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 7 of 15
Found at i:1011804 original size:20 final size:20
Alignment explanation
Indices: 1011779--1011852 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1011769 ACATCTTTTT
1011779 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
1011799 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
1011820 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
1011840 CATGTATCGATAC
1 CATGTATCGATAC
1011853 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:1011816 original size:41 final size:41
Alignment explanation
Indices: 1011759--1011852 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1011749 CTGCCAAGAA
1011759 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1011800 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1011841 ATGTATCGATAC
1 ATGTATCGATAC
1011853 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1012681 original size:22 final size:22
Alignment explanation
Indices: 1012654--1012711 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1012644 ATAACTTAAT
*
1012654 TTTAATTATT-TAGTTATAATAA
1 TTTAATTATTATAATT-TAATAA
* *
1012676 TTTAATAATTATAATTTAGTAA
1 TTTAATTATTATAATTTAATAA
1012698 TTTAATT-TTATAAT
1 TTTAATTATTATAAT
1012712 CTTTTTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTAATTATTATAATTTAATAA
Found at i:1012689 original size:14 final size:14
Alignment explanation
Indices: 1012672--1012711 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1012662 TTTAGTTATA
1012672 ATAATTTAATAATT
1 ATAATTTAATAATT
*
1012686 ATAATTTAGTAATT
1 ATAATTTAATAATT
*
1012700 -TAATTTTATAAT
1 ATAATTTAATAAT
1012712 CTTTTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATAATTTAATAATT
Found at i:1016768 original size:20 final size:20
Alignment explanation
Indices: 1016721--1016795 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1016711 AAAAAGACAT
*
1016721 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1016740 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1016761 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1016781 AATGTATCGATACAT
1 AATGTATCGATACAT
1016796 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1016789 original size:40 final size:39
Alignment explanation
Indices: 1016718--1016795 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1016708 GGTAAAAAGA
* *
1016718 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1016757 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1016796 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1017754 original size:115 final size:115
Alignment explanation
Indices: 1017309--1018122 Score: 1108
Period size: 115 Copynumber: 7.1 Consensus size: 115
1017299 ACAGTGGTGA
* * *
1017309 TTTGAAAAGGGTTGCCATTGACTTGCATAGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTT
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTT
* * * *
1017373 TGAAA-GAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
61 TGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
1017427 TTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAA-GGTACCACTGACTTGCGTGAGCTTTAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT--GTGGGCTTTGA
*
1017490 AAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC
64 AAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * * * *
1017544 TTTG-AAAGAGTGCCACTTAATTGTGGGCTTCG-CAATGGTGCCACTGACTTGTCGGCTTCGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
* *
1017607 GG-GTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGC
66 GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
1017656 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
*
1017721 GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
66 GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
1017771 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
*
1017836 GGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGC
66 GGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* * *
1017887 TTTG-AAAGGGTGCTACTGAGTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
** *
1017950 ATAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
*
1018001 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
** * *
1018065 AAAGTGCCACTGATTTATGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
66 GGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
1018116 TTTGAAA
1 TTTGAAA
1018123 GGGATGAACA
Statistics
Matches: 636, Mismatches: 50, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
112 36 0.06
113 26 0.04
114 152 0.24
115 303 0.48
116 36 0.06
117 79 0.12
118 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (115 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
GGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:1017896 original size:287 final size:286
Alignment explanation
Indices: 1017309--1018124 Score: 1212
Period size: 287 Copynumber: 2.8 Consensus size: 286
1017299 ACAGTGGTGA
* * *
1017309 TTTGAAAAGGGTTGCCATTGACTTGCATAGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTT
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTT
* * * *
1017374 G-AAAGAATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAA-GA
60 GAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1017436 GTGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT-AAAAGGAGTGCC
125 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAA-GAGTGCC
* *
1017500 ACTGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTTA
187 ACTGA-TT-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGA
* *
1017563 ATTGTGGGCTTCGCAATGGTGCCACTGACTTGTCGGC
250 ATTGTGGGCTTCGAAAGGGTGCCACTGACTTGTCGGC
* * *
1017600 TTCGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG
* *
1017665 AGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCA
66 AGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
*
1017730 CTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
131 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
*
1017795 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTT
196 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGAATTGTGGGCTT
* * *
1017860 TGAAAGGAGTGCCATTGACTTGTGGGC
261 CGAAAGG-GTGCCACTGACTTGTCGGC
* * *
1017887 TTTGAAAGGGTGCTACTGAGTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAT
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG
1017952 AGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
66 AGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
* *
1018017 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGATTTA
131 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
*
1018082 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG
196 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
1018125 GATGAACATT
Statistics
Matches: 482, Mismatches: 36, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
284 10 0.02
285 43 0.09
286 74 0.15
287 294 0.61
288 40 0.08
289 12 0.02
290 6 0.01
291 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (286 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAG
AGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGAATTGTGGGCTT
CGAAAGGGTGCCACTGACTTGTCGGC
Found at i:1018123 original size:29 final size:29
Alignment explanation
Indices: 1017338--1018124 Score: 1098
Period size: 29 Copynumber: 27.4 Consensus size: 29
1017328 GACTTGCATA
*
1017338 GGCTTTAAAAGG-GTGCCACTGACTTGCGTG
1 GGCTTTGAAAGGAGTGCCACTGACTT--GTG
* * *
1017368 GGCTTTGAAA-GAATGCCACTAACTCGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017396 GGCTTTGAAAGGA-TGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017424 GGCTTTGAAA-GAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017452 GGCTTTGAAAAG-GTACCACTGACTTGCGTG
1 GGCTTTGAAAGGAGTGCCACTGACTT--GTG
* *
1017482 AGCTTTAAAAGGAGTGCCACTGACTTGTGTG
1 GGCTTTGAAAGGAGTGCCACTGAC-T-TGTG
*
1017513 GGCTTTAAAAGG-GTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017541 GGCTTTGAAA-GAGTGCCACTTAATTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* * * *
1017569 GGCTTCGCAATG-GTGCCACTGACTTGTC
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
*
1017597 GGCTTCGAAAGG-GTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017625 GGCTCTGAAAGG-GTGCCACTAACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017653 GGCTTTGAAAAGAGTGCCACTGATTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017682 GGCTTTGAAAAGAGTGCCACTAACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017711 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
*
1017740 GGCTTTGAAAGG-GTGCCACTAACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017768 GGCTTTGAAAAGAGTGCCACTGATTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
*
1017797 GGCTTTGAAAAGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017826 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
*
1017855 GGCTTTGAAAGGAGTGCCATTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
* *
1017884 GGCTTTGAAAGG-GTGCTACTGAGTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017912 GGCTTTGAAAGG-GTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
** *
1017940 GGCTTTGAAAATAGTGCCACTGATTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017969 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1017998 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1018027 GGCTTTGAAAGG-GTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
** * *
1018055 GGCTTTGAAAAAAGTGCCACTGATTTATG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1018084 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1 GGCTTTGAAAGGAGTGCCACTGACTTGTG
1018113 GGCTTTGAAAGG
1 GGCTTTGAAAGG
1018125 GATGAACATT
Statistics
Matches: 682, Mismatches: 60, Indels: 31
0.88 0.08 0.04
Matches are distributed among these distances:
27 3 0.00
28 282 0.41
29 329 0.48
30 42 0.06
31 24 0.04
32 1 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
GGCTTTGAAAGGAGTGCCACTGACTTGTG
Found at i:1019357 original size:1 final size:1
Alignment explanation
Indices: 1019353--1019402 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
1019343 TTTTTTGCTA
* * * * *
1019353 TTTTTTTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1019403 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:1019368 original size:10 final size:10
Alignment explanation
Indices: 1019338--1019401 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
1019328 ATCTAGACCC
*
1019338 TTCTATTTTT
1 TTCTTTTTTT
* *
1019348 TGCTATTTTT
1 TTCTTTTTTT
1019358 TTCTTTTTTT
1 TTCTTTTTTT
*
1019368 TTGTTTTTTT
1 TTCTTTTTTT
*
1019378 GTTTTGTTTTTT
1 -TTCT-TTTTTT
*
1019390 TTGTTTTTTT
1 TTCTTTTTTT
1019400 TT
1 TT
1019402 TGGGTGTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
10 34 0.74
11 6 0.13
12 6 0.13
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:1033118 original size:20 final size:20
Alignment explanation
Indices: 1033071--1033145 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1033061 AAAAAGACAT
*
1033071 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1033090 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1033111 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1033131 AATGTATCGATACAT
1 AATGTATCGATACAT
1033146 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1033139 original size:40 final size:39
Alignment explanation
Indices: 1033068--1033145 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1033058 GGTAAAAAGA
* *
1033068 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1033107 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1033146 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1036118 original size:23 final size:23
Alignment explanation
Indices: 1036091--1036147 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1036081 TTCTAGAAAC
1036091 AAAAGAATGAGAGAGAATGAGAA
1 AAAAGAATGAGAGAGAATGAGAA
*
1036114 AAAAGAATAAGAGAGAATGAGAA
1 AAAAGAATGAGAGAGAATGAGAA
*
1036137 AAATGAA-GAGA
1 AAAAGAATGAGA
1036148 TATCTGTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (23 bp):
AAAAGAATGAGAGAGAATGAGAA
Found at i:1038298 original size:20 final size:20
Alignment explanation
Indices: 1038272--1038317 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1038262 AGCTTCTTTC
1038272 AGTTGTTGAAAAGCATTTAA
1 AGTTGTTGAAAAGCATTTAA
*
1038292 GGTTGTTGAAAAGCATTTAA
1 AGTTGTTGAAAAGCATTTAA
1038312 AGTTGT
1 AGTTGT
1038318 AAAAGTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (20 bp):
AGTTGTTGAAAAGCATTTAA
Found at i:1042686 original size:13 final size:13
Alignment explanation
Indices: 1042668--1042731 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
1042658 TACAAGCATC
1042668 ATGTATCGATACA
1 ATGTATCGATACA
1042681 ATGTATCGATACA
1 ATGTATCGATACA
1042694 A--T-TC-AT-C-
1 ATGTATCGATACA
* *
1042701 ATGCATCGATATA
1 ATGTATCGATACA
1042714 ATGTATCGATACA
1 ATGTATCGATACA
*
1042727 TTGTA
1 ATGTA
1042732 CCATGTATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 2 0.05
10 4 0.10
11 3 0.08
13 29 0.73
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1042701 original size:33 final size:33
Alignment explanation
Indices: 1042663--1042744 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
1042653 GCCGTTACAA
1042663 GCATCATGTATCGATACAATGTATCGATACAATT
1 GCATCATGTATCGATACAATGTATCGATAC-ATT
* *
1042697 -CATCATGCATCGATATAATGTATCGATACATT
1 GCATCATGTATCGATACAATGTATCGATACATT
* *
1042729 GTACCATGTATCGATA
1 GCATCATGTATCGATA
1042745 TAAACAGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 3 0.07
33 39 0.93
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (33 bp):
GCATCATGTATCGATACAATGTATCGATACATT
Found at i:1042800 original size:20 final size:20
Alignment explanation
Indices: 1042775--1042851 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
1042765 ACTACCAATC
1042775 TCATGTATCGATACAATTGT
1 TCATGTATCGATACAATTGT
1042795 TCATGTATCGATACAATTGT
1 TCATGTATCGATACAATTGT
*
1042815 TCATGTATCGATACAA-TGAA
1 TCATGTATCGATACAATTG-T
1042835 T-ATGTATCGATACAATT
1 TCATGTATCGATACAATT
1042852 TATCGATACA
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
19 16 0.30
20 38 0.70
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
TCATGTATCGATACAATTGT
Found at i:1042826 original size:40 final size:39
Alignment explanation
Indices: 1042775--1042851 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 39
1042765 ACTACCAATC
*
1042775 TCATGTATCGATACAATTG-TTCATGTATCGATACAATTGT
1 TCATGTATCGATACAA-TGAAT-ATGTATCGATACAATTGT
1042815 TCATGTATCGATACAATGAATATGTATCGATACAATT
1 TCATGTATCGATACAATGAATATGTATCGATACAATT
1042852 TATCGATACA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (39 bp):
TCATGTATCGATACAATGAATATGTATCGATACAATTGT
Found at i:1042861 original size:32 final size:33
Alignment explanation
Indices: 1042820--1042881 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1042810 ATTGTTCATG
*
1042820 TATCGATACAATGAAT-ATGTATCGATACAATT
1 TATCGATACAAAGAATAATGTATCGATACAATT
*
1042852 TATCGATACAAAGCATAATGTATCGATACA
1 TATCGATACAAAGAATAATGTATCGATACA
1042882 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (33 bp):
TATCGATACAAAGAATAATGTATCGATACAATT
Found at i:1043467 original size:22 final size:22
Alignment explanation
Indices: 1043405--1043460 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1043395 AGTTTTCATT
*
1043405 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
1043427 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
*
1043449 TTTCTCTCCCTT
1 TTTCTCCCCCTT
1043461 TGTCAAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.34, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:1046179 original size:50 final size:50
Alignment explanation
Indices: 1046120--1046220 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1046110 ATTGACAAGT
*
1046120 ACCAGAAGTGTTTTTTCTATCTATTTTACAACCACCAAAATCTGCATCCG
1 ACCAGAAGTGTTTTTTCTATCTATTTTACAACCACCAAAATCCGCATCCG
1046170 ACCAGAAGTGTTTTTTCTATCTATTTTACAACCACCAAAATCCGCATCCG
1 ACCAGAAGTGTTTTTTCTATCTATTTTACAACCACCAAAATCCGCATCCG
1046220 A
1 A
1046221 GTAAGCATGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.33
Consensus pattern (50 bp):
ACCAGAAGTGTTTTTTCTATCTATTTTACAACCACCAAAATCCGCATCCG
Found at i:1048469 original size:33 final size:33
Alignment explanation
Indices: 1048432--1048498 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1048422 TTCAACGATT
1048432 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1048465 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1048498 T
1 T
1048499 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:1048470 original size:13 final size:13
Alignment explanation
Indices: 1048452--1048476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1048442 CATAAAATGT
1048452 TGTATCGATACAA
1 TGTATCGATACAA
1048465 TGTATCGATACA
1 TGTATCGATACA
1048477 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:1048558 original size:13 final size:13
Alignment explanation
Indices: 1048540--1048564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1048530 ATTACTCAAA
1048540 TGTATCGATACAT
1 TGTATCGATACAT
1048553 TGTATCGATACA
1 TGTATCGATACA
1048565 CCGATCTTTG
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:1048629 original size:52 final size:52
Alignment explanation
Indices: 1048573--1048689 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
1048563 CACCGATCTT
* *
1048573 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAA
* *
1048625 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAA
1048677 TGTATCGATACAT
1 TGTATCGATACAT
1048690 ACAGATAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:1053590 original size:20 final size:20
Alignment explanation
Indices: 1053565--1053605 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1053555 GTTACAAGCA
*
1053565 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTATC
1053585 ATGTATCGATACAATGTATC
1 ATGTATCGATACAATGTATC
1053605 A
1 A
1053606 ATACATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATGTATC
Found at i:1053600 original size:33 final size:33
Alignment explanation
Indices: 1053563--1053631 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1053553 CCGTTACAAG
* *
1053563 CAATGTATCGATACAATT-TATCATGTATCGATA
1 CAATGTATCAATAC-ATTGTACCATGTATCGATA
*
1053596 CAATGTATCAATACATTGTACCATGTGTCGATA
1 CAATGTATCAATACATTGTACCATGTATCGATA
1053629 CAA
1 CAA
1053632 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:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACATTGTACCATGTATCGATA
Found at i:1053684 original size:20 final size:20
Alignment explanation
Indices: 1053659--1053732 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1053649 ACTGCCAATC
* *
1053659 TCATGTATCGATACAATTGT
1 TCATGTATCGATACAAGTGA
1053679 TCATGTATCGATAC-AGTGA
1 TCATGTATCGATACAAGTGA
* *
1053698 ACATGTATCGATACAAAG-CA
1 TCATGTATCGATAC-AAGTGA
*
1053718 TAATGTATCGATACA
1 TCATGTATCGATACA
1053733 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
19 17 0.37
20 27 0.59
21 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TCATGTATCGATACAAGTGA
Found at i:1053704 original size:19 final size:19
Alignment explanation
Indices: 1053660--1053712 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1053650 CTGCCAATCT
* **
1053660 CATGTATCGATACAATTGTT
1 CATGTATCGATAC-AGTGAA
1053680 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
1053699 CATGTATCGATACA
1 CATGTATCGATACA
1053713 AAGCATAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAGTGAA
Found at i:1054641 original size:21 final size:21
Alignment explanation
Indices: 1054611--1054651 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1054601 CATAAAGCAA
*
1054611 AAAAAAAAAAGAAAAAAATAGT
1 AAAAAAAAAA-AAAAGAATAGT
*
1054633 AAAAGAAAAAAAAAGAATA
1 AAAAAAAAAAAAAAGAATA
1054652 ATAGCTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAAAAAGAATAGT
Found at i:1059753 original size:15 final size:16
Alignment explanation
Indices: 1059733--1059763 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1059723 AAGGCTCTCG
1059733 TTAAAAAATTT-TCCC
1 TTAAAAAATTTCTCCC
1059748 TTAAAAAATTTCTCCC
1 TTAAAAAATTTCTCCC
1059764 CCTTGATAAT
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:1065860 original size:52 final size:52
Alignment explanation
Indices: 1065712--1065840 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1065702 CGAAATATGA
1065712 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1065764 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1065816 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1065841 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1065867 original size:13 final size:13
Alignment explanation
Indices: 1065849--1065873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1065839 CAAAGATCAG
1065849 TGTATCGATACAA
1 TGTATCGATACAA
1065862 TGTATCGATACA
1 TGTATCGATACA
1065874 TTTGAGTAAT
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:1071852 original size:19 final size:20
Alignment explanation
Indices: 1071812--1071861 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1071802 CAATTTCATA
**
1071812 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
1071832 TATCGATACAA-TGAACATG
1 TATCGATACAATTGAACATG
1071851 TATCGATACAA
1 TATCGATACAA
1071862 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:1071873 original size:20 final size:19
Alignment explanation
Indices: 1071828--1071878 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1071818 TACAATTGTC
*
1071828 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
1071847 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
1071868 -ATGTATCGATA
1 CATGTATCGATA
1071879 TATCTAGGTG
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:1073284 original size:47 final size:49
Alignment explanation
Indices: 1073233--1073351 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 49
1073223 ATTTTTACGT
* *
1073233 CATTTTCCATGACTTAG-GTTTTTTGTAT-CA-TTTCATGTCATTTTAGA
1 CATTTTCCATGACTTAGAGTTTTTT-CATGCATTTTCATATCATTTTAGA
* * * * *
1073280 CATTTTTCGTGACTTAGAG-ATTTTCATGCATTTTTATATCATTTTAGT
1 CATTTTCCATGACTTAGAGTTTTTTCATGCATTTTCATATCATTTTAGA
*
1073328 CATTTTCCATAACTTAGAGTTTTT
1 CATTTTCCATGACTTAGAGTTTTT
1073352 CATTATATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
46 2 0.04
47 21 0.37
48 31 0.54
49 3 0.05
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (49 bp):
CATTTTCCATGACTTAGAGTTTTTTCATGCATTTTCATATCATTTTAGA
Found at i:1073605 original size:116 final size:114
Alignment explanation
Indices: 1073417--1073730 Score: 373
Period size: 116 Copynumber: 2.7 Consensus size: 114
1073407 CTTCTATGTT
* * * * *
1073417 ATTTTATGAATTTTGATGTTATAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATTTTATG
1 ATTTTATGAATTTTGATGTCATTAAGTCATTTT-CATGATCTAGGAACTTTAATATAATTTTATG
* * * *
1073482 AATTTTGATATCATTTAAGTCA-TTTTCTATGACTT-GGGAACTTGGATCCA
65 AATTTTGATGTCATTTAAATCATTTTTC-ATGACTTAGAG-ACTTGGATACA
* * *
1073532 ATTTTATGATTTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTAATGTAATTTTAT
1 ATTTTATGAATTTTGATGTCAT-TAAGTCATTTT-CATGATCTAGGAACTTTAATATAATTTTAT
*
1073597 GAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACA
64 GAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTGGATACA
* * * * *
1073648 ATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGAC-TTAGATACAATTTTA
1 ATTTTATGAATTTTGATGTCA-TTAAGTCATTTTC-ATGATCTAGGAACTTTA-ATATAATTTTA
1073712 TGAATTTTGATGTCATTTA
63 TGAATTTTGATGTCATTTA
1073731 GTTTATTTTT
Statistics
Matches: 172, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
115 24 0.14
116 140 0.81
117 8 0.05
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (114 bp):
ATTTTATGAATTTTGATGTCATTAAGTCATTTTCATGATCTAGGAACTTTAATATAATTTTATGA
ATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGACTTGGATACA
Found at i:1073645 original size:174 final size:173
Alignment explanation
Indices: 1073412--1073727 Score: 442
Period size: 174 Copynumber: 1.8 Consensus size: 173
1073402 AAAGACTTCT
* * * *
1073412 ATGTTATTTTATGAATTTTGATGTTATAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATT
1 ATGTAATTTTATGAATTTTGATGTTATAAAGTCATTTTCCATGATCTAGGAACTTTGATACAATT
* * *
1073477 TTATGAATTTTGATATCATTTAAGTCATTTTCTATGACTT-GGGAACTTGGATCCAATTTTATGA
66 TTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTAGGG-ACTTAGATACAATTTTATGA
*
1073541 TTTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
130 ATTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
* *
1073585 ATGTAATTTTATGAATTTTGATGTCATTTAAA-TCATTTTTCATGA-CTTA-GAGACTTTGATAC
1 ATGTAATTTTATGAATTTTGATGT--TATAAAGTCATTTTCCATGATC-TAGGA-ACTTTGATAC
* * *
1073647 AATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGACTTAGATACAATTTTA
62 AATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTAGGGACTTAGATACAATTTTA
1073712 TGAATTTTGATGTCAT
127 TGAATTTTGATGTCAT
1073728 TTAGTTTATT
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
173 26 0.21
174 91 0.73
175 8 0.06
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (173 bp):
ATGTAATTTTATGAATTTTGATGTTATAAAGTCATTTTCCATGATCTAGGAACTTTGATACAATT
TTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTAGGGACTTAGATACAATTTTATGAA
TTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTA
Found at i:1073731 original size:58 final size:58
Alignment explanation
Indices: 1073417--1073730 Score: 323
Period size: 58 Copynumber: 5.4 Consensus size: 58
1073407 CTTCTATGTT
* * * * * * * * *
1073417 ATTTTATGAATTTTGATGTTA-TAAAGTTATTTTCCATGATCTAGGAATTTTGATATA
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATTTAGGGACTTAGATACA
* * * *
1073474 ATTTTATGAATTTTGATATCATTTAAGTCATTTTCTATGACTT-GGGAACTTGGATCCA
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATTTAGGG-ACTTAGATACA
* * * * * **
1073532 ATTTTATGATTTTTGATGTCATGTATGTCATTTTAC-ATGATCTAGGAACTTTA-ATGTA
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTT-CTATGATTTAGGGAC-TTAGATACA
* * * *
1073590 ATTTTATGAATTTTGATGTCATTTAAATCATTTT-TCATGACTTAGAGACTTTGATACA
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCT-ATGATTTAGGGACTTAGATACA
* *
1073648 ATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGGACTTAGATACA
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATTTAGGGACTTAGATACA
1073706 ATTTTATGAATTTTGATGTCATTTA
1 ATTTTATGAATTTTGATGTCATTTA
1073731 GTTTATTTTT
Statistics
Matches: 208, Mismatches: 40, Indels: 17
0.78 0.15 0.06
Matches are distributed among these distances:
57 23 0.11
58 179 0.86
59 6 0.03
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (58 bp):
ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCTATGATTTAGGGACTTAGATACA
Found at i:1073767 original size:116 final size:116
Alignment explanation
Indices: 1073375--1073801 Score: 325
Period size: 116 Copynumber: 3.7 Consensus size: 116
1073365 GTATAGTTTT
* * * * *** * *
1073375 TGTCATTTTAATCATTGTCAATGACTTAAAGAC-TTCTATGTTATTTTATGAATTTTGATGTTA-
1 TGTCATTTAAATCATTTTTAATGACTCAAAGACTTTC-ATACAATTTTATGAATTTTGAAGTCAT
* * * * * *
1073438 TAAAGTTATTTTCCATGATCTAGGAATTTTGATATAATTTTATGAATTTTGA
65 TTAAGTCATTTTCTATGATCTAGGAACTTTAATACAATTTTATGAATTTTGA
* * *** ** * * *
1073490 TATCATTTAAGTCATTTTCT-ATGACT-TGGGAACTTGGATCCAATTTTATGATTTTTGATGTCA
1 TGTCATTTAAATCATTTT-TAATGACTCAAAG-ACTTTCATACAATTTTATGAATTTTGAAGTCA
* * **
1073553 TGTATGTCATTTTAC-ATGATCTAGGAACTTTAATGTAATTTTATGAATTTTGA
64 TTTAAGTCATTTT-CTATGATCTAGGAACTTTAATACAATTTTATGAATTTTGA
* * * * *
1073606 TGTCATTTAAATCATTTTTCATGACTTAGAGACTTTGATACAATTTTATGAATTTTGACGTCATT
1 TGTCATTTAAATCATTTTTAATGACTCAAAGACTTTCATACAATTTTATGAATTTTGAAGTCATT
* * *
1073671 TAGGTCATTTTCTATGATTTAGGGAC-TTAGATACAATTTTATGAATTTTGA
66 TAAGTCATTTTCTATGATCTAGGAACTTTA-ATACAATTTTATGAATTTTGA
** * * *
1073722 TGTCATTTAGTTTATTTTTAATGA-TCCAAAGACTTTCATGA-AATTTCAT-ACATTTTAGAAAT
1 TGTCATTTAAATCATTTTTAATGACT-CAAAGACTTTCAT-ACAATTTTATGA-ATTTT-GAAGT
1073784 -ATTTAAGTCATTTTCTAT
62 CATTTAAGTCATTTTCTAT
1073802 AACTTAGGAA
Statistics
Matches: 252, Mismatches: 47, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
114 1 0.00
115 50 0.20
116 194 0.77
117 7 0.03
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (116 bp):
TGTCATTTAAATCATTTTTAATGACTCAAAGACTTTCATACAATTTTATGAATTTTGAAGTCATT
TAAGTCATTTTCTATGATCTAGGAACTTTAATACAATTTTATGAATTTTGA
Found at i:1073797 original size:174 final size:174
Alignment explanation
Indices: 1073465--1073797 Score: 408
Period size: 174 Copynumber: 1.9 Consensus size: 174
1073455 ATCTAGGAAT
* * * *
1073465 TTTGATATAATTTTATGAATTTTGATATCATTTAAGTCATTTTCTATGACTTGGGAACTTGGATC
1 TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATA
* * * * *
1073530 CAATTTTATGATTTTTGATGTCATGTATGTCATTTTACATGATCTAGGAACTTTAATGTAATTTT
66 CAATTTTATGAATTTTGATGTCATGTATGTCATTTTACATGATCAAAGAACTTTAATGAAATTTC
**
1073595 ATGAATTTTGATGTCATTTAAATCATTTTTCATGACTTAGAGAC
131 ATGAATTTTGAAATCATTTAAATCATTTTTCATGACTTAGAGAC
* * *
1073639 TTTGATACAATTTTATGAATTTTGACGTCATTTAGGTCATTTTCTATGATTTAGGG-ACTTAGAT
1 TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTT-GGGAACTTAGAT
* * *
1073703 ACAATTTTATGAATTTTGATGTCATTTA-GTTTATTTTTA-ATGATCCAAAG-ACTTTCATGAAA
65 ACAATTTTATGAATTTTGATGTCATGTATG-TCA-TTTTACATGAT-CAAAGAACTTTAATGAAA
*
1073765 TTTCAT-ACATTTTAGAAAT-ATTTAAGTCATTTT
127 TTTCATGA-ATTTT-GAAATCATTTAAATCATTTT
1073798 CTATAACTTA
Statistics
Matches: 135, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
173 2 0.01
174 119 0.88
175 14 0.10
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (174 bp):
TTTGATACAATTTTATGAATTTTGACATCATTTAAGTCATTTTCTATGACTTGGGAACTTAGATA
CAATTTTATGAATTTTGATGTCATGTATGTCATTTTACATGATCAAAGAACTTTAATGAAATTTC
ATGAATTTTGAAATCATTTAAATCATTTTTCATGACTTAGAGAC
Found at i:1075117 original size:19 final size:20
Alignment explanation
Indices: 1075069--1075122 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1075059 CTACCAATTT
*
1075069 CATATATCGATACAATTGAG
1 CATATATCGATACAATTGAA
* * *
1075089 TATGTATCGATATAA-TGAA
1 CATATATCGATACAATTGAA
1075108 CATATATCGATACAA
1 CATATATCGATACAA
1075123 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:1077614 original size:13 final size:13
Alignment explanation
Indices: 1077596--1077645 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
1077586 ATAGTCTCCT
*
1077596 TGTATCGATACAA
1 TGTATCAATACAA
1077609 TGTATCAATACAA
1 TGTATCAATACAA
1077622 TGTATCAATACAA
1 TGTATCAATACAA
1077635 TGTATCAATAC
1 TGTATCAATAC
1077646 TTAGAACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:1079730 original size:51 final size:51
Alignment explanation
Indices: 1079571--1079739 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
1079561 GAAATAACGA
* * *
1079571 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * *
1079623 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1079676 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1079727 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1079740 TCTCAGAAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 38 0.39
52 16 0.16
53 33 0.34
54 10 0.10
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1079766 original size:79 final size:79
Alignment explanation
Indices: 1079673--1079851 Score: 340
Period size: 79 Copynumber: 2.3 Consensus size: 79
1079663 AAAATAAAAT
1079673 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTAT
1079738 CCTCTCAGAAATAA
66 CCTCTCAGAAATAA
1079752 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTAT
*
1079817 CTTCTCAGAAATAA
66 CCTCTCAGAAATAA
*
1079831 CGGGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1079852 GATTAACGGG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 98 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGGGGTTGGAGTAT
CCTCTCAGAAATAA
Found at i:1079866 original size:27 final size:28
Alignment explanation
Indices: 1079803--1079878 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
1079793 AAAATAAAGT
1079803 CGGGGTTGGAGTATCTTCTC-A-GAAATAA
1 CGGGGTTGGAGTATC--CTCGATGAAATAA
*
1079831 CGGGGTTGGAGTATCCTCGATG-ATTAA
1 CGGGGTTGGAGTATCCTCGATGAAATAA
* *
1079858 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCTCGAT
1079879 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.07
27 24 0.56
28 16 0.37
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCGATGAAATAA
Found at i:1082361 original size:13 final size:13
Alignment explanation
Indices: 1082343--1082368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1082333 ACAAAGATCC
1082343 ATGTATCGATACA
1 ATGTATCGATACA
1082356 ATGTATCGATACA
1 ATGTATCGATACA
1082369 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1082367 original size:33 final size:33
Alignment explanation
Indices: 1082325--1082388 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1082315 ATTTCCAAAC
***
1082325 GTATCGATACAAAGATCCATGTATCGATACAAT
1 GTATCGATACAAAGAAAAATGTATCGATACAAT
*
1082358 GTATCGATACACAGAAAAATGTATCGATACA
1 GTATCGATACAAAGAAAAATGTATCGATACA
1082389 TTTCCTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (33 bp):
GTATCGATACAAAGAAAAATGTATCGATACAAT
Found at i:1082432 original size:19 final size:18
Alignment explanation
Indices: 1082408--1082475 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1082398 CAGTAGCTAA
1082408 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1082427 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1082442 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1082459 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1082476 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1082448 original size:13 final size:13
Alignment explanation
Indices: 1082430--1082454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1082420 ACAATACTTA
1082430 TGTATCGATACAT
1 TGTATCGATACAT
1082443 TGTATCGATACA
1 TGTATCGATACA
1082455 AAACTTATGT
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:1082452 original size:32 final size:32
Alignment explanation
Indices: 1082411--1082473 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1082401 TAGCTAATTA
*
1082411 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1082443 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1082474 AATTGTTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1082555 original size:21 final size:21
Alignment explanation
Indices: 1082531--1082587 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1082521 CATTTGTAGG
1082531 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1082552 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1082573 ATGTATCGATACATT
1 ATGTATCGATACATT
1082588 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1082616 original size:14 final size:14
Alignment explanation
Indices: 1082597--1082624 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1082587 TTAAATTTTT
1082597 TTTTTTTTTTTTCA
1 TTTTTTTTTTTTCA
1082611 TTTTTTTTTTTTCA
1 TTTTTTTTTTTTCA
1082625 AACACTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTCA
Found at i:1088835 original size:19 final size:18
Alignment explanation
Indices: 1088810--1088874 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
1088800 ATTTCAACGA
1088810 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1088828 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1088844 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1088860 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1088875 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:1088848 original size:32 final size:32
Alignment explanation
Indices: 1088812--1088887 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1088802 TTCAACGATT
1088812 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1088844 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1088876 TGTATCGCTACA
1 TGTATCGATACA
1088888 AAGCTACTGC
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:1088849 original size:13 final size:13
Alignment explanation
Indices: 1088831--1088888 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1088821 ACATAAGTGT
1088831 TGTATCGATACAA
1 TGTATCGATACAA
1088844 TGTATCGATACATAA
1 TGTATCGATAC--AA
1088859 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1088876 TGTATCGCTACAA
1 TGTATCGATACAA
1088889 AGCTACTGCC
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:1088945 original size:13 final size:13
Alignment explanation
Indices: 1088927--1088954 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1088917 ATTACTCAAA
1088927 TGTATCGATACAT
1 TGTATCGATACAT
1088940 TGTATCGATACAT
1 TGTATCGATACAT
1088953 TG
1 TG
1088955 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1089016 original size:52 final size:52
Alignment explanation
Indices: 1088960--1089088 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1088950 CATTGATCTT
* *
1088960 TGTATCGATACATGCAGGCAAATTTGTCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1089012 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1089064 TGTATTGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1089089 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1093544 original size:18 final size:18
Alignment explanation
Indices: 1093501--1093545 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1093491 ATGTTTTGGC
1093501 ATTCA-ATTTTTCAATTT
1 ATTCATATTTTTCAATTT
*
1093518 ATTCTTATTTTTCAATATT
1 ATTCATATTTTTCAAT-TT
1093537 -TTCATATTT
1 ATTCATATTT
1093546 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:1094708 original size:17 final size:15
Alignment explanation
Indices: 1094670--1094741 Score: 54
Period size: 16 Copynumber: 4.3 Consensus size: 15
1094660 AAAAATATTT
1094670 AAAATATAACATAAA
1 AAAATATAACATAAA
1094685 AATAATATACACATAACA
1 AA-AATATA-ACATAA-A
*
1094703 TAAATATATATATATAAA
1 -AAA-ATATA-ACATAAA
* *
1094721 AATATATAAAATAAA
1 AAAATATAACATAAA
1094736 ATAAAT
1 A-AAAT
1094742 TATTAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
15 9 0.20
16 14 0.30
17 8 0.17
18 3 0.07
19 12 0.26
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATATAACATAAA
Found at i:1094754 original size:36 final size:34
Alignment explanation
Indices: 1094669--1094762 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 34
1094659 TAAAAATATT
* * *
1094669 TAAA-ATATAACATAAAAATAATATACACATAACA
1 TAAATATATAATATAAAAAT-ATATACAAATAAAA
1094703 TAAATATATATATATAAAAATATATA-AAATAAAA
1 TAAATATATA-ATATAAAAATATATACAAATAAAA
1094737 TAAATTATTAATAATATAAAAATATA
1 TAAA-TA-T-ATAATATAAAAATATA
1094763 ATATTTTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
34 14 0.27
35 12 0.23
36 23 0.44
37 3 0.06
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (34 bp):
TAAATATATAATATAAAAATATATACAAATAAAA
Found at i:1094764 original size:16 final size:16
Alignment explanation
Indices: 1094704--1094765 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
1094694 CACATAACAT
1094704 AAATAT-ATATATATAA
1 AAATATAATA-ATATAA
* *
1094720 AAATATATAAAATAAAA
1 AAATATA-ATAATATAA
1094737 TAAATTATTAATAATATAA
1 -AAA-TA-TAATAATATAA
1094756 AAATATAATA
1 AAATATAATA
1094766 TTTTAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 11 0.30
17 7 0.19
18 8 0.22
19 9 0.24
20 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATAATAATATAA
Found at i:1094767 original size:22 final size:21
Alignment explanation
Indices: 1094729--1094783 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
1094719 AAAATATATA
1094729 AAAT-AAAATA-AATTATTAAT
1 AAATAAAAATATAATTATT-AT
*
1094749 AATATAAAAATATAA-TATTTT
1 AA-ATAAAAATATAATTATTAT
1094770 AAATAAAAATATAA
1 AAATAAAAATATAA
1094784 ATATAAACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 14 0.45
21 5 0.16
22 10 0.32
23 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAAAAATATAATTATTAT
Found at i:1094780 original size:28 final size:27
Alignment explanation
Indices: 1094716--1094790 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
1094706 ATATATATAT
1094716 ATAAAAATATATAAAATAAAATAAATTA
1 ATAAAAATATA-AAAATAAAATAAATTA
* * * **
1094744 TTAATAATATAAAAATATAATATTTTAA
1 ATAAAAATATAAAAATAAAATAAATT-A
*
1094772 ATAAAAATATAAATATAAA
1 ATAAAAATATAAAAATAAA
1094791 CACAAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 12 0.32
28 25 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAAAAATATAAAAATAAAATAAATTA
Found at i:1095414 original size:20 final size:20
Alignment explanation
Indices: 1095386--1095432 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1095376 AGCATAAAAA
*
1095386 AATTAAAAAAATTAAAATTT
1 AATTAAAAAAAGTAAAATTT
* * *
1095406 AATTTAAAATAGTAATATTT
1 AATTAAAAAAAGTAAAATTT
1095426 AATTAAA
1 AATTAAA
1095433 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:1095588 original size:28 final size:27
Alignment explanation
Indices: 1095553--1095608 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1095543 TTAATTTTAA
*
1095553 ATTTTTATAATATAAAAATAAATATTTT
1 ATTTTTATAAAATAAAAATAAA-ATTTT
* *
1095581 ATTTTTATAAAATTAATATAAAATTTT
1 ATTTTTATAAAATAAAAATAAAATTTT
1095608 A
1 A
1095609 AAAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTTTTATAAAATAAAAATAAAATTTT
Found at i:1095619 original size:19 final size:21
Alignment explanation
Indices: 1095583--1095622 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1095573 AATATTTTAT
1095583 TTTTATAAAATTAATATAAAA
1 TTTTATAAAATTAATATAAAA
*
1095604 TTTTA-AAAA-TATTATAAAA
1 TTTTATAAAATTAATATAAAA
1095623 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTATAAAATTAATATAAAA
Found at i:1096751 original size:18 final size:19
Alignment explanation
Indices: 1096718--1096753 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1096708 TTCATTTTCA
*
1096718 TAAAATTTAAATTTTATAT
1 TAAAATTTAAAATTTATAT
1096737 TAAAA-TTAAAATTTATA
1 TAAAATTTAAAATTTATA
1096754 AATTTAATAT
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:1096763 original size:27 final size:25
Alignment explanation
Indices: 1096718--1096767 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
1096708 TTCATTTTCA
*
1096718 TAAAATTTAAATTTTATATTAAAAT
1 TAAAATTTAAATTTAATATTAAAAT
1096743 TAAAATTTATAAATTTAATATTAAA
1 TAAAA-TT-TAAATTTAATATTAAA
1096768 CAAAATTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 15 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAAATTTAAATTTAATATTAAAAT
Found at i:1096772 original size:25 final size:27
Alignment explanation
Indices: 1096725--1096774 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1096715 TCATAAAATT
* *
1096725 TAAATTTTATATTAAAATTAAAATTTA
1 TAAATTTAATATTAAAATCAAAATTTA
1096752 TAAATTTAATATT-AAA-CAAAATT
1 TAAATTTAATATTAAAATCAAAATT
1096775 CACATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 3 0.14
27 12 0.57
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTTAATATTAAAATCAAAATTTA
Found at i:1097018 original size:15 final size:16
Alignment explanation
Indices: 1096998--1097028 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1096988 TTTATTTATT
1096998 TTATA-TATAAAAATC
1 TTATATTATAAAAATC
1097013 TTATATTATAAAAATC
1 TTATATTATAAAAATC
1097029 CTCATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATATTATAAAAATC
Found at i:1097916 original size:7 final size:7
Alignment explanation
Indices: 1097904--1097928 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1097894 CATAAAAAAA
1097904 AAATTTT
1 AAATTTT
1097911 AAATTTT
1 AAATTTT
1097918 AAATTTT
1 AAATTTT
1097925 AAAT
1 AAAT
1097929 GATTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:1099543 original size:88 final size:91
Alignment explanation
Indices: 1099451--1099862 Score: 275
Period size: 88 Copynumber: 4.6 Consensus size: 91
1099441 TTGCCACCTA
* *
1099451 GTCAGATTCCTTTTCATTCCGATTTGATC-TATGATTACCAACCCTGGTCAAA-CTAC-TCTCTC
1 GTCAGATTCCTTTTCATTCCGATTTGATCGTATGATTACCAACCCTGGTCAAATCTGCATATCTC
1099513 CTATCTAACGTATGGTTACCACCCTG
66 CTATCTAACGTATGGTTACCACCCTG
* * * * * * * *
1099539 GTCAGATTCTTTTTTCATTCC-AATTG-TACGTGGTGGTTA-CACCACCTAGTCAAATCTGCCTC
1 GTCAGATTC-CTTTTCATTCCGATTTGAT-CGT-ATGATTACCAAC-CCTGGTCAAATCTGCATA
* * *
1099601 CCTCCTATCTGACGTATGGTTACCA-CCAG
62 TCTCCTATCTAACGTATGGTTACCACCCTG
* * * * * * *
1099630 TTTAGA-TCCTTTTCATTCCGA-TTGA-CATATGATTACC-ACCGCCGGCCAAGTCTGCATATTT
1 GTCAGATTCCTTTTCATTCCGATTTGATCGTATGATTACCAACC-CTGGTCAAATCTGCATATCT
* * * *
1099691 CCTGTCTGATGTATGGTTACCACCTTG
65 CCTATCTAACGTATGGTTACCACCCTG
* * * ** * * *
1099718 GTTAGATT--TTATCATTCCGATTTGA-CGTATGGTTA-C-ACATTAGTCCCAAATCTGCTTATT
1 GTCAGATTCCTTTTCATTCCGATTTGATCGTATGATTACCAACCCTGGT--CAAATCTGCATATC
* * * *
1099778 TCCTGTCTAACATATGGTTACCAGCTTG
64 TCCTATCTAACGTATGGTTACCACCCTG
** *
1099806 GTCAGATT-CTTTTCATTTTGATTTGAT-GTATGATTACCACCACCTGGTCAAATCTGC
1 GTCAGATTCCTTTTCATTCCGATTTGATCGTATGATTACCAAC-CCTGGTCAAATCTGC
1099863 TTTTTTTCCT
Statistics
Matches: 250, Mismatches: 53, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
86 2 0.01
87 53 0.21
88 79 0.32
89 50 0.20
90 27 0.11
91 11 0.04
92 28 0.11
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (91 bp):
GTCAGATTCCTTTTCATTCCGATTTGATCGTATGATTACCAACCCTGGTCAAATCTGCATATCTC
CTATCTAACGTATGGTTACCACCCTG
Found at i:1101121 original size:32 final size:32
Alignment explanation
Indices: 1101058--1101210 Score: 236
Period size: 32 Copynumber: 4.7 Consensus size: 32
1101048 CACAATCCGA
* *
1101058 TTTTGTATCGATACATTGTA-CAATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
* *
1101089 TGTTGTATCGATACAATGTATTGATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
1101121 TTTTTGGTATCGATACAATGTATCGATACATAAG
1 -TTTT-GTATCGATACAATGTATCGATACATAAG
1101155 TTTTGTATCGATACAATGTATCGATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAG
1101187 TTTTGTATCGATACAAATGTATCG
1 TTTTGTATCGATAC-AATGTATCG
1101211 CGTACGAAGC
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
31 18 0.16
32 51 0.46
33 16 0.14
34 27 0.24
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (32 bp):
TTTTGTATCGATACAATGTATCGATACATAAG
Found at i:1101145 original size:13 final size:13
Alignment explanation
Indices: 1101127--1101182 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 13
1101117 TAAGTTTTTG
1101127 GTATCGATACAAT
1 GTATCGATACAAT
1101140 GTATCGATACATAAGTTTT
1 GTATCGATAC--AA----T
1101159 GTATCGATACAAT
1 GTATCGATACAAT
1101172 GTATCGATACA
1 GTATCGATACA
1101183 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:1101162 original size:66 final size:64
Alignment explanation
Indices: 1101058--1101210 Score: 236
Period size: 66 Copynumber: 2.4 Consensus size: 64
1101048 CACAATCCGA
* * *
1101058 TTTTGTATCGATACATTGTA-CAATACATAAGTGTTGTATCGATACAATGTATTGATACATAAG
1 TTTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAG
*
1101121 TTTTTGGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATGTATCGATACATAA
1 -TTTT-GTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAA
1101186 G
64 G
1101187 TTTTGTATCGATACAAATGTATCG
1 TTTTGTATCGATAC-AATGTATCG
1101211 CGTACGAAGC
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
64 14 0.17
65 28 0.34
66 40 0.49
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (64 bp):
TTTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAG
Found at i:1101163 original size:19 final size:19
Alignment explanation
Indices: 1101139--1101201 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1101129 ATCGATACAA
1101139 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTTT
1101158 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTTT
1101171 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTTT
1101190 TGTATCGATACA
1 TGTATCGATACA
1101202 AATGTATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTTT
Found at i:1108945 original size:13 final size:13
Alignment explanation
Indices: 1108927--1108951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1108917 CAAAGATCAG
1108927 TGTATCGATACAA
1 TGTATCGATACAA
1108940 TGTATCGATACA
1 TGTATCGATACA
1108952 TTTGAGTAAT
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:1109014 original size:13 final size:13
Alignment explanation
Indices: 1108996--1109111 Score: 61
Period size: 13 Copynumber: 7.5 Consensus size: 13
1108986 AGCTTCGTAG
1108996 CGATACATTGTAT
1 CGATACATTGTAT
1109009 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1109028 CGATACATTGTAT
1 CGATACATTGTAT
1109041 CGATACAAAACTTATGTAT
1 CGATAC---A--T-TGTAT
1109060 CGATACATTGTAT
1 CGATACATTGTAT
1109073 CGATACAAAACTTATGTAT
1 CGATAC---A--T-TGTAT
*
1109092 CAATACATTGTAT
1 CGATACATTGTAT
1109105 CGATACA
1 CGATACA
1109112 ACACTTATGT
Statistics
Matches: 83, Mismatches: 2, Indels: 36
0.69 0.02 0.30
Matches are distributed among these distances:
13 38 0.46
14 2 0.02
15 2 0.02
16 6 0.07
17 2 0.02
18 2 0.02
19 31 0.37
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1109028 original size:19 final size:18
Alignment explanation
Indices: 1109004--1109131 Score: 97
Period size: 19 Copynumber: 7.7 Consensus size: 18
1108994 AGCGATACAT
1109004 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1109023 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1109036 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1109055 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1109068 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
1109087 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
1109100 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
1109119 TGTATTGATACAA
1 TGTATCGATACAA
1109132 TGTATCGATA
Statistics
Matches: 88, Mismatches: 3, Indels: 36
0.69 0.02 0.28
Matches are distributed among these distances:
13 32 0.36
14 3 0.03
16 6 0.07
18 3 0.03
19 44 0.50
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1109037 original size:32 final size:32
Alignment explanation
Indices: 1108996--1109146 Score: 266
Period size: 32 Copynumber: 4.7 Consensus size: 32
1108986 AGCTTCGTAG
1108996 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1109028 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1109060 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1109092 CAATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1109124 TGATACAATGTATCGATACAAAA
1 CGATACATTGTATCGATACAAAA
1109147 TCGTTGAAAT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 113 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1109923 original size:82 final size:83
Alignment explanation
Indices: 1109740--1109941 Score: 216
Period size: 82 Copynumber: 2.4 Consensus size: 83
1109730 ACAAAAGATA
* *
1109740 AAAAGATTTACCTGGGACTAAGCTGACAGGTAAACAAGGGATGAAAGATTGTCTGGGATAAAACC
1 AAAAGATTTACCTGGGACTAAGCTGACAGGTAAACAAGAGATGAAAGATTATCTGGGATAAAACC
*
1109805 AATAAATCAAAAATGGAT
66 AACAAATCAAAAATGGAT
* * * **
1109823 AAAAGATTTACTTAGGACTAAGTTGACCA-GTAAAC-AGAGATAGAAAG-TTCATC-GGGATTGA
1 AAAAGATTTACCTGGGACTAAGCTGA-CAGGTAAACAAGAGAT-GAAAGATT-ATCTGGGATAAA
* *
1109884 ACCGACAAGTCAAAAGA-GGAT
63 ACCAACAAATCAAAA-ATGGAT
* * *
1109905 AAAAGATTTACCCGGGACTAAGCCGATAGGTAAACAA
1 AAAAGATTTACCTGGGACTAAGCTGACAGGTAAACAA
1109942 AGGATGAGGG
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
81 1 0.01
82 56 0.58
83 38 0.39
84 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.20
Consensus pattern (83 bp):
AAAAGATTTACCTGGGACTAAGCTGACAGGTAAACAAGAGATGAAAGATTATCTGGGATAAAACC
AACAAATCAAAAATGGAT
Found at i:1110331 original size:44 final size:44
Alignment explanation
Indices: 1110283--1110922 Score: 339
Period size: 44 Copynumber: 14.6 Consensus size: 44
1110273 AATGCAAGTC
* * *
1110283 ATTTGACCAAGGTGGTAACCATATGTTAAATAGGAA-AAAAGCAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAG-AG
* * *
1110327 ATTTGACCAGGGGTGGTAATCATACATCAAATCA-AAATGAAAAGA-
1 ATTTGACCA-GGGTGGTAACCATACGTCAAAT-AGGAA-GAAAAGAG
* * * * * * * *
1110372 ATCTGACCAAGCTGGTAACCATATGTTAGACAGGAA-ATAAGCAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAG-AG
* * * *
1110416 ATTTGACTAAGGT-GTAACCATACGTCAAATCGGAATGATAA-A-
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAA-GAAAAGAG
* * * * * * * *
1110458 ATCTAACCAAGGTGGTAACCATACATCAGACAGGAA-ATATGCAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAG-AG
* * * * *
1110502 ACTTGGCCA-GGTGGTAATCATATGTCAAATCGGAATGAAAAG-G
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAA-GAAAAGAG
* * * * ** *
1110545 ATCTAACTAGGGTGGTAACCATACGTCAGATAGG-AGGGAGGCAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAG-AG
* * *
1110589 ATTTGACTAGGGTGGTAACCACACGTCAAATTGGAATGAAAAGA-
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAA-GAAAAGAG
* * * * *
1110633 ATCTGACCAGGGTGGTAACCATACGTTAGATAGG-AGAGAGATAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGA-AAAGAG
* *
1110677 ATTTGACCAGGGTGGTAATCATA-GATCAAATCGGAATGAAAAGA-
1 ATTTGACCAGGGTGGTAACCATACG-TCAAATAGGAA-GAAAAGAG
* * * * * * * * *
1110721 ATCTGACTAGGGTGGCAATCATATGTTAAACAGG-AGAGAGGCAG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAG-AG
** * * *
1110765 ATTTGAATAGGGTGGTAACCATACGTCCAATTGAAATGAAAAGA-
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAA-GAAAAGAG
* * * * * *
1110809 ATCTGACCAAGGTGCTAACCATACGTCAGACAGGAAGGATAA-AG
1 ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAA-GAAAAGAG
* *
1110853 ATTTGACTAGGGTGGTAACCATACGTTAAATCA-GAATGAAAAGA-
1 ATTTGACCAGGGTGGTAACCATACGTCAAAT-AGGAA-GAAAAGAG
*
1110897 ATTTGACCAAGGTGGTAACCATACGT
1 ATTTGACCAGGGTGGTAACCATACGT
1110923 TAGACAGGAA
Statistics
Matches: 440, Mismatches: 123, Indels: 66
0.70 0.20 0.10
Matches are distributed among these distances:
41 3 0.01
42 23 0.05
43 73 0.17
44 280 0.64
45 45 0.10
46 11 0.03
47 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (44 bp):
ATTTGACCAGGGTGGTAACCATACGTCAAATAGGAAGAAAAGAG
Found at i:1110645 original size:88 final size:88
Alignment explanation
Indices: 1110286--1110949 Score: 699
Period size: 88 Copynumber: 7.6 Consensus size: 88
1110276 GCAAGTCATT
* * * * * * *
1110286 TGACCAAGGTGGTAACCATATGTTAAATAGGAAAAAAGCAGATTTGACCAGGGGTGGTAATCATA
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTA-GGGTGGTAACCATA
* **
1110351 CATCAAATCAAAATGAAAAGAATC
65 CGTCAAATCGGAATGAAAAGAATC
* * * * *
1110375 TGACCAAGCTGGTAACCATATGTTAGACAGGAAATAAGCAGATTTGACTAAGGT-GTAACCATAC
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
*
1110439 GTCAAATCGGAATGATAA-AATC
66 GTCAAATCGGAATGAAAAGAATC
* * * * * * * * * *
1110461 TAACCAAGGTGGTAACCATACATCAGACAGGAAATATGCAGACTTGGCCA-GGTGGTAATCATAT
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
*
1110525 GTCAAATCGGAATGAAAAGGATC
66 GTCAAATCGGAATGAAAAGAATC
* * * * * ** *
1110548 TAACTAGGGTGGTAACCATACGTCAGATAGGAGGGAGGCAGATTTGACTAGGGTGGTAACCACAC
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
*
1110613 GTCAAATTGGAATGAAAAGAATC
66 GTCAAATCGGAATGAAAAGAATC
* * * ** * *
1110636 TGACCAGGGTGGTAACCATACGTTAGATAGGAGAGAGATAGATTTGACCAGGGTGGTAATCATA-
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
1110700 GATCAAATCGGAATGAAAAGAATC
66 G-TCAAATCGGAATGAAAAGAATC
* * * * * * * *
1110724 TGACTAGGGTGGCAATCATATGTTAAACAGGAGAGAGGCAGATTTGAATAGGGTGGTAACCATAC
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
* * *
1110789 GTCCAATTGAAATGAAAAGAATC
66 GTCAAATCGGAATGAAAAGAATC
* * * ***
1110812 TGACCAAGGTGCTAACCATACGTCAGACAGGAAGGATAAAGATTTGACTAGGGTGGTAACCATAC
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
* * *
1110877 GTTAAATCAGAATGAAAAGAATT
66 GTCAAATCGGAATGAAAAGAATC
1110900 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGG-AGAGTTTGACTA
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGA-TTTGACTA
1110950 AGACCTAACA
Statistics
Matches: 480, Mismatches: 89, Indels: 13
0.82 0.15 0.02
Matches are distributed among these distances:
85 3 0.01
86 70 0.15
87 69 0.14
88 292 0.61
89 46 0.10
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (88 bp):
TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGCAGATTTGACTAGGGTGGTAACCATAC
GTCAAATCGGAATGAAAAGAATC
Found at i:1110946 original size:44 final size:43
Alignment explanation
Indices: 1110812--1110947 Score: 132
Period size: 44 Copynumber: 3.1 Consensus size: 43
1110802 GAAAAGAATC
* * *
1110812 TGACCAAGGTGCTAACCATACGTCAGACAGGAAGGATAA-AGATT
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGA-AAGAG-TT
* * * * *
1110856 TGACTAGGGTGGTAACCATACGTTAAATCA-GAATGAAAAGAATT
1 TGACCAAGGTGGTAACCATACGTTAGA-CAGGAAAG-AAAGAGTT
*
1110900 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAGGAGAGTT
1 TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGA-AAGAGTT
1110944 TGAC
1 TGAC
1110948 TAAGACCTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
43 3 0.04
44 67 0.91
45 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (43 bp):
TGACCAAGGTGGTAACCATACGTTAGACAGGAAAGAAAGAGTT
Found at i:1111019 original size:48 final size:48
Alignment explanation
Indices: 1110953--1111183 Score: 226
Period size: 48 Copynumber: 4.9 Consensus size: 48
1110943 TTGACTAAGA
* * *
1110953 CCTAACACGAATACAGTCAAACGAGGGATGAAAAGAATTTGACCAGGC
1 CCTAACACCAATATAGTCAAACAAGGGATGAAAAGAATTTGACCAGGC
* * *
1111001 CCTAAAACCAATATAGTCAAATAAGGGATGAAAAGAGTTTGACCAGGC
1 CCTAACACCAATATAGTCAAACAAGGGATGAAAAGAATTTGACCAGGC
* * * *
1111049 CCTAACACCAATATAGTC--A-AA-TGA-GAAAAGAGTTTGATCAGGT
1 CCTAACACCAATATAGTCAAACAAGGGATGAAAAGAATTTGACCAGGC
* * *
1111092 CCTAACACCAATATAGTCAAAC-GGGGGTAGAAAA-ATTTTGACCAGGC
1 CCTAACACCAATATAGTCAAACAAGGGAT-GAAAAGAATTTGACCAGGC
* * * **
1111139 CCTAAGACTAATACAGTCAAGTAAGGGATGAAAA-AAGTTTGACCA
1 CCTAACACCAATATAGTCAAACAAGGGATGAAAAGAA-TTTGACCA
1111184 AATACAGTCA
Statistics
Matches: 151, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
43 35 0.23
44 2 0.01
45 3 0.02
46 2 0.01
47 33 0.22
48 76 0.50
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (48 bp):
CCTAACACCAATATAGTCAAACAAGGGATGAAAAGAATTTGACCAGGC
Found at i:1111105 original size:91 final size:90
Alignment explanation
Indices: 1110982--1111158 Score: 230
Period size: 91 Copynumber: 2.0 Consensus size: 90
1110972 AACGAGGGAT
1110982 GAAAAGAATTTGACCAGGCCCTAAAACCAATATAGTCAAATAAGGGAT-GAAAAGAGTTTGACCA
1 GAAAAGAATTTGACCAGGCCCTAAAACCAATATAGTCAAA-AAGGGATAGAAAA-AGTTTGACCA
*
1111046 GGCCCTAACACCAATATAGTCAAATGA
64 GGCCCTAACACCAATACAGTCAAATGA
* * * * ** * *
1111073 GAAAAGAGTTTGATCAGGTCCTAACACCAATATAGTCAAACGGGGGTAGAAAAATTTTGACCAGG
1 GAAAAGAATTTGACCAGGCCCTAAAACCAATATAGTCAAAAAGGGATAGAAAAAGTTTGACCAGG
* *
1111138 CCCTAAGACTAATACAGTCAA
66 CCCTAACACCAATACAGTCAA
1111159 GTAAGGGATG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
90 33 0.45
91 41 0.55
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.20
Consensus pattern (90 bp):
GAAAAGAATTTGACCAGGCCCTAAAACCAATATAGTCAAAAAGGGATAGAAAAAGTTTGACCAGG
CCCTAACACCAATACAGTCAAATGA
Found at i:1112394 original size:6 final size:6
Alignment explanation
Indices: 1112383--1112420 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1112373 TCAAAAAGTA
1112383 TTTTGT TTTTGT TATTT-T TTTTGT TTTTGT TTTT-T TTT
1 TTTTGT TTTTGT T-TTTGT TTTTGT TTTTGT TTTTGT TTT
1112421 GTAAGCTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 7 0.23
6 20 0.67
7 3 0.10
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:1112422 original size:16 final size:18
Alignment explanation
Indices: 1112383--1112420 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1112373 TCAAAAAGTA
1112383 TTTTGTTTTTGTTATTTT
1 TTTTGTTTTTGTTATTTT
1112401 TTTTGTTTTTGTT-TTTT
1 TTTTGTTTTTGTTATTTT
1112418 TTT
1 TTT
1112421 GTAAGCTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87
Consensus pattern (18 bp):
TTTTGTTTTTGTTATTTT
Found at i:1112985 original size:16 final size:16
Alignment explanation
Indices: 1112964--1112994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1112954 ATTCTTTCCA
1112964 TTTTTTTCATTTTTTC
1 TTTTTTTCATTTTTTC
*
1112980 TTTTTTTCCTTTTTT
1 TTTTTTTCATTTTTT
1112995 TTATCATGCT
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:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTCATTTTTTC
Found at i:1115223 original size:22 final size:22
Alignment explanation
Indices: 1115195--1115238 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1115185 AATATGTTCT
1115195 CGAATTACTCCCAAGTTTGGAA
1 CGAATTACTCCCAAGTTTGGAA
*
1115217 CGAATTACTCCCGAGTTTGGAA
1 CGAATTACTCCCAAGTTTGGAA
1115239 AGAACAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (22 bp):
CGAATTACTCCCAAGTTTGGAA
Found at i:1116471 original size:18 final size:17
Alignment explanation
Indices: 1116448--1116484 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1116438 AACGGTTTTC
1116448 ATTTTAAAAGATCATAAA
1 ATTTTAAAAGATCA-AAA
*
1116466 ATTTTAAAAGGTCAAAA
1 ATTTTAAAAGATCAAAA
1116483 AT
1 AT
1116485 ATTCAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (17 bp):
ATTTTAAAAGATCAAAA
Found at i:1117420 original size:16 final size:15
Alignment explanation
Indices: 1117399--1117434 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1117389 GAATATTTAT
1117399 TTATTATTTTATCTTA
1 TTATTATTTT-TCTTA
*
1117415 TTATTATTTTTTTTA
1 TTATTATTTTTCTTA
1117430 TTATT
1 TTATT
1117435 GAAAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTATTTTTCTTA
Found at i:1118664 original size:11 final size:11
Alignment explanation
Indices: 1118648--1118693 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
1118638 TTTAGTTATA
1118648 TCTCTTTTTTT
1 TCTCTTTTTTT
1118659 TCTCTTTTTTCTT
1 TCTC-TTTTT-TT
*
1118672 TCTTTTTTTTT
1 TCTCTTTTTTT
1118683 TCTCTTTTTTT
1 TCTCTTTTTTT
1118694 CCTCCCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 16 0.52
12 10 0.32
13 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:1118673 original size:13 final size:12
Alignment explanation
Indices: 1118648--1118693 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
1118638 TTTAGTTATA
1118648 TCTC-TTTTTTT
1 TCTCTTTTTTTT
1118659 TCTCTTTTTTCTT
1 TCTCTTTTTT-TT
1118672 TCT-TTTTTTTT
1 TCTCTTTTTTTT
1118683 TCTCTTTTTTT
1 TCTCTTTTTTT
1118694 CCTCCCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.28
12 18 0.56
13 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TCTCTTTTTTTT
Found at i:1119804 original size:22 final size:22
Alignment explanation
Indices: 1119778--1119827 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1119768 TACTATTCAC
* * *
1119778 ATGTATTGATACATGAATAGTG
1 ATGTATTGATACATCAACAGTA
1119800 ATGTATTGATACATCAACAGTA
1 ATGTATTGATACATCAACAGTA
1119822 ATGTAT
1 ATGTAT
1119828 CAATTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (22 bp):
ATGTATTGATACATCAACAGTA
Found at i:1120237 original size:21 final size:21
Alignment explanation
Indices: 1120204--1120244 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1120194 CTAAGTAAAA
1120204 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1120225 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1120245 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1120310 original size:21 final size:20
Alignment explanation
Indices: 1120281--1120337 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1120271 AAAACCCTGA
**
1120281 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
1120301 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
1120322 ATAGTATCGATACACA
1 AAAGTATCGATACACA
1120338 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:1120408 original size:53 final size:53
Alignment explanation
Indices: 1120325--1120461 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
1120315 AGATTGCATA
* *
1120325 GTATCGATACACACAAATATGTATCGATACAGGACATTGGTAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
* *
1120379 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCTAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
1120432 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1120462 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 64 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:1120539 original size:31 final size:32
Alignment explanation
Indices: 1120485--1120572 Score: 135
Period size: 31 Copynumber: 2.8 Consensus size: 32
1120475 AATCTCATTT
1120485 TCACTATTCATCACTGTTCATGTATCGATGCA
1 TCACTATTCATCACTGTTCATGTATCGATGCA
*
1120517 TCACTATTCATCACT-TTCATGTATCGATTCA
1 TCACTATTCATCACTGTTCATGTATCGATGCA
* *
1120548 TCACTGTTCA-CACTGTTCACGTATC
1 TCACTATTCATCACTGTTCATGTATC
1120573 ACTATTCATG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 4 0.08
31 33 0.63
32 15 0.29
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (32 bp):
TCACTATTCATCACTGTTCATGTATCGATGCA
Found at i:1120599 original size:13 final size:13
Alignment explanation
Indices: 1120581--1120619 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1120571 TCACTATTCA
1120581 TGTATCGATACAT
1 TGTATCGATACAT
* *
1120594 TGTATCAATACAG
1 TGTATCGATACAT
1120607 TGTATCGATACAT
1 TGTATCGATACAT
1120620 CATAAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1124188 original size:21 final size:21
Alignment explanation
Indices: 1124170--1124210 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1124160 TTCATTTTGT
1124170 AACTCACTTATTTTCTTTTCC
1 AACTCACTTATTTTCTTTTCC
* *
1124191 AACTCATTTACTTTCTTTTC
1 AACTCACTTATTTTCTTTTC
1124211 AAGAGTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (21 bp):
AACTCACTTATTTTCTTTTCC
Found at i:1125944 original size:13 final size:13
Alignment explanation
Indices: 1125926--1125950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1125916 ACATTATGCT
1125926 TTGTATCGATACA
1 TTGTATCGATACA
1125939 TTGTATCGATAC
1 TTGTATCGATAC
1125951 GTGAAACTGG
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1126022 original size:33 final size:33
Alignment explanation
Indices: 1125985--1126047 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1125975 CCACTGTTTG
*
1125985 TATCGATACATGGT-ACATTGTATCGATACAATA
1 TATCGATACATGATGA-ATTGTATCGATACAATA
1126018 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGATGAATTGTATCGATACA
1126048 TTGCTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TATCGATACATGATGAATTGTATCGATACAATA
Found at i:1132217 original size:13 final size:13
Alignment explanation
Indices: 1132199--1132238 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1132189 ACAATATTCT
*
1132199 TTGTATTGATACA
1 TTGTATCGATACA
1132212 TTGTATCGATACA
1 TTGTATCGATACA
1132225 TTGTATCGATACA
1 TTGTATCGATACA
1132238 T
1 T
1132239 GAGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1132403 original size:20 final size:20
Alignment explanation
Indices: 1132365--1132404 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1132355 TTACAAATTT
1132365 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
1132386 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
1132405 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:1134749 original size:19 final size:19
Alignment explanation
Indices: 1134725--1134781 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1134715 TGAATCGATA
*
1134725 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGAT
*
1134744 CATTGTATCAATACATGGAT
1 CATTGTATCGATACAT-GAT
* *
1134764 AATTATATCGATACATGA
1 CATTGTATCGATACATGA
1134782 AACTGACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:1134777 original size:20 final size:20
Alignment explanation
Indices: 1134730--1134780 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1134720 CGATACATTG
* * *
1134730 TATCGATACAT-GTTCATTG
1 TATCGATACATGGATAATTA
*
1134749 TATCAATACATGGATAATTA
1 TATCGATACATGGATAATTA
1134769 TATCGATACATG
1 TATCGATACATG
1134781 AAACTGACAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (20 bp):
TATCGATACATGGATAATTA
Found at i:1134858 original size:10 final size:10
Alignment explanation
Indices: 1134843--1134874 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1134833 GATACATGAT
1134843 GAATTGTATC
1 GAATTGTATC
1134853 GAATTGTATC
1 GAATTGTATC
1134863 GAATTGTATC
1 GAATTGTATC
1134873 GA
1 GA
1134875 TACATTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (10 bp):
GAATTGTATC
Found at i:1135835 original size:36 final size:34
Alignment explanation
Indices: 1135751--1135848 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 34
1135741 CCTTGCAACA
*
1135751 CTATC-TTTC-AAGGCTAAGATAGAA-AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
1135781 CTATCTTTTCACAA-GCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCA-AAGGCTAAGATAGAA-CTCTCTCC
*
1135816 CTATCTTTTTCAAAGGCTAAGATGGAA-TCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACTCTCTC
1135849 AATCACTTAG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 12 0.21
33 2 0.03
34 7 0.12
35 11 0.19
36 17 0.29
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
Found at i:1137186 original size:164 final size:166
Alignment explanation
Indices: 1136996--1137518 Score: 573
Period size: 165 Copynumber: 3.2 Consensus size: 166
1136986 TATTAGATTC
** * * **
1136996 ATTTTAAAAATTGTATACCAAAGAAAATCCCCCTGAAAATATTTATG-GAATAG-AAACTCGGTT
1 ATTTTAAAAATTAAAAACC-AAGAAAATCCCCCTGAAAAAATTTATGAGAATAGAAAACTCCATT
* * * * *
1137059 TTTCAAGAAAAACAGAATTTTAAGAAAAAAATCCAAAACTCATGAAAATGAATGAATTTTTAAAA
65 TTTCAAGAAAAAGAGAATTTCAAGAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAA
* *
1137124 ACTGATTTAATATGAAATAAATAATAATATTTTATAGG
130 ACTAATTTATTATGAAATAAATAATAATATTTTAT-GG
* * * * *
1137162 A-TTTAAAAATTAAAAACCAAGAAAAATCTCCCC-AAAAAAAATT-TGCGAAGTAGAAAAATCTA
1 ATTTTAAAAATTAAAAACCAAG-AAAATC-CCCCTGAAAAAATTTATGAGAA-TAGAAAACTCCA
* *
1137224 TTTTT--TGAAAATAGGAAAATTTCAAGAAAAAGATTCAAAAACTCATGAAAATGAATTAATTTT
63 TTTTTCAAGAAAA-A-GAGAATTTCAAGAAAAA-ATTCAAAAACTCATGAAAATGAATTAATTTT
*
1137287 TCAAAACTAATTTATTATGAAATAAATAATAATA-TTTATGG
125 TAAAAACTAATTTATTATGAAATAAATAATAATATTTTATGG
* * ** *
1137328 ATTTTAAAAATTAAAAACTAAAAAAAT-CCTTTCGAAAAAATTTA-GAGAGTAGAAAACTCCATT
1 ATTTTAAAAATTAAAAACCAAGAAAATCCCCCT-GAAAAAATTTATGAGAATAGAAAACTCCATT
* * * **
1137391 TTTCAA-AATAAGAGAATTTCAAGGAAAAAATTTAAAAACTCATGAAAATGAATTATTTTTTTGA
65 TTTCAAGAAAAAGAGAATTTCAA-GAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAA
* *
1137455 AACTAATTTATTATGAAATAAATAACAATATTTGATGG
129 AACTAATTTATTATGAAATAAATAATAATATTTTATGG
*
1137493 ATTTTAAAAATTAAAAACTAAGAAAA
1 ATTTTAAAAATTAAAAACCAAGAAAA
1137519 ATCCTACCAA
Statistics
Matches: 302, Mismatches: 39, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
164 77 0.25
165 88 0.29
166 31 0.10
167 47 0.16
168 59 0.20
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.31
Consensus pattern (166 bp):
ATTTTAAAAATTAAAAACCAAGAAAATCCCCCTGAAAAAATTTATGAGAATAGAAAACTCCATTT
TTCAAGAAAAAGAGAATTTCAAGAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAA
CTAATTTATTATGAAATAAATAATAATATTTTATGG
Found at i:1138448 original size:23 final size:20
Alignment explanation
Indices: 1138422--1138487 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
1138412 TATCTACGAC
1138422 TCTCAATTTTGATTTCCTCTAAT
1 TCTCAATTTT--TTT-CTCTAAT
*
1138445 TCTCTATTTTTTTCTCTAAT
1 TCTCAATTTTTTTCTCTAAT
* * * *
1138465 TCTCTATTCTTCTCTCCAAT
1 TCTCAATTTTTTTCTCTAAT
1138485 TCT
1 TCT
1138488 TTATTCTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 27 0.69
21 3 0.08
23 9 0.23
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.56
Consensus pattern (20 bp):
TCTCAATTTTTTTCTCTAAT
Found at i:1138463 original size:20 final size:20
Alignment explanation
Indices: 1138438--1138494 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1138428 TTTTGATTTC
* *
1138438 CTCTAATTCTCTATTTTTTT
1 CTCTAATTCTCTATTCTTCT
1138458 CTCTAATTCTCTATTCTTCT
1 CTCTAATTCTCTATTCTTCT
* *
1138478 CTCCAATTCTTTATTCT
1 CTCTAATTCTCTATTCT
1138495 AAATTTCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (20 bp):
CTCTAATTCTCTATTCTTCT
Found at i:1141235 original size:16 final size:19
Alignment explanation
Indices: 1141214--1141257 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1141204 TTGCCACTTT
1141214 TAATTCTTA-T-TTC-CTC
1 TAATTCTTATTCTTCTCTC
1141230 TAATTCTCTATTCTTCTCTC
1 TAATTCT-TATTCTTCTCTC
1141250 TAATTCTT
1 TAATTCTT
1141258 TGTTCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 1 0.04
19 4 0.17
20 10 0.42
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTCTTATTCTTCTCTC
Found at i:1142944 original size:19 final size:19
Alignment explanation
Indices: 1142920--1142959 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1142910 GCTAGTCTTA
1142920 TTCCTTGTTCGAA-ACAGTT
1 TTCCTTGTTC-AATACAGTT
1142939 TTCCTTGTTCAATACAGTT
1 TTCCTTGTTCAATACAGTT
1142958 TT
1 TT
1142960 TTAGTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (19 bp):
TTCCTTGTTCAATACAGTT
Found at i:1144561 original size:22 final size:22
Alignment explanation
Indices: 1144534--1144591 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1144524 ATAACTTAAT
*
1144534 TTTAATTATT-TAGTTATAATAA
1 TTTAATTATTATAATT-TAATAA
* *
1144556 TTTAATAATTATAATTTAGTAA
1 TTTAATTATTATAATTTAATAA
1144578 TTTAATT-TTATAAT
1 TTTAATTATTATAAT
1144592 ATTTTTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 7 0.23
22 20 0.65
23 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTAATTATTATAATTTAATAA
Found at i:1144569 original size:14 final size:14
Alignment explanation
Indices: 1144552--1144591 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1144542 TTTAGTTATA
1144552 ATAATTTAATAATT
1 ATAATTTAATAATT
*
1144566 ATAATTTAGTAATT
1 ATAATTTAATAATT
*
1144580 -TAATTTTATAAT
1 ATAATTTAATAAT
1144592 ATTTTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATAATTTAATAATT
Found at i:1148126 original size:25 final size:24
Alignment explanation
Indices: 1148098--1148153 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 24
1148088 ACTTAGATTC
*
1148098 GAGAAACAAAAGAATGAGAGAGAAT
1 GAGAAA-AAAAGAATAAGAGAGAAT
*
1148123 GAG-AAAAATGAATAAGAGAGAAT
1 GAGAAAAAAAGAATAAGAGAGAAT
1148146 GAGAAAAA
1 GAGAAAAA
1148154 TGAAGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 19 0.68
24 6 0.21
25 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.09
Consensus pattern (24 bp):
GAGAAAAAAAGAATAAGAGAGAAT
Found at i:1148140 original size:23 final size:23
Alignment explanation
Indices: 1148105--1148157 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1148095 TTCGAGAAAC
*
1148105 AAAA-GAATGAGAGAGAATGAGA
1 AAAATGAATAAGAGAGAATGAGA
1148127 AAAATGAATAAGAGAGAATGAGA
1 AAAATGAATAAGAGAGAATGAGA
1148150 AAAATGAA
1 AAAATGAA
1148158 GAGATATCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.11
Consensus pattern (23 bp):
AAAATGAATAAGAGAGAATGAGA
Done.