Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 66 of 240
Found at i:21448352 original size:238 final size:238
Alignment explanation
Indices: 21447664--21448735 Score: 1803
Period size: 238 Copynumber: 4.5 Consensus size: 238
21447654 AAGTAGATTA
** *
21447664 TAAATTATATTTTATAGTACCATATATTAAGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
21447729 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAGATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
*
21447794 TTTATAGTATTATATATTATGATTATAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTC--ATAAGAATATTTAATATTAAGAATTTTA
* * *
21447859 TTAAATTATATACTTTTAATAAATTATACTTAATAATAATTATTT
194 TTAAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
21447904 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
21447969 AAGAATTTTATTAAATTATATCTTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
21448034 TTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTATT
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
* *
21448098 AAATTATATA-TTTTACTAATTTATATTTTTAATAATTATTATTT
196 AAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
* * *
21448142 TAAATTATATTTTATAGTGTTATATATTGTGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
21448207 AAGAATTTTATTAAATTATATA-TTTTATTAACTTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
21448271 TTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTATT
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
21448335 AAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTT
196 AAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
*
21448380 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
21448445 AAGAATTTTATTAAATTATATATTTTTATTAAATTTTATTTAATAATAATTATTTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
*
21448510 TTTATAGTATTATATATTATGA-TTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTC--ATAAGAATATTTAATATTAAGAATTTTA
* *
21448574 TTAAATTATATGTTTTTATTAAATTATATTTAATAATAATTATTT
194 TTAAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
* *
21448619 TAAATTATATTTTATAGTATTATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
21448684 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
21448736 TGTTAAAATA
Statistics
Matches: 793, Mismatches: 32, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
236 13 0.02
237 154 0.19
238 226 0.28
239 190 0.24
240 157 0.20
241 53 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (238 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
AAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
Found at i:21448965 original size:45 final size:44
Alignment explanation
Indices: 21448880--21448975 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
21448870 ATTACAATAT
*
21448880 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
* *
21448924 CATTACATTCAACCAAACA-ATTGAATTACTATTACGTCTCTATTC
1 CATTACATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTC
21448969 CATTACA
1 CATTACA
21448976 GCTCTATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.45
45 25 0.53
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (44 bp):
CATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:21448980 original size:16 final size:16
Alignment explanation
Indices: 21448961--21448992 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21448951 ACTATTACGT
21448961 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
21448977 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
21448993 TGAACCAAAC
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:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:21457786 original size:2 final size:2
Alignment explanation
Indices: 21457779--21457852 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
21457769 TTAATAAAAT
21457779 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21457821 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
21457853 AGGTTTCTAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21484240 original size:22 final size:23
Alignment explanation
Indices: 21484198--21484243 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21484188 TAAAGCGAAT
*
21484198 AAATATTTATGTTTTTAATTTTA
1 AAATATTTATGTATTTAATTTTA
*
21484221 AAAT-TTTATGTAATTTATTTTTA
1 AAATATTTATGT-ATTTAATTTTA
21484244 TTTTCTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
AAATATTTATGTATTTAATTTTA
Found at i:21487089 original size:7 final size:7
Alignment explanation
Indices: 21487077--21487102 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21487067 TAGTCGATTC
21487077 GTATTTA
1 GTATTTA
21487084 GTATTTA
1 GTATTTA
21487091 GTATTTA
1 GTATTTA
21487098 GTATT
1 GTATT
21487103 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:21487751 original size:18 final size:18
Alignment explanation
Indices: 21487728--21487771 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21487718 ATGCCAAGTG
* *
21487728 TGTATCCTATCCCTTTTA
1 TGTATCCTAACCCTTATA
21487746 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
21487764 TGTTTCCT
1 TGTATCCT
21487772 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:21488037 original size:21 final size:21
Alignment explanation
Indices: 21488013--21488059 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21488003 CAACACTGAT
* *
21488013 AACCA-AATCCCTTACCGGAGG
1 AACCAGAATCCC-CACCGGAGC
21488034 AACCAGAATCCCCACCGGAGC
1 AACCAGAATCCCCACCGGAGC
21488055 AACCA
1 AACCA
21488060 CAACCCCCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.38, G:0.17, T:0.09
Consensus pattern (21 bp):
AACCAGAATCCCCACCGGAGC
Found at i:21488067 original size:21 final size:21
Alignment explanation
Indices: 21488026--21488067 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21488016 CAAATCCCTT
* * *
21488026 ACCGGAGGAACCAGAATCCCC
1 ACCGGAGCAACCACAACCCCC
21488047 ACCGGAGCAACCACAACCCCC
1 ACCGGAGCAACCACAACCCCC
21488068 GTCGAAAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.45, G:0.19, T:0.02
Consensus pattern (21 bp):
ACCGGAGCAACCACAACCCCC
Found at i:21490858 original size:242 final size:243
Alignment explanation
Indices: 21490433--21490888 Score: 734
Period size: 242 Copynumber: 1.9 Consensus size: 243
21490423 TTGGGGCTGA
* *
21490433 GCTCTTGAGGTGGATCCACATCGGGCTCATCTTCTAACCCACCATCATCTGCAACGTACAAGGTC
1 GCTCTTGAGGTGGATCCACATCGGACTCATATTCTAACCCACCATCATCTGCAACGTACAAGGTC
* * * * * *
21490498 CCCTCACTAATGGACGTCCTAGGGAATACATTATCCCTTCTTCTGGGCGTTTCATAACGTCTTCA
66 CCCTCACCAATAGACGTCCTAGGGAATACATCATCCCCTCTTCTGGGCGTTTCATAACATCTCCA
*
21490563 TTTGGATGTAGATTGCCAACCACTAGAAGTTGATGTCATTCCCCAGTACGTATTTTC-GCATCAA
131 ATTGGATGTAGATTGCCAACCACTAGAAGTTGATGTCATTCCCCAGTACGTATTTTCAGCATCAA
* *
21490627 ACATCAATCTACCGAGGTGTTGTGTAACTTTTGCACCATCAGGTCCGG
196 ACATCAACCCACCGAGGTGTTGTGTAACTTTTGCACCATCAGGTCCGG
* * *
21490675 GCTCTTGAGGTGGATCCACATCGGACTCATATTCTAACCCACTATCATCTGCAACGTACGAGGTT
1 GCTCTTGAGGTGGATCCACATCGGACTCATATTCTAACCCACCATCATCTGCAACGTACAAGGTC
* *
21490740 CCCTCACCGATAGACGTCGTAGGGAATACATCATCCCCTCTTCTGGGCGTTTCATAACATCTCCA
66 CCCTCACCAATAGACGTCCTAGGGAATACATCATCCCCTCTTCTGGGCGTTTCATAACATCTCCA
* *
21490805 ATTGGATGTAGATTGCCAACTACTAGAAGTTGATGTCGTTCCCCAGTACGTATTTTCAGCATCAA
131 ATTGGATGTAGATTGCCAACCACTAGAAGTTGATGTCATTCCCCAGTACGTATTTTCAGCATCAA
*
21490870 ACATCGACCCACCGAGGTG
196 ACATCAACCCACCGAGGTG
21490889 CATATCCCAT
Statistics
Matches: 194, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
242 171 0.88
243 23 0.12
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (243 bp):
GCTCTTGAGGTGGATCCACATCGGACTCATATTCTAACCCACCATCATCTGCAACGTACAAGGTC
CCCTCACCAATAGACGTCCTAGGGAATACATCATCCCCTCTTCTGGGCGTTTCATAACATCTCCA
ATTGGATGTAGATTGCCAACCACTAGAAGTTGATGTCATTCCCCAGTACGTATTTTCAGCATCAA
ACATCAACCCACCGAGGTGTTGTGTAACTTTTGCACCATCAGGTCCGG
Found at i:21491694 original size:126 final size:125
Alignment explanation
Indices: 21491466--21491881 Score: 634
Period size: 126 Copynumber: 3.3 Consensus size: 125
21491456 CAGGCCAAAT
* *
21491466 AGGAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
1 AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
** *
21491531 TCCTGCTTGAAATGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATTCTTTTTTT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATT-TTTTTTC
* *
21491592 AGGAACTACTGTAGCAAAAGAACGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
1 AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
* * * *
21491657 TCTTGTTTGAAGCGTTTTTGACACTATTTGCTTAGAAACATCTTCTCAAAATTATTTTTTC
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATT-TTTTTTC
* * * *
21491718 AGAAACTACTATAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGACAATGCA
1 AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
* * * * *
21491783 TCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACCTCTTTTCAAAATTATTTTTC
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATTTTTTTTC
21491843 AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTT
1 AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTT
21491882 TTTTAAATTA
Statistics
Matches: 264, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
125 43 0.16
126 221 0.84
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (125 bp):
AGGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACATTGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTATCAAAATTTTTTTTC
Found at i:21492192 original size:97 final size:97
Alignment explanation
Indices: 21491958--21492327 Score: 524
Period size: 97 Copynumber: 4.0 Consensus size: 97
21491948 CTTAAAACCT
*
21491958 TAAACCCTAATCT-ATTTTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCCAAACCCTAAT
1 TAAACCCTAATCTAATTTTTTT-AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAAT
*
21492022 TTATTTGATTTTTTCCTTAAAAACCCTAAACCC
65 TTATTTGATTTTTTCCTTAAAAACCCTAAACAC
21492055 TAAA--C--A-CTAATTTTTTT-AAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATT
1 TAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATT
21492114 TATTTGATTTTTT-CTTAAAAACCCTAAACAC
66 TATTTGATTTTTTCCTTAAAAACCCTAAACAC
21492145 TAAACCCTAATCTAATTTTTTTCAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAAT
1 TAAACCCTAATCTAATTTTTTT-AAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAAT
* *
21492210 TTATTTAATTTTTTTCCTTAAAAACCATAAACAC
65 TTATTTGA-TTTTTTCCTTAAAAACCCTAAACAC
* * *
21492244 TAAACCCTAATCTAA-TTTTTTAAAATTTATAATT-A---AC-CTA--AACCCTAAACCTTTATT
1 TAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATT
21492301 TATTT-ATTTTTTCCTT-AAAACCCTAAA
66 TATTTGATTTTTTCCTTAAAAACCCTAAA
21492328 ATCTAAAAAT
Statistics
Matches: 255, Mismatches: 8, Indels: 30
0.87 0.03 0.10
Matches are distributed among these distances:
87 10 0.04
88 10 0.04
89 1 0.00
90 41 0.16
91 54 0.21
92 5 0.02
93 11 0.04
94 1 0.00
95 12 0.05
96 1 0.00
97 65 0.25
98 12 0.05
99 32 0.13
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.41
Consensus pattern (97 bp):
TAAACCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATT
TATTTGATTTTTTCCTTAAAAACCCTAAACAC
Found at i:21493750 original size:18 final size:18
Alignment explanation
Indices: 21493729--21493766 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
21493719 GAATTGTTAT
21493729 AAATATT-TTGAGTTTTAA
1 AAATATTATT-AGTTTTAA
*
21493747 AAATATTATTATTTTTAA
1 AAATATTATTAGTTTTAA
21493765 AA
1 AA
21493767 TTTTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
AAATATTATTAGTTTTAA
Found at i:21493992 original size:16 final size:16
Alignment explanation
Indices: 21493973--21494005 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21493963 TCGAGTTTTG
21493973 GTCACTCGTAGTTTAA
1 GTCACTCGTAGTTTAA
21493989 GTCACTCGTAGTTTAA
1 GTCACTCGTAGTTTAA
21494005 G
1 G
21494006 ATAGCTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (16 bp):
GTCACTCGTAGTTTAA
Found at i:21494643 original size:7 final size:8
Alignment explanation
Indices: 21494624--21494650 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
21494614 TTTGATTTAA
21494624 AAAAAATT
1 AAAAAATT
21494632 AAAAAATT
1 AAAAAATT
21494640 AAAAAATT
1 AAAAAATT
21494648 AAA
1 AAA
21494651 GTTTTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:21494846 original size:17 final size:17
Alignment explanation
Indices: 21494824--21494874 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
21494814 AAAAATTAAA
*
21494824 AAAATTATAATATTTTT
1 AAAATTATAATATTTTG
*
21494841 AAAATTCAAAATATTTATG
1 AAAATT-ATAATATTT-TG
*
21494860 AAAATT-TAAAATTTT
1 AAAATTATAATATTTT
21494875 ATATTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 1 0.04
17 12 0.43
18 8 0.29
19 7 0.25
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AAAATTATAATATTTTG
Found at i:21494863 original size:19 final size:19
Alignment explanation
Indices: 21494832--21494876 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
21494822 AAAAAATTAT
*
21494832 AATATTT-TTAAAATTCAA
1 AATATTTATGAAAATTCAA
*
21494850 AATATTTATGAAAATTTAA
1 AATATTTATGAAAATTCAA
21494869 AAT-TTTAT
1 AATATTTAT
21494877 ATTTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AATATTTATGAAAATTCAA
Found at i:21494875 original size:18 final size:17
Alignment explanation
Indices: 21494824--21494877 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
21494814 AAAAATTAAA
*
21494824 AAAATTATAATATTTT-T
1 AAAATT-TAAAATTTTAT
*
21494841 AAAATTCAAAATATTTAT
1 AAAATTTAAAAT-TTTAT
21494859 GAAAATTTAAAATTTTAT
1 -AAAATTTAAAATTTTAT
21494877 A
1 A
21494878 TTTTTCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 6 0.19
19 11 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AAAATTTAAAATTTTAT
Found at i:21495160 original size:14 final size:14
Alignment explanation
Indices: 21495141--21495180 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
21495131 TTAATTTTTT
21495141 AATTTAACTCGAAC
1 AATTTAACTCGAAC
*
21495155 AATTTAACTTGAAC
1 AATTTAACTCGAAC
*
21495169 AATTTCACTCGA
1 AATTTAACTCGA
21495181 TTCGATTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTTAACTCGAAC
Found at i:21498403 original size:58 final size:58
Alignment explanation
Indices: 21498313--21498448 Score: 236
Period size: 58 Copynumber: 2.3 Consensus size: 58
21498303 AGTAATAGCC
*
21498313 TCTTTCATCTATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
* * *
21498371 TCTTTCATCCATGGTATTACACTGTATACCTTATACCTTTTACCATGTTGTCATGGCA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
21498429 TCTTTCATCCATGGTCTTAC
1 TCTTTCATCCATGGTCTTAC
21498449 GCAACGTACC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (58 bp):
TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
Found at i:21499773 original size:85 final size:85
Alignment explanation
Indices: 21499656--21499817 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
21499646 CCTGTACTTG
* * ** * *
21499656 CATAAAATGTCTAATGTGGTACTTGTACTTTGAAAATGTTTATTATGGTATATGAACTATTAATA
1 CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
21499721 TATGTTTTATTATGCTCTTT
66 TATGTTTTATTATGCTCTTT
* * * *
21499741 CATAAAATGTCCAATGTGGTACATGTAGTTTGAAAATGTCCAATGTGGTATCCGAACTATTTATA
1 CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
*
21499806 TGTGTTTTATTA
66 TATGTTTTATTA
21499818 CGGTACTTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (85 bp):
CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
TATGTTTTATTATGCTCTTT
Found at i:21502957 original size:14 final size:16
Alignment explanation
Indices: 21502938--21502969 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
21502928 TTAACTTCTC
21502938 ATTTAATT-TTT-AAA
1 ATTTAATTGTTTCAAA
21502952 ATTTAATTGTTTCAAA
1 ATTTAATTGTTTCAAA
21502968 AT
1 AT
21502970 AGATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTAATTGTTTCAAA
Found at i:21503603 original size:3 final size:3
Alignment explanation
Indices: 21503548--21503586 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
21503538 TTTGGAATTG
21503548 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21503587 AAGAAACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21511328 original size:16 final size:16
Alignment explanation
Indices: 21511307--21511343 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
21511297 TAATTAACAT
21511307 AGATAAAAA-TAATTAA
1 AGATAAAAATTAATT-A
21511323 AGATAAAAATTAATTA
1 AGATAAAAATTAATTA
21511339 AGATA
1 AGATA
21511344 TAAGATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (16 bp):
AGATAAAAATTAATTA
Found at i:21515352 original size:13 final size:13
Alignment explanation
Indices: 21515334--21515358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21515324 ATTAAGAAAA
21515334 AAATATCAAATTC
1 AAATATCAAATTC
21515347 AAATATCAAATT
1 AAATATCAAATT
21515359 AGATGAAAAA
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAAATTC
Found at i:21519708 original size:51 final size:51
Alignment explanation
Indices: 21519591--21519850 Score: 396
Period size: 51 Copynumber: 5.1 Consensus size: 51
21519581 CTTGCGTATG
* * *
21519591 ATCACTTATCACTTGTCCCTGATAAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
21519641 ATCACTTGCCATTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
21519692 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
21519743 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
21519794 ATCACTTGTCATTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
21519845 ATCACT
1 ATCACT
21519851 GATCAGAAGT
Statistics
Matches: 190, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
50 32 0.17
51 158 0.83
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:21525967 original size:227 final size:228
Alignment explanation
Indices: 21525571--21526013 Score: 710
Period size: 227 Copynumber: 1.9 Consensus size: 228
21525561 AAAATAAGCA
* * * * *
21525571 TTAGCGGTGTTTCTGAAAAAGCGTCGCAAAAATACTTCAGTCCAACGATGTCGTTTTCTGAGCTG
1 TTAGCGGCGTTTCTGAAAAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
21525636 AGAAGGATTTAGTGGCATTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGG
66 AGAAGGATTTAGTGGCATTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGG
* * * *
21525701 GAAAGCGCCGCAAAAATACTTCAGTCTAACAACGCCGTTTT-TCGAGCTGAGAAGGATTTAGTGG
131 GAAAGCCCCGCAAAAATACTTCAGCCCAACAACGCCGTTTTCT-GAGCTGAGAAGGATTTAGTAG
21525765 CGTTTTTATGTAAGCACCGCTACTGGTCAGGTCT
195 CGTTTTTATGTAAGCACCGCTACTGGTCAGGTCT
* *
21525799 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAATAC-TCAGCCCAACGACGCCGTTTTCTGAGCTG
1 TTAGCGGCGTTTCTGAAAAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
* * * *
21525863 AGAATGATTTAGTGGCGTTTTTATGTAAGCGCCGCTAGTGGTCAGGTCTTTAGCGGCGTTTTTGG
66 AGAAGGATTTAGTGGCATTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGG
*
21525928 GAAAGCCCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGC
131 GAAAGCCCCGCAAAAATACTTCAGCCCAACAACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGC
*
21525993 GTTTTTATGTAAGCGCCGCTA
196 GTTTTTATGTAAGCACCGCTA
21526014 ATACTCAGGG
Statistics
Matches: 197, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
227 165 0.84
228 32 0.16
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (228 bp):
TTAGCGGCGTTTCTGAAAAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTG
AGAAGGATTTAGTGGCATTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGG
GAAAGCCCCGCAAAAATACTTCAGCCCAACAACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGC
GTTTTTATGTAAGCACCGCTACTGGTCAGGTCT
Found at i:21526022 original size:114 final size:114
Alignment explanation
Indices: 21525588--21526013 Score: 694
Period size: 114 Copynumber: 3.7 Consensus size: 114
21525578 TGTTTCTGAA
* * * * *
21525588 AAAGCGTCGCAAAAATACTTCAGTCCAACGATGTCGTTTTCTGAGCTGAGAAGGATTTAGTGGCA
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTGGCG
*
21525653 TTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
66 TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
* * *
21525702 AAAGCGCCGCAAAAATACTTCAGTCTAACAACGCCGTTTT-TCGAGCTGAGAAGGATTTAGTGGC
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCT-GAGCTGAGAAGGATTTAGTGGC
* *
21525766 GTTTTTATGTAAGCACCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGA
65 GTTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
*
21525816 AAAGCGCCGCAAAAATAC-TCAGCCCAACGACGCCGTTTTCTGAGCTGAGAATGATTTAGTGGCG
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTGGCG
*
21525880 TTTTTATGTAAGCGCCGCTAGTGGTCAGGTCTTTAGCGGCGTTTTTGGG
66 TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
* *
21525929 AAAGCCCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGCG
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTGGCG
21525994 TTTTTATGTAAGCGCCGCTA
66 TTTTTATGTAAGCGCCGCTA
21526014 ATACTCAGGG
Statistics
Matches: 290, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
113 104 0.36
114 186 0.64
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (114 bp):
AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTGGCG
TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
Found at i:21526289 original size:14 final size:15
Alignment explanation
Indices: 21526256--21526289 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21526246 TAAGTTTTAT
21526256 AGATTATGGAATTAG
1 AGATTATGGAATTAG
21526271 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
21526285 GGATT
1 AGATT
21526290 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:21526331 original size:14 final size:14
Alignment explanation
Indices: 21526312--21526356 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
21526302 TTAATGTGAT
* *
21526312 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
21526326 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
21526340 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
21526354 TTA
1 TTA
21526357 GATGTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:21526357 original size:7 final size:7
Alignment explanation
Indices: 21526323--21526357 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
21526313 TAAGGTTTAT
*
21526323 GGGTTAA
1 GGGTTAG
21526330 GGGTTAG
1 GGGTTAG
21526337 GGGTTAG
1 GGGTTAG
21526344 GGGTTAG
1 GGGTTAG
21526351 GGGTTAG
1 GGGTTAG
21526358 ATGTTAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.54, T:0.29
Consensus pattern (7 bp):
GGGTTAG
Found at i:21526363 original size:21 final size:21
Alignment explanation
Indices: 21526323--21526373 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
21526313 TAAGGTTTAT
* * *
21526323 GGGTTAAGGGTTAGGGGTTAG
1 GGGTTAGGGGTTAGAGGTTAA
*
21526344 GGGTTAGGGGTTAGATGTTAA
1 GGGTTAGGGGTTAGAGGTTAA
*
21526365 GAGTTAGGG
1 GGGTTAGGG
21526374 ATTTAGGGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.49, T:0.29
Consensus pattern (21 bp):
GGGTTAGGGGTTAGAGGTTAA
Found at i:21526482 original size:14 final size:14
Alignment explanation
Indices: 21526459--21526488 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21526449 ATATATTAAA
*
21526459 TAAGGTTTAGGGGT
1 TAAGGGTTAGGGGT
21526473 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
21526487 TA
1 TA
21526489 GGGATCGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (14 bp):
TAAGGGTTAGGGGT
Found at i:21526511 original size:88 final size:82
Alignment explanation
Indices: 21526408--21526634 Score: 208
Period size: 88 Copynumber: 2.7 Consensus size: 82
21526398 TTCGGTGTTA
* *
21526408 GGTTAGAGTTTAGGGTTTAGATTAATTAATATGTTTTAA-TTATATATTAAATAAGGTTTAGGGG
1 GGTTAGGGTTTAGGGTTTAGATTAATTAATATTTTTTAATTTATATATTAAATAAGGTTTAGGGG
* * *
21526472 TTAAGG-GTTAGGGGTTAG
66 TTAGGGAGTTA-GAG-TCG
* * * * *
21526490 GGATCGGGTTATGGTTTAGGGTTTAGATTAATTAGA-ATTTTTTAATTTATATATTAAAAAAAGT
1 GGTTAGGGTT-TAG-----GGTTTAGATTAATTA-ATATTTTTTAATTTATATATTAAATAAGGT
*
21526554 TTAGGGGTTAGGGATTTAGAGTCG
59 TTAGGGGTTAGGGAGTTAGAGTCG
* * * *
21526578 GGTTAGGGTTTAAGATTTGGATTAATTAGTACTTTTTTAATTTATATATTAAATAAG
1 GGTTAGGGTTTAGGGTTTAGATTAATTAATA-TTTTTTAATTTATATATTAAATAAG
21526635 TTCTTTATAT
Statistics
Matches: 114, Mismatches: 20, Indels: 21
0.74 0.13 0.14
Matches are distributed among these distances:
82 21 0.18
83 25 0.22
87 1 0.01
88 33 0.29
89 31 0.27
90 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.25, T:0.43
Consensus pattern (82 bp):
GGTTAGGGTTTAGGGTTTAGATTAATTAATATTTTTTAATTTATATATTAAATAAGGTTTAGGGG
TTAGGGAGTTAGAGTCG
Found at i:21526614 original size:82 final size:83
Alignment explanation
Indices: 21526476--21526630 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 83
21526466 TAGGGGTTAA
* * * *
21526476 GGGTTAGGGGTTAGGGATCGGGTTATGGTTTAGGGTTTAGATTAATTAGAA-TTTTTTAATTTAT
1 GGGTTAGGGGTTAGAGATCGGGTTAGGGTTTAAGATTTAGATTAATTAGAACTTTTTTAATTTAT
21526540 ATATTAAAAAAAGTTTAG
66 ATATTAAAAAAAGTTTAG
* * *
21526558 GGGTTAGGGATTTAGAG-TCGGGTTAGGGTTTAAGATTTGGATTAATTAGTACTTTTTTAATTTA
1 GGGTTAGGG-GTTAGAGATCGGGTTAGGGTTTAAGATTTAGATTAATTAGAACTTTTTTAATTTA
21526622 TATATTAAA
65 TATATTAAA
21526631 TAAGTTCTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
82 38 0.59
83 26 0.41
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (83 bp):
GGGTTAGGGGTTAGAGATCGGGTTAGGGTTTAAGATTTAGATTAATTAGAACTTTTTTAATTTAT
ATATTAAAAAAAGTTTAG
Found at i:21526735 original size:21 final size:21
Alignment explanation
Indices: 21526682--21526735 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
21526672 TAAAGATTAT
21526682 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
21526703 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
21526724 TAATTTAAAATT
1 TAATTTAAAATT
21526736 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:21526744 original size:9 final size:9
Alignment explanation
Indices: 21526730--21526772 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
21526720 ATAATAATTT
21526730 AAAATTGTA
1 AAAATTGTA
21526739 AAAATTGT-
1 AAAATTGTA
21526747 AAAATTGTAAA
1 AAAATTGT--A
21526758 AAAATTGTA
1 AAAATTGTA
21526767 AAAATT
1 AAAATT
21526773 ACAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.26
9 15 0.48
11 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (9 bp):
AAAATTGTA
Found at i:21526751 original size:17 final size:18
Alignment explanation
Indices: 21526725--21526769 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
21526715 TGAATATAAT
21526725 AATT-TAAAATTGT-AAA
1 AATTGTAAAATTGTAAAA
21526741 AATTGTAAAATTGTAAAAA
1 AATTGTAAAATTGT-AAAA
21526760 AATTGTAAAA
1 AATTGTAAAA
21526770 ATTACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 9 0.35
19 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (18 bp):
AATTGTAAAATTGTAAAA
Found at i:21526769 original size:8 final size:8
Alignment explanation
Indices: 21526725--21526758 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
21526715 TGAATATAAT
21526725 AATT-TAA
1 AATTGTAA
21526732 AATTGTAAA
1 AATTGT-AA
21526741 AATTGTAA
1 AATTGTAA
21526749 AATTGTAA
1 AATTGTAA
21526757 AA
1 AA
21526759 AAATTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.16
8 13 0.52
9 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (8 bp):
AATTGTAA
Found at i:21526778 original size:19 final size:19
Alignment explanation
Indices: 21526738--21526781 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
21526728 TTAAAATTGT
*
21526738 AAAAATTGTAAAATTGTAA
1 AAAAATTGTAAAAATGTAA
21526757 AAAAATTGTAAAAAT-TACA
1 AAAAATTGTAAAAATGTA-A
21526776 AAAAAT
1 AAAAAT
21526782 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAAATTGTAAAAATGTAA
Found at i:21526796 original size:18 final size:18
Alignment explanation
Indices: 21526775--21526821 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
21526765 TAAAAATTAC
21526775 AAAAAATAAAATAA-AAAT
1 AAAAAATAAAA-AAGAAAT
21526793 AAAAAATAAAAAAGAAAT
1 AAAAAATAAAAAAGAAAT
21526811 AAAAAACTAAA
1 AAAAAA-TAAA
21526822 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.07
18 21 0.78
19 4 0.15
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (18 bp):
AAAAAATAAAAAAGAAAT
Found at i:21526860 original size:46 final size:47
Alignment explanation
Indices: 21526810--21526905 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 47
21526800 AAAAAAGAAA
** *
21526810 TAAAAAACT-AAATTTTTATTTTTACCTAA-TTTTTATAAATATTA-C
1 TAAAAAACTAAAATTGATAATTTTACCTAATTTTTTA-AAATATTACC
* *
21526855 TTAAAAACTAAAATTGATAATTTTATCTAATTTTTTAAAATATTACC
1 TAAAAAACTAAAATTGATAATTTTACCTAATTTTTTAAAATATTACC
21526902 TAAA
1 TAAA
21526906 TTAACAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
45 8 0.19
46 24 0.57
47 10 0.24
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (47 bp):
TAAAAAACTAAAATTGATAATTTTACCTAATTTTTTAAAATATTACC
Found at i:21527260 original size:75 final size:74
Alignment explanation
Indices: 21527101--21527264 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 74
21527091 CATTTGATAA
*
21527101 AAAACTGCGCCGTTTTATTATTTGCTTTTAGTGGCACTTTAGAAAAACGTCGCAAATTAATGTAA
1 AAAACTGCGTCGTTTTATTATTTGCTTTTAGTGGCACTTTAGAAAAACGTCGCAAATTAATGTAA
21527166 CTGTTAAGG
66 CTGTTAAGG
* * *
21527175 AAAACGGCGTCGTTTTATTATTTGCTTTTAGTGGGGACTTTTGAAAAACG-CGGCAAA-T-ATGT
1 AAAACTGCGTCGTTTTATTATTTGCTTTTAGT-GGCACTTTAGAAAAACGTC-GCAAATTAATGT
21527237 ATTA-TGGGTTAAGG
64 A--ACT--GTTAAGG
21527251 -AAACTGCGTCGTTT
1 AAAACTGCGTCGTTT
21527265 CAGTTTTTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
73 5 0.06
74 33 0.42
75 34 0.43
76 7 0.09
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (74 bp):
AAAACTGCGTCGTTTTATTATTTGCTTTTAGTGGCACTTTAGAAAAACGTCGCAAATTAATGTAA
CTGTTAAGG
Found at i:21529038 original size:7 final size:7
Alignment explanation
Indices: 21529026--21529084 Score: 100
Period size: 7 Copynumber: 8.3 Consensus size: 7
21529016 TGTTTCTTTA
21529026 TTTTCTG
1 TTTTCTG
21529033 TTTTCTG
1 TTTTCTG
21529040 TTTTCTG
1 TTTTCTG
21529047 TTTTCTG
1 TTTTCTG
21529054 TTTTCTG
1 TTTTCTG
21529061 TTTTCTG
1 TTTTCTG
*
21529068 TTTTGCTA
1 TTTT-CTG
21529076 TTTTCTG
1 TTTTCTG
21529083 TT
1 TT
21529085 GAATGAAGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
7 43 0.88
8 6 0.12
ACGTcount: A:0.02, C:0.14, G:0.14, T:0.71
Consensus pattern (7 bp):
TTTTCTG
Found at i:21529672 original size:13 final size:13
Alignment explanation
Indices: 21529654--21529798 Score: 89
Period size: 13 Copynumber: 11.0 Consensus size: 13
21529644 ATTTACTCTT
*
21529654 AATATATTACTTG
1 AATATATTACTTA
21529667 AATATATTACTTA
1 AATATATTACTTA
21529680 AATATATTACTTA
1 AATATATTACTTA
*
21529693 CTAA-A-ATTTCGTTA
1 --AATATATTAC-TTA
*
21529707 AATTTATTACTTA
1 AATATATTACTTA
* *
21529720 AATATGTTACTCA
1 AATATATTACTTA
* * *
21529733 GATACATCACTTA
1 AATATATTACTTA
* **
21529746 CTAAAAT-TTGGTTA
1 --AATATATTACTTA
* *
21529760 AATTTTTTACTTA
1 AATATATTACTTA
*
21529773 AATATGTTACTTA
1 AATATATTACTTA
*
21529786 AATACATTACTTA
1 AATATATTACTTA
21529799 CTAAAATTTA
Statistics
Matches: 98, Mismatches: 26, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
12 5 0.05
13 77 0.79
14 12 0.12
15 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:21529730 original size:53 final size:53
Alignment explanation
Indices: 21529636--21529807 Score: 229
Period size: 53 Copynumber: 3.2 Consensus size: 53
21529626 AACATATTTT
* * * * *
21529636 TTACTAAAATTTAC-TCTTAATATATTACTTGAATATATTACTTAAATATATTAC
1 TTACTAAAATTT-CGT-TAAATTTATTACTTAAATATGTTACTTAAATACATTAC
* * *
21529690 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTCAGATACATCAC
1 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
* *
21529743 TTACTAAAATTTGGTTAAATTTTTTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
21529796 TTACTAAAATTT
1 TTACTAAAATTT
21529808 AAGTATATAT
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
53 91 0.88
54 13 0.12
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (53 bp):
TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
Found at i:21529953 original size:9 final size:9
Alignment explanation
Indices: 21529939--21530258 Score: 202
Period size: 9 Copynumber: 35.8 Consensus size: 9
21529929 TAAGTACAAG
21529939 AACTTACAT
1 AACTTACAT
*
21529948 AACTTA-TT
1 AACTTACAT
*
21529956 AATATTTACAT
1 -A-ACTTACAT
21529967 AAACTTACAT
1 -AACTTACAT
*
21529977 AACTATCACAAA
1 AACT-T-AC-AT
*
21529989 AACTTATATGT
1 AACTTACA--T
21530000 AAACTTACAT
1 A-ACTTACAT
21530010 AA--TACAT
1 AACTTACAT
* *
21530017 AATTTACAC
1 AACTTACAT
21530026 AACTTACAT
1 AACTTACAT
*
21530035 AACCTACAT
1 AACTTACAT
21530044 AACTTACAT
1 AACTTACAT
21530053 AA--TACA-
1 AACTTACAT
21530059 AAGCTTACAT
1 AA-CTTACAT
* *
21530069 AACTGAAAT
1 AACTTACAT
* *
21530078 AGCTTACAC
1 AACTTACAT
21530087 AACTTACAT
1 AACTTACAT
21530096 AACTTACAT
1 AACTTACAT
*
21530105 AACTTACAC
1 AACTTACAT
21530114 AACTTACAT
1 AACTTACAT
*
21530123 AATACATA-AT
1 -A-ACTTACAT
21530133 AACTTAC--
1 AACTTACAT
21530140 AACTTACAT
1 AACTTACAT
*
21530149 AACATACAT
1 AACTTACAT
* **
21530158 TACTTTGAT
1 AACTTACAT
21530167 AACTTACAT
1 AACTTACAT
*
21530176 AAGTTACAT
1 AACTTACAT
*
21530185 AA--TACAC
1 AACTTACAT
21530192 AACTTACAT
1 AACTTACAT
** *
21530201 AGTTTACTT
1 AACTTACAT
21530210 AA--TACAT
1 AACTTACAT
21530217 AACTTACAT
1 AACTTACAT
21530226 AACTT--AT
1 AACTTACAT
*
21530233 ACACGTACAT
1 A-ACTTACAT
21530243 AACTTACAT
1 AACTTACAT
*
21530252 AATTTAC
1 AACTTAC
21530259 TTAATACATA
Statistics
Matches: 240, Mismatches: 44, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.01
7 33 0.14
8 8 0.03
9 152 0.63
10 23 0.10
11 11 0.05
12 11 0.05
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:21530044 original size:34 final size:33
Alignment explanation
Indices: 21530005--21530128 Score: 85
Period size: 34 Copynumber: 3.6 Consensus size: 33
21529995 TATGTAAACT
21530005 TACATAA-TACATAATTTACACAA-CTTACATAACC
1 TACATAACTACATAA--TACA-AAGCTTACATAACC
21530039 TACATAACTTACATAATACAAAGCTTACATAA-C
1 TACATAAC-TACATAATACAAAGCTTACATAACC
* * * *
21530072 TGAAATAGCTTACACAACTTACATAA-CTTACATAACT
1 T-ACATAAC-TACATAA--TACA-AAGCTTACATAACC
*
21530109 TACACAACTTACATAATACA
1 TACATAAC-TACATAATACA
21530129 TAATAACTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
33 4 0.05
34 36 0.49
36 31 0.42
37 3 0.04
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (33 bp):
TACATAACTACATAATACAAAGCTTACATAACC
Found at i:21530157 original size:53 final size:51
Alignment explanation
Indices: 21530082--21530201 Score: 152
Period size: 53 Copynumber: 2.3 Consensus size: 51
21530072 TGAAATAGCT
*
21530082 TACACAACTTACATAACTTACATAACTTACACAACTTACATAA-TACATAA
1 TACACAACTTACATAACATACATAACTTACACAACTTACATAAGTACATAA
* ** *
21530132 TAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAAGTTACATAA
1 T-AC--ACAACTTACATAACATACATAACTTACACAACTTACATAAG-TACATAA
21530187 TACACAACTTACATA
1 TACACAACTTACATA
21530202 GTTTACTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 1 0.02
51 2 0.03
52 12 0.20
53 35 0.58
54 2 0.03
55 8 0.13
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (51 bp):
TACACAACTTACATAACATACATAACTTACACAACTTACATAAGTACATAA
Found at i:21530207 original size:25 final size:25
Alignment explanation
Indices: 21530109--21530266 Score: 106
Period size: 25 Copynumber: 6.2 Consensus size: 25
21530099 TTACATAACT
21530109 TACACAACTTACATAA--TACATAA
1 TACACAACTTACATAATTTACATAA
** *
21530132 TAACTTACAACTTACATAACATACATTACT
1 T-AC--ACAACTTACATAATTTACA-TA-A
** * *
21530162 TTGATAACTTACATAAGTTACATAA
1 TACACAACTTACATAATTTACATAA
* *
21530187 TACACAACTTACATAGTTTACTTAA
1 TACACAACTTACATAATTTACATAA
* **
21530212 TACATAACTTACATAACTTATACA-CG
1 TACACAACTTACATAA-TT-TACATAA
* *
21530238 TACATAACTTACATAATTTACTTAA
1 TACACAACTTACATAATTTACATAA
21530263 TACA
1 TACA
21530267 TAAATATATA
Statistics
Matches: 104, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
23 1 0.01
24 5 0.05
25 39 0.38
26 33 0.32
27 19 0.18
28 4 0.04
29 2 0.02
30 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.34
Consensus pattern (25 bp):
TACACAACTTACATAATTTACATAA
Found at i:21530258 original size:51 final size:50
Alignment explanation
Indices: 21530005--21530269 Score: 162
Period size: 52 Copynumber: 5.1 Consensus size: 50
21529995 TATGTAAACT
* * * * *
21530005 TACATAA--TACATAATTTACACAACTTACATAACCTACATAACTTACATAA
1 TACATAACTTACATAACTTACACAA--TACACAACTTACATAATTTACTTAA
* * * * * *
21530055 TACA-AAGCTTACATAACTGAAATAGCTTACACAACTTACATAACTTACATAA
1 TACATAA-CTTACATAACTTACACA--ATACACAACTTACATAATTTACTTAA
* * ** *
21530107 CTTACACAACTTACATAA--TACATAATAACTTACAACTTACATAACATACATTACT
1 --TACATAACTTACATAACTTACACAAT-AC--ACAACTTACATAATTTAC-TTA-A
** * * *
21530162 TTGATAACTTACATAAGTTACATAATACACAACTTACATAGTTTACTTAA
1 TACATAACTTACATAACTTACACAATACACAACTTACATAATTTACTTAA
* * *
21530212 TACATAACTTACATAACTTATACACGTACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACACA-ATACACAACTTACATAATTTACTTAA
21530263 TACATAA
1 TACATAA
21530270 ATATATATCA
Statistics
Matches: 171, Mismatches: 28, Indels: 31
0.74 0.12 0.13
Matches are distributed among these distances:
49 2 0.01
50 24 0.14
51 35 0.20
52 53 0.31
53 30 0.18
54 17 0.10
55 10 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (50 bp):
TACATAACTTACATAACTTACACAATACACAACTTACATAATTTACTTAA
Found at i:21535787 original size:66 final size:66
Alignment explanation
Indices: 21535704--21535834 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
21535694 CACAGATGAG
* *
21535704 GTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGTAGT-GAGAGAAGCAG
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCA-TCGAGAGAAGCAG
21535768 AA
65 AA
* *
21535770 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCTGATGCGGCATCGAGAGAAGCAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCATCGAGAGAAGCAGA
21535835 GCAGAGCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.16
Consensus pattern (66 bp):
GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCATCGAGAGAAGCAGA
A
Found at i:21535858 original size:66 final size:66
Alignment explanation
Indices: 21535707--21535871 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 66
21535697 AGATGAGGTT
* * * *
21535707 CAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGTAGTGAGAGAAGCAGAAGT
1 CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGTGAGAGAAGCAGAAGA
*
21535772 T
66 G
* * *
21535773 CAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCTGATGCGGCA-TCGAGAGAAGCAGAGC
1 CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGT-GAGAGAAGCAGA--
21535837 AGAG
63 AGAG
* *
21535841 C-AAA-AAGTACGACGAACTCCAGC-AGCAACTT
1 CAAAAGAAATACGAAGAACTCCAGCTA-CAACTT
21535872 CAGAGTATGA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.02
66 78 0.91
67 3 0.03
68 3 0.03
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (66 bp):
CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGTGAGAGAAGCAGAAGA
G
Found at i:21536202 original size:42 final size:41
Alignment explanation
Indices: 21536155--21536292 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 41
21536145 TTGAACAAAA
* * * *
21536155 GTTCTTTAGCGGCGCTTAATAAAAAATGCCACCAAAGATCAT
1 GTTCTTTAGCGGCGCTTAA-AAAAAAAGCCGCTAAAGAACAT
* *
21536197 GTTCTTTAGCGACGATTAGAAAAAAAAGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTA-AAAAAAAAGCCGCTAAAGAACAT
* *
21536239 GTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTA-AAAAAAAAGCCGCTAAAGAACAT
21536281 -TATCTTTAGCGG
1 GT-TCTTTAGCGG
21536293 TATTTTTGTT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 82 0.98
43 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
GTTCTTTAGCGGCGCTTAAAAAAAAAGCCGCTAAAGAACAT
Found at i:21539512 original size:3 final size:3
Alignment explanation
Indices: 21539446--21539499 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
21539436 GAGGAGGAAA
* *
21539446 TGG TGG TGG AGG TGG AGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
21539494 TGG TGG
1 TGG TGG
21539500 AGGAAATGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.04, C:0.00, G:0.67, T:0.30
Consensus pattern (3 bp):
TGG
Found at i:21539615 original size:3 final size:3
Alignment explanation
Indices: 21539607--21539657 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
21539597 CACTGTAGTT
* * * * *
21539607 GTG GTG GTG G-G GGG GCG GGG GTG GTG GTG GTG GTG GTG GAG GTG GAG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
21539654 GTG G
1 GTG G
21539658 AAATGGAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.04, C:0.02, G:0.73, T:0.22
Consensus pattern (3 bp):
GTG
Found at i:21545314 original size:15 final size:15
Alignment explanation
Indices: 21545294--21545323 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21545284 AGCTGGTACT
*
21545294 TCTTCTTCCTCCTCA
1 TCTTCTTCATCCTCA
21545309 TCTTCTTCATCCTCA
1 TCTTCTTCATCCTCA
21545324 CGTTTCTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTTCTTCATCCTCA
Found at i:21550118 original size:131 final size:130
Alignment explanation
Indices: 21549753--21550150 Score: 469
Period size: 131 Copynumber: 3.0 Consensus size: 130
21549743 GATGAGATCG
* * *
21549753 TTCATGATGTTAAATCGAATGAACTTAGGCTATAATATTAAATTAACGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTAGCGAGCCTTAACATTATTAG
* * * *
21549818 CTGCGATCTTATATCAGTGAGCTATTTAGAGTAGCAATATTAAATCAACTAACTCAAA-TAAAAT
66 CTGCGATCTTAAATCAG-GAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAAAT
21549882 T
130 T
* * * * * *
21549883 ATTTATGATATTAAATTGAATAAACTT-GGCTACGATATTAAATT-GACGAGCTTTAACATTATC
1 -TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTAG-CGAGCCTTAACATTATT
* * * * * * * *
21549946 AGCTGCAATATTAAATCAGTAACTTATTTAAAGTAGTGATATTAAATCGGGTAACTCAAAGAAAA
64 AGCTGCGATCTTAAATCAGGAGC-TATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAA
21550011 ATT
128 ATT
* * *
21550014 TTCATGATATTAAATCGAATGAACTTAGGCTGTGATTTTAAATTAGTGAGCCTTAACATTATTAG
1 TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTAGCGAGCCTTAACATTATTAG
* * * * *
21550079 TTGTGATCTTAAATTAGCGAGCTATTTAGAGTAACGATATTAAATCAGCTAACTCAAAGAAAATT
66 CTGCGATCTTAAATCAG-GAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAAAT
21550144 T
130 T
21550145 TTCATG
1 TTCATG
21550151 TTAGATAAAC
Statistics
Matches: 218, Mismatches: 43, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
129 2 0.01
130 99 0.45
131 114 0.52
132 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (130 bp):
TTCATGATATTAAATCGAATGAACTTAGGCTATGATATTAAATTAGCGAGCCTTAACATTATTAG
CTGCGATCTTAAATCAGGAGCTATTTAGAGTAGCGATATTAAATCAGCTAACTCAAAGAAAAATT
Found at i:21557747 original size:14 final size:14
Alignment explanation
Indices: 21557730--21557756 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21557720 TTATATTTAG
21557730 TTAATTTTTATTTC
1 TTAATTTTTATTTC
21557744 TTAATTTTTATTT
1 TTAATTTTTATTT
21557757 TATATTTCAC
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:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TTAATTTTTATTTC
Found at i:21561348 original size:29 final size:31
Alignment explanation
Indices: 21561279--21561351 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
21561269 ATTCAAAAAA
* *
21561279 TACAATGACTAAAATTAATCAATATGTAAAG
1 TACAAGGACTAAAATTAATCAATATGCAAAG
*
21561310 TAC-AGAGACTAAAATTGATCAA-AT-CAAAG
1 TACAAG-GACTAAAATTAATCAATATGCAAAG
21561339 TACAAGGACTAAA
1 TACAAGGACTAAA
21561352 CTCACAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 14 0.38
30 5 0.14
31 18 0.49
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (31 bp):
TACAAGGACTAAAATTAATCAATATGCAAAG
Found at i:21563806 original size:36 final size:33
Alignment explanation
Indices: 21563766--21563861 Score: 93
Period size: 36 Copynumber: 2.8 Consensus size: 33
21563756 ATGTATATAT
* *
21563766 ATTGCCATGGCCCAACCATGGTCTTATGTCTATAC
1 ATTGCCATGGCCCAACTATGGTCTTATG--TAAAC
* *** *
21563801 AATTGCCATAGCCTTGCTATGGTCTTACGTAAAC
1 -ATTGCCATGGCCCAACTATGGTCTTATGTAAAC
*
21563835 ATTGCCATGGTCCAACTATGGTCTTAT
1 ATTGCCATGGCCCAACTATGGTCTTAT
21563862 ACATTTTTAC
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
33 21 0.45
34 4 0.09
36 22 0.47
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (33 bp):
ATTGCCATGGCCCAACTATGGTCTTATGTAAAC
Found at i:21567199 original size:22 final size:21
Alignment explanation
Indices: 21567171--21567214 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
21567161 TCTCTCTATT
*
21567171 TTCTCTCAATCTCTCTTTCAAA
1 TTCTCTCAAACT-TCTTTCAAA
*
21567193 TTCTCTCAAACTTCTTTGAAA
1 TTCTCTCAAACTTCTTTCAAA
21567214 T
1 T
21567215 ATTTGGTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (21 bp):
TTCTCTCAAACTTCTTTCAAA
Found at i:21583416 original size:16 final size:16
Alignment explanation
Indices: 21583391--21583428 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21583381 TTTTAAAAAG
*
21583391 AAAATACTTGTAGA-A
1 AAAATACTTGAAGAGA
21583406 AAAAGTACTTGAAGAGA
1 AAAA-TACTTGAAGAGA
21583423 AAAATA
1 AAAATA
21583429 ATTTGTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (16 bp):
AAAATACTTGAAGAGA
Found at i:21589949 original size:6 final size:6
Alignment explanation
Indices: 21589938--21589979 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
21589928 GAAATAAATT
21589938 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
21589980 TATACTCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTTC
Found at i:21598662 original size:21 final size:21
Alignment explanation
Indices: 21598638--21598680 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
21598628 ATAGAGCCCG
21598638 TCGACTTTCTATTTTATTTAA
1 TCGACTTTCTATTTTATTTAA
21598659 TCGACTTTCTATTTTATTTAA
1 TCGACTTTCTATTTTATTTAA
21598680 T
1 T
21598681 TAACTCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.58
Consensus pattern (21 bp):
TCGACTTTCTATTTTATTTAA
Found at i:21613377 original size:20 final size:20
Alignment explanation
Indices: 21613352--21613421 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
21613342 ATTATTAGAG
21613352 TAAACTACACCATTAGTCAT
1 TAAACTACACCATTAGTCAT
* ** * * *
21613372 TAAACTATGATTTATTATTAGAG
1 TAAACTA-CA-CCATTAGT-CAT
21613395 TAAACTACACCATTAGTCAT
1 TAAACTACACCATTAGTCAT
21613415 TAAACTA
1 TAAACTA
21613422 TGGGTAAGTT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 15 0.43
21 6 0.17
22 6 0.17
23 8 0.23
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (20 bp):
TAAACTACACCATTAGTCAT
Found at i:21613399 original size:43 final size:43
Alignment explanation
Indices: 21613338--21613423 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
21613328 CTAAGAGATA
21613338 ATTTATTATTAGAGTAAACTACACCATTAGTCATTAAACTATG
1 ATTTATTATTAGAGTAAACTACACCATTAGTCATTAAACTATG
21613381 ATTTATTATTAGAGTAAACTACACCATTAGTCATTAAACTATG
1 ATTTATTATTAGAGTAAACTACACCATTAGTCATTAAACTATG
21613424 GGTAAGTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (43 bp):
ATTTATTATTAGAGTAAACTACACCATTAGTCATTAAACTATG
Found at i:21615627 original size:8 final size:8
Alignment explanation
Indices: 21615614--21615643 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
21615604 CCAGAAAAGC
21615614 TAATATAT
1 TAATATAT
21615622 TAATATAT
1 TAATATAT
21615630 TAATATAT
1 TAATATAT
21615638 TAATAT
1 TAATAT
21615644 TTGGTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAATATAT
Found at i:21615670 original size:68 final size:68
Alignment explanation
Indices: 21615561--21615695 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
21615551 TCCAGAAGAG
21615561 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
1 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
21615626 ATA
66 ATA
*
21615629 TTAATATATTAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
1 TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
21615694 AT
66 AT
21615696 CTAAAAAGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (68 bp):
TTAATATATCAATATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAAT
ATA
Found at i:21615714 original size:68 final size:68
Alignment explanation
Indices: 21615574--21615714 Score: 219
Period size: 68 Copynumber: 2.1 Consensus size: 68
21615564 ATATATCAAT
* * * **
21615574 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATTAATATATT
1 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
*
21615639 AAT
66 AAA
*
21615642 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATCTAAAAAGAAC
1 ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
21615707 AAA
66 AAA
21615710 ATTTG
1 ATTTG
21615715 TGATGGTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (68 bp):
ATTTGGTAGTAAAAAAATTAGTTGAAAGCTCCAGAAAAGCTAATATATTAATATATAAAAAGAAC
AAA
Found at i:21624681 original size:17 final size:17
Alignment explanation
Indices: 21624659--21624723 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
21624649 CATCAAAGGC
21624659 TACAATTAGAACCTGTA
1 TACAATTAGAACCTGTA
21624676 TACAATTAGAACTCTAAG-A
1 TACAATTAGAAC-CT--GTA
* * **
21624695 CACAATTATAAGTTGTA
1 TACAATTAGAACCTGTA
21624712 TACAATTAGAAC
1 TACAATTAGAAC
21624724 TCTAAGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
16 1 0.03
17 22 0.59
18 3 0.08
19 10 0.27
20 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (17 bp):
TACAATTAGAACCTGTA
Found at i:21629572 original size:48 final size:48
Alignment explanation
Indices: 21629501--21629595 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
21629491 TTCTTTGCTT
21629501 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGACTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGACTCAACAGC
* * *
21629549 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGACTCAACAG
21629596 AATTCCCTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.17
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGACTCAACAGC
Found at i:21630740 original size:29 final size:29
Alignment explanation
Indices: 21630665--21630740 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
21630655 CTAGTACTCA
*
21630665 CCACAAAGGCTTTCCTATCCAGAGTTGTG
1 CCACAAAGGCTTTCCTTTCCAGAGTTGTG
* * *
21630694 CCACAAAGGCTTAT-CTTTCTAGAGTTTTT
1 CCACAAAGGCTT-TCCTTTCCAGAGTTGTG
21630723 CCACAAAGG-TTGTCCTTT
1 CCACAAAGGCTT-TCCTTT
21630741 AACAAGTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 3 0.08
29 36 0.90
30 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (29 bp):
CCACAAAGGCTTTCCTTTCCAGAGTTGTG
Found at i:21630960 original size:53 final size:53
Alignment explanation
Indices: 21630879--21631037 Score: 237
Period size: 53 Copynumber: 3.0 Consensus size: 53
21630869 TTTTTTAATT
* * * * *
21630879 TTTCCATATGATTCCATAACCCATCAGTTATGATCTTACATGATATGGTCTTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
* *
21630932 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACAATATGGTATTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
* *
21630985 TTTCCATATGATGTCATAACTCACCAGTTACGGTCTTACACGATATGGTCTTC
1 TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
21631038 AATGCCATGG
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 95 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (53 bp):
TTTCCATATGATTTCATAACCCACCAGTTACGGTCTTACACGATATGGTCTTC
Found at i:21650606 original size:23 final size:22
Alignment explanation
Indices: 21650573--21650629 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
21650563 CAATGATAAT
*
21650573 ATTTTGTTTTTACTTCTCTTTTAC
1 ATTTT-TTTTTACTTCT-TTTTAA
**
21650597 ATTTTTTTTTGTTTCTTTTTAA
1 ATTTTTTTTTACTTCTTTTTAA
*
21650619 ATATTTTTTTA
1 ATTTTTTTTTA
21650630 TGTAAATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 14 0.50
23 9 0.32
24 5 0.18
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.72
Consensus pattern (22 bp):
ATTTTTTTTTACTTCTTTTTAA
Found at i:21650616 original size:22 final size:23
Alignment explanation
Indices: 21650586--21650628 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
21650576 TTGTTTTTAC
* *
21650586 TTCTCTTTTACATTTTTTTTTGT
1 TTCTCTTTTAAATATTTTTTTGT
21650609 TTCT-TTTTAAATATTTTTTT
1 TTCTCTTTTAAATATTTTTTT
21650629 ATGTAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (23 bp):
TTCTCTTTTAAATATTTTTTTGT
Found at i:21655738 original size:133 final size:132
Alignment explanation
Indices: 21655512--21655888 Score: 565
Period size: 133 Copynumber: 2.8 Consensus size: 132
21655502 TTAGTGCTTT
* * * * *
21655512 TATCCTCGAGTCTTAGGTTCAATTCTTCTCCTACCCACATTTTGTACTTTTTTTATTTCATGTTG
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACA-TTTGTATTTTTTTTATTTCATGTTG
* * *
21655577 CTTCAAACTTTTTAAATTTTTAATTAATTTTTTGAACATATTAGTTTTTTGGTTAGATGGTTGCA
65 CTTCAAACTTTTTTAATTTTTAATTAATTTTTT-AACATATTAGTTCTTTGGTTAGATAGTTGCA
21655642 ATTA
129 ATTA
*
21655646 TATCCTTGAGTCTCAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
21655711 TTCAAACTTTTTTAATTTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAAT
66 TTCAAACTTTTTTAATTTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAAT
21655776 TA
131 TA
* * * *
21655778 CATCCTTGAGTCTTGAGTTTAATTCCTCTCCTACTCACATTTGCATTTTGTTTTATTTCATGTTG
1 TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTT-TTTTATTTCATGTTG
* *
21655843 CTTCAAGCTTTTCTTTTATTTTTAATTAATTTTTTTAACATATTAG
65 CTTCAAAC-TTT-TTTAATTTTTAATTAA-TTTTTTAACATATTAG
21655889 CTTGTTTCCT
Statistics
Matches: 223, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
132 77 0.35
133 78 0.35
134 37 0.17
135 15 0.07
136 16 0.07
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (132 bp):
TATCCTTGAGTCTTAAGTTTAATTCTTCTCCTACTCACATTTGTATTTTTTTTATTTCATGTTGC
TTCAAACTTTTTTAATTTTTAATTAATTTTTTAACATATTAGTTCTTTGGTTAGATAGTTGCAAT
TA
Found at i:21656053 original size:20 final size:19
Alignment explanation
Indices: 21655996--21656089 Score: 95
Period size: 19 Copynumber: 4.7 Consensus size: 19
21655986 TGTTTCAAGC
21655996 TTTTTTATTTTTAATTAAT
1 TTTTTTATTTTTAATTAAT
21656015 GTTTTGATGATATTTTTAATT-A-
1 -TTTT--T--TATTTTTAATTAAT
*
21656037 -CTTTTATTTTTAATTAATAT
1 TTTTTTATTTTTAATT-A-AT
21656057 TTTTTTATTTTTAATTAAT
1 TTTTTTATTTTTAATTAAT
21656076 TTTTTTATTTTTAA
1 TTTTTTATTTTTAA
21656090 CTCTTAACCA
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
16 11 0.17
18 1 0.02
19 17 0.27
20 7 0.11
21 14 0.22
22 1 0.02
23 1 0.02
24 11 0.17
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTATTTTTAATTAAT
Found at i:21656062 original size:16 final size:16
Alignment explanation
Indices: 21656025--21656078 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
21656015 GTTTTGATGA
*
21656025 TATTTTTAATTACTTT
1 TATTTTTAATTAATTT
21656041 TATTTTTAATTAATATTTTTT
1 TATTTTTAATT-A-A---TTT
21656062 TATTTTTAATTAATTT
1 TATTTTTAATTAATTT
21656078 T
1 T
21656079 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 15 0.47
17 1 0.03
19 1 0.03
20 1 0.03
21 14 0.44
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTAATTAATTT
Found at i:21656082 original size:40 final size:40
Alignment explanation
Indices: 21655996--21656089 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
21655986 TGTTTCAAGC
*
21655996 TTTTTTATTTTTAATTAATGTTTTGATGATATTTTTAATTA
1 TTTTTTATTTTTAATTAATATTTT-ATGATATTTTTAATTA
* *
21656037 -CTTTTATTTTTAATTAATATTTT-T-TTATTTTTAATTAA
1 TTTTTTATTTTTAATTAATATTTTATGATATTTTTAATT-A
21656075 TTTTTTTATTTTTAA
1 -TTTTTTATTTTTAA
21656090 CTCTTAACCA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
37 11 0.24
38 2 0.04
40 33 0.72
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (40 bp):
TTTTTTATTTTTAATTAATATTTTATGATATTTTTAATTA
Found at i:21656166 original size:30 final size:31
Alignment explanation
Indices: 21656125--21656192 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
21656115 CATGCTTATA
21656125 AAAATAATTAAAAATA-A-AAAATACATTAATT
1 AAAA-AATTAAAAATACATAAAA-ACATTAATT
*
21656156 AAAAAATTAAAAATATCATCAAAACATTAATT
1 AAAAAATTAAAAATA-CATAAAAACATTAATT
21656188 AAAAA
1 AAAAA
21656193 TAAACTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 11 0.33
31 4 0.12
32 15 0.45
33 3 0.09
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (31 bp):
AAAAAATTAAAAATACATAAAAACATTAATT
Found at i:21656991 original size:20 final size:20
Alignment explanation
Indices: 21656966--21657020 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
21656956 GCAAAAAAAA
* *
21656966 TTATTGTTCTTTTTACTGTT
1 TTATTGTTATTTTTACCGTT
*
21656986 TTATTGCTGTTTTTTTACCGTT
1 TTATTG-T-TATTTTTACCGTT
*
21657008 TTGTTGTTATTTT
1 TTATTGTTATTTT
21657021 CTTGTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 16 0.55
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (20 bp):
TTATTGTTATTTTTACCGTT
Found at i:21664033 original size:15 final size:15
Alignment explanation
Indices: 21663990--21664033 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21663980 TTTAATTCAT
*
21663990 TTTAAATTATTCAAG
1 TTTAAATTATTTAAG
*
21664005 TTTAGATTATTTTAAG
1 TTTAAATTA-TTTAAG
*
21664021 TTTAAATCATTTA
1 TTTAAATTATTTA
21664034 TACTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTAAATTATTTAAG
Found at i:21668616 original size:9 final size:9
Alignment explanation
Indices: 21668604--21668644 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
21668594 TTTGAATTTT
21668604 ATAATTCGA
1 ATAATTCGA
* *
21668613 ATAACTCAA
1 ATAATTCGA
*
21668622 ATAATTTGA
1 ATAATTCGA
21668631 ATAATTCGA
1 ATAATTCGA
21668640 ATAAT
1 ATAAT
21668645 AGATTGGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (9 bp):
ATAATTCGA
Found at i:21668824 original size:21 final size:20
Alignment explanation
Indices: 21668782--21668826 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
21668772 ATATTTTTTT
*
21668782 AAAAAATATAAAAAATTCTA
1 AAAAAATATAAAAAAGTCTA
21668802 AAAAATATATAAAGAAAGT-TA
1 AAAAA-ATATAAA-AAAGTCTA
21668823 AAAA
1 AAAA
21668827 TTTCCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATATAAAAAAGTCTA
Found at i:21669083 original size:5 final size:5
Alignment explanation
Indices: 21669043--21669081 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
21669033 ATAATTTCTC
* *
21669043 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAC TCGAC TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
21669082 CTTGAATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (5 bp):
TCGAT
Found at i:21673104 original size:25 final size:24
Alignment explanation
Indices: 21673076--21673203 Score: 73
Period size: 24 Copynumber: 5.2 Consensus size: 24
21673066 GTATAATAGA
21673076 AAGCTCATATGAGCCATGTAACGGG
1 AAGCTCATATGAGCCAT-TAACGGG
* * * ** *
21673101 AAGCTGATCTGGGCTGTATAACAGG
1 AAGCTCATATGAGCCAT-TAACGGG
* *
21673126 AAGATCATAAGAGCCA-TAACCGGG
1 AAGCTCATATGAGCCATTAA-CGGG
** *
21673150 AAGCTCATGCGAGCCAATAACGGG
1 AAGCTCATATGAGCCATTAACGGG
* *
21673174 TAGCTTCGA-A-GAGCTATTAACGGG
1 AAGC-TC-ATATGAGCCATTAACGGG
21673198 AAGCTC
1 AAGCTC
21673204 CGGATAGCCA
Statistics
Matches: 76, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
23 5 0.07
24 38 0.50
25 32 0.42
26 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (24 bp):
AAGCTCATATGAGCCATTAACGGG
Found at i:21673291 original size:26 final size:25
Alignment explanation
Indices: 21673244--21673301 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
21673234 ATCCATATCG
* *
21673244 GGAAGCTCCAGAGAGCAATTAATTA
1 GGAAGCTCCAAAGAGCAATTAATCA
** *
21673269 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTC-CAAAGAGCAATTAATCA
21673295 GGAAGCT
1 GGAAGCT
21673302 AAAGAAGAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (25 bp):
GGAAGCTCCAAAGAGCAATTAATCA
Found at i:21673334 original size:25 final size:25
Alignment explanation
Indices: 21673306--21673354 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
21673296 GAAGCTAAAG
* *
21673306 AAGAGCCATATAATGGAAAGCTCGC
1 AAGAACCATATAAAGGAAAGCTCGC
* *
21673331 AAGAACTATATAAAGGGAAGCTCG
1 AAGAACCATATAAAGGAAAGCTCG
21673355 AGATGGCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (25 bp):
AAGAACCATATAAAGGAAAGCTCGC
Found at i:21680640 original size:13 final size:14
Alignment explanation
Indices: 21680607--21680640 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
21680597 ATCTTATATA
21680607 TTTTTTTGTTTTCT
1 TTTTTTTGTTTTCT
*
21680621 TTGTTTTG-TTTCT
1 TTTTTTTGTTTTCT
21680634 TTTTTTT
1 TTTTTTT
21680641 TTGTGTTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTTTTGTTTTCT
Found at i:21682065 original size:12 final size:13
Alignment explanation
Indices: 21682042--21682070 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21682032 ATCTAAAAAA
21682042 AGAAGTGAAATGT
1 AGAAGTGAAATGT
21682055 AGAAG-GAAATGT
1 AGAAGTGAAATGT
21682067 AGAA
1 AGAA
21682071 ACCTATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (13 bp):
AGAAGTGAAATGT
Found at i:21696613 original size:23 final size:23
Alignment explanation
Indices: 21696539--21696613 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
21696529 TTGAGAACAT
* ** *
21696539 TAAACAAACATATTCACAAATGT
1 TAAACAAACATGTTTGCAAATGC
* ** *
21696562 TAAAAAGAACATGTTTGTGAATAC
1 TAAACA-AACATGTTTGCAAATGC
*
21696586 CAAACAAACATGTTTGCAAATGC
1 TAAACAAACATGTTTGCAAATGC
21696609 TAAAC
1 TAAAC
21696614 GAATTGATCC
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (23 bp):
TAAACAAACATGTTTGCAAATGC
Found at i:21703271 original size:15 final size:15
Alignment explanation
Indices: 21703251--21703280 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21703241 CTTATCAAAT
*
21703251 GGAACCTTTTACAAC
1 GGAACCTCTTACAAC
21703266 GGAACCTCTTACAAC
1 GGAACCTCTTACAAC
21703281 CTTAGCTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.23
Consensus pattern (15 bp):
GGAACCTCTTACAAC
Found at i:21711022 original size:40 final size:40
Alignment explanation
Indices: 21710978--21711098 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
21710968 GAAAGTTTGT
* *
21710978 TCAGGGGTACAAAAGTACAAATAGGGGCACGTATG-GTCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTG-CAA
*
21711018 TCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
* * **
21711058 TCAGGGGTACCGAAGTACAAACAGGGGAAATTATGTGCAA
1 TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
21711098 T
1 T
21711099 AATTTAATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 72 0.99
41 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.18
Consensus pattern (40 bp):
TCAGGGGTACAGAAGTACAAACAGGGGCACGTATGTGCAA
Found at i:21711023 original size:20 final size:20
Alignment explanation
Indices: 21711000--21711064 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
21710990 AAGTACAAAT
21711000 AGGGGCACGTATGGT-CAATC
1 AGGGGCACGTAT-GTACAATC
* * *
21711020 AGGGGTAC-TGAAGTACAAAC
1 AGGGGCACGT-ATGTACAATC
*
21711040 AGGGGCACGTATGTGCAATC
1 AGGGGCACGTATGTACAATC
21711060 AGGGG
1 AGGGG
21711065 TACCGAAGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.09
20 31 0.89
21 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.37, T:0.17
Consensus pattern (20 bp):
AGGGGCACGTATGTACAATC
Found at i:21711082 original size:20 final size:20
Alignment explanation
Indices: 21711019--21711084 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
21711009 TATGGTCAAT
*
21711019 CAGGGGTACTGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * *
21711039 CAGGGGCA-CGTATGTGCAAT
1 CAGGGGTACCG-AAGTACAAA
21711059 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
21711079 CAGGGG
1 CAGGGG
21711085 AAATTATGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.91
21 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.35, T:0.14
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:21711123 original size:21 final size:22
Alignment explanation
Indices: 21711099--21711139 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21711089 TATGTGCAAT
*
21711099 AATTTAATT-ATTAACTATAGA
1 AATTTAATTAAATAACTATAGA
21711120 AATTTAATTAAATAACTATA
1 AATTTAATTAAATAACTATA
21711140 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTAATTAAATAACTATAGA
Found at i:21717034 original size:17 final size:17
Alignment explanation
Indices: 21717012--21717046 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21717002 GTTTTTAATG
21717012 TAAACCAAGACCAAAAT
1 TAAACCAAGACCAAAAT
21717029 TAAACCAAGACCAAAAT
1 TAAACCAAGACCAAAAT
21717046 T
1 T
21717047 CTCTATCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.06, T:0.14
Consensus pattern (17 bp):
TAAACCAAGACCAAAAT
Found at i:21721389 original size:42 final size:43
Alignment explanation
Indices: 21721342--21721424 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 43
21721332 AGTTACACGG
21721342 CGTGTGTCCCTGTTTCGAATACTCACACGGCC-GAGACATGAC
1 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATGAC
21721384 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATG
1 CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATG
21721425 GGCGTGTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 32 0.80
43 8 0.20
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.25
Consensus pattern (43 bp):
CGTGTGTCCCTGTTTCGAATACTCACACGGCCTGAGACATGAC
Found at i:21726401 original size:42 final size:42
Alignment explanation
Indices: 21726322--21726404 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
21726312 TCAAAAAAAA
*
21726322 TCAAAAATCCCAAAAATATTTTCCATCTTTGTCTTTAATTTT
1 TCAAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTT
* * *
21726364 TCAAAAAT-CCAAAAATATTTTTCTTCATTGTTTTTTAATTT
1 TCAAAAATCCCAAAAATATTTTCCATCATTG-TCTTTAATTT
21726405 GTGTTATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 19 0.53
42 17 0.47
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (42 bp):
TCAAAAATCCCAAAAATATTTTCCATCATTGTCTTTAATTTT
Found at i:21735026 original size:26 final size:26
Alignment explanation
Indices: 21734991--21735050 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
21734981 ATTTTTCTTG
*
21734991 AAATTTTACCGGGGGTAAAATCATCA
1 AAATTTTACCGAGGGTAAAATCATCA
* *
21735017 AATTTTTACCGAGGGTAAAATTATCA
1 AAATTTTACCGAGGGTAAAATCATCA
21735043 AAATTTTA
1 AAATTTTA
21735051 TTGAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATCATCA
Found at i:21743447 original size:13 final size:13
Alignment explanation
Indices: 21743425--21743472 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
21743415 CAAAGGAGTA
*
21743425 TTTTTATTTTATT
1 TTTTTGTTTTATT
*
21743438 TTTTTGTTTTGCTT
1 TTTTTGTTTT-ATT
* *
21743452 TTTCTGTTTTTTT
1 TTTTTGTTTTATT
21743465 TTTTTGTT
1 TTTTTGTT
21743473 GAAAAGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.83
Consensus pattern (13 bp):
TTTTTGTTTTATT
Found at i:21743917 original size:7 final size:6
Alignment explanation
Indices: 21743901--21743951 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
21743891 TGTTTCCTGC
* *
21743901 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
21743951 A
1 A
21743952 GGAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 7 0.18
8 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:21746287 original size:21 final size:20
Alignment explanation
Indices: 21746263--21746302 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
21746253 AGTATTTTTA
*
21746263 TTTTTATTTTTTTTGTTTTGC
1 TTTTTATGTTTTTT-TTTTGC
*
21746284 TTTTTCTGTTTTTTTTTTG
1 TTTTTATGTTTTTTTTTTG
21746303 TTGAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.03, C:0.05, G:0.10, T:0.82
Consensus pattern (20 bp):
TTTTTATGTTTTTTTTTTGC
Found at i:21746749 original size:7 final size:6
Alignment explanation
Indices: 21746733--21746783 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
21746723 TGTTTCCTGC
* *
21746733 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
21746783 A
1 A
21746784 GGAAAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.56
7 7 0.18
8 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:21749157 original size:31 final size:29
Alignment explanation
Indices: 21749089--21749160 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
21749079 CTCAAGTTAT
* *
21749089 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTCAAATGTAAC
* **
21749118 GTTTTAGTCACTTATGTTATCATGTTGTAAC
1 ATTTTAGTCACTTATGTT-TCA-AATGTAAC
21749149 ATTTTAGTCACT
1 ATTTTAGTCACT
21749161 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 16 0.46
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTCAAATGTAAC
Found at i:21751825 original size:44 final size:44
Alignment explanation
Indices: 21751767--21751855 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
21751757 ATGGCCAAAT
21751767 CTTAAATAGGTGGCACTTTGAAATAAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGAAATAAACACAGGTTTTGTTCTTA
* *
21751811 CTTAAATAGGTGGCACTTTGGAATGAACACAGGTTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGAAATAAACACAGGTTTTGTTCTTA
21751855 C
1 C
21751856 ATATGCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (44 bp):
CTTAAATAGGTGGCACTTTGAAATAAACACAGGTTTTGTTCTTA
Found at i:21758854 original size:17 final size:17
Alignment explanation
Indices: 21758804--21758854 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
21758794 AAATGATGAA
*
21758804 AAGATAAAAAG-TATAT
1 AAGATAAAAAGAAATAT
*
21758820 CAA-ATAAAAA-AAAGAT
1 -AAGATAAAAAGAAATAT
21758836 AAGATAAAAAGAAATAT
1 AAGATAAAAAGAAATAT
21758853 AA
1 AA
21758855 TTAACCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.07
16 17 0.61
17 9 0.32
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.18
Consensus pattern (17 bp):
AAGATAAAAAGAAATAT
Found at i:21763168 original size:11 final size:11
Alignment explanation
Indices: 21763105--21763166 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
21763095 ATAAATCCTT
21763105 TCTCTAATTTCC
1 TCTC-AATTTCC
21763117 TCTCAATTTCC
1 TCTCAATTTCC
* *
21763128 ACTCAATTTGC
1 TCTCAATTTCC
*
21763139 TCTCAATTTGC
1 TCTCAATTTCC
21763150 TCTCAAATTT-C
1 TCTC-AATTTCC
21763161 TCTCAA
1 TCTCAA
21763167 ATCCCTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
10 2 0.04
11 35 0.76
12 9 0.20
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:21765821 original size:29 final size:27
Alignment explanation
Indices: 21765762--21765825 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
21765752 TTCTTGATTT
*
21765762 ATATTATAAAAATATTATTTAATTAAA
1 ATATTATAAAAATATTATTAAATTAAA
* *
21765789 ATATTATAAATTATATTAATTAAATTAAG
1 ATATTATAAA-AATATT-ATTAAATTAAA
21765818 ATATTATA
1 ATATTATA
21765826 TTATTAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 10 0.31
28 5 0.16
29 17 0.53
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATATTATAAAAATATTATTAAATTAAA
Found at i:21766817 original size:3 final size:3
Alignment explanation
Indices: 21766809--21766837 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21766799 ATTAGGTAAG
21766809 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21766838 AGATGAGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21768078 original size:8 final size:8
Alignment explanation
Indices: 21768065--21768091 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
21768055 TAAAATATTA
21768065 TATGATTT
1 TATGATTT
21768073 TATGATTT
1 TATGATTT
21768081 TATGATTT
1 TATGATTT
21768089 TAT
1 TAT
21768092 TTTAATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TATGATTT
Found at i:21771501 original size:124 final size:130
Alignment explanation
Indices: 21771316--21771614 Score: 403
Period size: 134 Copynumber: 2.3 Consensus size: 130
21771306 CAGGCCATGC
* * * *
21771316 GCCACTGTAGTAAAAGCACGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATTTT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCTT
*
21771381 GCTTAAA-G-C-A-TTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTT-TCAGGA
66 GCTTAAAGGTCAACTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTCTCAGAA
* * * *
21771441 GCTACTGTAGCAAAAGCGCATCCACGTGGAAG-TTTTTTTAGTACTTCTGCTGACAAAGCATCTT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCTT
21771505 GCTTAAAGTGTCTTAAAACGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTC
66 GCTTAAAG-GTC----AAC-TTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTC
21771570 TCAGAA
125 TCAGAA
**
21771576 GCCACTGTAGCAAAAGCGCGTCCACGTGGGTGCTTCTTT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGAAGCTTCTTT
21771615 AAATTAACAA
Statistics
Matches: 148, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
124 36 0.24
125 27 0.18
126 1 0.01
127 1 0.01
132 1 0.01
134 44 0.30
135 33 0.22
136 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (130 bp):
GCCACTGTAGCAAAAGCGCGTCCACGTGGAAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCTT
GCTTAAAGGTCAACTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATTATTTTCTCAGAA
Found at i:21776493 original size:23 final size:19
Alignment explanation
Indices: 21776467--21776516 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 19
21776457 CCGGCCCATT
21776467 TTTTAATAAACACAAAAAATTTA
1 TTTTAA-AAACA-AAAAAA--TA
*
21776490 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
21776509 TTTTAAAA
1 TTTTAAAA
21776517 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
21 6 0.23
22 4 0.15
23 6 0.23
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Found at i:21776510 original size:19 final size:18
Alignment explanation
Indices: 21776488--21776523 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
21776478 ACAAAAAATT
21776488 TATTTTAAAAATAAAAAAA
1 TATTTT-AAAATAAAAAAA
21776507 TATTTTAAAATAAAAAA
1 TATTTTAAAATAAAAAA
21776524 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TATTTTAAAATAAAAAAA
Found at i:21776528 original size:25 final size:26
Alignment explanation
Indices: 21776494--21776544 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
21776484 AATTTATTTT
21776494 AAAAATAAAAAAATAT-TTTAAAATA
1 AAAAATAAAAAAATATATTTAAAATA
*
21776519 AAAAATAAAAAAATATATTTATAATA
1 AAAAATAAAAAAATATATTTAAAATA
21776545 TTCGGGCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATAAAAAAATATATTTAAAATA
Found at i:21779704 original size:18 final size:18
Alignment explanation
Indices: 21779677--21779713 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21779667 AAGTGACAAG
*
21779677 TGGTAGCTTTAGCTACAC
1 TGGTAACTTTAGCTACAC
21779695 TGGTAACTTTAGCTACAC
1 TGGTAACTTTAGCTACAC
21779713 T
1 T
21779714 TATCTGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (18 bp):
TGGTAACTTTAGCTACAC
Found at i:21779846 original size:45 final size:45
Alignment explanation
Indices: 21779704--21779877 Score: 255
Period size: 46 Copynumber: 3.9 Consensus size: 45
21779694 CTGGTAACTT
*
21779704 TAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC
1 TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
21779749 TCAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
1 T-AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
* *
21779795 TTAGCTACACTTATCTGATCAAGT-AAAAAGGTGACAAGTGGTAGTC
1 -TAGCTACACTTATCTGATCAAGTGAAAAA-GTGATAAGTGGTAGCC
* *
21779841 TAGCTACACTTATCTGATTAAG-G-ACAAGTGATAAGTG
1 TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
21779878 ATCATACGTA
Statistics
Matches: 119, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
43 9 0.08
44 3 0.03
45 27 0.23
46 79 0.66
47 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (45 bp):
TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGGTAGCC
Found at i:21782474 original size:21 final size:22
Alignment explanation
Indices: 21782448--21782502 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
21782438 AAATAGGGTG
21782448 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
21782469 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
*
21782490 GCAGTGAGATTAG
1 GCGGTGAGATTAG
21782503 AAACAACAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.90
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:21786715 original size:12 final size:13
Alignment explanation
Indices: 21786692--21786730 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
21786682 TTTGCAACCC
*
21786692 AAGGGGAAGGGGA
1 AAGGGAAAGGGGA
21786705 AA-GGAAAGGGGA
1 AAGGGAAAGGGGA
21786717 AAGGGGAAAGGGGA
1 AA-GGGAAAGGGGA
21786731 GAAGAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (13 bp):
AAGGGAAAGGGGA
Done.