Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold164
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: 2248410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1150328 original size:20 final size:20
Alignment explanation
Indices: 1150302--1150347 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1150292 AGCTTCTTTC
1150302 AGTTGTTGAAAAACATTTAA
1 AGTTGTTGAAAAACATTTAA
* *
1150322 GGTTGTTGAAAAGCATTTAA
1 AGTTGTTGAAAAACATTTAA
1150342 AGTTGT
1 AGTTGT
1150348 AAAAGTCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTTGTTGAAAAACATTTAA
Found at i:1154777 original size:33 final size:33
Alignment explanation
Indices: 1154702--1154779 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
1154692 TTACAAGCAT
*
1154702 CATGTATCGATAAAATGTATCGATACAATTCAT
1 CATGTATCGATAAAATGTATCGATACAATTCAC
* * * *
1154735 TATGCATCGATATAATGTATCGATAC-ATTGTAC
1 CATGTATCGATAAAATGTATCGATACAATT-CAC
1154768 CATGTATCGATA
1 CATGTATCGATA
1154780 CAAACAGTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
32 3 0.08
33 34 0.92
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
CATGTATCGATAAAATGTATCGATACAATTCAC
Found at i:1154835 original size:20 final size:20
Alignment explanation
Indices: 1154810--1154886 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
1154800 ACTACCAATC
1154810 TCATGTATCGATACAATTGT
1 TCATGTATCGATACAATTGT
1154830 TCATGTATCGATACAATTGT
1 TCATGTATCGATACAATTGT
*
1154850 TCATGTATCGATACAA-TGA
1 TCATGTATCGATACAATTGT
*
1154869 ACATGTATCGATACAATT
1 TCATGTATCGATACAATT
1154887 TATCGATACA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 17 0.31
20 37 0.69
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (20 bp):
TCATGTATCGATACAATTGT
Found at i:1154885 original size:39 final size:40
Alignment explanation
Indices: 1154810--1154886 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
1154800 ACTACCAATC
**
1154810 TCATGTATCGATACAATTGTTCATGTATCGATACAATTGT
1 TCATGTATCGATACAATTGAACATGTATCGATACAATTGT
1154850 TCATGTATCGATACAA-TGAACATGTATCGATACAATT
1 TCATGTATCGATACAATTGAACATGTATCGATACAATT
1154887 TATCGATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (40 bp):
TCATGTATCGATACAATTGAACATGTATCGATACAATTGT
Found at i:1154913 original size:33 final size:32
Alignment explanation
Indices: 1154855--1154916 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1154845 ATTGTTCATG
*
1154855 TATCGATACAATGAACATGTATCGATACAATT
1 TATCGATACAAAGAACATGTATCGATACAATT
1154887 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
1154917 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAATT
Found at i:1155502 original size:22 final size:22
Alignment explanation
Indices: 1155440--1155495 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1155430 AGTTTTCATT
* *
1155440 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTCATCAAAGAA
*
1155462 TTTCTCCCCCTTCATCAAAGCA
1 TTTCTCCCCCTTCATCAAAGAA
*
1155484 TTTCTCTCCCTT
1 TTTCTCCCCCTT
1155496 TGTCAAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.36, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTCTCCCCCTTCATCAAAGAA
Found at i:1161975 original size:20 final size:20
Alignment explanation
Indices: 1161950--1161990 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1161940 GTTACAAGCA
* *
1161950 ATGTATCGATACAATTTATC
1 ATGTATCAATACAATGTATC
1161970 ATGTATCAATACAATGTATC
1 ATGTATCAATACAATGTATC
1161990 A
1 A
1161991 ATACATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (20 bp):
ATGTATCAATACAATGTATC
Found at i:1161985 original size:33 final size:33
Alignment explanation
Indices: 1161948--1162016 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1161938 CCGTTACAAG
* *
1161948 CAATGTATCGATACAATT-TATCATGTATCAATA
1 CAATGTATCAATAC-ATTGTACCATGTATCAATA
*
1161981 CAATGTATCAATACATTGTACCATGTATCGATA
1 CAATGTATCAATACATTGTACCATGTATCAATA
1162014 CAA
1 CAA
1162017 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACATTGTACCATGTATCAATA
Found at i:1161986 original size:13 final size:13
Alignment explanation
Indices: 1161970--1162000 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1161960 ACAATTTATC
1161970 ATGTATCAATACA
1 ATGTATCAATACA
1161983 ATGTATCAATACA
1 ATGTATCAATACA
*
1161996 TTGTA
1 ATGTA
1162001 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1162089 original size:19 final size:19
Alignment explanation
Indices: 1162045--1162117 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1162035 CTGCCAATCT
**
1162045 CATGTATCGATACAATTGTT
1 CATGTATCGATACAA-TGAA
*
1162065 CATGTATCGATACAGTGAA
1 CATGTATCGATACAATGAA
*
1162084 CATGTATCGATACAAAGAA
1 CATGTATCGATACAATGAA
*
1162103 TAATGTATCGATACA
1 -CATGTATCGATACA
1162118 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1167645 original size:17 final size:18
Alignment explanation
Indices: 1167623--1167661 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1167613 GCTTAAGTCA
1167623 ACAAATA-ATGTATCGAT
1 ACAAATACATGTATCGAT
1167640 ACAAATACCTATGTATCGAT
1 ACAAATA-C-ATGTATCGAT
1167660 AC
1 AC
1167662 TTTGAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
20 12 0.63
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (18 bp):
ACAAATACATGTATCGAT
Found at i:1168146 original size:15 final size:16
Alignment explanation
Indices: 1168126--1168156 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1168116 AAGGCTCTCG
1168126 TTAAAAAATTT-TCCC
1 TTAAAAAATTTCTCCC
1168141 TTAAAAAATTTCTCCC
1 TTAAAAAATTTCTCCC
1168157 CTTTGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAAATTTCTCCC
Found at i:1169913 original size:19 final size:21
Alignment explanation
Indices: 1169889--1169927 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1169879 TTTGTTGATA
1169889 ATTTTG-A-TGAAAATGAAGT
1 ATTTTGAAGTGAAAATGAAGT
1169908 ATTTTGAAGTGAAAATGAAG
1 ATTTTGAAGTGAAAATGAAG
1169928 AAATTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTGAAAATGAAGT
Found at i:1174255 original size:52 final size:52
Alignment explanation
Indices: 1174106--1174234 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1174096 CGAAATATGA
*
1174106 AAATTTGCCTGCATGTATCAATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1174158 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1174210 AAATTTGCCTGCACGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1174235 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1174300 original size:19 final size:19
Alignment explanation
Indices: 1174276--1174404 Score: 114
Period size: 19 Copynumber: 7.7 Consensus size: 19
1174266 TAGCTTACAT
1174276 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1174295 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1174308 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1174327 TGTATCGAT---ACA-TTA
1 TGTATCGATACAACACTTA
1174342 --TATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1174359 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1174372 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
*
1174392 TGCATCGATACAA
1 TGTATCGATACAA
1174405 ATCGTTGAAA
Statistics
Matches: 90, Mismatches: 1, Indels: 37
0.70 0.01 0.29
Matches are distributed among these distances:
13 25 0.28
14 2 0.02
15 3 0.03
16 18 0.20
17 3 0.03
18 1 0.01
19 26 0.29
20 12 0.13
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1174312 original size:32 final size:32
Alignment explanation
Indices: 1174271--1174403 Score: 239
Period size: 32 Copynumber: 4.1 Consensus size: 32
1174261 GGCAGTAGCT
1174271 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1174303 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1174335 TACATTATATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1174367 TACATTGTATCGATACAACACTTTATGCATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1174400 TACA
1 TACA
1174404 AATCGTTGAA
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 83 0.86
33 14 0.14
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1174313 original size:13 final size:13
Alignment explanation
Indices: 1174295--1174383 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 13
1174285 ACAACACTTA
1174295 TGTATCGATACAT
1 TGTATCGATACAT
1174308 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1174326 ATGTATCGATACAT
1 -TGTATCGATACAT
*
1174340 TATATCGATACAACACTT
1 TGTATCGAT---ACA--T
1174358 ATGTATCGATACAT
1 -TGTATCGATACAT
1174372 TGTATCGATACA
1 TGTATCGATACA
1174384 ACACTTTATG
Statistics
Matches: 62, Mismatches: 2, Indels: 24
0.70 0.02 0.27
Matches are distributed among these distances:
13 29 0.47
14 2 0.03
16 12 0.19
18 2 0.03
19 17 0.27
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1176624 original size:19 final size:19
Alignment explanation
Indices: 1176585--1176668 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
1176575 TTTCAACGAT
1176585 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
1176605 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1176624 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
1176638 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1176656 TTGTATCGATACA
1 TTGTATCGATACA
1176669 ATTTAAGCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 2 0.03
19 29 0.50
20 14 0.24
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1176643 original size:13 final size:13
Alignment explanation
Indices: 1176625--1176649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1176615 ACATAAGTGT
1176625 TGTATCGATACAA
1 TGTATCGATACAA
1176638 TGTATCGATACA
1 TGTATCGATACA
1176650 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:1176647 original size:32 final size:32
Alignment explanation
Indices: 1176606--1176670 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1176596 CATAAAGTGT
1176606 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1176638 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1176670 T
1 T
1176671 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1176729 original size:13 final size:13
Alignment explanation
Indices: 1176711--1176735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1176701 ATTACTCAAC
1176711 TGTATCGATACAT
1 TGTATCGATACAT
1176724 TGTATCGATACA
1 TGTATCGATACA
1176736 CTGATCTTTG
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:1183700 original size:19 final size:20
Alignment explanation
Indices: 1183660--1183709 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1183650 CAATTTCATA
**
1183660 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
1183680 TATCGATACAA-TGAACATG
1 TATCGATACAATTGAACATG
1183699 TATCGATACAA
1 TATCGATACAA
1183710 AGCATAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:1183721 original size:20 final size:19
Alignment explanation
Indices: 1183676--1183726 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1183666 TACAATTGTC
*
1183676 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
1183695 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
1183716 -ATGTATCGATA
1 CATGTATCGATA
1183727 TATCTGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.55
20 12 0.41
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1184043 original size:20 final size:20
Alignment explanation
Indices: 1184018--1184068 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1184008 ATCCTAACAA
* * *
1184018 TATCGATACATTTATACATG
1 TATCGATACATTAAAAAATG
1184038 TATCGATACATTAAAAAATG
1 TATCGATACATTAAAAAATG
1184058 TATCGATACAT
1 TATCGATACAT
1184069 CTGGGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCGATACATTAAAAAATG
Found at i:1185355 original size:20 final size:20
Alignment explanation
Indices: 1185309--1185348 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1185299 CATGATCTAG
*
1185309 GAATTTTGATATAATTTTAT
1 GAATTTTGATATAATTTAAT
*
1185329 GAATTTTGATATCATTTAAT
1 GAATTTTGATATAATTTAAT
1185349 TCATTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (20 bp):
GAATTTTGATATAATTTAAT
Found at i:1185450 original size:116 final size:114
Alignment explanation
Indices: 1185265--1185593 Score: 376
Period size: 116 Copynumber: 2.8 Consensus size: 114
1185255 CTTCTATGTT
* * * *
1185265 ATTTTATGAATTTTGATGTCATAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATTTTATG
1 ATTTTATGAATTTTGATGTCATTAAGTCATTTT-CATGATCTAGGAACTTTAATATAATTTTATG
* * * *
1185330 AATTTTGATATCATTTAATTCA-TTTTCTATTACTT-GGGAACTTGGATCCA
65 AATTTTGATGTCATTTAATTCATTTTTC-ATGACTTAGAG-ACTTGGATACA
* * *
1185380 ATTTTATGATTTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTAATGTAATTTTAT
1 ATTTTATGAATTTTGATGTCAT-TAAGTCATTTT-CATGATCTAGGAACTTTAATATAATTTTAT
* * *
1185445 AAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACA
64 GAATTTTGATGTCATTTAATTCATTTTTCATGACTTAGAGACTTGGATACA
* * * *
1185496 ATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGAC-TTAGATATAATTTTA
1 ATTTTATGAATTTTGATGTCA-TTAAGTCATTTTC-ATGATCTAGGAACTTTA-ATATAATTTTA
* * *
1185560 TGAATTTTGATGTCATTTAGTTTATTTTTAATGA
63 TGAATTTTGATGTCATTTAATTCATTTTTCATGA
1185594 TCTAAAGACT
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
115 25 0.14
116 149 0.82
117 8 0.04
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (114 bp):
ATTTTATGAATTTTGATGTCATTAAGTCATTTTCATGATCTAGGAACTTTAATATAATTTTATGA
ATTTTGATGTCATTTAATTCATTTTTCATGACTTAGAGACTTGGATACA
Found at i:1185594 original size:58 final size:57
Alignment explanation
Indices: 1185265--1185594 Score: 281
Period size: 58 Copynumber: 5.7 Consensus size: 57
1185255 CTTCTATGTT
** * * * * *
1185265 ATTTTATGAATTTTGATGTCATAAAGTT-ATTTTCCATGATCTAGGAATTTTGATATA
1 ATTTTATGAATTTTGATGTCATTTAGTTCATTTT-TATGATTTAGGGACTTAGATATA
* * * * * **
1185322 ATTTTATGAATTTTGATATCATTTAATTCATTTTCTATTACTT-GGGAACTTGGATCCA
1 ATTTTATGAATTTTGATGTCATTTAGTTCATTTT-TATGATTTAGGG-ACTTAGATATA
* * * * * *
1185380 ATTTTATGATTTTTGATGTCATGTA-TGTCATTTTACATGATCTAGGAACTTTA-ATGTA
1 ATTTTATGAATTTTGATGTCATTTAGT-TCATTTT-TATGATTTAGGGAC-TTAGATATA
* ** * * * *
1185438 ATTTTATAAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACA
1 ATTTTATGAATTTTGATGTCATTTAGTTCATTTTT-ATGATTTAGGGACTTAGATATA
* *
1185496 ATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGACTTAGATATA
1 ATTTTATGAATTTTGATGTCATTTAGTTCATTTT-TATGATTTAGGGACTTAGATATA
*
1185554 ATTTTATGAATTTTGATGTCATTTAGTTTATTTTTAATGAT
1 ATTTTATGAATTTTGATGTCATTTAGTTCATTTTT-ATGAT
1185595 CTAAAGACTT
Statistics
Matches: 215, Mismatches: 48, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
57 30 0.14
58 180 0.84
59 5 0.02
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (57 bp):
ATTTTATGAATTTTGATGTCATTTAGTTCATTTTTATGATTTAGGGACTTAGATATA
Found at i:1185597 original size:174 final size:173
Alignment explanation
Indices: 1185260--1185575 Score: 415
Period size: 174 Copynumber: 1.8 Consensus size: 173
1185250 AAAGACTTCT
* * * * *
1185260 ATGTTATTTTATGAATTTTGATGTCATAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATT
1 ATGTAATTTTATAAATTTTGATGTCATAAAGTCATTTTCCATGATCTAGGAACTTTGATACAATT
* * * * * *
1185325 TTATGAATTTTGATATCATTTAATTCATTTTCTATTACTTGGGAACTTGGATCCAATTTTATGAT
66 TTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATACAATTTTATGAA
1185390 TTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
131 TTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
*
1185433 ATGTAATTTTATAAATTTTGATGTCATTTAAA-TCATTTTTCATGA-CTTA-GAGACTTTGATAC
1 ATGTAATTTTATAAATTTTGATGTCA--TAAAGTCATTTTCCATGATC-TAGGA-ACTTTGATAC
* * * *
1185495 AATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGG-ACTTAGATATAATTTT
62 AATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTT-GGGAACTTAGATACAATTTT
1185559 ATGAATTTTGATGTCAT
126 ATGAATTTTGATGTCAT
1185576 TTAGTTTATT
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
173 27 0.22
174 88 0.72
175 7 0.06
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (173 bp):
ATGTAATTTTATAAATTTTGATGTCATAAAGTCATTTTCCATGATCTAGGAACTTTGATACAATT
TTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATACAATTTTATGAA
TTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
Found at i:1185615 original size:116 final size:113
Alignment explanation
Indices: 1185265--1185649 Score: 366
Period size: 116 Copynumber: 3.3 Consensus size: 113
1185255 CTTCTATGTT
* * * * *
1185265 ATTTTATGAATTTTGATGTCA-TAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATTTTAT
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATCTAGGAACTTAGATATAATTTTAT
* * * * * *
1185329 GAATTTTGATATCATTTAATTCATTTTCTATTACTTGGGAACTTGGATCCA
66 GAATTTTGATGTCATTTAATTCATTTT-TATGACTAGAG-ACTTTGAT-AA
* * * *
1185380 ATTTTATGATTTTTGATGTCATGTATGTCATTTTAC-ATGATCTAGGAACTTTA-ATGTAATTTT
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTT-CTATGATCTAGGAAC-TTAGATATAATTTT
* *
1185443 ATAAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACA
64 ATGAATTTTGATGTCATTTAATTCATTTTT-ATGAC-TAGAGACTTTGATA-A
* * * *
1185496 ATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGACTTAGATATAATTTTAT
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATCTAGGAACTTAGATATAATTTTAT
* * * *
1185561 GAATTTTGATGTCATTTAGTTTATTTTTAATGATCTAAAGACTTTCATGAA
66 GAATTTTGATGTCATTTAATTCATTTTT-ATGA-CTAGAGACTTTGAT-AA
* **
1185612 ATTTCAT-ACATTTTAGAAAT-ATTTAAGTCATTTTCTAT
1 ATTTTATGA-ATTTT-GATGTCATTTAAGTCATTTTCTAT
1185650 AACTTAGGAA
Statistics
Matches: 224, Mismatches: 34, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
115 26 0.12
116 187 0.83
117 11 0.05
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (113 bp):
ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATCTAGGAACTTAGATATAATTTTAT
GAATTTTGATGTCATTTAATTCATTTTTATGACTAGAGACTTTGATAA
Found at i:1185645 original size:174 final size:174
Alignment explanation
Indices: 1185313--1185645 Score: 397
Period size: 174 Copynumber: 1.9 Consensus size: 174
1185303 ATCTAGGAAT
* * * * * *
1185313 TTTGATATAATTTTATGAATTTTGATATCATTTAATTCATTTTCTATTACTTGGGAACTTGGATC
1 TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATA
* * * *
1185378 CAATTTTATGATTTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTAATGTAATTTT
66 CAATTTTATGAATTTTGATGTCATGTATGTCATTTTACATGATCTAAGAACTTTAATGAAATTTC
**
1185443 ATAAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGAC
131 ATAAATTTTGAAATCATTTAAATCATTTTTCATGACTTAGAGAC
* * *
1185487 TTTGATACAATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGG-ACTTAGAT
1 TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTT-GGGAACTTAGAT
* * * *
1185551 ATAATTTTATGAATTTTGATGTCATTTA-GTTTATTTTTA-ATGATCTAA-AGACTTTCATGAAA
65 ACAATTTTATGAATTTTGATGTCATGTATG-TCA-TTTTACATGATCTAAGA-ACTTTAATGAAA
* *
1185613 TTTCATACATTTTAGAAAT-ATTTAAGTCATTTT
127 TTTCATAAATTTT-GAAATCATTTAAATCATTTT
1185646 CTATAACTTA
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
173 2 0.02
174 120 0.90
175 11 0.08
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (174 bp):
TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATA
CAATTTTATGAATTTTGATGTCATGTATGTCATTTTACATGATCTAAGAACTTTAATGAAATTTC
ATAAATTTTGAAATCATTTAAATCATTTTTCATGACTTAGAGAC
Found at i:1185657 original size:116 final size:116
Alignment explanation
Indices: 1185223--1185657 Score: 264
Period size: 116 Copynumber: 3.8 Consensus size: 116
1185213 GTATAGTTTT
* * * *** * **
1185223 TGTCATTTTAATCATTGTCAATGACTTAAAGAC-TTCTATGTTATTTTATGAATTTTGATGTCA-
1 TGTCATTTAAATCATTTTTAATGACTTAAAGACTTTC-ATACAATTTCATGAATTTTGAAATCAT
* * * * * * * *
1185286 TAAAGTTATTTTCCATGA-TCTAGGAATTTTGATATAATTTTATGAATTTTGA
65 TTAAGTCATTTTCTATAACT-TAGGGACTTAGATATAATTTTATAAATTTTGA
* * * ** ** * * * **
1185338 TATCATTTAATTCATTTTCT-ATTACTT-GGGAACTTGGATCCAATTTTATGATTTTTGATGTCA
1 TGTCATTTAAATCATTTT-TAATGACTTAAAG-ACTTTCATACAATTTCATGAATTTTGAAATCA
* * * * *
1185401 TGTATGTCATTTTAC-ATGA-TCTAGGAACTTTA-ATGTAATTTTATAAATTTTGA
64 TTTAAGTCATTTT-CTATAACT-TAGGGAC-TTAGATATAATTTTATAAATTTTGA
* * * * **
1185454 TGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACAATTTTATGAATTTTGACGTCATT
1 TGTCATTTAAATCATTTTTAATGACTTAAAGACTTTCATACAATTTCATGAATTTTGAAATCATT
* * * *
1185519 TAGGTCATTTTCTATGATTTAGGGACTTAGATATAATTTTATGAATTTTGA
66 TAAGTCATTTTCTATAACTTAGGGACTTAGATATAATTTTATAAATTTTGA
** *
1185570 TGTCATTTAGTTTATTTTTAATGA-TCTAAAGACTTTCATGA-AATTTCAT-ACATTTTAGAAAT
1 TGTCATTTAAATCATTTTTAATGACT-TAAAGACTTTCAT-ACAATTTCATGA-ATTTT-GAAAT
1185632 -ATTTAAGTCATTTTCTATAACTTAGG
62 CATTTAAGTCATTTTCTATAACTTAGG
1185658 AATTATTATT
Statistics
Matches: 258, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
114 1 0.00
115 51 0.20
116 196 0.76
117 10 0.04
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (116 bp):
TGTCATTTAAATCATTTTTAATGACTTAAAGACTTTCATACAATTTCATGAATTTTGAAATCATT
TAAGTCATTTTCTATAACTTAGGGACTTAGATATAATTTTATAAATTTTGA
Found at i:1186965 original size:19 final size:20
Alignment explanation
Indices: 1186917--1186970 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1186907 CTACCAATTT
*
1186917 CATATATCGATACAATTGAG
1 CATATATCGATACAATTGAA
* * *
1186937 TATGTATCGATATAA-TGAA
1 CATATATCGATACAATTGAA
1186956 CATATATCGATACAA
1 CATATATCGATACAA
1186971 AGCATAATCT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
CATATATCGATACAATTGAA
Found at i:1189461 original size:13 final size:13
Alignment explanation
Indices: 1189443--1189479 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1189433 ATAGTCTCCT
*
1189443 TGTATCGATACAA
1 TGTATCAATACAA
1189456 TGTATCAATACAA
1 TGTATCAATACAA
1189469 TGTATCAATAC
1 TGTATCAATAC
1189480 TTAGAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:1195833 original size:19 final size:19
Alignment explanation
Indices: 1195809--1195876 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1195799 AATTCAACAA
1195809 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1195828 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1195843 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1195860 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1195877 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1195848 original size:13 final size:13
Alignment explanation
Indices: 1195830--1195854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195820 ACATAAGTTT
1195830 TGTATCGATACAA
1 TGTATCGATACAA
1195843 TGTATCGATACA
1 TGTATCGATACA
1195855 TAAGTATTGT
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:1195852 original size:32 final size:32
Alignment explanation
Indices: 1195811--1195873 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1195801 TTCAACAATT
*
1195811 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1195843 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1195874 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1195934 original size:13 final size:13
Alignment explanation
Indices: 1195916--1195941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1195906 CATTTTTCTG
1195916 TGTATCGATACAT
1 TGTATCGATACAT
1195929 TGTATCGATACAT
1 TGTATCGATACAT
1195942 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:1195938 original size:33 final size:33
Alignment explanation
Indices: 1195896--1195962 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1195886 GCCAAGGAAA
***
1195896 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1195929 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1195962 T
1 T
1195963 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
Found at i:1198401 original size:27 final size:28
Alignment explanation
Indices: 1198368--1198443 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
1198358 ATTTTCTATA
1198368 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1198395 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1198423 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
1198444 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1198544 original size:52 final size:50
Alignment explanation
Indices: 1198426--1198648 Score: 225
Period size: 52 Copynumber: 4.3 Consensus size: 50
1198416 TTATTTCTGA
* * * *** *
1198426 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTA-TTCTAAAACACCAATTTTTCACAATC
*
1198477 GGGGATACTCCAACCCC-AGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGA-TTTTATT-CTAAAACACCAATTTTT-CACAATC
* *
1198529 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTC-CTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTTCAC---AATC
* *
1198582 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTTCACAATC
*
1198634 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1198649 TTATTATTTC
Statistics
Matches: 146, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
50 4 0.03
51 36 0.25
52 60 0.41
53 28 0.19
54 17 0.12
55 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTTCACAATC
Found at i:1198631 original size:105 final size:103
Alignment explanation
Indices: 1198426--1198648 Score: 279
Period size: 105 Copynumber: 2.1 Consensus size: 103
1198416 TTATTTCTGA
* *** *
1198426 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAAC
* * *
1198491 CCCAGTTTTATTGCTAAAACACTAATTTTTCCACAATC
66 CCCAGTTTTATTCCAAAAACACCAATTTTTCCACAATC
* * *
1198529 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTT-TCC-ATAATCGGGGATACTCCA
*
1198594 ACTCC-GATTTTATTTCCAAAAACACCAATTTTT-CACAATC
64 ACCCCAG-TTTTA-TTCCAAAAACACCAATTTTTCCACAATC
*
1198634 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1198649 TTATTATTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 36 0.35
104 3 0.03
105 47 0.46
106 17 0.17
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATCGGGGATACTCCAAC
CCCAGTTTTATTCCAAAAACACCAATTTTTCCACAATC
Found at i:1200323 original size:19 final size:18
Alignment explanation
Indices: 1200298--1200362 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
1200288 ATTTCAATGA
1200298 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1200316 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1200332 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1200348 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1200363 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 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 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1200337 original size:13 final size:13
Alignment explanation
Indices: 1200319--1200376 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1200309 ACATAAGTGT
1200319 TGTATCGATACAA
1 TGTATCGATACAA
1200332 TGTATCGATACATAA
1 TGTATCGATAC--AA
1200347 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1200364 TGTATCGCTACAA
1 TGTATCGATACAA
1200377 AGCTACTACC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1200341 original size:32 final size:32
Alignment explanation
Indices: 1200300--1200375 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1200290 TTCAATGATT
1200300 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1200332 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1200364 TGTATCGCTACA
1 TGTATCGATACA
1200376 AAGCTACTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1200433 original size:13 final size:13
Alignment explanation
Indices: 1200415--1200439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1200405 ATTACTCAAA
1200415 TGTATCGATACAT
1 TGTATCGATACAT
1200428 TGTATCGATACA
1 TGTATCGATACA
1200440 CTGATCTTTG
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:1200492 original size:52 final size:51
Alignment explanation
Indices: 1200428--1200576 Score: 194
Period size: 52 Copynumber: 2.9 Consensus size: 51
1200418 ATCGATACAT
** *
1200428 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGTCCAGA
1 TGTATCGATACACTGAT-AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1200480 TGTATCGATACACT-ATAAAATGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGAT--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
1200532 TGTATCGATACACAATGA-AATGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACAC--TGATAATGTATCGATACATGCAGGCAAATTT
1200577 TCATATTTCG
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
51 2 0.02
52 82 0.95
54 1 0.01
55 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTGATAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1205015 original size:18 final size:18
Alignment explanation
Indices: 1204972--1205016 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1204962 ATGTTTTGGC
1204972 ATTCA-ATTTTTCAATTT
1 ATTCATATTTTTCAATTT
*
1204989 ATTCTTATTTTTCAATATT
1 ATTCATATTTTTCAAT-TT
1205008 -TTCATATTT
1 ATTCATATTT
1205017 ATTTATAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTCATATTTTTCAATTT
Found at i:1206155 original size:16 final size:16
Alignment explanation
Indices: 1206134--1206198 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
1206124 AAATATTTAA
1206134 AATATAACATAAAAAT
1 AATATAACATAAAAAT
1206150 AATATACACATGACATAAAT
1 AATATA-ACAT-A-A-AAAT
*
1206170 -ATAT-ATATAAAAAT
1 AATATAACATAAAAAT
*
1206184 ATATATAAAATAAAA
1 A-ATATAACATAAAA
1206199 TAAATTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 4 0.10
15 1 0.03
16 11 0.28
17 14 0.35
18 1 0.03
19 5 0.12
20 4 0.10
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.28
Consensus pattern (16 bp):
AATATAACATAAAAAT
Found at i:1206185 original size:12 final size:12
Alignment explanation
Indices: 1206118--1206193 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
1206108 ATATAATGTT
1206118 TATAAAAA-ATA
1 TATAAAAATATA
*
1206129 T-TTAAAATATAA
1 TATAAAAATAT-A
*
1206141 CATAAAAATA-A
1 TATAAAAATATA
* * *
1206152 TATACACAT-GA
1 TATAAAAATATA
* *
1206163 CATAAATATATA
1 TATAAAAATATA
1206175 TATAAAAATATA
1 TATAAAAATATA
1206187 TATAAAA
1 TATAAAA
1206194 TAAAATAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
10 5 0.10
11 17 0.35
12 19 0.40
13 7 0.15
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.30
Consensus pattern (12 bp):
TATAAAAATATA
Found at i:1206227 original size:17 final size:17
Alignment explanation
Indices: 1206174--1206228 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 17
1206164 ATAAATATAT
1206174 ATATAAAAATATATATAAA
1 ATATAAAAATATA-AT-AA
*
1206193 ATAAAATAAATTATTAATAA
1 ATATAA-AAA-TA-TAATAA
1206213 ATATAAAAATATAATA
1 ATATAAAAATATAATA
1206229 TTTTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 5 0.16
18 2 0.06
19 8 0.26
20 10 0.32
21 4 0.13
22 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAATATAATAA
Found at i:1206880 original size:20 final size:20
Alignment explanation
Indices: 1206852--1206898 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1206842 AGCATAAAAA
*
1206852 AATTAAAAAAATTAAAATTT
1 AATTAAAAAAAGTAAAATTT
* * *
1206872 AATTTAAAATAGTAATATTT
1 AATTAAAAAAAGTAAAATTT
1206892 AATTAAA
1 AATTAAA
1206899 TTTTGGTATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTAAAAAAAGTAAAATTT
Found at i:1207043 original size:46 final size:49
Alignment explanation
Indices: 1206941--1207050 Score: 136
Period size: 50 Copynumber: 2.3 Consensus size: 49
1206931 TTTATTTTAT
**
1206941 TTATTTTATTTTTATTTATATATTAAAAAATTATAATTATTTAAATAAA
1 TTATTTTATTTTTATTTATATATTAAAAAATTATAATTATAAAAATAAA
* ***
1206990 TTAATTTTATTTTTATTTA-ATTTTAAATTTTTATAA-TATAAAAATAAA
1 TT-ATTTTATTTTTATTTATATATTAAAAAATTATAATTATAAAAATAAA
1207038 -TATTTTATTTTTA
1 TTATTTTATTTTTA
1207051 AATTAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
46 12 0.22
47 1 0.02
48 10 0.19
49 15 0.28
50 16 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (49 bp):
TTATTTTATTTTTATTTATATATTAAAAAATTATAATTATAAAAATAAA
Found at i:1207066 original size:19 final size:19
Alignment explanation
Indices: 1207044--1207082 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1207034 TAAATATTTT
* *
1207044 ATTTTTAAATTAATATAAA
1 ATTTTAAAAATAATATAAA
*
1207063 ATTTTAAAAATATTATAAA
1 ATTTTAAAAATAATATAAA
1207082 A
1 A
1207083 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAAAAATAATATAAA
Found at i:1207068 original size:46 final size:47
Alignment explanation
Indices: 1206941--1207068 Score: 134
Period size: 46 Copynumber: 2.7 Consensus size: 47
1206931 TTTATTTTAT
** **
1206941 TTATTTTATTTTTATTTATATATTAAAAAATTATAATTATTTAAATAAA
1 TTATTTTATTTTTATTTA-ATA-TAAAATTTTATAATTATAAAAATAAA
* *
1206990 TTAATTTTATTTTTATTTAATTTTAAATTTTTATAA-TATAAAAATAAA
1 TT-ATTTTATTTTTATTTAA-TATAAAATTTTATAATTATAAAAATAAA
*
1207038 -TATTTTATTTTTAAATTAATATAAAATTTTA
1 TTATTTTATTTTT-ATTTAATATAAAATTTTA
1207069 AAAATATTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
46 21 0.31
47 6 0.09
48 10 0.15
49 13 0.19
50 17 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (47 bp):
TTATTTTATTTTTATTTAATATAAAATTTTATAATTATAAAAATAAA
Found at i:1207091 original size:47 final size:46
Alignment explanation
Indices: 1206942--1207089 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 46
1206932 TTATTTTATT
* ** * * **
1206942 TATTTTATTTTTATTTATATATTAAAAAATTATAATTATTTAAATAAA
1 TATTTTATTTTTAATTA-ATA-TAAAATTTTAAAAATATAAAAATAAA
* * * * *
1206990 TTAATTTTATTTTTATTTAATTTTAAATTTTTATAATATAAAAATAAA
1 -T-ATTTTATTTTTAATTAATATAAAATTTTAAAAATATAAAAATAAA
* *
1207038 TATTTTATTTTTAAATTAATATAAAATTTTAAAAATATTATAA-AAA
1 TATTTTATTTTT-AATTAATATAAAATTTTAAAAATATAAAAATAAA
1207084 TATTTT
1 TATTTT
1207090 TAAAAAATTT
Statistics
Matches: 80, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
46 20 0.25
47 24 0.30
48 17 0.21
49 3 0.04
50 16 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (46 bp):
TATTTTATTTTTAATTAATATAAAATTTTAAAAATATAAAAATAAA
Found at i:1207456 original size:21 final size:21
Alignment explanation
Indices: 1207408--1207457 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1207398 CATCTAAAAT
1207408 TAATTT-AATTAAAAAAATAA
1 TAATTTGAATTAAAAAAATAA
* * * *
1207428 AAACTTGAATTTAAAAAGTAA
1 TAATTTGAATTAAAAAAATAA
1207449 TAATTTGAA
1 TAATTTGAA
1207458 ATAGCACAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (21 bp):
TAATTTGAATTAAAAAAATAA
Found at i:1208206 original size:18 final size:19
Alignment explanation
Indices: 1208173--1208208 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1208163 TTCATTTTCA
*
1208173 TAAAATTTAAATTTTATAT
1 TAAAATTTAAAATTTATAT
1208192 TAAAA-TTAAAATTTATA
1 TAAAATTTAAAATTTATA
1208209 AATTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATTTAAAATTTATAT
Found at i:1208215 original size:27 final size:26
Alignment explanation
Indices: 1208173--1208223 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
1208163 TTCATTTTCA
1208173 TAAAATTTAAATTTT-ATATTAAAAT
1 TAAAATTTAAATTTTAATATTAAAAT
1208198 TAAAATTTATAAATTTTAATATTAAA
1 TAAAA-TT-TAAATTTTAATATTAAA
1208224 CAAAATTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 8 0.35
28 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAAATTTAAATTTTAATATTAAAAT
Found at i:1208473 original size:15 final size:16
Alignment explanation
Indices: 1208453--1208482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1208443 TTTTATTTAT
1208453 TTATA-TATAAAAATA
1 TTATATTATAAAAATA
1208468 TTATATTATAAAAAT
1 TTATATTATAAAAAT
1208483 CCTCATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTATATTATAAAAATA
Found at i:1209392 original size:8 final size:7
Alignment explanation
Indices: 1209370--1209408 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
1209360 ATCATAAAAA
1209370 AAAATTT
1 AAAATTT
1209377 AAAATTT
1 AAAATTT
1209384 AAAATTT
1 AAAATTT
*
1209391 TAAATGATT
1 AAAAT--TT
1209400 AAAATTT
1 AAAATTT
1209407 AA
1 AA
1209409 TTCATTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 22 0.79
9 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:1210446 original size:24 final size:24
Alignment explanation
Indices: 1210419--1210465 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1210409 ATTGCATATT
1210419 ATATAATTT-TAATGTATTATATAA
1 ATATAATTTGT-ATGTATTATATAA
* *
1210443 ATATACTTTGTTTGTATTATATA
1 ATATAATTTGTATGTATTATATA
1210466 TAAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
ATATAATTTGTATGTATTATATAA
Found at i:1211268 original size:25 final size:24
Alignment explanation
Indices: 1211240--1211293 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
1211230 TATGAAATTG
1211240 AATAA-TATAATTATATATTGAATA-A
1 AATAATTA-AATTATA-ATT-AATATA
1211265 AATAATTAAATTATAATTAATATA
1 AATAATTAAATTATAATTAATATA
1211289 AATAA
1 AATAA
1211294 AAATATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.15
24 9 0.33
25 12 0.44
26 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AATAATTAAATTATAATTAATATA
Found at i:1211302 original size:23 final size:24
Alignment explanation
Indices: 1211240--1211302 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
1211230 TATGAAATTG
1211240 AATAATATAAT-TATATATTGAATAA
1 AATAATA-AATATATA-ATTGAATAA
1211265 AATAATTAAAT-TATAATT-AATATA
1 AATAA-TAAATATATAATTGAATA-A
1211289 AATAA-AAATATATA
1 AATAATAAATATATA
1211303 CTTTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.11
23 8 0.23
24 9 0.26
25 12 0.34
26 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AATAATAAATATATAATTGAATAA
Found at i:1213376 original size:15 final size:15
Alignment explanation
Indices: 1213347--1213399 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1213337 TGTATTTATA
*
1213347 ATATATATT-ATATT
1 ATATATTTTAATATT
1213361 ATATATTTTAATATT
1 ATATATTTTAATATT
1213376 ATA-ATATTTAATTATT
1 ATATAT-TTTAA-TATT
*
1213392 TTATATTT
1 ATATATTT
1213400 ATATAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 10 0.30
15 13 0.39
16 8 0.24
17 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATTTTAATATT
Found at i:1213423 original size:44 final size:43
Alignment explanation
Indices: 1213350--1213438 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 43
1213340 ATTTATAATA
* *
1213350 TATATTATATTATATATTTTAATATTATAATATTTA-ATTATTT
1 TATATTATATTATAAATTTTAATATTATAAAATTTATATT-TTT
1213393 TATATT-TA-TATAAATTTTAATAAATTTATAAAATTTATATTTTT
1 TATATTATATTATAAATTTTAAT--A-TTATAAAATTTATATTTTT
1213437 TA
1 TA
1213439 GTGGTGTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
41 12 0.30
42 2 0.05
43 7 0.17
44 16 0.40
45 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (43 bp):
TATATTATATTATAAATTTTAATATTATAAAATTTATATTTTT
Found at i:1213426 original size:9 final size:10
Alignment explanation
Indices: 1213396--1213432 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1213386 ATTATTTTAT
1213396 ATTTATATAA
1 ATTTATATAA
1213406 ATTT-TAATAA
1 ATTTAT-ATAA
1213416 ATTTATA-AA
1 ATTTATATAA
1213425 ATTTATAT
1 ATTTATAT
1213433 TTTTTAGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 10 0.42
10 13 0.54
11 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTATATAA
Found at i:1213679 original size:3 final size:3
Alignment explanation
Indices: 1213671--1213699 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1213661 CCTGAATCTC
1213671 TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1213700 GTTTAATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:1216583 original size:29 final size:30
Alignment explanation
Indices: 1216527--1216588 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
1216517 ATTTTAGACC
* * *
1216527 AAACTTTAGGAGGATAAATAAGTATTTTTT
1 AAACGTTAGGAGGATAAATAAATATTTTAT
*
1216557 AAACGTTAGGAGG-TAAATAAATTTTTTAT
1 AAACGTTAGGAGGATAAATAAATATTTTAT
1216586 AAA
1 AAA
1216589 ACTTTAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (30 bp):
AAACGTTAGGAGGATAAATAAATATTTTAT
Found at i:1216596 original size:30 final size:30
Alignment explanation
Indices: 1216527--1216596 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
1216517 ATTTTAGACC
*
1216527 AAACTTTAGGAGGATAAATAAGTATTTTTT
1 AAACTTTAGGAGGATAAATAAATATTTTTT
*
1216557 AAACGTTAGGAGG-TAAATAAAT-TTTTTAT
1 AAACTTTAGGAGGATAAATAAATATTTTT-T
1216586 AAAACTTTAGG
1 -AAACTTTAGG
1216597 GATAAGTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.14
29 9 0.26
30 21 0.60
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (30 bp):
AAACTTTAGGAGGATAAATAAATATTTTTT
Found at i:1217192 original size:23 final size:22
Alignment explanation
Indices: 1217165--1217213 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
1217155 TTTAAAAGTT
1217165 TATTTTATTATTTATTAT-ATTAA
1 TATTTTA-TATTT-TTATAATTAA
1217188 TATTTTATATTTTTATAATTAA
1 TATTTTATATTTTTATAATTAA
1217210 -ATTT
1 TATTT
1217214 AAATAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.32
22 10 0.40
23 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTATATTTTTATAATTAA
Found at i:1217672 original size:2 final size:2
Alignment explanation
Indices: 1217665--1217702 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1217655 AATTAAACTG
1217665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1217703 GGAAGATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1219140 original size:22 final size:23
Alignment explanation
Indices: 1219101--1219146 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1219091 ATAAGTATAA
*
1219101 TAATATATATTAATATGTTGTAT
1 TAATATATATTAATATGTCGTAT
1219124 TAATCATAT-TTAA-ATGTCGTAT
1 TAAT-ATATATTAATATGTCGTAT
1219146 T
1 T
1219147 TTTTATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (23 bp):
TAATATATATTAATATGTCGTAT
Found at i:1220147 original size:20 final size:20
Alignment explanation
Indices: 1220119--1220170 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1220109 ATCGATACAT
* **
1220119 TGTAACGATACATGACTAAA
1 TGTATCGATACATGAAAAAA
*
1220139 TGTATCGATACTTGAAAAAA
1 TGTATCGATACATGAAAAAA
1220159 TGTATCGATACA
1 TGTATCGATACA
1220171 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1220245 original size:32 final size:33
Alignment explanation
Indices: 1220204--1220266 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1220194 AGCCAAATTT
*
1220204 GTATCGATACACAC-AATATGTATCGATACAAA
1 GTATCGATACACACAAAAATGTATCGATACAAA
*
1220236 GTATCGATACACCCAAAAATGTATCGATACA
1 GTATCGATACACACAAAAATGTATCGATACA
1220267 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.24
Consensus pattern (33 bp):
GTATCGATACACACAAAAATGTATCGATACAAA
Found at i:1221740 original size:28 final size:28
Alignment explanation
Indices: 1221684--1221760 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1221674 GGAATAAAGC
*** **
1221684 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1221712 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1221740 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1221761 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1221747 original size:106 final size:106
Alignment explanation
Indices: 1221606--1221839 Score: 278
Period size: 107 Copynumber: 2.2 Consensus size: 106
1221596 AAAAAAAAAT
* * * *
1221606 CGGGATTGGAGTATCCCTTCGA-AAATAATGGGGTTGGAGTATCC-C-AGTTATGAGAAATCAAT
1 CGGGGTTGGAGTATCCC--CGATAAATAACGAGGTTGGAGTATCCTCGA-TTATGAAAAATCAAT
** * * **
1221668 -ATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
63 GATTTTGAAAATAAAACCGGGGTTGGAGTAT-CCCTCGAAAATAA
* * *
1221712 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATGT
1 CGGGGTTGGAGTATCCCCGAT-AAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATGA
1221777 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCTCGAAAATAA
65 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCTCGAAAATAA
1221819 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1221840 TATGAGAAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
104 3 0.03
106 36 0.33
107 44 0.40
108 27 0.25
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (106 bp):
CGGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTATCCTCGATTATGAAAAATCAATGAT
TTTGAAAATAAAACCGGGGTTGGAGTATCCCTCGAAAATAA
Found at i:1221850 original size:79 final size:79
Alignment explanation
Indices: 1221713--1221993 Score: 392
Period size: 79 Copynumber: 3.6 Consensus size: 79
1221703 CGGAGGTAAC
* * * *
1221713 GGGGTTGGAGTAT-CCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATG
1 GGGGTTGGAGTATCCCCTCGA--AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAAT-
* * *
1221776 TTTTTGAAAATAAAACC
63 ATTTTGAAAATAAAGCA
1221793 GGGGTTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
*
1221857 TTGGAAATAAAGCA
66 TTGAAAATAAAGCA
*
1221871 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
1221936 TT-AAGAATAAAGCA
66 TTGAA-AATAAAGCA
*
1221950 GGGGTTGGAGTATCCCCTC-AAAGGTAACGGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCCCTCGAAA-ATAACGGGGTTGGAGTATCCC
1221994 TGATGAAATA
Statistics
Matches: 186, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
78 30 0.16
79 137 0.74
80 16 0.09
81 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
TTGAAAATAAAGCA
Found at i:1221889 original size:186 final size:185
Alignment explanation
Indices: 1221522--1221918 Score: 555
Period size: 186 Copynumber: 2.1 Consensus size: 185
1221512 TTTTGGAGAT
* ** * * *
1221522 AATAATGGGGTTGGAGTATCCCCTTTAAAATAACGGGGCTGGAGTATCCCTGGTTGTGAGAAATT
1 AATAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGCTGGAGTATCCCTGATTGTGAAAAATT
* * *
1221587 GATGATTAGAAAAAAAAATCGGGATTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCA
66 AATGATTAGAAAAAAAAACCGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCA
* * *
1221652 GTTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGA
131 GTTATGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAA
** * *
1221707 GGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT-CCTCGATTGTGAAAAAT
1 AATAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGCTGGAGTATCCCT-GATTGTGAAAAAT
* * * *
1221771 TAATGTTTTTGAAAATAAAACCGGGGTTGGAGTATCCC-TCGAAAATAACGGGGTTGGAGTATCC
65 TAATG-ATTAGAAAAAAAAACCGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCC
* *
1221835 CCGATTATGAGAAATTAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAA
129 CAG-TTATGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAA
1221893 AATAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
1221919 TATGAGAAAT
Statistics
Matches: 185, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
184 3 0.02
185 81 0.44
186 101 0.55
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (185 bp):
AATAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGCTGGAGTATCCCTGATTGTGAAAAATT
AATGATTAGAAAAAAAAACCGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCA
GTTATGAGAAATCAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAA
Found at i:1221967 original size:265 final size:266
Alignment explanation
Indices: 1221528--1222259 Score: 1150
Period size: 266 Copynumber: 2.8 Consensus size: 266
1221518 AGATAATAAT
** * * * * *
1221528 GGGGTTGGAGTATCCCCTTTAAAATAACGGGGCTGGAGTATCCCTGGTTGTGAGAAATTGATGA-
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAAT-AT
* * * * * * *
1221592 TTAGAAAAAAAAATC-GGGATTGGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCAG-TT
65 TTTG-GAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATT
** *
1221655 ATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTG
129 ATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTG
*
1221720 GAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTTGAAA
194 GAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTTAAAA
1221785 ATAAAACC
259 ATAAAACC
1221793 GGGGTTGGAGTAT-CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
*
1221857 TTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT
66 TTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTAT
**
1221922 GAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCAAAGGTAACGGGGTTGGA
131 GAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGA
* *
1221987 GTATCCCTGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTAAAAAT
196 GTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTTAAAAAT
1222052 AAAACC
261 AAAACC
*
1222058 GGGGTT-TAGGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 GGGGTTGGA-GTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
*
1222122 TTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTTGAGTATCCCCGATTA
65 TTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTA
* **
1222187 TGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGG
130 TGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGG
1222252 AGTATCCC
195 AGTATCCC
1222260 GGATTATAGA
Statistics
Matches: 431, Mismatches: 31, Indels: 9
0.92 0.07 0.02
Matches are distributed among these distances:
263 8 0.02
264 87 0.20
265 155 0.36
266 181 0.42
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (266 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
TTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTAT
GAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGA
GTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTTAAAAAT
AAAACC
Found at i:1222003 original size:107 final size:107
Alignment explanation
Indices: 1221871--1222101 Score: 281
Period size: 108 Copynumber: 2.1 Consensus size: 107
1221861 AAATAAAGCA
* *
1221871 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-AT
1 GGGGTTGGAGTAT-CCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAATGAT
* * *
1221935 TTTAAGAATAAAGCAGGGGTTG-GAGTATCCCCTC-AAAGGTAAC
65 TTTAAAAATAAAACAGGGGTTGAG-GTATCCCCTCGAAA-ATAAC
* * ** *
1221978 GGGGTTGGAGTATCCCT-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGATGT
1 GGGGTTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAATGA
* *
1222042 TTTTAAAAATAAAACCGGGGTTTAGGTATCCCCTCGAAAATAAC
64 TTTTAAAAATAAAACAGGGGTTGAGGTATCCCCTCGAAAATAAC
1222086 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1222102 CGATTATGAG
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
105 2 0.02
106 4 0.04
107 48 0.45
108 49 0.46
109 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (107 bp):
GGGGTTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAATGATT
TTAAAAATAAAACAGGGGTTGAGGTATCCCCTCGAAAATAAC
Found at i:1222095 original size:108 final size:106
Alignment explanation
Indices: 1221871--1222101 Score: 279
Period size: 107 Copynumber: 2.2 Consensus size: 106
1221861 AAATAAAGCA
* *
1221871 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATT
1 GGGGTTGGAGTAT-CCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
* * * *
1221936 TTAAGAATAAAGCAGGGGTTGGAGTATCCCCTCAAAGGTAAC
65 TTAAAAATAAAACAGGGGTTAGAGTATCCCCTCAAAGATAAC
* * ** *
1221978 GGGGTTGGAGTATCCCT-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGATGT
1 GGGGTTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAAT-A
*
1222042 TTTTAAAAATAAAACCGGGGTTTAG-GTATCCCCTCGAAA-ATAAC
63 TTTTAAAAATAAAACAGGGG-TTAGAGTATCCCCTC-AAAGATAAC
1222086 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1222102 CGATTATGAG
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
105 2 0.02
106 4 0.04
107 48 0.45
108 47 0.44
109 6 0.06
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (106 bp):
GGGGTTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATCAATATTT
TAAAAATAAAACAGGGGTTAGAGTATCCCCTCAAAGATAAC
Found at i:1222105 original size:187 final size:185
Alignment explanation
Indices: 1221792--1222180 Score: 552
Period size: 187 Copynumber: 2.1 Consensus size: 185
1221782 AAAATAAAAC
* *
1221792 CGGGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
1 CGGGGTTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAATATT
** * *
1221857 TTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT
66 TTAAAAATAAAACAGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT
*
1221922 GAGAAATCAATATTTTA-AGAATAAAGCAGGGGTTGGAGTATCCCCTC-AAAGGTAA
131 GAGAAATCAATATTTTAGA-AATAAAGCAGGGGTTGGAGTATCCCCTCGAAA-ATAA
* * *
1221977 CGGGGTTGGAGTATCCCT-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGATG
1 CGGGGTTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAAT-
* *
1222041 TTTTTAAAAATAAAACCGGGGTTTAG-GTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
63 ATTTTAAAAATAAAACAGGGG-TTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
* *
1222105 TTATGAGAAATTAATATTTTGGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAA
127 TTATGAGAAATCAATATTTTAGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAA
* *
1222164 TGGGGTTTGAGTATCCC
1 CGGGGTTGGAGTATCCC
1222181 CGATTATGAG
Statistics
Matches: 182, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
184 2 0.01
185 18 0.10
186 36 0.20
187 119 0.65
188 7 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (185 bp):
CGGGGTTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAATATT
TTAAAAATAAAACAGGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT
GAGAAATCAATATTTTAGAAATAAAGCAGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:1222116 original size:80 final size:79
Alignment explanation
Indices: 1221978--1222271 Score: 362
Period size: 79 Copynumber: 3.7 Consensus size: 79
1221968 CAAAGGTAAC
* * * * *
1221978 GGGGTTGGAGTAT-CCCT-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGATG
1 GGGGTTGGAGTATCCCCTCGA--AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAAT-
* * *
1222041 TTTTTAAAAATAAAACC
63 ATTTTAAAAATAAAGCA
*
1222058 GGGGTT-TAGGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 GGGGTTGGA-GTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
**
1222122 TTTGGAAATAAAGCA
65 TTTAAAAATAAAGCA
* * *
1222137 GGGGTTGGAGTATCCCCTCGAAAATAATGGGGTTTGAGTATCCCCGATTATGAGAAATCAATATT
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
*
1222202 TTAAGAATAAAGCA
66 TTAAAAATAAAGCA
* * *
1222216 GGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCGGATTAT-AGAAA
1 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAA
1222272 AATAGTGTTT
Statistics
Matches: 187, Mismatches: 23, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.03
79 129 0.69
80 47 0.25
81 4 0.02
82 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATT
TTAAAAATAAAGCA
Found at i:1224692 original size:13 final size:13
Alignment explanation
Indices: 1224674--1224699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1224664 ACAAAGATCG
1224674 ATGTATCGATACA
1 ATGTATCGATACA
1224687 ATGTATCGATACA
1 ATGTATCGATACA
1224700 TTTCCTTAAT
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:1224710 original size:21 final size:21
Alignment explanation
Indices: 1224689--1224769 Score: 153
Period size: 21 Copynumber: 3.9 Consensus size: 21
1224679 TCGATACAAT
*
1224689 GTATCGATACATTTCCTTAAT
1 GTATCGATACATTTCCTTAAA
1224710 GTATCGATACATTTCCTTAAA
1 GTATCGATACATTTCCTTAAA
1224731 GTATCGATACATTTCCTTAAA
1 GTATCGATACATTTCCTTAAA
1224752 GTATCGATACATTTCCTT
1 GTATCGATACATTTCCTT
1224770 GGCAGTAGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
GTATCGATACATTTCCTTAAA
Found at i:1224818 original size:19 final size:19
Alignment explanation
Indices: 1224794--1224843 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1224784 AGCGATACAT
1224794 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1224813 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1224832 TGTATCGATACA
1 TGTATCGATACA
1224844 TTTACTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1230802 original size:8 final size:8
Alignment explanation
Indices: 1230789--1230814 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1230779 ATTTGATTAA
1230789 ATTTTGTG
1 ATTTTGTG
1230797 ATTTTGTG
1 ATTTTGTG
1230805 ATTTTGTG
1 ATTTTGTG
1230813 AT
1 AT
1230815 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1231035 original size:13 final size:13
Alignment explanation
Indices: 1231017--1231055 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1231007 CAACATTCTC
1231017 TGTATCGATACAA
1 TGTATCGATACAA
*
1231030 TGTATCGATACAG
1 TGTATCGATACAA
1231043 TGTATCGATACAA
1 TGTATCGATACAA
1231056 GGGGTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1231532 original size:21 final size:21
Alignment explanation
Indices: 1231488--1231529 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1231478 CCCCTAGGCA
*
1231488 GCACCCACTAGGTCGCGACCG
1 GCACCCACTAGGTCGCAACCG
*
1231509 GCACCCTC-AGGTCGCAACCG
1 GCACCCACTAGGTCGCAACCG
1231529 G
1 G
1231530 GCAGCCCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.19, C:0.43, G:0.29, T:0.10
Consensus pattern (21 bp):
GCACCCACTAGGTCGCAACCG
Found at i:1232932 original size:22 final size:22
Alignment explanation
Indices: 1232907--1232951 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1232897 CGAAATTGTT
*
1232907 AAATTATTTT-ATTGAGGGGGAG
1 AAATT-TTTTGATTAAGGGGGAG
1232929 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGATTAAGGGGGAG
1232951 A
1 A
1232952 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (22 bp):
AAATTTTTTGATTAAGGGGGAG
Found at i:1233546 original size:20 final size:20
Alignment explanation
Indices: 1233521--1233570 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1233511 CGATACGTTA
**
1233521 TATCGATACATGACTAAATG
1 TATCGATACATGAAAAAATG
*
1233541 TATCGATACTTGAAAAAATG
1 TATCGATACATGAAAAAATG
1233561 TATCGATACA
1 TATCGATACA
1233571 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
TATCGATACATGAAAAAATG
Found at i:1234976 original size:51 final size:51
Alignment explanation
Indices: 1234895--1235095 Score: 210
Period size: 51 Copynumber: 3.9 Consensus size: 51
1234885 TCGAAAACAA
*
1234895 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGT
1 CGGGATTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGT
* *
1234946 CGGGATTGGAGTATCCCCGATTGTGGAAAATCGATGCTTTAGAAATAAGGC
1 CGGGATTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGT
* * * * * **
1234997 CGGGGTTGGAGTATCCTCGATTGT-AAGAAATTGGTG-TTTTGAAAATAAAAT
1 CGGGATTGGAGTATCCCCGATTGTGGA-AAATTGATGCTTTAG-AAATAAGGT
* * * * **
1235048 C-AGAGTTGGAGTATCCCCTATTATGGAAAATTGGTATTTTAGAAATAA
1 CGGGA-TTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAA
1235096 AATCGAGGTT
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
50 6 0.05
51 114 0.91
52 5 0.04
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (51 bp):
CGGGATTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGT
Found at i:1235075 original size:102 final size:102
Alignment explanation
Indices: 1234895--1235078 Score: 239
Period size: 102 Copynumber: 1.8 Consensus size: 102
1234885 TCGAAAACAA
* ** *
1234895 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGTCGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTAGAAAATTGATGCTTTAGAAATAAAATCGAGATTGGAGTAT
*
1234960 CCCCGATTGTGGAAAATCGATGCTTTAGAAATAAGGC
66 CCCCGATTATGGAAAATCGATGCTTTAGAAATAAGGC
* * *
1234997 CGGGGTTGGAGTATCCTCGATTGTA-AGAAATTGGTG-TTTTGAAAATAAAATC-AGAGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTGTAGA-AAATTGATGCTTTAG-AAATAAAATCGAGA-TTGGAG
*
1235059 TATCCCCTATTATGGAAAAT
63 TATCCCCGATTATGGAAAAT
1235079 TGGTATTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
101 7 0.10
102 63 0.90
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (102 bp):
CGGGGTTGGAGTATCCCCGATTGTAGAAAATTGATGCTTTAGAAATAAAATCGAGATTGGAGTAT
CCCCGATTATGGAAAATCGATGCTTTAGAAATAAGGC
Found at i:1235152 original size:28 final size:28
Alignment explanation
Indices: 1235121--1235177 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1235111 ATCCCTTCAA
*
1235121 AAATAACGGGATTAGAGTATCCCCGATG
1 AAATAACGGGATTAGAGTACCCCCGATG
* *
1235149 AAATAACGGGGTTGGAGTACCCCCGATG
1 AAATAACGGGATTAGAGTACCCCCGATG
1235177 A
1 A
1235178 TGAAAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (28 bp):
AAATAACGGGATTAGAGTACCCCCGATG
Found at i:1235251 original size:28 final size:28
Alignment explanation
Indices: 1235208--1235309 Score: 136
Period size: 28 Copynumber: 3.6 Consensus size: 28
1235198 GATATAAAGC
1235208 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
* ***
1235236 CGAGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
1235264 CGGGGTTGGAGTAT--CCTCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCG--GAAATAA
1235292 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1235310 AATTGTGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.03
28 58 0.94
30 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAA
Found at i:1238236 original size:15 final size:14
Alignment explanation
Indices: 1238212--1238258 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
1238202 TGAGAGACTC
1238212 GTTATTTATATTTA
1 GTTATTTATATTTA
1238226 GTTATTTTATATTTA
1 GTTA-TTTATATTTA
1238241 --TA-TTATATTTA
1 GTTATTTATATTTA
*
1238252 TTTATTT
1 GTTATTT
1238259 TAATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.31
13 4 0.14
14 6 0.21
15 10 0.34
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (14 bp):
GTTATTTATATTTA
Found at i:1238248 original size:26 final size:25
Alignment explanation
Indices: 1238213--1238330 Score: 87
Period size: 26 Copynumber: 4.4 Consensus size: 25
1238203 GAGAGACTCG
1238213 TTAT-TTATATTTAGTTATTTTATAT
1 TTATATTATATTTA-TTATTTTATAT
1238238 TTATATTATATTTATTTATTTTAATAT
1 TTATATTATATTTA-TTATTTT-ATAT
* *
1238265 ATTATAATCAAATTTATAATATTTTATAT
1 -TTAT-ATTATATTTAT--TATTTTATAT
* * *
1238294 TTA-ATAAAATTTATTATATTAATAAT
1 TTATATTATATTTATTAT-TTTAT-AT
*
1238320 TTTTATTATAT
1 TTATATTATAT
1238331 AAATTTTTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.04
25 8 0.11
26 30 0.39
27 9 0.12
28 8 0.11
29 12 0.16
30 6 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (25 bp):
TTATATTATATTTATTATTTTATAT
Found at i:1238256 original size:21 final size:22
Alignment explanation
Indices: 1238214--1238254 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1238204 AGAGACTCGT
1238214 TATTTATATT-TAGTTATTTTA
1 TATTTATATTATAGTTATTTTA
*
1238235 TATTTATATTATATTTATTT
1 TATTTATATTATAGTTATTT
1238255 ATTTTAATAT
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:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TATTTATATTATAGTTATTTTA
Found at i:1238300 original size:17 final size:17
Alignment explanation
Indices: 1238276--1238325 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1238266 TTATAATCAA
1238276 ATTT-ATAATATTTTAT
1 ATTTAATAATATTTTAT
*
1238292 ATTTAATAA-AATTTATT
1 ATTTAATAATATTTTA-T
1238309 ATATTAATAAT-TTTTAT
1 AT-TTAATAATATTTTAT
1238326 TATATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATAATATTTTAT
Found at i:1238317 original size:18 final size:18
Alignment explanation
Indices: 1238288--1238330 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1238278 TTATAATATT
1238288 TTATATTTAATAAAATTTA
1 TTATA-TTAATAAAATTTA
**
1238307 TTATATTAATAATTTTTA
1 TTATATTAATAAAATTTA
1238325 TTATAT
1 TTATAT
1238331 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATATTAATAAAATTTA
Found at i:1238333 original size:32 final size:31
Alignment explanation
Indices: 1238300--1238362 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
1238290 ATATTTAATA
1238300 AAATTTATT-ATATTAATAATTTTTATTATAT
1 AAATTT-TTAATATTAATAATTTTTATTATAT
1238331 AAATTTTTAAATATT-ATATATTTTTATTATAT
1 AAATTTTT-AATATTAATA-ATTTTTATTATAT
1238363 TTTAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.07
31 9 0.31
32 18 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
AAATTTTTAATATTAATAATTTTTATTATAT
Found at i:1238335 original size:15 final size:15
Alignment explanation
Indices: 1238303--1238362 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 15
1238293 TTTAATAAAA
1238303 TTTATTATATTAATAATT
1 TTTATTATA-T-A-AATT
1238321 TTTATTATATAAATT
1 TTTATTATATAAATT
* *
1238336 TTTAAATATTATATATT
1 TTT-ATTA-TATAAATT
1238353 TTTATTATAT
1 TTTATTATAT
1238363 TTTAATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.27
16 7 0.19
17 11 0.30
18 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATATAAATT
Found at i:1238362 original size:18 final size:17
Alignment explanation
Indices: 1238303--1238363 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 17
1238293 TTTAATAAAA
1238303 TTTATTATATTAATAATT
1 TTTATTATATTAAT-ATT
1238321 TTTATTATA-TAA-ATT
1 TTTATTATATTAATATT
*
1238336 TTTA-AATATTATATATT
1 TTTATTATATTA-ATATT
1238353 TTTATTATATT
1 TTTATTATATT
1238364 TTAATTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 3 0.08
15 9 0.24
16 1 0.03
17 10 0.27
18 14 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATTATATTAATATT
Found at i:1238377 original size:32 final size:30
Alignment explanation
Indices: 1238304--1238377 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 30
1238294 TTAATAAAAT
1238304 TTATTATATTAATAATTTTTATTATATAAA
1 TTATTATATTAATAATTTTTATTATATAAA
* *
1238334 TTTTTAAATATT-ATATATTTTTATTATATTTTAA
1 TTATT--ATATTAATA-ATTTTTATTATA--TAAA
1238368 TTATTATATT
1 TTATTATATT
1238378 TGTCATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
30 4 0.11
31 3 0.08
32 22 0.61
34 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATTATATTAATAATTTTTATTATATAAA
Found at i:1238697 original size:18 final size:17
Alignment explanation
Indices: 1238654--1238701 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1238644 TTTTTTCTAA
*
1238654 TTTT-AATTTATTAATT
1 TTTTAAATTTAATAATT
*
1238670 TTTAATAATTTAATATATT
1 TTTTA-AATTTAATA-ATT
1238689 TTTTAAATTTAAT
1 TTTTAAATTTAAT
1238702 TTTAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
18 16 0.62
19 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTAATAATT
Found at i:1238803 original size:19 final size:20
Alignment explanation
Indices: 1238763--1238807 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
1238753 TATATATTTT
1238763 TATATAATAAAAATTATATAA
1 TATATAATAAAAA-TATATAA
1238784 TATATAAATAAAAA-AT-TAA
1 TATAT-AATAAAAATATATAA
1238803 TATAT
1 TATAT
1238808 TATTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 2 0.09
21 5 0.22
22 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAATAAAAATATATAA
Found at i:1238814 original size:48 final size:51
Alignment explanation
Indices: 1238731--1238827 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 51
1238721 AATATATTTT
* * * *
1238731 TAATATTTACAATACAATATTATATATATTTTTATATAA-TAAAAATTATA
1 TAATATATACAATAAAAAATTATATATATTATTATATAATTAAAAATTATA
1238781 TAATATATA-AATAAAAAATTA-ATATATTATTATATAATTAAAAATTA
1 TAATATATACAATAAAAAATTATATATATTATTATATAATTAAAAATTA
1238828 AGCTGCGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 15 0.36
49 19 0.45
50 8 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (51 bp):
TAATATATACAATAAAAAATTATATATATTATTATATAATTAAAAATTATA
Found at i:1238828 original size:26 final size:26
Alignment explanation
Indices: 1238749--1238828 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
1238739 ACAATACAAT
*
1238749 ATTATATATATTTTTATATAA-TAAAA
1 ATTA-ATATATTATTATATAATTAAAA
* *
1238775 ATT-ATATAATA-TATA-AATAAAAA
1 ATTAATATATTATTATATAATTAAAA
1238798 ATTAATATATTATTATATAATTAAAA
1 ATTAATATATTATTATATAATTAAAA
1238824 ATTAA
1 ATTAA
1238829 GCTGCGTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
22 2 0.04
23 11 0.24
24 13 0.29
25 4 0.09
26 15 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAATATATTATTATATAATTAAAA
Found at i:1238915 original size:19 final size:19
Alignment explanation
Indices: 1238870--1238931 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
1238860 ATTCAATTAA
* *
1238870 TTTTTAAA-TTAGTCATAT
1 TTTTTAAACTTAATCTTAT
1238888 TTTTT--ACTTAATCTTAT
1 TTTTTAAACTTAATCTTAT
*
1238905 TTTTTAAACTTAATATT-T
1 TTTTTAAACTTAATCTTAT
1238923 TTATTTAAA
1 TT-TTTAAA
1238932 TCTTTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.03
17 13 0.35
18 8 0.22
19 15 0.41
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAACTTAATCTTAT
Found at i:1239353 original size:24 final size:23
Alignment explanation
Indices: 1239326--1239371 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1239316 GGATTTTTTT
1239326 ATAAAAT-TTAAAAATTTTCATCAC
1 ATAAAATGTT-AAAATTTT-ATCAC
*
1239350 ATAATATGTTAAAATTTTATCA
1 ATAAAATGTTAAAATTTTATCA
1239372 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAAATGTTAAAATTTTATCAC
Found at i:1241162 original size:20 final size:20
Alignment explanation
Indices: 1241137--1241210 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
1241127 TTTTACCTAG
*
1241137 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
*** *
1241157 ATGTATCGATACATGGATGA
1 ATGTATCGATACATTCTTCA
*
1241177 ATGTATCGACACATTCTTCA
1 ATGTATCGATACATTCTTCA
1241197 ATGTATCGATACAT
1 ATGTATCGATACAT
1241211 CTAGTTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1245255 original size:15 final size:16
Alignment explanation
Indices: 1245228--1245257 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1245218 TTTTCAATAT
1245228 ATAAAACTTTTTCTTA
1 ATAAAACTTTTTCTTA
1245244 ATAAAA-TTTTTCTT
1 ATAAAACTTTTTCTT
1245258 CCCCTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAAACTTTTTCTTA
Found at i:1245382 original size:30 final size:30
Alignment explanation
Indices: 1245346--1245406 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1245336 AAAACAAATT
*
1245346 TATTTCAAAATGTTTCTC-CTCTTTTTCATC
1 TATTTCAAAATATTTCTCTC-CTTTTTCATC
1245376 TATTTCAAAATATTTCTCTCCTTTTTCATC
1 TATTTCAAAATATTTCTCTCCTTTTTCATC
1245406 T
1 T
1245407 CTCCCACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTTCAAAATATTTCTCTCCTTTTTCATC
Found at i:1245810 original size:52 final size:52
Alignment explanation
Indices: 1245754--1245882 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1245744 CACTGATCTT
*
1245754 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1245806 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1245858 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1245883 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1248999 original size:17 final size:17
Alignment explanation
Indices: 1248977--1249025 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
1248967 TTCATGTAGA
1248977 ATATATTGCATTCATGT
1 ATATATTGCATTCATGT
1248994 ATATATTGCATTCATGT
1 ATATATTGCATTCATGT
1249011 ATATATTGCATTCAT
1 ATATATTGCATTCAT
1249026 ATAGAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
ATATATTGCATTCATGT
Found at i:1249242 original size:16 final size:16
Alignment explanation
Indices: 1249218--1249248 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1249208 GATGGTGATG
*
1249218 AGTCGAGCGTCCATTA
1 AGTCAAGCGTCCATTA
1249234 AGTCAAGCGTCCATT
1 AGTCAAGCGTCCATT
1249249 GAAGAAACAA
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:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (16 bp):
AGTCAAGCGTCCATTA
Found at i:1250775 original size:33 final size:33
Alignment explanation
Indices: 1250725--1250790 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1250715 AATAATTTCC
* *
1250725 ATATATCGATACAAAGAACGCAGTATTGATACA
1 ATATATCAATACAAAGAACGCAGTATCGATACA
*
1250758 ATATATCAATACTAAGAACGCAGTATCGATACA
1 ATATATCAATACAAAGAACGCAGTATCGATACA
1250791 TCTGGGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (33 bp):
ATATATCAATACAAAGAACGCAGTATCGATACA
Found at i:1253701 original size:79 final size:79
Alignment explanation
Indices: 1253590--1253796 Score: 272
Period size: 79 Copynumber: 2.6 Consensus size: 79
1253580 GAGATAATAA
* * * * * * *
1253590 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
1253655 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAT
* *
1253669 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* * * *
1253734 TTTGGAAATAAAGT
66 TTAGAAAAAAAAAT
*
1253748 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1253797 GATCAACGGG
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 1 0.01
79 110 0.99
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAT
Found at i:1253812 original size:27 final size:26
Alignment explanation
Indices: 1253748--1253823 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
1253738 GAAATAAAGT
1253748 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
1253776 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
1253803 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1253824 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:1253867 original size:109 final size:107
Alignment explanation
Indices: 1253669--1253874 Score: 263
Period size: 109 Copynumber: 1.9 Consensus size: 107
1253659 AAAAAAAAAT
1253669 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
* *
1253734 TTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAAATAA
66 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAA
* ** * * **
1253776 CGGGGTTGGAGTAT-CCC-CGATGATCAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATGGGT
1 CGGGATTGGAGTATCCCCTCGAAAAT-AACGGGGTTGGAGTATCCCCAATTATG-AGAAAT--CA
* *
1253839 GTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
62 ATATTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1253875 GATTATAGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
105 5 0.06
106 28 0.33
107 19 0.23
109 32 0.38
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (107 bp):
CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAA
Done.