Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011753.1 Corchorus capsularis cultivar CVL-1 contig11774, whole genome shotgun sequence
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: 159131
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1397 original size:19 final size:19
Alignment explanation
Indices: 1375--1411 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1365 CTACAGTACC
*
1375 TAATCTAATCTGTACAGTG
1 TAATCTAATCTATACAGTG
*
1394 TAATCTTATCTATACAGT
1 TAATCTAATCTATACAGT
1412 TGTTAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTATACAGTG
Found at i:2366 original size:5 final size:5
Alignment explanation
Indices: 2356--2393 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
2346 TCGTCTCTCT
*
2356 TTTTC TTTTC TTTTC TTTTC TTTTC ATTT- TTTT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
2394 AGATTTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 7 0.23
5 23 0.77
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:4227 original size:103 final size:103
Alignment explanation
Indices: 4044--4295 Score: 450
Period size: 103 Copynumber: 2.4 Consensus size: 103
4034 TAGGGCGTGG
*
4044 CCAAACCAAAACCAAATAATGCAGCTGAGTTTTGAACCAGCAACTAAGAATACCAACTAGGGCAA
1 CCAAACCAAATCCAAATAATGCAGCTGAGTTTTGAACCAGCAACTAAGAATACCAACTAGGGCAA
* *
4109 ATGTTATTGTGCAATTCATTTGCCCTCTTAACCAGATT
66 ATGTTATTGTCCAATTCATTTGCCCTCTTAACCAGAAT
* *
4147 CCAAACCAAATCCAAATAATGCAGTTGAGTTTTGAACCAGCAACTAAGAATACTAACTAGGGCAA
1 CCAAACCAAATCCAAATAATGCAGCTGAGTTTTGAACCAGCAACTAAGAATACCAACTAGGGCAA
4212 ATGTTATTGTCCAATTCATTTGCCCTCTTAACCAGAAT
66 ATGTTATTGTCCAATTCATTTGCCCTCTTAACCAGAAT
*
4250 CCAAACCAAATCCAAATAATGCAGCTGGGTTTTGAACCAGCAACTA
1 CCAAACCAAATCCAAATAATGCAGCTGAGTTTTGAACCAGCAACTA
4296 GGGCAAATGT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 142 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (103 bp):
CCAAACCAAATCCAAATAATGCAGCTGAGTTTTGAACCAGCAACTAAGAATACCAACTAGGGCAA
ATGTTATTGTCCAATTCATTTGCCCTCTTAACCAGAAT
Found at i:5176 original size:21 final size:22
Alignment explanation
Indices: 5142--5203 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
5132 TCGATGAGAG
*
5142 TAAAATTGGTTACTGTACATG-
1 TAAAATTTGTTACTGTACATGA
* * *
5163 TTAGATTTGTTACTATACA-GA
1 TAAAATTTGTTACTGTACATGA
5184 TAAAATTTGTTACTGTACAT
1 TAAAATTTGTTACTGTACAT
5204 ATGAGAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (22 bp):
TAAAATTTGTTACTGTACATGA
Found at i:25014 original size:32 final size:32
Alignment explanation
Indices: 24968--25037 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
24958 CGTGACCTTA
* *
24968 CCACCTGGCATTTTTTGTCCAACATGGCATTG
1 CCACGTGGCATTTTTGGTCCAACATGGCATTG
**
25000 CCACGTGGCATTTTTGGTCTGACATGGCATTG
1 CCACGTGGCATTTTTGGTCCAACATGGCATTG
*
25032 CAACGT
1 CCACGT
25038 CAGCATTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (32 bp):
CCACGTGGCATTTTTGGTCCAACATGGCATTG
Found at i:31387 original size:29 final size:30
Alignment explanation
Indices: 31287--31384 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
31277 TTGAGGGGGT
* *
31287 AAAACGTCCCAAAATTGAAGTTCAG-GGGAC
1 AAAACGTCCCAAAATTGATGTTCAGAGAG-C
*
31317 AAAACGTCCCAAAATTGATATTCAGAGAGC
1 AAAACGTCCCAAAATTGATGTTCAGAGAGC
31347 AAAACGT-CCAAAATTGATGTTCAGAGAGC
1 AAAACGTCCCAAAATTGATGTTCAGAGAGC
31376 AAAACGTCC
1 AAAACGTCC
31385 AAACGCTACA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
29 28 0.45
30 32 0.52
31 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.18
Consensus pattern (30 bp):
AAAACGTCCCAAAATTGATGTTCAGAGAGC
Found at i:33508 original size:19 final size:19
Alignment explanation
Indices: 33484--33527 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
33474 TATTGACTAT
33484 GAGAGAG-C-AAGTGGGAG
1 GAGAGAGACTAAGTGGGAG
* *
33501 GAGAGAGACTTAGTGGGGG
1 GAGAGAGACTAAGTGGGAG
33520 GAGAGAGA
1 GAGAGAGA
33528 AGAGGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 1 0.04
19 15 0.65
ACGTcount: A:0.34, C:0.05, G:0.52, T:0.09
Consensus pattern (19 bp):
GAGAGAGACTAAGTGGGAG
Found at i:38834 original size:70 final size:70
Alignment explanation
Indices: 38721--38862 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
38711 ATAATCGCCG
38721 TTTTGTCACCGCCGGTTAGCTTTTTCCTCTTTTCCTTCTTTACCTTTTAACTGTTTATTTTCATT
1 TTTTGTCACCGCCGGTTAGCTTTTTCCTCTTTTCCTTCTTTACCTTTTAACTGTTTATTTTCATT
38786 ACTAT
66 ACTAT
38791 TTTTGTCACCGCCGGTTAGCTTTTTCCTCTTTTCCTTCTTTACCTTTTAACTGTTTATTTTCATT
1 TTTTGTCACCGCCGGTTAGCTTTTTCCTCTTTTCCTTCTTTACCTTTTAACTGTTTATTTTCATT
38856 ACTAT
66 ACTAT
38861 TT
1 TT
38863 GAAGAATGAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.13, C:0.24, G:0.08, T:0.55
Consensus pattern (70 bp):
TTTTGTCACCGCCGGTTAGCTTTTTCCTCTTTTCCTTCTTTACCTTTTAACTGTTTATTTTCATT
ACTAT
Found at i:39148 original size:36 final size:36
Alignment explanation
Indices: 39101--39171 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
39091 AATATGAATA
39101 TCTTCCATTACCTGTCATTGCAATGATAGTTGTTTC
1 TCTTCCATTACCTGTCATTGCAATGATAGTTGTTTC
39137 TCTTCCATTACCTGTCATTGCAATGATAGTTGTTT
1 TCTTCCATTACCTGTCATTGCAATGATAGTTGTTT
39172 ATCTGTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTTCCATTACCTGTCATTGCAATGATAGTTGTTTC
Found at i:40026 original size:38 final size:39
Alignment explanation
Indices: 39970--40044 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
39960 TGTTCTTTGC
*
39970 TTCTGTTAAGTTGTTAATTAACTTC-TTTTGACTCTAAA
1 TTCTATTAAGTTGTTAATTAACTTCTTTTTGACTCTAAA
40008 TTCTATTAAGTTGTTAATTAACTTCTTTTTGACTCTA
1 TTCTATTAAGTTGTTAATTAACTTCTTTTTGACTCTA
40045 CTTCTGATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.52
Consensus pattern (39 bp):
TTCTATTAAGTTGTTAATTAACTTCTTTTTGACTCTAAA
Found at i:47000 original size:183 final size:183
Alignment explanation
Indices: 46692--47058 Score: 734
Period size: 183 Copynumber: 2.0 Consensus size: 183
46682 CGGCATCTAT
46692 TTTCAACTTTGAGTTACTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAAATTGAAGTGT
1 TTTCAACTTTGAGTTACTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAAATTGAAGTGT
46757 TGTTCACGGCATCTATTTTCTTTGTTCATAATAATTGAACCGGAAACCTTACTTAAAAGGAACAG
66 TGTTCACGGCATCTATTTTCTTTGTTCATAATAATTGAACCGGAAACCTTACTTAAAAGGAACAG
46822 AGCTCCTCCTTAAATTAAGAATTTGTGGTGAGTTCCACCTATTATTTTAAACC
131 AGCTCCTCCTTAAATTAAGAATTTGTGGTGAGTTCCACCTATTATTTTAAACC
46875 TTTCAACTTTGAGTTACTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAAATTGAAGTGT
1 TTTCAACTTTGAGTTACTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAAATTGAAGTGT
46940 TGTTCACGGCATCTATTTTCTTTGTTCATAATAATTGAACCGGAAACCTTACTTAAAAGGAACAG
66 TGTTCACGGCATCTATTTTCTTTGTTCATAATAATTGAACCGGAAACCTTACTTAAAAGGAACAG
47005 AGCTCCTCCTTAAATTAAGAATTTGTGGTGAGTTCCACCTATTATTTTAAACC
131 AGCTCCTCCTTAAATTAAGAATTTGTGGTGAGTTCCACCTATTATTTTAAACC
47058 T
1 T
47059 CATACGATTC
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 184 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TTTCAACTTTGAGTTACTACTAATAGTAAGAAACGGTTACAAAATCGACTTTGAAATTGAAGTGT
TGTTCACGGCATCTATTTTCTTTGTTCATAATAATTGAACCGGAAACCTTACTTAAAAGGAACAG
AGCTCCTCCTTAAATTAAGAATTTGTGGTGAGTTCCACCTATTATTTTAAACC
Found at i:54315 original size:57 final size:57
Alignment explanation
Indices: 54227--54340 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
54217 TTACTAGCCT
54227 TCTCATTTTATGTATTCACCAGTAATTACAATGATAGGAATGTGAGCGATGCTAGGC
1 TCTCATTTTATGTATTCACCAGTAATTACAATGATAGGAATGTGAGCGATGCTAGGC
54284 TCTCATTTTATGTATTCACCAGTAATTACAATGATAGGAATGTGAGCGATGCTAGGC
1 TCTCATTTTATGTATTCACCAGTAATTACAATGATAGGAATGTGAGCGATGCTAGGC
54341 CAGTATTCCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (57 bp):
TCTCATTTTATGTATTCACCAGTAATTACAATGATAGGAATGTGAGCGATGCTAGGC
Found at i:56326 original size:174 final size:174
Alignment explanation
Indices: 55995--56895 Score: 1576
Period size: 174 Copynumber: 5.2 Consensus size: 174
55985 ATGACACCAC
* * * *
55995 TATACCTTTGTGTATAGTAGGAATGCCACCATGTTA---TGCCTTTAACTGCATATTAAAAATTC
1 TATACCTTTATGTATAATAGGAACGCCA-C-TGTTATTGTGCCTTTAACTGCATAATAAAAATTC
* *
56057 TCATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCAATCACTTCTG
64 TCATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTG
*
56122 CTACAAATAGAAATTCCCGTCAGCAACCTTTATTCAGATGCGCCAT
129 CTACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
* *
56168 TATACCTTTATGTATAATAGGAACGCCACTTTTATTGTGCCCTTAACTGCATAATAAAAATTCTC
1 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
56233 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
66 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
* *
56298 ACAAATAGAAATTCCCGTCAACAACCTTTATCCAGATGCGCCAT
131 ACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
56342 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
1 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
*
56407 ATTATACCTTTATTTAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
66 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
*
56472 ACAAACAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
131 ACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
*
56516 TATACCTTTATGTATAATAGGAACGCCACTATTATTGTGCCTTTAACTGCATAATAAAAATTCTC
1 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
* *
56581 ATTATACCTTTATTTAGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCGCTTTTGCT
66 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
*
56646 ACAAATAGAAATTCCCGTCGCCAACCTTTATTCAGATGCGCCAT
131 ACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
*
56690 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAAGTGCATAAT-AAAATTCTC
1 TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
*
56754 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCCCTTTTGCT
66 ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
*
56819 ACAAATAGAAATTCCCGTCACCTACCTTTATTCAGATGCGCCAT
131 ACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
56863 TATACCTTTATGTATAATAGGAACGCCACTGTT
1 TATACCTTTATGTATAATAGGAACGCCACTGTT
56896 GTGCGCTTTA
Statistics
Matches: 699, Mismatches: 26, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
171 4 0.01
172 1 0.00
173 172 0.25
174 522 0.75
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (174 bp):
TATACCTTTATGTATAATAGGAACGCCACTGTTATTGTGCCTTTAACTGCATAATAAAAATTCTC
ATTATACCTTTATTTGGATGCACCATTATACCTTGATGTATAATAGGAATGCCATCACTTTTGCT
ACAAATAGAAATTCCCGTCACCAACCTTTATTCAGATGCGCCAT
Found at i:58990 original size:31 final size:31
Alignment explanation
Indices: 58936--59017 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
58926 TATGATGTTG
**
58936 ACGTGGCATGATACGTCAGCCGAAAATTGCT-
1 ACGTGGCATGCCACGTCAGCCGAAAA-TGCTC
* * * *
58967 AGGTGGCATGCCATGTCATCCGAAAATGGTC
1 ACGTGGCATGCCACGTCAGCCGAAAATGCTC
58998 ACGTGGCATGCCACGTCAGC
1 ACGTGGCATGCCACGTCAGC
59018 ATAAAAGAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (31 bp):
ACGTGGCATGCCACGTCAGCCGAAAATGCTC
Found at i:63501 original size:15 final size:15
Alignment explanation
Indices: 63481--63561 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
63471 TTTAAATGAG
63481 CTCATCGTCTGAATC
1 CTCATCGTCTGAATC
* * *
63496 CTCATCATCTGGATG
1 CTCATCGTCTGAATC
*
63511 CTCATCGTCAGAATC
1 CTCATCGTCTGAATC
* * *
63526 CTCCTCCTCACCTAAATC
1 CTCATCGT---CTGAATC
*
63544 CTCACCGTCTGAATC
1 CTCATCGTCTGAATC
63559 CTC
1 CTC
63562 CTCATTATAA
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
15 38 0.79
18 10 0.21
ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30
Consensus pattern (15 bp):
CTCATCGTCTGAATC
Found at i:67214 original size:15 final size:15
Alignment explanation
Indices: 67194--67224 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
67184 CCCTTAAGTT
67194 TGTACGGATTGCCAC
1 TGTACGGATTGCCAC
67209 TGTACGGATTGCCAC
1 TGTACGGATTGCCAC
67224 T
1 T
67225 TTACCCCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (15 bp):
TGTACGGATTGCCAC
Found at i:67423 original size:31 final size:33
Alignment explanation
Indices: 67387--67485 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 33
67377 TTTTGTTCAC
*
67387 GTGGCATGCCACGTGCCA-TTTTTTG-AAACAT
1 GTGGCATGCCACGTGCCACTTTTTGGTAAACAT
*
67418 GTGGCATGCCACGTGTCACTTTTTGGTAAACA-
1 GTGGCATGCCACGTGCCACTTTTTGGTAAACAT
* * * *
67450 -TGGCGTGACATGTGTCACTTTTTGGT--ACAT
1 GTGGCATGCCACGTGCCACTTTTTGGTAAACAT
67480 GTGGCA
1 GTGGCA
67486 CGACTTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
29 3 0.05
31 44 0.76
32 6 0.10
33 5 0.09
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (33 bp):
GTGGCATGCCACGTGCCACTTTTTGGTAAACAT
Found at i:73421 original size:21 final size:21
Alignment explanation
Indices: 73383--73422 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
73373 GAAAGAAAGA
*
73383 AAGAAAAACTAAATAACAATG
1 AAGAAAAAATAAATAACAATG
73404 AAGAAAAGAATAAA-AACAA
1 AAGAAAA-AATAAATAACAA
73423 GAGGAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (21 bp):
AAGAAAAAATAAATAACAATG
Found at i:85756 original size:63 final size:64
Alignment explanation
Indices: 85657--85783 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 64
85647 GAAAAAAAAA
85657 GATGATGCGCTGGTTATAATGGGTTACGATTTTATGATTTTTCA-TTTTTTAAAGTAATTAGAC
1 GATGATGCGCTGGTTATAATGGGTTACGATTTTATGATTTTTCATTTTTTTAAAGTAATTAGAC
*
85720 GATGATGTGCTGGTTATAATGGGTTACGATTTTATGATTTTTCATTTTTTTAAAGTAATTAGAC
1 GATGATGCGCTGGTTATAATGGGTTACGATTTTATGATTTTTCATTTTTTTAAAGTAATTAGAC
85784 AAATTAAAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 43 0.69
64 19 0.31
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (64 bp):
GATGATGCGCTGGTTATAATGGGTTACGATTTTATGATTTTTCATTTTTTTAAAGTAATTAGAC
Found at i:87632 original size:30 final size:29
Alignment explanation
Indices: 87585--87653 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
87575 CATAACATAA
*
87585 GGGCTTATCTGGCCAAAATTGATAGTCCAG
1 GGGCTTATTTGGCCAAAATTGA-AGTCCAG
* * *
87615 GGGTTTATTTGGTCAAAATTGAAGTTCAG
1 GGGCTTATTTGGCCAAAATTGAAGTCCAG
*
87644 TGGCTTATTT
1 GGGCTTATTT
87654 AACCATTGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (29 bp):
GGGCTTATTTGGCCAAAATTGAAGTCCAG
Found at i:87714 original size:3 final size:3
Alignment explanation
Indices: 87706--87732 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
87696 TAAAAATAGT
87706 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
87733 CAAAATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:88356 original size:109 final size:109
Alignment explanation
Indices: 88160--88434 Score: 428
Period size: 109 Copynumber: 2.5 Consensus size: 109
88150 ACTATTATAG
* * *
88160 TTTTATTATACTATAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
88225 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
88274 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
88339 TTACCAAAAAATTTGGATATATTAAATTTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
88383 TTTTATTCAACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
88435 TAATTTTTTT
Statistics
Matches: 154, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
108 7 0.05
109 122 0.79
110 3 0.02
111 2 0.01
114 20 0.13
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:89665 original size:1 final size:1
Alignment explanation
Indices: 89659--89685 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
89649 CTCTTTTCAC
89659 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
89686 GATATATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:91094 original size:41 final size:40
Alignment explanation
Indices: 91037--91118 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 40
91027 CGTGCGGCTG
91037 TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAA-AAA
*
91078 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAAAAA
91118 T
1 T
91119 GAAATTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 4 0.10
41 36 0.90
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (40 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAATTAAAAA
Found at i:91114 original size:14 final size:14
Alignment explanation
Indices: 91048--91114 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
91038 TTTATTTTAT
*
91048 AAATTCTTTTAAGA
1 AAATTCATTTAAGA
*
91062 AAATTCAATTAAGA
1 AAATTCATTTAAGA
* * * *
91076 AATTTTATTTTA-T
1 AAATTCATTTAAGA
*
91089 AAATTCTTTTAAGA
1 AAATTCATTTAAGA
*
91103 AAATTCAGTTAA
1 AAATTCATTTAA
91115 AAATGAAATT
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
13 8 0.21
14 30 0.79
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (14 bp):
AAATTCATTTAAGA
Found at i:91444 original size:11 final size:11
Alignment explanation
Indices: 91430--91467 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
91420 ATTCATAACA
91430 AATTTATAATT
1 AATTTATAATT
91441 AATTTATAATT
1 AATTTATAATT
91452 -ATTTGATAATT
1 AATTT-ATAATT
*
91463 TATTT
1 AATTT
91468 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:95672 original size:75 final size:75
Alignment explanation
Indices: 95577--95725 Score: 262
Period size: 75 Copynumber: 2.0 Consensus size: 75
95567 TACAATACCA
* *
95577 TAAATTTCATTTTTATTATGGGTTTAAATTCTATTAGAATCATCCTAAAAATGGGTGGTTTTAGG
1 TAAATTTCATTTTCATTATGGGTTTAAATTCTATTAGAATCATCCTAAAAATGAGTGGTTTTAGG
95642 ATTCCATTAC
66 ATTCCATTAC
*
95652 TAAATTTCATTTTCATTATGGGTTTAAATTCTATTAGAATCATCCTAAAAATGAGTGTTTTTAGG
1 TAAATTTCATTTTCATTATGGGTTTAAATTCTATTAGAATCATCCTAAAAATGAGTGGTTTTAGG
*
95717 ATTTCATTA
66 ATTCCATTA
95726 AGATGGTGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (75 bp):
TAAATTTCATTTTCATTATGGGTTTAAATTCTATTAGAATCATCCTAAAAATGAGTGGTTTTAGG
ATTCCATTAC
Found at i:103947 original size:89 final size:89
Alignment explanation
Indices: 103847--104026 Score: 342
Period size: 89 Copynumber: 2.0 Consensus size: 89
103837 GCACAAACAT
*
103847 ATCTTACTACTATATAAAATCACGAATTCAAAAATTATAATTGGGAAATTTCATAAATACCCTTA
1 ATCTTACTACTATATAAAATCACGAACTCAAAAATTATAATTGGGAAATTTCATAAATACCCTTA
*
103912 GTATTATGGTATAATAATTTTTTA
66 GTATTATAGTATAATAATTTTTTA
103936 ATCTTACTACTATATAAAATCACGAACTCAAAAATTATAATTGGGAAATTTCATAAATACCCTTA
1 ATCTTACTACTATATAAAATCACGAACTCAAAAATTATAATTGGGAAATTTCATAAATACCCTTA
104001 GTATTATAGTATAATAATTTTTTA
66 GTATTATAGTATAATAATTTTTTA
104025 AT
1 AT
104027 AAGTATTCTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (89 bp):
ATCTTACTACTATATAAAATCACGAACTCAAAAATTATAATTGGGAAATTTCATAAATACCCTTA
GTATTATAGTATAATAATTTTTTA
Found at i:105122 original size:334 final size:333
Alignment explanation
Indices: 104194--106200 Score: 1608
Period size: 334 Copynumber: 6.1 Consensus size: 333
104184 ATAATTACTT
* * * *
104194 CATTTGAATCCTGTTTGGATTTAATTAGAAATAAATTCGAGAAAAAAAAATGGAAAAACGATATT
1 CATTTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAG-AAAAAAAATGGAAAAACGATATT
* * *
104259 AGAAGCGTGAAAAGTCCGTCAATCTTTTTGG-GATTGAATTAAATATTTTTCTTACTATTGTGGC
65 AGAAGCGTGAAAAGTCCGTCAATTTTTTTGGCG-TTGAATTATATATTTTTCTGACTATTGTGGC
** ** * * * *
104323 AAAAAAATTGAGTAAAAATTTTTCGGGTCAGTTTTTCCAAAATTTTAGTTGAAATGGTGTACT--
129 AAAAAAAAGGAAAAAAAAATTTT-GGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAA
* * * * **
104386 GCATCGCGATTTTTTGCTAAAAAACGCGTTCTGGAGCCCCGATTCAGTTTTGCATGATTTTTGGC
193 CCATCACGGTTTTTTGCT-AAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGC
* * ** * ** * * *
104451 GTAAATAATTCTTTCAATATCTATATTTATGGAAGCAAATCTCACCCACATTGGATATAAGGATT
257 GTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATT
104516 TGTTTTTACGAG
322 TGTTTTTACGAG
* * * * * * *
104528 AATCTT-AATCTTGTTTCGATTTAATTAGAAATTAATTC--G-GAAAAAATAGAAAAATGATATT
1 CAT-TTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATT
* * ** * * * **
104589 AGAGGCGTGAAAAGTCCGTCAATCTTTTTGGTATTAAATTATATATTTTT-TCAGTATTGTCACA
65 AGAAGCGTGAAAAGTCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTGGCA
* * * *
104653 AAAAAATA-TAAAAAAGAAATTTCGGGTAAG----T------TTTTAG-CTGAAATCGTTTACTA
130 AAAAAA-AGGAAAAAA-AAATTTTGGGTCAGTTTTTGCAAAATTTTAGTC-GAAATCGTGTACTA
* * * * * * * *
104706 ATCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTTTTGCATGATTTTTGG
192 ACCATCACGGTTTTT-TGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGG
* * * * ** *
104771 CATAAAAACTCCTTGAAATATCTATATTCATCTAACCAAATTTCAGTTACATTGGATTTAAGAAT
256 CGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT
*
104836 TTGTTTTTATGAG
321 TTGTTTTTACGAG
* *
104849 TATTTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAG-AAAAAAA-GGGAAAACGATATTA
1 CATTTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATTA
** * * * * *
104912 GAAATGTGAAAAATTCTTCAATTTTTTTTGCGTTGAATTATGTATTTTTTCTGACTATTGTGGCA
66 GAAGCGTGAAAAGTCCGTCAATTTTTTTGGCGTTGAATTATATA-TTTTTCTGACTATTGTGGCA
* * * *
104977 AAAAAAAGGAGGAAAAAAATTATTAGGTCATTTTTTGCAAAATTTTAATCGAAATCGTGTACTAA
130 AAAAAAAGGA-AAAAAAAATT-TTGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAA
105042 CCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG
193 CCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * * *
105107 TAAAGGCTTCTTGAAATATCTATATTCATCGAATCAAATCTCAACCACATTGGATATAAGTATTT
258 TAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
105172 GTTTTTACGAG
323 GTTTTTACGAG
* * *
105183 CATCTGAATTTTGATTTCTAATTTAATTAGAAATTAAA-TCT---AAAAAAATGGAAAAAACGAT
1 CATTTGAATCTT-ATTT-TGATTTAATTAGAAA-TAAATTCTAGAAAAAAAATGG-AAAAACGAT
* * *
105244 ATTAGAAGCGTGAAAAGTCCGTCAATATTTTTGGCGTTGAATTATATAATTTTTTTGAGC-AATG
62 ATTAGAAGCGTGAAAAGTCCGTCAATTTTTTTGGCGTTGAATTATAT-ATTTTTCTGA-CTATTG
* * * * *
105308 TGGCAAAAATTTCAGAA-AAAAAAAAAATTTCGGATCA------GC----GTTTAGCCGAAATCG
125 TGGCAAAAA----A-AAGGAAAAAAAAATTTTGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCG
* * * * * *
105362 TGTACT-----TTACAGTTTTTTGTCTAAAAATGCTTTCCGGGGCCCCGGCTCAGTTTTACATGA
185 TGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGA
* ** * ** *
105422 TTTTTGCCAAAAATACACCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACATTCGG-T
249 TTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GGAT
* * * *
105486 TTAAGGATTTATTTTTGCTAC
313 TTAAGGATTTGTTTTTACGAG
** * * *
105507 CATCCG-ATCTTATTTTGATTTAATTA-AAATTTTAATT-TGGAAAAAGAAATGAAAAAACGATA
1 CATTTGAATCTTATTTTGATTTAATTAGAAA--TAAATTCTAGAAAAA-AAATGGAAAAACGATA
* * *
105569 TTAGAAGCGTGAAAAG-CCAGTCAATCTTTTTGGCGTTGAATTATATATTTTT-TGAGTATTGCG
63 TTAGAAGCGTGAAAAGTCC-GTCAATTTTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTG
* ** * * *
105632 GCAAAGAATTGAGAAAAAAAAATTTTTGGATCAGTTTTTGCAAAATTTTAGCCGAAATTGTGTAC
127 GCAAAAAAAAG-GAAAAAAAAA-TTTTGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTAC
* * * * * * * *
105697 TAACTATCACGGTTTATGGCTAAAAACGCATTTCGGTGCCCCGGCTCAGTTTTGTATGCTTTTTG
190 TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTG
*
105762 GCGTAAAGAATTCTTGAAATATCTATATTCATCTAACCAAAT-TCCAGCCACATTGGATTTAAGG
255 GCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCT-CAGCCACATTGGATTTAAGG
105826 ATTTGTTTTTACGAG
319 ATTTGTTTTTACGAG
* * * * * * * *
105841 CATTTTAATTTTGTTTCGATTTAATTAAAAATTAA-TCTGGAAAAAAAATGGAAAAATGATATTA
1 CATTTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATTA
* * * * *
105905 GAAGCGTGAAGAGCCCGTC-ATTCTTTTTGACGTTGAATTATATATTATTCTGAATATTGTGGC-
66 GAAGCGTGAAAAGTCCGTCAATT-TTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTGGCA
** * ** *
105968 AAAAAATTGAGAAAAACCTTTTCGGGTCAG----T------TTTTAGCCGAAATCGTGTACTAAC
130 AAAAAAAGGAAAAAAAAATTTT-GGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
* * * * * ** * *
106023 CATCACAGTTTTTGGCTAAAAACGCCTTCCGGGGCCACATCTCTA-TTTTGCATGGTTTTTGGTG
194 CATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTC-AGTTTTGCATGATTTTTGGCG
*** * * * * *
106087 CCGAGA-TTCCTTGAAATATCGT-TATTCATCTAATCAAATCTGAGACATATTCGATTTAAGGAT
258 TAAAGACTT-CTTGAAATATC-TATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT
*
106150 TTCTTTTTACGAG
321 TTGTTTTTACGAG
* * * * *
106163 CACTTAAATCTTGTTTCGATTTAATTAGAAATTAATTC
1 CATTTGAATCTTATTTTGATTTAATTAGAAATAAATTC
106201 AAAAAATATG
Statistics
Matches: 1352, Mismatches: 240, Indels: 173
0.77 0.14 0.10
Matches are distributed among these distances:
318 1 0.00
319 26 0.02
320 14 0.01
321 156 0.12
322 229 0.17
323 41 0.03
324 184 0.14
325 17 0.01
326 2 0.00
328 19 0.01
329 27 0.02
330 88 0.07
331 4 0.00
332 18 0.01
333 65 0.05
334 284 0.21
335 65 0.05
336 88 0.07
337 6 0.00
338 5 0.00
339 9 0.01
340 2 0.00
341 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (333 bp):
CATTTGAATCTTATTTTGATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATTA
GAAGCGTGAAAAGTCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTGGCAA
AAAAAAGGAAAAAAAAATTTTGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCA
TCACGGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAA
AGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
TTTACGAG
Found at i:105672 original size:658 final size:654
Alignment explanation
Indices: 104211--105983 Score: 2026
Period size: 658 Copynumber: 2.7 Consensus size: 654
104201 ATCCTGTTTG
*
104211 GATTTAATTAGAAATAAATTCGAGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGTCC
1 GATTTAATTAGAAATAAATTCTAG-AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CC
* * *
104276 GTCAATCTTTTTGG-GATTGAATTAAATATTTTTCTTACTATTGTGGCAAAAAAATTGAG--TAA
64 GTCAATCTTTTTGGCG-TTGAATTATATATTTTTCTGACTATTGTGGC-AAAAAATTGAGAAAAA
* * * * * *
104338 AAATTTTTCGGGTCAGTTTTTCCAAAATTTTAGTTGAAATGGTGTACT--GCATCGCGATTTTTT
127 AAATTTTT--GGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTT
* ** * **
104401 GCTAAAAAACGCGTTCTGGAGCCCCGATTCAGTTTTGCATGATTTTTGGCGTAAATAATTCTTTC
190 GCT-AAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGAATTCTTGA
* * * * *
104466 AATATCTATATTTATGGAAGCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACGAGAAT
254 AATATCTATATTCATCGAACCAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACGAGCAT
* * ** * *
104531 CTTAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGAAAAATGATATTAGAGGCG
319 CTTAATTTTGTTTCGATTTAATTAGAAATTAAATCTAAAAAAATGGAAAAATGATATTAGAAGCG
** * * **
104596 TGAAAAGTCCGTCAATCTTTTTGGTATTAAATTATATA-TTTTTTCAGTATTGTCACAAAAA--A
384 TGAAAAGTCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTTGAGTATTGTGGCAAAAATTA
* * * * ** * *
104658 ATATAAAAAAGAAATTTCGGGTAAGTTTTTAGCTGAAATCGTTTACTAATCATCATGGTTTTTGG
449 AGAAAAAAAAAAAATTTCGGATAAGCGTTTAGCCGAAATCGTGTACT-ATCATCA-GGTTTTTGG
* * * * *
104723 GCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTTTTGCATGATTTTTGGCATAAAAACTCCTTGAA
512 GCTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTACATGATTTTTGCCATAAAAACACCTTGAA
* * ** * ** *
104788 ATATCTATATTCATCTAACCAAATTTCAGTTACATTGGATTTAAGAATTTGTTTTTATGAGTATT
577 ATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTATGACCATC
*
104853 TGAATCTTATTTT
642 CGAATCTTATTTT
* ** ** *
104866 GATTTAATTAGAAATAAATTCTAG-AAAAAAA-GGGAAAACGATATTAGAAATGTGAAAAATTCT
1 GATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAGCCG
* * * ** *
104929 TCAATTTTTTTTGCGTTGAATTATGTATTTTTTCTGACTATTGTGGCAAAAAAAAGGAGGAAAAA
65 TCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGACTATTGTGGC-AAAAAATTGAGAAAAAA
* * *
104994 AATTATTAGGTCATTTTTTGCAAAATTTTAATCGAAATCGTGTACTAACCATCACGGTTTTTTGC
128 AATT-TTTGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTTGC
**
105059 TAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGGCTTCTTGAAAT
192 TAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGAATTCTTGAAAT
* * *
105124 ATCTATATTCATCGAATCAAATCTCAACCACATTGGATATAAGTATTTGTTTTTACGAGCATCTG
257 ATCTATATTCATCGAACCAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACGAGCATCTT
* *
105189 AATTTTGATTTCTAATTTAATTAGAAATTAAATCTAAAAAAATGGAAAAAACGATATTAGAAGCG
322 AATTTTG-TTTC-GATTTAATTAGAAATTAAATCTAAAAAAATGG-AAAAATGATATTAGAAGCG
* * *
105254 TGAAAAGTCCGTCAATATTTTTGGCGTTGAATTATATAATTTTTTTGAGCAATGTGGCAAAAATT
384 TGAAAAGTCCGTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTTTGAGTATTGTGGCAAAAA-T
* * * *
105319 TCAGAAAAAAAAAAAATTTCGGATCAGCGTTTAGCCGAAATCGTGTACT-TTA-CA-GTTTTTTG
447 TAAGAAAAAAAAAAAATTTCGGATAAGCGTTTAGCCGAAATCGTGTACTATCATCAGGTTTTTGG
* * *
105381 TCTAAAAATGC-TTTCCGGGGCCCCGGCTCAGTTTTACATGATTTTTGCCA-AAAATACACCTTG
512 GCTAAAAACGCGTTT-CGGGGCCCCAGCTCAGTTTTACATGATTTTTGCCATAAAA-ACACCTTG
* *
105444 AAATATATATATTCATCTAACCAAATCTCAGCCACATTCGG-TTTAAGGATTTATTTTTGCT-AC
575 AAATATATATATTCATCTAACCAAATCTCAGCCACATT-GGATTTAAGAATTTATTTTT-ATGAC
105507 CATCCG-ATCTTATTTT
638 CATCCGAATCTTATTTT
* * *
105523 GATTTAATTA-AAATTTTAATT-TGGAAAAAGAAATGAAAAAACGATATTAGAAGCGTGAAAAGC
1 GATTTAATTAGAAA--TAAATTCTAGAAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAGC
* * *
105586 CAGTCAATCTTTTTGGCGTTGAATTATATATTTTT-TGAGTATTGCGGCAAAGAATTGAGAAAAA
63 C-GTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTGGCAAAAAATTGAG-AAAA
* * * * *
105650 AAAATTTTTGGATCAGTTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACTATCACGGTTTATG
126 AAAATTTTTGG-TCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTT
* * * * *
105715 GCTAAAAACGCATTTCGGTGCCCCGGCTCAGTTTTGTATGCTTTTTGGCGTAAAGAATTCTTGAA
190 GCTAAAAACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGAATTCTTGAA
* * *
105780 ATATCTATATTCATCTAACCAAAT-TCCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
255 ATATCTATATTCATCGAACCAAATCT-CAACCACATTGGATATAAGGATTTGTTTTTACGAGCAT
* *
105844 TTTAATTTTGTTTCGATTTAATTAAAAATT-AATCTGGAAAAAAAATGGAAAAATGATATTAGAA
319 CTTAATTTTGTTTCGATTTAATTAGAAATTAAATCT---AAAAAAATGGAAAAATGATATTAGAA
* * * * * * *
105908 GCGTGAAGAGCCCGTCATTCTTTTTGACGTTGAATTATATATTATTCTGAATATTGTGGCAAAAA
381 GCGTGAAAAGTCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTTGAGTATTGTGGC-AAAA
*
105973 ATTGAGAAAAA
445 ATTAAGAAAAA
105984 CCTTTTCGGG
Statistics
Matches: 944, Mismatches: 141, Indels: 65
0.82 0.12 0.06
Matches are distributed among these distances:
652 42 0.04
653 40 0.04
654 33 0.03
655 155 0.16
656 62 0.07
657 128 0.14
658 364 0.39
659 17 0.02
660 63 0.07
661 2 0.00
663 38 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (654 bp):
GATTTAATTAGAAATAAATTCTAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCGT
CAATCTTTTTGGCGTTGAATTATATATTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAAAT
TTTTGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAA
AACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTAAAGAATTCTTGAAATATCT
ATATTCATCGAACCAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACGAGCATCTTAATT
TTGTTTCGATTTAATTAGAAATTAAATCTAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAG
TCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTTGAGTATTGTGGCAAAAATTAAGAAAAA
AAAAAAATTTCGGATAAGCGTTTAGCCGAAATCGTGTACTATCATCAGGTTTTTGGGCTAAAAAC
GCGTTTCGGGGCCCCAGCTCAGTTTTACATGATTTTTGCCATAAAAACACCTTGAAATATATATA
TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTATGACCATCCGAATCTTA
TTTT
Found at i:106552 original size:380 final size:380
Alignment explanation
Indices: 105845--106609 Score: 1266
Period size: 380 Copynumber: 2.0 Consensus size: 380
105835 TACGAGCATT
* * ** *
105845 TTAATTTTGTTTCGATTTAATTAAAAATTAATCTGGAAAAAAAATGGAAAAATGATATTAGAAGC
1 TTAATCTTGTTTCGATTTAATTAAAAATTAATCTGCAAAAAAAATGGAAAAACAATATTAGAAAC
*
105910 GTGAAGAGCCCGTCATTCTTTTTGACGTTGAATTATATATTATTCTGAATATTGTGGCAAAAAAT
66 GTGAAGAGCCCGTCATTCTTTTTGACATTGAATTATATATTATTCTGAATATTGTGGCAAAAAAT
**
105975 TGAGAAAAACCTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
131 TGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
*
106040 AAAAACGCCTTCCGGGGCCACATCTCTATTTTGCATGGTTTTTGGTGCCGAGATTCCTTGAAATA
196 AAAAACGCCTTCCGGGGCCACATCTCTATTTTGCATGGTTTTTGGTGCCGAGACTCCTTGAAATA
* *
106105 TCGTTATTCATCTAATCAAATCTGAGACATATTCGATTTAAGGATTTCTTTTTACGAGCACTTAA
261 TCGTTATTCATCTAATCAAAACAGAGACATATTCGATTTAAGGATTTCTTTTTACGAGCACTTAA
*
106170 ATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAA-ACCAAAATTTGA
326 ATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAACA-AAAAATTTGA
* * *
106225 TTAATCTTGTTTCGGTTTAATTAAAAATTAAT-T-CAGAAAAAATGGAAAAGCAATATTAGAAAC
1 TTAATCTTGTTTCGATTTAATTAAAAATTAATCTGCAAAAAAAATGGAAAAACAATATTAGAAAC
* * *
106288 GTGAAGAGCCCGTCATTCTTTTTGGCATTGAATTATATATATTTTTTTGAATATTGTGGCAAAAA
66 GTGAAGAGCCCGTCATTCTTTTTGACATTGAA-T-TATATATTATTCTGAATATTGTGGCAAAAA
*
106353 ATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTGACCATCACAGTTTTTGG
129 ATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
* *
106418 CTAAAAACGCTTTCCGGGGCCACATCTCTATTTTGCATGGTTTTTTGTGCCGAGACTCCTTGAAA
194 CTAAAAACGCCTTCCGGGGCCACATCTCTATTTTGCATGGTTTTTGGTGCCGAGACTCCTTGAAA
* *
106483 TATCGTTATTCATCTAATCAAAACAGAGACATATTCGATTTAAGGATTTGTTTTTACGAGTACTT
259 TATCGTTATTCATCTAATCAAAACAGAGACATATTCGATTTAAGGATTTCTTTTTACGAGCACTT
*
106548 AAATCTTGTTTCGATTTAATTAGAAATTAATTTAAAAAATATGAACAAAAAATTTGA
324 AAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAACAAAAAATTTGA
106605 TTAAT
1 TTAAT
106610 TTATTCTCAA
Statistics
Matches: 358, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
378 54 0.15
379 2 0.01
380 301 0.84
381 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (380 bp):
TTAATCTTGTTTCGATTTAATTAAAAATTAATCTGCAAAAAAAATGGAAAAACAATATTAGAAAC
GTGAAGAGCCCGTCATTCTTTTTGACATTGAATTATATATTATTCTGAATATTGTGGCAAAAAAT
TGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
AAAAACGCCTTCCGGGGCCACATCTCTATTTTGCATGGTTTTTGGTGCCGAGACTCCTTGAAATA
TCGTTATTCATCTAATCAAAACAGAGACATATTCGATTTAAGGATTTCTTTTTACGAGCACTTAA
ATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAATATGAACAAAAAATTTGA
Found at i:111598 original size:6 final size:6
Alignment explanation
Indices: 111589--111620 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
111579 CCCCATCCCC
111589 ATCACT ATCACT ATCACT ATCACT ATCACT AT
1 ATCACT ATCACT ATCACT ATCACT ATCACT AT
111621 ATTCACTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCACT
Found at i:124338 original size:2 final size:2
Alignment explanation
Indices: 124331--124355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
124321 AAACTACTCA
124331 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
124356 ATTCAACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125523 original size:334 final size:330
Alignment explanation
Indices: 124947--126111 Score: 957
Period size: 334 Copynumber: 3.4 Consensus size: 330
124937 TTAAAAGCCT
* * * * * *
124947 TTTTCAGGCTTCAAATAT-AGTTTTCCTTTTTTTATTTCCAAATTAATTTTTGATTAATTCGAAA
1 TTTTCACGCTTCTAATATCA-TTTTCCCTATTTT-TTT-CAAATTAATTTTTAATTAAATCGAAA
* * * *
125011 CAAGAATTCGAAA--CTCGTTAAAACAAATCCTTAAATACAATGTCA-CTAAGATTTGGTTAGCT
63 CAAG-ATTC-AAATGCTCGTAAAAACAAATCCTTAAATCCAATGT-AGCTGAGATTTGGTTAGAT
* * * * **
125073 GAATATAAATATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCAAAA-TTGACACAGAAACCCG
125 GAATAT--AGATATTTCAAGGAGTCTTGCCACCAAAAATCATGCAAAACTT-AC-C-GGGACCCG
* * ** * * * *
125137 AAACACGTTTTTTGA-CAAAAAAAAACC-CCATGA-TGGTACAAGATTATGGCTAAACATTTTGC
185 AAACGCG--TTTTGAGCCAAAAAAAACCGTGATAATTAGTACACGATTTTGGCTAAA-ATTTTGC
125199 AAAAATTGACCCAGAATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCA
247 AAAAATTGACCCAGAATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCA
*
125264 ACGCGAAAAAGATTGAAGGG
312 ATGC-AAAAAGATTGAAGGG
125284 TTTCTCACGCTTCTAATATCATTTTCCCTATTTTTTTCAAATTAATTTTTAATTAAATCGAAACA
1 TTT-TCACGCTTCTAATATCATTTTCCCTATTTTTTTCAAATTAATTTTTAATTAAATCGAAACA
* * * *
125349 TG-TTGTAAATGCTCGTAAAAACAAATCCTTAAATCCAATTTAG-TTAGGATTTGGTTAGATGAA
65 AGATT-CAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGA-GATTTGGTTAGATGAA
* * *
125412 TATATATATTTCAAGGAGTTTTGCCACCAAAAATCATGCAAAACTTACTCGGGACCCCAAACGCG
128 TATAGATATTTCAAGGAGTCTTGCCACCAAAAATCATGCAAAACTTAC-CGGGACCCGAAACGCG
* *
125477 TTTTGAGCCAAAAAAAACCGTGATAATTAGTACACGATTTTGGCTAAAATTTTGTAAATAAATGA
192 TTTTGAGCCAAAAAAAACCGTGATAATTAGTACACGATTTTGGCTAAAATTTTGCAAA-AATTGA
* * * ** * * * *
125542 CCCAAAATTTTTTTCTTCAATTTTTCGATAAAATACTCATAAAATATAAATAATTCAATGCCAAA
256 CCCAGAATATTTTTC-TCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAATGCAAAA
* *
125607 AGTTTTGGAGGAG
320 AG-ATTGAAGG-G
* * * * * * *
125620 TCTTCACGCTTTTAATATCATTTTTCATATTTTTCT-AAATTAATTTATAATTAAATTGAAACAA
1 TTTTCACGCTTCTAATATCATTTTCCCTATTTTTTTCAAATTAATTTTTAATTAAATCGAAACAA
** * *
125684 GATTCAGGTGCTCGTAAAAA-AAATCCTTAAATGCC-ATGTGGCTGAGATTTGATTAGATGAATA
66 GATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CCAATGTAGCTGAGATTTGGTTAGATGAATA
* *** * * **
125747 TAGATATTTCAAGGAGTCTCGATGTCC-AAAATCATGCAAAACTGAGCCGGTGTCCCGAAACGTA
130 TAGATATTTCAAGGAGTCTTG-CCACCAAAAATCATGCAAAACTTA-CCGG-GACCCGAAACGCG
* * * ** *
125811 TTTTTAG-C--AAAAAACCGTGATGATTGAATTATATAATTTTTACACGATCTCAGCTAGAATTT
192 TTTTGAGCCAAAAAAAACC--G-TGA-T--A--AT-T-A---GTACACGATTTTGGCTAAAATTT
* * ** * *
125873 TGCAAAAATTGACTC-GAA-AGTTATTTCCTAAAATTTTTTTCCACAATACTCATAAAAATTGTA
244 TGCAAAAATTGACCCAGAATA-TT-TTT-CT-CAATTTTTAGCCACAATACTCATAAAAAATATA
*
125936 TAATTCAATTCCAAAAAGATTGAAGGG
305 TAATTCAA-TGCAAAAAGATTGAAGGG
* ** * ** *
125963 CTTTTCATGCTTCTAATATCATTTTTTCTATTATTTTTCGAATTAATTTTTAATTAAATTAAAAT
1 -TTTTCACGCTTCTAATATCATTTTCCCTATT-TTTTTCAAATTAATTTTTAATTAAATCGAAAC
* * ***
126028 ATGATTCAAATGCTTGT-TTTACAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTAGATGAAT
64 AAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTAGATGAAT
*
126092 ATAGATATTTCAAGCAGTCT
129 ATAGATATTTCAAGGAGTCT
126112 CGGCGGCGAA
Statistics
Matches: 670, Mismatches: 114, Indels: 79
0.78 0.13 0.09
Matches are distributed among these distances:
331 14 0.02
332 11 0.02
333 96 0.14
334 149 0.22
335 81 0.12
336 75 0.11
337 7 0.01
338 24 0.04
339 3 0.00
340 1 0.00
341 1 0.00
342 4 0.01
343 12 0.02
344 87 0.13
345 14 0.02
346 91 0.14
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (330 bp):
TTTTCACGCTTCTAATATCATTTTCCCTATTTTTTTCAAATTAATTTTTAATTAAATCGAAACAA
GATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTAGATGAATAT
AGATATTTCAAGGAGTCTTGCCACCAAAAATCATGCAAAACTTACCGGGACCCGAAACGCGTTTT
GAGCCAAAAAAAACCGTGATAATTAGTACACGATTTTGGCTAAAATTTTGCAAAAATTGACCCAG
AATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAATGCAAAAAGATTG
AAGGG
Found at i:126533 original size:19 final size:19
Alignment explanation
Indices: 126522--126558 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
126512 AATTTTTAAG
126522 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
126541 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
126559 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:127799 original size:2 final size:2
Alignment explanation
Indices: 127792--127821 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
127782 GTAAGTCAGC
*
127792 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127822 TACCGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128282 original size:6 final size:6
Alignment explanation
Indices: 128271--128310 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
128261 TTGTTCTCCA
*
128271 ATCTTC ATCTTC ATCTTC ATTTTC ATCTTC ATCTTC ATCT
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCT
128311 AACCCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
ATCTTC
Found at i:128339 original size:6 final size:6
Alignment explanation
Indices: 128330--128369 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
128320 TCACCTTCAC
* **
128330 CTTCGT CTTCGT CTTCGT CTTCGT CTACAC CTTCGT CTTC
1 CTTCGT CTTCGT CTTCGT CTTCGT CTTCGT CTTCGT CTTC
128370 ACCTTCACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.05, C:0.38, G:0.12, T:0.45
Consensus pattern (6 bp):
CTTCGT
Found at i:128372 original size:12 final size:12
Alignment explanation
Indices: 128336--128387 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
128326 TCACCTTCGT
**
128336 CTTCGTCTTCGT
1 CTTCGTCTTCAC
*
128348 CTTCGTCTACAC
1 CTTCGTCTTCAC
128360 CTTCGTCTTCAC
1 CTTCGTCTTCAC
**
128372 CTTCACCTTCAC
1 CTTCGTCTTCAC
128384 CTTC
1 CTTC
128388 TAATCCACCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.10, C:0.42, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTCGTCTTCAC
Found at i:128378 original size:18 final size:18
Alignment explanation
Indices: 128342--128381 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
128332 TCGTCTTCGT
**
128342 CTTCGTCTTCGTCTACAC
1 CTTCGTCTTCACCTACAC
*
128360 CTTCGTCTTCACCTTCAC
1 CTTCGTCTTCACCTACAC
128378 CTTC
1 CTTC
128382 ACCTTCTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.42, G:0.07, T:0.40
Consensus pattern (18 bp):
CTTCGTCTTCACCTACAC
Found at i:142111 original size:1 final size:1
Alignment explanation
Indices: 142105--142144 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
142095 CAAAATCTTC
*
142105 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
142145 CAGTGTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:145780 original size:29 final size:29
Alignment explanation
Indices: 145738--145794 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
145728 AACTATCCAC
145738 TTTGGGACAAATTGACCCCTTAACTTTTT
1 TTTGGGACAAATTGACCCCTTAACTTTTT
*
145767 TTTGGGACAAATTGGCCCCTTAACTTTT
1 TTTGGGACAAATTGACCCCTTAACTTTT
145795 AAAAACGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (29 bp):
TTTGGGACAAATTGACCCCTTAACTTTTT
Found at i:146559 original size:31 final size:29
Alignment explanation
Indices: 146487--146567 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
146477 TCTCGTTTTT
*
146487 AAAAGTTAAGGGACCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
*
146516 AAAAATTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
* *
146545 TGAATAGTTAAGGGGCTAATTTG
1 --AAAAGTTAAGGGGCCAATTTG
146568 GGTATTAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 27 0.60
31 18 0.40
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.25
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:148678 original size:28 final size:29
Alignment explanation
Indices: 148646--148701 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
148636 TTTCTTACTT
148646 AGTTATTAA-AAAGCTTTAGATTTTAAAA
1 AGTTATTAAGAAAGCTTTAGATTTTAAAA
*
148674 AGTTATTAAGAAAGTTTTAGATTTTAAA
1 AGTTATTAAGAAAGCTTTAGATTTTAAA
148702 TTAAATGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (29 bp):
AGTTATTAAGAAAGCTTTAGATTTTAAAA
Found at i:156564 original size:22 final size:22
Alignment explanation
Indices: 156520--156563 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
156510 TTTTAAACCC
* *
156520 ATCAAAAGCGTGTTGCCCAAAA
1 ATCAAAAGCCTGTTGCCAAAAA
156542 ATCAAAAGCCT-TTGCCAAAAA
1 ATCAAAAGCCTGTTGCCAAAAA
156563 A
1 A
156564 AAAACCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (22 bp):
ATCAAAAGCCTGTTGCCAAAAA
Found at i:156843 original size:23 final size:24
Alignment explanation
Indices: 156817--156871 Score: 103
Period size: 23 Copynumber: 2.3 Consensus size: 24
156807 ACCTTCCCCA
156817 AAATCAATCAAAAACA-ACAATAT
1 AAATCAATCAAAAACACACAATAT
156840 AAATCAATCAAAAACACACAATAT
1 AAATCAATCAAAAACACACAATAT
156864 AAATCAAT
1 AAATCAAT
156872 GATCATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (24 bp):
AAATCAATCAAAAACACACAATAT
Done.