Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold287
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: 796744
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 2 of 5
Found at i:117149 original size:18 final size:19
Alignment explanation
Indices: 117128--117166 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
117118 TATAAACTAT
117128 ATAAATATT-AAT-ATAAAA
1 ATAAAT-TTAAATAATAAAA
117146 ATAAATTTAAATAATAAAA
1 ATAAATTTAAATAATAAAA
117165 AT
1 AT
117167 TATTATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 9 0.47
19 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATTTAAATAATAAAA
Found at i:117243 original size:11 final size:11
Alignment explanation
Indices: 117229--117253 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
117219 TATGTAAAAT
117229 ATATGAATATA
1 ATATGAATATA
117240 ATATGAATATA
1 ATATGAATATA
117251 ATA
1 ATA
117254 ATTTAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
ATATGAATATA
Found at i:117821 original size:13 final size:13
Alignment explanation
Indices: 117803--117827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
117793 TTCAATGATT
117803 TGTATCGATACAA
1 TGTATCGATACAA
117816 TGTATCGATACA
1 TGTATCGATACA
117828 TAAGTGTTGT
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:117916 original size:13 final size:13
Alignment explanation
Indices: 117898--117956 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
117888 CATTATTCTA
117898 TGTATCGATACAT
1 TGTATCGATACAT
117911 TGTATCGATACA-
1 TGTATCGATACAT
*
117923 TG----GAT-CTT
1 TGTATCGATACAT
117931 TGTATCGATACAT
1 TGTATCGATACAT
117944 TGTATCGATACAT
1 TGTATCGATACAT
117957 GGATCTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 1 0.03
8 5 0.13
12 5 0.13
13 27 0.71
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:117922 original size:33 final size:33
Alignment explanation
Indices: 117880--117977 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
117870 CAAGGAAATA
* *
117880 TATCGATACAT-TATTCTATGTATCGATACATTG
1 TATCGATACATGGA-TCTTTGTATCGATACATTG
117913 TATCGATACATGGATCTTTGTATCGATACATTG
1 TATCGATACATGGATCTTTGTATCGATACATTG
117946 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTTTGTATCGATACATT
117978 TGGGAAGTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 61 0.98
34 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
TATCGATACATGGATCTTTGTATCGATACATTG
Found at i:117935 original size:20 final size:20
Alignment explanation
Indices: 117910--117976 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
117900 TATCGATACA
117910 TTGTATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
117930 TTGTATCGATAC----A---
1 TTGTATCGATACATGGATCT
117943 TTGTATCGATACATGGATCT
1 TTGTATCGATACATGGATCT
117963 TTGTATCGATACAT
1 TTGTATCGATACAT
117977 TTGGGAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.30
16 1 0.03
17 1 0.03
20 26 0.65
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATGGATCT
Found at i:120367 original size:51 final size:51
Alignment explanation
Indices: 120302--120427 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
120292 TTTCTCAATT
* * * * *
120302 TTTCTTAATTGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCTA-T
1 TTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACC
120352 TTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACC
1 TTT-CATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACC
*
120404 TTTCACAATCGGGGATACTCCAAC
1 TTTCATAATCGGGGATACTCCAAC
120428 CCCGTTATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.04
51 62 0.91
52 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
TTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACC
Found at i:120488 original size:40 final size:40
Alignment explanation
Indices: 120433--120508 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
120423 CCAACCCCGT
120433 TATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAA
1 TATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAA
120473 TATTTTCGAGGGGATACTCCAACCCCGGTTTTATTT
1 TATTTTCGAGGGGATACTCCAACCCCGGTTTTATTT
120509 TTAAAACACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (40 bp):
TATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAA
Found at i:120617 original size:31 final size:28
Alignment explanation
Indices: 120533--120606 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
120523 CTCCACAATC
*
120533 GGGGATACTCCAACCCCGTTA-TTTC-A
1 GGGGATACTCCAACCTCGTTATTTTCGA
120559 TCGGGGATACTCCAACCTCGTTATTTTCGA
1 --GGGGATACTCCAACCTCGTTATTTTCGA
120589 GGGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
120607 GCTTTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 38 0.88
29 4 0.09
30 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCTCGTTATTTTCGA
Found at i:120665 original size:51 final size:51
Alignment explanation
Indices: 120589--120706 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
120579 TTATTTTCGA
* *
120589 GGGGATACTCCAACCTCGGCTTTATTT-TCAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCT-AAAATATTGATTTCTCACAATC
* * *
120640 GGGGATACTTCAACCCCGGCCTTATTTCTACAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCACAATC
120691 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
120707 TTTTATTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCACAATC
Found at i:120805 original size:130 final size:130
Alignment explanation
Indices: 120558--120806 Score: 281
Period size: 130 Copynumber: 1.9 Consensus size: 130
120548 CCGTTATTTC
* * * *
120558 ATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCGGCTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCTCGTTATTTTCGAGGAGATACTCCAACCCCGACTTTATTTTCAAAAC
* * * *
120623 ATTGATTTCTCACAATCGGGGATACTTCAACCCCGGCCTTATTTCTACAATATTGATTTCTCATA
66 ATCGATTTCTCACAATCGGGGATACTTCAACCCCGGCCTTATCTCCAAAATATTGATTTCTCATA
* * * *
120688 ATCGGGGATACTCCAACC-CTTTTATTTTC-ACGGAGATACTTCAACCCCGATTTTATTTTTAAA
1 ATCGGGGATACTCCAACCTC-GTTATTTTCGA-GGAGATACTCCAACCCCGACTTTATTTTCAAA
* * ***
120751 ACATCGATTT-TCTATAATCGGGGATA-TTCCAGCCCCGTTGTTATCTCCAAAATATT
64 ACATCGATTTCTC-ACAATCGGGGATACTT-CAACCCCGGCCTTATCTCCAAAATATT
120807 AAATTTTTCA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
129 6 0.06
130 92 0.94
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.35
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCTCGTTATTTTCGAGGAGATACTCCAACCCCGACTTTATTTTCAAAAC
ATCGATTTCTCACAATCGGGGATACTTCAACCCCGGCCTTATCTCCAAAATATTGATTTCTCATA
Found at i:133175 original size:12 final size:12
Alignment explanation
Indices: 133158--133204 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
133148 CATTCTTTTT
133158 AAAAAAAAAACA
1 AAAAAAAAAACA
133170 AAAAAAAAAACA
1 AAAAAAAAAACA
133182 AAAAAAACAAA-A
1 AAAAAAA-AAACA
133194 AAAAGAAAAAA
1 AAAA-AAAAAA
133205 GAGAGAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 27 0.82
13 6 0.18
ACGTcount: A:0.91, C:0.06, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:133219 original size:1 final size:1
Alignment explanation
Indices: 133158--133204 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
133148 CATTCTTTTT
* * * *
133158 AAAAAAAAAACAAAAAAAAAAACAAAAAAAACAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
133205 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.91, C:0.06, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:134291 original size:55 final size:54
Alignment explanation
Indices: 134177--134438 Score: 373
Period size: 55 Copynumber: 4.7 Consensus size: 54
134167 TCCTTTCACT
134177 TTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACG-C---T--TTTCAAAGCCCACACAAGTTGGTGGCA-C
*
134238 TTTCAGTCCTCAAAGAGTAGGACGCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGGCA-C
* *
134293 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
134347 TTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTC-AGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGGCAC
134402 TTTCTAGTCCTCAAAGAGCAGGACGCCTTTT-AAAGCC
1 TTTC-AGTCCTCAAAGAGCAGGACG-CTTTTCAAAGCC
134439 TGTTGTAACG
Statistics
Matches: 194, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
54 4 0.02
55 161 0.83
56 4 0.02
57 1 0.01
60 1 0.01
61 23 0.12
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:134377 original size:27 final size:27
Alignment explanation
Indices: 134347--134431 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
134337 TTGGTGGCAT
134347 TTTCTAGTCCTCAAAGAGCAGGACGCC
1 TTTCTAGTCCTCAAAGAGCAGGACGCC
* * * * ** ** *
134374 TTTCAAAGCCCACACA-AGTTGGTGGCAT
1 TTTC-TAGTCCTCAAAGAGCAGGACGC-C
134402 TTTCTAGTCCTCAAAGAGCAGGACGCC
1 TTTCTAGTCCTCAAAGAGCAGGACGCC
134429 TTT
1 TTT
134432 TAAAGCCTGT
Statistics
Matches: 37, Mismatches: 18, Indels: 6
0.61 0.30 0.10
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (27 bp):
TTTCTAGTCCTCAAAGAGCAGGACGCC
Found at i:137563 original size:52 final size:51
Alignment explanation
Indices: 137485--137633 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
137475 CGAAACATGA
*
137485 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTAGGC
* *
137537 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTAGGC
**
137589 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
137634 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
Found at i:137640 original size:13 final size:13
Alignment explanation
Indices: 137622--137646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137612 CAAAGATCAG
137622 TGTATCGATACAA
1 TGTATCGATACAA
137635 TGTATCGATACA
1 TGTATCGATACA
137647 TTTAAGTGAT
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:137727 original size:13 final size:13
Alignment explanation
Indices: 137709--137733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137699 CAAAAAAATA
137709 TGTATCGATACAT
1 TGTATCGATACAT
137722 TGTATCGATACA
1 TGTATCGATACA
137734 AATCGTTGAA
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:138615 original size:58 final size:58
Alignment explanation
Indices: 138506--138615 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
138496 TGAAGAAAAA
* * **
138506 TGCCAATGTGCTGAGGCAAGGCCAGCGACATCGGGCTTAGGAATGTTAAAGATGAAGG
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATCGGACTTAAGAATGACAAAGATGAAGG
** *
138564 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA-AGATGACAAAGA
1 TGCCAATGTGCTGAGGCAAGGCCAGCGACATCGGACTTAAGA-ATGACAAAGA
138616 CGCCAATATG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 1 0.02
58 43 0.98
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (58 bp):
TGCCAATGTGCTGAGGCAAGGCCAGCGACATCGGACTTAAGAATGACAAAGATGAAGG
Found at i:138763 original size:32 final size:32
Alignment explanation
Indices: 138647--138781 Score: 161
Period size: 31 Copynumber: 4.3 Consensus size: 32
138637 CCAGCTATAT
* *
138647 TGGGC-TTA-GAAGGGTGGCCACCGACTTGTG
1 TGGGCTTTAGGAAGGGTTGCCACCAACTTGTG
**
138677 TGGGCTTTAGAGAATAGTTGCCACCAACTTGTG
1 TGGGCTTTAG-GAAGGGTTGCCACCAACTTGTG
*
138710 TGGCCTTTGAGG--GGGTTGCCACCAACTTGTG
1 TGGGCTTT-AGGAAGGGTTGCCACCAACTTGTG
* *
138741 TGGGCTTTAGGAAGGGTTGCCACCGACTAGTG
1 TGGGCTTTAGGAAGGGTTGCCACCAACTTGTG
138773 TGGGCTTTA
1 TGGGCTTTA
138782 AAAAGGGTGA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
30 8 0.09
31 27 0.30
32 26 0.29
33 26 0.29
34 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGGAAGGGTTGCCACCAACTTGTG
Found at i:138788 original size:32 final size:32
Alignment explanation
Indices: 138656--138789 Score: 135
Period size: 32 Copynumber: 4.2 Consensus size: 32
138646 TTGGGCTTAG
* * *
138656 AAGGGTGGCCACCGACTTGTGTGGGCTTTAGAG
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTA-AA
** * *
138689 AATAGTTGCCACCAACTTGTGTGGCCTTT-GA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAA
** **
138720 GGGGGTTGCCACCAACTTGTGTGGGCTTTAGG
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAA
* *
138752 AAGGGTTGCCACCGACTAGTGTGGGCTTTAAA
1 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAA
138784 AAGGGT
1 AAGGGT
138790 GAAAGATGCC
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
31 24 0.30
32 33 0.41
33 24 0.30
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (32 bp):
AAGGGTTGCCACCAACTTGTGTGGGCTTTAAA
Found at i:138877 original size:36 final size:35
Alignment explanation
Indices: 138791--138954 Score: 175
Period size: 36 Copynumber: 4.9 Consensus size: 35
138781 AAAAAGGGTG
*
138791 AAAGA-TGCCACGAAGTTGTGGAC-TTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* *
138824 TAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAA-GGAA
* *
138859 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
* *
138891 -AAG-GTGCCACGGAGTCGTGGAC-TTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
*
138923 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTT-AAAA
138955 AGATGCCACT
Statistics
Matches: 108, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
29 4 0.04
30 18 0.17
31 3 0.03
33 24 0.22
34 24 0.22
35 9 0.08
36 26 0.24
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (35 bp):
AAAGAGTGCCACGGAGTTGTGGACTTTAAAAGGAA
Found at i:138937 original size:64 final size:65
Alignment explanation
Indices: 138825--138963 Score: 219
Period size: 64 Copynumber: 2.2 Consensus size: 65
138815 TAAAAGGAAT
*
138825 AAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
1 AAGGTGCCACGAAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
* *
138890 GAAGGTGCCACGGAGTCGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 -AAGGTGCCACGAAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
138953 A
65 A
*
138954 AAGATGCCAC
1 AAGGTGCCAC
138964 TGACTTGTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
63 9 0.13
64 35 0.51
65 5 0.07
66 20 0.29
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.19
Consensus pattern (65 bp):
AAGGTGCCACGAAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA
Found at i:138957 original size:66 final size:68
Alignment explanation
Indices: 138772--138957 Score: 213
Period size: 64 Copynumber: 2.8 Consensus size: 68
138762 ACCGACTAGT
* ** * * * *
138772 GTGGGCTTTAAAAAGGGTGAAAGA-TGCCACGAAGTTGTGGAC-TTAAAAGGAATAAGGTGCCAC
1 GTGGACTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAA--AAGAAGGTGCCAC
*
138835 GAAGTT
63 GAAGTC
*
138841 GTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG--AAAGAAGGTGCCACGGA
1 GTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAGAAGGTGCCACGAA
138904 GTC
66 GTC
*
138907 GTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
1 GTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
138958 TGCCACTGAC
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
64 32 0.31
65 5 0.05
66 27 0.26
68 13 0.13
69 24 0.23
70 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (68 bp):
GTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAGAAGGTGCCACGAA
GTC
Found at i:138971 original size:29 final size:30
Alignment explanation
Indices: 138856--138978 Score: 142
Period size: 30 Copynumber: 4.0 Consensus size: 30
138846 CTTTAAAAGG
138856 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* * *
138886 GAAAGAAG-GTGCCACGGAGTCGTGGACTTAGAAG
1 GAAA-AAGAGTGCCACGGAGTTGTGGGCTT----T
138920 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
138950 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
138979 TGAAGGGTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
29 19 0.24
30 31 0.39
31 3 0.04
33 3 0.04
34 23 0.29
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (30 bp):
GAAAAAGAGTGCCACGGAGTTGTGGGCTTT
Found at i:152397 original size:51 final size:51
Alignment explanation
Indices: 152337--152457 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
152327 CAATTTTTCT
* * *
152337 TAATCGGGGATACTCTAACTCCGATTTTATTTCTAAAACACCTA-TATTCCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACT-TTCCA
* *
152388 TAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAACACCGACTTTTCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACTTTCCA
*
152439 CAATCGGGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
152458 CCCGTTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 62 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACTTTCCA
Found at i:152524 original size:79 final size:79
Alignment explanation
Indices: 152392--152567 Score: 234
Period size: 79 Copynumber: 2.2 Consensus size: 79
152382 ATTCCATAAT
* * * *
152392 CGGGGATACTCCAA-CTCTGATTTTATTTCCAAAACACCGACTTTTCACAATCGGGGATACTCCA
1 CGGGGATACTCCAACCCCAGATTTTATTTCCAAAACACCGAATTTCCACAATCGGGGATACTCCA
152456 ACCCCGTTATTTTCGA
66 ACCCCGTTA-TTTC-A
* *
152472 -GGGGATACTCCAACCCCAG-TTTTATTTCTAAAACACC-AATTCTCCACAATCGGGGATACTCT
1 CGGGGATACTCCAACCCCAGATTTTATTTCCAAAACACCGAATT-TCCACAATCGGGGATACTCC
152534 AACCCCGTTATTTCA
65 AACCCCGTTATTTCA
152549 TCGGGGATACTCCAACCCC
1 -CGGGGATACTCCAACCCC
152568 GTTATTTTTG
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
77 1 0.01
78 7 0.08
79 75 0.87
80 3 0.03
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCAGATTTTATTTCCAAAACACCGAATTTCCACAATCGGGGATACTCCA
ACCCCGTTATTTCA
Found at i:152560 original size:28 final size:27
Alignment explanation
Indices: 152520--152596 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 27
152510 ATTCTCCACA
*
152520 ATCGGGGATACTCTAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
152547 CATCGGGGATACTCCAACCCCGTTATTT
1 -ATCGGGGATACTCCAACCCCGTTATTT
* *
152575 TTGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
152597 GCTTTATTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTT
Found at i:152627 original size:107 final size:107
Alignment explanation
Indices: 152441--152647 Score: 301
Period size: 107 Copynumber: 1.9 Consensus size: 107
152431 ACTTTTCACA
* *
152441 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAAC
*
152506 ACCAATTCTCCACAATCGGGGATA-CTCTAACCCCGTTATTTC
66 ACCAATTCTCCACAATCGAGGATACCTC-AACCCCGTTATTTC
* * *
152548 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAAC
***
152613 ATTGATT-TCTCACAATCGAGGATACCTCAACCCCG
66 ACCAATTCTC-CACAATCGAGGATACCTCAACCCCG
152648 GCCTTATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
106 2 0.02
107 84 0.94
108 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (107 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAAC
ACCAATTCTCCACAATCGAGGATACCTCAACCCCGTTATTTC
Found at i:152644 original size:51 final size:51
Alignment explanation
Indices: 152581--152696 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
152571 ATTTTTGAGG
*
152581 GGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCGA
1 GGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCGA
* * *
152632 GGATAC-CTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATCGG
1 GGATACTC-CAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCGA
152683 GGATACTCCAACCC
1 GGATACTCCAACCC
152697 TATTATTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCGGCCTTATTTCCAAAATATTGATTTCTCACAATCGA
Found at i:152793 original size:130 final size:130
Alignment explanation
Indices: 152548--152796 Score: 281
Period size: 130 Copynumber: 1.9 Consensus size: 130
152538 CCGTTATTTC
* * * *
152548 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTTCAGGGGATACTCCAACCCCGGATTTATTTCCAAAAC
* * *
152613 ATTGATTTCTCACAATCGAGGATACCTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATA
66 ATCGATTTCTCACAATCGAGGATACCTCAACCCCGGCCTTATCTCCAAAATATTGATTTCTCATA
* * **
152678 ATCGGGGATACTCCAACCCTATTA-TTTTCACGGGGATACTCCAACCTC-GATTGTATTTTTAAA
1 ATCGGGGATACTCCAACCCCATTATTTTTCA-GGGGATACTCCAACCCCGGATT-TATTTCCAAA
* * * ***
152741 ACATCGATTT-TCTATAATCGGGGATA-CTCCAGCCCCGTTGTTATCTCCAAAATATT
64 ACATCGATTTCTC-ACAATCGAGGATACCT-CAACCCCGGCCTTATCTCCAAAATATT
152797 AAATTTTTCA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
129 12 0.12
130 86 0.88
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCATTATTTTTCAGGGGATACTCCAACCCCGGATTTATTTCCAAAAC
ATCGATTTCTCACAATCGAGGATACCTCAACCCCGGCCTTATCTCCAAAATATTGATTTCTCATA
Found at i:163090 original size:20 final size:20
Alignment explanation
Indices: 163067--163123 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
163057 AAGTACCCAG
*
163067 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTCA
163087 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
163107 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
163124 ATCTTTTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:177151 original size:20 final size:21
Alignment explanation
Indices: 177123--177165 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
177113 TGTCCTCCAT
*
177123 ACAAAAAAAAACAAAGAAAAA
1 ACAAAAAAAACCAAAGAAAAA
*
177144 ACAAAAAAAACCAAGGAAAAA
1 ACAAAAAAAACCAAAGAAAAA
177165 A
1 A
177166 ATAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
ACAAAAAAAACCAAAGAAAAA
Found at i:178448 original size:28 final size:28
Alignment explanation
Indices: 178405--178487 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
178395 CGTTCATCTC
*
178405 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
178433 TTCAAAACCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
178461 TTCAAAGCCCACAAGTCAGTGGCACCC
1 TTCAAAGCCCACAAGTCAGTGGCACCC
178488 ACAAGTCAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:178490 original size:17 final size:17
Alignment explanation
Indices: 178468--178501 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
178458 CCTTTCAAAG
178468 CCCACAAGTCAGTGGCA
1 CCCACAAGTCAGTGGCA
178485 CCCACAAGTCAGTGGCA
1 CCCACAAGTCAGTGGCA
178502 TCCTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (17 bp):
CCCACAAGTCAGTGGCA
Found at i:178507 original size:45 final size:45
Alignment explanation
Indices: 178439--178532 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
178429 CCCTTTCAAA
178439 ACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
* *
178484 ACCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
1 ACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
178529 ACCC
1 ACCC
178533 TTTCAAAACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (45 bp):
ACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:178526 original size:28 final size:28
Alignment explanation
Indices: 178485--178913 Score: 606
Period size: 28 Copynumber: 15.2 Consensus size: 28
178475 GTCAGTGGCA
178485 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
178513 CCCACAAGTTAGTGGCACCCTTTCAAAA
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
178541 CCCACAAGTCAATGGCATCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
178569 CCTACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
178597 CCCACGAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
178625 CCCACAAGTTAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
178653 CCCACGAGACAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* *
178681 CCCACGAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
178709 CCCACGAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
178737 CCCACGAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
178765 CCCACGAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
178793 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
* * *
178821 CCCACACAAGTCAGTGACACTCTTTTTAAAG
1 -CC-CACAAGTCAGTGGCA-TCCTTTCAAAG
* * *
178852 CCCACAAGTTAATGGCCTCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
*
178880 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTTCAAAG
178908 CCCACA
1 CCCACA
178914 CAAGTTGGTG
Statistics
Matches: 361, Mismatches: 37, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
28 323 0.89
29 13 0.04
30 16 0.04
31 9 0.02
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCATCCTTTCAAAG
Found at i:179804 original size:20 final size:20
Alignment explanation
Indices: 179779--179855 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
179769 AAGTACCCAG
*
179779 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTCA
* *
179799 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
179819 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
179839 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
179856 ATCTTTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:187944 original size:21 final size:21
Alignment explanation
Indices: 187891--187952 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
187881 AGGTAAAAAA
* *
187891 CCTAGAATGTATCGATCCATT
1 CCTAGAATGTATCGATACAAT
** *
187912 GAT-GATTGTATCGATACAAT
1 CCTAGAATGTATCGATACAAT
*
187932 CCTAGAATGTATCGAAACAAT
1 CCTAGAATGTATCGATACAAT
187953 TGCTTAAGTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTAGAATGTATCGATACAAT
Found at i:195076 original size:62 final size:62
Alignment explanation
Indices: 194988--195654 Score: 539
Period size: 62 Copynumber: 10.7 Consensus size: 62
194978 TAACACCTTT
* * * * **
194988 TTTTTAAAGCCCACAC-ACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGGATGTTTTTTTC
1 TTTTTAAAGCCCACACGA-GTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
* * **
195050 TTTTTAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTTAAAGAGTAGGACACCTTTTT-
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
* * * **** *
195111 TTTTCAAAG-TC-CACGACTCCCCGGCACCCCTTTTAAACTTTTAGTCTTCAAAGA-TCAGGATG
1 TTTTTAAAGCCCACACGAGTTGGTGGCA---C-------CTTTTAGTCCTCAAAGAGT-AGGATG
*
195173 CCTTTTCC
55 CCTTTTTC
* * ** *
195181 TTTTTAAAGTCCATATAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGTAGGATGCCTTTCTC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGTAGGATGCCTTTTTC
* * * * *
195243 TTTTCAAAGCGCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCTAGGACGTCTTTTCC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAG-TAGGATGCCTTTTTC
* * * ** * *
195306 TTTTTAAAGCCCACACGAGTTGGCGGCACCCTTTAGTCCTCAAAGAGCAAAACGTCTTTCTT-
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTT-TTC
* * * * * * *
195368 TTTTCAAAGCCCACACAAGTTGGTGGCA-ATTTT-TTTCTCAAAGAGCAGGACGCCTTTTTC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
* * *
195428 -TTTTAAAGCCCACACGAGTTGGTGGTAACTTTTAGTCCTCAAAGAGTAGGATACCTTTTTC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
* * * *
195489 TTTTTAAAGCCTACACGAGTTAGTGGCAACTCTTAG-CCTTCAAAGAGTAGGATGCCTTTTTC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCC-TCAAAGAGTAGGATGCCTTTTTC
* * * ** * * **
195551 -TTTTAAAACCCATACGAGTTGGTGGAAATTTTTAGTCTTCAAAGAGCAGGATGTTTTTTTC
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
* * * *
195612 CTTTCAAAGCCCACACGAGTTGGTGGCGCTTTTTAGTCCTCAA
1 TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAA
195655 GAAATAGGAC
Statistics
Matches: 482, Mismatches: 96, Indels: 54
0.76 0.15 0.09
Matches are distributed among these distances:
59 36 0.07
60 23 0.05
61 88 0.18
62 231 0.48
63 62 0.13
68 1 0.00
69 25 0.05
70 8 0.02
71 1 0.00
72 7 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (62 bp):
TTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTC
Found at i:195663 original size:123 final size:123
Alignment explanation
Indices: 194985--195664 Score: 488
Period size: 123 Copynumber: 5.5 Consensus size: 123
194975 GAATAACACC
* * * * **
194985 TTTT-TTTT-AAAGCCCACAC-ACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGGATGTTTTT
1 TTTTCTTTTCAAAGCCCACACGA-GTTGGTGGCACTTTTTAGTCCTC-AAAAATAGGACGCCTTT
* * * * * **
195047 TTCTTTTTAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTTAAAGAGTAGGACACCT
64 TCCTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGGATGCCT
* * **** * *
195107 TTTT-TTTTCAAAG-TC-CACGACTCCCCGGCACCCCTTTTAAACTTTTAGTCTTCAAAGATCAG
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA---C---T----TTTTAGTCCTCAAAAAT-AG
* * * ** *
195169 GATGCCTTTTCCTTTTTAAAGTCCATATAAGTTGGTGGC-ACTTTTCAGTCCTCAAAGAGTAGGA
55 GACGCCTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTT-AGTCCTCAAAGAGCAGGA
195233 TGCCT
119 TGCCT
* * * * *
195238 TTCTCTTTTCAAAGCGCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCTAGGACGTCTTT
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAA-A-ATAGGACGCCTTT
* * * ** * *
195303 TCCTTTTTAAAGCCCACACGAGTTGGCGGCACCCTTTAGTCCTCAAAGAGCAAAACGTCT
64 TCCTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * **
195363 TTCTT-TTTTCAAAGCCCACACAAGTTGGTGGCAATTTTT--TTCTCAAAGAGCAGGACGCCTTT
1 TT-TTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAA-AATAGGACGCCTTT
* * * *
195425 TTC-TTTTAAAGCCCACACGAGTTGGTGGTAACTTTTAGTCCTCAAAGAGTAGGATACCT
64 TCCTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGGATGCCT
* * * * * *
195484 TTTTCTTTTTAAAGCCTACACGAGTTAGTGGCAAC-TCTTAG-CCTTCAAAGAGTAGGATGCCTT
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGC-ACTTTTTAGTCC-TCAAA-AATAGGACGCCTT
* * * * * * **
195547 TTTC-TTTTAAAACCCATACGAGTTGGTGGAAATTTTTAGTCTTCAAAGAGCAGGATGTTT
63 TTCCTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGGATGCCT
* *
195607 TTTTCCTTTCAAAGCCCACACGAGTTGGTGGCGCTTTTTAGTCCTCAAGAAATAGGAC
1 TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAA-AAATAGGAC
195665 ACTTTCCTCA
Statistics
Matches: 437, Mismatches: 92, Indels: 57
0.75 0.16 0.10
Matches are distributed among these distances:
120 2 0.00
121 82 0.19
122 25 0.06
123 124 0.28
124 17 0.04
125 84 0.19
126 6 0.01
130 10 0.02
131 67 0.15
132 9 0.02
133 1 0.00
134 10 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (123 bp):
TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAAATAGGACGCCTTTTC
CTTTTTAAAGCCCACACGAGTTGGTGGCAACTTTTAGTCCTCAAAGAGCAGGATGCCT
Found at i:195790 original size:41 final size:42
Alignment explanation
Indices: 195716--195804 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 42
195706 ATGACGCAAT
* *
195716 TTTATTTTCTTTTCTCTTTTGTCCTTAAAGAGTAGAACACAC
1 TTTATTTCCTTTTCTCTTTTGTCCTCAAAGAGTAGAACACAC
* * *
195758 TTTATTTCCTTTTTTC-TTTGTCCTCAAAGAGTAGGACGCAC
1 TTTATTTCCTTTTCTCTTTTGTCCTCAAAGAGTAGAACACAC
195799 TTTATT
1 TTTATT
195805 CCCTCATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 28 0.67
42 14 0.33
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.48
Consensus pattern (42 bp):
TTTATTTCCTTTTCTCTTTTGTCCTCAAAGAGTAGAACACAC
Found at i:196073 original size:62 final size:61
Alignment explanation
Indices: 195993--196171 Score: 227
Period size: 62 Copynumber: 2.9 Consensus size: 61
195983 AAAGAGAATA
195993 ACACC-TTTTTTTTTAAAGCCCACACACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGG
1 ACACCTTTTTTTTTTAAAGCCCACACACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGG
**** * * * * * *
196053 ATGTTTTTTTCTTTTTAAAGCCTACACGA-GTTGGTGGCACCTTTTAGTCCTTAAAGAGTAGG
1 ACACCTTTTT-TTTTTAAAGCCCACAC-ACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGG
*
196115 ACACCTTTTTTTTTCAAAGCCCACACACATTAGTGGCACCTTTTAGTCCTCAAAAAA
1 ACACCTTTTTTTTTTAAAGCCCACACACATTAGTGGCACCTTTTAGTCCTCAAAAAA
196172 ATGGATTTTT
Statistics
Matches: 94, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
60 2 0.02
61 42 0.45
62 49 0.52
63 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (61 bp):
ACACCTTTTTTTTTTAAAGCCCACACACATTAGTGGCACCTTTTAGTCCTCAAAAAATAGG
Found at i:196451 original size:13 final size:13
Alignment explanation
Indices: 196433--196457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196423 ATTACTCAAA
196433 TGTATCGATACAT
1 TGTATCGATACAT
196446 TGTATCGATACA
1 TGTATCGATACA
196458 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:196561 original size:52 final size:52
Alignment explanation
Indices: 196466--196593 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
196456 CACTGATCTT
* *
196466 TGTATCGATACACGCAGCCAAA-TTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
196517 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
196569 TGTATCGATATATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
196594 TCATATTTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 20 0.27
52 53 0.73
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:199274 original size:17 final size:17
Alignment explanation
Indices: 199252--199287 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
199242 CATTTCATAT
* *
199252 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
199269 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
199286 TT
1 TT
199288 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:199382 original size:19 final size:20
Alignment explanation
Indices: 199354--199394 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
199344 AAACCGGCGA
*
199354 CCGGCCACCA-CGTCGGTCG
1 CCGGCCACCACCGTCGGCCG
*
199373 CCGGCGACCACCGTCGGCCG
1 CCGGCCACCACCGTCGGCCG
199393 CC
1 CC
199395 ACTCAACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.10, C:0.51, G:0.32, T:0.07
Consensus pattern (20 bp):
CCGGCCACCACCGTCGGCCG
Found at i:200575 original size:32 final size:32
Alignment explanation
Indices: 200526--201159 Score: 1056
Period size: 32 Copynumber: 19.8 Consensus size: 32
200516 AAAATAGTGA
* * *
200526 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
200558 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200590 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
200622 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200654 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200686 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
200718 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
200750 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
200782 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200814 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200846 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200878 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200910 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200942 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
200974 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
201006 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
201038 TTTGGAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
201070 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
201102 TTTGAAATGGGTTGCCACTGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
201134 TTTGAAATGGG-TGCCACGGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
201160 GATTTAAAAG
Statistics
Matches: 578, Mismatches: 22, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
31 14 0.02
32 563 0.97
33 1 0.00
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:201176 original size:27 final size:27
Alignment explanation
Indices: 201145--201571 Score: 508
Period size: 27 Copynumber: 15.6 Consensus size: 27
201135 TTGAAATGGG
201145 TGCCACGGAGTTGTGGATTTAAAAGGA
1 TGCCACGGAGTTGTGGATTTAAAAGGA
* *
201172 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGATTTAAAAGGA
* *
201199 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGATTTAAAAGGA
201226 TGCCACGGAGTTGTGG-TCTTAAAAGGGA
1 TGCCACGGAGTTGTGGAT-TTAAAA-GGA
* *
201254 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGATTTAAAAGGA
* *
201281 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGATTTAAAAGGA
**
201308 TGCCACGGAGTTGTGGGCTTAAAA-GA
1 TGCCACGGAGTTGTGGATTTAAAAGGA
*
201334 GTGCCACGGAGTTGTGGACTTAAAAAGG-
1 -TGCCACGGAGTTGTGGA-TTTAAAAGGA
* *
201362 TGCTACGGAGTTGTGGACTTTAAAA-AA
1 TGCCACGGAGTTGTGGA-TTTAAAAGGA
* *
201389 GTGCCACGGAGTTGTGGACTTT-GAAGGG
1 -TGCCACGGAGTTGTGGA-TTTAAAAGGA
* *
201417 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGATTTAAAAGGA
*
201444 TGTCACGGAGTTGTGGACTTTAAAA-GA
1 TGCCACGGAGTTGTGGA-TTTAAAAGGA
201471 GTGCCACGGAGTTGTGGACTTTAAAA-GA
1 -TGCCACGGAGTTGTGGA-TTTAAAAGGA
*
201499 GTGCCACGGAGTTGTGGATTTAAAAGGG
1 -TGCCACGGAGTTGTGGATTTAAAAGGA
**
201527 TGCCACAAAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGA-TTTAAAAGGA
201555 TGCCACGGAGTTGTGGA
1 TGCCACGGAGTTGTGGA
201572 CTTCAAAAAG
Statistics
Matches: 356, Mismatches: 30, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.01
27 228 0.64
28 124 0.35
29 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGATTTAAAAGGA
Found at i:201277 original size:82 final size:82
Alignment explanation
Indices: 201127--201579 Score: 676
Period size: 82 Copynumber: 5.5 Consensus size: 82
201117 CACTGACTTG
* * * *
201127 TGTGGGCTTTGAAATGGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTT
1 TGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT
201192 AAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGT
*
201210 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTT
201274 AAAAGGGTGCCACGGAGT
65 AAAAGGGTGCCACGGAGT
* *
201292 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
* *
201356 AAAAGGTGCTACGGAGT
66 AAAGGGTGCCACGGAGT
** **
201373 TGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTTGTGGACTTA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
*
201438 AAAGGGTGTCACGGAGT
66 AAAGGGTGCCACGGAGT
* * *
201455 TGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT
**
201520 AAAAGGGTGCCACAAAGT
65 AAAAGGGTGCCACGGAGT
*
201538 TGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTCAAAA
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAA
201580 AGAAATGCCA
Statistics
Matches: 338, Mismatches: 28, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
81 73 0.22
82 182 0.54
83 83 0.25
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.25
Consensus pattern (82 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
AAAGGGTGCCACGGAGT
Found at i:201279 original size:55 final size:54
Alignment explanation
Indices: 201142--201579 Score: 660
Period size: 55 Copynumber: 8.0 Consensus size: 54
201132 GCTTTGAAAT
* *
201142 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
201196 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
201250 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* *
201305 GGGTGCCACGGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* * ** **
201359 AGGTGCTACGGAGTTGTGGACTTTAAAAAAGTGCCACGGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
201414 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGTCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
201469 GAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
** *
201524 GGGTGCCACAAAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAA
201580 AGAAATGCCA
Statistics
Matches: 350, Mismatches: 29, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
54 145 0.41
55 177 0.51
56 28 0.08
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (54 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:209408 original size:17 final size:17
Alignment explanation
Indices: 209386--209421 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
209376 CATTTCATAT
* *
209386 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
209403 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
209420 TT
1 TT
209422 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:209517 original size:19 final size:20
Alignment explanation
Indices: 209489--209529 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
209479 AAACCGGCGA
*
209489 CCGGCCACCA-CGTCGGTCG
1 CCGGCCACCACCGTCGGCCG
*
209508 CCGGCGACCACCGTCGGCCG
1 CCGGCCACCACCGTCGGCCG
209528 CC
1 CC
209530 ACTCAACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.10, C:0.51, G:0.32, T:0.07
Consensus pattern (20 bp):
CCGGCCACCACCGTCGGCCG
Found at i:213400 original size:44 final size:40
Alignment explanation
Indices: 213341--213527 Score: 149
Period size: 42 Copynumber: 4.7 Consensus size: 40
213331 AGACGTACTC
213341 CTTTTTT--TTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCT
1 CTTTTTTCCTTTGTCCTCAAAGAGCAGGAC-CA-TTCATTT--T
* * * *
213383 CCTTTTCCCTTTGTCCTC-AAGTAGCAAGACACATTCCTTTTT
1 CTTTTTTCCTTTGTCCTCAAAG-AGCAGGAC-CATT-CATTTT
* *
213425 CTTTTTTTCCTTCGTCCTCAAGGAGCAGGACCTATTTCATTTT
1 C-TTTTTTCCTTTGTCCTCAAAGAGCAGGACC-A-TTCATTTT
*
213468 CTTTTTTCCTTTGTCCTCGAAGAGCAGGA-CA-T-A--TT
1 CTTTTTTCCTTTGTCCTCAAAGAGCAGGACCATTCATTTT
*
213503 C-CTTTTCCTTTGTCCTCAAAGAGCA
1 CTTTTTTCCTTTGTCCTCAAAGAGCA
213528 AGGCGCCCTA
Statistics
Matches: 121, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
34 22 0.18
35 3 0.02
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
42 33 0.27
43 33 0.27
44 26 0.21
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.41
Consensus pattern (40 bp):
CTTTTTTCCTTTGTCCTCAAAGAGCAGGACCATTCATTTT
Found at i:213493 original size:42 final size:41
Alignment explanation
Indices: 213341--213498 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 41
213331 AGACGTACTC
* *
213341 CTTTTTT--TTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCT
1 CTTTTTTCCTTTGTCCTC-AAGAGCAGGACACATTTCATTT--T
* * * * *
213383 CCTTTTCCCTTTGTCCTCAAGTAGCAAGACACATTCCTTTTT
1 CTTTTTTCCTTTGTCCTCAAG-AGCAGGACACATTTCATTTT
*
213425 CTTTTTTTCCTTCGTCCTCAAGGAGCAGGAC-CTATTTCATTTT
1 C-TTTTTTCCTTTGTCCTCAA-GAGCAGGACAC-ATTTCATTTT
213468 CTTTTTTCCTTTGTCCTCGAAGAGCAGGACA
1 CTTTTTTCCTTTGTCCTC-AAGAGCAGGACA
213499 TATTCCTTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
42 33 0.35
43 37 0.39
44 24 0.26
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (41 bp):
CTTTTTTCCTTTGTCCTCAAGAGCAGGACACATTTCATTTT
Found at i:213506 original size:85 final size:86
Alignment explanation
Indices: 213339--213513 Score: 218
Period size: 85 Copynumber: 2.1 Consensus size: 86
213329 CAAGACGTAC
213339 TCCTTTTTTT--TT-GTCCTCAAAGAGCAGGACGCACTTCATTTCCTCCTTTTCCCTTTGTCCTC
1 TCCTTTTTTTCCTTCGTCCTCAAAGAGCAGGACGCACTTCATTT-CTCCTTTTCCCTTTGTCCTC
213401 AAGTAGCAAGACACATTCCTTT
65 AAGTAGCAAGACACATTCCTTT
* * * * *
213423 TTCTTTTTTTCCTTCGTCCTCAAGGAGCAGGAC-CTATTTCATTT-TCTTTTTTCCTTTGTCCTC
1 TCCTTTTTTTCCTTCGTCCTCAAAGAGCAGGACGC-ACTTCATTTCTCCTTTTCCCTTTGTCCTC
* *
213486 GAAG-AGCAGGACATATTCCTTT
65 -AAGTAGCAAGACACATTCCTTT
213508 TCCTTT
1 TCCTTT
213514 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
84 9 0.12
85 38 0.49
86 6 0.08
87 25 0.32
ACGTcount: A:0.17, C:0.27, G:0.13, T:0.43
Consensus pattern (86 bp):
TCCTTTTTTTCCTTCGTCCTCAAAGAGCAGGACGCACTTCATTTCTCCTTTTCCCTTTGTCCTCA
AGTAGCAAGACACATTCCTTT
Found at i:214330 original size:19 final size:19
Alignment explanation
Indices: 214243--214339 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 19
214233 CTGCCAAGGA
** *
214243 AATGTATCGATACATAAGTA
1 AATGTATCGATACAT-TCTC
214263 AATGTATCGATACATT-TAC
1 AATGTATCGATACATTCT-C
* * * *
214282 TATTTATATTGATACATTTTTC
1 -A-ATGTATCGATACA-TTCTC
*
214304 ATTGTATCGATACATTCTC
1 AATGTATCGATACATTCTC
*
214323 AATGTATCGATATATTC
1 AATGTATCGATACATTC
214340 AAGCATTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
18 1 0.02
19 19 0.31
20 27 0.44
21 11 0.18
22 3 0.05
23 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (19 bp):
AATGTATCGATACATTCTC
Found at i:216813 original size:79 final size:78
Alignment explanation
Indices: 216680--217046 Score: 330
Period size: 79 Copynumber: 4.7 Consensus size: 78
216670 TCATTGATGT
*
216680 TTTTATTTCTAAAATATCGATTTTCTACCATCGGAGATACTCCAACCCCGTTATTTTTGAGGGGA
1 TTTTATTTCTAAAATATCGATTTTCTACCATCGGAGATACTCCAACCCCATTATTTTTGAGGGGA
*
216745 TACTCCAACTCTGA
66 TACTCCAAC-CCGA
* * *
216759 TTTTATTTCTAAAATATCTATTTTCTATCATCGGAGATACTCCAACTCCATTATTTTTGAGGGGA
1 TTTTATTTCTAAAATATCGATTTTCTACCATCGGAGATACTCCAACCCCATTATTTTTGAGGGGA
*
216824 TACTCCAACCCGG
66 TACTCCAACCCGA
* * * * ** *
216837 TTTTATTTCGAAAACA-CTGATTTT-TCACCATC-AAGGATACTCTAACCCTGTTATTTTTGAAG
1 TTTTATTTCTAAAATATC-GATTTTCT-ACCATCGGA-GATACTCCAACCCCATTATTTTTGAGG
* * **
216899 AGATACTCAAATCCTAA
63 GGATACTCCAA-CCCGA
* * * * * ** * *
216916 TTTTATTTATAAAACACCGATTTT-TCACCATCGGGGAAACTCCAACCCTGTTATTTTCGAAGGG
1 TTTTATTTCTAAAATATCGATTTTCT-ACCATCGGAGATACTCCAACCCCATTATTTTTGAGGGG
*
216980 ATATTCCAACCCCGA
65 ATACTCCAA-CCCGA
* * * * * *
216995 TTTTGTTTCCAAAATATCAACTTTTC-ACCATTGGGGATACTCTAACCCCATT
1 TTTTATTTCTAAAATATCGA-TTTTCTACCATCGGAGATACTCCAACCCCATT
217047 TTTATTTCTA
Statistics
Matches: 235, Mismatches: 45, Indels: 16
0.79 0.15 0.05
Matches are distributed among these distances:
77 3 0.01
78 57 0.24
79 170 0.72
80 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (78 bp):
TTTTATTTCTAAAATATCGATTTTCTACCATCGGAGATACTCCAACCCCATTATTTTTGAGGGGA
TACTCCAACCCGA
Found at i:217032 original size:51 final size:51
Alignment explanation
Indices: 216977--217137 Score: 191
Period size: 51 Copynumber: 3.2 Consensus size: 51
216967 TATTTTCGAA
* * *
216977 GGGATATTCCAACCCCGA-TTTTGTTTCCAAAATATCAACTTT-TCACCATTG
1 GGGATACTCCAACCCC-ATTTTTATTTCCAAAATATCAA-TTTATCACCATCG
* *
217028 GGGATACTCTAACCCCATTTTTATTTCTAAAATATCAATTTATCACCATCG
1 GGGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTATCACCATCG
* * ** *
217079 GGAATACTCCAACCCCATTTTTATTTTCAAAATATTGATTTCTCACCATCG
1 GGGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTATCACCATCG
*
217130 GAGATACT
1 GGGATACT
217138 TCAATTCCAT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 4 0.04
51 90 0.96
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (51 bp):
GGGATACTCCAACCCCATTTTTATTTCCAAAATATCAATTTATCACCATCG
Found at i:220549 original size:3 final size:3
Alignment explanation
Indices: 220537--220580 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
220527 GTGAATTTTA
220537 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
220581 GCTGTCGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:221257 original size:3 final size:3
Alignment explanation
Indices: 221249--221274 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
221239 TTCGGAAACT
221249 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
221275 CGACGATGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:224840 original size:26 final size:23
Alignment explanation
Indices: 224793--224850 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
224783 AAGTGGGAGG
*
224793 AAGATTTTGTTGTCTTTGACTAC
1 AAGATTTTGTTGTCCTTGACTAC
224816 AAGATTTTGTTGTCCTTGACTAC
1 AAGATTTTGTTGTCCTTGACTAC
*
224839 TAGATTTTGTTG
1 AAGATTTTGTTG
224851 GGGTAGTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (23 bp):
AAGATTTTGTTGTCCTTGACTAC
Found at i:225156 original size:163 final size:163
Alignment explanation
Indices: 224886--225214 Score: 640
Period size: 163 Copynumber: 2.0 Consensus size: 163
224876 GGCCAAAAGG
224886 AATAGTACGTATTGCTAGGACGATAAAATCTCATTTCAATGACTATAGTTGTAGCAAGATGGGGC
1 AATAGTACGTATTGCTAGGACGATAAAATCTCATTTCAATGACTATAGTTGTAGCAAGATGGGGC
224951 CAAATGGCTGATTGGCTTGGTTACTCATATGAGAGAATTGCTTGCCAGTCAAATCGGCTTCTGGT
66 CAAATGGCTGATTGGCTTGGTTACTCATATGAGAGAATTGCTTGCCAGTCAAATCGGCTTCTGGT
*
225016 CATTAGCTATCATATTTGGTTGTAGGTGAGTGA
131 CATTAGCTATCATATTTGGTTGTAGGAGAGTGA
*
225049 AATAGTACGTATTGCTAGGATGATAAAATCTCATTTCAATGACTATAGTTGTAGCAAGATGGGGC
1 AATAGTACGTATTGCTAGGACGATAAAATCTCATTTCAATGACTATAGTTGTAGCAAGATGGGGC
225114 CAAATGGCTGATTGGCTTGGTTACTCATATGAGAGAATTGCTTGCCAGTCAAATCGGCTTCTGGT
66 CAAATGGCTGATTGGCTTGGTTACTCATATGAGAGAATTGCTTGCCAGTCAAATCGGCTTCTGGT
225179 CATTAGCTATCATATTTGGTTGTAGGAGAGTGA
131 CATTAGCTATCATATTTGGTTGTAGGAGAGTGA
225212 AAT
1 AAT
225215 GGCTCATCGG
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (163 bp):
AATAGTACGTATTGCTAGGACGATAAAATCTCATTTCAATGACTATAGTTGTAGCAAGATGGGGC
CAAATGGCTGATTGGCTTGGTTACTCATATGAGAGAATTGCTTGCCAGTCAAATCGGCTTCTGGT
CATTAGCTATCATATTTGGTTGTAGGAGAGTGA
Found at i:228477 original size:14 final size:13
Alignment explanation
Indices: 228458--228508 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
228448 TATATAATGT
228458 TTTTCTTTCTTTAA
1 TTTTCTTTCTTT-A
*
228472 TTTTCTTTCTGT-
1 TTTTCTTTCTTTA
*
228484 TTTTC-CTCTTTCA
1 TTTTCTTTCTTT-A
228497 TTTTCTTTCTTT
1 TTTTCTTTCTTT
228509 GGTGCCGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 5 0.17
14 16 0.53
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTCTTTCTTTA
Found at i:228493 original size:25 final size:26
Alignment explanation
Indices: 228455--228506 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
228445 CAATATATAA
*
228455 TGTTTTTCTTTCTTTAATTTTCTTTC
1 TGTTTTTCTCTCTTTAATTTTCTTTC
*
228481 TGTTTTTC-CTCTTTCATTTTCTTTC
1 TGTTTTTCTCTCTTTAATTTTCTTTC
228506 T
1 T
228507 TTGGTGCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (26 bp):
TGTTTTTCTCTCTTTAATTTTCTTTC
Found at i:235191 original size:2 final size:2
Alignment explanation
Indices: 235184--235211 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
235174 CACCATTTAC
235184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
235212 CTCATATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:239445 original size:19 final size:20
Alignment explanation
Indices: 239398--239445 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 20
239388 AGATAAATAA
239398 TAAAATAATAT--ATATTGT
1 TAAAATAATATAAATATTGT
239416 TAAAAT--T-TAAATATT-T
1 TAAAATAATATAAATATTGT
239432 TAAAATAATATAAA
1 TAAAATAATATAAA
239446 AATCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.04
16 8 0.32
17 5 0.20
18 7 0.28
19 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATAATATAAATATTGT
Found at i:239890 original size:36 final size:36
Alignment explanation
Indices: 239844--239931 Score: 158
Period size: 36 Copynumber: 2.4 Consensus size: 36
239834 ATATATTTAC
*
239844 TTAATATAATAAATATGAAATAGTAATAGTAATAAT
1 TTAATTTAATAAATATGAAATAGTAATAGTAATAAT
239880 TTAATTTAATAAATATGAAATAGTAATAGTAATAAT
1 TTAATTTAATAAATATGAAATAGTAATAGTAATAAT
239916 TTAATTTAATGAAATA
1 TTAATTTAAT-AAATA
239932 AAATATTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 45 0.90
37 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (36 bp):
TTAATTTAATAAATATGAAATAGTAATAGTAATAAT
Found at i:241351 original size:16 final size:16
Alignment explanation
Indices: 241327--241361 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
241317 AATTAGGTCA
* *
241327 TTTTGAGTTTAAATTT
1 TTTTAAGTTAAAATTT
241343 TTTTAAGTTAAAATTT
1 TTTTAAGTTAAAATTT
241359 TTT
1 TTT
241362 GAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (16 bp):
TTTTAAGTTAAAATTT
Found at i:245285 original size:19 final size:20
Alignment explanation
Indices: 245261--245298 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
245251 AAATATAAAT
245261 TGATTAATTGAA-AAATTAA
1 TGATTAATTGAACAAATTAA
245280 TGATTAATTGAACAAATTA
1 TGATTAATTGAACAAATTA
245299 TGTTCATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (20 bp):
TGATTAATTGAACAAATTAA
Found at i:247276 original size:14 final size:14
Alignment explanation
Indices: 247257--247287 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
247247 CATGTAAACT
247257 TCTATATATCTATA
1 TCTATATATCTATA
247271 TCTATATATCTATA
1 TCTATATATCTATA
247285 TCT
1 TCT
247288 TACTCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (14 bp):
TCTATATATCTATA
Found at i:247297 original size:20 final size:20
Alignment explanation
Indices: 247261--247299 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
247251 TAAACTTCTA
*
247261 TATATCTATATCTATATATC
1 TATATCTATATCCATATATC
247281 TATATCT-TACTCCATATAT
1 TATATCTATA-TCCATATAT
247300 ATATGTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATCTATATCCATATATC
Found at i:249390 original size:3 final size:3
Alignment explanation
Indices: 249382--249415 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
249372 ATATATATAT
249382 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
249416 GGGTCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:250129 original size:22 final size:25
Alignment explanation
Indices: 250094--250148 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 25
250084 AAAAATATTT
**
250094 TATTTTAATTTATTT-T-TAAAAA-
1 TATTTTAAAATATTTGTATAAAAAG
250116 TATTTTAAAATATTTGTATAAAAAG
1 TATTTTAAAATATTTGTATAAAAAG
*
250141 TTTTTTAA
1 TATTTTAA
250149 TATTTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.48
23 1 0.04
24 6 0.22
25 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTTTAAAATATTTGTATAAAAAG
Found at i:250803 original size:11 final size:10
Alignment explanation
Indices: 250786--250843 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
250776 AGTATTAGAG
250786 TTTTTATTTA
1 TTTTTATTTA
*
250796 TATTTTATCTA
1 T-TTTTATTTA
*
250807 TTTTTAATTA
1 TTTTTATTTA
*
250817 TTTTTAAATTA
1 TTTTT-ATTTA
*
250828 GTTTTATTTA
1 TTTTTATTTA
250838 TTTTTA
1 TTTTTA
250844 AGTTACTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 22 0.55
11 18 0.45
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:250844 original size:21 final size:22
Alignment explanation
Indices: 250787--250844 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
250777 GTATTAGAGT
*
250787 TTTTATTTATATTTT--ATCTAT
1 TTTTATTTAT-TTTTAAATCTAG
*
250808 TTTTAATTATTTTTAAAT-TAG
1 TTTTATTTATTTTTAAATCTAG
250829 TTTTATTTATTTTTAA
1 TTTTATTTATTTTTAA
250845 GTTACTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTTATTTTTAAATCTAG
Found at i:254354 original size:11 final size:11
Alignment explanation
Indices: 254330--254364 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
254320 AGATACTTTC
* *
254330 ATATCGAAGAT
1 ATATCAAAGGT
254341 ATATCAAAGGT
1 ATATCAAAGGT
254352 ATATCAAAGGT
1 ATATCAAAGGT
254363 AT
1 AT
254365 TTTTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (11 bp):
ATATCAAAGGT
Found at i:256612 original size:22 final size:22
Alignment explanation
Indices: 256584--256626 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
256574 AAAGTTTAGG
256584 CTACCAAAACTGGCATTTTTGC
1 CTACCAAAACTGGCATTTTTGC
256606 CTACCAAAACTGGCATTTTTG
1 CTACCAAAACTGGCATTTTTG
256627 AAAATTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
CTACCAAAACTGGCATTTTTGC
Found at i:259096 original size:21 final size:21
Alignment explanation
Indices: 259057--259096 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
259047 TGAAAAGTTA
*
259057 AGAAAATATCAATATTTCAAG
1 AGAAAATATCAATACTTCAAG
**
259078 AGAAAATATTGATACTTCA
1 AGAAAATATCAATACTTCA
259097 CCTTTTAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AGAAAATATCAATACTTCAAG
Found at i:265867 original size:23 final size:23
Alignment explanation
Indices: 265825--265884 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
265815 TAGTGGTTAT
* *
265825 GTAAAATGTATATATTGTTTTCA
1 GTAAAATGTAAATATCGTTTTCA
*
265848 -TAAAATGTACAATATCGTTTTTA
1 GTAAAATGTA-AATATCGTTTTCA
265871 GT-AAATGTAAATAT
1 GTAAAATGTAAATAT
265885 GCTATAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 14 0.44
23 17 0.53
24 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (23 bp):
GTAAAATGTAAATATCGTTTTCA
Found at i:270285 original size:35 final size:35
Alignment explanation
Indices: 270246--270313 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
270236 TATATATATA
*
270246 TATATTTAAACTCTTAAAAAGATTATAATTTTTAC
1 TATATTTAAACTCTTAAAAAGATAATAATTTTTAC
* * * *
270281 TATATTTAACCTCTTGAAGAGGTAATAATTTTT
1 TATATTTAAACTCTTAAAAAGATAATAATTTTT
270314 CTACGTAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (35 bp):
TATATTTAAACTCTTAAAAAGATAATAATTTTTAC
Found at i:277310 original size:37 final size:36
Alignment explanation
Indices: 276938--277310 Score: 130
Period size: 37 Copynumber: 9.8 Consensus size: 36
276928 ATTCTCAAGG
* **
276938 CAAGATGATTTTTGAATTCTCAA-CCTTTTTTTGTCAA
1 CAAGATGATTTTTGAATTCTCAAGCC-TTTGTCATC-A
* * * * *
276975 CGAGGTTATGATTTTTGAATTCTCAAACATTTGTCGTAGA
1 C-AAG--ATGATTTTTGAATTCTCAAGCCTTTGTCAT-CA
* * * *
277015 CAAAATGATTTTTTAATTCTCAATCATTTGTCGTATGCGA
1 CAAGATGATTTTTGAATTCTCAAGCCTTTGTC--AT-C-A
* * * *
277055 GATA-ATAATTTTTGAATT-TCTAAACCTTTGTCATGA
1 CA-AGATGATTTTTGAATTCTC-AAGCCTTTGTCATCA
** * **
277091 GGGAGATGATACTTTTGAATTCTCAAACCTTTACCATTGGCA
1 -CAAGATGAT--TTTTGAATTCTCAAGCCTTTGTCA-T--CA
* *
277133 -AAG-TGATTTTTTGAATTCTTAAGCCTTTGTCGTCA
1 CAAGATGA-TTTTTGAATTCTCAAGCCTTTGTCATCA
* * * * * **
277168 GCCAA-AT-ATTTTTTTAATTCTCAAGTCTCTATCGTGGG
1 --CAAGATGA-TTTTTGAATTCTCAAGCCTTTGTCAT-CA
*
277206 CAAGGTGATTTTTGAATTCTCAAGCCTTTGTCATCA
1 CAAGATGATTTTTGAATTCTCAAGCCTTTGTCATCA
* *
277242 CTAAGATAATAGTTTTGAATTCTCAAGCCTTTGTCGATGA
1 C-AAGATGAT--TTTTGAATTCTCAAGCCTTTGTC-ATCA
* * *
277282 CAAGATGATTTTTAAATTCTTAAACCTTT
1 CAAGATGATTTTTGAATTCTCAAGCCTTT
277311 TTCGTCAGTG
Statistics
Matches: 255, Mismatches: 51, Indels: 60
0.70 0.14 0.16
Matches are distributed among these distances:
35 2 0.01
36 6 0.02
37 101 0.40
38 27 0.11
39 56 0.22
40 60 0.24
41 2 0.01
42 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
CAAGATGATTTTTGAATTCTCAAGCCTTTGTCATCA
Found at i:280502 original size:28 final size:28
Alignment explanation
Indices: 280462--280518 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
280452 ATACTCGATC
280462 TATTATAAATCTCTATTTTTCTATTTGA
1 TATTATAAATCTCTATTTTTCTATTTGA
280490 TATTATAAATCTCTATTTTTCTATTTGA
1 TATTATAAATCTCTATTTTTCTATTTGA
280518 T
1 T
280519 TGATCTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (28 bp):
TATTATAAATCTCTATTTTTCTATTTGA
Found at i:283924 original size:21 final size:21
Alignment explanation
Indices: 283900--283971 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 21
283890 CATGGTCCTA
* *
283900 TATCGATACATTTGAGATATG
1 TATCGATACATTTCACATATG
*
283921 TATCGATACA-TTCACTTATG
1 TATCGATACATTTCACATATG
283941 TATCGATACA-TTCAC-TAATTG
1 TATCGATACATTTCACAT-A-TG
283962 TATCGATACA
1 TATCGATACA
283972 AATTATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 23 0.50
21 22 0.48
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TATCGATACATTTCACATATG
Found at i:283942 original size:20 final size:20
Alignment explanation
Indices: 283917--283971 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
283907 ACATTTGAGA
283917 TATGTATCGATACATTCACT
1 TATGTATCGATACATTCACT
283937 TATGTATCGATACATTCACT
1 TATGTATCGATACATTCACT
*
283957 AATTGTATCGATACA
1 TA-TGTATCGATACA
283972 AATTATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
TATGTATCGATACATTCACT
Found at i:288078 original size:150 final size:154
Alignment explanation
Indices: 287916--288254 Score: 345
Period size: 150 Copynumber: 2.2 Consensus size: 154
287906 CATTAAGGAT
* * *
287916 GAACCTATCCTAAATATATACCTTTGGCGTAAAAGCGACTCGGTAACTA-TCTAAGACTCATTTC
1 GAACCTATCCTAAATATATACCTTTGGCATAAAAGCAACTCGGTAACTACT-TAAGACTCAGTTC
*
287980 -AA-GAAAATTTACTAAAA-AACCCCAAGATATA-CTTCGAC-TAAAATTATC-TCGAAACCCTA
65 TAAGGAAAA-TTACTAAAATAACCCCAAGATATACCTTCGACGTAAAAGTATCTTCGAAACCCTA
*
288039 AAGGACACAAAAATATTATAAAAAGAG
129 AAAGACACAAAAATATTATAAAAA-AG
* ** * * *
288066 GAACCTATCCTAAACT-TAT-TCTATCAGCATAAAAGCAACTCGGTGACTACTTAGGACTCGGTT
1 GAACCTATCCTAAA-TATATACCT-TTGGCATAAAAGCAACTCGGTAACTACTTAAGACTCAGTT
* * * ** * * * * *
288129 CTAAGGGAAATTATTAAAATATCCTTAAGGTGTACCTTCGACGTGAAAGTATCTTGGTAACCCTA
64 CTAAGGAAAATTACTAAAATAACCCCAAGATATACCTTCGACGTAAAAGTATCTTCGAAACCCTA
*
288194 AAAGACACGAAAATATTATAAAAAAG
129 AAAGACACAAAAATATTATAAAAAAG
* * *
288220 GAACTTATCCTAAACATATACCTTTGACATAAAAG
1 GAACCTATCCTAAATATATACCTTTGGCATAAAAG
288255 TGAGCAGGTG
Statistics
Matches: 150, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
149 2 0.01
150 48 0.32
151 12 0.08
152 13 0.09
153 7 0.05
154 35 0.23
155 33 0.22
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (154 bp):
GAACCTATCCTAAATATATACCTTTGGCATAAAAGCAACTCGGTAACTACTTAAGACTCAGTTCT
AAGGAAAATTACTAAAATAACCCCAAGATATACCTTCGACGTAAAAGTATCTTCGAAACCCTAAA
AGACACAAAAATATTATAAAAAAG
Found at i:289293 original size:82 final size:81
Alignment explanation
Indices: 289144--289298 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 81
289134 ACAAAAACGC
* *
289144 CCCAAAAAAGTTAAAAACATACAAATCACATTTAAACGTGATAAATACACTTGAAAAACACCCTT
1 CCCAAAAAAGTTAAAAACATACAAATCAAATTTAAACGTGATAAATACACATGAAAAACACCCTT
289209 AAAGGTGTATAAGTAAT
66 AAA-GTGTATAAGTAAT
* * * * **
289226 CCCAAAAAGGTTAGAAACATACGAATCAAATTTAAATGTGATAAATACACATGAAAAACACTTTT
1 CCCAAAAAAGTTAAAAACATACAAATCAAATTTAAACGTGATAAATACACATGAAAAACACCCTT
289291 AAAGTGTA
66 AAAGTGTA
289299 CAAATGATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 5 0.08
82 60 0.92
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (81 bp):
CCCAAAAAAGTTAAAAACATACAAATCAAATTTAAACGTGATAAATACACATGAAAAACACCCTT
AAAGTGTATAAGTAAT
Found at i:291990 original size:41 final size:41
Alignment explanation
Indices: 291925--292050 Score: 121
Period size: 41 Copynumber: 3.1 Consensus size: 41
291915 CATGTTAGAG
* *
291925 GGGTT-ACCAAGGTAAAACTGATAAAGTTAACCAATTAAAA
1 GGGTTGACTAAGGCAAAACTGATAAAGTTAACCAATTAAAA
* * ** * ** *
291965 GGGTTGACTAAGGCGAAACTAATAAAGCCAATCGGTT-AGA
1 GGGTTGACTAAGGCAAAACTGATAAAGTTAACCAATTAAAA
* *
292005 GAGGTTGACTAGGGCAAAACTGATAAAGTTAACCAATTAAAG
1 G-GGTTGACTAAGGCAAAACTGATAAAGTTAACCAATTAAAA
292047 GGGT
1 GGGT
292051 CAGCTAAGAC
Statistics
Matches: 63, Mismatches: 20, Indels: 5
0.72 0.23 0.06
Matches are distributed among these distances:
40 8 0.13
41 53 0.84
42 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (41 bp):
GGGTTGACTAAGGCAAAACTGATAAAGTTAACCAATTAAAA
Found at i:292032 original size:82 final size:81
Alignment explanation
Indices: 291918--292450 Score: 271
Period size: 82 Copynumber: 6.5 Consensus size: 81
291908 AAGCTAGCAT
* * *
291918 GTTAGAGGGGTT-ACCAAGGTAAAACTGATAAAGTTAACCAATTAAAAGGGTTGACTAAGGCGAA
1 GTTAGAGGAGTTGACCAGGGCAAAACTGATAAAGTTAACCAATT-AAAGGGTTGACTAAGGCGAA
*
291982 A-CTAATAAAGCCAATC-G
65 ATC-AATAAAACCAA-CAG
* * * *
291999 GTTAGA-GAGGTTGACTAGGGCAAAACTGATAAAGTTAACCAATTAAAGGGGTCAGCTAAGACGA
1 GTTAGAGGA-GTTGACCAGGGCAAAACTGATAAAGTTAACCAATTAAAGGGTTGA-CTAAGGCGA
*
292063 AATCGATAAAACCAACAG
64 AATCAATAAAACCAACAG
* * * * *
292081 GTTAGAGGAGTTGACCAGGGCAAAATTAATAAAGTTAACTAATTAAAGAGGTTGACCAAGGAGAA
1 GTTAGAGGAGTTGACCAGGGCAAAACTGATAAAGTTAACCAATTAAAG-GGTTGACTAAGGCGAA
* **
292146 ATCGATAAAGTCAACTA-
65 ATCAATAAAACCAAC-AG
* * * * * * * * * * *
292163 ATTA-AAGAGGTTGATCAAGGCGAAA-TAGATAAAGTCAACTAATTAGAGAGG-TCACCTAGGGT
1 GTTAGAGGA-GTTGACCAGGGCAAAACT-GATAAAGTTAACCAATTAAAG-GGTTGA-CTAAGGC
* * *
292225 GAAATCAATAAAGCAAACAA
62 GAAATCAATAAAACCAACAG
* * * ** * * * * **
292245 GTTAG-GGATGTTAACTAAGGCAAAACCAATAAAGTCAACAAATTATAAGGGTTGGCTAGGGAAA
1 GTTAGAGGA-GTTGACCAGGGCAAAACTGATAAAGTTAACCAATTA-AAGGGTTGACTAAGGCGA
* * *
292309 AACCGATAAAACCAACAA
64 AATCAATAAAACCAACAG
* * * * * * * * *** *
292327 GTAAAAAGG-GTTGACTAGGGCGAAACTGATAAAGTCAACTAATTAAAGATGTTGGCCGCGGTGA
1 GT-TAGAGGAGTTGACCAGGGCAAAACTGATAAAGTTAACCAATTAAAG-GGTTGACTAAGGCGA
* *
292391 AA-CTAATAAAGCCAATAG
64 AATC-AATAAAACCAACAG
* * *
292409 GTTAGAAGG-GTTGACCAGGGCAAAACTAATAATGTCAACCAA
1 GTTAG-AGGAGTTGACCAGGGCAAAACTGATAAAGTTAACCAA
292451 ATAGAAAGGT
Statistics
Matches: 352, Mismatches: 79, Indels: 41
0.75 0.17 0.09
Matches are distributed among these distances:
80 1 0.00
81 30 0.09
82 307 0.87
83 12 0.03
84 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (81 bp):
GTTAGAGGAGTTGACCAGGGCAAAACTGATAAAGTTAACCAATTAAAGGGTTGACTAAGGCGAAA
TCAATAAAACCAACAG
Found at i:292229 original size:41 final size:41
Alignment explanation
Indices: 292109--292214 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
292099 GGCAAAATTA
* *
292109 ATAAAGTTAACTAATTAAAGAGGTTGACCAAGGAGAAATCG
1 ATAAAGTCAACTAATTAAAGAGGTTGACCAAGGAGAAATAG
* *
292150 ATAAAGTCAACTAATTAAAGAGGTTGATCAAGGCGAAATAG
1 ATAAAGTCAACTAATTAAAGAGGTTGACCAAGGAGAAATAG
*
292191 ATAAAGTCAACTAATTAGAGAGGT
1 ATAAAGTCAACTAATTAAAGAGGT
292215 CACCTAGGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (41 bp):
ATAAAGTCAACTAATTAAAGAGGTTGACCAAGGAGAAATAG
Found at i:292236 original size:41 final size:41
Alignment explanation
Indices: 292090--292237 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 41
292080 GGTTAGAGGA
* * *
292090 GTTGACCAGGGCA-AAATTAATAAAGTTAACTAATTAAAGAG
1 GTTGACCAAGG-AGAAATCAATAAAGTCAACTAATTAAAGAG
*
292131 GTTGACCAAGGAGAAATCGATAAAGTCAACTAATTAAAGAG
1 GTTGACCAAGGAGAAATCAATAAAGTCAACTAATTAAAGAG
* * *
292172 GTTGATCAAGGCGAAAT-AGATAAAGTCAACTAATTAGAGAG
1 GTTGACCAAGGAGAAATCA-ATAAAGTCAACTAATTAAAGAG
* * *
292213 G-TCACCTAGGGTGAAATCAATAAAG
1 GTTGACC-AAGGAGAAATCAATAAAG
292238 CAAACAAGTT
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.04
41 86 0.95
42 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (41 bp):
GTTGACCAAGGAGAAATCAATAAAGTCAACTAATTAAAGAG
Found at i:292311 original size:41 final size:41
Alignment explanation
Indices: 292266--292373 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 41
292256 TAACTAAGGC
* * *
292266 AAAACCAATAAAGTCAACAAATTATAAGGGTTGGCTAGGGA
1 AAAACCGATAAAGTCAACAAATTAAAAGGGTTGACTAGGGA
** * * *
292307 AAAACCGATAAAACCAACAAGTAAAAAGGGTTGACTAGGGC
1 AAAACCGATAAAGTCAACAAATTAAAAGGGTTGACTAGGGA
* * *
292348 GAAACTGATAAAGTCAACTAATTAAA
1 AAAACCGATAAAGTCAACAAATTAAA
292374 GATGTTGGCC
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.18
Consensus pattern (41 bp):
AAAACCGATAAAGTCAACAAATTAAAAGGGTTGACTAGGGA
Found at i:292433 original size:164 final size:163
Alignment explanation
Indices: 292220--292644 Score: 387
Period size: 164 Copynumber: 2.6 Consensus size: 163
292210 GAGGTCACCT
* * * * * * *
292220 AGGGTGAAATCAATAAAGCAAACAAGTTAG-GGATGTTAACTAAGGCAAAACCAATAAAGTCAAC
1 AGGGTGAAACCAATAAAGCCAATAGGTTAGAGG--GTTGACCAAGGCAAAACTAATAAAGTCAAC
* * *
292284 AAATTATAAGGGTTGGCTAGGGAAAAACCGATAAAACCAACAAGTAAAAAG-GGTTGACTAGGGC
64 AAATTATAAGGGTTAGCTAGGGAAAAACCGATAAAACCAACAAGT-AAAAGTGGTTGACTAGAGA
* ** * * * *
292348 GAAACTGATAAAGTCAACTA-ATTA-AAGATGTTGGC
128 AAAACCAATAAAGTCAACCAGAATAGAAG-GGTTAGC
* * * *
292383 CGCGGTGAAACTAATAAAGCCAATAGGTTAGAAGGGTTGACCAGGGCAAAACTAATAATGTCAAC
1 AG-GGTGAAACCAATAAAGCCAATAGGTTAG-AGGGTTGACCAAGGCAAAACTAATAAAGTCAA-
* * ** * * * * *
292448 CAAA-TAGAAAGGTTAGCTAGGGCCAAACCCATAAAAGCAACAAGTTAGAGTGGTTTACTAGAGA
63 CAAATTATAAGGGTTAGCTAGGGAAAAACCGATAAAACCAACAAGTAAAAGTGGTTGACTAGAGA
* *
292512 AAAACCAATAAAGTTAGCCAGAATAGAAGGGTTAGC
128 AAAACCAATAAAGTCAACCAGAATAGAAGGGTTAGC
* ** *
292548 AGGGTGAAACCAATAAAGCTAATAGGTTAGAGGGTTGACCAAGGTGAAACTAATAAAGTCAACCA
1 AGGGTGAAACCAATAAAGCCAATAGGTTAGAGGGTTGACCAAGGCAAAACTAATAAAGTCAACAA
* *
292613 ATT-TGAAGGGTTAGCTAAGGTAAAA-CGATAAA
66 ATTAT-AAGGGTTAGCTAGGGAAAAACCGATAAA
292645 GTCAACCAAT
Statistics
Matches: 207, Mismatches: 46, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
162 9 0.04
163 49 0.24
164 131 0.63
165 13 0.06
166 5 0.02
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.19
Consensus pattern (163 bp):
AGGGTGAAACCAATAAAGCCAATAGGTTAGAGGGTTGACCAAGGCAAAACTAATAAAGTCAACAA
ATTATAAGGGTTAGCTAGGGAAAAACCGATAAAACCAACAAGTAAAAGTGGTTGACTAGAGAAAA
ACCAATAAAGTCAACCAGAATAGAAGGGTTAGC
Found at i:292482 original size:82 final size:81
Alignment explanation
Indices: 291918--292629 Score: 257
Period size: 82 Copynumber: 8.7 Consensus size: 81
291908 AAGCTAGCAT
* * * * * * * *
291918 GTTAGAGGGGTT-ACCAAGGTAAAACTGATAAAGTTAACCAATTAAAAGGGTT-GACTAAGGCGA
1 GTTAGA-GGGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAGGGTTAG-CTAGGGCCA
* *
291981 AACTAATAAAGCCAATCG
64 AACCAATAAAGCCAATAG
* * * * * * * * *
291999 GTTAGAGAGGTTGACTAGGGCAAAACTGATAAAGTTAACCAATTA-AAGGGGTCAGCTAAGACGA
1 GTTAGAG-GGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAA-GGGTTAGCTAGGGCCA
* * * *
292063 AATCGATAAAACCAACAG
64 AACCAATAAAGCCAATAG
* * * * * * *
292081 GTTAGAGGAGTTGACCAGGGCAAAATTAATAAAGTTAACTAATTA-AAGAGGTTGACCAAGGAG-
1 GTTAGAGG-GTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAG-GGTT-AGCTAGG-GC
* * *
292144 -AAATCGATAAAGTCAACTA-
62 CAAACCAATAAAGCCAA-TAG
* * * * ** * * * * **
292163 ATTAAAGAGGTTGATCAAGGCGAAA-TAGATAAAGTCAACTAATTAG-AGAGGTCACCTAGGGTG
1 GTTAGAG-GGTTGACCAGGGAAAAACTA-ATAAAGTCAACCAAATAGAAG-GGTTAGCTAGGGCC
* * * *
292226 AAATCAATAAAGCAAACAA
63 AAACCAATAAAGCCAATAG
* * * * * * * **
292245 GTTAG-GGATGTTAACTAAGGCAAAACCAATAAAGTCAA-CAAATTATAAGGGTTGGCTAGGGAA
1 GTTAGAGG--GTTGACCAGGGAAAAACTAATAAAGTCAACCAAA-TAGAAGGGTTAGCTAGGGCC
* * * *
292308 AAACCGATAAAACCAACAA
63 AAACCAATAAAGCCAATAG
* * * ** * * * * * * **
292327 GTAAAAAGGGTTGACTAGGGCGAAACTGATAAAGTCAACTAATTA-AAGATGTTGGC-CGCGGTG
1 GT-TAGAGGGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAG-GGTTAGCTAG-GGCC
*
292390 AAACTAATAAAGCCAATAG
63 AAACCAATAAAGCCAATAG
* * *
292409 GTTAGAAGGGTTGACCAGGGCAAAACTAATAATGTCAACCAAATAGAAAGGTTAGCTAGGGCCAA
1 GTTAG-AGGGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAGGGTTAGCTAGGGCCAA
* * *
292474 ACCCATAAAAG-CAACAA
65 ACCAAT-AAAGCCAATAG
* * * * * * **
292491 GTTAGAGTGGTTTACTAGAGAAAAACCAATAAAGTTAGCCAGAATAGAAGGGTTAGC-AGGGTGA
1 GTTAGAG-GGTTGACCAGGGAAAAACTAATAAAGTCAACCA-AATAGAAGGGTTAGCTAGGGCCA
*
292555 AACCAATAAAGCTAATAG
64 AACCAATAAAGCCAATAG
* ** * *
292573 GTTAGAGGGTTGACCAAGGTGAAACTAATAAAGTCAACCAATTTGAAGGGTTAGCTA
1 GTTAGAGGGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAGGGTTAGCTA
292630 AGGTAAAACG
Statistics
Matches: 482, Mismatches: 116, Indels: 66
0.73 0.17 0.10
Matches are distributed among these distances:
80 16 0.03
81 62 0.13
82 368 0.76
83 34 0.07
84 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (81 bp):
GTTAGAGGGTTGACCAGGGAAAAACTAATAAAGTCAACCAAATAGAAGGGTTAGCTAGGGCCAAA
CCAATAAAGCCAATAG
Found at i:292699 original size:82 final size:82
Alignment explanation
Indices: 292613--292821 Score: 212
Period size: 82 Copynumber: 2.5 Consensus size: 82
292603 AAGTCAACCA
*
292613 ATTTGAAGGGTT-AGCTAAGG-TAAAACGATAAAGTCAACCAATTTA-AAAGGGTTGGCTAAGGC
1 ATTTGAAGGGTTGA-CTAAGGCCAAAACGATAAAGTCAACCAA-TTAGAAA-GGTTGGCTAAGGC
*
292675 AAAATCAATAAAACCAATAG
63 AAAACCAATAAAACCAATAG
* * * **
292695 ATTTGAGGGGTTGACTACGGCCAAAATGATAAAGTCAACCAATTAGAAAGGTTGGCTAAGGTGAA
1 ATTTGAAGGGTTGACTAAGGCCAAAACGATAAAGTCAACCAATTAGAAAGGTTGGCTAAGGCAAA
*
292760 ACCAATAAAGCCAATAG
66 ACCAATAAAACCAATAG
* * * * * *
292777 -GTTAAAGGGACTGACCAAGG-CAAAATCGATAAGGTCAACTAATTA
1 ATTTGAAGGG-TTGACTAAGGCCAAAA-CGATAAAGTCAACCAATTA
292822 AAGGGGTTAA
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
81 11 0.10
82 71 0.68
83 23 0.22
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (82 bp):
ATTTGAAGGGTTGACTAAGGCCAAAACGATAAAGTCAACCAATTAGAAAGGTTGGCTAAGGCAAA
ACCAATAAAACCAATAG
Found at i:292768 original size:41 final size:41
Alignment explanation
Indices: 292588--292769 Score: 122
Period size: 41 Copynumber: 4.4 Consensus size: 41
292578 AGGGTTGACC
* * *
292588 AAGGTG-AAACTAATAAAGTCAACCAATTTGAAGGGTTAGCT
1 AAGGTGAAAAC-AATAAAGTCAACCAATTAGAAAGGTTGGCT
*
292629 AAGGT-AAAACGATAAAGTCAACCAATTTA-AAAGGGTTGGCT
1 AAGGTGAAAACAATAAAGTCAACCAA-TTAGAAA-GGTTGGCT
* ** * * ** *
292670 AAGG-CAAAATCAATAAAACCAA-TAGATTTGAGGGGTTGACT
1 AAGGTGAAAA-CAATAAAGTCAACCA-ATTAGAAAGGTTGGCT
* ** **
292711 ACGGCCAAAATGATAAAGTCAACCAATTAGAAAGGTTGGCT
1 AAGGTGAAAACAATAAAGTCAACCAATTAGAAAGGTTGGCT
*
292752 AAGGTGAAACCAATAAAG
1 AAGGTGAAAACAATAAAG
292770 CCAATAGGTT
Statistics
Matches: 104, Mismatches: 28, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
40 16 0.15
41 71 0.68
42 17 0.16
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (41 bp):
AAGGTGAAAACAATAAAGTCAACCAATTAGAAAGGTTGGCT
Found at i:293457 original size:21 final size:20
Alignment explanation
Indices: 293420--293458 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
293410 AAATTTTCAT
*
293420 TAACAGCCGAAATAAAATGA
1 TAACAGCCGAAAAAAAATGA
*
293440 TAACAAGCTGAAAAAAAAT
1 TAAC-AGCCGAAAAAAAAT
293459 AACATGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (20 bp):
TAACAGCCGAAAAAAAATGA
Found at i:293519 original size:76 final size:75
Alignment explanation
Indices: 293335--293935 Score: 265
Period size: 76 Copynumber: 8.1 Consensus size: 75
293325 TGGTTTTCAC
* * **
293335 AATTTCCCATCAATAG-TGGAAACAAACTGATGACAAGTTAAAGAAAAAAACACAATGGGGAATA
1 AATTT-CCATCAATAGCT-GAAACAAACTGATAACAAGCTAAAGAAAAAAACATGATGGGGAATA
*
293399 TGTGATTTCTAA
64 TGTGGTTTCTAA
* * * * * *
293411 AATTTTCATTAACAGCCGAAATAAAATGATAACAAGCTGAAA-AAAAATAACATGATGGGGAATA
1 AATTTCCATCAATAGCTGAAACAAACTGATAACAAGCT-AAAGAAAAA-AACATGATGGGGAATA
293475 TGTGGTTTCTAA
64 TGTGGTTTCTAA
* * * **
293487 AGTTTCCATCAATAGCTAAAACAAACTAATAAC-AGCCTAAAGAAGAAAGAACATGATACGGAAT
1 AATTTCCATCAATAGCTGAAACAAACTGATAACAAG-CTAAAGAA-AAA-AACATGATGGGGAAT
*
293551 ATGTTG-TTCTAA
63 ATGTGGTTTCTAA
*** * ** * * * * ** * *
293563 AATTTTTGTCAACAGCCAAAACAAACTGATAATAGGTTGAAGGAAAAGTACGTGATGTGG-A-A-
1 AATTTCCATCAATAGCTGAAACAAACTGATAACAAGCT-AAAGAAAAAAACATGATGGGGAATAT
* *
293625 -----TCCAAA
65 GTGGTTTCTAA
** * * ** * * *
293631 AATTTTTATCAATAG-TCAAACAAACTAATAA-TGGCCTTAAGGAAAAGGAACATGAT-AGGAAT
1 AATTTCCATCAATAGCTGAAACAAACTGATAACAAG-C-TAAAGAAAA-AAACATGATGGGGAAT
* *
293693 ATGTTGTTTCTAC
63 ATGTGGTTTCTAA
* * * * * * * * *
293706 AATTTCCCATCTACAACTGAAACAAACTGAAAATAAACTGAAGAAAAAGAACATGTTGGGAAATA
1 AATTT-CCATCAATAGCTGAAACAAACTGATAACAAGCTAAAGAAAAA-AACATGATGGGGAATA
* *
293771 TAG-AGTTTCTAT
64 T-GTGGTTTCTAA
* ** * * *
293783 AATTTCCATCACTAGCCAAAACAAACTGATAATAAGCT---G-AAAAAA-ATTATGAGGAATATG
1 AATTTCCATCAATAGCTGAAACAAACTGATAACAAGCTAAAGAAAAAAACATGATGGGGAATATG
293843 TGGTTTCTAA
66 TGGTTTCTAA
* * * * * * * *
293853 AATCTACCATCAAT-GGTCGAAACAAATTAATAATAAGCTAAAGGAAAATAACATGATAGAGAAT
1 AAT-TTCCATCAATAGCT-GAAACAAACTGATAACAAGCTAAA-GAAAAAAACATGATGGGGAAT
*
293917 ATGTGGTTTCTAC
63 ATGTGGTTTCTAA
293930 AATTTC
1 AATTTC
293936 TGGTCGTCAA
Statistics
Matches: 389, Mismatches: 102, Indels: 68
0.70 0.18 0.12
Matches are distributed among these distances:
66 2 0.01
67 23 0.06
68 26 0.07
69 2 0.01
70 21 0.05
71 28 0.07
72 4 0.01
73 2 0.01
74 1 0.00
75 51 0.13
76 146 0.38
77 82 0.21
78 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (75 bp):
AATTTCCATCAATAGCTGAAACAAACTGATAACAAGCTAAAGAAAAAAACATGATGGGGAATATG
TGGTTTCTAA
Found at i:293692 original size:67 final size:68
Alignment explanation
Indices: 293561--293692 Score: 146
Period size: 67 Copynumber: 2.0 Consensus size: 68
293551 ATGTTGTTCT
* * * * *
293561 AAAATTTTTGTCAACAGCCAAAACAAACTGATAATAGGTTGAAGGAAAAGTACGTGATGTGGAAT
1 AAAATTTTTATCAACAGCCAAAACAAACTAATAATAGGTTGAAGGAAAAGAACATGATGAGGAAT
293626 CCA
66 CCA
* *
293629 AAAATTTTTATCAATAGTC-AAACAAACTAATAAT-GGCCTT-AAGGAAAAGGAACATGAT-AGG
1 AAAATTTTTATCAACAGCCAAAACAAACTAATAATAGG--TTGAAGGAAAA-GAACATGATGAGG
293690 AAT
63 AAT
293693 ATGTTGTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
66 2 0.04
67 27 0.50
68 25 0.46
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (68 bp):
AAAATTTTTATCAACAGCCAAAACAAACTAATAATAGGTTGAAGGAAAAGAACATGATGAGGAAT
CCA
Found at i:293752 original size:143 final size:144
Alignment explanation
Indices: 293494--293754 Score: 312
Period size: 144 Copynumber: 1.8 Consensus size: 144
293484 TAAAGTTTCC
293494 ATCAATAGCTAAAACAAACTAATAACAGCCTAAAGAAGAAAGAACATGATACGGAATATGTTGTT
1 ATCAATAGCTAAAACAAACTAATAACAGCCTAAAGAAGAAAGAACATGATACGGAATATGTTGTT
*** * * ***
293559 CTAAAATTTTTGTCAACAGCCAAAACAAACTGATAATAGGTTGAAGGAAAAGTACGTGATGTGGA
66 CTAAAATTTCCATCAACAACCAAAACAAACTGAAAATAAACTGAAGGAAAAGTACGTGATGTGGA
293624 ATCCAAAAATTTTT
131 ATCCAAAAATTTTT
* ** * *
293638 ATCAATAG-TCAAACAAACTAATAATGGCCTTAAGGAA-AAGGAACATGATA-GGAATATGTTGT
1 ATCAATAGCTAAAACAAACTAATAACAGCC-TAAAGAAGAAAGAACATGATACGGAATATGTTG-
* * ** *
293700 TTCTACAATTTCCCATCTACAACTGAAACAAACTGAAAATAAACTGAAGAAAAAG
64 TTCTAAAATTT-CCATCAACAACCAAAACAAACTGAAAATAAACTGAAGGAAAAG
293755 AACATGTTGG
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
142 11 0.11
143 40 0.42
144 45 0.47
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (144 bp):
ATCAATAGCTAAAACAAACTAATAACAGCCTAAAGAAGAAAGAACATGATACGGAATATGTTGTT
CTAAAATTTCCATCAACAACCAAAACAAACTGAAAATAAACTGAAGGAAAAGTACGTGATGTGGA
ATCCAAAAATTTTT
Found at i:294173 original size:60 final size:61
Alignment explanation
Indices: 294113--294530 Score: 336
Period size: 60 Copynumber: 7.0 Consensus size: 61
294103 CGTAATCAAA
* * * * *
294113 ACTCAATGAAATGGCTTGGATAAAACCAAAAGCCT-AACAATGACTTAGGGTAAAGCCAAA
1 ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
* * * * * * * *
294173 ACTCAATAAAATGACCTAAATAAAACTAGAAACCTAAATAATGACTTA-GGAAAAACCAAG
1 ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
* ** * * *
294233 ACTAAACAAAATGG-TCTAGATGAAACCAAAAACCTATACAATAACTT-GGGCAAAACCAAG
1 ACTCAATGAAATGGCT-TAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
* * ** * * ** **
294293 ATTCAAAGAAAT-TATCTAGATAAAATCAAAAACCTAAACAAAGA-TCCGGGTGAAACCAAG
1 ACTCAATGAAATGGCT-TAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
* * * * * *
294353 ATTCAACGAAATGGCTTGGATAAAACCAAAACCCTAAATAATGACTT-GAGCAAAACCAAG
1 ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
* * * * ** *
294413 ACTCAA-AAAATGGCTTAGATAAAACCAGAAACTTAAACAATAACATTA--GCGTAATCAAG
1 ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGAC-TTAGGGCAAAACCAAG
* *
294472 ACTCAATGAAATGGCTTAGATAAAACCAAAAACGTAAA-AATGACTTGGGGCAAAACCAA
1 ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAA
294531 AACTTAAAAT
Statistics
Matches: 278, Mismatches: 68, Indels: 24
0.75 0.18 0.06
Matches are distributed among these distances:
58 2 0.01
59 51 0.18
60 212 0.76
61 13 0.05
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (61 bp):
ACTCAATGAAATGGCTTAGATAAAACCAAAAACCTAAACAATGACTTAGGGCAAAACCAAG
Found at i:298220 original size:60 final size:60
Alignment explanation
Indices: 298153--298480 Score: 293
Period size: 60 Copynumber: 5.5 Consensus size: 60
298143 ATTGACTTAA
* *
298153 GCAAAACCAAGACTCAACAAAATGGCCTGGATAAAACCAGCAACCTAAACAATAACTTGG
1 GCAAAACCAAGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATAACTTGG
* * * ** * * *
298213 GCAAAACCAAAATTCAAAAAAATGATCTAGATAAAATCAGAAACCTAAATAA-AGATTTGG
1 GCAAAACCAAGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATA-ACTTGG
** * * * * * **
298273 GTGAAACAAAGATTCAACGAAATGGCCAAGATAAAACCACAAACCTAAACAATAACTTAC
1 GCAAAACCAAGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATAACTTGG
* * * * * *
298333 GCAAAACCATAG-CT-AAAAAAATGGCTTGGATAAAACCAAAAACCTAAACAATGACTTAG
1 GCAAAACCA-AGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATAACTTGG
** ** * * * * *
298392 ATAAAACCAAGACTCAAGGAAAGGGCCTAAATGAAACTAGAAACCTAAATAATAACTTGGG
1 GCAAAACCAAGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATAACTT-GG
*
298453 GCAAAACCAAAACTCAACAAAATGGCCT
1 GCAAAACCAAGACTCAACAAAATGGCCT
298481 TAGCAAAAAT
Statistics
Matches: 205, Mismatches: 57, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
58 2 0.01
59 47 0.23
60 130 0.63
61 26 0.13
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.16
Consensus pattern (60 bp):
GCAAAACCAAGACTCAACAAAATGGCCTAGATAAAACCAGAAACCTAAACAATAACTTGG
Found at i:298397 original size:30 final size:30
Alignment explanation
Indices: 298301--298401 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
298291 GAAATGGCCA
* *
298301 AGATAAAACCACAAACCTAAACAATAACTT
1 AGATAAAACCAAAAACCTAAACAATGACTT
* * * * *
298331 ACG-CAAAACC--ATAGCTAAAAAAATGGCTT
1 A-GATAAAACCAAAAACCT-AAACAATGACTT
*
298360 GGATAAAACCAAAAACCTAAACAATGACTT
1 AGATAAAACCAAAAACCTAAACAATGACTT
298390 AGATAAAACCAA
1 AGATAAAACCAA
298402 GACTCAAGGA
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
28 5 0.09
29 15 0.28
30 28 0.53
31 5 0.09
ACGTcount: A:0.54, C:0.21, G:0.09, T:0.16
Consensus pattern (30 bp):
AGATAAAACCAAAAACCTAAACAATGACTT
Found at i:298438 original size:119 final size:120
Alignment explanation
Indices: 298155--298476 Score: 326
Period size: 119 Copynumber: 2.7 Consensus size: 120
298145 TGACTTAAGC
* ** * **
298155 AAAACCAAGACTCAACAAAATGGCCTGGATAAAACCAGCAACCTAAACAATAACTTGGGCAAAAC
1 AAAACCAAGACTCAACGAAATGGCCTAAATAAAACCAGAAACCTAAACAATAACTTACGCAAAAC
* * * * * * *
298220 CAAAATTCAAAAAAATGATCTAGATAAAATCAGAAACCTAAATAAAGATTTGGGT
66 CAAAACTCAAAAAAATGATCTAGATAAAACCAAAAACCTAAACAAAGACTTAGAT
* * * *
298275 GAAACAAAGATTCAACGAAATGGCC-AAGATAAAACCACAAACCTAAACAATAACTTACGCAAAA
1 AAAACCAAGACTCAACGAAATGGCCTAA-ATAAAACCAGAAACCTAAACAATAACTTACGCAAAA
* * * * *
298339 CCATAGCT-AAAAAAATG-GCTTGGATAAAACCAAAAACCTAAACAATGACTTAGAT
65 CCAAAACTCAAAAAAATGATC-TAGATAAAACCAAAAACCTAAACAAAGACTTAGAT
* * * * * **
298394 AAAACCAAGACTCAAGGAAAGGGCCTAAATGAAACTAGAAACCTAAATAATAACTTGGGGCAAAA
1 AAAACCAAGACTCAACGAAATGGCCTAAATAAAACCAGAAACCTAAACAATAACTT-ACGCAAAA
*
298459 CCAAAACTCAACAAAATG
65 CCAAAACTCAAAAAAATG
298477 GCCTTAGCAA
Statistics
Matches: 161, Mismatches: 36, Indels: 9
0.78 0.17 0.04
Matches are distributed among these distances:
118 1 0.01
119 80 0.50
120 72 0.45
121 8 0.05
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (120 bp):
AAAACCAAGACTCAACGAAATGGCCTAAATAAAACCAGAAACCTAAACAATAACTTACGCAAAAC
CAAAACTCAAAAAAATGATCTAGATAAAACCAAAAACCTAAACAAAGACTTAGAT
Found at i:298652 original size:113 final size:116
Alignment explanation
Indices: 298513--298918 Score: 335
Period size: 120 Copynumber: 3.5 Consensus size: 116
298503 AATGAGACTT
*
298513 AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTTGGGCGAAACCAAGATTCAAC-T
1 AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTTGGGCGAAAACAAGATTCAACAT
* * *
298577 -CTA-GATAAAATCAAAAACCTAAATAAAGATTCAGGTGAAACCAAGATTC
66 GATACGATAAAATCAAAAACCTAAACAAAGATTCAGGTGAAACCAAAATTC
* * * * * * *
298626 AACAAAATAGCTTGGATGAAACCAAAAGCCTAAACAATAATTTGGGTGAAAATAAGATTCAACGA
1 AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTTGGGCGAAAACAAGATTCAAC--
* * *
298691 AATGATACGGATAAAATCAAAAACCTAAACAGAGATTCGGGTGAAACTAAAATTC
64 -ATGATAC-GATAAAATCAAAAACCTAAACAAAGATTCAGGTGAAACCAAAATTC
* * * *
298746 AACAAAATGGCCTAGATAAAACC-AAAACCATAAACAATGACTTAGGAC-AAAACAAAGACTCAA
1 AACAAAATGGCCTGGATAAAACCAAAAACC-TAAACAATAACTT-GGGCGAAAAC-AAGATTC-A
* * * * * *
298809 AGAACTGGCAT-GGATAAAACCAAAAACCTAAACAATGACTT-AGGTAAAACCAAGACTT-
62 A-CA-T-G-ATACGATAAAATCAAAAACCTAAACAAAGA-TTCAGGTGAAACCAA-AATTC
** * * * * * *
298867 AAGGAAATGGCCTAGATGAAACC-ATAACCTAAATAATGACTTGGGCCAAAAC
1 AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTTGGGCGAAAAC
298919 CAAAGCTCAA
Statistics
Matches: 235, Mismatches: 40, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
113 55 0.23
117 1 0.00
118 2 0.01
119 8 0.03
120 93 0.40
121 66 0.28
122 8 0.03
123 2 0.01
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (116 bp):
AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTTGGGCGAAAACAAGATTCAACAT
GATACGATAAAATCAAAAACCTAAACAAAGATTCAGGTGAAACCAAAATTC
Found at i:298683 original size:60 final size:58
Alignment explanation
Indices: 298513--298783 Score: 200
Period size: 60 Copynumber: 4.6 Consensus size: 58
298503 AATGAGACTT
* * *
298513 AACAAAATGGCCTGGATAAAACCAAAAACCTAAACAATAACTT-GGGCGAAACCAAGATTC
1 AACAAAAT-GCTTGGATAAAACC-AAAACCTAAACAATAA-TTCGGGTGAAACTAAGATTC
* * * * *
298573 AAC----T-C-TAGATAAAATCAAAAACCTAAATAA-AGATTCAGGTGAAACCAAGATTC
1 AACAAAATGCTTGGATAAAA-CCAAAACCTAAACAATA-ATTCGGGTGAAACTAAGATTC
* * *
298626 AACAAAATAGCTTGGATGAAACCAAAAGCCTAAACAATAATTTGGGTGAAAATAAGATTC
1 AACAAAAT-GCTTGGATAAAACCAAAA-CCTAAACAATAATTCGGGTGAAACTAAGATTC
* * * * * *
298686 AACGAAATGATACGGATAAAATCAAAAACCTAAACAGA-GATTCGGGTGAAACTAAAATTC
1 AACAAAATGCT-TGGATAAAA-CCAAAACCTAAACA-ATAATTCGGGTGAAACTAAGATTC
* *
298746 AACAAAATGGCCTAGATAAAACCAAAACCATAAACAAT
1 AACAAAAT-GCTTGGATAAAACCAAAACC-TAAACAAT
298784 GACTTAGGAC
Statistics
Matches: 165, Mismatches: 28, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
52 3 0.02
53 39 0.24
54 2 0.01
56 1 0.01
57 1 0.01
59 16 0.10
60 95 0.58
61 8 0.05
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (58 bp):
AACAAAATGCTTGGATAAAACCAAAACCTAAACAATAATTCGGGTGAAACTAAGATTC
Found at i:298798 original size:31 final size:31
Alignment explanation
Indices: 298760--298861 Score: 90
Period size: 30 Copynumber: 3.4 Consensus size: 31
298750 AAATGGCCTA
298760 GATAAAACCAAAACCATAAACAATGACTTAG
1 GATAAAACCAAAACCATAAACAATGACTTAG
* * * *
298791 GACAAAA-CAAAGACTCA-AAGA-ACTGGCAT-G
1 GATAAAACCAAA-AC-CATAA-ACAATGACTTAG
298821 GATAAAACCAAAAACC-TAAACAATGACTTAG
1 GATAAAACC-AAAACCATAAACAATGACTTAG
298852 G-TAAAACCAA
1 GATAAAACCAA
298862 GACTTAAGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
29 3 0.05
30 26 0.47
31 20 0.36
32 6 0.11
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.14
Consensus pattern (31 bp):
GATAAAACCAAAACCATAAACAATGACTTAG
Found at i:298966 original size:120 final size:119
Alignment explanation
Indices: 298746--299247 Score: 398
Period size: 120 Copynumber: 4.2 Consensus size: 119
298736 ACTAAAATTC
*
298746 AACAAAATGGCCTAGATAAAACCAAAACCATAAACAATGACTTAGGACAAAA-CAAAGACTCAAA
1 AACAAAATGGCCTAGATGAAACCAAAACC-TAAACAATGACTTAGG-CAAAACCAAAGACTCAAA
* *
298810 GAACTGGCATGGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTT
64 GAAATGGCATGAATAAAACCAAAAACCTAAACAATGACTTA-GTAAAACCAAGACTT
** * * *
298867 AAGGAAATGGCCTAGATGAAACCATAACCTAAATAATGACTTGGGCCAAAACCAAAG-CTCAACA
1 AACAAAATGGCCTAGATGAAACCAAAACCTAAACAATGACTTAGG-CAAAACCAAAGACTCAA-A
* * * * * **
298931 -AAATGGCTTGAATGAAACTAGAAACCTAAATAATGACTTAGTCGAACCAAGACTT
64 GAAATGGCATGAATAAAACCAAAAACCTAAACAATGACTTAGTAAAACCAAGACTT
* * *
298986 AACAAAATGGCCTAGATGAAACCAGAAACCTAAACAATAACTTAGGCAAAACC-AAGATTCAATG
1 AACAAAATGGCCTAGATGAAACCA-AAACCTAAACAATGACTTAGGCAAAACCAAAGACTCAAAG
* * * * * * * * **
299050 AAAAGATC-TGGATAAAATCAGAAATCTAAATAAAT-A-TTCGAGTGAAACCATTA-TT
65 AAATG-GCATGAATAAAACCAAAAACCTAAA-CAATGACTT--AGTAAAACCAAGACTT
** * * * * * *
299105 CAATGAATTGGCCAAGAT-AAGACCAAAACCCTAAATAATGACTTGGGCAAAA-CTAAGATTCAA
1 -AACAAAATGGCCTAGATGAA-ACCAAAA-CCTAAACAATGACTTAGGCAAAACCAAAGACTCAA
** * * *
299168 AGAAATCCCCT-ATATAAAACCAAAAACCTAAACAATGACTTAGGTAAAATCAAGACTG
63 AGAAATGGCATGA-ATAAAACCAAAAACCTAAACAATGACTTA-GTAAAACCAAGACTT
*
299226 AA-AGAAATGGCCTAGATAAAAC
1 AACA-AAATGGCCTAGATGAAAC
299248 TAGAAGCCTA
Statistics
Matches: 300, Mismatches: 60, Indels: 43
0.74 0.15 0.11
Matches are distributed among these distances:
118 5 0.02
119 81 0.27
120 178 0.59
121 36 0.12
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (119 bp):
AACAAAATGGCCTAGATGAAACCAAAACCTAAACAATGACTTAGGCAAAACCAAAGACTCAAAGA
AATGGCATGAATAAAACCAAAAACCTAAACAATGACTTAGTAAAACCAAGACTT
Found at i:298993 original size:59 final size:59
Alignment explanation
Indices: 298746--299042 Score: 262
Period size: 60 Copynumber: 4.9 Consensus size: 59
298736 ACTAAAATTC
* * * *
298746 AACAAAATGGCCTAGATAAAACCA-AAACCATAAACAATGACTTAGGACAAAACAAAGACTC
1 AACAAAATGGCCTAGATGAAACCAGAAACC-TAAACAATGACTTA-GTC-AAACCAAGACTT
* * * * * *
298807 AA-AGAACTGGCATGGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTT
1 AACA-AAATGGCCTAGATGAAACCAGAAACCTAAACAATGACTTA-GTCAAACCAAGACTT
** * * * * *
298867 AAGGAAATGGCCTAGATGAAACCA-TAACCTAAATAATGACTTGGGCCAAAACCAA-AGCTC
1 AACAAAATGGCCTAGATGAAACCAGAAACCTAAACAATGACTT-AGTC-AAACCAAGA-CTT
* * * *
298927 AACAAAATGG-CTTGAATGAAACTAGAAACCTAAATAATGACTTAGTCGAACCAAGACTT
1 AACAAAATGGCCTAG-ATGAAACCAGAAACCTAAACAATGACTTAGTCAAACCAAGACTT
* *
298986 AACAAAATGGCCTAGATGAAACCAGAAACCTAAACAATAACTTAGGCAAAACCAAGA
1 AACAAAATGGCCTAGATGAAACCAGAAACCTAAACAATGACTTAGTC-AAACCAAGA
299043 TTCAATGAAA
Statistics
Matches: 192, Mismatches: 33, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
59 67 0.35
60 68 0.35
61 52 0.27
62 5 0.03
ACGTcount: A:0.49, C:0.20, G:0.15, T:0.16
Consensus pattern (59 bp):
AACAAAATGGCCTAGATGAAACCAGAAACCTAAACAATGACTTAGTCAAACCAAGACTT
Found at i:299230 original size:60 final size:60
Alignment explanation
Indices: 298756--299247 Score: 221
Period size: 60 Copynumber: 8.2 Consensus size: 60
298746 AACAAAATGG
* * **
298756 CCTAGATAAAACC-AAAACCATAAACAATGACTTAGGACAAAACAAAGACTCAAAGAACTGG
1 CCTAGATAAAACCAAAAACC-TAAACAATGACTTAGG-CAAAACTAAGACTCAAAGAAATCC
* * * * * * **
298817 CATGGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTTAAGGAAATGG
1 CCTAGATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACTAAGACTCAAAGAAATCC
* * * * * *
298877 CCTAGATGAAACC-ATAACCTAAATAATGACTTGGGCCAAAACCAA-AGCTCAACA-AAAT-G
1 CCTAGATAAAACCAAAAACCTAAACAATGACTTAGG-CAAAACTAAGA-CTCAA-AGAAATCC
* * * * * * * * * * **
298936 GCTTGAATGAAACTAGAAACCTAAATAATGACTTAGTC-GAACCAAGACTTAACA-AAATGG
1 CCTAG-ATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACTAAGACTCAA-AGAAATCC
* * * * * * ***
298996 CCTAGATGAAACCAGAAACCTAAACAATAACTTAGGCAAAACCAAGATTCAATGAAAAGA
1 CCTAGATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACTAAGACTCAAAGAAATCC
* * * * * * * ** * ** * * * **
299056 TCTGGATAAAATCAGAAATCTAAATAAAT-A-TTCGAGTGAAACCATTATTCAATGAATTGG
1 CCTAGATAAAACCAAAAACCTAAA-CAATGACTTAG-GCAAAACTAAGACTCAAAGAAATCC
* * * * * *
299116 CCAAGATAAGACCAAAACCCTAAATAATGACTTGGGCAAAACTAAGATTCAAAGAAATCC
1 CCTAGATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACTAAGACTCAAAGAAATCC
* * * **
299176 CCTATATAAAACCAAAAACCTAAACAATGACTTAGGTAAAA-TCAAGACTGAAAGAAATGG
1 CCTAGATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACT-AAGACTCAAAGAAATCC
299236 CCTAGATAAAAC
1 CCTAGATAAAAC
299248 TAGAAGCCTA
Statistics
Matches: 334, Mismatches: 82, Indels: 31
0.75 0.18 0.07
Matches are distributed among these distances:
59 75 0.22
60 202 0.60
61 51 0.15
62 6 0.02
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (60 bp):
CCTAGATAAAACCAAAAACCTAAACAATGACTTAGGCAAAACTAAGACTCAAAGAAATCC
Found at i:299280 original size:360 final size:358
Alignment explanation
Indices: 298615--299319 Score: 857
Period size: 360 Copynumber: 2.0 Consensus size: 358
298605 ATTCAGGTGA
* * * * * *
298615 AACCAAGATTCAACAAAATAGCTTGGATGAAACCAAAAGCCTAAACAATAATTTGGGTGAAAATA
1 AACCAAGATTCAACAAAATAGCCTAGATGAAACCAAAAGCCTAAACAATAACTTAGGTCAAAACA
* * * *
298680 AGATTCAACGAAATGATACGGATAAAATCAAAAACCTAAACAGAGATTCGGGTGAAACTAAAATT
66 AGATTCAACGAAAAGATACGGATAAAATCAAAAACCTAAACAAAGATTCGAGTGAAACCAAAATT
*
298745 CAACAAAATGGCCTAGATAAAACCAAAACCATAAACAATGACTTAGGACAAAACAAAGACTCAAA
131 CAACAAAATGGCCAAGATAAAACCAAAACCATAAACAATGACTTAGGACAAAACAAAGACTCAAA
* ** * * *
298810 GAACTGGCATGGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTTAAGGAAAT
196 GAAATCCCATAGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTGAAAGAAAT
* * * * *
298875 GGCCTAGATGAAACCATAACCTAAATAATGACTTGGGCCAAAACCAAAGCTCAACAAAATGGCTT
261 GGCCTAGATAAAACCAGAACCTAAATAATGACTT-GGCCAAAACCAAAACTCAA-AAAATGACCT
298940 GAATGAA-ACTAGAAACCTAAATAATGACTTAGTCG
324 GAAT-AATACTAGAAACCTAAATAATGACTTAGTCG
*
298975 AACCAAGACTT-AACAAAATGGCCTAGATGAAACCAGAAA-CCTAAACAATAACTTAGG-CAAAA
1 AACCAAGA-TTCAACAAAATAGCCTAGATGAAACCA-AAAGCCTAAACAATAACTTAGGTCAAAA
* * * * * *
299037 CCAAGATTCAATGAAAAGAT-CTGGATAAAATCAGAAATCTAAATAAATATTCGAGTGAAACCAT
64 -CAAGATTCAACGAAAAGATAC-GGATAAAATCAAAAACCTAAACAAAGATTCGAGTGAAACCAA
* ** * * * * * * *
299101 TATTCAATGAATTGGCCAAGATAAGACCAAAACCCTAAATAATGACTT-GGGCAAAACTAAGATT
127 AATTCAACAAAATGGCCAAGATAAAACCAAAACCATAAACAATGACTTAGGACAAAACAAAGACT
* * *
299165 CAAAGAAATCCCCTATATAAAACCAAAAACCTAAACAATGACTTAGGTAAAATCAAGACTGAAAG
192 CAAAGAAATCCCATAGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTGAAAG
* * *
299230 AAATGGCCTAGATAAAACTAGAAGCCTAGATAAATGACTT-GCATAAAACCAAAACTCAAAAAAT
257 AAATGGCCTAGATAAAACCAGAA-CCTAAAT-AATGACTTGGC-CAAAACCAAAACTCAAAAAAT
*
299294 GACCTGGATAATACTAGAAACCTAAA
319 GACCTGAATAATACTAGAAACCTAAA
299320 CCATGACTAT
Statistics
Matches: 291, Mismatches: 46, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
358 2 0.01
359 121 0.42
360 155 0.53
361 13 0.04
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (358 bp):
AACCAAGATTCAACAAAATAGCCTAGATGAAACCAAAAGCCTAAACAATAACTTAGGTCAAAACA
AGATTCAACGAAAAGATACGGATAAAATCAAAAACCTAAACAAAGATTCGAGTGAAACCAAAATT
CAACAAAATGGCCAAGATAAAACCAAAACCATAAACAATGACTTAGGACAAAACAAAGACTCAAA
GAAATCCCATAGATAAAACCAAAAACCTAAACAATGACTTAGGTAAAACCAAGACTGAAAGAAAT
GGCCTAGATAAAACCAGAACCTAAATAATGACTTGGCCAAAACCAAAACTCAAAAAATGACCTGA
ATAATACTAGAAACCTAAATAATGACTTAGTCG
Found at i:300125 original size:13 final size:13
Alignment explanation
Indices: 300107--300132 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300097 CAATTTTTTG
300107 TGTATCGATACAT
1 TGTATCGATACAT
300120 TGTATCGATACAT
1 TGTATCGATACAT
300133 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:300836 original size:40 final size:40
Alignment explanation
Indices: 300792--300910 Score: 103
Period size: 40 Copynumber: 3.1 Consensus size: 40
300782 ATTTGTACAT
300792 TCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTA
1 TCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTA
* * * * *
300832 TCTCCCTCGTTTATTAA--TAAAT-A-G--TT-TGTAC-AT-
1 TCTCCC-C-CTTAATAAGGTAAATCACGCATTCTCTCCTTTA
*
300865 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTA
1 TCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTA
300905 TCTCCC
1 TCTCCC
300911 TCGTTTATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 22
0.63 0.12 0.24
Matches are distributed among these distances:
31 6 0.11
32 1 0.02
33 10 0.18
34 2 0.04
35 4 0.07
36 2 0.04
37 2 0.04
38 4 0.07
39 2 0.04
40 17 0.30
41 1 0.02
42 6 0.11
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.39
Consensus pattern (40 bp):
TCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTA
Found at i:300902 original size:73 final size:73
Alignment explanation
Indices: 300783--300926 Score: 279
Period size: 73 Copynumber: 2.0 Consensus size: 73
300773 ATTTAACGAA
300783 TTTGTACATTCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTATCTCCCTCGTTTATTA
1 TTTGTACATTCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTATCTCCCTCGTTTATTA
300848 ATAAATAG
66 ATAAATAG
*
300856 TTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCTCGTTTATTA
1 TTTGTACATTCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTATCTCCCTCGTTTATTA
300921 ATAAAT
66 ATAAAT
300927 CTCCCCCTTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.41
Consensus pattern (73 bp):
TTTGTACATTCTCCCCCTTAATAAGGTAAATCACGCATTCTCTCCTTTATCTCCCTCGTTTATTA
ATAAATAG
Found at i:302771 original size:13 final size:13
Alignment explanation
Indices: 302753--302791 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
302743 ATAATCACCC
302753 TGTATCGATACAA
1 TGTATCGATACAA
302766 TGTATCGATACAA
1 TGTATCGATACAA
302779 TGTATCGATACAA
1 TGTATCGATACAA
302792 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:304892 original size:15 final size:15
Alignment explanation
Indices: 304872--304902 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
304862 ATTTCGTTTG
*
304872 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
304887 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
304902 G
1 G
304903 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:306735 original size:21 final size:21
Alignment explanation
Indices: 306706--306750 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
306696 AAGTTTTCAT
*
306706 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
306726 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
306748 TTT
1 TTT
306751 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:308986 original size:13 final size:13
Alignment explanation
Indices: 308968--308993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
308958 CAATTTTTTG
308968 TGTATCGATACAT
1 TGTATCGATACAT
308981 TGTATCGATACAT
1 TGTATCGATACAT
308994 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:310178 original size:88 final size:87
Alignment explanation
Indices: 310074--310421 Score: 353
Period size: 88 Copynumber: 4.0 Consensus size: 87
310064 ATATGCACAT
* * *
310074 GAAATGGTGTAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATTATGCAAATACCAATG
1 GAAATGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATG
*
310139 TCATCCAAAGTATAGATGTGTG
66 TCATCTAAAGTATAGATGTGTG
*
310161 CGAAATGATGCAAATGCAAGCATCAATAAAGTGGTAAATGCATATGAAAT-ATTGCAAATACCAA
1 -GAAATGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGA-TGCAAATACCAA
* *
310225 TGTCATCTAAAGTACAGATGTACAT-
64 TGTCATCTAAAGTATAGATGT--GTG
** * ** * * *
310250 GAAATGATGCAGCTGCAAGCATCAATAAAGTAGCAGTTGCATATGAAATGATGTAAATGCCAACG
1 GAAATGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATG
* * * *
310315 TTATCTAAAAT-TCAAATATGCATG
66 TCATCTAAAGTAT-AGATGTG--TG
* * ** * * *
310339 G-AATGATGCCACTATAAGCATTAATAAAGTGGAAAATGCATATGAAATGATGCAAATGCCAATG
1 GAAATGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATG
*
310403 TCATCTAAAGGTGTAGATG
66 TCATCTAAA-GTATAGATG
310422 CACATAAAAT
Statistics
Matches: 214, Mismatches: 36, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
87 1 0.00
88 205 0.96
89 6 0.03
90 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (87 bp):
GAAATGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATG
TCATCTAAAGTATAGATGTGTG
Found at i:310210 original size:44 final size:44
Alignment explanation
Indices: 310048--310440 Score: 143
Period size: 44 Copynumber: 8.9 Consensus size: 44
310038 GAGGAAAATG
* * * * *
310048 TGTCATCTAATGAT-GCATATGCACATGAAATGGTGTAAATGCAA
1 TGTCATCTAAAG-TGGCAAATGCATATGAAATGATGCAAATGCAA
* *
310092 -G-CATCAATAAAGTGGCAAATGCATATGAAATTATGCAAATACCAA
1 TGTCATC--TAAAGTGGCAAATGCATATGAAATGATGCAAAT-GCAA
* ** * ** **
310137 TGTCATCCAAAGT-ATAGATGTGTGCGAAATGATGCAAATGCAA
1 TGTCATCTAAAGTGGCAAATGCATATGAAATGATGCAAATGCAA
* *
310180 -G-CATCAATAAAGTGGTAAATGCATATGAAAT-ATTGCAAATACCAA
1 TGTCATC--TAAAGTGGCAAATGCATATGAAATGA-TGCAAAT-GCAA
* * * * **
310225 TGTCATCTAAAGT-ACAGATGTACATGAAATGATGCAGCTGCAA
1 TGTCATCTAAAGTGGCAAATGCATATGAAATGATGCAAATGCAA
* ** *
310268 -G-CATCAATAAAGTAGCAGTTGCATATGAAATGATGTAAATGCCAA
1 TGTCATC--TAAAGTGGCAAATGCATATGAAATGATGCAAATG-CAA
* * * * * * * **
310313 CGTTATCTAAAAT-TCAAAT--ATGCATGGAATGATGCCACTATAA
1 TGTCATCTAAAGTGGCAAATGCAT--ATGAAATGATGCAAATGCAA
* *
310356 -G-CATTAATAAAGTGGAAAATGCATATGAAATGATGCAAATGCCAA
1 TGTCA-T-CTAAAGTGGCAAATGCATATGAAATGATGCAAATG-CAA
* * * *
310401 TGTCATCTAAAG-GTGTAGATGCACATAAAATGATGCAAAT
1 TGTCATCTAAAGTG-GCAAATGCATATGAAATGATGCAAAT
310441 ACAGATGATA
Statistics
Matches: 252, Mismatches: 66, Indels: 61
0.66 0.17 0.16
Matches are distributed among these distances:
41 9 0.04
42 10 0.04
43 27 0.11
44 131 0.52
45 55 0.22
46 7 0.03
47 13 0.05
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (44 bp):
TGTCATCTAAAGTGGCAAATGCATATGAAATGATGCAAATGCAA
Done.