Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 95 of 126
Found at i:29292120 original size:86 final size:85
Alignment explanation
Indices: 29291966--29292132 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 85
29291956 CGAACCCCAA
* ** * * *
29291966 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAATATGGTTAGCTTCTTGATGAGATACT
1 CTTCCTGATGAGATACAGAGAAGCAAATCGAAACAATAATACGGTTAGCTTCTTGATAAGATACT
*
29292031 GAGAAGTAGACCAAATTCGT
66 GAGAAGAAGACCAAATTCGT
* * * *
29292051 CTTCCTGATGAGATACAGAGATGCAAATTGAAACAAGTCATACGGTTATCTTGC-TGATAAGATA
1 CTTCCTGATGAGATACAGAGAAGCAAATCGAAACAA-TAATACGGTTAGCTT-CTTGATAAGATA
29292115 CTGAGAAGAAGACCAAAT
64 CTGAGAAGAAGACCAAAT
29292133 CAAACCTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 30 0.43
86 38 0.55
87 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGCAAATCGAAACAATAATACGGTTAGCTTCTTGATAAGATACT
GAGAAGAAGACCAAATTCGT
Found at i:29292429 original size:201 final size:201
Alignment explanation
Indices: 29291897--29292522 Score: 797
Period size: 201 Copynumber: 3.1 Consensus size: 201
29291887 CGAGGCGATT
* * * * *
29291897 ATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAAGGTTCAAAGTGAGCAAATCTTCGAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAACGCTCGATGTGAGCAAATCTTCGAACC
* * *
29291962 CCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAATATGGTTAGCTTCTTGATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * ** * * *
29292027 TACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGATGCAAATTGAAACAAGTCAT
131 TACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTAAG
*
29292092 ACGGTT
196 ACGGTC
* * * * * * * *
29292098 ATCTTGCTGATAAGATACTGAGAAGAAGACCAAATCAAACCTATGCGCGATATGAGCAAATCTTC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-AA-C---GCTCGATGTGAGCAAATCTTC
29292163 GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
61 GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
29292228 TGAGATACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAA
126 TGAGATACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAA
* *
29292293 GTGAGACAGTC
191 GTAAGACGGTC
* * *
29292304 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGACGCTCGATGGGAGCAAATCTTTGAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAACGCTCGATGTGAGCAAATCTTCGAACC
* * * *
29292369 TCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCCTGATGAGG
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * * * * * * *
29292434 TACGGAGAAG-TGAACCAAATCCGTCCTCCTAATGAAACACAGAGAAGTGGATCAAAACAAGTAA
131 TACTGAGAAGTTG-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTAA
*
29292498 TG-TGGTC
195 -GACGGTC
29292505 ATCTTCCTGATGAGATAC
1 ATCTTCCTGATGAGATAC
29292523 TAAGAAGGCC
Statistics
Matches: 367, Mismatches: 51, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
200 2 0.01
201 185 0.50
202 3 0.01
204 1 0.00
205 1 0.00
206 175 0.48
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (201 bp):
ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAACGCTCGATGTGAGCAAATCTTCGAACC
CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
TACTGAGAAGTTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGTAAG
ACGGTC
Found at i:29292888 original size:6 final size:6
Alignment explanation
Indices: 29292832--29292948 Score: 70
Period size: 6 Copynumber: 20.2 Consensus size: 6
29292822 CCGGGCCCCT
* * * * *
29292832 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTGAA TTTAAA ATT-AT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
29292877 TTTAAA TTTAAA TTT--A TTCTAAAA TTTAAA TTTAAT TTTATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TT-T-AAA TTTAAA TTTAAA TTTAAA TTTAAA
*
29292925 TTTAAA ATT--A TTATAAA TTTAAA T
1 TTTAAA TTTAAA TT-TAAA TTTAAA T
29292949 AATAAAATGT
Statistics
Matches: 84, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
4 5 0.06
5 14 0.17
6 58 0.69
7 4 0.05
8 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:29292903 original size:18 final size:17
Alignment explanation
Indices: 29292832--29292928 Score: 124
Period size: 17 Copynumber: 5.6 Consensus size: 17
29292822 CCGGGCCCCT
29292832 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
29292850 -TTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
29292866 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
*
29292883 TTTAAATTTATTCTAAAA
1 TTTAAATTTATT-TTAAA
*
29292901 TTTAAATTTAATTTTATA
1 TTTAAATTT-ATTTTAAA
29292919 TTTAAATTTA
1 TTTAAATTTA
29292929 AAATTATTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.01
17 40 0.58
18 25 0.36
19 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:29292943 original size:17 final size:17
Alignment explanation
Indices: 29292832--29292947 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 17
29292822 CCGGGCCCCT
*
29292832 TTTAAATTTATTTTAAGA
1 TTTAAAATTATTTTAA-A
* *
29292850 -TTAAATTTATTTTGAA
1 TTTAAAATTATTTTAAA
29292866 TTTAAAATTATTTTAAA
1 TTTAAAATTATTTTAAA
* *
29292883 TTTAAATTTATTCTAAAA
1 TTTAAAATTATT-TTAAA
29292901 TTTAAATTTAATTTTATATTTAAA
1 TTT-AA---AA--TTAT-TTTAAA
*
29292925 TTTAAAATTATTATAAA
1 TTTAAAATTATTTTAAA
29292942 TTTAAA
1 TTTAAA
29292948 TAATAAAATG
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.01
17 50 0.62
18 11 0.14
19 2 0.02
20 2 0.02
22 1 0.01
23 2 0.02
24 11 0.14
25 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:29293206 original size:25 final size:25
Alignment explanation
Indices: 29293178--29293233 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
29293168 CTACTGTTGC
* *
29293178 CCACCCGCTTCAACCTGTTCTGCCA
1 CCACCAGCTTCAACCTGCTCTGCCA
29293203 CCACCAGCTTCAACCTGCTCTGCCA
1 CCACCAGCTTCAACCTGCTCTGCCA
*
29293228 TCACCA
1 CCACCA
29293234 CCACTATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.48, G:0.11, T:0.21
Consensus pattern (25 bp):
CCACCAGCTTCAACCTGCTCTGCCA
Found at i:29293698 original size:10 final size:10
Alignment explanation
Indices: 29293680--29293709 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29293670 TAACGGTAAT
*
29293680 AATAATATTA
1 AATATTATTA
29293690 AATATTATTA
1 AATATTATTA
29293700 AATATTATTA
1 AATATTATTA
29293710 CATTTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATTATTA
Found at i:29294876 original size:29 final size:29
Alignment explanation
Indices: 29294825--29294935 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
29294815 CCCTAAACCG
** * *
29294825 TCCAAAAATTAAAATTTTAACCCCGAACT
1 TCCAAAAATTCCATTTTTGACCCCGAACT
29294854 TCCAAAAATTCCATTTTTGACCCCGAAACAT
1 TCCAAAAATTCCATTTTTGACCCCG-AAC-T
*
29294885 T-CAAAAATCACCA-TTTTG-CCCTCGAA-T
1 TCCAAAAAT-TCCATTTTTGACCC-CGAACT
* *
29294912 GTCCAAAAATTCTATTTTCGACCC
1 -TCCAAAAATTCCATTTTTGACCC
29294936 AATTTTTTCT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.02
28 3 0.05
29 37 0.56
30 20 0.30
31 5 0.08
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTGACCCCGAACT
Found at i:29296722 original size:27 final size:30
Alignment explanation
Indices: 29296662--29296725 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
29296652 TATTTCAAAA
*
29296662 TTTTTCATTTAAGTCACTAGATTATTTGGGAG
1 TTTTTCATTTAAGTCACAAGATTATTT--GAG
29296694 TTTTT-ATTTAAGTCACAAGATTA-TT-AG
1 TTTTTCATTTAAGTCACAAGATTATTTGAG
29296721 TTTTT
1 TTTTT
29296726 TGTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
30 2 0.06
31 17 0.55
32 5 0.16
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (30 bp):
TTTTTCATTTAAGTCACAAGATTATTTGAG
Found at i:29297739 original size:17 final size:18
Alignment explanation
Indices: 29297713--29297746 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29297703 TATTTTTTTG
*
29297713 TAATATTTTAT-ATTTAT
1 TAATAATTTATGATTTAT
29297730 TAATAATTTATGATTTA
1 TAATAATTTATGATTTA
29297747 ATCGTTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATAATTTATGATTTAT
Found at i:29303025 original size:31 final size:29
Alignment explanation
Indices: 29302990--29303085 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 29
29302980 ACCTCAAAAT
* * *
29302990 TATACATGAATTTTGATTTAATGTACAATTG
1 TATACATGAACTTTAATTT-A-GTACAATTA
29303021 TATACATGAACTTTAATTTAGTACAATTA
1 TATACATGAACTTTAATTTAGTACAATTA
* * **
29303050 TATACATAAACTTTAATTTGGTGTAATTA
1 TATACATGAACTTTAATTTAGTACAATTA
29303079 TATACAT
1 TATACAT
29303086 AAAATTCTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 40 0.69
30 1 0.02
31 17 0.29
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAGTACAATTA
Found at i:29303086 original size:29 final size:29
Alignment explanation
Indices: 29303012--29303102 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
29303002 TTGATTTAAT
* *
29303012 GTACAATTGTATACATGAACTTTAATTTA
1 GTACAATTATATACATAAACTTTAATTTA
*
29303041 GTACAATTATATACATAAACTTTAATTTG
1 GTACAATTATATACATAAACTTTAATTTA
** *
29303070 GTGTAATTATATACATAAAATTCTAATTGTA
1 GTACAATTATATACATAAACTT-TAATT-TA
29303101 GT
1 GT
29303103 TCAAACGTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
29 45 0.85
30 5 0.09
31 3 0.06
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (29 bp):
GTACAATTATATACATAAACTTTAATTTA
Found at i:29303804 original size:11 final size:11
Alignment explanation
Indices: 29303788--29303820 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29303778 TTTTTTTTAT
29303788 AAAAATTGTAA
1 AAAAATTGTAA
*
29303799 AAAAATTAT-A
1 AAAAATTGTAA
29303809 AAAAATTGTAA
1 AAAAATTGTAA
29303820 A
1 A
29303821 CTTTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (11 bp):
AAAAATTGTAA
Found at i:29303827 original size:20 final size:21
Alignment explanation
Indices: 29303782--29303833 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
29303772 ATTAGATTTT
29303782 TTTTAT-AAAAATTGTAAAAA
1 TTTTATAAAAAATTGTAAAAA
** *
29303802 AATTATAAAAAATTGT-AAAC
1 TTTTATAAAAAATTGTAAAAA
29303822 TTTTATAAAAAA
1 TTTTATAAAAAA
29303834 AATTATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
TTTTATAAAAAATTGTAAAAA
Found at i:29304061 original size:29 final size:30
Alignment explanation
Indices: 29304008--29304104 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 30
29303998 TTACATTTTC
* * *
29304008 TATAATTTTCTTACAACTTTA-TAAAATTT
1 TATAATTTTTTTATAATTTTATTAAAATTT
* **
29304037 TATAATTTTTTTCTAATTTT-TTAAAAAAT
1 TATAATTTTTTTATAATTTTATTAAAATTT
* *
29304066 TAAATATTTTTTTATCATTTTATTAAAATTT
1 TATA-ATTTTTTTATAATTTTATTAAAATTT
*
29304097 AATAATTT
1 TATAATTT
29304105 GTATAACTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 25 0.48
30 18 0.35
31 9 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
TATAATTTTTTTATAATTTTATTAAAATTT
Found at i:29313585 original size:28 final size:27
Alignment explanation
Indices: 29313554--29313618 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
29313544 TAATATAAAC
29313554 ATAAAATAAATAA-AATAGAAATATATT
1 ATAAAATAAA-AATAATAGAAATATATT
* **
29313581 AATAATATAAAAATAATATTAATATATT
1 -ATAAAATAAAAATAATAGAAATATATT
29313609 AT-AAATAAAA
1 ATAAAATAAAA
29313619 TATATAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 7 0.22
27 4 0.12
28 21 0.66
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
ATAAAATAAAAATAATAGAAATATATT
Found at i:29313598 original size:22 final size:24
Alignment explanation
Indices: 29313566--29313623 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 24
29313556 AAAATAAATA
29313566 AAATAGAAATATATTAATA-A-TAT
1 AAATA-AAATATATTAATATATTAT
*
29313589 AAA-AATA-ATATTAATATATTAT
1 AAATAAAATATATTAATATATTAT
29313611 AAATAAAATATAT
1 AAATAAAATATAT
29313624 AAATGAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 9 0.31
21 3 0.10
22 7 0.24
23 6 0.21
24 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATAAAATATATTAATATATTAT
Found at i:29313615 original size:39 final size:39
Alignment explanation
Indices: 29313518--29313596 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
29313508 AATGAAAAGG
* *
29313518 AAATAAATGAAATAGAAATAGATAAATAATATAAACATA
1 AAATAAATAAAATAGAAATAGATAAATAATATAAAAATA
* *
29313557 AAATAAATAAAATAGAAATATATTAATAATATAAAAATA
1 AAATAAATAAAATAGAAATAGATAAATAATATAAAAATA
29313596 A
1 A
29313597 TATTAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.25
Consensus pattern (39 bp):
AAATAAATAAAATAGAAATAGATAAATAATATAAAAATA
Found at i:29313616 original size:20 final size:20
Alignment explanation
Indices: 29313542--29313604 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
29313532 GAAATAGATA
* * *
29313542 AATAATATAAACATAAAATA
1 AATAATATAAAAATAATATT
* *
29313562 AATAAAATAGAAAT-ATATT
1 AATAATATAAAAATAATATT
29313581 AATAATATAAAAATAATATT
1 AATAATATAAAAATAATATT
29313601 AATA
1 AATA
29313605 TATTATAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAATATAAAAATAATATT
Found at i:29313640 original size:34 final size:33
Alignment explanation
Indices: 29313584--29313647 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
29313574 ATATATTAAT
*
29313584 AATATAAAAATAATATTAATATATTATAAATAA
1 AATATAAAAATAATATTAATATATAATAAATAA
*
29313617 AATATATAAATGAAT-TCTAATATATAATAAA
1 AATATAAAAAT-AATAT-TAATATATAATAAA
29313648 AATCTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (33 bp):
AATATAAAAATAATATTAATATATAATAAATAA
Found at i:29315872 original size:24 final size:24
Alignment explanation
Indices: 29315845--29315893 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29315835 AATGACGAGG
29315845 AATGATAATTGATATATGTATGTA
1 AATGATAATTGATATATGTATGTA
29315869 AATGATAATTGATATATGTATGTA
1 AATGATAATTGATATATGTATGTA
29315893 A
1 A
29315894 GTGTGTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (24 bp):
AATGATAATTGATATATGTATGTA
Found at i:29316210 original size:3 final size:3
Alignment explanation
Indices: 29316157--29316191 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29316147 CTTTTAAGTT
29316157 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29316192 TCGTTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29316414 original size:20 final size:20
Alignment explanation
Indices: 29316378--29316421 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29316368 ATAATTCAAG
*
29316378 AATTTAAAAATGTTATAAAT
1 AATTTAAAAATGTTATAAAA
*
29316398 AATTTAAAGAT-TGTATAAAA
1 AATTTAAAAATGT-TATAAAA
29316418 AATT
1 AATT
29316422 ATAATTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
AATTTAAAAATGTTATAAAA
Found at i:29316625 original size:52 final size:54
Alignment explanation
Indices: 29316532--29316643 Score: 131
Period size: 52 Copynumber: 2.1 Consensus size: 54
29316522 AAATATAAAA
* * *
29316532 TATTTATATAAGATACAAGATTTGAACAAAACAATAAAAATAAATATTTAT-TT
1 TATTTATATAAAATACAAGATTTAAACAAAACAATAAAAATAAACATTTATATT
* * **
29316585 T-TTTATATAAAATATCAA-ATTTAAACAAATCACTTTAAATAAACATTTATATT
1 TATTTATATAAAATA-CAAGATTTAAACAAAACAATAAAAATAAACATTTATATT
29316638 TATTTA
1 TATTTA
29316644 AAACATCAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
52 38 0.78
53 7 0.14
54 4 0.08
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (54 bp):
TATTTATATAAAATACAAGATTTAAACAAAACAATAAAAATAAACATTTATATT
Found at i:29320466 original size:15 final size:15
Alignment explanation
Indices: 29320429--29320469 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29320419 TTTTCTTTGA
29320429 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
29320445 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
29320457 TTTCACAATTTAA
1 TTTCACAATTTAA
29320470 AGCTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:29326727 original size:45 final size:46
Alignment explanation
Indices: 29326677--29326763 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
29326667 CAAAATAAGT
*
29326677 TTAATATGTAAAACTAAAAGAAAATTAATA-TT-GAAATTTTAAGAG
1 TTAATATCTAAAACTAAAAGAAAATTAA-AGTTCGAAATTTTAAGAG
** * *
29326722 TTAATATCTAATGCTAAAGGAAAGTTAAAGTTCGAAATTTTA
1 TTAATATCTAAAACTAAAAGAAAATTAAAGTTCGAAATTTTA
29326764 CAACTAGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.03
45 25 0.71
46 9 0.26
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (46 bp):
TTAATATCTAAAACTAAAAGAAAATTAAAGTTCGAAATTTTAAGAG
Found at i:29331376 original size:60 final size:60
Alignment explanation
Indices: 29331283--29331403 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
29331273 GATTATACCT
29331283 GCTTATAAGTAGGATTATTGGCTTAGATCCGAAGGTCTGTCCGAAATTTGAGAGGGTTTG
1 GCTTATAAGTAGGATTATTGGCTTAGATCCGAAGGTCTGTCCGAAATTTGAGAGGGTTTG
29331343 GCTTATAAGTAGGATTATTGGCTTAGATCCGAAGGTCTGTCCGAAATTTGAGAGGGTTTG
1 GCTTATAAGTAGGATTATTGGCTTAGATCCGAAGGTCTGTCCGAAATTTGAGAGGGTTTG
29331403 G
1 G
29331404 GTAAAAAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.33
Consensus pattern (60 bp):
GCTTATAAGTAGGATTATTGGCTTAGATCCGAAGGTCTGTCCGAAATTTGAGAGGGTTTG
Found at i:29333041 original size:20 final size:20
Alignment explanation
Indices: 29332990--29333041 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
29332980 TTTATTAATT
* **
29332990 TTTTGAA-TTTTAAAAATTG
1 TTTTGAATTTTTTAAAATCA
* *
29333009 TTTTAAATATTTTAAAATCA
1 TTTTGAATTTTTTAAAATCA
29333029 TTTTGAATTTTTT
1 TTTTGAATTTTTT
29333042 GTAATTTTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATCA
Found at i:29334433 original size:28 final size:28
Alignment explanation
Indices: 29334378--29334439 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
29334368 TTTGTGAACA
* * * *
29334378 TTAAACAAACGAACATGAACATATAATT
1 TTAAATAAACAAACATGAACAAAAAATT
*
29334406 TTAAATAAACAAACATGAATAAAAAATT
1 TTAAATAAACAAACATGAACAAAAAATT
*
29334434 TGAAAT
1 TTAAAT
29334440 TCTTAACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (28 bp):
TTAAATAAACAAACATGAACAAAAAATT
Found at i:29336595 original size:6 final size:6
Alignment explanation
Indices: 29336584--29336650 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
29336574 AGGGTCGCTA
* * * *
29336584 TGTGTT TGTGTT TGTGTT TGTGTT TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
29336632 TGTGTG TGTGTG TGTGTG T
1 TGTGTG TGTGTG TGTGTG T
29336651 ATATATATAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.00, C:0.00, G:0.43, T:0.57
Consensus pattern (6 bp):
TGTGTG
Found at i:29338989 original size:29 final size:29
Alignment explanation
Indices: 29338907--29339113 Score: 192
Period size: 29 Copynumber: 7.2 Consensus size: 29
29338897 AGACTGCACA
* * *
29338907 ACAAAGGCATTTCCTTTTCAGAGATAGCC
1 ACAAAGGCATTTCCTTTACAGAGATTGAC
29338936 ACAAAGGC--TTCCTTTAACAGAGATTGAC
1 ACAAAGGCATTTCCTTT-ACAGAGATTGAC
* **
29338964 ACAAAGGCATTTCCATTACAGAGATTTCC
1 ACAAAGGCATTTCCTTTACAGAGATTGAC
**
29338993 ACAAAGGTGTTTCCTTTACAGAGATT-ACC
1 ACAAAGGCATTTCCTTTACAGAGATTGA-C
* * * * *
29339022 ATAAAGGCATTTCATTAACAAAGA-TCACC
1 ACAAAGGCATTTCCTTTACAGAGATTGA-C
*
29339051 ACAAAGGCATTTCCTTTACAGAGATTGCC
1 ACAAAGGCATTTCCTTTACAGAGATTGAC
*
29339080 ACAAAGGCATTT-CTTTAACAAAGATT-ACC
1 ACAAAGGCATTTCCTTT-ACAGAGATTGA-C
29339109 ACAAA
1 ACAAA
29339114 AGTGTTTCAT
Statistics
Matches: 146, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
27 7 0.05
28 22 0.15
29 110 0.75
30 7 0.05
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (29 bp):
ACAAAGGCATTTCCTTTACAGAGATTGAC
Found at i:29339034 original size:58 final size:58
Alignment explanation
Indices: 29338944--29339145 Score: 246
Period size: 58 Copynumber: 3.5 Consensus size: 58
29338934 CCACAAAGGC
* *
29338944 TTCCTTTAACAGAGATTGA-CACAAAGGCATTTCCATT-ACAGAGATTTCCACAAAGGTGT
1 TTCCTTT-ACAGAGATT-ACCACAAAGGCATTT-CATTAACAAAGATTACCACAAAGGTGT
* * **
29339003 TTCCTTTACAGAGATTACCATAAAGGCATTTCATTAACAAAGATCACCACAAAGGCAT
1 TTCCTTTACAGAGATTACCACAAAGGCATTTCATTAACAAAGATTACCACAAAGGTGT
* * *
29339061 TTCCTTTACAGAGATTGCCACAAAGGCATTTCTTTAACAAAGATTACCACAAAAGTGT
1 TTCCTTTACAGAGATTACCACAAAGGCATTTCATTAACAAAGATTACCACAAAGGTGT
* * * *
29339119 TTCATTTACAAAGATTTCCAGAAAGGC
1 TTCCTTTACAGAGATTACCACAAAGGC
29339146 GTTCTTTAAG
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
57 5 0.04
58 112 0.90
59 7 0.06
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (58 bp):
TTCCTTTACAGAGATTACCACAAAGGCATTTCATTAACAAAGATTACCACAAAGGTGT
Found at i:29339072 original size:87 final size:85
Alignment explanation
Indices: 29338907--29339133 Score: 262
Period size: 87 Copynumber: 2.6 Consensus size: 85
29338897 AGACTGCACA
* * * * *
29338907 ACAAAGGCATTTCCTTTTCAGAGA-TAGCCACAAAGGCTTCCTTTAACAGAGATTGACACAAAGG
1 ACAAAGGCATTTCCTTTACAGAGATTA-CCACAAAGGCTTTCATTAACAAAGA-TCACACAAAGG
*
29338971 CATTTCCATTACAGAGATTTCC
64 CATTTCCATTACAGAGATTGCC
** *
29338993 ACAAAGGTGTTTCCTTTACAGAGATTACCATAAAGGCATTTCATTAACAAAGATCACCACAAAGG
1 ACAAAGGCATTTCCTTTACAGAGATTACCACAAAGGC-TTTCATTAACAAAGATCA-CACAAAGG
*
29339058 CATTTCCTTTACAGAGATTGCC
64 CATTTCCATTACAGAGATTGCC
* *
29339080 ACAAAGGCATTT-CTTTAACAAAGATTACCACAAAAGTG-TTTCATTTACAAAGAT
1 ACAAAGGCATTTCCTTT-ACAGAGATTACCAC-AAAG-GCTTTCATTAACAAAGAT
29339134 TTCCAGAAAG
Statistics
Matches: 120, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
86 36 0.30
87 79 0.66
88 4 0.03
89 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (85 bp):
ACAAAGGCATTTCCTTTACAGAGATTACCACAAAGGCTTTCATTAACAAAGATCACACAAAGGCA
TTTCCATTACAGAGATTGCC
Found at i:29339121 original size:29 final size:28
Alignment explanation
Indices: 29338907--29339153 Score: 187
Period size: 29 Copynumber: 8.6 Consensus size: 28
29338897 AGACTGCACA
* *
29338907 ACAAAGGCATTTCCTTTTCAGAGA-TAGCC
1 ACAAAGGCATTT-CTTTACAAAGATTA-CC
* *
29338936 ACAAAGGC-TTCCTTTAACAGAGATTGA-C
1 ACAAAGGCATTTCTTT-ACAAAGATT-ACC
* * *
29338964 ACAAAGGCATTTCCATTACAGAGATTTCC
1 ACAAAGGCATTT-CTTTACAAAGATTACC
** *
29338993 ACAAAGGTGTTTCCTTTACAGAGATTACC
1 ACAAAGGCATTT-CTTTACAAAGATTACC
* * *
29339022 ATAAAGGCATTTCATTAACAAAGATCACC
1 ACAAAGGCATTTC-TTTACAAAGATTACC
* *
29339051 ACAAAGGCATTTCCTTTACAGAGATTGCC
1 ACAAAGGCATTT-CTTTACAAAGATTACC
29339080 ACAAAGGCATTTCTTTAACAAAGATTACC
1 ACAAAGGCATTTCTTT-ACAAAGATTACC
* ** *
29339109 ACAAAAGTGTTTCATTTACAAAGATTTCC
1 ACAAAGGCATTTC-TTTACAAAGATTACC
* *
29339138 AGAAAGGC-GTTCTTTA
1 ACAAAGGCATTTCTTTA
29339154 AGAGGTTTAT
Statistics
Matches: 178, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
27 8 0.04
28 25 0.14
29 137 0.77
30 8 0.04
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (28 bp):
ACAAAGGCATTTCTTTACAAAGATTACC
Found at i:29339621 original size:15 final size:15
Alignment explanation
Indices: 29339601--29339654 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29339591 ACTATACATT
29339601 GACTTATTCATAACA
1 GACTTATTCATAACA
* * *
29339616 GACTTACTAATGACA
1 GACTTATTCATAACA
*
29339631 GACATT-TTCACAACA
1 GAC-TTATTCATAACA
29339646 GACTTATTC
1 GACTTATTC
29339655 GTATTGGACT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.31
Consensus pattern (15 bp):
GACTTATTCATAACA
Found at i:29341294 original size:21 final size:21
Alignment explanation
Indices: 29341270--29341318 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
29341260 TAACGGGTTG
29341270 TCAAATTGATAAATGTGTTTA
1 TCAAATTGATAAATGTGTTTA
*
29341291 TCAAATTGATAAATGTGTTTG
1 TCAAATTGATAAATGTGTTTA
29341312 TCAAATT
1 TCAAATT
29341319 AAATATTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (21 bp):
TCAAATTGATAAATGTGTTTA
Found at i:29341949 original size:24 final size:24
Alignment explanation
Indices: 29341902--29341949 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29341892 GTGATAATTT
** *
29341902 TAAAATAAAATTATTTTTTTAATA
1 TAAAATAAAATTATTACTTGAATA
29341926 TAAAATAAAATTATTACTTGAATA
1 TAAAATAAAATTATTACTTGAATA
29341950 GAATTCTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TAAAATAAAATTATTACTTGAATA
Found at i:29344459 original size:23 final size:23
Alignment explanation
Indices: 29344433--29344488 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
29344423 ATGCCAGTTG
*
29344433 GAAATTTTTAAATTAATTTTTTT
1 GAAACTTTTAAATTAATTTTTTT
*
29344456 GAAACTTTTAGATTAATTTTTTT
1 GAAACTTTTAAATTAATTTTTTT
*
29344479 AAAACTTTTA
1 GAAACTTTTA
29344489 CTTCAATGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (23 bp):
GAAACTTTTAAATTAATTTTTTT
Found at i:29345887 original size:18 final size:18
Alignment explanation
Indices: 29345866--29345907 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
29345856 ATTTTTTTAA
29345866 AAAAAT-TAAATAAATATT
1 AAAAATATAAA-AAATATT
* *
29345884 AAAAATATGAAAAATGTT
1 AAAAATATAAAAAATATT
29345902 AAAAAT
1 AAAAAT
29345908 GATTAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATATAAAAAATATT
Found at i:29347349 original size:17 final size:17
Alignment explanation
Indices: 29347322--29347389 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
29347312 TTTAATCTTA
*
29347322 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
29347338 AATTTAAGTTTAAATTTG
1 AATTTAA-TTTAAATTTC
29347356 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
29347373 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
29347390 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.13
17 21 0.47
18 18 0.40
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:29347371 original size:12 final size:11
Alignment explanation
Indices: 29347299--29347375 Score: 66
Period size: 12 Copynumber: 6.8 Consensus size: 11
29347289 AACCATTTGA
*
29347299 AAATTAAATTT
1 AAATTTAATTT
*
29347310 -ATTTTAATCTT
1 AAATTTAAT-TT
*
29347321 AAATTTACTTT
1 AAATTTAATTT
*
29347332 AAATTCAATTT
1 AAATTTAATTT
*
29347343 AAGTTTAAATTT
1 AAATTT-AATTT
*
29347355 GAATTTAATTT
1 AAATTTAATTT
29347366 AAAATTTAAT
1 -AAATTTAAT
29347376 ATTATTATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
10 6 0.12
11 22 0.43
12 23 0.45
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:29347583 original size:15 final size:15
Alignment explanation
Indices: 29347563--29347609 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
29347553 GCCTATGCTA
29347563 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
29347578 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
29347593 CCAT-CCACCACCAGCT
1 -C-TGCCACCACCAGCT
29347609 C
1 C
29347610 CACCATGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 16 0.53
16 13 0.43
17 1 0.03
ACGTcount: A:0.21, C:0.55, G:0.11, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:29347602 original size:16 final size:17
Alignment explanation
Indices: 29347564--29347611 Score: 75
Period size: 16 Copynumber: 3.0 Consensus size: 17
29347554 CCTATGCTAC
29347564 TGCCACCACCAGCT-C-
1 TGCCACCACCAGCTCCA
29347579 TGCCACCACCAGCTCCA
1 TGCCACCACCAGCTCCA
29347596 T-CCACCACCAGCTCCA
1 TGCCACCACCAGCTCCA
29347612 CCATGCCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.45
16 16 0.52
17 1 0.03
ACGTcount: A:0.23, C:0.54, G:0.10, T:0.12
Consensus pattern (17 bp):
TGCCACCACCAGCTCCA
Found at i:29347613 original size:12 final size:14
Alignment explanation
Indices: 29347563--29347628 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 14
29347553 GCCTATGCTA
29347563 CTGCCACCACCAGC
1 CTGCCACCACCAGC
29347577 TCTGCCACCACCAG-
1 -CTGCCACCACCAGC
29347591 CT-CCATCCACCA-C
1 CTGCCA-CCACCAGC
* *
29347604 CAG-CTCCACCATGCC
1 CTGCCACCACCA-G-C
29347619 CTGCCACCAC
1 CTGCCACCAC
29347629 TGACTTGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
12 9 0.22
13 10 0.25
15 16 0.40
16 5 0.12
ACGTcount: A:0.21, C:0.56, G:0.11, T:0.12
Consensus pattern (14 bp):
CTGCCACCACCAGC
Found at i:29349231 original size:30 final size:30
Alignment explanation
Indices: 29349190--29349409 Score: 370
Period size: 30 Copynumber: 7.3 Consensus size: 30
29349180 CCCCAAACAA
29349190 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
29349221 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
29349251 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
29349281 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
29349311 TCCAAAATTATATTTTGACCCCAAACCTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* *
29349341 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
29349371 TCCAAAATTACATTTTGACCCCAAAAC-TT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
29349400 TCAAAAATTA
1 TCCAAAATTA
29349410 CCATTTTACC
Statistics
Matches: 181, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
29 11 0.06
30 166 0.92
31 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Found at i:29349445 original size:60 final size:55
Alignment explanation
Indices: 29349339--29349777 Score: 322
Period size: 59 Copynumber: 7.5 Consensus size: 55
29349329 CCCCAAACCT
* * * * *
29349339 TTTCCAAAATTA-CATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAA
1 TTTCAAAAATTACCATTTTACCCCCGAAACTTTT--AAAATTCCATTTTGACCCC--GA
* *
29349397 CTTTCAAAAATTACCATTTTACCCCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGA
1 -TTTCAAAAATTACCATTTTA-CCCC-CGAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * * ** * *
29349456 TTACACTAAAATTACCATTTTATCCTCGAAACTTCCAAAATTCCATTTTTAACCCTGA
1 TTTCA--AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * * *
29349514 TTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTCATTTCTAACCCCGA
1 TTTCA---AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTT-TGACCCCGA
* * *
29349573 TTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAAATCCATTTTTGACCTCGA
1 TTT---CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * ** *
29349632 TTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCTGTTTTTAACCCCGA
1 TTTCA---AAAATTACCATTTTACCCCCGAAACTTTTAAAATTC-CATTTTGACCCCGA
* * * *
29349691 TTTCACCGAAAATTACCATTTTACCCCAGAATCTTTTAAGATTCCATTTTCAACCCCGA
1 TTTCA---AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTT-GACCCCGA
* *
29349750 TTACACCAAAATTACCATTTTGCCCCCG
1 TTTCA--AAAATTACCATTTTACCCCCG
29349778 GGTATCCATA
Statistics
Matches: 318, Mismatches: 45, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
58 63 0.20
59 198 0.62
60 33 0.10
61 12 0.04
62 10 0.03
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (55 bp):
TTTCAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTTGACCCCGA
Found at i:29349555 original size:59 final size:59
Alignment explanation
Indices: 29349403--29349777 Score: 493
Period size: 59 Copynumber: 6.4 Consensus size: 59
29349393 AAAACTTTCA
* * *
29349403 AAAATTACCATTTTACCCCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACA-CT
1 AAAATTACCATTTTA-CCCC-CGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * *
29349463 AAAATTACCATTTTATCCTCGAAACTTCCAAAATTCCATTTTTAACCCTGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
29349522 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTCATTTCTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
29349581 AAAATTACCATTTTACCCCCGAATCTTTTAAAAATCCATTTTTGACCTCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* **
29349640 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCTGTTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * * *
29349699 AAAATTACCATTTTACCCCAGAATCTTTTAAGATTCCATTTTCAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
*
29349757 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
29349778 GGTATCCATA
Statistics
Matches: 273, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
58 51 0.19
59 207 0.76
60 15 0.05
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:29361813 original size:68 final size:68
Alignment explanation
Indices: 29361701--29362364 Score: 1080
Period size: 68 Copynumber: 9.8 Consensus size: 68
29361691 TGCAGGTCAC
*
29361701 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29361766 GAG
66 GAG
* *
29361769 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTAAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29361834 GAG
66 GAG
* * *
29361837 CAACGTCATCCCC-TGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29361901 GAG
66 GAG
* *
29361904 TAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29361969 GAG
66 GAG
* * *
29361972 CAACGTCATCCCCTCGAAATTGAAGTAGAGCGGATAACAAGTCTTGATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29362037 GAG
66 GAG
* *
29362040 CAACGTCAT-CCCTTGAAATTGAAGTAGAGCGGATAACAAGTCTTGATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29362104 GAG
66 GAG
*
29362107 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29362172 GAG
66 GAG
* *
29362175 CAACGTCATCCCCTTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGGAGTA
1 CAACGTCATCCCC-TTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTA
29362240 AGAG
65 AGAG
* * *
29362244 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
29362309 GAG
66 GAG
* * * *
29362312 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAAC-AAGTCTTAATCTC
29362365 CCTGAAGAGC
Statistics
Matches: 556, Mismatches: 35, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
67 127 0.23
68 348 0.63
69 72 0.13
70 9 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (68 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTAATCTCTGAAATTGAAGTAA
GAG
Found at i:29361961 original size:135 final size:136
Alignment explanation
Indices: 29361701--29362364 Score: 1118
Period size: 135 Copynumber: 4.9 Consensus size: 136
29361691 TGCAGGTCAC
*
29361701 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAGTCTCTGAAATTGAAGTAA
*
29361766 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTAAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
29361831 TAAGAG
131 TAAGAG
*
29361837 CAACGTCATCCCC-TGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAGTCTCTGAAATTGAAGTAA
* * *
29361901 GAGTAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
29361966 TAAGAG
131 TAAGAG
* * *
29361972 CAACGTCATCCCCTCGAAATTGAAGTAGAGCGGATAACAAGTCTT-GATCTCTGAAATTGAAGTA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAG-TCTCTGAAATTGAAGTA
*
29362036 AGAGCAACGTCAT-CCCTTGAAATTGAAGTAGAGCGGATAACAAGTCTTGATCTCTGAAATTGAA
65 AGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAA
29362100 GTAAGAG
130 GTAAGAG
*
29362107 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAGTCTCTGAAATTGAAGTAA
*
29362172 GAGCAACGTCATCCCCTTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGGA
66 GAGCAACGTCATCCCC-TTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAA
29362237 GTAAGAG
130 GTAAGAG
*
29362244 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAGTCTCTGAAATTGAAGTAA
* * * *
29362309 GAGCAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
66 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATAAC-AAGTCTTGATCTC
29362365 CCTGAAGAGC
Statistics
Matches: 495, Mismatches: 26, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
135 257 0.52
136 88 0.18
137 138 0.28
138 12 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (136 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAGTCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
TAAGAG
Found at i:29362051 original size:203 final size:203
Alignment explanation
Indices: 29361701--29362348 Score: 1154
Period size: 203 Copynumber: 3.2 Consensus size: 203
29361691 TGCAGGTCAC
29361701 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
*
29361766 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTAAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
29361831 TAAGAGCAACGTCATCCCCTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGA
131 TAAGAGCAACGTCATCCCCTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGA
29361896 AGTAAGAG
196 AGTAAGAG
*
29361904 TAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
* *
29361969 GAGCAACGTCATCCCCTCGAAATTGAAGTAGAGCGGATAACAAGTCTTGATCTCTGAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
* * * *
29362034 TAAGAGCAACGTCATCCCTTGAAATTGAAGTAGAGCGGATAACAAGTCTT-GATCTCTGAAATTG
131 TAAGAGCAACGTCATCCCCTGAAATTGAAGTAGAGTGGATAACACGCCTTAG-TCTCTGAAATTG
29362098 AAGTAAGAG
195 AAGTAAGAG
29362107 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
*
29362172 GAGCAACGTCATCCCCTTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGGA
66 GAGCAACGTCATCCCC-TTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAA
29362237 GTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATT
130 GTAAGAGCAACGTCATCCCC-TGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATT
29362302 GAAGTAAGAG
194 GAAGTAAGAG
* *
29362312 CAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATA
1 CAACGTCATCCCCTTGAAATTGAAGTAGAG-TGGATA
29362349 GCAAAGTCTT
Statistics
Matches: 422, Mismatches: 18, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
202 1 0.00
203 273 0.65
204 64 0.15
205 77 0.18
206 7 0.02
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (203 bp):
CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTAATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTGATCTCTGAAATTGAAG
TAAGAGCAACGTCATCCCCTGAAATTGAAGTAGAGTGGATAACACGCCTTAGTCTCTGAAATTGA
AGTAAGAG
Found at i:29362688 original size:17 final size:17
Alignment explanation
Indices: 29362661--29362728 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
29362651 TTTAATCTTA
*
29362661 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
29362677 AATTTAAGTTTAAATTTG
1 AATTTAA-TTTAAATTTC
29362695 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
29362712 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
29362729 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.13
17 21 0.47
18 18 0.40
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:29362710 original size:12 final size:11
Alignment explanation
Indices: 29362638--29362714 Score: 66
Period size: 12 Copynumber: 6.8 Consensus size: 11
29362628 AACCATTTGA
*
29362638 AAATTAAATTT
1 AAATTTAATTT
*
29362649 -ATTTTAATCTT
1 AAATTTAAT-TT
*
29362660 AAATTTACTTT
1 AAATTTAATTT
*
29362671 AAATTCAATTT
1 AAATTTAATTT
*
29362682 AAGTTTAAATTT
1 AAATTT-AATTT
*
29362694 GAATTTAATTT
1 AAATTTAATTT
29362705 AAAATTTAAT
1 -AAATTTAAT
29362715 ATTATTATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
10 6 0.12
11 22 0.43
12 23 0.45
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:29362944 original size:19 final size:16
Alignment explanation
Indices: 29362905--29362966 Score: 101
Period size: 16 Copynumber: 3.9 Consensus size: 16
29362895 TATGCTGCTG
29362905 CCACCACCAGCT-C-T
1 CCACCACCAGCTCCAT
29362919 GCCACCACCAGCTCCAT
1 -CCACCACCAGCTCCAT
29362936 CCACCACCAGCTCCAT
1 CCACCACCAGCTCCAT
29362952 CCACCACCAGCTCCA
1 CCACCACCAGCTCCA
29362967 CCATGCCCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.27
16 32 0.71
17 1 0.02
ACGTcount: A:0.24, C:0.56, G:0.08, T:0.11
Consensus pattern (16 bp):
CCACCACCAGCTCCAT
Found at i:29364628 original size:59 final size:60
Alignment explanation
Indices: 29364557--29364715 Score: 261
Period size: 59 Copynumber: 2.7 Consensus size: 60
29364547 TCCAAAAATT
*
29364557 ATTTTGACCCCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTAC
*
29364617 ATTTTGA-CCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTAC
*
29364676 ATTTTGACCCCAAAAC-TTTCAAAAATTACCATTTT-ACCCC
1 ATTTTGACCCCAAAACTTTTCCAAAATTA-CATTTTGACCCC
29364716 CTGAATCTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
59 72 0.77
60 21 0.23
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (60 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTAC
Found at i:29364637 original size:29 final size:30
Alignment explanation
Indices: 29364557--29364715 Score: 261
Period size: 30 Copynumber: 5.4 Consensus size: 30
29364547 TCCAAAAATT
*
29364557 ATTTTGACCCCAAAACTTTTCCAAAATTAT
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
29364587 ATTTTGACCCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
29364617 ATTTTGA-CCCAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
29364646 ATTTTGACCCTAAAACTTTTCCAAAATTAC
1 ATTTTGACCCCAAAACTTTTCCAAAATTAC
*
29364676 ATTTTGACCCCAAAAC-TTTCAAAAATTACC
1 ATTTTGACCCCAAAACTTTTCCAAAATTA-C
29364706 ATTTT-ACCCC
1 ATTTTGACCCC
29364716 CTGAATCTTT
Statistics
Matches: 123, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
29 45 0.37
30 78 0.63
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTGACCCCAAAACTTTTCCAAAATTAC
Found at i:29364731 original size:59 final size:55
Alignment explanation
Indices: 29364633--29365070 Score: 333
Period size: 59 Copynumber: 7.5 Consensus size: 55
29364623 ACCCAAAACT
* ** * *
29364633 TTTCCAAAATTA-CATTTTGA-CCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAA
1 TTTCAAAAATTACCATTTT-ACCCCCGAAACTTTT--AAAATTCCATTTTGACCCC--GA
* *
29364691 CTTTCAAAAATTACCATTTTACCCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGA
1 -TTTCAAAAATTACCATTTTACCCCC-GAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * * * * *
29364749 TTACACTAAAATTACAATTTTATCCTCGAAACTTCTAAAATTCCATTTTTAACCCCGA
1 TTTCA--AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * * * *
29364807 TTTCACCAAAAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTCTAACCCTGA
1 TTT---CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTT-TGACCCCGA
*
29364866 TTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTGACCCCGA
1 TTTCA---AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCA-TTTTGACCCCGA
* * * * *
29364925 TTTCACCAAAAATTACCATTTTA-CCCCTAAGCTTCTAAAATTCCGTTTTTAACCCCGA
1 TTT---CAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCC-ATTTTGACCCCGA
* * *
29364983 TTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAGATTCCATTTTCAACCCCGA
1 TTTCA---AAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTT-GACCCCGA
* *
29365042 TTACACCAAAATTACCATTTTGCCCCCGA
1 TTTCA--AAAATTACCATTTTACCCCCGA
29365071 GTATCCATAA
Statistics
Matches: 320, Mismatches: 36, Indels: 47
0.79 0.09 0.12
Matches are distributed among these distances:
55 2 0.01
56 2 0.01
57 4 0.01
58 108 0.34
59 172 0.54
60 21 0.07
61 9 0.03
62 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (55 bp):
TTTCAAAAATTACCATTTTACCCCCGAAACTTTTAAAATTCCATTTTGACCCCGA
Found at i:29364736 original size:29 final size:29
Alignment explanation
Indices: 29364697--29365070 Score: 183
Period size: 29 Copynumber: 12.8 Consensus size: 29
29364687 AAAACTTTCA
*
29364697 AAAATTACCATTTTACCCCCTGAATCTTTT
1 AAAATTACCATTTTACCCCC-GAATCTTCT
* * *
29364727 AAAATT-CCATTTTTAACCCCGATTAC-ACT
1 AAAATTACCA-TTTTACCCCCGAAT-CTTCT
* * * *
29364756 AAAATTACAATTTTATCCTCGAAACTTCT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* * ** *
29364785 AAAATT-CCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTACCCCCGA-ATCTTCT
* *
29364815 AAAATTACCATTTTACCCTCGAAGCTTCT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* * * ** *
29364844 AAAATT-CCATTTCTAACCCTGATTTCACCG
1 AAAATTACCATTT-TACCCCCGA-ATCTTCT
*
29364874 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* ** *
29364903 AAAATT-CCATTTTTGA-CCCCGATTTCACCA
1 AAAATTACCA-TTTT-ACCCCCGA-ATCTTCT
* *
29364933 AAAATTACCATTTTA-CCCCTAAGCTTCT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* * * ** *
29364961 AAAATT-CCGTTTTTAACCCCGATTTCACCG
1 AAAATTACC-ATTTTACCCCCGA-ATCTTCT
*
29364991 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* * * * *
29365020 AAGATT-CCATTTTCAACCCCGATTAC-ACC
1 AAAATTACCATTTT-ACCCCCGAAT-CTTCT
*
29365049 AAAATTACCATTTTGCCCCCGA
1 AAAATTACCATTTTACCCCCGA
29365071 GTATCCATAA
Statistics
Matches: 249, Mismatches: 74, Indels: 43
0.68 0.20 0.12
Matches are distributed among these distances:
27 2 0.01
28 32 0.13
29 110 0.44
30 91 0.37
31 14 0.06
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATCTTCT
Found at i:29364760 original size:118 final size:117
Alignment explanation
Indices: 29364638--29365068 Score: 450
Period size: 117 Copynumber: 3.7 Consensus size: 117
29364628 AAACTTTTCC
* * *
29364638 AAAATTA-CATTTTGACCCTAAAACTTTTCCAAAATTACA-TTTTGACCCCAAAACTTT-CAAAA
1 AAAATTACCATTTT-ACCCTGAAACTTTT-CAAAATTCCATTTTTGACCCC--GA-TTTCCAAAA
* * * *
29364700 ATTACCATTTTACCCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGATTACA-CT
61 ATTACCATTTTACCCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * *
29364756 AAAATTACAATTTTATCCTCGAAACTTCT-AAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
1 AAAATTACCATTTTACCCT-GAAACTTTTCAAAATTCCATTTTTGACCCCGATTT--CCAAAAAT
* * *
29364820 TACCATTTTACCCTC-GAAGCTTCTAAAATTCCATTTCTAACCCTGATTTCACCG
63 TACCATTTTACCCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* *
29364874 AAAATTACCATTTTACCCCCGAATCTTTT-AAAATTCCATTTTTGACCCCGATTTCACCAAAAAT
1 AAAATTACCATTTTA-CCCTGAAACTTTTCAAAATTCCATTTTTGACCCCGATTT--CCAAAAAT
*
29364938 TACCATTTTA-CCCCT-AAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCG
63 TACCATTTTACCCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
* * * ** * *
29364991 AAAATTACCATTTTACCCCCGAATCTTTT-AAGATTCCATTTTCAACCCCGATTACACCAAAATT
1 AAAATTACCATTTTA-CCCTGAAACTTTTCAAAATTCCATTTTTGACCCCGATTTC-CAAAAATT
*
29365055 ACCATTTTGCCCCC
64 ACCATTTTACCCCC
29365069 GAGTATCCAT
Statistics
Matches: 272, Mismatches: 30, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
115 4 0.01
116 16 0.06
117 131 0.48
118 107 0.39
119 14 0.05
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAATTACCATTTTACCCTGAAACTTTTCAAAATTCCATTTTTGACCCCGATTTCCAAAAATTAC
CATTTTACCCCCTGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:29365006 original size:117 final size:117
Alignment explanation
Indices: 29364695--29365067 Score: 543
Period size: 117 Copynumber: 3.2 Consensus size: 117
29364685 CCAAAACTTT
* * * *
29364695 CAAAAATTACCATTTTACCCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGATTACA-CTAAA
1 CAAAAATTACCATTTTA-CCCCT-AAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAA
* * * * *
29364759 ATTACAATTTTATCCTCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCAC
64 ATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
29364813 CAAAAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTCTAACCCTGATTTCACCGAAAA
1 CAAAAATTACCATTTTACCC-CTAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAA
*
29364878 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTGACCCCGATTTCAC
65 TTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAC
*
29364931 CAAAAATTACCATTTTACCCCTAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCGAAAAT
1 CAAAAATTACCATTTTACCCCTAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAAT
* * *
29364996 TACCATTTTACCCCCGAATCTTTTAAGATTCCATTTTCAACCCCGATTACAC
66 TACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAC
*
29365048 C-AAAATTACCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
29365068 CGAGTATCCA
Statistics
Matches: 231, Mismatches: 22, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
116 18 0.08
117 123 0.53
118 90 0.39
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (117 bp):
CAAAAATTACCATTTTACCCCTAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCGAAAAT
TACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:29365068 original size:58 final size:59
Alignment explanation
Indices: 29364695--29365070 Score: 515
Period size: 59 Copynumber: 6.4 Consensus size: 59
29364685 CCAAAACTTT
* *
29364695 CAAAAATTACCATTTTACCCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGATTACA-
1 CAAAAATTACCATTTTACCCCC-GAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
29364754 CTAAAATTACAATTTTATCCTCGAAACTTCTAAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * * *
29364813 CAAAAATTACCATTTTACCCTCGAAGCTTCTAAAATTCCATTTCTAACCCTGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
29364872 CGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTGACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * *
29364931 CAAAAATTACCATTTTA-CCCCTAAGCTTCTAAAATTCCGTTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
29364989 CGAAAATTACCATTTTACCCCCGAATCTTTTAAGATTCCATTTTCAACCCCGATTACAC
1 CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
*
29365048 C-AAAATTACCATTTTGCCCCCGA
1 CAAAAATTACCATTTTACCCCCGA
29365071 GTATCCATAA
Statistics
Matches: 280, Mismatches: 35, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
58 106 0.38
59 174 0.62
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:29368038 original size:51 final size:51
Alignment explanation
Indices: 29367967--29368158 Score: 267
Period size: 51 Copynumber: 3.8 Consensus size: 51
29367957 CCATATAGGA
* * * * * *
29367967 ATTCATATACTCACGATGACACTGAGTCATCGGACCTTTAATCCATGATGG
1 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
* * * * * *
29368018 ATTCATGTACTCACTATGACACTTAGTTATCGGACCTTTAATCTGTAAAAG
1 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
*
29368069 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
29368120 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTT
29368159 TCGTTTATAG
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 125 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGG
Found at i:29395144 original size:24 final size:22
Alignment explanation
Indices: 29395097--29395144 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
29395087 TGATAATTAC
*
29395097 ATGACTTAAATGTTAGGTTGTA
1 ATGACTTAAATGTTAAGTTGTA
29395119 ATGACATTGAAATGTTTAAGTT-TA
1 ATGAC-TT-AAATG-TTAAGTTGTA
29395143 AT
1 AT
29395145 TGATGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
24 9 0.41
25 6 0.27
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (22 bp):
ATGACTTAAATGTTAAGTTGTA
Found at i:29398116 original size:28 final size:28
Alignment explanation
Indices: 29398079--29398163 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
29398069 AGACACTTTC
* *
29398079 CCATAAGCATAGATAGCCACAAAGGTGT
1 CCATAAGCATAGATAACCACAAAGGCGT
* *
29398107 TCATAAGCATAGATAACTACAAAGGCGT
1 CCATAAGCATAGATAACCACAAAGGCGT
*
29398135 CCATTAA-CATAGATAACCACAAAGACGT
1 CCA-TAAGCATAGATAACCACAAAGGCGT
29398163 C
1 C
29398164 ATTCACACTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 46 0.94
29 3 0.06
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.19
Consensus pattern (28 bp):
CCATAAGCATAGATAACCACAAAGGCGT
Found at i:29398243 original size:29 final size:29
Alignment explanation
Indices: 29398192--29398330 Score: 92
Period size: 29 Copynumber: 4.9 Consensus size: 29
29398182 GGAACCTCAT
* *
29398192 TTTAATAGAATCAGTCACGAAGGC-TTAA
1 TTTAACAGAATCAGTCACAAAGGCTTTAA
29398220 CTTTAACAGAATCAG-CTACAAAGGCTTTAA
1 -TTTAACAGAATCAGTC-ACAAAGGCTTTAA
* * * *
29398250 TTTAACATAATCTA-CCACAAA-GATAT-A
1 TTTAACAGAATC-AGTCACAAAGGCTTTAA
* ** * *
29398277 TTTAACAAAATCAAACACAAAGGATCT-A
1 TTTAACAGAATCAGTCACAAAGGCTTTAA
* *
29398305 TTTAATAGAATCAGGCACAAAGGCTT
1 TTTAACAGAATCAGTCACAAAGGCTT
29398331 CACTTTTTTG
Statistics
Matches: 90, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
26 1 0.01
27 18 0.20
28 29 0.32
29 36 0.40
30 6 0.07
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (29 bp):
TTTAACAGAATCAGTCACAAAGGCTTTAA
Found at i:29398316 original size:28 final size:28
Alignment explanation
Indices: 29398249--29398327 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
29398239 AAAGGCTTTA
* * *
29398249 ATTTAACATAATCTACCACAAA-GATAT
1 ATTTAACAAAATCAAACACAAAGGATAT
*
29398276 ATTTAACAAAATCAAACACAAAGGATCT
1 ATTTAACAAAATCAAACACAAAGGATAT
* * **
29398304 ATTTAATAGAATCAGGCACAAAGG
1 ATTTAACAAAATCAAACACAAAGG
29398328 CTTCACTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 19 0.44
28 24 0.56
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (28 bp):
ATTTAACAAAATCAAACACAAAGGATAT
Found at i:29400063 original size:10 final size:10
Alignment explanation
Indices: 29400027--29400085 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 10
29400017 AACTTTTGTG
29400027 ATTTTTATAA
1 ATTTTTATAA
*
29400037 TTTGTTATATAA
1 ATT-TT-TATAA
29400049 TATTTTTATAA
1 -ATTTTTATAA
29400060 A-TTTTA-AA
1 ATTTTTATAA
29400068 TATTTTTAATAA
1 -ATTTTT-ATAA
29400080 ATTTTT
1 ATTTTT
29400086 TTGATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
8 2 0.05
9 6 0.15
10 7 0.17
11 14 0.35
12 9 0.22
13 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTTTATAA
Found at i:29400071 original size:19 final size:20
Alignment explanation
Indices: 29400047--29400084 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
29400037 TTTGTTATAT
29400047 AATATTTTT-ATAAATTTTA
1 AATATTTTTAATAAATTTTA
29400066 AATATTTTTAATAAATTTT
1 AATATTTTTAATAAATTTT
29400085 TTTGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTTTAATAAATTTTA
Found at i:29403496 original size:21 final size:22
Alignment explanation
Indices: 29403443--29403501 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
29403433 CGATACCTAT
* *
29403443 GACAGTTCTAGCGATACAAGTGA
1 GACA-TTCTACCGATACAAGTCA
29403466 GACATT-TACCGATACAAGTCA
1 GACATTCTACCGATACAAGTCA
* *
29403487 TAC-TTCTACCAATAC
1 GACATTCTACCGATAC
29403502 TAAAAACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 23 0.74
22 2 0.06
23 4 0.13
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (22 bp):
GACATTCTACCGATACAAGTCA
Found at i:29405862 original size:33 final size:32
Alignment explanation
Indices: 29405810--29405885 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
29405800 GATGACATCG
*
29405810 TGTGTCAAG-GAGGTCTCGACCATCCCCAAGCCA
1 TGTGTCAAGTG-GGTCTCGACCA-ACCCAAGCCA
* * *
29405843 TGTGTCAAGTGGGTGTCGACCAACCCAGGCCG
1 TGTGTCAAGTGGGTCTCGACCAACCCAAGCCA
29405875 TGTGTC-AGTGG
1 TGTGTCAAGTGG
29405886 CCTAATGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 5 0.13
32 13 0.34
33 19 0.50
34 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.21
Consensus pattern (32 bp):
TGTGTCAAGTGGGTCTCGACCAACCCAAGCCA
Found at i:29405970 original size:15 final size:15
Alignment explanation
Indices: 29405924--29405970 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
29405914 CCAACGAGTC
* *
29405924 TAAAAAATTAAAAAA
1 TAAATAATTAAAAAT
**
29405939 T-AATAATTAAATTT
1 TAAATAATTAAAAAT
29405953 TAAATAATTAAAAAT
1 TAAATAATTAAAAAT
29405968 TAA
1 TAA
29405971 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATAATTAAAAAT
Found at i:29405972 original size:21 final size:23
Alignment explanation
Indices: 29405943--29405988 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
29405933 AAAAAATAAT
29405943 AATTAAATTTTAAAT-AATTA-AA
1 AATTAAA-TTTAAATAAATTACAA
29405965 AATT-AATTTAAATAAATTACAA
1 AATTAAATTTAAATAAATTACAA
29405987 AA
1 AA
29405989 AATAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTAAATTTAAATAAATTACAA
Found at i:29407290 original size:20 final size:20
Alignment explanation
Indices: 29407255--29407314 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
29407245 ATAGGGCAAG
*
29407255 ATATATTTTT-TAATTTTTAA
1 ATATATTTTTAT-ATTTTCAA
*
29407275 ATATATTTTTATATTTTCGA
1 ATATATTTTTATATTTTCAA
*
29407295 A-ATATTTTTACATTTTCAA
1 ATATATTTTTATATTTTCAA
29407314 A
1 A
29407315 ATCTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.49
20 17 0.49
21 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATATTTTTATATTTTCAA
Found at i:29409095 original size:59 final size:59
Alignment explanation
Indices: 29408972--29409105 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 59
29408962 CAGTGGTTAC
* * ** * *
29408972 CAAACACCAAAAAAATTATTTTTTAATTCGTATTTTTATGAGTGTTGGCCATTAGTTGT
1 CAAACACAAAAAAAATTATTTTTTAATTCATATTTTTATGAGTGTTAACCATTAGATGG
* * * * *
29409031 TAAACACAAAAAAAATTATTTTTTTATTCATATTTTTTGTGGGTGTTAATCA-TAGATGG
1 CAAACACAAAAAAAATTATTTTTTAATTCATA-TTTTTATGAGTGTTAACCATTAGATGG
29409090 CAAACA-AAAAAAAATT
1 CAAACACAAAAAAAATT
29409106 TGGAGAACTA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
58 10 0.16
59 38 0.61
60 14 0.23
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (59 bp):
CAAACACAAAAAAAATTATTTTTTAATTCATATTTTTATGAGTGTTAACCATTAGATGG
Found at i:29410318 original size:24 final size:22
Alignment explanation
Indices: 29410283--29410326 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
29410273 TTTATGAGCT
*
29410283 TTTTATAATTTAATTTATTTTA
1 TTTTATAATTTAAATTATTTTA
29410305 TTTTATAAACTTTAAATTATTT
1 TTTTAT-AA-TTTAAATTATTT
29410327 ATTACCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATAATTTAAATTATTTTA
Found at i:29420221 original size:41 final size:42
Alignment explanation
Indices: 29420136--29420227 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 42
29420126 CAGTATGAGT
* **
29420136 TTGGTATTCGCCAATGGGTGAGCTGTGTAAGGTCTGTTTATG
1 TTGGTATTCGCCAATGGGTGAACTGTGTAAGGTCTACTTATG
* *
29420178 TT-GTATTCGCTAATAGGG-GAACTGTGTAAGGTCTACTTGTG
1 TTGGTATTCGCCAAT-GGGTGAACTGTGTAAGGTCTACTTATG
29420219 TTGGTATTC
1 TTGGTATTC
29420228 AGTAATGGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 32 0.74
42 11 0.26
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.39
Consensus pattern (42 bp):
TTGGTATTCGCCAATGGGTGAACTGTGTAAGGTCTACTTATG
Found at i:29422055 original size:120 final size:120
Alignment explanation
Indices: 29421838--29422065 Score: 357
Period size: 120 Copynumber: 1.9 Consensus size: 120
29421828 TACAATTCAA
* *
29421838 AATTTCATCCTCATGTCTGTATCAACTTTGTTACCAGTATACGATGCTGCTCACATGAGCTGTCG
1 AATTTCATCCTCATGTCTGTATCAACTTTATTACCAATATACGATGCTGCTCACATGAGCTGTCG
* *
29421903 GGAACTCACAACATATACGGTACCCCAACCATCGATACGGTATGCTAGAATCTAG
66 AGAAATCACAACATATACGGTACCCCAACCATCGATACGGTATGCTAGAATCTAG
* * *
29421958 AATTTCATTCTCATGTTTGTATCAACTTTATTACCAATATATGATGCTGCTCACATGAGCTGTCG
1 AATTTCATCCTCATGTCTGTATCAACTTTATTACCAATATACGATGCTGCTCACATGAGCTGTCG
* * * *
29422023 AGAAATCGCAACATATGCGGTACCTCAGCCATCGATACGGTAT
66 AGAAATCACAACATATACGGTACCCCAACCATCGATACGGTAT
29422066 TTATGCATAT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (120 bp):
AATTTCATCCTCATGTCTGTATCAACTTTATTACCAATATACGATGCTGCTCACATGAGCTGTCG
AGAAATCACAACATATACGGTACCCCAACCATCGATACGGTATGCTAGAATCTAG
Found at i:29426162 original size:28 final size:28
Alignment explanation
Indices: 29426106--29426166 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
29426096 ACATCCCGAA
* *
29426106 GGACTTACCTCGTATTTACTGTCCCAGT
1 GGACTTACCTCATATTTACTATCCCAGT
* *
29426134 GGACTTACCTCATGTTTACTATCCTAGT
1 GGACTTACCTCATATTTACTATCCCAGT
29426162 GGACT
1 GGACT
29426167 CTATTTGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (28 bp):
GGACTTACCTCATATTTACTATCCCAGT
Found at i:29426215 original size:31 final size:31
Alignment explanation
Indices: 29426177--29426262 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 31
29426167 CTATTTGTTA
*
29426177 TGTGTTTATTGTCCCGATGGACTA-TCTATTT
1 TGTGTTTACTGTCCC-ATGGACTACTCTATTT
*
29426208 TGTGTTTACTGTCCCAGTGGAATATCTCTATTT
1 TGTGTTTACTGTCCCA-TGGACTA-CTCTATTT
*
29426241 TGTGTTTACTGTCCAATGGACT
1 TGTGTTTACTGTCCCATGGACT
29426263 TTCTTTGTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.02
31 20 0.42
32 5 0.10
33 22 0.46
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (31 bp):
TGTGTTTACTGTCCCATGGACTACTCTATTT
Found at i:29427754 original size:21 final size:22
Alignment explanation
Indices: 29427728--29427779 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29427718 ATAATAAAAT
29427728 AAAAATAAATAAAAGTT-ATAA
1 AAAAATAAATAAAAGTTAATAA
* * *
29427749 AAAAATTATTAAAATTTAATAA
1 AAAAATAAATAAAAGTTAATAA
*
29427771 AAATATAAA
1 AAAAATAAA
29427780 AATATTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAAATAAAAGTTAATAA
Found at i:29427781 original size:19 final size:20
Alignment explanation
Indices: 29427725--29427835 Score: 58
Period size: 20 Copynumber: 5.7 Consensus size: 20
29427715 TTGATAATAA
*
29427725 AATAAAAATAAATAAAAGTTAT
1 AATAAAAAT--ATAAAAATTAT
*
29427747 AA-AAAAATTATTAAAATT-T
1 AATAAAAA-TATAAAAATTAT
29427766 AATAAAAATATAAAAA-TAT
1 AATAAAAATATAAAAATTAT
* *
29427785 -TTAAAATTTATTAAAAATTAT
1 AATAAAA-ATA-TAAAAATTAT
* *
29427806 -A-AAATATATAGAAA-TAT
1 AATAAAAATATAAAAATTAT
*
29427823 AA-AAAATTATAAA
1 AATAAAAATATAAA
29427836 TTTTATAAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.04
18 20 0.29
19 15 0.21
20 21 0.30
21 8 0.11
22 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAAAAATATAAAAATTAT
Found at i:29427789 original size:10 final size:8
Alignment explanation
Indices: 29427767--29427827 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 8
29427757 TTAAAATTTA
29427767 ATAAAAAT
1 ATAAAAAT
29427775 ATAAAAAT
1 ATAAAAAT
*
29427783 ATTTAAAATTT
1 A--TAAAA-AT
29427794 ATTAAAAATT
1 A-TAAAAA-T
29427804 ATAAAATAT
1 ATAAAA-AT
*
29427813 ATAGAAAT
1 ATAAAAAT
29427821 ATAAAAA
1 ATAAAAA
29427828 ATTATAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 17 0.39
9 11 0.25
10 14 0.32
11 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
ATAAAAAT
Found at i:29427789 original size:28 final size:28
Alignment explanation
Indices: 29427749--29427835 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
29427739 AAAGTTATAA
29427749 AAAAAT-TATTAAAATTTAATAAAAATAT
1 AAAAATAT-TTAAAATTTAATAAAAATAT
*
29427777 AAAAATATTTAAAATTTATTAAAAAT-T
1 AAAAATATTTAAAATTTAATAAAAATAT
* * *
29427804 ATAAAATATATAGAAATATAA-AAAATTAT
1 A-AAAATATTTA-AAATTTAATAAAAATAT
29427833 AAA
1 AAA
29427836 TTTTATAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.04
28 39 0.78
29 9 0.18
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATATTTAAAATTTAATAAAAATAT
Found at i:29427815 original size:38 final size:38
Alignment explanation
Indices: 29427749--29427832 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
29427739 AAAGTTATAA
*
29427749 AAAAATTATTAAAATTTAATAAAAATATAAAAATATTT
1 AAAAATTATTAAAAATTAATAAAAATATAAAAATATTT
* * *
29427787 AAAATTTATTAAAAATT-ATAAAATATATAGAAATA-TA
1 AAAAATTATTAAAAATTAATAAAA-ATATAAAAATATTT
29427824 AAAAATTAT
1 AAAAATTAT
29427833 AAATTTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 15 0.38
38 25 0.62
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (38 bp):
AAAAATTATTAAAAATTAATAAAAATATAAAAATATTT
Found at i:29427842 original size:27 final size:28
Alignment explanation
Indices: 29427797--29427865 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
29427787 AAAATTTATT
29427797 AAAAATTATAAAATATATAGAAATA-T-A
1 AAAAATTATAAAATATATA-AAATAGTAA
* * *
29427824 AAAAATTATAAATTTTATAAAGTAGTAA
1 AAAAATTATAAAATATATAAAATAGTAA
29427852 AAAAATTATTAAAA
1 AAAAATTA-TAAAA
29427866 ATGTAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 4 0.11
27 18 0.51
28 9 0.26
29 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAATAGTAA
Found at i:29427894 original size:11 final size:10
Alignment explanation
Indices: 29427738--29427907 Score: 71
Period size: 9 Copynumber: 17.9 Consensus size: 10
29427728 AAAAATAAAT
*
29427738 AAAAGTTATAA
1 AAAAATTAT-A
29427749 AAAAATTAT-
1 AAAAATTATA
*
29427758 TAAAATT-TA
1 AAAAATTATA
*
29427767 ATAAAAATATA
1 A-AAAATTATA
29427778 AAAATATT-T-
1 AAAA-ATTATA
* *
29427787 AAAATTTATT
1 AAAAATTATA
29427797 AAAAATTATA
1 AAAAATTATA
*
29427807 AAATA-TAT-
1 AAAAATTATA
*
29427815 AGAAA-TATA
1 AAAAATTATA
29427824 AAAAATTAT-
1 AAAAATTATA
**
29427833 AAATTTTATA
1 AAAAATTATA
** *
29427843 AAGTAGTA-A
1 AAAAATTATA
*
29427852 AAAAATTATT
1 AAAAATTATA
29427862 AAAAATGTA-A
1 AAAAAT-TATA
*
29427872 ATAAA-TAT-
1 AAAAATTATA
29427880 -AAAATTCATA
1 AAAAATT-ATA
29427890 AAAAATTAT-
1 AAAAATTATA
29427899 AAAAATTAT
1 AAAAATTAT
29427908 CGTGTCTCTC
Statistics
Matches: 119, Mismatches: 24, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
7 3 0.03
8 12 0.10
9 42 0.35
10 41 0.34
11 21 0.18
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAAATTATA
Found at i:29427899 original size:19 final size:18
Alignment explanation
Indices: 29427726--29427904 Score: 82
Period size: 19 Copynumber: 9.4 Consensus size: 18
29427716 TGATAATAAA
29427726 ATAAAAATA-AATAAAAGTT
1 ATAAAAATATAA-AAAA-TT
* *
29427745 ATAAAAAAATTATTAAAATTT
1 AT--AAAAA-TATAAAAAATT
29427766 AATAAAAATATAAAAATATT
1 -ATAAAAATATAAAAA-ATT
* *
29427786 -TAAAATTTATTAAAAATT
1 ATAAAA-ATATAAAAAATT
*
29427804 AT-AAAATATATAGAAA-T
1 ATAAAAATATA-AAAAATT
* *
29427821 ATAAAAA-ATTATAAATT
1 ATAAAAATATAAAAAATT
* *
29427838 TTATAAAGTAGTAAAAAAATT
1 ATA-AAAATA-T-AAAAAATT
*
29427859 ATTAAAAATGTAAATAAA-T
1 A-TAAAAATATAAA-AAATT
*
29427878 ATAAAATTCATAAAAAATT
1 ATAAAAAT-ATAAAAAATT
29427897 ATAAAAAT
1 ATAAAAAT
29427905 TATCGTGTCT
Statistics
Matches: 120, Mismatches: 21, Indels: 38
0.67 0.12 0.21
Matches are distributed among these distances:
16 4 0.03
17 11 0.09
18 31 0.26
19 35 0.29
20 12 0.10
21 17 0.14
22 9 0.08
23 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAAAAATATAAAAAATT
Found at i:29428524 original size:23 final size:22
Alignment explanation
Indices: 29428491--29428533 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29428481 TGAGTGCAAC
**
29428491 AAAAAAATTAATTACTTTTCTT
1 AAAAAAATTAAAAACTTTTCTT
29428513 AAAAAAATTTAAAAACTTTTC
1 AAAAAAA-TTAAAAACTTTTC
29428534 ACATCGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAAATTAAAAACTTTTCTT
Found at i:29430948 original size:76 final size:76
Alignment explanation
Indices: 29430819--29431033 Score: 295
Period size: 76 Copynumber: 2.8 Consensus size: 76
29430809 GAGTTAAAAG
* * * * *
29430819 GATTGATTTTTACGCATTAGGATGAAAAATGATCATGTCTCCTATTTTTTCTCCTCTCATCATTC
1 GATTGATTTTTATGCATTAGGATGGAAAATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTC
*
29430884 CAATTTGGAAT
66 CAATTTGGAAA
* * *
29430895 GATTGATTTTTATGCATTATGATGGAAAATGATCATCTCTCTTATTTTCTCTCCTCTCATCGTTT
1 GATTGATTTTTATGCATTAGGATGGAAAATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTC
29430960 CAATTTGGAAA
66 CAATTTGGAAA
* * * * *
29430971 CACTGATTTTTATGCATCAGGATGGAAAAATGATCATCTCTCTTATTTTCTCTTCTCTAATCA
1 GATTGATTTTTATGCATTAGGATGG-AAAATGATCATCTCTCTTATTTTCTCTCCTCTCATCA
29431034 GAATTTTATA
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
76 88 0.72
77 34 0.28
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (76 bp):
GATTGATTTTTATGCATTAGGATGGAAAATGATCATCTCTCTTATTTTCTCTCCTCTCATCATTC
CAATTTGGAAA
Found at i:29432596 original size:28 final size:28
Alignment explanation
Indices: 29432560--29432617 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
29432550 TTTGATACTT
*
29432560 TCTTTGTAAAATATAGGCAGATAAGTTA
1 TCTTCGTAAAATATAGGCAGATAAGTTA
29432588 TCTTCGTAAAATATAGGCAGATAAGTTA
1 TCTTCGTAAAATATAGGCAGATAAGTTA
29432616 TC
1 TC
29432618 GTAGGAGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (28 bp):
TCTTCGTAAAATATAGGCAGATAAGTTA
Found at i:29438606 original size:27 final size:26
Alignment explanation
Indices: 29438537--29438615 Score: 122
Period size: 26 Copynumber: 3.0 Consensus size: 26
29438527 AGAAAAGAAT
* * *
29438537 AAATACGAGAAAGTTTAAAAAATTTG
1 AAATAAGAGAAGGTTTAAAAAAATTG
29438563 AAATAAGAGAAGGTTTAAAAAAATTG
1 AAATAAGAGAAGGTTTAAAAAAATTG
*
29438589 AAATAAGAGAAGGTTTTAAAAAATTG
1 AAATAAGAGAAGGTTTAAAAAAATTG
29438615 A
1 A
29438616 GATTTTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.56, C:0.01, G:0.18, T:0.25
Consensus pattern (26 bp):
AAATAAGAGAAGGTTTAAAAAAATTG
Found at i:29439834 original size:48 final size:48
Alignment explanation
Indices: 29439768--29439873 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
29439758 TTAGGTGAGA
* * * * *
29439768 GTTTAGATAAGGGCAATCCTGTTAATAGCAGCCCAGATATAAGAGAGG
1 GTTTAGATAAAGGCAATCCTATCAATAACAGCCCAAATATAAGAGAGG
*
29439816 GTTTAGATAAAGGTAATCCTATCAATAACAGCCCAAATATAAGAGAGG
1 GTTTAGATAAAGGCAATCCTATCAATAACAGCCCAAATATAAGAGAGG
*
29439864 ATTTAGATAA
1 GTTTAGATAA
29439874 GGGTGTGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (48 bp):
GTTTAGATAAAGGCAATCCTATCAATAACAGCCCAAATATAAGAGAGG
Found at i:29439979 original size:27 final size:27
Alignment explanation
Indices: 29439945--29440025 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
29439935 TGAGAAGGAG
* *
29439945 GGGAGGAAGCTATTCCAAAGAGAGATA
1 GGGAGGAAGCTATTCCAGAGGGAGATA
* *
29439972 GGGAGGAAGCTGTTCCAGTGGGAGATA
1 GGGAGGAAGCTATTCCAGAGGGAGATA
* * *
29439999 TGAAAGAAGCTATTCCAGAGGGAGATA
1 GGGAGGAAGCTATTCCAGAGGGAGATA
29440026 ATGATAGTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (27 bp):
GGGAGGAAGCTATTCCAGAGGGAGATA
Found at i:29444692 original size:18 final size:19
Alignment explanation
Indices: 29444665--29444708 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29444655 GACTTTTTTT
*
29444665 TTCGAATTTTGAGTTCGAA
1 TTCGAGTTTTGAGTTCGAA
**
29444684 -TCGAGTTTTGTTTTCGAA
1 TTCGAGTTTTGAGTTCGAA
29444702 TTCGAGT
1 TTCGAGT
29444709 AACTTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.45
Consensus pattern (19 bp):
TTCGAGTTTTGAGTTCGAA
Found at i:29445831 original size:21 final size:18
Alignment explanation
Indices: 29445807--29445854 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
29445797 TTCCGAAATG
29445807 TATTGATACCAATATGGTTTT
1 TATTGATACC-ATAT--TTTT
* *
29445828 TATTAATACCTTATTTTT
1 TATTGATACCATATTTTT
29445846 TATTGATAC
1 TATTGATAC
29445855 TAAAACTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.50
20 3 0.12
21 9 0.38
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (18 bp):
TATTGATACCATATTTTT
Found at i:29465938 original size:20 final size:18
Alignment explanation
Indices: 29465902--29465940 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29465892 AAATTTGTAT
*
29465902 TTTTTAAAAAATTATATA
1 TTTTTAAAAAATAATATA
29465920 TTTTTAAAAAACCTAATATA
1 TTTTTAAAAAA--TAATATA
29465940 T
1 T
29465941 ATATATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
20 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTTAAAAAATAATATA
Found at i:29466443 original size:60 final size:60
Alignment explanation
Indices: 29466372--29466610 Score: 283
Period size: 60 Copynumber: 4.0 Consensus size: 60
29466362 TTTTTTTAGT
* *
29466372 GTCACTGC-ATGGCCGACACCTCCTTTTCTCGTGAAAAAAATTTAAATTTTTTTGGTGTTG
1 GTCACT-CAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTA
*
29466432 GTCACTGC-ATGGCCGACACCTCCTTTTCTCGAG-AAAAAATTTAAATTTTTTTTGTGTTA
1 GTCACT-CAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTA
* *
29466491 GTC-GTCAAATGGCCGACACC-CCTTATTCTAGAGAAAAAAATTTTAAATTTTTTTTGGTGTTA
1 GTCACTC-AATGGCCGACACCTCCTT-TTCTCGAGAAAAAAA-TTTAAA-TTTTTTTGGTGTTA
* * * * *
29466553 GCCA-TCAAATGGCCAACACCCCCTTTTTTCGAGAAAAAAATTTAAATTTTTTTCGTGT
1 GTCACTC-AATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGT
29466611 CGGCCATCAC
Statistics
Matches: 160, Mismatches: 11, Indels: 16
0.86 0.06 0.09
Matches are distributed among these distances:
57 1 0.01
58 5 0.03
59 46 0.29
60 49 0.31
61 12 0.08
62 43 0.27
63 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (60 bp):
GTCACTCAATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTA
Found at i:29466572 original size:62 final size:61
Alignment explanation
Indices: 29466380--29466605 Score: 302
Period size: 59 Copynumber: 3.7 Consensus size: 61
29466370 GTGTCACTGC
* *
29466380 ATGGCCGACACCTCCTTTTCTCGTGAAAAAAATTTAAA-TTTTTTTGGTGTTGGTCACTGC--
1 ATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTTGGTGTTAGTCA-T-CAA
*
29466440 ATGGCCGACACCTCCTTTTCTCGAG-AAAAAATTTAAATTTTTTTT-GTGTTAGTCGTCAA
1 ATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTTGGTGTTAGTCATCAA
* *
29466499 ATGGCCGACACC-CCTTATTCTAGAGAAAAAAATTTTAAATTTTTTTTGGTGTTAGCCATCAA
1 ATGGCCGACACCTCCTT-TTCTCGAGAAAAAAA-TTTAAATTTTTTTTGGTGTTAGTCATCAA
* * *
29466561 ATGGCCAACACCCCCTTTTTTCGAGAAAAAAATTTAAATTTTTTT
1 ATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTT
29466606 CGTGTCGGCC
Statistics
Matches: 149, Mismatches: 9, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
57 1 0.01
58 5 0.03
59 39 0.26
60 37 0.25
61 27 0.18
62 36 0.24
63 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (61 bp):
ATGGCCGACACCTCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTTGGTGTTAGTCATCAA
Found at i:29470385 original size:11 final size:12
Alignment explanation
Indices: 29470345--29470393 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
29470335 TATTTGTGTA
29470345 AAAATTAATTTG
1 AAAATTAATTTG
29470357 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
29470371 TTGAAATTAATTTG
1 --AAAATTAATTTG
29470385 AAAATTAAT
1 AAAATTAAT
29470394 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:29470717 original size:83 final size:83
Alignment explanation
Indices: 29470524--29471046 Score: 777
Period size: 83 Copynumber: 6.3 Consensus size: 83
29470514 AAAAAGATAG
* * * * * * * *
29470524 TTATTATATTACAATTTATATCAAATATTATATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTAT-TAATTTT-
* *
29470589 ATA--TTTAAGGTATAAA-TTA
64 ATATCTTTAA-ATA-AAATTTT
* * * *
29470608 TTATTATATTATAATTTTTATTATATAATATATTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
29470673 ATCTTTAAATAAAATTTT
66 ATCTTTAAATAAAATTTT
29470691 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
29470756 ATCTTTAAATAAAATTTT
66 ATCTTTAAATAAAATTTT
*
29470774 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTATAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
29470839 ATCTTTAAAT-AAA-TTT
66 ATCTTTAAATAAAATTTT
*
29470855 TTATTATATTACAATTTTTATCATATAATGTGTTGATCTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
*
29470920 ATCTTTAAATAAAACTTT
66 ATCTTTAAATAAAATTTT
* * *
29470938 TTATTATATTATAATTTTTGTCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
*
29471003 ATCTTTAAATAAATTTTT
66 ATCTTTAAATAAAATTTT
*
29471021 TTATTATATTACAATTTTTATAATAT
1 TTATTATATTACAATTTTTATCATAT
29471047 TTTATATTTA
Statistics
Matches: 408, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
81 76 0.19
82 12 0.03
83 266 0.65
84 54 0.13
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (83 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
ATCTTTAAATAAAATTTT
Found at i:29470924 original size:164 final size:164
Alignment explanation
Indices: 29470524--29471046 Score: 782
Period size: 164 Copynumber: 3.2 Consensus size: 164
29470514 AAAAAGATAG
* * * * * * * *
29470524 TTATTATATTACAATTTATATCAAATATTATATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTAT-TAATTTT-
* * * * *
29470589 ATA--TTTAAGGTATAAATTATTATTATATTATAATTTTTATTATATAATATATTGATTTGACAA
64 ATATCTTTAA-ATA-AAATTTTTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAA
29470652 TACAATATTTATTAATTTTATATCTTTAAATAAAATTTT
127 TACAATATTTATTAATTTTATATCTTTAAAT-AAATTTT
29470691 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
*
29470756 ATCTTTAAATAAAATTTTTTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATAC
66 ATCTTTAAATAAAA-TTTTTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
*
29470821 AATATTTATTAATTATATATCTTTAAATAAA-TTT
130 AATATTTATTAATTTTATATCTTTAAATAAATTTT
*
29470855 TTATTATATTACAATTTTTATCATATAATGTGTTGATCTGACAATACAATATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
*
29470920 ATCTTTAAATAAAACTTTTTATTATATTATAATTTTTGTCATATAATGTGTTGATTTGACAATAC
66 ATCTTTAAATAAAA-TTTTTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
*
29470985 ATTATTTATTAATTTTATATCTTTAAATAAATTTTT
130 AATATTTATTAATTTTATATCTTTAAATAAA-TTTT
*
29471021 TTATTATATTACAATTTTTATAATAT
1 TTATTATATTACAATTTTTATCATAT
29471047 TTTATATTTA
Statistics
Matches: 329, Mismatches: 22, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
164 158 0.48
165 9 0.03
166 108 0.33
167 54 0.16
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (164 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTATTAATTTTAT
ATCTTTAAATAAAATTTTTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACA
ATATTTATTAATTTTATATCTTTAAATAAATTTT
Found at i:29470964 original size:247 final size:248
Alignment explanation
Indices: 29470524--29471046 Score: 800
Period size: 247 Copynumber: 2.1 Consensus size: 248
29470514 AAAAAGATAG
* * * *
29470524 TTATTATATTACAATTTATATCAAATATTATATTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATATATTAATTTGACAATACAATATTTATCAAATTTTC
* * *
29470589 ATATTTAAGGTATAAATTATTATTATATTATAATTTTTATTATATAATATATTGATTTGACAATA
66 ATATTTAA-G-ATAAATTATTATTATATTACAATTTTTATCATATAATATATTGATCTGACAATA
*
29470654 CAATATTTATTAATTTTATATCTTTAAATAAAATTTTTTATTATATTACAATTTTTATCATATAA
129 CAATATTTATTAATTTTATATCTTTAAATAAAACTTTTTATTATATTACAATTTTTATCATATAA
29470719 TGTGTTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAATTTT
194 TGTGTTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAATTTT
* * * *
29470774 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACAATATTTAT-TAATTATA
1 TTATTATATTACAATTTTTATCATATAATATATTAATTTGACAATACAATATTTATCAAATT-T-
* * * *
29470838 T-ATCTTTAA-ATAAATTTTTATTATATTACAATTTTTATCATATAATGTGTTGATCTGACAATA
64 TCATATTTAAGATAAATTATTATTATATTACAATTTTTATCATATAATATATTGATCTGACAATA
* *
29470901 CAATATTTATTAATTTTATATCTTTAAATAAAACTTTTTATTATATTATAATTTTTGTCATATAA
129 CAATATTTATTAATTTTATATCTTTAAATAAAACTTTTTATTATATTACAATTTTTATCATATAA
* *
29470966 TGTGTTGATTTGACAATACATTATTTATTAATTTTATATCTTTAAATAAATTTTT
194 TGTGTTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAATTTT
*
29471021 TTATTATATTACAATTTTTATAATAT
1 TTATTATATTACAATTTTTATCATAT
29471047 TTTATATTTA
Statistics
Matches: 250, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
247 188 0.75
249 4 0.02
250 57 0.23
251 1 0.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (248 bp):
TTATTATATTACAATTTTTATCATATAATATATTAATTTGACAATACAATATTTATCAAATTTTC
ATATTTAAGATAAATTATTATTATATTACAATTTTTATCATATAATATATTGATCTGACAATACA
ATATTTATTAATTTTATATCTTTAAATAAAACTTTTTATTATATTACAATTTTTATCATATAATG
TGTTGATTTGACAATACAATATTTATTAATTTTATATCTTTAAATAAAATTTT
Found at i:29473491 original size:30 final size:30
Alignment explanation
Indices: 29473451--29473516 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
29473441 TCCCTTTACT
* *
29473451 TTTTAGATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
29473481 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
29473511 TTTTAA
1 TTTTAA
29473517 TTTTTCTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
30 29 0.91
31 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:29473532 original size:30 final size:30
Alignment explanation
Indices: 29473479--29473548 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
29473469 ATTTCGTTTT
* * *
29473479 TATTTTAAATTTAATTTCGAATTTCTTGTA
1 TATTTTAATTTTAATTTCGAATTTCATGCA
** *
29473509 TATTTTAATTTTTCTTTCTAATTTCATGCA
1 TATTTTAATTTTAATTTCGAATTTCATGCA
*
29473539 TATTCTAATT
1 TATTTTAATT
29473549 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (30 bp):
TATTTTAATTTTAATTTCGAATTTCATGCA
Found at i:29474437 original size:59 final size:61
Alignment explanation
Indices: 29474365--29474685 Score: 221
Period size: 59 Copynumber: 5.4 Consensus size: 61
29474355 ATGAGAAGTT
*
29474365 GGTGTCGGCCATTTAATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTCGAGAAA-AGAG
1 GGTGTC-GCCATTTAATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAAAAATAGAG
* * * *
29474425 GGTGTCGCCATTTGATGGCCGACACCAAAAGAATTTGAAATTTTTTTCTCGAAAAATAGGG
1 GGTGTCGCCATTTAATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAAAAATAGAG
* ** *
29474486 GGTATCGACCATTTAATGGCCAACATCC--AAAAA-TACAAA-TTTTTT-T-G--AAATAGGG
1 GGTGTCG-CCATTTAATGGCCAACA-CCAAAAAAATTTGAAATTTTTTTCTCGAAAAATAGAG
** * * * *
29474541 GGTGTCGGCCATTGCATGGCCGACACC-CAAAAA--TGCAATTTTTTT-TTG--AAATAG-G
1 GGTGTC-GCCATTTAATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAAAAATAGAG
* ** * * *
29474596 GAGTGTCGGTCATGCAATGGCCAACACCCAAAAATTTTGAAATTTTTTT-TCTGACAAAAAAGA-
1 G-GTGTC-GCCATTTAATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTC-GA-AAAATAGAG
**
29474659 GGTGTCGGCCATTGCATGGCCAACACC
1 GGTGTC-GCCATTTAATGGCCAACACC
29474686 CCAAATTTTT
Statistics
Matches: 212, Mismatches: 32, Indels: 32
0.77 0.12 0.12
Matches are distributed among these distances:
54 4 0.02
55 41 0.19
56 29 0.14
57 5 0.02
58 1 0.00
59 45 0.21
60 29 0.14
61 13 0.06
62 37 0.17
63 8 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (61 bp):
GGTGTCGCCATTTAATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAAAAATAGAG
Found at i:29474616 original size:56 final size:56
Alignment explanation
Indices: 29474478--29474630 Score: 186
Period size: 56 Copynumber: 2.8 Consensus size: 56
29474468 TTTTCTCGAA
* * * * *
29474478 AAATAGGGGGTATCGACCATT-TAATGGCCAACATCCAAAAATACAAATTTTTTTG
1 AAATAGGGAGTGTCGGCCATTGCAATGGCCAACACCCAAAAATACAAATTTTTTTG
* * * *
29474533 AAATAGGGGGTGTCGGCCATTGC-ATGGCCGACACCCAAAAATGCAATTTTTTTTTG
1 AAATAGGGAGTGTCGGCCATTGCAATGGCCAACACCCAAAAATACAA-ATTTTTTTG
*
29474589 AAATAGGGAGTGTCGGTCA-TGCAATGGCCAACACCCAAAAAT
1 AAATAGGGAGTGTCGGCCATTGCAATGGCCAACACCCAAAAAT
29474631 TTTGAAATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
55 42 0.49
56 43 0.51
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (56 bp):
AAATAGGGAGTGTCGGCCATTGCAATGGCCAACACCCAAAAATACAAATTTTTTTG
Found at i:29474678 original size:62 final size:59
Alignment explanation
Indices: 29474365--29474686 Score: 254
Period size: 55 Copynumber: 5.5 Consensus size: 59
29474355 ATGAGAAGTT
** * *
29474365 GGTGTCGGCCATTTAATGGCCAACACCAAAAAAATTT-AAATTTTTTTCTCGAGAAAA-GA
1 GGTGTCGGCCATTGCATGGCCAACACC-CAAAAATTTGAAATTTTTTTCT-GAAAAAAGGA
* * *
29474424 GGGTGTC-GCCATTTG-ATGGCCGACACCAAAAGAATTTGAAATTTTTTTCTCGAAAAATAGGG
1 -GGTGTCGGCCA-TTGCATGGCCAACACCCAAA-AATTTGAAATTTTTTTCT-GAAAAA-AGGA
* * ** * ** * *
29474486 GGTATCGACCATTTAATGGCCAACATCCAAAAA-TACAAA-TTTTTT-TG-AAATAGGG
1 GGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGAAATTTTTTTCTGAAAAAAGGA
* * * * *
29474541 GGTGTCGGCCATTGCATGGCCGACACCCAAAAA--TGCAATTTTTTTTTGAAATAGGGA
1 GGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGAAATTTTTTTCTGAAAAAAGGA
* *
29474598 -GTGTCGGTCA-TGCAATGGCCAACACCCAAAAATTTTGAAATTTTTTTTCTGACAAAAAAGA
1 GGTGTCGGCCATTGC-ATGGCCAACACCCAAAAA-TTTGAAA-TTTTTTTCTGA-AAAAAGGA
29474659 GGTGTCGGCCATTGCATGGCCAACACCC
1 GGTGTCGGCCATTGCATGGCCAACACCC
29474687 CAAATTTTTT
Statistics
Matches: 210, Mismatches: 34, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
54 2 0.01
55 40 0.19
56 31 0.15
57 5 0.02
58 5 0.02
59 30 0.14
60 40 0.19
61 15 0.07
62 39 0.19
63 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGGCCAACACCCAAAAATTTGAAATTTTTTTCTGAAAAAAGGA
Found at i:29476609 original size:21 final size:23
Alignment explanation
Indices: 29476555--29476611 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
29476545 ATTAATTTTT
*
29476555 AATTTTATAAAAAAATTCATTAAG
1 AATTATATAAAAAAATTCA-TAAG
29476579 -ATTATA-AAAAAAATT-A-AAG
1 AATTATATAAAAAAATTCATAAG
29476598 AATTATATAAAAAA
1 AATTATATAAAAAA
29476612 TAAGTTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 6 0.20
21 7 0.23
22 9 0.30
23 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AATTATATAAAAAAATTCATAAG
Found at i:29476687 original size:19 final size:18
Alignment explanation
Indices: 29476663--29476711 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
29476653 TATATTATTT
*
29476663 GTTTTCTATTATTTAATAA
1 GTTTTCTATTATTT-AGAA
29476682 GTTTTC-ATT-TTTAGAA
1 GTTTTCTATTATTTAGAA
29476698 GTTTT-TATCTATTT
1 GTTTTCTAT-TATTT
29476712 TTTGTATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 6 0.23
19 6 0.23
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.61
Consensus pattern (18 bp):
GTTTTCTATTATTTAGAA
Found at i:29477281 original size:47 final size:47
Alignment explanation
Indices: 29477211--29477304 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
29477201 ATACCAATAG
29477211 TCACTCAACTTTGATTTAAGGAAACAAACAGTCACCTTGTTTACATT
1 TCACTCAACTTTGATTTAAGGAAACAAACAGTCACCTTGTTTACATT
** *
29477258 TCACTCAACTTTGATTTGGGGAAACAAATAGTCACCTTGTTTACATT
1 TCACTCAACTTTGATTTAAGGAAACAAACAGTCACCTTGTTTACATT
29477305 ATCGAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (47 bp):
TCACTCAACTTTGATTTAAGGAAACAAACAGTCACCTTGTTTACATT
Found at i:29478550 original size:26 final size:26
Alignment explanation
Indices: 29478500--29478550 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
29478490 TATTTGTATA
* ***
29478500 TTCTCTTCTTCTTCTTCTTCTCCTTT
1 TTCTCCTCTTCTTCTTCTAAACCTTT
29478526 TTCTCCTCTTCTTCTTCTAAACCTT
1 TTCTCCTCTTCTTCTTCTAAACCTT
29478551 AATCGTCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (26 bp):
TTCTCCTCTTCTTCTTCTAAACCTTT
Found at i:29479098 original size:14 final size:15
Alignment explanation
Indices: 29479072--29479101 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29479062 GTGGGATGAG
29479072 AATAAATTTTAATTA
1 AATAAATTTTAATTA
29479087 AATAAA-TTTAATTA
1 AATAAATTTTAATTA
29479101 A
1 A
29479102 TTGAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTTTAATTA
Found at i:29481397 original size:11 final size:11
Alignment explanation
Indices: 29481383--29481416 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29481373 AAATTGATAT
29481383 AAAATTATAAA
1 AAAATTATAAA
29481394 AAAA-TATAAA
1 AAAATTATAAA
*
29481404 AAAATCATAAA
1 AAAATTATAAA
29481415 AA
1 AA
29481417 CTTGAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:29481401 original size:10 final size:10
Alignment explanation
Indices: 29481383--29481416 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
29481373 AAATTGATAT
*
29481383 AAAATTATAA
1 AAAAATATAA
29481393 AAAAATATAA
1 AAAAATATAA
29481403 AAAAATCATAA
1 AAAAAT-ATAA
29481414 AAA
1 AAA
29481417 CTTGAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
AAAAATATAA
Found at i:29481817 original size:9 final size:9
Alignment explanation
Indices: 29481795--29481870 Score: 53
Period size: 10 Copynumber: 7.9 Consensus size: 9
29481785 ATAATTCAAG
29481795 TTTTTATAA
1 TTTTTATAA
29481804 TTTTTTATAA
1 -TTTTTATAA
29481814 TTTTTATAA
1 TTTTTATAA
*
29481823 GTTTATATCAA
1 -TTTTTAT-AA
*
29481834 TTTTAATACA
1 TTTTTATA-A
* **
29481844 TTTAATATTT
1 TTT-TTATAA
*
29481854 TTTTTATGA
1 TTTTTATAA
29481863 TTTTTATA
1 TTTTTATA
29481871 GAATTTTAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
9 20 0.39
10 27 0.53
11 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29481819 original size:19 final size:20
Alignment explanation
Indices: 29481790--29481837 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
29481780 AATCAATAAT
* *
29481790 TCAAGTTTTTATAATTTTTTA
1 TCAA-TTTTTATAAGTTTATA
29481811 T-AATTTTTATAAGTTTATA
1 TCAATTTTTATAAGTTTATA
29481830 TCAATTTT
1 TCAATTTT
29481838 AATACATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 15 0.62
20 8 0.33
21 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
TCAATTTTTATAAGTTTATA
Found at i:29481838 original size:19 final size:19
Alignment explanation
Indices: 29481795--29481900 Score: 61
Period size: 20 Copynumber: 5.3 Consensus size: 19
29481785 ATAATTCAAG
* *
29481795 TTTTTATAATTTTTTATAA
1 TTTTTATAAGTTTATATAA
29481814 TTTTTATAAGTTTATATCAA
1 TTTTTATAAGTTTATAT-AA
* **
29481834 TTTTAATACA-TTTAATATTT
1 TTTTTATA-AGTTT-ATATAA
** *
29481854 TTTTTATGATTTTTATAGAA
1 TTTTTAT-AAGTTTATATAA
* *
29481874 TTTTAATACAGTTTTATAAAA
1 TTTTTATA-AG-TTTATATAA
29481895 TTTTTA
1 TTTTTA
29481901 ATATTTAAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
19 16 0.25
20 27 0.42
21 22 0.34
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTATAAGTTTATATAA
Found at i:29482810 original size:18 final size:16
Alignment explanation
Indices: 29482774--29482815 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
29482764 TATAATTAAT
*
29482774 TAATTTTTTAAGAAAA
1 TAATTTTTTAAAAAAA
29482790 TAATTTTTTAAAAAATTA
1 TAATTTTTTAAAAAA--A
29482808 TAATTTTT
1 TAATTTTT
29482816 AGAGAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.61
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTTTTTAAAAAAA
Found at i:29490887 original size:18 final size:15
Alignment explanation
Indices: 29490860--29490900 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 15
29490850 CAATTTTCTG
29490860 TAAAAAAATTAATATTT
1 TAAAAAAATT-A-ATTT
29490877 TAAATAAAATTAATTT
1 TAAA-AAAATTAATTT
29490893 TAAAAAAA
1 TAAAAAAA
29490901 ATAAGTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 5 0.22
18 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAAATTAATTT
Found at i:29490894 original size:16 final size:17
Alignment explanation
Indices: 29490860--29490902 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
29490850 CAATTTTCTG
29490860 TAAAAAAATTAATATTT
1 TAAAAAAATTAATATTT
29490877 TAAATAAAATTAAT-TTT
1 TAAA-AAAATTAATATTT
*
29490894 AAAAAAAAT
1 TAAAAAAAT
29490903 AAGTGATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAAAATTAATATTT
Found at i:29492722 original size:21 final size:22
Alignment explanation
Indices: 29492689--29492750 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
29492679 TTTAATTAGT
* *
29492689 TTTAAGGTTTTTTAAATTAGGG
1 TTTAGGGTATTTTAAATTAGGG
* *
29492711 TTT-TGGTATTTTAAATAAGGG
1 TTTAGGGTATTTTAAATTAGGG
29492732 TTTAGGGTATTTTAAATTA
1 TTTAGGGTATTTTAAATTA
29492751 ATGGTTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (22 bp):
TTTAGGGTATTTTAAATTAGGG
Done.