTAT
1 TAAA-ATAAAATTAAAATT-TTAT
*
1597625 T-TAATAAAATTAAAATTTTAT
1 TAAAATAAAATTAAAATTTTAT
*
1597646 TAAAATAAAAATAAAA
1 TAAAATAAAATTAAAA
1597662 AGCTCCTAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 5 0.16
22 24 0.77
23 1 0.03
24 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATAAAATTAAAATTTTAT
Found at i:1597649 original size:17 final size:17
Alignment explanation
Indices: 1597624--1597657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1597614 ATAATTATTA
*
1597624 TTTAATAAAATTAAAAT
1 TTTAATAAAATAAAAAT
*
1597641 TTTATTAAAATAAAAAT
1 TTTAATAAAATAAAAAT
1597658 AAAAAGCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAATAAAATAAAAAT
Found at i:1598437 original size:15 final size:14
Alignment explanation
Indices: 1598410--1598436 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1598400 ATTAAGTTAA
1598410 AAAAGTAAAAAAAG
1 AAAAGTAAAAAAAG
1598424 AAAAGTAAAAAAA
1 AAAAGTAAAAAAA
1598437 AATATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AAAAGTAAAAAAAG
Found at i:1599132 original size:63 final size:62
Alignment explanation
Indices: 1599065--1599356 Score: 200
Period size: 62 Copynumber: 4.6 Consensus size: 62
1599055 ATAATTTATT
* **
1599065 AAAAAAATA-AATAAA-ATTACTAATTAATATTATAAAAAATTTATTGATTTCAAAATTTTTTTA
1 AAAAAAATATAATAAATATTACT-ATTAATATCA-AAAAAATTTATTGATTTCAAAA-AATTTTA
** * * * *
1599128 AAAAATTTATAATAAATATTAGTATTTATGTCAAAAAAATTTATTGATTTTAAAAAATTTTA
1 AAAAAAATATAATAAATATTACTATTAATATCAAAAAAATTTATTGATTTCAAAAAATTTTA
* * ** * * *
1599190 AAAAAAATCTATAATAAATATTAATATTTATGTAAAAAAATTAAATTTATTAATTTTAAAAAA-A
1 AAAAAAA--TATAATAAATATTACTA-TTA-ATATCAAAA--AAATTTATTGATTTCAAAAAATT
1599254 TTA
60 TTA
* * ** * **
1599257 AAAAAATTCATAATAAATATTAAC-ATTTACGT-AAAAAAATTTATTAATTTTTTAAAAATTTTA
1 AAAAAAAT-ATAATAAATATT-ACTATTAATATCAAAAAAATTTATTGA-TTTCAAAAAATTTTA
* * *
1599320 AAAAATATATAATAAATATTAATATTTATAT-AAAAAA
1 AAAAAAATATAATAAATATTACTATTAATATCAAAAAA
1599357 TTATATATAT
Statistics
Matches: 183, Mismatches: 33, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
61 12 0.07
62 43 0.23
63 41 0.22
64 29 0.16
65 10 0.05
66 18 0.10
67 10 0.05
68 20 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (62 bp):
AAAAAAATATAATAAATATTACTATTAATATCAAAAAAATTTATTGATTTCAAAAAATTTTA
Found at i:1599190 original size:62 final size:61
Alignment explanation
Indices: 1599098--1599356 Score: 293
Period size: 62 Copynumber: 4.1 Consensus size: 61
1599088 TTAATATTAT
* * ** *
1599098 AAAAAATTTATTGATTTCAAAATTTTTTTAAAAAATTTATAATAAATATTAGTATTTATGTCA
1 AAAAAATTTATTAATTTTAAAA-AATTTTAAAAAATTTATAATAAATATTAATATTTATGT-A
* *
1599161 AAAAAATTTATTGATTTTAAAAAATTTTAAAAAAAATCTATAATAAATATTAATATTTATGTAAA
1 AAAAAATTTATTAATTTTAAAAAATTTT--AAAAAATTTATAATAAATATTAATATTTATGT---
1599226 A
61 A
* * * * *
1599227 AAATTAAATTTATTAATTTTAAAAAAATTAAAAAAATTCATAATAAATATTAACATTTACGTA
1 AAA--AAATTTATTAATTTTAAAAAATTTTAAAAAATTTATAATAAATATTAATATTTATGTA
* * *
1599290 AAAAAATTTATTAATTTTTTAAAAATTTTAAAAAATATATAATAAATATTAATATTTATATA
1 AAAAAATTTATTAA-TTTTAAAAAATTTTAAAAAATTTATAATAAATATTAATATTTATGTA
1599352 AAAAA
1 AAAAA
1599357 TTATATATAT
Statistics
Matches: 168, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
61 11 0.07
62 48 0.29
63 25 0.15
64 30 0.18
66 32 0.19
68 22 0.13
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (61 bp):
AAAAAATTTATTAATTTTAAAAAATTTTAAAAAATTTATAATAAATATTAATATTTATGTA
Found at i:1599349 original size:21 final size:21
Alignment explanation
Indices: 1599325--1599369 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1599315 TTTTAAAAAA
1599325 TATATAATAAATATTA-ATAT-T
1 TATATAA-AAA-ATTATATATAT
1599346 TATATAAAAAATTATATATAT
1 TATATAAAAAATTATATATAT
1599367 TAT
1 TAT
1599370 GTCGACGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
21 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATAAAAAATTATATATAT
Found at i:1599392 original size:130 final size:129
Alignment explanation
Indices: 1599127--1599368 Score: 337
Period size: 130 Copynumber: 1.9 Consensus size: 129
1599117 AAATTTTTTT
* ** * *
1599127 AAAAAATTTATAATAAATATTAGTATTTATGTCAAAAAAATTTATTGATTTTAAAAAATTTTAAA
1 AAAAAATTCATAATAAATATTAACATTTACGTCAAAAAAATTTATTAATTTTAAAAAATTTT-AA
* * * **
1599192 AAAAATCTATAATAAATATTAATATTTATGTAAAAAAATTAAATTTATTAATTTTAAAAAAATTA
65 AAAAATATATAATAAATATTAATATTTATATAAAAAAATTAAATATATTAATTCGAAAAAAATTA
*
1599257 AAAAAATTCATAATAAATATTAACATTTACGT-AAAAAAATTTATTAATTTTTTAAAAATTTT-A
1 AAAAAATTCATAATAAATATTAACATTTACGTCAAAAAAATTTATTAA-TTTTAAAAAATTTTAA
*
1599320 AAAAATATATAATAAATATTAATATTTATAT-AAAAAATTATATATATTA
65 AAAAATATATAATAAATATTAATATTTATATAAAAAAATTAAATATATTA
1599369 TGTCGACGTA
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
127 16 0.16
128 30 0.30
129 14 0.14
130 41 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (129 bp):
AAAAAATTCATAATAAATATTAACATTTACGTCAAAAAAATTTATTAATTTTAAAAAATTTTAAA
AAAATATATAATAAATATTAATATTTATATAAAAAAATTAAATATATTAATTCGAAAAAAATTA
Found at i:1600199 original size:21 final size:18
Alignment explanation
Indices: 1600154--1600201 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
1600144 ATTTATTTTG
*
1600154 AAATATTGTTTAATTAAT
1 AAATATTATTTAATTAAT
1600172 AAGATATTATTTAAATTTAATT
1 AA-ATATTATTT-AA-TTAA-T
1600194 AAATATTA
1 AAATATTA
1600202 ATATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 8 0.32
20 2 0.08
21 10 0.40
22 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
AAATATTATTTAATTAAT
Found at i:1601289 original size:2 final size:2
Alignment explanation
Indices: 1601282--1601316 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1601272 TCAGTTCATT
*
1601282 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1601317 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1605160 original size:19 final size:21
Alignment explanation
Indices: 1605114--1605167 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
1605104 TTTTAACAAT
1605114 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
1605135 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
1605154 TTGTATCGATACAA
1 TTGTATCGATACAA
1605168 TGTATCGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:1622295 original size:17 final size:19
Alignment explanation
Indices: 1622261--1622304 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 19
1622251 TTACTTAAAG
1622261 ATATTAAAATATTATTTTT
1 ATATTAAAATATTATTTTT
1622280 ATATT--AATA-TATTTTT
1 ATATTAAAATATTATTTTT
1622296 ATAATTAAA
1 AT-ATTAAA
1622305 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
19 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAAAATATTATTTTT
Found at i:1623450 original size:20 final size:21
Alignment explanation
Indices: 1623421--1623470 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1623411 TCTATTTATG
*
1623421 TAAAATTATA-TCAAAATTTA
1 TAAAAATATATTCAAAATTTA
* *
1623441 TAAAAATATATTTAAATTTTA
1 TAAAAATATATTCAAAATTTA
1623462 TATAAAATA
1 TA-AAAATA
1623471 ACTGATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.36
21 10 0.40
22 6 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATATTCAAAATTTA
Found at i:1623469 original size:12 final size:11
Alignment explanation
Indices: 1623414--1623469 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
1623404 ATTTAAATCT
*
1623414 ATTTATGTAAA
1 ATTTATATAAA
1623425 A-TTATATCAAA
1 ATTTATAT-AAA
1623436 ATTTATA-AAA
1 ATTTATATAAA
* *
1623446 ATATATTTAAA
1 ATTTATATAAA
*
1623457 TTTTATATAAA
1 ATTTATATAAA
1623468 AT
1 AT
1623470 AACTGATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 13 0.37
11 17 0.49
12 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
ATTTATATAAA
Found at i:1623486 original size:19 final size:17
Alignment explanation
Indices: 1623473--1623506 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1623463 ATAAAATAAC
*
1623473 TGATTTTTTTTAAAAGA
1 TGATTTTTTTTAAAAAA
*
1623490 TGATTTTTTTCAAAAAA
1 TGATTTTTTTTAAAAAA
1623507 AAGTGAACTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (17 bp):
TGATTTTTTTTAAAAAA
Found at i:1629427 original size:2 final size:2
Alignment explanation
Indices: 1629422--1629454 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1629412 GAAAAGTTTG
1629422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1629455 AATAAGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1631616 original size:15 final size:16
Alignment explanation
Indices: 1631588--1631620 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1631578 ATATTATCGA
*
1631588 AAAACTTTTTAAAAAT
1 AAAACTTTTAAAAAAT
1631604 AAAA-TTTTAAAAAAT
1 AAAACTTTTAAAAAAT
1631619 AA
1 AA
1631621 CTATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAACTTTTAAAAAAT
Found at i:1631683 original size:20 final size:21
Alignment explanation
Indices: 1631655--1631694 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1631645 TAGAACTTTT
*
1631655 AAAACAATT-TTTATTATTTG
1 AAAACAATTATTTATCATTTG
*
1631675 AAAATAATTATTTATCATTT
1 AAAACAATTATTTATCATTT
1631695 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
AAAACAATTATTTATCATTTG
Found at i:1634882 original size:6 final size:6
Alignment explanation
Indices: 1634871--1634906 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1634861 TTATGATTAA
*
1634871 TAATTT TAATTT TAATTT TAATTT T-ATCT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
1634907 GAAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
TAATTT
Found at i:1636500 original size:20 final size:19
Alignment explanation
Indices: 1636459--1636501 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1636449 AAATTACCCA
*
1636459 TTTAGGGCATTTAAGACCT
1 TTTAGGGCATTTAAGACAT
1636478 TTTAGGGACATTTCAAG-CAT
1 TTTAGGG-CATTT-AAGACAT
1636498 TTTA
1 TTTA
1636502 AGTCATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (19 bp):
TTTAGGGCATTTAAGACAT
Found at i:1636593 original size:29 final size:29
Alignment explanation
Indices: 1636515--1636714 Score: 132
Period size: 29 Copynumber: 6.9 Consensus size: 29
1636505 CATTTTAAGA
* ** *
1636515 TCAAAGTGTAATTTAAAAAAAATTAAGGG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* *
1636544 TTAAAGTGTAATTTTGAAAAGTTTAGGGG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* *
1636573 TCAAAGTGTTATTTTAAAAAGTTTAGAGG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* * * * * ***
1636602 TCCATGTGCAATTTTGAAAATTTTAAAAG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* ** * *
1636631 TCAAAGTGCAATTTTGGAAAGTTTTGAGG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* * * *
1636660 TTAGAGCGTAATTTTAAAAAGTTTA-GAG
1 TCAAAGTGTAATTTTAAAAAGTTTAGGGG
* ** *
1636688 TTAAAAAGTAATTTTGAAAAGTTTAGG
1 TCAAAGTGTAATTTTAAAAAGTTTAGG
1636715 AACTTAGTAG
Statistics
Matches: 132, Mismatches: 38, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
28 22 0.17
29 110 0.83
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (29 bp):
TCAAAGTGTAATTTTAAAAAGTTTAGGGG
Found at i:1637352 original size:154 final size:153
Alignment explanation
Indices: 1636829--1637382 Score: 471
Period size: 154 Copynumber: 3.6 Consensus size: 153
1636819 ATACTTGTAT
* * * * * * * ** *
1636829 GTCGAAGGTATATCTT-AAGAGTATTTTCGTAATTTTTTAAAAATTGAGTCTAAAGTTGTCACCG
1 GTCGAAAGTATACCTTAAAG-GCATTTTAGTAATTTTTTTAAAA-TAAGTCTTAAGTCATCATCG
* * * * *
1636893 GATCGCTTTTATGCCAAATGTGTGCATTTAGGATAGGTTAGTCATTTTCTTTATATTTTTCGTAT
64 GGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTC-TTATCTTTTTCATAT
** * *
1636958 CCTTTAAAGTTACTG-GATACTTTTAT
128 CCTTTAGGGTTAC-GAGATACTTTCAC
* ** * * *
1636984 ATCGAAAGTATATCC-TATGGGCATGTTT-GTAATTTTTTTAAATTGAA-TCTTAGGTCGTCATC
1 GTCGAAAGTATA-CCTTAAAGGCAT-TTTAGTAATTTTTTTAAAAT-AAGTCTTAAGTCATCATC
* * * * * *
1637046 GAGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGATCAGTCTTTTTCTTATCTTTTTCCTGT
63 GGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTCTTATCTTTTTCATAT
**
1637111 CCTTTAGGGTTATTAGGATACTTTCAC
128 CCTTTAGGGTTACGA-GATACTTTCAC
** * *
1637138 GTCGAAAGTATACCTT-AAGAGCATTTTCA-TAATTTTCCTAAAATGAGTCTTAAATCATCATCG
1 GTCGAAAGTATACCTTAAAG-GCATTTT-AGTAATTTTTTTAAAATAAGTCTTAAGTCATCATCG
* * * *
1637201 GGTCCCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCCTTTTCATTATCTTGTTCATAA
64 GGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTC-TTATCTTTTTCATAT
1637266 CCTTTAGGGTGT-CGAGATACTTTCAC
128 CCTTTAGGGT-TACGAGATACTTTCAC
* * * * * **
1637292 GTTGAAAGTATA-CTTAAAGGCATTTTAGTAATTTTTTTAGAACTAAGTCTGATGTAATCATTAG
1 GTCGAAAGTATACCTTAAAGGCATTTTAGTAATTTTTTTA-AAATAAGTCTTAAGTCATCATCGG
*
1637356 GTCACTTTTATGTCGAAA-GTGTGCATT
65 GTCACTTTTATG-CCAAAGGTGTGCATT
1637383 AAGAGTAAGT
Statistics
Matches: 319, Mismatches: 63, Indels: 35
0.76 0.15 0.08
Matches are distributed among these distances:
152 1 0.00
153 48 0.15
154 210 0.66
155 54 0.17
156 6 0.02
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.41
Consensus pattern (153 bp):
GTCGAAAGTATACCTTAAAGGCATTTTAGTAATTTTTTTAAAATAAGTCTTAAGTCATCATCGGG
TCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTCTTATCTTTTTCATATCCT
TTAGGGTTACGAGATACTTTCAC
Found at i:1637717 original size:16 final size:16
Alignment explanation
Indices: 1637664--1637710 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1637654 TTTGAACTCG
*
1637664 AAATGACCTAAACCTA
1 AAATGACCTGAACCTA
* *
1637680 AAATGATCTGAACCCA
1 AAATGACCTGAACCTA
1637696 AAATGACCTGAACCT
1 AAATGACCTGAACCT
1637711 GGAATGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (16 bp):
AAATGACCTGAACCTA
Found at i:1637740 original size:32 final size:32
Alignment explanation
Indices: 1637641--1637740 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
1637631 GATCGATCCA
* * *
1637641 AACCTGAAAATAATTTGAACTCGAAATGACCTA
1 AACCT-AAAATGATTTGAACCCGAAATGACCTG
* *
1637674 AACCTAAAATGATCTGAACCCAAAATGACCTG
1 AACCTAAAATGATTTGAACCCGAAATGACCTG
** * *
1637706 AACCTGGAATGATTTAAACCCGAAATGACTTG
1 AACCTAAAATGATTTGAACCCGAAATGACCTG
1637738 AAC
1 AAC
1637741 AAATAACTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
32 51 0.91
33 5 0.09
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (32 bp):
AACCTAAAATGATTTGAACCCGAAATGACCTG
Found at i:1638619 original size:16 final size:16
Alignment explanation
Indices: 1638600--1638671 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
1638590 GAACCCGAAG
1638600 TGACCCAAACCCAAAA
1 TGACCCAAACCCAAAA
* *
1638616 TGACTCGAA-CC-AAA
1 TGACCCAAACCCAAAA
*
1638630 TGA-CCATAACCCGAAA
1 TGACCCA-AACCCAAAA
* *
1638646 TGACCTAAACTCAAAA
1 TGACCCAAACCCAAAA
*
1638662 GTGACTCAAA
1 -TGACCCAAA
1638672 AATTTTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
13 1 0.02
14 8 0.19
15 4 0.10
16 20 0.48
17 9 0.21
ACGTcount: A:0.46, C:0.29, G:0.11, T:0.14
Consensus pattern (16 bp):
TGACCCAAACCCAAAA
Found at i:1641743 original size:10 final size:10
Alignment explanation
Indices: 1641713--1641746 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1641703 TGATGATCGA
*
1641713 TTTAAAAATA
1 TTTAAAAATC
1641723 TTTCAAAAATC
1 TTT-AAAAATC
1641734 TTTAAAAATC
1 TTTAAAAATC
1641744 TTT
1 TTT
1641747 TCCTAGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATC
Found at i:1643676 original size:65 final size:66
Alignment explanation
Indices: 1643555--1643677 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 66
1643545 AAAATATATC
* * *
1643555 GATACATCTGGGTAAATAGACAGAATGTATCGATACATTGAAAACTGCATCGATACATTCATACT
1 GATACATCTGGGTAAATAGACAGAATGTATCGATACATTAAAAAATGCATCAATACATTCATACT
1643620 T
66 T
* * *
1643621 GATACATCTGGGTAAA-AGATAGAATGTATCGATATATTAAAAAATGTATCAATACAT
1 GATACATCTGGGTAAATAGACAGAATGTATCGATACATTAAAAAATGCATCAATACAT
1643678 CTAGGTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
65 35 0.69
66 16 0.31
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (66 bp):
GATACATCTGGGTAAATAGACAGAATGTATCGATACATTAAAAAATGCATCAATACATTCATACT
T
Found at i:1644086 original size:18 final size:18
Alignment explanation
Indices: 1644063--1644102 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1644053 GTACCTTTTT
*
1644063 TTAAAAAAA-AAGTTTAAA
1 TTAAAAAAATAAGCTT-AA
1644081 TTAAAAAAATAAGCTTAA
1 TTAAAAAAATAAGCTTAA
1644099 TTAA
1 TTAA
1644103 TTCGAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
TTAAAAAAATAAGCTTAA
Found at i:1657585 original size:20 final size:20
Alignment explanation
Indices: 1657524--1657586 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1657514 TAATTTATAG
*
1657524 TATAAATTTAATTTAATTTAAA
1 TATAAATAT-ATTT-ATTTAAA
* **
1657546 AATAAATAT-TTTATAAAAA
1 TATAAATATATTTATTTAAA
*
1657565 TATGAATATATTTATTTAAA
1 TATAAATATATTTATTTAAA
1657585 TA
1 TA
1657587 AATTTAGGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 12 0.38
20 13 0.41
22 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAAATATATTTATTTAAA
Found at i:1657880 original size:40 final size:39
Alignment explanation
Indices: 1657836--1657914 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
1657826 ATACTAAAAT
* *
1657836 ATTTTTATAAAAATAATATTTATATTTTAATA-AATTATTA
1 ATTTTTATAAAAAT-A-ATTTAAATTATAATATAATTATTA
1657876 ATTTTTATAAAAATAATTTAAATTATAATATAATTATTA
1 ATTTTTATAAAAATAATTTAAATTATAATATAATTATTA
1657915 TTTATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 13 0.36
39 9 0.25
40 14 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (39 bp):
ATTTTTATAAAAATAATTTAAATTATAATATAATTATTA
Found at i:1658693 original size:33 final size:33
Alignment explanation
Indices: 1658656--1658722 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1658646 TTCAACGATT
1658656 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1658689 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1658722 T
1 T
1658723 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:1658694 original size:13 final size:13
Alignment explanation
Indices: 1658676--1658700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1658666 CATAAAATGT
1658676 TGTATCGATACAA
1 TGTATCGATACAA
1658689 TGTATCGATACA
1 TGTATCGATACA
1658701 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:1658781 original size:13 final size:13
Alignment explanation
Indices: 1658763--1658787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1658753 ATTACTCAAA
1658763 TGTATCGATACAT
1 TGTATCGATACAT
1658776 TGTATCGATACA
1 TGTATCGATACA
1658788 CTGATCTCTG
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):
TGTATCGATACAT
Found at i:1658852 original size:52 final size:52
Alignment explanation
Indices: 1658796--1658920 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1658786 CACTGATCTC
*
1658796 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1658848 TGTATCGATACATGCAGGCAAATTTGCCCGGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1658900 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1658921 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1664090 original size:25 final size:24
Alignment explanation
Indices: 1664060--1664106 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1664050 TCATCTAATA
*
1664060 TAAATTTATTATATAATATAATATT
1 TAAATTTATTAT-TAACATAATATT
*
1664085 TAAATTTGTTATTAACATAATA
1 TAAATTTATTATTAACATAATA
1664107 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATTTATTATTAACATAATATT
Found at i:1668641 original size:126 final size:126
Alignment explanation
Indices: 1668416--1668665 Score: 473
Period size: 126 Copynumber: 2.0 Consensus size: 126
1668406 CTGGACAGAA
*
1668416 GGAAAATGAGTCTATTCTCTCTGGATAATTGGTTCTTATCATCTCTTCAAAGATAAATGTTTTGA
1 GGAAAATGAGTCTATTCTCTCTGGATAATTGGTTCGTATCATCTCTTCAAAGATAAATGTTTTGA
1668481 TGAGAAAAAACAAAACTTAAAGTGCTTATGAAAATTGCAACAAGTATACCTAACATACCAC
66 TGAGAAAAAACAAAACTTAAAGTGCTTATGAAAATTGCAACAAGTATACCTAACATACCAC
*
1668542 GGAAAATGAGTCTGTTCTCTCTGGATAATTGGTTCGTATCATCTCTTCAAAGATAAATGTTTTGA
1 GGAAAATGAGTCTATTCTCTCTGGATAATTGGTTCGTATCATCTCTTCAAAGATAAATGTTTTGA
*
1668607 TGAGCAAAAACAAAACTTAAAGTGCTTATGAAAATTGCAACAAGTATACCTAACATACC
66 TGAGAAAAAACAAAACTTAAAGTGCTTATGAAAATTGCAACAAGTATACCTAACATACC
1668666 GTCAACCATT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 121 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (126 bp):
GGAAAATGAGTCTATTCTCTCTGGATAATTGGTTCGTATCATCTCTTCAAAGATAAATGTTTTGA
TGAGAAAAAACAAAACTTAAAGTGCTTATGAAAATTGCAACAAGTATACCTAACATACCAC
Found at i:1671537 original size:3 final size:3
Alignment explanation
Indices: 1671524--1671557 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1671514 TGACATTTTT
*
1671524 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1671558 CAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1676264 original size:21 final size:21
Alignment explanation
Indices: 1676238--1676280 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1676228 TAAAAATTAT
*
1676238 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTAAATA
1676259 TTTTATAATTAAATTTAAATA
1 TTTTATAATTAAATTTAAATA
1676280 T
1 T
1676281 AAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATAATTAAATTTAAATA
Found at i:1676309 original size:26 final size:27
Alignment explanation
Indices: 1676246--1676310 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
1676236 ATTTTTATAT
*
1676246 TAAT-ATTTATATATTTTATAATTAAA
1 TAATAATTTAAATATTTTATAATTAAA
* * *
1676272 T-TTAAATATAAATATTTT-TTATTAAA
1 TAAT-AATTTAAATATTTTATAATTAAA
1676298 TAATAATTTAAAT
1 TAATAATTTAAAT
1676311 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
25 1 0.03
26 17 0.57
27 12 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATAATTTAAATATTTTATAATTAAA
Found at i:1678721 original size:112 final size:112
Alignment explanation
Indices: 1678515--1678739 Score: 351
Period size: 112 Copynumber: 2.0 Consensus size: 112
1678505 ATCTTTGAAG
* * * **
1678515 GGTATATTTCGTAATGGGTTCTTAGGTATAATAAATAAATGCTGAATGTGCTAGTCTAGTAGGAT
1 GGTAAATTACGTAATAGGTTCTTAGGTATAATAAATAAATGCTGAATGCACTAGTCTAGTAGGAT
1678580 GGTTTCTATATTAGTTTTTTCGGCTGACTAAGTTTTAGCTGCCATTT
66 GGTTTCTATATTAGTTTTTTCGGCTGACTAAGTTTTAGCTGCCATTT
* * ** *
1678627 GGTAAATTACGTAATAGGTTCTTAGGTATAATAATTAAATGGTTTATGCACTAGTGTAGTAGGAT
1 GGTAAATTACGTAATAGGTTCTTAGGTATAATAAATAAATGCTGAATGCACTAGTCTAGTAGGAT
*
1678692 GGTTTCTATATTAGTTTTTTCGTCTGACTAAGTTTTAGCTGCCATTT
66 GGTTTCTATATTAGTTTTTTCGGCTGACTAAGTTTTAGCTGCCATTT
1678739 G
1 G
1678740 TTTTTTTGTT
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 102 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (112 bp):
GGTAAATTACGTAATAGGTTCTTAGGTATAATAAATAAATGCTGAATGCACTAGTCTAGTAGGAT
GGTTTCTATATTAGTTTTTTCGGCTGACTAAGTTTTAGCTGCCATTT
Found at i:1681715 original size:20 final size:20
Alignment explanation
Indices: 1681690--1681728 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1681680 GGGCGTACAA
1681690 AATAATAATGCATGCATGCG
1 AATAATAATGCATGCATGCG
1681710 AATAATAATGCATGCATGC
1 AATAATAATGCATGCATGC
1681729 ATCTCTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (20 bp):
AATAATAATGCATGCATGCG
Found at i:1682264 original size:27 final size:32
Alignment explanation
Indices: 1682210--1682276 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 32
1682200 TTAAAAATTT
1682210 ATATTTAAGTTTTTATTAATTTAAAAATAA-A
1 ATATTTAAGTTTTTATTAATTTAAAAATAAGA
1682241 ATATTT-A-TTTTTA-T-ATTTAAAAATAAGA
1 ATATTTAAGTTTTTATTAATTTAAAAATAAGA
*
1682269 ATAATTAA
1 ATATTTAA
1682277 AGAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 12 0.36
28 7 0.21
29 7 0.21
30 1 0.03
31 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (32 bp):
ATATTTAAGTTTTTATTAATTTAAAAATAAGA
Found at i:1683627 original size:14 final size:15
Alignment explanation
Indices: 1683608--1683657 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
1683598 TCATAACATT
1683608 TTTTGACAAAAATA-
1 TTTTGACAAAAATAC
*
1683622 TTTTGACAAAAGTAC
1 TTTTGACAAAAATAC
* *
1683637 TTTTGACAATAACAC
1 TTTTGACAAAAATAC
1683652 TTTTGA
1 TTTTGA
1683658 GACAAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (15 bp):
TTTTGACAAAAATAC
Found at i:1683640 original size:15 final size:14
Alignment explanation
Indices: 1683608--1683673 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
1683598 TCATAACATT
*
1683608 TTTTGACAAAAATA
1 TTTTGACAAAAGTA
1683622 TTTTGACAAAAGTA
1 TTTTGACAAAAGTA
*
1683636 CTTTTGACAATAA-CA
1 -TTTTGACAA-AAGTA
1683651 CTTTTGAGACAAAAGTA
1 -TTTT--GACAAAAGTA
1683668 TTTTGA
1 TTTTGA
1683674 TAGCAACGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 15 0.34
15 15 0.34
16 8 0.18
17 6 0.14
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (14 bp):
TTTTGACAAAAGTA
Found at i:1684998 original size:36 final size:34
Alignment explanation
Indices: 1684944--1685014 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 34
1684934 AAGAATTAAA
* *
1684944 TTTGAAATTCAAAGAAATATGGATTAAATTTTTT
1 TTTGAAATTCAAAGAAATATGAATTAAAATTTTT
1684978 TTTGTAAAGTTCAAAGAAATATGAATTAAAATTTTT
1 TTTG-AAA-TTCAAAGAAATATGAATTAAAATTTTT
1685014 T
1 T
1685015 AATTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 4 0.12
35 3 0.09
36 26 0.79
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (34 bp):
TTTGAAATTCAAAGAAATATGAATTAAAATTTTT
Found at i:1686023 original size:25 final size:26
Alignment explanation
Indices: 1685987--1686036 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1685977 ATTATTCTCT
1685987 AAATCAATTTAA-TTTAAAATATTTA
1 AAATCAATTTAATTTTAAAATATTTA
*
1686012 AAATACAA-TTAATTTTAATATATTT
1 AAAT-CAATTTAATTTTAAAATATTT
1686037 TTTCCCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATCAATTTAATTTTAAAATATTTA
Found at i:1686679 original size:16 final size:16
Alignment explanation
Indices: 1686660--1686690 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1686650 TTAAAGTGGA
1686660 TAATTATTAAATTAAG
1 TAATTATTAAATTAAG
*
1686676 TAATTTTTAAATTAA
1 TAATTATTAAATTAA
1686691 AGTAGCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATTATTAAATTAAG
Found at i:1687025 original size:17 final size:17
Alignment explanation
Indices: 1686997--1687049 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
1686987 GGGTGAAGTA
1686997 ATAAATAATT-AAATATAT
1 ATAAA-AATTAAAATA-AT
1687015 ATAAAAATTAAAATAAT
1 ATAAAAATTAAAATAAT
*
1687032 AAAAAAATTAAAAGTAAT
1 ATAAAAATTAAAA-TAAT
1687050 TGAAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAAAATTAAAATAAT
Found at i:1689242 original size:13 final size:12
Alignment explanation
Indices: 1689221--1689260 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1689211 ATAATGTATG
1689221 ATTTTTTCTTAA
1 ATTTTTTCTTAA
1689233 ATTATTTTCTT-A
1 ATT-TTTTCTTAA
1689245 A-TTTTTCTTAA
1 ATTTTTTCTTAA
1689256 ATTTT
1 ATTTT
1689261 CTTATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 8 0.32
13 7 0.28
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTTCTTAA
Found at i:1689268 original size:23 final size:23
Alignment explanation
Indices: 1689223--1689268 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1689213 AATGTATGAT
*
1689223 TTTTTCTTAAATTATTTTCTTAA
1 TTTTTCTTAAATTATTTTATTAA
1689246 TTTTTCTTAAATT-TTCTTATTAA
1 TTTTTCTTAAATTATT-TTATTAA
1689269 AAAAATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTCTTAAATTATTTTATTAA
Found at i:1689430 original size:2 final size:2
Alignment explanation
Indices: 1689423--1689447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1689413 TTGGTAGTTT
1689423 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1689448 GCATGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1689733 original size:21 final size:21
Alignment explanation
Indices: 1689707--1689780 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
1689697 CATAATTTTA
1689707 TATATTTATTATATTATTAAT
1 TATATTTATTATATTATTAAT
* *
1689728 TATATTAATT-TATT-TAAAT
1 TATATTTATTATATTATTAAT
* *
1689747 AATATATTT-TAATATTAAT-AT
1 --TATATTTATTATATTATTAAT
*
1689768 TATAATTATTATA
1 TATATTTATTATA
1689781 AATAATAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 11
0.68 0.14 0.19
Matches are distributed among these distances:
19 10 0.25
20 9 0.22
21 21 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTTATTATATTATTAAT
Found at i:1689888 original size:17 final size:17
Alignment explanation
Indices: 1689862--1689897 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1689852 TAAATAATTA
1689862 TACATATATTAATT-TT
1 TACATATATTAATTATT
1689878 TACACTATATTAATTATT
1 TACA-TATATTAATTATT
1689896 TA
1 TA
1689898 AAATAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 10 0.56
18 4 0.22
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (17 bp):
TACATATATTAATTATT
Found at i:1690535 original size:16 final size:16
Alignment explanation
Indices: 1690516--1690574 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
1690506 TTTTATCCAT
1690516 TTTTAAAAAATAATTA
1 TTTTAAAAAATAATTA
1690532 TTTTATAAAATATAATTTAA
1 TTTTA-AAAA-ATAA-TT-A
1690552 TTTATAAAAAAATAA--A
1 TTT-T-AAAAAATAATTA
1690568 TTTTAAA
1 TTTTAAA
1690575 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.08
15 1 0.03
16 9 0.24
17 4 0.11
18 4 0.11
19 2 0.05
20 8 0.22
21 5 0.14
22 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAAAAATAATTA
Found at i:1690546 original size:18 final size:19
Alignment explanation
Indices: 1690514--1690562 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1690504 TGTTTTATCC
1690514 ATTTT-TAAAAAATAA-TT
1 ATTTTATAAAAAATAATTT
*
1690531 ATTTTATAAAATATAATTT
1 ATTTTATAAAAAATAATTT
*
1690550 AATTTATAAAAAA
1 ATTTTATAAAAAA
1690563 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTATAAAAAATAATTT
Found at i:1690572 original size:22 final size:23
Alignment explanation
Indices: 1690538--1690583 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1690528 ATTATTTTAT
*
1690538 AAAATATAATTT-AATTTATAAA
1 AAAATATAATTTAAATTAATAAA
1690560 AAAATA-AATTTTAAATTAATAAA
1 AAAATATAA-TTTAAATTAATAAA
1690583 A
1 A
1690584 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 9 0.43
23 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATATAATTTAAATTAATAAA
Found at i:1691144 original size:27 final size:28
Alignment explanation
Indices: 1691114--1691167 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1691104 AATTATATGT
1691114 TTTATAAA-TTA-TTATTTAATATTTAAA
1 TTTATAAATTTATTTATTTAAT-TTTAAA
*
1691141 TTTATAAATTTATTTTTTTAATTTTAA
1 TTTATAAATTTATTTATTTAATTTTAA
1691168 TATGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 8 0.33
29 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATAAATTTATTTATTTAATTTTAAA
Found at i:1691192 original size:15 final size:16
Alignment explanation
Indices: 1691172--1691204 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1691162 TTTTAATATG
1691172 AAAATAAAAT-TTATA
1 AAAATAAAATATTATA
1691187 AAAATAAAATATTATA
1 AAAATAAAATATTATA
1691203 AA
1 AA
1691205 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAAAATATTATA
Found at i:1692377 original size:20 final size:22
Alignment explanation
Indices: 1692344--1692388 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1692334 ATTTTAAAAA
1692344 ATATAATCATAATCT-TATAAT
1 ATATAATCATAATCTATATAAT
1692365 ATATAAT-ATAATCTAATATAAT
1 ATATAATCATAATCT-ATATAAT
1692387 AT
1 AT
1692389 TATTCTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAATCATAATCTATATAAT
Found at i:1694618 original size:305 final size:306
Alignment explanation
Indices: 1694040--1694624 Score: 908
Period size: 305 Copynumber: 1.9 Consensus size: 306
1694030 CATCTCCTAA
* * * * *
1694040 AAAGGATATCTTAAGTCTATTCACGGATATTAAGAAAAGTCAGATTATATATTAAAAAAAGTATC
1 AAAGGATATCTAAAGTCCATCCAAGGATATTAAGAAAAGTCAGATTATACATTAAAAAAAGTATC
* * * * * *
1694105 ATGGTTTATAAGATAATCGAAGATGATTTGACATTTTGACTATTCTTAGTTTGCATCGAGTCAGC
66 ATGGTTTATAAGATAATCGAAAATGATTTAACATTTTGACCATTCTCAATTTGCATCGAGCCAGC
* *
1694170 ATCATGCACACCTTGCTTTTACCATTTAACTTATTTATCCATCACTTGCTTACTCAATTATTTAC
131 ATCATGCACACCTTGCTTTTACCACTTAACTTATTTATCCACCACTTGCTTACTCAATTATTTAC
1694235 CTATCACTTCTCTCAACAACTTGTATATATTTTCTTACCATATCACGTACAACAATTTTATGGTT
196 CTATCACTTCTCTCAACAACTTGTATATATTTTCTTACCATATCACGTACAACAATTTTATGGTT
**
1694300 ATCCATTACTTTTTCTTTACCTACCACAATTTTATGGATATCTTGT
261 ATCCACCACTTTTTCTTTACCTACCACAATTTTATGGATATCTTGT
1694346 AAAGGATATC-AAAGTCCATCCAAGGATATTAAGAAAAGTC-GAATTATACATTAAAAAATA-TA
1 AAAGGATATCTAAAGTCCATCCAAGGATATTAAGAAAAGTCAG-ATTATACATTAAAAAA-AGTA
* *
1694408 TTATGGTTTATAAGATAATCGAAAATGATTTAATATTTTGACCATTCTCAATTTGCATCGAGCCA
64 TCATGGTTTATAAGATAATCGAAAATGATTTAACATTTTGACCATTCTCAATTTGCATCGAGCCA
* *
1694473 GCATCATGCACACTTTGCTTTTACCACTTAACTTATTTATCCACCACTTGTTTACTCAATTATTT
129 GCATCATGCACACCTTGCTTTTACCACTTAACTTATTTATCCACCACTTGCTTACTCAATTATTT
* * *
1694538 A-CTCATTACTTCTCTCAATAACTTGTATATATTTTCTTACCATATCACGTACAATAATTTTATG
194 ACCT-ATCACTTCTCTCAACAACTTGTATATATTTTCTTACCATATCACGTACAACAATTTTATG
*
1694602 GTTATCTACCACTTTTTCTTTAC
258 GTTATCCACCACTTTTTCTTTAC
1694625 TAACTACAAT
Statistics
Matches: 253, Mismatches: 23, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
304 3 0.01
305 239 0.94
306 11 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (306 bp):
AAAGGATATCTAAAGTCCATCCAAGGATATTAAGAAAAGTCAGATTATACATTAAAAAAAGTATC
ATGGTTTATAAGATAATCGAAAATGATTTAACATTTTGACCATTCTCAATTTGCATCGAGCCAGC
ATCATGCACACCTTGCTTTTACCACTTAACTTATTTATCCACCACTTGCTTACTCAATTATTTAC
CTATCACTTCTCTCAACAACTTGTATATATTTTCTTACCATATCACGTACAACAATTTTATGGTT
ATCCACCACTTTTTCTTTACCTACCACAATTTTATGGATATCTTGT
Found at i:1695159 original size:19 final size:21
Alignment explanation
Indices: 1695137--1695178 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1695127 ATAATAAATC
1695137 TAATAATA-TAA-ATAAAAAA
1 TAATAATAGTAATATAAAAAA
1695156 TAATAATAGTAATATAAAAAA
1 TAATAATAGTAATATAAAAAA
1695177 TA
1 TA
1695179 TTAACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.38
20 3 0.14
21 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATAATAGTAATATAAAAAA
Found at i:1695189 original size:18 final size:18
Alignment explanation
Indices: 1695168--1695230 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
1695158 ATAATAGTAA
1695168 TATAAAAAATATTAACAT
1 TATAAAAAATATTAACAT
* *
1695186 TATAATAAATA--AAAAT
1 TATAAAAAATATTAACAT
1695202 TA-ATAAAAATATTAACAT
1 TATA-AAAAATATTAACAT
*
1695220 TATAATAAATA
1 TATAAAAAATA
1695231 AAAATTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 1 0.03
16 12 0.33
18 22 0.61
19 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAAAATATTAACAT
Found at i:1695193 original size:21 final size:20
Alignment explanation
Indices: 1695145--1695204 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1695135 TCTAATAATA
* *
1695145 TAAATAAAAAATAATAATAG
1 TAAATAAAAAATATTAACAG
*
1695165 TAATATAAAAAATATTAACAT
1 TAA-ATAAAAAATATTAACAG
*
1695186 TATAATAAATAAAAATTAA
1 TA-AATAAA-AAATATTAA
1695205 TAAAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.09
21 21 0.64
22 9 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAATAAAAAATATTAACAG
Found at i:1695210 original size:34 final size:34
Alignment explanation
Indices: 1695172--1695272 Score: 152
Period size: 34 Copynumber: 3.0 Consensus size: 34
1695162 TAGTAATATA
1695172 AAAAATATTAACATTATAATAAATAAAAATTAAT
1 AAAAATATTAACATTATAATAAATAAAAATTAAT
1695206 AAAAATATTAACATTATAATAAATAAAAATTAAT
1 AAAAATATTAACATTATAATAAATAAAAATTAAT
* *
1695240 AAGAATATTATAAATT-TAATAAA-AAAAACTTAA
1 AAAAATATTA-ACATTATAATAAATAAAAA-TTAA
1695273 CAAATTATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.08
34 54 0.86
35 4 0.06
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (34 bp):
AAAAATATTAACATTATAATAAATAAAAATTAAT
Found at i:1695808 original size:13 final size:13
Alignment explanation
Indices: 1695790--1695823 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1695780 TTAATAGTTT
1695790 AATTAATATATAA
1 AATTAATATATAA
*
1695803 AATTAAAATATAA
1 AATTAATATATAA
1695816 AATATAAT
1 AAT-TAAT
1695824 TGGCAGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAATATATAA
Found at i:1698266 original size:27 final size:27
Alignment explanation
Indices: 1698228--1698280 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1698218 TGCAACTTTC
* *
1698228 ACTGTTTTAAATTGAATTTCATAATTT
1 ACTGTTTCAAATTGAATTTCAAAATTT
1698255 ACTGTTTCAAATTGAATTTCAAAATT
1 ACTGTTTCAAATTGAATTTCAAAATT
1698281 GACGGCACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTT
Found at i:1702991 original size:27 final size:27
Alignment explanation
Indices: 1702941--1702992 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1702931 AAACATATAA
*
1702941 TGTTTCAAATTAAATTTCATAATTTAC
1 TGTTTCAAATTAAATTTCAAAATTTAC
* *
1702968 TGTTTTAAATTAAATTTTAAAATTT
1 TGTTTCAAATTAAATTTCAAAATTT
1702993 TAGGCACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (27 bp):
TGTTTCAAATTAAATTTCAAAATTTAC
Found at i:1705303 original size:37 final size:35
Alignment explanation
Indices: 1705262--1705354 Score: 91
Period size: 35 Copynumber: 2.6 Consensus size: 35
1705252 ATTGGCCATC
1705262 AATATTTAAATAAATTAAATAAATTATAAAATATATA
1 AATATTTAAATAAATT-AATAAATT-TAAAATATATA
** **
1705299 AATA-TTAATATAAATTTTTAAATTTTTAATATATA
1 AATATTTAA-ATAAATTAATAAATTTAAAATATATA
* *
1705334 TAT-TTTAAATAAATTTATAAA
1 AATATTTAAATAAATTAATAAA
1705355 AGTTATTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
34 12 0.25
35 15 0.31
36 10 0.21
37 11 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
AATATTTAAATAAATTAATAAATTTAAAATATATA
Found at i:1705327 original size:21 final size:22
Alignment explanation
Indices: 1705303--1705343 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1705293 TATATAAATA
1705303 TTAATATAAAT-TTTTAAATTT
1 TTAATATAAATATTTTAAATTT
*
1705324 TTAATATATATATTTTAAAT
1 TTAATATAAATATTTTAAAT
1705344 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATATAAATATTTTAAATTT
Found at i:1705338 original size:23 final size:20
Alignment explanation
Indices: 1705303--1705343 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1705293 TATATAAATA
1705303 TTAATATAAATTTTTAAATTT
1 TTAATATAAA-TTTTAAATTT
1705324 TTAATATATATATTTTAAAT
1 TTAATATA-A-ATTTTAAAT
1705344 AAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 9 0.50
23 1 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATATAAATTTTAAATTT
Found at i:1705829 original size:23 final size:24
Alignment explanation
Indices: 1705803--1705850 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1705793 TTAATTCAAT
1705803 TAAAAATTTATAAAAAAT-TAAAA
1 TAAAAATTTATAAAAAATATAAAA
* *
1705826 TAAAATTTTATAATAAATATAAAA
1 TAAAAATTTATAAAAAATATAAAA
1705850 T
1 T
1705851 TAAGATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAAAATTTATAAAAAATATAAAA
Done.