Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 63 of 136
Found at i:20918821 original size:27 final size:26
Alignment explanation
Indices: 20918771--20918822 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20918761 ATAGTTTATT
* *
20918771 AAATAAAAATAAAATAATATTTTTTG
1 AAATAAAAACAAAATAATAATTTTTG
*
20918797 AAATTAAAACAAAATAATAAATTTTT
1 AAATAAAAACAAAATAAT-AATTTTT
20918823 TTGACAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATAAAAACAAAATAATAATTTTTG
Found at i:20935787 original size:7 final size:7
Alignment explanation
Indices: 20935775--20935801 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20935765 AAAAAAACTT
20935775 ATAAATA
1 ATAAATA
20935782 ATAAATA
1 ATAAATA
20935789 ATAAATA
1 ATAAATA
20935796 ATAAAT
1 ATAAAT
20935802 TTTAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:20936201 original size:179 final size:178
Alignment explanation
Indices: 20935910--20936265 Score: 459
Period size: 179 Copynumber: 2.0 Consensus size: 178
20935900 AAAAATCCCT
* * *
20935910 TTAACAATTAACTTTAACTATTGATCGTTAAAGTTAACGACCCCTAGTTTTTTCAATTAAAGTCA
1 TTAACAATTAACTTTAACTATTAATCATTAAAGTTAACGACCCCTAGTTTTTTAAATTAAAGTCA
** ** * *
20935975 TTGCGTGTCGTAACACAACATGACATGTGGCGAAAATGATAAAAAAAAAATCAATAAAAGTTATA
66 TCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTATA
* * *
20936040 GAAAAATTAT-AAAATGCTTCTTTGGTATGGTAATTTTTAT-AATTTTTTC
131 GAAAAATTATGAAAAT--TT-TTTGATACGATAATTTTTATAAATTTTTTC
* *
20936089 TTAACAATTAACTTTAATTGTTAATCATTAAAGTTAAACGACCCCTAGTTTGTTTAAATTAAAGT
1 TTAACAATTAACTTTAACTATTAATCATTAAAGTT-AACGACCCCTAGTTT-TTTAAATTAAAGT
* * *** *
20936154 CATCATGTGTCACAACATAGTGTGACATGTAGC-AAAA-AATGAAAAAAAAATCAATAAAAGTTA
64 CATCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTA
20936217 TAGAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTT
129 TAGAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTT
20936266 TACGAAATTT
Statistics
Matches: 153, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
177 17 0.11
178 10 0.07
179 67 0.44
180 24 0.16
181 35 0.23
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (178 bp):
TTAACAATTAACTTTAACTATTAATCATTAAAGTTAACGACCCCTAGTTTTTTAAATTAAAGTCA
TCACGTGTCACAACACAACATGACATGTAGCGAAAATAATAAAAAAAAAATCAATAAAAGTTATA
GAAAAATTATGAAAATTTTTTGATACGATAATTTTTATAAATTTTTTC
Found at i:20942668 original size:16 final size:16
Alignment explanation
Indices: 20942647--20942681 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20942637 CTAATTATTG
20942647 ATTACAACTCTATTCT
1 ATTACAACTCTATTCT
*
20942663 ATTACAACTCTATTTT
1 ATTACAACTCTATTCT
20942679 ATT
1 ATT
20942682 CCAATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:20945113 original size:30 final size:30
Alignment explanation
Indices: 20945053--20945113 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20945043 TTTATCATCT
* * **
20945053 AAAACTCGTGCTTTTTGAACTATTACCAAA
1 AAAACTCGTGCTTCTTGAACCAAAACCAAA
*
20945083 AAAACTCGTGCTTCTTGAACCAAAAGCAAA
1 AAAACTCGTGCTTCTTGAACCAAAACCAAA
20945113 A
1 A
20945114 GCTGTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (30 bp):
AAAACTCGTGCTTCTTGAACCAAAACCAAA
Found at i:20950334 original size:2 final size:2
Alignment explanation
Indices: 20950285--20950323 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20950275 CAATCAAAGA
20950285 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20950324 GTTTGTCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:20952790 original size:3 final size:3
Alignment explanation
Indices: 20952782--20952856 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
20952772 TAATAAAGCG
20952782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20952829 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
20952857 GTAATGCATT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20955204 original size:83 final size:83
Alignment explanation
Indices: 20955065--20955230 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
20955055 TTCACCACTT
20955065 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
1 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
20955130 AAGAGTTAGCTGTACCAG
66 AAGAGTTAGCTGTACCAG
* *
20955148 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGTTTCCTGCAAATATAAAGCAGGTCATCTTAC
1 AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
20955213 AAGAGTTAGCTGTACCAG
66 AAGAGTTAGCTGTACCAG
20955231 CAAAGTCAGT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (83 bp):
AAGGTTTGTGTGATTGAAGTTGCAGATTTAATAGCTTCCTGCAAATATAAAGCAGGTCATCTTAA
AAGAGTTAGCTGTACCAG
Found at i:20971342 original size:10 final size:10
Alignment explanation
Indices: 20971327--20971355 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
20971317 GGTTATATGT
20971327 TTTGGGAGTG
1 TTTGGGAGTG
20971337 TTTGGGAGTG
1 TTTGGGAGTG
20971347 TTTGGGAGT
1 TTTGGGAGT
20971356 TCCCAAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.41
Consensus pattern (10 bp):
TTTGGGAGTG
Found at i:20975464 original size:27 final size:27
Alignment explanation
Indices: 20975426--20975812 Score: 478
Period size: 27 Copynumber: 14.3 Consensus size: 27
20975416 TGCGATTCGT
*
20975426 GGTAAAATGACTGAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* *
20975453 GGTAAAATGACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
20975480 GGTAAAA-TAATCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
* ** * * *
20975507 GGTAATACGATTGAAATTCCCTTGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
20975534 GGTAAAATTA-TCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
* *
20975561 GGTAAAATGACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
20975588 GGTAAAATTACTAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* * *
20975615 GGTAAAATAACTAAAATACCCATCAAAG
1 GGTAAAATTACTGAAATACCC-TCGAAG
* *
20975643 GGTAAAATGACTGAAATACGCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
20975670 GGTAAAATTA-TCGAAATACTCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
20975697 GGTAAAATTACTGAAATACCC-CTGAAG
1 GGTAAAATTACTGAAATACCCTC-GAAG
*
20975724 AGTAAAATTA-TCGAAATACCCTCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
*
20975751 GGTAAAATTACGGAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* *
20975778 GGTAAAATTACCGAAATACCCCCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
20975805 GGTAAAAT
1 GGTAAAAT
20975813 GGCTGTTATA
Statistics
Matches: 318, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
26 6 0.02
27 284 0.89
28 28 0.09
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (27 bp):
GGTAAAATTACTGAAATACCCTCGAAG
Found at i:20982814 original size:15 final size:15
Alignment explanation
Indices: 20982794--20982822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20982784 TAGCCATGGG
20982794 ATGTCACGACACACT
1 ATGTCACGACACACT
20982809 ATGTCACGACACAC
1 ATGTCACGACACAC
20982823 CCCTAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (15 bp):
ATGTCACGACACACT
Found at i:20987350 original size:6 final size:6
Alignment explanation
Indices: 20987339--20987383 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
20987329 ATCTTTATTA
* * * *
20987339 GTATCT GTATCT GTATTT GTATTT GTATTT GTATCT ATATCT GTA
1 GTATCT GTATCT GTATCT GTATCT GTATCT GTATCT GTATCT GTA
20987384 ACTCATCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.56
Consensus pattern (6 bp):
GTATCT
Found at i:20987350 original size:18 final size:18
Alignment explanation
Indices: 20987329--20987383 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
20987319 CAGTATATGC
20987329 ATCTTTATTAGTATCTGT
1 ATCTTTATTAGTATCTGT
* * *
20987347 ATCTGTATTTGTATTTGT
1 ATCTTTATTAGTATCTGT
20987365 AT-TTGTATCTA-TATCTGT
1 ATCTT-TAT-TAGTATCTGT
20987383 A
1 A
20987384 ACTCATCTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (18 bp):
ATCTTTATTAGTATCTGT
Found at i:20988700 original size:21 final size:22
Alignment explanation
Indices: 20988670--20988716 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
20988660 TTGAATGTAT
* *
20988670 AAAAGCAAAATGAGTACAAAGA
1 AAAAGCAAAAGGAGTAAAAAGA
*
20988692 AAAAG-AAAAGGTGTAAAAAGA
1 AAAAGCAAAAGGAGTAAAAAGA
20988713 AAAA
1 AAAA
20988717 AAACAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGCAAAAGGAGTAAAAAGA
Found at i:20989233 original size:11 final size:12
Alignment explanation
Indices: 20989203--20989231 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20989193 AATTAATTAG
20989203 GTTTTTAATTTA
1 GTTTTTAATTTA
20989215 GTTTTTAATTTA
1 GTTTTTAATTTA
20989227 GTTTT
1 GTTTT
20989232 AAATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (12 bp):
GTTTTTAATTTA
Found at i:20997903 original size:18 final size:18
Alignment explanation
Indices: 20997880--20997915 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20997870 ATATCATGAT
* *
20997880 AATGCCGTCGATGCTAAG
1 AATGCCATCGACGCTAAG
20997898 AATGCCATCGACGCTAAG
1 AATGCCATCGACGCTAAG
20997916 GATAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (18 bp):
AATGCCATCGACGCTAAG
Found at i:21000625 original size:13 final size:13
Alignment explanation
Indices: 21000607--21000631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21000597 CAAATTTTAT
21000607 AACAATATATTAA
1 AACAATATATTAA
21000620 AACAATATATTA
1 AACAATATATTA
21000632 CATTAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AACAATATATTAA
Found at i:21000677 original size:13 final size:13
Alignment explanation
Indices: 21000650--21000683 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21000640 ATTAAGGTGT
*
21000650 AGTAT-TTATAAC
1 AGTATATTAAAAC
21000662 AGTATATTAAAAC
1 AGTATATTAAAAC
21000675 AGTATATTA
1 AGTATATTA
21000684 CATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:21000922 original size:27 final size:27
Alignment explanation
Indices: 21000704--21000914 Score: 422
Period size: 27 Copynumber: 7.8 Consensus size: 27
21000694 TAAGGTGCAG
21000704 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000731 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000758 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000785 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000812 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000839 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000866 TATTTATAACAGTATATTAAAATAGTA
1 TATTTATAACAGTATATTAAAATAGTA
21000893 TATTTATAACAGTATATTAAAA
1 TATTTATAACAGTATATTAAAA
21000915 CCGTATATAT
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 184 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
TATTTATAACAGTATATTAAAATAGTA
Found at i:21001286 original size:11 final size:11
Alignment explanation
Indices: 21001272--21001302 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
21001262 TCAATCATAC
21001272 TAGAAAGAGAA
1 TAGAAAGAGAA
21001283 TAGAAAGAGAA
1 TAGAAAGAGAA
21001294 TAGAAAGAG
1 TAGAAAGAG
21001303 CCTTCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (11 bp):
TAGAAAGAGAA
Found at i:21011031 original size:32 final size:32
Alignment explanation
Indices: 21010989--21011117 Score: 206
Period size: 32 Copynumber: 4.1 Consensus size: 32
21010979 CATAGCCATG
* *
21010989 TGTCAGACACGGATGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
* *
21011021 TGTCGCACACGGTTGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
*
21011053 TGTCACACACGGCTGAGACACACG-TCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
21011084 TGTCACACACGGCTGAGACACACGCCCGTGTC
1 TGTCACACACGGCTGAGACACACGCCCGTGTC
21011116 TG
1 TG
21011118 AGGCTGTGTG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 30 0.34
32 59 0.66
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (32 bp):
TGTCACACACGGCTGAGACACACGCCCGTGTC
Found at i:21011101 original size:63 final size:64
Alignment explanation
Indices: 21010989--21011117 Score: 206
Period size: 63 Copynumber: 2.0 Consensus size: 64
21010979 CATAGCCATG
* * *
21010989 TGTCAGACACGGATGAGACACACGCCCGTGTCTGTCGCACACGGTTGAGACACACGCCCGTGTC
1 TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
* *
21011053 TGTCACACACGGCTGAGACACACG-TCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
1 TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
21011116 TG
1 TG
21011118 AGGCTGTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 38 0.63
64 22 0.37
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (64 bp):
TGTCACACACGGATGAGACACACGCCCGTGTCTGTCACACACGGCTGAGACACACGCCCGTGTC
Found at i:21012989 original size:29 final size:29
Alignment explanation
Indices: 21012956--21013118 Score: 136
Period size: 29 Copynumber: 5.6 Consensus size: 29
21012946 CATGGTTGTT
*
21012956 ACCATCCCTTTTCATAGTTGATGGTCATC
1 ACCATCCCTTTTCATAATTGATGGTCATC
* * *
21012985 ACCATCCCTTTTCATAATCGATAG-C-TGA
1 ACCATCCCTTTTCATAATTGATGGTCAT-C
* * * * *
21013013 AGCTATCCCTTTTCATAATCGGTAGTCGA-A
1 A-CCATCCCTTTTCATAATTGATGGTC-ATC
* * *
21013043 ACTATCCCTTTTCAT-ATTCAATGGTCGTC
1 ACCATCCCTTTTCATAATT-GATGGTCATC
* *
21013072 ACCATCCTTTTTCATAGTTGATGGTCATC
1 ACCATCCCTTTTCATAATTGATGGTCATC
21013101 ACCATCCCTTTTCATAAT
1 ACCATCCCTTTTCATAAT
21013119 CGATAGCCGA
Statistics
Matches: 107, Mismatches: 19, Indels: 16
0.75 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 4 0.04
29 97 0.91
30 5 0.05
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATAATTGATGGTCATC
Found at i:21013077 original size:87 final size:87
Alignment explanation
Indices: 21012959--21013144 Score: 225
Period size: 87 Copynumber: 2.1 Consensus size: 87
21012949 GGTTGTTACC
* *
21012959 ATCCCTTTTCATAGTTGATGGTCATCACCATCCCTTTTCATAATCGATAG-C-TGAAGCTATCCC
1 ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATCGATAGTCAT-AA-CCATCCC
* *
21013022 TTTTCATAATCGGTAGTCGAAACT
64 TTTTCATAATCGATAGCCGAAACT
* * * * * *
21013046 ATCCCTTTTCATA-TTCAATGGTCGTCACCATCCTTTTTCATAGTTGATGGTCATCACCATCCCT
1 ATCCCTTTTCATAGTT-AATGGTCATCACCATCCCTTTTCATAATCGATAGTCATAACCATCCCT
*
21013110 TTTCATAATCGATAGCCGAAGCT
65 TTTCATAATCGATAGCCGAAACT
21013133 ATCCCTTTTCAT
1 ATCCCTTTTCAT
21013145 TGGTTGATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 80 0.94
88 2 0.02
89 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (87 bp):
ATCCCTTTTCATAGTTAATGGTCATCACCATCCCTTTTCATAATCGATAGTCATAACCATCCCTT
TTCATAATCGATAGCCGAAACT
Found at i:21016522 original size:11 final size:11
Alignment explanation
Indices: 21016506--21016538 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
21016496 AATCAGTCCC
21016506 TTGACCCACTA
1 TTGACCCACTA
*
21016517 TTGACCCACTG
1 TTGACCCACTA
21016528 TTGACCCACTA
1 TTGACCCACTA
21016539 AGGGAATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.27
Consensus pattern (11 bp):
TTGACCCACTA
Found at i:21024647 original size:40 final size:41
Alignment explanation
Indices: 21024603--21024682 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
21024593 TAACAGTTTG
* *
21024603 GGCCTTAGCCCATCTCAGTA-CAGTATCAAAT-ATGCAGTAA
1 GGCCTTAGCCCATCACAGTATCAGTAGC-AATCATGCAGTAA
21024643 GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
1 GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTA
21024683 TTCAGTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 22 0.61
41 14 0.39
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (41 bp):
GGCCTTAGCCCATCACAGTATCAGTAGCAATCATGCAGTAA
Found at i:21027691 original size:14 final size:14
Alignment explanation
Indices: 21027672--21027698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21027662 ATTAGCATTA
21027672 CATTTCATTACATG
1 CATTTCATTACATG
21027686 CATTTCATTACAT
1 CATTTCATTACAT
21027699 AAAAAGTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
CATTTCATTACATG
Found at i:21029205 original size:32 final size:32
Alignment explanation
Indices: 21029166--21029233 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
21029156 GCCTTGCCTG
21029166 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
1 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
* *
21029198 GAAGAGGAAGGAATTGGAAAAGAAGCACTAAA
1 GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
21029230 GAAG
1 GAAG
21029234 GAAAACACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.53, C:0.07, G:0.34, T:0.06
Consensus pattern (32 bp):
GAAGAGGAAGGAACTGGAAAAGAAGCACGAAA
Found at i:21030299 original size:16 final size:16
Alignment explanation
Indices: 21030273--21030313 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
21030263 AGATATAACC
21030273 ATTTATTTTTA-TTTTT
1 ATTT-TTTTTATTTTTT
21030289 ATTCTTTTTTATTTTTT
1 ATT-TTTTTTATTTTTT
21030306 ATTTTTTT
1 ATTTTTTT
21030314 CTTTCTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
ATTTTTTTTATTTTTT
Found at i:21037840 original size:45 final size:47
Alignment explanation
Indices: 21037677--21037848 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 47
21037667 TATTTCTGTG
* * * *** * *
21037677 TTCTCGAGTCCACAACGTATGTAGGAGCTCAAAACCTAAT-CCTATA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* *
21037723 TTCTCGAGTCCGCAACGTATGCAAGAGCTCGGAACCTAATATTG-TA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* * *
21037769 TTCTCAAGTCTGCAACATATGCAAGAGCTTGGAACCT-AT-TCGATA
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
* * *
21037814 TTCTCGAGTCCGCAATGTACGTAAGAGCTTGGAAC
1 TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAAC
21037849 TTGGGCAAAG
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.02
45 33 0.31
46 70 0.67
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (47 bp):
TTCTCGAGTCCGCAACGTATGCAAGAGCTTGGAACCTAATATCGATA
Found at i:21046403 original size:27 final size:27
Alignment explanation
Indices: 21046372--21046649 Score: 303
Period size: 27 Copynumber: 10.3 Consensus size: 27
21046362 AGAGGTCAAT
21046372 AAATGACTGAAATACCCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
21046399 AAATGACCGAAATACGCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
***
21046426 AAATGA-TCGAAATACCCTTGTAGGGTA
1 AAATGACT-GAAATACCCCCATAGGGTA
* *
21046453 AAATGACTGGAATACCGCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* *
21046480 AAATGACCGAAATACCGCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * *
21046507 AAATAACTGAAATACCCCCACAAGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
* * * *
21046534 AAATGA-TCATATTACTCCCATAAGGTA
1 AAATGACTGA-AATACCCCCATAGGGTA
* * *
21046561 AAATGACCGTATTACCCCCA-ATGGGTA
1 AAATGACTGAAATACCCCCATA-GGGTA
* *
21046588 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
*
21046615 AAATGACCGAAATA-CCCCATAGGGTA
1 AAATGACTGAAATACCCCCATAGGGTA
21046641 AAATGACTG
1 AAATGACTG
21046650 TTATACCCTT
Statistics
Matches: 211, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
26 22 0.10
27 187 0.89
28 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCATAGGGTA
Found at i:21046888 original size:26 final size:26
Alignment explanation
Indices: 21046812--21046892 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
21046802 TGGAGGAAGT
* * *
21046812 ATACTGTTATTGGCAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
* * * * *
21046838 ATATTTTTACTGGAAACCTTACTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
*
21046864 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGGAAGCTTTGCTGCG
21046890 ATA
1 ATA
21046893 TTGGTGTGTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGAAGCTTTGCTGCG
Found at i:21048720 original size:42 final size:42
Alignment explanation
Indices: 21048573--21048730 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 42
21048563 TAACAATGTC
* *
21048573 ATATCCCAAATATGGTC-TACATGTAATCTCATATCGATGCCA
1 ATATCCCAAACATGGTCTTACACG-AATCTCATATCGATGCCA
* ** * *
21048615 ATAGCCCAGCCATGGTCTTACACGAAATCACATATCGATGCCG
1 ATATCCCAAACATGGTCTTACACG-AATCTCATATCGATGCCA
* * *
21048658 ATGTCCCAAACATGGTCTTACACGAAGTTTCATATCGATGTC-
1 ATATCCCAAACATGGTCTTACACGAA-TCTCATATCGATGCCA
* *
21048700 ATATCCCAGATATGGTCTTACACGTAATCTC
1 ATATCCCAAACATGGTCTTACACG-AATCTC
21048731 GGTAAACCTA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 39 0.41
43 55 0.59
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
ATATCCCAAACATGGTCTTACACGAATCTCATATCGATGCCA
Found at i:21052879 original size:3 final size:3
Alignment explanation
Indices: 21052871--21052998 Score: 256
Period size: 3 Copynumber: 42.7 Consensus size: 3
21052861 TATTCTTTAA
21052871 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21052919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21052967 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21052999 AATTACTAAA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 125 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21054217 original size:17 final size:17
Alignment explanation
Indices: 21054195--21054234 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
21054185 ACAAATTATT
21054195 TTTGGGCTT-GTTGGGTA
1 TTTGGGCTTGGTT-GGTA
21054212 TTTGGGCTTGGTTGGTA
1 TTTGGGCTTGGTTGGTA
21054229 TTTGGG
1 TTTGGG
21054235 TTAGGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.05, C:0.05, G:0.42, T:0.47
Consensus pattern (17 bp):
TTTGGGCTTGGTTGGTA
Found at i:21054428 original size:29 final size:30
Alignment explanation
Indices: 21054379--21054438 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
21054369 AGTATAAGGT
21054379 TTAAATTTTTAAAAATAAAAG-TATAAAAA
1 TTAAATTTTTAAAAATAAAAGATATAAAAA
**
21054408 TTAAA-TTTTAAATTTATAAAGAATATAAAAA
1 TTAAATTTTTAAAAATA-AAAG-ATATAAAAA
21054439 CTTATCACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 9 0.35
29 9 0.35
31 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAAATTTTTAAAAATAAAAGATATAAAAA
Found at i:21056773 original size:7 final size:7
Alignment explanation
Indices: 21056731--21056771 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
21056721 TTGGTAATTG
21056731 GTTGATA
1 GTTGATA
21056738 GTTGATA
1 GTTGATA
21056745 GTTGATA
1 GTTGATA
21056752 GTTGATA
1 GTTGATA
*
21056759 GTTGATT
1 GTTGATA
21056766 GTTGAT
1 GTTGAT
21056772 TGCAGTGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.46
Consensus pattern (7 bp):
GTTGATA
Found at i:21058847 original size:5 final size:5
Alignment explanation
Indices: 21058837--21058866 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21058827 ACGATTTCGG
*
21058837 TTTCT TTTCT TTTCT TTTCT TTTCT CTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
21058867 GCGTTCAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:21072217 original size:44 final size:44
Alignment explanation
Indices: 21072166--21072539 Score: 152
Period size: 44 Copynumber: 8.1 Consensus size: 44
21072156 AGTGTAAGGA
* * *
21072166 AGCAGATTTAAGCCA-CAGGTCTTATCTCCCTGAGATTACAGCGG
1 AGCAGATTGAAGCCAGCA-ATCCTATCTCCCTGAGATTACAGCGG
* * *
21072210 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * * * * * *
21072254 AGCGGATTAAAATG-AAG-GAT-TTATCTCTCTGA-AGTTACAATAGAGTAG
1 AGCAGATT-GAA-GCCAGCAATCCTATCTCCCTGAGA-TTAC---AGCG--G
* * *
21072302 ATCGCATCAGATGGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGG
1 A--G---CAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * *
21072351 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
** *** * * *
21072395 AGTGGATT-AAAATAG-AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAG
1 AGCAGATTGAAGCCAGCA--ATCCTATCTCCCTGAGA-TTAC---AGCG--G
** *
21072444 ATCACGTCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGG
1 ---A-G-CAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
* * *
21072493 AGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
21072537 AGC
1 AGC
21072540 GGGTTAAAAT
Statistics
Matches: 251, Mismatches: 45, Indels: 68
0.69 0.12 0.19
Matches are distributed among these distances:
42 2 0.01
43 20 0.08
44 145 0.58
45 6 0.02
46 5 0.02
47 4 0.02
48 2 0.01
49 4 0.02
50 1 0.00
51 7 0.03
52 5 0.02
53 7 0.03
54 37 0.15
55 5 0.02
56 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
AGCAGATTGAAGCCAGCAATCCTATCTCCCTGAGATTACAGCGG
Found at i:21072507 original size:142 final size:142
Alignment explanation
Indices: 21072185--21072588 Score: 677
Period size: 142 Copynumber: 2.9 Consensus size: 142
21072175 AAGCCACAGG
21072185 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* *
21072250 GTGGAGCGGATTAAAAT-GAAGGAT-TTATCTCTCTGAAGTTACAATAGAGTAGATCGCATCAGA
66 GTGGAGCGGATTAAAATAG-AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGA
*
21072313 TGGAAGCCAGAAA
130 TGGAAGCCAAAAA
21072326 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* *
21072391 GTGGAGTGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACGTCAGAT
66 GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGAT
*
21072456 TGAAGCCAAAAA
131 GGAAGCCAAAAA
21072468 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
* * * * * *
21072533 GTGGAGCGGGTTAAAATAAAAGATCTTATCTCTCTGAACTTATAGCAGAGTAGATC
66 GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC
21072589 GCATTAGGTC
Statistics
Matches: 248, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
141 86 0.35
142 162 0.65
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (142 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAATAGAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGAT
GGAAGCCAAAAA
Found at i:21072532 original size:98 final size:97
Alignment explanation
Indices: 21072353--21072534 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
21072343 TACAGCGGAG
* ** * ** *
21072353 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAGAGGATCTT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAGA-GATCCT
*
21072418 ATCTCTCTGAAGTTACAGTAGAGTAGATCACGT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCACGT
* **
21072451 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA-ATCC
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAG-AGATCC
21072515 TATCTCCCTG-AGATTACAGT
64 TATCTCCCTGAAG-TTACAGT
21072535 GGAGCGGGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 2 0.03
98 62 0.89
99 5 0.07
100 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (97 bp):
CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAGAGATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCACGT
Found at i:21072563 original size:44 final size:44
Alignment explanation
Indices: 21072463--21072569 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
21072453 GATTGAAGCC
**
21072463 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
1 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
** * * * *
21072507 AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGGTT-AAAAT
1 AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
*
21072550 AAAAGATCTTATCTCTCTGA
1 AAAA-ATCTTATCTCCCTGA
21072570 ACTTATAGCA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
43 5 0.10
44 45 0.90
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
AAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAAAT
Found at i:21076348 original size:20 final size:19
Alignment explanation
Indices: 21076323--21076361 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21076313 TCTACTATAC
21076323 TTACATATGTAATTTAATTT
1 TTACAT-TGTAATTTAATTT
* *
21076343 TTACATTTTAATTTCATTT
1 TTACATTGTAATTTAATTT
21076362 AATTTGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
TTACATTGTAATTTAATTT
Found at i:21076615 original size:50 final size:50
Alignment explanation
Indices: 21076559--21076664 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
21076549 CTTGAATTAA
21076559 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
1 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
21076609 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
1 TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
21076659 TTAATA
1 TTAATA
21076665 GGCTTTGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (50 bp):
TTAATAATATTACGAAAATAGAAGAATCAAATCATATTAAATTGCGAAGG
Found at i:21076645 original size:27 final size:27
Alignment explanation
Indices: 21076565--21076647 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
21076555 TTAATTAATA
21076565 ATATTACGAAAATAGAAGAATCAAATC
1 ATATTACGAAAATAGAAGAATCAAATC
* * * * *
21076592 ATATT---AAATTGCGAAG-GT-TAATA
1 ATATTACGAAAAT-AGAAGAATCAAATC
21076615 ATATTACGAAAATAGAAGAATCAAATC
1 ATATTACGAAAATAGAAGAATCAAATC
21076642 ATATTA
1 ATATTA
21076648 AATTGCGAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 8 0.20
24 5 0.12
25 8 0.20
26 5 0.12
27 14 0.35
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (27 bp):
ATATTACGAAAATAGAAGAATCAAATC
Found at i:21077086 original size:112 final size:113
Alignment explanation
Indices: 21076949--21077173 Score: 434
Period size: 112 Copynumber: 2.0 Consensus size: 113
21076939 TAAACATAAT
*
21076949 AAAATGATCATAACTATAAAATGATTTAAAATTTTTTATATCTAATGAGAACATTTTTCATTTAA
1 AAAATGATCATAACTATAAAATGATTTAAAATATTTTATATCTAATGAGAACATTTTTCATTTAA
21077014 TTTACTAAAAAAGTAATATTTTTAAAAGGATTTTTTTAATTAATGAAA
66 TTTACTAAAAAAGTAATATTTTTAAAAGGATTTTTTTAATTAATGAAA
21077062 AAAATGATCA-AACTATAAAATGATTTAAAATATTTTATATCTAATGAGAACATTTTTCATTTAA
1 AAAATGATCATAACTATAAAATGATTTAAAATATTTTATATCTAATGAGAACATTTTTCATTTAA
21077126 TTTACTAAAAAAGTAATATTTTTAAAAGGATTTTTTTAATTAATGAAA
66 TTTACTAAAAAAGTAATATTTTTAAAAGGATTTTTTTAATTAATGAAA
21077174 CAATATTTTC
Statistics
Matches: 111, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
112 101 0.91
113 10 0.09
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (113 bp):
AAAATGATCATAACTATAAAATGATTTAAAATATTTTATATCTAATGAGAACATTTTTCATTTAA
TTTACTAAAAAAGTAATATTTTTAAAAGGATTTTTTTAATTAATGAAA
Found at i:21079269 original size:20 final size:20
Alignment explanation
Indices: 21079244--21079298 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
21079234 AATTACAAAA
21079244 AAAATAATTTTAAAAAATTC
1 AAAATAATTTTAAAAAATTC
* *
21079264 AAAATAATTTT-TAAAATTT
1 AAAATAATTTTAAAAAATTC
21079283 AAAAT-ATTTATAAAAA
1 AAAATAATTT-TAAAAA
21079299 TCAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 14 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTAAAAAATTC
Found at i:21079281 original size:19 final size:19
Alignment explanation
Indices: 21079244--21079305 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
21079234 AATTACAAAA
*
21079244 AAAATAATTTTAAAAAATTC
1 AAAATAATTTT-TAAAATTC
*
21079264 AAAATAATTTTTAAAATTT
1 AAAATAATTTTTAAAATTC
* *
21079283 AAAAT-ATTTATAAAAATC
1 AAAATAATTTTTAAAATTC
21079301 AAAAT
1 AAAAT
21079306 TTTATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.41
19 11 0.30
20 11 0.30
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTC
Found at i:21079296 original size:18 final size:18
Alignment explanation
Indices: 21079252--21079333 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 18
21079242 AAAAAATAAT
* *
21079252 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTTAAAAT-A
*
21079271 TTTTTAAAATTTAAAATA
1 TTTATAAAATTTAAAATA
* *
21079289 TTTATAAAAATCAAAAT-
1 TTTATAAAATTTAAAATA
**
21079306 TTTAT-ATTTTTAAAA-A
1 TTTATAAAATTTAAAATA
*
21079322 ATTATAAAATTT
1 TTTATAAAATTT
21079334 TTCAAACAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
16 10 0.21
17 9 0.19
18 15 0.31
19 14 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATAAAATTTAAAATA
Found at i:21079344 original size:20 final size:19
Alignment explanation
Indices: 21079311--21079349 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
21079301 AAAATTTTAT
21079311 ATTTTTAAAAAATTATAAA
1 ATTTTTAAAAAATTATAAA
* *
21079330 ATTTTTCAAACAATTCTAAA
1 ATTTTT-AAAAAATTATAAA
21079350 GAATACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTTTAAAAAATTATAAA
Found at i:21084532 original size:34 final size:35
Alignment explanation
Indices: 21084465--21084586 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 35
21084455 TAAAGAGTGT
21084465 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
1 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
* * *
21084500 GCCCAGCGCTAGTCGGAT-AACTGAC-GATAGTTGT
1 GCCCAGCACTAGTCAGATAAACTGACAGA-AGTTGC
* * * *
21084534 GCCCAGTACTAATCAGATAAATTGACAGAAATTGC
1 GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
**
21084569 GCCCAGTGCTAGTCAGAT
1 GCCCAGCACTAGTCAGAT
21084587 GAATCGACAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
33 2 0.03
34 26 0.36
35 42 0.58
36 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (35 bp):
GCCCAGCACTAGTCAGATAAACTGACAGAAGTTGC
Found at i:21084666 original size:20 final size:21
Alignment explanation
Indices: 21084626--21084674 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
21084616 AGTCCATAAA
21084626 ATCACATTTCATAACCTCAAT
1 ATCACATTTCATAACCTCAAT
21084647 ATCACATTTCATAA-CTCAAT
1 ATCACATTTCATAACCTCAAT
21084667 ATCACATT
1 ATCACATT
21084675 CACTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.35
Consensus pattern (21 bp):
ATCACATTTCATAACCTCAAT
Found at i:21091404 original size:22 final size:22
Alignment explanation
Indices: 21091374--21091425 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
21091364 AATGGCTAAG
* * *
21091374 AGCCGTAAATAGGATAGCTATA
1 AGCCATAAATAGAATAGCTACA
* *
21091396 AGCTATAAATAGAATGGCTACA
1 AGCCATAAATAGAATAGCTACA
21091418 AGCCATAA
1 AGCCATAA
21091426 GTACAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (22 bp):
AGCCATAAATAGAATAGCTACA
Found at i:21091470 original size:32 final size:32
Alignment explanation
Indices: 21091432--21091552 Score: 140
Period size: 32 Copynumber: 3.8 Consensus size: 32
21091422 ATAAGTACAA
* * *
21091432 TAATATGATTGGCACAAAGCCATCAGTAGTAG
1 TAATATGATCGACACAAAGCCATCAGTAATAG
21091464 TAATATGATCGACACATAA-CCATCAGTAATAG
1 TAATATGATCGACACA-AAGCCATCAGTAATAG
* * *
21091496 TAGTATGATCAACACAAAGCCATCAGTAATGG
1 TAATATGATCGACACAAAGCCATCAGTAATAG
21091528 TAATATGATTCGGACAC--AGCCATCA
1 TAATATGA-TC-GACACAAAGCCATCA
21091553 ATAGTATCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.03
32 67 0.87
33 4 0.05
34 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (32 bp):
TAATATGATCGACACAAAGCCATCAGTAATAG
Found at i:21091775 original size:24 final size:25
Alignment explanation
Indices: 21091748--21091811 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
21091738 CAAATCACAA
* *
21091748 ACAAATCAGTCATTTACATCTC-GG
1 ACAAATCAATCATTTACATCACAGG
*
21091772 ACAAATCATTCATTTACATCACAGG
1 ACAAATCAATCATTTACATCACAGG
21091797 A-AAATCAATCATTTA
1 ACAAATCAATCATTTA
21091812 ACCCCGAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 33 0.92
25 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (25 bp):
ACAAATCAATCATTTACATCACAGG
Found at i:21091861 original size:27 final size:27
Alignment explanation
Indices: 21091830--21092135 Score: 337
Period size: 27 Copynumber: 11.3 Consensus size: 27
21091820 GGGTAAAATA
* *
21091830 GTCATTTTACCCTACAAGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
21091857 ATCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
21091884 ATCTTTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
21091911 ATCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
21091938 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
21091965 GTCATTTTACCCTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
21091992 GTCATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* **
21092019 GTCATTTTACCCTATAGGGAAATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
21092046 GTCATTTTACCC-ATC-GAGGGTATTTCG
1 GTCATTTTACCCTA-CAG-GGGCATTACG
** * *
21092073 GTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * **
21092100 ATAATTTTACCCTTCAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
21092127 GTCATTTTA
1 GTCATTTTA
21092136 TCATTCGGTG
Statistics
Matches: 244, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 241 0.99
28 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:21092107 original size:54 final size:54
Alignment explanation
Indices: 21091858--21092190 Score: 192
Period size: 54 Copynumber: 6.2 Consensus size: 54
21091848 GACATTACGA
* * * ** * * *
21091858 TCATTTTACCCTATAGGGGCATTACGATCTTTTTACCCTAC-AGGGGTATTACGA
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
** * * * * * * * *
21091912 TCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTAC-AGGGGCATTACGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
** * * * * * ** * *
21091966 TCATTTTACCCTACAGAGGCATTACGGTCATTTTA-CCTTATAGGGGCATTACGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
* ** * * * *
21092020 TCATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGG
*
21092074 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTC-AGGGGTATTTTGG
1 TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGA-GGGTATTTCGG
* * * *
21092128 TCATTTTA-TCATTCGGTGGTATTTC-AGTAATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTTAGG-GGTATTTCGA-TAATTTTACCCTTCGAGGGTATTTCGG
*
21092182 TAATTTTAC
1 TCATTTTAC
21092191 AACCTTTTTG
Statistics
Matches: 239, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
53 10 0.04
54 224 0.94
55 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (54 bp):
TCATTTTACCCTTTAGGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGG
Found at i:21092149 original size:81 final size:81
Alignment explanation
Indices: 21091855--21092190 Score: 249
Period size: 81 Copynumber: 4.1 Consensus size: 81
21091845 AAGGACATTA
* ** * * * *
21091855 CGATCATTTTACCCTATAGGGGCATTACGATCTTTTTACCC-TAC-AGGGGTATTACGATCATTT
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCAT-CGA-GGGTATTTCGGTCATTT
** * * *
21091918 TACCCTACAAGGGCATTA
64 TACCCTTTAGGGGTATTT
* * * ** * *
21091936 CGGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCC-TAC-AGAGGCATTACGGTCATTT
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCAT-CGAG-GGTATTTCGGTCATTT
* *
21091999 TA-CCTTATAGGGGCATTA
64 TACCCTT-TAGGGGTATTT
* *
21092017 CGGTCATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
1 CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
21092082 CCCTTTAGGGGTATTT
66 CCCTTTAGGGGTATTT
** ** * * *
21092098 CGATAATTTTACCCT-TCAGGGGTATTTTGGTCATTTTA-TCATTCG-GTGGTATTTCAGTAATT
1 CGATAATTTTACCCTAT-AGGGAAATTACGGTCATTTTACCCA-TCGAG-GGTATTTCGGTCATT
*
21092160 TTACCC-TTCGAGGGTATTT
63 TTACCCTTTAG-GGGTATTT
21092179 CGATAATTTTAC
1 CGATAATTTTAC
21092191 AACCTTTTTG
Statistics
Matches: 220, Mismatches: 26, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
80 11 0.05
81 202 0.92
82 7 0.03
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (81 bp):
CGATAATTTTACCCTATAGGGAAATTACGGTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
CCCTTTAGGGGTATTT
Found at i:21092160 original size:27 final size:26
Alignment explanation
Indices: 21092049--21092190 Score: 142
Period size: 27 Copynumber: 5.3 Consensus size: 26
21092039 AATTACGGTC
* * *
21092049 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCTTCG-GGGTATTTCGATA
*
21092076 ATTTTACCCTTTAGGGGTATTTCGATA
1 ATTTTACCC-TTCGGGGTATTTCGATA
* * *
21092103 ATTTTACCCTTCAGGGGTATTTTGGTC
1 ATTTTACCCTTC-GGGGTATTTCGATA
* *
21092130 ATTTTATCATTCGGTGGTATTTC-AGTA
1 ATTTTACCCTTCGG-GGTATTTCGA-TA
21092157 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCG-GGGTATTTCGATA
21092184 ATTTTAC
1 ATTTTAC
21092191 AACCTTTTTG
Statistics
Matches: 94, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
26 4 0.04
27 86 0.91
28 4 0.04
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTTCGGGGTATTTCGATA
Found at i:21095175 original size:15 final size:15
Alignment explanation
Indices: 21095136--21095167 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21095126 TAGATACATC
21095136 AAGACAGAGTTTGTA
1 AAGACAGAGTTTGTA
*
21095151 AAGATAGAGTTTGTA
1 AAGACAGAGTTTGTA
21095166 AA
1 AA
21095168 AGCAGAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (15 bp):
AAGACAGAGTTTGTA
Found at i:21099130 original size:42 final size:42
Alignment explanation
Indices: 21099064--21099223 Score: 123
Period size: 42 Copynumber: 3.8 Consensus size: 42
21099054 AAACTCGTAC
* * *
21099064 AATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATC-AATAT
1 AATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* *
21099105 CGATGCCACTGTCCCAGACAAGGTCTTACACGAAATCAAATAT
1 -AATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* * * *
21099148 AATGTCGA-TGTCCCAGACATGGTCTTATACATAAATCTCAAAT-C
1 AATG-CCACTGTCCCAGACATGGTCTTACAC-GAAA--TCAAATAT
* *
21099192 GATGCCAAC-GTCCCAGACGTGGTCTTACACGA
1 AATGCC-ACTGTCCCAGACATGGTCTTACACGA
21099224 TAACACATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 51 0.54
43 12 0.13
44 23 0.24
45 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (42 bp):
AATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
Found at i:21108184 original size:6 final size:6
Alignment explanation
Indices: 21108173--21108206 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
21108163 TCTACTTTAT
*
21108173 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCT CTTC
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTC
21108207 ATTTGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CTTCCC
Found at i:21108235 original size:13 final size:13
Alignment explanation
Indices: 21108217--21108242 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21108207 ATTTGCATGT
21108217 AGTTCCTTGGGAA
1 AGTTCCTTGGGAA
21108230 AGTTCCTTGGGAA
1 AGTTCCTTGGGAA
21108243 TAGGTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
AGTTCCTTGGGAA
Found at i:21118395 original size:40 final size:40
Alignment explanation
Indices: 21118351--21118512 Score: 179
Period size: 40 Copynumber: 4.2 Consensus size: 40
21118341 GTACCTAGCG
* * * *
21118351 CTAGTCAGACAAACTGACGATATCAAATGTGTGTCCAGCA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
*
21118391 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCATCA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
* * * * *
21118431 CTAGTCGGATAAACTGAC-A-AT-AAAT-TACGCCTAACA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
* * *
21118467 CTAGTCGGATAAACCGACGATATCAAATGTGTGCCCAGAA
1 CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
21118507 CTAGTC
1 CTAGTC
21118513 GGGTAAACTG
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
36 25 0.25
37 5 0.05
38 4 0.04
39 5 0.05
40 63 0.62
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (40 bp):
CTAGTCAGATAAACCGACGATATCAAATGTATGCCCAGCA
Found at i:21123517 original size:24 final size:24
Alignment explanation
Indices: 21123490--21123537 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21123480 GATGAGATAC
* *
21123490 CGACCTTTTCGTTGATATCCTTTT
1 CGACCTTTTCATTGATATCATTTT
*
21123514 CGACCTTTTCATTTATATCATTTT
1 CGACCTTTTCATTGATATCATTTT
21123538 TAATCTTCTT
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:0.17, C:0.23, G:0.08, T:0.52
Consensus pattern (24 bp):
CGACCTTTTCATTGATATCATTTT
Found at i:21123756 original size:40 final size:40
Alignment explanation
Indices: 21123706--21123841 Score: 113
Period size: 40 Copynumber: 3.5 Consensus size: 40
21123696 AGTTTCATGC
*
21123706 CCAGCGCTAGTCAGATAAACTGACGATATCAAATGTGTGT
1 CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
* * * ** * * *
21123746 CCAGCACTAGTCGGATAAATTGA-TA-AT--GTTTTGCGC
1 CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
*
21123782 CCGGCGA-TAGT-AGGATAAACTGACGATATCAAATGTGTGT
1 CCAGC-ACTAGTCA-GATAAACTGACGATATCAAATGTGTGT
*
21123822 CTAGCACTAGTCAGATAAAC
1 CCAGCACTAGTCAGATAAAC
21123842 CGACAATGAT
Statistics
Matches: 68, Mismatches: 20, Indels: 16
0.65 0.19 0.15
Matches are distributed among these distances:
36 21 0.31
37 2 0.03
38 4 0.06
39 2 0.03
40 38 0.56
41 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (40 bp):
CCAGCACTAGTCAGATAAACTGACGATATCAAATGTGTGT
Found at i:21124035 original size:27 final size:27
Alignment explanation
Indices: 21124004--21124057 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21123994 ATATATTTCC
21124004 ATAGCATTACATTTAAAATACTAATCA
1 ATAGCATTACATTTAAAATACTAATCA
21124031 ATAGCATTACATTTAAAATACTAATCA
1 ATAGCATTACATTTAAAATACTAATCA
21124058 TTTGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (27 bp):
ATAGCATTACATTTAAAATACTAATCA
Found at i:21128930 original size:76 final size:75
Alignment explanation
Indices: 21128804--21129176 Score: 473
Period size: 76 Copynumber: 4.9 Consensus size: 75
21128794 TTCTTGGCGA
**
21128804 GCAAATATTTGTCGATTAATCCGACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
1 GCAAATATTTGTC-ATTAATCTAACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
21128869 TAGCGCAGGGC
65 TAGCGCAGGGC
*
21128880 GCAAATATTTGTCATTTAATCTAAGTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
1 GCAAATATTTGTCA-TTAATCTAACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
21128945 TAGCGCAGGGC
65 TAGCGCAGGGC
*
21128956 GCAAATATTTGTCATTTAATCTAAGTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
1 GCAAATATTTGTCA-TTAATCTAACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGAC
* *
21129021 TAGTGCTGGGC
65 TAGCGCAGGGC
* * * * * *
21129032 ACAAATAGTTGACGGTTAAT-TCGACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCTGA
1 GCAAATATTTGTC-ATTAATCT-AACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGA
* *
21129096 CTAGCGCTGGAC
64 CTAGCGCAGGGC
* * * * * *
21129108 GCAAATCTTTGTCGATTAAT-TCGACAAGTGTTGGGCACAC-TTTTACTATCGTCGGTTTATCCA
1 GCAAATATTTGTC-ATTAATCT-AACTAGTGTTGGGCACACATTTAAC-ATCGTCGGTTCATCCG
21129171 ACTAGC
63 ACTAGC
21129177 ACTGAGTGCA
Statistics
Matches: 269, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
75 7 0.03
76 262 0.97
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (75 bp):
GCAAATATTTGTCATTAATCTAACTAGTGTTGGGCACACATTTAACATCGTCGGTTCATCCGACT
AGCGCAGGGC
Found at i:21136590 original size:19 final size:18
Alignment explanation
Indices: 21136561--21136610 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
21136551 GTATATGTTT
21136561 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
21136579 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
*
21136598 TAAGTTTTATTTA
1 TAA-ATTTATTTA
21136611 TATTCTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 23 0.79
20 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:21137917 original size:31 final size:31
Alignment explanation
Indices: 21137882--21138057 Score: 239
Period size: 31 Copynumber: 5.7 Consensus size: 31
21137872 GTATATATTT
*
21137882 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
21137913 TATACATTGCCGAATTTGATTTATATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
21137944 TATACATTGTCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
21137975 TATACATTGCCGAA-TTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
21138005 TATACATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
21138036 TATATATTTCTGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
21138058 GGCATTGGAT
Statistics
Matches: 126, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
30 35 0.28
31 91 0.72
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATGGA
Found at i:21138023 original size:61 final size:61
Alignment explanation
Indices: 21137882--21138057 Score: 244
Period size: 61 Copynumber: 2.9 Consensus size: 61
21137872 GTATATATTT
* * * *
21137882 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTATATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTGTATATAGA
* * *
21137944 TATACATTGTCAAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGA
* * * *
21138005 TATACATTGCCGAATTTGATTCGTATATGGATATATATTTCTGAATTGATTTG
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTG
21138058 GGCATTGGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
61 59 0.58
62 42 0.42
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (61 bp):
TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGA
Found at i:21138286 original size:44 final size:44
Alignment explanation
Indices: 21138175--21138286 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 44
21138165 TCCGAGGTGT
* **
21138175 GATTTCATGTAAGACCATAGT-TGAGCTATTGGCATCAATTTGA
1 GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
* * * *
21138218 CATTTCGTGTAAGACCATAG-CTGGGCTATTGTCATCGATACGA
1 GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
21138261 GATTTCCATGTAAGACCAT-GTCTGGG
1 GATTT-CATGTAAGACCATAGTCTGGG
21138287 ACATGGCATT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
43 40 0.70
44 17 0.30
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (44 bp):
GATTTCATGTAAGACCATAGTCTGGGCTATTGGCATCAATACGA
Found at i:21140721 original size:20 final size:20
Alignment explanation
Indices: 21140696--21140734 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21140686 TGAGTTATTT
21140696 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
21140716 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
21140735 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:21145485 original size:23 final size:23
Alignment explanation
Indices: 21145453--21145500 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
21145443 CCTATTTATC
*
21145453 CTTAATTTCGTCATGTTTTGATA
1 CTTAAATTCGTCATGTTTTGATA
21145476 CTTAAATTCGTCATGTTTTGATA
1 CTTAAATTCGTCATGTTTTGATA
21145499 CT
1 CT
21145501 GATGTCGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (23 bp):
CTTAAATTCGTCATGTTTTGATA
Found at i:21147462 original size:45 final size:45
Alignment explanation
Indices: 21147398--21147539 Score: 277
Period size: 45 Copynumber: 3.2 Consensus size: 45
21147388 CCTATCCCAA
21147398 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
1 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
21147443 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
1 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
21147488 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
1 ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
21147533 AC-ATTGA
1 ACAATTGA
21147540 CTCACTAATC
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
44 5 0.05
45 92 0.95
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (45 bp):
ACAATTGATCTGCTAAGAAGCCCTACATAGAAACTAATTAATCAC
Found at i:21147562 original size:14 final size:14
Alignment explanation
Indices: 21147543--21147571 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21147533 ACATTGACTC
21147543 ACTAATCCCCTATT
1 ACTAATCCCCTATT
21147557 ACTAATCCCCTATT
1 ACTAATCCCCTATT
21147571 A
1 A
21147572 AGAGGATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ACTAATCCCCTATT
Found at i:21158978 original size:23 final size:23
Alignment explanation
Indices: 21158952--21158996 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
21158942 CAAATTGATG
21158952 AATAA-AAAATAAAACATTTTCAA
1 AATAACAAAA-AAAACATTTTCAA
*
21158975 AATAAGCAAAAAAAATATTTTC
1 AATAA-CAAAAAAAACATTTTC
21158997 TTTTCCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAACAAAAAAAACATTTTCAA
Found at i:21170316 original size:3 final size:3
Alignment explanation
Indices: 21170308--21170372 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
21170298 ATATTGCATC
21170308 ATT ATT ATT A-T ATT A-T ATT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
21170352 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
21170373 TCTATACATA
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.88
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21181269 original size:46 final size:46
Alignment explanation
Indices: 21181213--21181781 Score: 405
Period size: 46 Copynumber: 12.4 Consensus size: 46
21181203 GATTTTTTAT
* * * * * * *
21181213 TGCTGTAAATTGAGGTGTATAAACGTTGTTAACTGAGATGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
*
21181259 TGCTGCAAATTGAAGTGTTTAAATATTGTAAATTGA-AGTGTTTAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * ** * * * * *
21181305 TACTGCAAGTTGAAGTGTTTAGTTGCTGGAAATTAAGATGTTTTAC
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
** * * ** * * * *
21181351 TGCTTTAAATTGAGGTGTATAAACATTATTAATTGAGATGTTAAAA
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * *
21181397 TGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTGA-AGTGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
** *
21181443 CACTGCAAATTGAAGTGTTTCAATGTTGTAAATTGA-AGTGTTTAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * ** * * *
21181489 TACTACAAATTGAAGTG-TTAGTTGTTGGAAATTGAGATGTTTTAT
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
** * * * * *
21181534 TGCTATAAATTGAGGTGTATAAACGTTGTTAATTGAGATGTTAAAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * *
21181580 TGTTGCGAATTGAAGTGTTTAAATGTTGTAAATT-AAAGTGTTTAAC
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
* * * * * * * *
21181626 TACTACAAATTGAACTGTTTAATTGCTGGAAATTGAGATGTTTTAT
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
* * * * * *
21181672 TGTTGTAAATTAAAGTGTATAAACGTTGTTAATTGAGATG-TTACAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTA-AG
* * *
21181718 TGCTGCAAAATGAAGTGTTTAAATATTGTAAATTGA-AGTGTTTGAG
1 TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGA-TGTTTAAG
*
21181764 TGCTGCAAATTGAGGTGT
1 TGCTGCAAATTGAAGTGT
21181782 ACAAATGAGT
Statistics
Matches: 391, Mismatches: 122, Indels: 20
0.73 0.23 0.04
Matches are distributed among these distances:
45 41 0.10
46 345 0.88
47 5 0.01
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (46 bp):
TGCTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAGATGTTTAAG
Found at i:21181277 original size:23 final size:23
Alignment explanation
Indices: 21181213--21181781 Score: 140
Period size: 23 Copynumber: 24.8 Consensus size: 23
21181203 GATTTTTTAT
*
21181213 TGCTGTAAATTGAGGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
* *
21181238 T--TGTTAACTG-AGATGTTAAAG
1 TGCTGTAAATTGAAG-TGTTAAAG
*
21181259 TGCTGCAAATTGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
** *
21181282 TATTGTAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGAAGTGTTAAAG
* * * *
21181305 TACTGCAAGTTGAAGTGTT-TAG
1 TGCTGTAAATTGAAGTGTTAAAG
* ** *
21181327 TTGCTGGAAATT-AAGATGTTTTAC
1 -TGCTGTAAATTGAAG-TGTTAAAG
* * *
21181351 TGCTTTAAATTGAGGTGTATAAACA
1 TGCTGTAAATTGAAGTGT-TAAA-G
* * *
21181376 T--TATTAATTG-AGATGTTAAAA
1 TGCTGTAAATTGAAG-TGTTAAAG
* * *
21181397 TGTTGCAAAATGAAGTGCTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
*
21181420 TGTTGTAAATTGAAGTGTTAAAG
1 TGCTGTAAATTGAAGTGTTAAAG
** * *
21181443 CACTGCAAATTGAAGTGTTTCAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
* *
21181466 TGTTGTAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGAAGTGTTAAAG
* **
21181489 TACTACAAATTGAAGTGTT--AG
1 TGCTGTAAATTGAAGTGTTAAAG
* * ** *
21181510 TTGTTGGAAATTG-AGATGTTTTAT
1 -TGCTGTAAATTGAAG-TGTTAAAG
* *
21181534 TGCTATAAATTGAGGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
*
21181559 T--TGTTAATTG-AGATGTTAAAG
1 TGCTGTAAATTGAAG-TGTTAAAG
* **
21181580 TGTTGCGAATTGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
* * * *
21181603 TGTTGTAAATTAAAGTGTTTAAC
1 TGCTGTAAATTGAAGTGTTAAAG
* ** * * *
21181626 TACTACAAATTGAACTGTTTAAT
1 TGCTGTAAATTGAAGTGTTAAAG
* ** *
21181649 TGCTGGAAATTG-AGATGTTTTAT
1 TGCTGTAAATTGAAG-TGTTAAAG
* *
21181672 TGTTGTAAATTAAAGTGTATAAACG
1 TGCTGTAAATTGAAGTGT-TAAA-G
* *
21181697 T--TGTTAATTG-AGATGTTACAG
1 TGCTGTAAATTGAAG-TGTTAAAG
* *
21181718 TGCTGCAAAATGAAGTGTTTAAA-
1 TGCTGTAAATTGAAGTG-TTAAAG
** **
21181741 TATTGTAAATTGAAGTGTTTGAG
1 TGCTGTAAATTGAAGTGTTAAAG
* *
21181764 TGCTGCAAATTGAGGTGT
1 TGCTGTAAATTGAAGTGT
21181782 ACAAATGAGT
Statistics
Matches: 398, Mismatches: 103, Indels: 88
0.68 0.17 0.15
Matches are distributed among these distances:
21 12 0.03
22 58 0.15
23 279 0.70
24 45 0.11
25 4 0.01
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
TGCTGTAAATTGAAGTGTTAAAG
Found at i:21181411 original size:138 final size:138
Alignment explanation
Indices: 21181161--21181462 Score: 417
Period size: 138 Copynumber: 2.2 Consensus size: 138
21181151 TAATGCCCTA
* ** * *
21181161 TTTAAATACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGGTGATTTTTTATTGCTGTAAATTGA
1 TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGAAGATGTTTTACTGCTGTAAATTGA
* * * * *
21181226 GGTGTATAAACGTTGTTAACTGAGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATATTGTAAA
66 GGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAAA
21181291 TTGAAGTG
131 TTGAAGTG
* * * *
21181299 TTTAAGTACTGCAAGTTGAAGTGTTTAGTTGCTGGAAA-TTAAGATGTTTTACTGCTTTAAATTG
1 TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCT-AAAAGTGAAGATGTTTTACTGCTGTAAATTG
* * *
21181363 AGGTGTATAAACATTATTAATTGAGATGTTAAAATGTTGCAAAATGAAGTGCTTAAATGTTGTAA
65 AGGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAA
21181428 ATTGAAGTG
130 ATTGAAGTG
* *
21181437 TTAAAGCACTGCAAATTGAAGTGTTT
1 TTTAAGTACTGCAAATTGAAGTGTTT
21181463 CAATGTTGTA
Statistics
Matches: 143, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
138 140 0.98
139 3 0.02
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (138 bp):
TTTAAGTACTGCAAATTGAAGTGTTTAGTTGCTAAAAGTGAAGATGTTTTACTGCTGTAAATTGA
GGTGTATAAACATTATTAACTGAGATGTTAAAATGCTGCAAAATGAAGTGCTTAAATATTGTAAA
TTGAAGTG
Found at i:21181499 original size:138 final size:138
Alignment explanation
Indices: 21181219--21181782 Score: 499
Period size: 138 Copynumber: 4.1 Consensus size: 138
21181209 TTATTGCTGT
** * * * **
21181219 AAATTGAGGTGTATAAACGTTGTTAACTGAGATGTTAAAGTGCTGCAAATTGAAGTGTTTAAATA
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* * ** * *
21181284 TTGTAAATTGA-AGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTTGCTGGAAATT-AAGATGTT
66 TTGTAAATTGAGA-TGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAG-TGTT
* * **
21181347 TTACTGCTTT
129 TAACTACTAC
* *** * * * *
21181357 AAATTGAGGTGTATAAACATTATTAATTGAGATGTTAAAATGTTGCAAAATGAAGTGCT-TAAAT
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTG-TATAAAC
* *
21181421 GTTGTAAATTGA-AGTGTTAAAGCACTGCAAATTGAAGTGTTTCAATGTTGTAAATTGAAGTGTT
65 GTTGTAAATTGAGA-TGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTT
*
21181485 TAAGTACTAC
129 TAACTACTAC
* *** ** ** *
21181495 AAATTGAAGTGT-TAGTTGTTGGAAATTGAGATGTTTTATTGCTATAAATTGAGGTGTATAAACG
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* ** * *
21181559 TTGTTAATTGAGATGTTAAAGTGTTGCGAATTGAAGTGTTTAAATGTTGTAAATTAAAGTGTTTA
66 TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
21181624 ACTACTAC
131 ACTACTAC
** * ** * ** * * *
21181632 AAATTGAACTGTTTAATTGCTGGAAATTGAGATGTTTTATTGTTGTAAATTAAAGTGTATAAACG
1 AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
* * * * * *
21181697 TTGTTAATTGAGATGTTACAGTGCTGCAAAATGAAGTGTTTAAATATTGTAAATTGAAGTGTTTG
66 TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
* * *
21181762 AGTGCTGC
131 ACTACTAC
21181770 AAATTGAGGTGTA
1 AAATTGAGGTGTA
21181783 CAAATGAGTC
Statistics
Matches: 356, Mismatches: 65, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
136 1 0.00
137 108 0.30
138 243 0.68
139 4 0.01
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (138 bp):
AAATTGAGGTGTATAAACGTTGGAAATTGAGATGTTAAATTGCTGCAAATTGAAGTGTATAAACG
TTGTAAATTGAGATGTTAAAGTACTGCAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTA
ACTACTAC
Found at i:21181508 original size:69 final size:68
Alignment explanation
Indices: 21181265--21181781 Score: 252
Period size: 69 Copynumber: 7.5 Consensus size: 68
21181255 AAAGTGCTGC
* * * * * **
21181265 AAATTGAAGTGTTTAAATATTGTAAATTGAAGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTTG
1 AAATTGAAGTGTTT-AATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
* *
21181330 CTGG
65 TTGT
* * ***
21181334 AAATT-AAGATGTTT--TACTGCTTTAAATTGAGGTGTATAAACAT--TATTAATTG-AGATGTT
1 AAATTGAAG-TGTTTAATACTGC---AAATTGAAGTGT-TAAA-GTGCTGCAAATTGAAG-TGTT
* *
21181393 AAAATGTTGC
59 TAAATGTTGT
* * ** * ** *
21181403 AAAATGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGCACTGCAAATTGAAGTGTTTCAATG
1 AAATTGAAGTG-TTTAATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATG
21181468 TTGT
65 TTGT
* * * * *
21181472 AAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTT--AGTTGTTGGAAATTG-AGATGTTTTAT
1 AAATTGAAGTGTTTAA-TACTGCAAATTGAAGTGTTAAAG-TGCTGCAAATTGAAG-TGTTTAAA
* *
21181534 TGCTAT
63 TGTTGT
* * ** * *
21181540 AAATTGAGGTGTATAA-ACGTTGTTAATTG-AGATGTTAAAGTGTTGCGAATTGAAGTGTTTAAA
1 AAATTGAAGTGTTTAATAC--TGCAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
21181603 TGTTGT
63 TGTTGT
* * * * * * * *
21181609 AAATTAAAGTGTTTAACTACTACAAATTGAACTGTTTAATTGCTGGAAATTG-AGATGTTTTATT
1 AAATTGAAGTGTTTAA-TACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAG-TGTTTAAAT
21181673 GTTGT
64 GTTGT
* * ** * *
21181678 AAATTAAAGTGTATAA-ACGTTGTTAATTG-AGATGTTACAGTGCTGCAAAATGAAGTGTTTAAA
1 AAATTGAAGTGTTTAATAC--TGCAAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAA
*
21181741 TATTGT
63 TGTTGT
* * *
21181747 AAATTGAAGTGTTTGAGTGCTGCAAATTGAGGTGT
1 AAATTGAAGTGTTT-AATACTGCAAATTGAAGTGT
21181782 ACAAATGAGT
Statistics
Matches: 327, Mismatches: 87, Indels: 68
0.68 0.18 0.14
Matches are distributed among these distances:
66 6 0.02
67 8 0.02
68 58 0.18
69 229 0.70
70 19 0.06
71 4 0.01
72 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (68 bp):
AAATTGAAGTGTTTAATACTGCAAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGT
TGT
Found at i:21181661 original size:183 final size:183
Alignment explanation
Indices: 21181264--21181648 Score: 576
Period size: 183 Copynumber: 2.1 Consensus size: 183
21181254 TAAAGTGCTG
* * *
21181264 CAAATTGAAGTGTTTAAATATTGTAAATTGAAGTGTTTAAGTACTGCAAGTTGAAGTGTTTAGTT
1 CAAATTGAAGTGTTT-AATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTT
*
21181329 GCTGGAAATTAAGATGTTTTACTGCTTTAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
65 GCTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
* *
21181394 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTGAAGTGTTAAAGCACTG
130 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGCACTA
21181448 CAAATTGAAGTGTTTCAATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTG-TTAGTT
1 CAAATTGAAGTGTTT-AATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTT
* * * * *
21181512 GTTGGAAATTGAGATGTTTTATTGCTATAAATTGAGGTGTATAAACGTTGTTAATTGAGATGTTA
65 GCTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTA
* * * * *
21181577 AAGTGTTGCGAATTGAAGTGTTTAAATGTTGTAAATTAAAGTGTTTAA-CTACTA
130 AAATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGC-ACTA
*
21181631 CAAATTGAACTGTTTAAT
1 CAAATTGAAGTGTTTAAT
21181649 TGCTGGAAAT
Statistics
Matches: 182, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
182 4 0.02
183 124 0.68
184 54 0.30
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (183 bp):
CAAATTGAAGTGTTTAATGTTGTAAATTGAAGTGTTTAAGTACTACAAATTGAAGTGTTTAGTTG
CTGGAAATTAAGATGTTTTACTGCTATAAATTGAGGTGTATAAACATTATTAATTGAGATGTTAA
AATGTTGCAAAATGAAGTGCTTAAATGTTGTAAATTAAAGTGTTAAAGCACTA
Found at i:21186577 original size:11 final size:11
Alignment explanation
Indices: 21186561--21186590 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21186551 TATATATACT
21186561 TAAAAATTATA
1 TAAAAATTATA
*
21186572 TAAAAATAATA
1 TAAAAATTATA
21186583 TAAAAATT
1 TAAAAATT
21186591 TAATATGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:21190173 original size:32 final size:32
Alignment explanation
Indices: 21190137--21190197 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
21190127 AAATAAACAC
21190137 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
21190169 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
21190198 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:21190915 original size:20 final size:20
Alignment explanation
Indices: 21190886--21190928 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21190876 NNNNNNNNNN
* **
21190886 TATAATTATTCATTTAATAT
1 TATAACTATTCAAATAATAT
21190906 TATAACTATTCAAATAATAT
1 TATAACTATTCAAATAATAT
21190926 TAT
1 TAT
21190929 TTAAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAACTATTCAAATAATAT
Found at i:21190941 original size:32 final size:32
Alignment explanation
Indices: 21190887--21190947 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
21190877 NNNNNNNNNT
21190887 ATAATTATTCATTTAATATTATAACTATTCAA
1 ATAATTATTCATTTAATATTATAACTATTCAA
*
21190919 ATAA-TATT-ATTTAAATAGTTATAATTATT
1 ATAATTATTCATTT-AATA-TTATAACTATT
21190948 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATTATTCATTTAATATTATAACTATTCAA
Found at i:21192102 original size:30 final size:29
Alignment explanation
Indices: 21192064--21192122 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
21192054 GAGGTGGGAT
*
21192064 GTGAAGGGAATAAAAGTTTTAGGGAAAAA
1 GTGAAGGGAATAAAAATTTTAGGGAAAAA
* * *
21192093 GTGAGAGGGAGTAAAAATTTTGGGGGAAAA
1 GTGA-AGGGAATAAAAATTTTAGGGAAAAA
21192123 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (29 bp):
GTGAAGGGAATAAAAATTTTAGGGAAAAA
Found at i:21200561 original size:3 final size:3
Alignment explanation
Indices: 21200553--21200589 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21200543 CAAATGGAAT
21200553 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
21200590 GATGATGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21202313 original size:15 final size:15
Alignment explanation
Indices: 21202289--21202332 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
21202279 AAGTAGCCTA
*
21202289 TCTTTTTTCCTTCTT
1 TCTTTCTTCCTTCTT
21202304 TCTTTCTTCCTTCCTT
1 TCTTTCTTCCTT-CTT
21202320 TC-TTCTT-CTTCTT
1 TCTTTCTTCCTTCTT
21202333 CTTGTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 3 0.11
15 16 0.59
16 5 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TCTTTCTTCCTTCTT
Found at i:21222045 original size:232 final size:232
Alignment explanation
Indices: 21221676--21222121 Score: 614
Period size: 232 Copynumber: 1.9 Consensus size: 232
21221666 TAACCGTGAA
*
21221676 TAAACCTCACAGCAGCTAGGAAGCTCACTCGAATTAAGTAATTCAATTGAACTTCAAAAAAAGAC
1 TAAACCTCACAG-AGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAACTTCAAAAAAAGAC
* * * * * *
21221741 TAAAACTTGCATAGTTTTTTGTACAGATACCCTAATTCAACCAAATTTCTAGAACCTCGCATCTA
65 GAAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTAGAAACTCGCATCTA
* * * *
21221806 ATTACGAACTAACTTCCTCTAAGAAAGCGATTTCA-AG-AAAGAGGTTTATGACGCCCAATTAAA
130 ATTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAATTAAA
*
21221869 ACCCAAAATCCTAAGGAAAGAAAAGGCTTAAGTGCAAG
195 ACCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
*
21221907 TAAACCTCACAG-GCTAGGAAGCTCGCTCAAATTAAGTAATTCAATTGAACTTTCAGAAAACAAA
1 TAAACCTCACAGAGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAAC-TTC--AAAA-AAA
* *
21221971 TACGGAAACTTACAAAG-TTCTTGTACACATACCCTAATTCAACCAAATTTC-AGGAAACTCGCA
62 GACGAAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTA-GAAACTCGCA
** * **
21222034 TCTAATTACGAACTAACTTCCTCTGGGAAAGCAAATTCATAGAAAAGAGGTTCATGATACCCTTT
126 TCTAATTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAAT
*
21222099 TAAAACCTAAAATACTAAGGAAA
191 TAAAACCCAAAATACTAAGGAAA
21222122 CACAAAAAAG
Statistics
Matches: 187, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
229 36 0.19
230 3 0.02
231 13 0.07
232 80 0.43
233 17 0.09
234 38 0.20
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (232 bp):
TAAACCTCACAGAGCTAGGAAGCTCACTCAAATTAAGTAATTCAATTGAACTTCAAAAAAAGACG
AAAACTTACAAAGTTTCTTGTACACATACCCTAATTCAACCAAATTTCTAGAAACTCGCATCTAA
TTACGAACTAACTTCCTCTAAGAAAGCAAATTCATAGAAAAGAGGTTCATGACACCCAATTAAAA
CCCAAAATACTAAGGAAAGAAAAGGCTTAAGTGCAAG
Found at i:21223515 original size:30 final size:31
Alignment explanation
Indices: 21223467--21223525 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
21223457 GAATTATTCA
21223467 AAAGTTTTCATGCAAGTCACT-GGACTATTTG
1 AAAGTTTTCATGCAAGTCACTAGG-CTATTTG
*
21223498 AAAGTTTT-ATTCAAGTCACTAGGCTATT
1 AAAGTTTTCATGCAAGTCACTAGGCTATT
21223526 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (31 bp):
AAAGTTTTCATGCAAGTCACTAGGCTATTTG
Found at i:21223991 original size:17 final size:18
Alignment explanation
Indices: 21223971--21224006 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21223961 TTAGAAGTTA
21223971 AATC-TATTACTAAATTC
1 AATCATATTACTAAATTC
21223988 AATCATATTACTAAATTC
1 AATCATATTACTAAATTC
21224006 A
1 A
21224007 CATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
AATCATATTACTAAATTC
Found at i:21228809 original size:24 final size:24
Alignment explanation
Indices: 21228759--21228812 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
21228749 TTTGTAGGTC
* * **
21228759 AAATAAATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
21228783 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
21228807 AAATAT
1 AAATAT
21228813 TCTAGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:21232808 original size:24 final size:24
Alignment explanation
Indices: 21232771--21232834 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
21232761 TTACTTTTTT
* * *
21232771 TAAAATTATAATGTATTTTTATTA
1 TAAATTTATTATGTATTATTATTA
* *
21232795 TAAGTTTATTATGTATTATTATTT
1 TAAATTTATTATGTATTATTATTA
21232819 TAAATTTATTATGTAT
1 TAAATTTATTATGTAT
21232835 CACTACTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
TAAATTTATTATGTATTATTATTA
Found at i:21234339 original size:14 final size:14
Alignment explanation
Indices: 21234310--21234338 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21234300 TAAAGAATAT
21234310 AATAAATTATTAAA
1 AATAAATTATTAAA
21234324 AATAAA-TATTAAA
1 AATAAATTATTAAA
21234337 AA
1 AA
21234339 AAGACATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAAATTATTAAA
Found at i:21236343 original size:2 final size:2
Alignment explanation
Indices: 21236336--21236374 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21236326 GGTCATCATG
21236336 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
21236375 TGTGTGTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21238402 original size:22 final size:22
Alignment explanation
Indices: 21238359--21238401 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
21238349 AGGACAAAAA
21238359 AATGCTATTTTTTTGTTGTTTT
1 AATGCTATTTTTTTGTTGTTTT
21238381 AATGCT-TTTTCTTT-TTGTTTT
1 AATGCTATTTT-TTTGTTGTTTT
21238402 TTTCCCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.70
Consensus pattern (22 bp):
AATGCTATTTTTTTGTTGTTTT
Found at i:21242539 original size:20 final size:22
Alignment explanation
Indices: 21242497--21242541 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
21242487 GACCAAGGAT
*
21242497 TCCCTTTAGTGGTATCGCGATA
1 TCCCTTTAGTGGTATCGCAATA
*
21242519 TCCCTTT-G-GGTATGGCAATA
1 TCCCTTTAGTGGTATCGCAATA
21242539 TCC
1 TCC
21242542 ACCTCTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (22 bp):
TCCCTTTAGTGGTATCGCAATA
Found at i:21244533 original size:2 final size:2
Alignment explanation
Indices: 21244526--21244560 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21244516 TGTTACACAA
21244526 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21244561 AAGGGTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21245913 original size:65 final size:63
Alignment explanation
Indices: 21245825--21245961 Score: 188
Period size: 65 Copynumber: 2.2 Consensus size: 63
21245815 GTTCAACTAT
* * *
21245825 TATTAAATTTAATTACTTCAATATTAAATTAATATAATACATATCAGGATAAGTGATTAAATTTA
1 TATTAAATATAATTACTTCAATATTAAATTAATAAAATAC-TATCAAGATAAGT-ATTAAA-TTA
21245890 A
63 A
* *
21245891 TATTAAA-ATAATTACTTTAATATTAAATTAATAAAATACTATTAAGATAAGTATTAAATTAA
1 TATTAAATATAATTACTTCAATATTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAA
21245953 -ATTAAATAT
1 TATTAAATAT
21245962 TAAATTTATT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
61 6 0.09
62 6 0.09
63 6 0.09
64 11 0.17
65 29 0.45
66 7 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (63 bp):
TATTAAATATAATTACTTCAATATTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAA
Found at i:21245977 original size:17 final size:17
Alignment explanation
Indices: 21245880--21245967 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
21245870 AGGATAAGTG
*
21245880 ATTAAATTTAATATTAA
1 ATTAAATTAAATATTAA
* *
21245897 AATAATTACTTTAATATTAA
1 ATTAA--A-TTAAATATTAA
* *
21245917 ATT-AATAAAATACT--
1 ATTAAATTAAATATTAA
*
21245931 ATTAAGA-TAAGTATTAA
1 ATTAA-ATTAAATATTAA
21245948 ATTAAATTAAATATTAA
1 ATTAAATTAAATATTAA
21245965 ATT
1 ATT
21245968 TATTAAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
14 3 0.06
15 6 0.11
16 8 0.15
17 22 0.41
19 2 0.04
20 13 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTAAATTAAATATTAA
Found at i:21245980 original size:68 final size:65
Alignment explanation
Indices: 21245844--21245983 Score: 149
Period size: 68 Copynumber: 2.1 Consensus size: 65
21245834 TAATTACTTC
* * ***
21245844 AATATTAAATTAATATAATACATATCAGGATAAGTGATTAAATTTAATATTAAAATAATTACTTT
1 AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAATTTAATATTAAAATAATTAAAAT
* * *
21245909 AATATTAAATTAATAAAATAC-TATTAAGATAAGT-ATTAAATTAAATTAAATATTAAATTTATT
1 AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAA-T---TT-AATATTAAAATAATT
21245972 AAAAT
61 AAAAT
21245977 AATATTA
1 AATATTA
21245984 TTTTTAGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
63 6 0.10
64 12 0.19
65 20 0.32
67 2 0.03
68 22 0.35
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (65 bp):
AATATTAAATTAATAAAATACATATCAAGATAAGTGATTAAATTTAATATTAAAATAATTAAAAT
Found at i:21248449 original size:5 final size:5
Alignment explanation
Indices: 21248439--21248465 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21248429 AAAAGGACAT
21248439 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
21248466 CAAAGGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:21249034 original size:46 final size:46
Alignment explanation
Indices: 21248975--21249083 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 46
21248965 AATTTTAGAC
* * *
21248975 TCATTTGTA-CACCTTAATGTGTAGCACTTAAACACTTCAATTTACA
1 TCATTTG-AGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
*
21249021 TCATTTGAGCACCTCAATTTGCAGCAATTAAACACTTCAATTTACA
1 TCATTTGAGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
* *
21249067 GCATTTAAGCACCTCAA
1 TCATTTGAGCACCTCAA
21249084 CTGACAACAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 1 0.02
46 55 0.98
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (46 bp):
TCATTTGAGCACCTCAATGTGCAGCAATTAAACACTTCAATTTACA
Found at i:21249060 original size:23 final size:23
Alignment explanation
Indices: 21248997--21249729 Score: 319
Period size: 23 Copynumber: 31.8 Consensus size: 23
21248987 CTTAATGTGT
*
21248997 AGCACTTAAACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * * *
21249020 ATCATTTGAGCACCTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
21249043 AGCAATTAAACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * *
21249066 AGCATTTAAGCACCTCAACTGAC
1 AGCATTTAAACACTTCAATTTAC
* * *
21249089 AACACTTT-AACA-TCCCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* * * *
21249112 AACAGTTATACACCTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
* *
21249134 ATAG-A-TAAAACA-TCTCAATTTCC
1 --AGCATTTAAACACT-TCAATTTAC
* ** *
21249157 TGCAACTAAACAATTCAATTTGA-
1 AGCATTTAAACACTTCAATTT-AC
* * * *
21249180 TGTAATTAAAACACTTCAATTCAC
1 AG-CATTTAAACACTTCAATTTAC
* *
21249204 AACATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
21249227 AGCACTTTAAA-ACTTCAATTCT-C
1 AGCA-TTTAAACACTTCAATT-TAC
* * *
21249250 AACATTTAAACACCTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
21249273 AACACTTT-AACACTTCAATTTAC
1 AGCA-TTTAAACACTTCAATTTAC
*
21249296 AGCATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
* *
21249319 AGAACTTT-AACA-TCTCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* ** * *
21249342 AACATTTATGCACCTCAA-TTAT
1 AGCATTTAAACACTTCAATTTAC
* *
21249364 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ATTTAAACACT-TCAATTTAC
** * **
21249387 AGCAACTAAACAATTCAATTTTT
1 AGCATTTAAACACTTCAATTTAC
* * *
21249410 AGTACTTAAAACACTTCAATTTGC
1 AGCA-TTTAAACACTTCAATTTAC
*
21249434 AGCATTTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
21249457 AGCACTTT-AACACTTCAATTCAC
1 AGCA-TTTAAACACTTCAATTTAC
* * * *
21249480 AACATTTAAATAGTACTTCAATGTGC
1 AGCATTT-AA-A-CACTTCAATTTAC
*
21249506 AACACTTT-AACACTTCAATTTAC
1 AGCA-TTTAAACACTTCAATTTAC
* * *
21249529 AACATTTAAGCACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
21249552 AGCACTTT-AACATCTT-AATTAAC
1 AGCA-TTTAAACA-CTTCAATTTAC
* * *
21249575 AACATTTATACACCTCAA-TTAC
1 AGCATTTAAACACTTCAATTTAC
* *
21249597 AGCGA-TAAAACATCTT-AATTTCC
1 AGC-ATTTAAACA-CTTCAATTTAC
** *
21249620 AGCAACTAAACACTTCAATTTGC
1 AGCATTTAAACACTTCAATTTAC
*
21249643 AGCACTTT-AACA-TGTCAATTAAC
1 AGCA-TTTAAACACT-TCAATTTAC
* * *
21249666 AACGTTTATACACTTCAATTTAC
1 AGCATTTAAACACTTCAATTTAC
* * * *
21249689 AGAAATAAAACA-TCTCAATTTGC
1 AGCATTTAAACACT-TCAATTTAC
**
21249712 AGCAACTAAACACTTCAA
1 AGCATTTAAACACTTCAA
21249730 ATTGCAGTAC
Statistics
Matches: 526, Mismatches: 132, Indels: 104
0.69 0.17 0.14
Matches are distributed among these distances:
21 1 0.00
22 74 0.14
23 371 0.71
24 62 0.12
25 2 0.00
26 13 0.02
27 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.31
Consensus pattern (23 bp):
AGCATTTAAACACTTCAATTTAC
Found at i:21249400 original size:230 final size:231
Alignment explanation
Indices: 21248997--21249641 Score: 906
Period size: 230 Copynumber: 2.8 Consensus size: 231
21248987 CTTAATGTGT
* * * * * *
21248997 AGCAC-TTAAACACTTCAATT-TACATCATTTGAGCACCTCAATTTGCAGCAATTAAACACTTCA
1 AGCACTTTAAA-ACTTCAATTCT-CAACATTTAAACACCTCAATTTGCAACACTTTAACACTTCA
* * * *
21249060 ATTTACAGCATTTAAGCACCTCAA-CTGACA-ACACTTTAACATCCCAATTAACAACAGTTATAC
64 ATTTACAGCATTTAAGCACTTCAATTTG-CAGA-ACTTTAACATCTCAATTAACAACATTTATAC
** *
21249123 ACCTCAATTACATAGATAAAACATCTCAATTTCCTGCAACTAAACAATTCAATTTGAT-GTAATT
127 ACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGATAGTAATT
21249187 AAAACACTTCAATTCACAACATTTAAACACTTCAATTTGC
192 AAAACACTTCAATTCACAACATTTAAACACTTCAATTTGC
21249227 AGCACTTTAAAACTTCAATTCTCAACATTTAAACACCTCAATTTGCAACACTTTAACACTTCAAT
1 AGCACTTTAAAACTTCAATTCTCAACATTTAAACACCTCAATTTGCAACACTTTAACACTTCAAT
* *
21249292 TTACAGCATTTAAACACTTCAATTTGCAGAACTTTAACATCTCAATTAACAACATTTATGCACCT
66 TTACAGCATTTAAGCACTTCAATTTGCAGAACTTTAACATCTCAATTAACAACATTTATACACCT
* * *
21249357 CAATTATAGCGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTT-TTAGTACTTAAAA
131 CAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGATAGTAATTAAAA
** *
21249421 CACTTCAATTTGCAGCATTTAAACACTTCAATTTGC
196 CACTTCAATTCACAACATTTAAACACTTCAATTTGC
* * * * *
21249457 AGCACTTTAACACTTCAATTCACAACATTTAAATAGTACTTCAATGTGCAACACTTTAACACTTC
1 AGCACTTTAAAACTTCAATTCTCAACATTT-AA-A-CACCTCAATTTGCAACACTTTAACACTTC
* * *
21249522 AATTTACAACATTTAAGCACTTCAATTTGCAGCACTTTAACATCTTAATTAACAACATTTATACA
63 AATTTACAGCATTTAAGCACTTCAATTTGCAGAACTTTAACATCTCAATTAACAACATTTATACA
* *
21249587 CCTCAATTACAGCGATAAAACATCTTAATTTCCAGCAACTAAACACTTCAATTTG
128 CCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTG
21249642 CAGCACTTTA
Statistics
Matches: 372, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
229 1 0.00
230 222 0.60
231 11 0.03
232 1 0.00
233 137 0.37
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (231 bp):
AGCACTTTAAAACTTCAATTCTCAACATTTAAACACCTCAATTTGCAACACTTTAACACTTCAAT
TTACAGCATTTAAGCACTTCAATTTGCAGAACTTTAACATCTCAATTAACAACATTTATACACCT
CAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACAATTCAATTTGATAGTAATTAAAA
CACTTCAATTCACAACATTTAAACACTTCAATTTGC
Found at i:21249517 original size:49 final size:47
Alignment explanation
Indices: 21249189--21249686 Score: 370
Period size: 46 Copynumber: 10.8 Consensus size: 47
21249179 ATGTAATTAA
*
21249189 AACACTTCAATTCACAACATTTAAA-CACTTCAATTTGCAGCACTTT
1 AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* ** * *
21249235 AAAACTTCAATTCTCAACATTTAAA-CACCTCAATTTGCAACACTTT
1 AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* * *
21249281 AACACTTCAATTTACAGCATTTAAA-CACTTCAATTTGCAGAACTTT
1 AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* * **
21249327 AACA-TCTCAATTAACAACATTT-ATGCACCTCAATTAT--AGCGA-TAA
1 AACACT-TCAATTAACAACATTTAAAGCACTTCAATT-TGCAGC-ACTTT
** * ** * ** * *
21249372 AACA-TCTCAATTTCCAGCAACTAAA-CAATTCAATTTTTAGTACTTAA
1 AACACT-TCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTT-T
** *
21249419 AACACTTCAATTTGCAGCATTTAAA-CACTTCAATTTGCAGCACTTT
1 AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* * * *
21249465 AACACTTCAATTCACAACATTTAAATAGTACTTCAATGTGCAACACTTT
1 AACACTTCAATTAACAACATTT-AA-AGCACTTCAATTTGCAGCACTTT
*
21249514 AACACTTCAATTTACAACATTT-AAGCACTTCAATTTGCAGCACTTT
1 AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* * * **
21249560 AACATCTT-AATTAACAACATTTATA-CACCTCAA-TTACAGCGA-TAA
1 AACA-CTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGC-ACTTT
** * **
21249605 AACATCTT-AATTTCCAGCAACTAAA-CACTTCAATTTGCAGCACTTT
1 AACA-CTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
* *
21249651 AACA-TGTCAATTAACAACGTTTATA-CACTTCAATTT
1 AACACT-TCAATTAACAACATTTAAAGCACTTCAATTT
21249687 ACAGAAATAA
Statistics
Matches: 363, Mismatches: 69, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.01
45 66 0.18
46 209 0.58
47 45 0.12
48 2 0.01
49 39 0.11
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (47 bp):
AACACTTCAATTAACAACATTTAAAGCACTTCAATTTGCAGCACTTT
Found at i:21250250 original size:15 final size:15
Alignment explanation
Indices: 21250230--21250263 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
21250220 AATGTTTTAA
21250230 TACAACATAAATACT
1 TACAACATAAATACT
*
21250245 TACAACATGAATACT
1 TACAACATAAATACT
21250260 TACA
1 TACA
21250264 TTTTAATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (15 bp):
TACAACATAAATACT
Found at i:21256174 original size:16 final size:16
Alignment explanation
Indices: 21256153--21256184 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21256143 ATCTGTACAT
21256153 AAAATGCGTATAAGAC
1 AAAATGCGTATAAGAC
21256169 AAAATGCGTATAAGAC
1 AAAATGCGTATAAGAC
21256185 TGTACATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATGCGTATAAGAC
Found at i:21258895 original size:23 final size:24
Alignment explanation
Indices: 21258865--21258920 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
21258855 TGACTTGAAA
**
21258865 ATTAATTTTAA-AATTTTTTTAAT
1 ATTAATTTTAATAATTTCATTAAT
21258888 ATTAA-TTTAATTAATTTCATTAAT
1 ATTAATTTTAA-TAATTTCATTAAT
21258912 -TTAATTTTA
1 ATTAATTTTA
21258921 CTTGATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.18
23 9 0.32
24 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTAATTTTAATAATTTCATTAAT
Found at i:21258900 original size:9 final size:9
Alignment explanation
Indices: 21258888--21258917 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
21258878 TTTTTTTAAT
21258888 ATTAATTTA
1 ATTAATTTA
*
21258897 ATTAATTTC
1 ATTAATTTA
21258906 ATTAATTTA
1 ATTAATTTA
21258915 ATT
1 ATT
21258918 TTACTTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:21282883 original size:29 final size:29
Alignment explanation
Indices: 21282816--21282890 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
21282806 TGTTAATAGT
*
21282816 TGGATTAAATTTTAAAATATGAAAAGTAA
1 TGGATTAAATTCTAAAATATGAAAAGTAA
* *
21282845 AGTGACTAAATTCCTAAAA-AT-AAAAGTACA
1 TG-GATTAAATT-CTAAAATATGAAAAGTA-A
21282875 TGGATTAAATTCTAAA
1 TGGATTAAATTCTAAA
21282891 TTTTTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 12 0.32
31 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGATTAAATTCTAAAATATGAAAAGTAA
Found at i:21285537 original size:14 final size:14
Alignment explanation
Indices: 21285481--21285537 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
21285471 TTCGACAATG
* * *
21285481 ATATTGCAACGATT
1 ATATTGTAACGGTC
21285495 ATATTGTAACGGTC
1 ATATTGTAACGGTC
* **
21285509 AGATTCCAACGGTC
1 ATATTGTAACGGTC
*
21285523 ATATTGTAACAGTC
1 ATATTGTAACGGTC
21285537 A
1 A
21285538 GATTTTTGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (14 bp):
ATATTGTAACGGTC
Found at i:21286705 original size:67 final size:67
Alignment explanation
Indices: 21286597--21286728 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
21286587 TTTCCAATTC
**
21286597 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
21286662 CA
66 CA
*
21286664 AGAGAGCACACTCCCGTGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
21286729 TAATATAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGAAGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:21288541 original size:12 final size:11
Alignment explanation
Indices: 21288512--21288555 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
21288502 AATCATTTAA
*
21288512 TAATAAAATAA
1 TAATAAAATAT
*
21288523 TACTAAAAATAT
1 TAAT-AAAATAT
21288535 TAATAAAATAT
1 TAATAAAATAT
*
21288546 TAATTAAATA
1 TAATAAAATA
21288556 ACATTTATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:21295482 original size:29 final size:29
Alignment explanation
Indices: 21295430--21295488 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
21295420 ATTAGACGTA
** *
21295430 TATGACTAATTAGGTGAATGAAATTTGTT
1 TATGACTAATTAGGTGAACAAAATTCGTT
21295459 TATGACTAATTAGGTGAACAAAATTCGTT
1 TATGACTAATTAGGTGAACAAAATTCGTT
21295488 T
1 T
21295489 TAGGTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (29 bp):
TATGACTAATTAGGTGAACAAAATTCGTT
Found at i:21296404 original size:27 final size:27
Alignment explanation
Indices: 21296366--21296420 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
21296356 TCACTAGAAG
21296366 TAAGAATTATGTAATCGTACTTATAAA
1 TAAGAATTATGTAATCGTACTTATAAA
*
21296393 TAAGAATTATGTAATCGTATTTATAAA
1 TAAGAATTATGTAATCGTACTTATAAA
21296420 T
1 T
21296421 TGTTGTCATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (27 bp):
TAAGAATTATGTAATCGTACTTATAAA
Found at i:21296606 original size:18 final size:18
Alignment explanation
Indices: 21296583--21296623 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
21296573 TAATTTTGTG
21296583 TTATTCTATAGGTGTTCT
1 TTATTCTATAGGTGTTCT
*
21296601 TTATTCTGTAGGTGTTCT
1 TTATTCTATAGGTGTTCT
21296619 TTATT
1 TTATT
21296624 TACGTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (18 bp):
TTATTCTATAGGTGTTCT
Done.