Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 146 of 193
Found at i:45546761 original size:18 final size:18
Alignment explanation
Indices: 45546738--45546778 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45546728 TTTAATATGA
45546738 CTTTTT-GGTTCAAAAGTG
1 CTTTTTAGGTT-AAAAGTG
*
45546756 CTTTTTATGTTAAAAGTG
1 CTTTTTAGGTTAAAAGTG
45546774 CTTTT
1 CTTTT
45546779 AAAAAGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (18 bp):
CTTTTTAGGTTAAAAGTG
Found at i:45553367 original size:6 final size:6
Alignment explanation
Indices: 45553356--45553394 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
45553346 TGATCAAAAT
* * *
45553356 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
45553395 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:45561021 original size:16 final size:16
Alignment explanation
Indices: 45561002--45561040 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
45560992 ATATAAATAT
45561002 TTTTTAATGCATTATA
1 TTTTTAATGCATTATA
* *
45561018 TTTTTAGTGGATTATA
1 TTTTTAATGCATTATA
45561034 TTTTTAA
1 TTTTTAA
45561041 ATAAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (16 bp):
TTTTTAATGCATTATA
Found at i:45569399 original size:24 final size:24
Alignment explanation
Indices: 45569372--45569422 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45569362 AAAATTTAAA
* *
45569372 ATTTATTAGCATAATATATTTGTT
1 ATTTACTAGCATAAAATATTTGTT
*
45569396 ATTTACTAGCATAAAATCTTTGTT
1 ATTTACTAGCATAAAATATTTGTT
45569420 ATT
1 ATT
45569423 ACTTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTACTAGCATAAAATATTTGTT
Found at i:45570481 original size:33 final size:33
Alignment explanation
Indices: 45570443--45570520 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
45570433 CCCCTAAATG
* * *
45570443 ATTGTTTATTTTATTAATTTTATTTTCATTAAA
1 ATTGTTTATTTTACTAATTTCATTTTCACTAAA
* * *
45570476 TTTG-TTATTTTCCTAATTTCATTTTGACTAAA
1 ATTGTTTATTTTACTAATTTCATTTTCACTAAA
*
45570508 ATTATTTATTTTA
1 ATTGTTTATTTTA
45570521 AGTAAATAGG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTGTTTATTTTACTAATTTCATTTTCACTAAA
Found at i:45589081 original size:35 final size:35
Alignment explanation
Indices: 45589035--45589105 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
45589025 AAATTTAACA
* *
45589035 TAGTTATATTAACAATGTAGGACTGCAGGAACACG
1 TAGTTATATTAACAATATAGAACTGCAGGAACACG
45589070 TAGTTATATTAACAATATAGAACTGCAGGAACACG
1 TAGTTATATTAACAATATAGAACTGCAGGAACACG
45589105 T
1 T
45589106 CTTTAGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
TAGTTATATTAACAATATAGAACTGCAGGAACACG
Found at i:45591322 original size:86 final size:86
Alignment explanation
Indices: 45591228--45591397 Score: 304
Period size: 86 Copynumber: 2.0 Consensus size: 86
45591218 CTTTTTTGTC
*
45591228 AAGTTATTTTAAAATGAATGAAAAAATTAACGTTTGTAAATTTTATTGATGCAGCATGCTCATAG
1 AAGTTATTTTAAAATGAATGAAAAAATTAACGTTTATAAATTTTATTGATGCAGCATGCTCATAG
45591293 ATTACCATGTAAATGACATAA
66 ATTACCATGTAAATGACATAA
*
45591314 AAGTTATTTTAAAATGAATGGAAAAATTAACGTTTATAAATTTTATTGATGCAGCATGCTCATAG
1 AAGTTATTTTAAAATGAATGAAAAAATTAACGTTTATAAATTTTATTGATGCAGCATGCTCATAG
* *
45591379 ATTACTATGTAGATGACAT
66 ATTACCATGTAAATGACAT
45591398 GTTATTATTC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (86 bp):
AAGTTATTTTAAAATGAATGAAAAAATTAACGTTTATAAATTTTATTGATGCAGCATGCTCATAG
ATTACCATGTAAATGACATAA
Found at i:45593829 original size:2 final size:2
Alignment explanation
Indices: 45593822--45593858 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45593812 ACAAGTATCT
45593822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45593859 TTTTTAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45595272 original size:14 final size:15
Alignment explanation
Indices: 45595244--45595272 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45595234 ATTGTTAAAA
45595244 TTGTTAAAGTTTTTT
1 TTGTTAAAGTTTTTT
45595259 TTGTTAAA-TTTTTT
1 TTGTTAAAGTTTTTT
45595273 GTGTGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTAAAGTTTTTT
Found at i:45597094 original size:17 final size:17
Alignment explanation
Indices: 45597072--45597138 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
45597062 ACCATTTTAG
*
45597072 AATTTACTTTAAAATTA
1 AATTTAATTTAAAATTA
* *
45597089 AATTTATTTTAAATTTA
1 AATTTAATTTAAAATTA
*
45597106 AATTTAATTT-AAGTTA
1 AATTTAATTTAAAATTA
45597122 GAATTTAATTTAAAATT
1 -AATTTAATTTAAAATT
45597139 TAATATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
16 5 0.12
17 34 0.79
18 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAAATTA
Found at i:45597142 original size:12 final size:12
Alignment explanation
Indices: 45597088--45597142 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
45597078 CTTTAAAATT
*
45597088 AAATTT-ATTTT
1 AAATTTAATTTA
45597099 AAATTTAAATTT-
1 AAATTT-AATTTA
*
45597111 -AATTTAAGTTA
1 AAATTTAATTTA
*
45597122 GAATTTAATTTA
1 AAATTTAATTTA
45597134 AAATTTAAT
1 AAATTTAAT
45597143 ATTATTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.11
11 11 0.30
12 18 0.49
13 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:45597883 original size:21 final size:21
Alignment explanation
Indices: 45597846--45597888 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45597836 AATAACGTTT
*
45597846 TAATATCAATACTATTATTAA
1 TAATATCAATACTATTAATAA
*
45597867 TAATATTAATGAC-ATTAATAA
1 TAATATCAAT-ACTATTAATAA
45597888 T
1 T
45597889 TATTAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TAATATCAATACTATTAATAA
Found at i:45598148 original size:16 final size:16
Alignment explanation
Indices: 45598127--45598160 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
45598117 GTTTTGAATC
45598127 TTTTTCCAGATCTAGG
1 TTTTTCCAGATCTAGG
*
45598143 TTTTTCCAGATCTGGG
1 TTTTTCCAGATCTAGG
45598159 TT
1 TT
45598161 CGGTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (16 bp):
TTTTTCCAGATCTAGG
Found at i:45598971 original size:162 final size:162
Alignment explanation
Indices: 45598704--45599042 Score: 570
Period size: 162 Copynumber: 2.1 Consensus size: 162
45598694 AGCTTTCAGT
* * * * **
45598704 TTAGTCCTTTGACTGTTTGACTGTACTAGAGGTTGCCACGTGTCACTTTTTGGATTATTTTTGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCACTTTTTAGATTATTTACGCA
45598769 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
*
45598834 AATTGGCCCAAGAATTTTTCAAGGTTTATAAA
131 AATTGGCCCAAGAATTTTTCAAGGTTTACAAA
* *
45598866 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGTTACCACGTGTCACTTTTTAGCTTATTTACGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCACTTTTTAGATTATTTACGCA
45598931 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
* *
45598996 AATTGGCCCAAGAATTTTTCGAGGTTTACAAT
131 AATTGGCCCAAGAATTTTTCAAGGTTTACAAA
*
45599028 TTAATCCTTTGACTG
1 TTAGTCCTTTGACTG
45599043 CTGGATGCCT
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 165 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGAGGTTACCACGTGTCACTTTTTAGATTATTTACGCA
TTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
AATTGGCCCAAGAATTTTTCAAGGTTTACAAA
Found at i:45599177 original size:29 final size:28
Alignment explanation
Indices: 45599111--45599190 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
45599101 CCCCAAACAG
*
45599111 TCCAAAAATTGCATTTTGACCCTAAAAT
1 TCCAAAAATTACATTTTGACCCTAAAAT
** * *
45599139 TTTAGGAAATTACATTTTGACCCTGAAACT
1 TCCA-AAAATTACATTTTGACCCT-AAAAT
45599169 TCCAAAAATTACCATTTT-ACCC
1 TCCAAAAATTA-CATTTTGACCC
45599191 CCGAACCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 2 0.05
29 27 0.66
30 12 0.29
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (28 bp):
TCCAAAAATTACATTTTGACCCTAAAAT
Found at i:45599205 original size:29 final size:28
Alignment explanation
Indices: 45599145--45599417 Score: 146
Period size: 29 Copynumber: 9.4 Consensus size: 28
45599135 AAATTTTAGG
* * *
45599145 AAATTACATTTTGA-CCCTGAAACTTCCAA
1 AAATTCCATTTT-ACCCCCGAATCTTCC-A
* *
45599174 AAATTACCATTTTACCCCCGAACCTTCTA
1 AAATT-CCATTTTACCCCCGAATCTTCCA
* *
45599203 AAATTTCATTTTTAACCCCG-AT-TTCACCGA
1 AAATTCCA-TTTTACCCCCGAATCTT--CC-A
* * *
45599233 AAATTACCATTTTACCCTCGAACCTTCTA
1 AAATT-CCATTTTACCCCCGAATCTTCCA
* ** *
45599262 AAATTCCATTTTTAACCCCTGTTTC-ACCA
1 AAATTCCA-TTTT-ACCCCCGAATCTTCCA
* * *
45599291 AAATTACCATTTTACCCCTGAAACTTCTA
1 AAATT-CCATTTTACCCCCGAATCTTCCA
* *
45599320 AAATTCCATTTTTAACCCCG-GT-TTCACCA
1 AAATTCCA-TTTTACCCCCGAATCTT--CCA
45599349 AAATTACCATTTTACCCCCGAATCTTCCA
1 AAATT-CCATTTTACCCCCGAATCTTCCA
***
45599378 AAATTCCATTTTTGACCCGAAT-TTCTCA
1 AAATTCCATTTTACCCCCGAATCTTC-CA
*
45599406 AAATTACATTTT
1 AAATTCCATTTT
45599418 TGCCCCTAAG
Statistics
Matches: 188, Mismatches: 36, Indels: 41
0.71 0.14 0.15
Matches are distributed among these distances:
27 7 0.04
28 44 0.23
29 85 0.45
30 45 0.24
31 5 0.03
32 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.35
Consensus pattern (28 bp):
AAATTCCATTTTACCCCCGAATCTTCCA
Found at i:45599207 original size:58 final size:58
Alignment explanation
Indices: 45599173--45599417 Score: 354
Period size: 58 Copynumber: 4.2 Consensus size: 58
45599163 GAAACTTCCA
*
45599173 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTTCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACC
*
45599231 GAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCCCTG-TTTCACC
1 -AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCC-GATTTCACC
* * *
45599290 AAAATTACCATTTTACCCCTGAAACTTCTAAAATTCCATTTTTAACCCCGGTTTCACC
1 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
45599348 AAAATTACCATTTTACCCCCGAATCTTCCAAAATTCCATTTTTGA-CCCGAATTTC-TC
1 AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCG-ATTTCACC
45599405 AAAATTA-CATTTT
1 AAAATTACCATTTT
45599418 TGCCCCTAAG
Statistics
Matches: 172, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
56 6 0.03
57 13 0.08
58 98 0.57
59 54 0.31
60 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACCTTCTAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:45599396 original size:28 final size:27
Alignment explanation
Indices: 45599319--45599419 Score: 87
Period size: 28 Copynumber: 3.6 Consensus size: 27
45599309 TGAAACTTCT
* *
45599319 AAAATTCCATTTTTAACCCCG-GTTTCACC
1 AAAATTCCATTTTTGA-CCCGAATTT--CC
***
45599348 AAAATTACCATTTTACCCCCGAATCTTCC
1 AAAATT-CCATTTTTGACCCGAAT-TTCC
45599377 AAAATTCCATTTTTGACCCGAATTTCTC
1 AAAATTCCATTTTTGACCCGAATTTC-C
*
45599405 AAAATTACATTTTTG
1 AAAATTCCATTTTTG
45599420 CCCCTAAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.05
28 29 0.48
29 18 0.30
30 8 0.13
31 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (27 bp):
AAAATTCCATTTTTGACCCGAATTTCC
Found at i:45604054 original size:17 final size:18
Alignment explanation
Indices: 45604026--45604071 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
45604016 AAACCCAAAT
*
45604026 AAAAAAAGAAAAAAG-AG
1 AAAAAAACAAAAAAGAAG
*
45604043 AACAAAAC-AAAAAGAAG
1 AAAAAAACAAAAAAGAAG
45604060 AAAAAAACAAAA
1 AAAAAAACAAAA
45604072 CAAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.83, C:0.07, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAGAAG
Found at i:45604054 original size:22 final size:21
Alignment explanation
Indices: 45604028--45604077 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 21
45604018 ACCCAAATAA
45604028 AAAAAGAAAAAAGAGAACAAAAC
1 AAAAAGAAAAAA-A-AACAAAAC
45604051 AAAAAGAAGAAAAAAACAAAAC
1 AAAAAGAA-AAAAAAACAAAAC
45604073 AAAAA
1 AAAAA
45604078 AAAGGAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.50
23 9 0.35
24 4 0.15
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAGAAAAAAAAACAAAAC
Found at i:45606222 original size:28 final size:27
Alignment explanation
Indices: 45606165--45606250 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 27
45606155 GCACCACAAT
**
45606165 GTAAAATGGAATTTTGGGAAGTTTGGGG
1 GTAAAATGGAATTTT-GGAAGTTTTAGG
45606193 GTAAAATGGTAATTTTGGAAGTTTTAGG
1 GTAAAATGG-AATTTTGGAAGTTTTAGG
*
45606221 GTCAAAAATGAAATTTTGGAAAG-TTTAGG
1 GT--AAAATGGAATTTTGG-AAGTTTTAGG
45606250 G
1 G
45606251 ATCAGAATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 21 0.41
29 21 0.41
30 9 0.18
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.34
Consensus pattern (27 bp):
GTAAAATGGAATTTTGGAAGTTTTAGG
Found at i:45606227 original size:29 final size:28
Alignment explanation
Indices: 45606167--45606265 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 28
45606157 ACCACAATGT
* **
45606167 AAAATGGAATTTTGGGAAGTTTGGGGGT-
1 AAAATGTAATTTT-GGAAGTTTTAGGGTC
45606195 AAAATGGTAATTTTGGAAGTTTTAGGGTC
1 AAAAT-GTAATTTTGGAAGTTTTAGGGTC
*
45606224 AAAAATGAAATTTTGGAAAG-TTTAGGGATC
1 -AAAATGTAATTTTGG-AAGTTTTAGGG-TC
*
45606254 AGAATGTAATTT
1 AAAATGTAATTT
45606266 CCTAAAACTT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
28 17 0.28
29 33 0.55
30 10 0.17
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAGTTTTAGGGTC
Found at i:45606667 original size:163 final size:163
Alignment explanation
Indices: 45606367--45606709 Score: 483
Period size: 163 Copynumber: 2.1 Consensus size: 163
45606357 AGGCATCCAG
* * * *
45606367 CAGTCAAGGGACTAA-ATTATAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAG
1 CAGTCAAAGGACTAATTTTAAAAAGCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAG
** * * * *
45606431 TTGATTTAAGGATTAAATGAAAACAAATTAAAAATGTCAGGGACTAAATGCACAAATAAGCTTAA
66 TTGATTTAAGGATTAAATGAAAACAAATTAAAAATAACAGGGACCAAATACACAAATAAACTCAA
*
45606496 AAGTGACACGTGGCAGCCTCTGGTGCAGTCAAA
131 AAGTGACACGTAGCAGCCTCTGGTGCAGTCAAA
* * *
45606529 CAGTCAAAGGACTAATTTTAAAAAGCTTGATAAATTCTTGGGCTAATTTTGTAATTAAATAAAAG
1 CAGTCAAAGGACTAATTTTAAAAAGCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAG
* * * * *
45606594 TTGATTTAGGGATTAAATTAAAACAATTTAAAAATAACAGGGACCAGATACATAAATAAAC-CAA
66 TTGATTTAAGGATTAAATGAAAACAAATTAAAAATAACAGGGACCAAATACACAAATAAACTCAA
45606658 GAAGTGACACGTAGCAGCCTCTGGTGCAGTCAAA
131 -AAGTGACACGTAGCAGCCTCTGGTGCAGTCAAA
45606692 CAGTCAAAGGACTGAATT
1 CAGTCAAAGGACT-AATT
45606710 GAAAACTAAT
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
162 16 0.10
163 139 0.87
164 4 0.03
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (163 bp):
CAGTCAAAGGACTAATTTTAAAAAGCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAG
TTGATTTAAGGATTAAATGAAAACAAATTAAAAATAACAGGGACCAAATACACAAATAAACTCAA
AAGTGACACGTAGCAGCCTCTGGTGCAGTCAAA
Found at i:45606985 original size:9 final size:9
Alignment explanation
Indices: 45606959--45606988 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
45606949 CAAAAATTCT
*
45606959 CTCTTCTCT
1 CTCTTCTCA
45606968 CTCTTCTCA
1 CTCTTCTCA
45606977 CTCTTCTCA
1 CTCTTCTCA
45606986 CTC
1 CTC
45606989 CTAATGGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.47, G:0.00, T:0.47
Consensus pattern (9 bp):
CTCTTCTCA
Found at i:45608251 original size:11 final size:11
Alignment explanation
Indices: 45608235--45608310 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
45608225 TTATAATAAT
45608235 ATTAAATTTAA
1 ATTAAATTTAA
*
45608246 ATTAAATTCAA
1 ATTAAATTTAA
*
45608257 ATTAAAATTAAA
1 ATT-AAATTTAA
*
45608269 ATTGAATTTAA
1 ATTAAATTTAA
*
45608280 AATAAATTTAA
1 ATTAAATTTAA
*
45608291 GATTAAA-ATAA
1 -ATTAAATTTAA
*
45608302 ATTTAATTT
1 ATTAAATTT
45608311 TCAAATGGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
10 5 0.10
11 32 0.62
12 15 0.29
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:45608258 original size:17 final size:16
Alignment explanation
Indices: 45608219--45608310 Score: 71
Period size: 17 Copynumber: 5.5 Consensus size: 16
45608209 ACTTTTCTTT
45608219 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
45608236 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
*
45608252 TTCAAATTAAAATTAAAA
1 TT-AAATTTAAATT-AAA
* *
45608270 TTGAATTTAAAATAAA
1 TTAAATTTAAATTAAA
*
45608286 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
45608303 TTTAATTT
1 TTAAATTT
45608311 TCAAATGGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.02
16 13 0.21
17 43 0.68
18 6 0.10
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:45610676 original size:6 final size:6
Alignment explanation
Indices: 45610665--45610709 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
45610655 TGATCAAAAT
*
45610665 TGAAAG TGAAAG TGAAAG TGAAAG TG-AAG TTGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG -TGAAAG TGAAAG TGA
45610710 TATGAATTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 3 0.09
6 30 0.86
7 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:45620837 original size:59 final size:58
Alignment explanation
Indices: 45620751--45621172 Score: 468
Period size: 58 Copynumber: 7.2 Consensus size: 58
45620741 ACCCGAGGGC
* * *
45620751 AAAATGGTAA-TTTTGGTGAAGTCGGGGTTAAAAAATAGAATTTTTGAGAGTTCGGGGCT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTAGAGAGTTCGGGG-T
* * *
45620810 -AAACGGTAATTTTTGATGAAA-CTGGGGTTAAAAAT-GATATTTTAGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGA-ATTTTAGAGAGTTC-GGGGT
* ** *
45620868 AAAATGGTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGA-AGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTCG-GGGT
* * *
45620926 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGAAATTTTGGA-AGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTCG-GGGT
* *
45620983 AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGA-AGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTC-GGGGT
* * * * * *
45621041 AAAATGGTAATTTTCGATGAAA-CTGAGGTTAAAAATGGTATTTTAGAAGATTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTAG-AGAGTTCGGGGT
*
45621100 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GGGAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAG-AGTTC-GGGGT
45621159 AAAATGGTAATTTT
1 AAAATGGTAATTTT
45621173 GGAAGTTTAG
Statistics
Matches: 318, Mismatches: 29, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
57 60 0.19
58 132 0.42
59 120 0.38
60 6 0.02
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAGAGTTCGGGGT
Found at i:45621144 original size:232 final size:233
Alignment explanation
Indices: 45620744--45621172 Score: 661
Period size: 232 Copynumber: 1.8 Consensus size: 233
45620734 TTTGGACACC
* * *
45620744 CGAGGGCAAAATGGTAATTTTGGTGAAGTCGGGGTTAAAAAATAGAATTTTTGAGAGTTCGGGGC
1 CGAGGGCAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGGC
* *
45620809 TAAACGGTAATTTTTGATGAAACTGGGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
66 TAAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
45620874 GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTT-GGAAGTTC-GAGGGTAAAATGGTAAT
131 GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGGAAGTTCAG-GGGTAAAATGGTAAT
45620937 TTTTGGTGAAATCGAGGTTAAAATGAAATTTTGGAAGTT
195 TTTTGGTGAAATCGAGGTTAAAATGAAATTTTGGAAGTT
* *
45620976 CGAGGGTAAAATGGTAAATTTTGGTGAAATCGAGGTT-AAAAATGGAATTTTAGA-AGTTCGGGG
1 CGAGGGCAAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGG
* * * *
45621039 GTAAAATGGTAATTTTCGATGAAACTGAGGTTAAAAATGGTATTTTAG-AAGATTTAGGGGTAAA
65 CT-AAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAG-TTCAGGGGTAAA
* **
45621103 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCAGGGGTAAAATGGTA
128 ATGGTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGGAAGTTCAGGGGTAAAATGGTA
45621168 ATTTT
193 ATTTT
45621173 GGAAGTTTAG
Statistics
Matches: 178, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
231 13 0.07
232 119 0.67
233 45 0.25
234 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (233 bp):
CGAGGGCAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGGC
TAAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGGAAGTTCAGGGGTAAAATGGTAATT
TTTGGTGAAATCGAGGTTAAAATGAAATTTTGGAAGTT
Found at i:45621194 original size:29 final size:27
Alignment explanation
Indices: 45620856--45621215 Score: 132
Period size: 29 Copynumber: 12.4 Consensus size: 27
45620846 ATATTTTAGA
45620856 AAGTTCAGGGGTAAAATGGTAATCTTTGGTG
1 AAGTTCAGGGGTAAAATGG-AAT-TTT-G-G
* **
45620887 AA-ATC-GGGGTTAAAAATAAAATTTTGG
1 AAGTTCAGGGG-T-AAAATGGAATTTTGG
45620914 AAGTTC-GAGGGTAAAATGGTAATTTTTGGTG
1 AAGTTCAG-GGGTAAAATGG-AA-TTTT-G-G
* * *
45620945 AA-ATC-GAGGTTAAAATGAAATTTTGG
1 AAGTTCAG-GGGTAAAATGGAATTTTGG
45620971 AAGTTC-GAGGGTAAAATGGTAAATTTTGGTG
1 AAGTTCAG-GGGTAAAATGG--AATTTT-G-G
* * *
45621002 AA-ATC-GAGGTTAAAAATGGAATTTTAG
1 AAGTTCAG-GGGT-AAAATGGAATTTTGG
*
45621029 AAGTTCGGGGGTAAAATGGTAATTTTCGATG
1 AAGTTCAGGGGTAAAATGG-AATTTT-G--G
** * * * *
45621060 AAACTGA-GGTTAAAAATGGTATTTTAG
1 AAGTTCAGGGGT-AAAATGGAATTTTGG
*
45621087 AAGATTTAGGGGTAAAATGGTAATTTTTGGTG
1 AAG-TTCAGGGGTAAAATGG-AA-TTTT-G-G
*
45621119 AA-ATC-GGGGTTAAAAATGGAATTTTGGG
1 AAGTTCAGGGG-T-AAAATGGAATTTT-GG
45621147 AAGTTCAGGGGTAAAATGGTAATTTTGG
1 AAGTTCAGGGGTAAAATGG-AATTTTGG
*
45621175 AAGTTTA-GGGTCAAATATGGAATTTTGG
1 AAGTTCAGGGGT-AAA-ATGGAATTTTGG
*
45621203 AAAGTTCGGGGGT
1 -AAGTTCAGGGGT
45621216 CAGAATGTAA
Statistics
Matches: 256, Mismatches: 37, Indels: 73
0.70 0.10 0.20
Matches are distributed among these distances:
26 3 0.01
27 39 0.15
28 60 0.23
29 61 0.24
30 52 0.20
31 38 0.15
32 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (27 bp):
AAGTTCAGGGGTAAAATGGAATTTTGG
Found at i:45621201 original size:232 final size:233
Alignment explanation
Indices: 45620744--45621228 Score: 646
Period size: 232 Copynumber: 2.1 Consensus size: 233
45620734 TTTGGACACC
* * * *
45620744 CGAGGGCAAAATGGTAATTTTGGTGAAGTCGGGGTTAAAAAATAGAATTTTTGAGAGTTCGGGGC
1 CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGGC
* *
45620809 TAAACGGTAATTTTTGATGAAACTGGGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
66 TAAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
45620874 GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGAAGTTCGAGGGTAAAATGGTAATTT
131 GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGAAGTTCGAGGGTAAAATGGTAATTT
*
45620939 TTGGTGAAATCGAGGTTAAAATGAAATTTTGG-AAGTT
196 TTGGTGAAATCGAGGTCAAAATGAAATTTTGGAAAGTT
*
45620976 CGAGGGTAAAATGGTAAATTTTGGTGAAATCGAGGTT-AAAAATGGAATTTTAGA-AGTTCGGGG
1 CGAGGGTAAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGG
* * * *
45621039 GTAAAATGGTAATTTTCGATGAAACTGAGGTTAAAAATGGTATTTTAG-AAGATTTAGGGGTAAA
65 CT-AAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAG-TTCAGGGGTAAA
* **
45621103 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTC-AGGGGTAAAATGGT
128 ATGGTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTT-GGAAGTTCGA-GGGTAAAATGGT
* ** *
45621167 AA-TTTT-G-GAAGTTTAGGGTCAAATATGGAATTTTGGAAAGTT
191 AATTTTTGGTGAAATCGA-GGTCAAA-ATGAAATTTTGGAAAGTT
* *
45621209 CGGGGGTCAGAAT-GTAATTT
1 CGAGGGT-AAAATGGTAATTT
45621229 CCTAAAATTT
Statistics
Matches: 223, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
230 5 0.02
231 20 0.09
232 140 0.63
233 54 0.24
234 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (233 bp):
CGAGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAAATAGAATTTTAGAGAGTTCGGGGC
TAAACGGTAATTTTCGATGAAACTGAGGTTAAAAATGATATTTTAGAAAGTTCAGGGGTAAAATG
GTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGAAGTTCGAGGGTAAAATGGTAATTT
TTGGTGAAATCGAGGTCAAAATGAAATTTTGGAAAGTT
Found at i:45621215 original size:57 final size:57
Alignment explanation
Indices: 45620751--45621228 Score: 455
Period size: 58 Copynumber: 8.2 Consensus size: 57
45620741 ACCCGAGGGC
* * * * * *
45620751 AAAATGGTAATTTTGGTGAAGTCGGGGTTAAAAAATAGAATTTTTGAGAGTTCGGGGCT
1 AAAATGGTAATTTTGGTGAAATTGAGGTT-AAAAATGGAATTTTGGA-AGTTCGGGGGT
* * * * * *
45620810 -AAACGGTAATTTTTGATGAAACTGGGGTTAAAAAT-GATATTTTAGAAAGTTCAGGGGT
1 AAAATGGTAA-TTTTGGTGAAATTGAGGTTAAAAATGGA-ATTTT-GGAAGTTCGGGGGT
* * ** *
45620868 AAAATGGTAATCTTTGGTGAAATCGGGGTTAAAAATAAAATTTTGGAAGTTCGAGGGT
1 AAAATGGTAAT-TTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGT
* * *
45620926 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGAAATTTTGGAAGTTCGAGGGT
1 AAAATGGTAA-TTTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGT
* *
45620983 AAAATGGTAAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGTTCGGGGGT
1 AAAATGGT-AATTTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGT
* * * * **
45621041 AAAATGGTAATTTTCGATGAAACTGAGGTTAAAAATGGTATTTTAGAAGATTTAGGGGT
1 AAAATGGTAATTTT-GGTGAAATTGAGGTTAAAAATGGAATTTTGGAAG-TTCGGGGGT
* * *
45621100 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCAGGGGT
1 AAAATGGTAA-TTTTGGTGAAATTGAGGTTAAAAATGGAATTTT-GGAAGTTCGGGGGT
* * * *
45621159 AAAATGGTAATTTT-G-GAAGTTTAGGGTCAAATATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATTGA-GGTTAAAAATGGAATTTTGG-AAGTTCGGGGGT
*
45621216 CAGAAT-GTAATTT
1 -AAAATGGTAATTT
45621229 CCTAAAATTT
Statistics
Matches: 360, Mismatches: 43, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
56 6 0.02
57 96 0.27
58 139 0.39
59 110 0.31
60 9 0.03
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTGAAATTGAGGTTAAAAATGGAATTTTGGAAGTTCGGGGGT
Found at i:45621227 original size:29 final size:28
Alignment explanation
Indices: 45621014--45621228 Score: 111
Period size: 28 Copynumber: 7.4 Consensus size: 28
45621004 ATCGAGGTTA
* *
45621014 AAAATGGAATTTTAGAAGTTCGGGGGT-
1 AAAATGGAATTTTGGAAGTTCAGGGGTC
** * * *
45621041 AAAATGGTAATTTTCGATGAAACTGA-GGTTA
1 AAAATGG-AATTTT-G--GAAGTTCAGGGGTC
* * *
45621072 AAAATGGTATTTTAGAAGATTTAGGGGT-
1 AAAATGGAATTTTGGAAG-TTCAGGGGTC
* *
45621100 AAAATGGTAATTTTTGGTGAA-ATC-GGGGTTA
1 AAAATGG-AA-TTTT-G-GAAGTTCAGGGG-TC
45621131 AAAATGGAATTTTGGGAAGTTCAGGGGT-
1 AAAATGGAATTTT-GGAAGTTCAGGGGTC
*
45621159 AAAATGGTAATTTTGGAAGTTTA-GGGTC
1 AAAATGG-AATTTTGGAAGTTCAGGGGTC
*
45621187 AAATATGGAATTTTGGAAAGTTCGGGGGTC
1 AAA-ATGGAATTTTGG-AAGTTCAGGGGTC
* *
45621217 AGAATGTAATTT
1 AAAATGGAATTT
45621229 CCTAAAATTT
Statistics
Matches: 146, Mismatches: 22, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
27 14 0.10
28 44 0.30
29 40 0.27
30 27 0.18
31 18 0.12
32 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAGTTCAGGGGTC
Found at i:45621544 original size:163 final size:164
Alignment explanation
Indices: 45621361--45621678 Score: 503
Period size: 163 Copynumber: 1.9 Consensus size: 164
45621351 AAATCTTAAA
* *
45621361 AAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATTAAAATAAATTAA
1 AAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGAGATTAAATTAAAACAAATTAA
** * * * *
45621426 AAATGTCAGGGACTAAATGCACAAATAAGCCAAAAAGTGACACGTGGTAGCCTCTGGTGCAGTCA
66 AAATAACAGGGACCAAATACACAAATAAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCA
*
45621491 AACAGTCAAAGGACT-AATTTAAAAAAGCTTGAT
131 AACAGTCAAAGGACTGAATTGAAAAAAGCTTGAT
*
45621524 AAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGAGATTAAATTAAAACAATTTAA
1 AAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGAGATTAAATTAAAACAAATTAA
* * * *
45621589 AAATAACAGGGACCAGATACATAAATAAACCAAGAAGTGACACGTGGCAGCCTCTGGTGCGGTCA
66 AAATAACAGGGACCAAATACACAAATAAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCA
45621654 AACAGTCAAAGGACTGAATTGAAAA
131 AACAGTCAAAGGACTGAATTGAAAA
45621679 CCAATTAAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
163 132 0.94
164 8 0.06
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (164 bp):
AAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGAGATTAAATTAAAACAAATTAA
AAATAACAGGGACCAAATACACAAATAAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCA
AACAGTCAAAGGACTGAATTGAAAAAAGCTTGAT
Found at i:45623230 original size:6 final size:6
Alignment explanation
Indices: 45623221--45623310 Score: 52
Period size: 6 Copynumber: 15.8 Consensus size: 6
45623211 GACTTTTCTT
*
45623221 TTTAAA TTTATAA --TAATA TT-AAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
45623267 -TTAAA ATTGAA TTTAAA -ATAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
45623311 TTTTCAAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
4 1 0.02
5 25 0.38
6 36 0.55
7 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:45623244 original size:17 final size:16
Alignment explanation
Indices: 45623222--45623313 Score: 80
Period size: 17 Copynumber: 5.5 Consensus size: 16
45623212 ACTTTTCTTT
45623222 TTAAATTTATAA-TAATA
1 TTAAATTTA-AATTAA-A
45623239 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
45623255 TTCAAATTTAAATTAAAA
1 TT-AAATTTAAATT-AAA
* *
45623273 TTGAATTTAAAATAAA
1 TTAAATTTAAATTAAA
*
45623289 TTTAAGA-TTAAAATAAA
1 -TTAA-ATTTAAATTAAA
*
45623306 TTTAATTT
1 TTAAATTT
45623314 TCAAATGGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.02
16 13 0.20
17 45 0.69
18 6 0.09
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:45623254 original size:11 final size:11
Alignment explanation
Indices: 45623238--45623313 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 11
45623228 TTATAATAAT
45623238 ATTAAATTTAA
1 ATTAAATTTAA
*
45623249 ATTAAATTCAA
1 ATTAAATTTAA
*
45623260 ATTTAAATTAAA
1 A-TTAAATTTAA
*
45623272 ATTGAATTTAA
1 ATTAAATTTAA
*
45623283 AATAAATTTAA
1 ATTAAATTTAA
*
45623294 GATTAAA-ATAA
1 -ATTAAATTTAA
*
45623305 ATTTAATTT
1 ATTAAATTT
45623314 TCAAATGGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
10 5 0.10
11 32 0.62
12 15 0.29
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:45623280 original size:34 final size:34
Alignment explanation
Indices: 45623224--45623290 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
45623214 TTTTCTTTTT
* *
45623224 AAATTTATAATAATATTAAATTTAAATTAAATTC
1 AAATTTATAATAAAATTAAATTTAAAATAAATTC
*
45623258 AAATTTA-AATTAAAATTGAATTTAAAATAAATT
1 AAATTTATAA-TAAAATTAAATTTAAAATAAATT
45623291 TAAGATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AAATTTATAATAAAATTAAATTTAAAATAAATTC
Found at i:45625063 original size:25 final size:25
Alignment explanation
Indices: 45625035--45625222 Score: 225
Period size: 25 Copynumber: 7.5 Consensus size: 25
45625025 CTTAAAAGAT
*
45625035 ATATTTTGTCTGGCTCGTAAGAGCG
1 ATATTCTGTCTGGCTCGTAAGAGCG
* *
45625060 ATATTCTGTTTAGCTCGTAAGAGCG
1 ATATTCTGTCTGGCTCGTAAGAGCG
* * *
45625085 ATATTTTGTTTGGGTCGTAAGAGCG
1 ATATTCTGTCTGGCTCGTAAGAGCG
* * *
45625110 ATATTTTGTCTAGCTCGTAA-AGTAG
1 ATATTCTGTCTGGCTCGTAAGAG-CG
**
45625135 ATATTCTAACTGGCTCGTAAGAGCG
1 ATATTCTGTCTGGCTCGTAAGAGCG
* * *
45625160 ATATTCTGACTGGCTTGTAAGAGTG
1 ATATTCTGTCTGGCTCGTAAGAGCG
45625185 ATATTCTGTCTGGCTCGTAAGAGCG
1 ATATTCTGTCTGGCTCGTAAGAGCG
*
45625210 TTATTCTGTCTGG
1 ATATTCTGTCTGG
45625223 GCTTATATTA
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
24 2 0.01
25 135 0.97
26 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (25 bp):
ATATTCTGTCTGGCTCGTAAGAGCG
Found at i:45628733 original size:17 final size:17
Alignment explanation
Indices: 45628680--45628736 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
45628670 GATGTTCAAT
*
45628680 CTTTAATCTCCCTTGAC
1 CTTTAACCTCCCTTGAC
* * *
45628697 TTTTAACTTTCCTT---
1 CTTTAACCTCCCTTGAC
45628711 CTTTAACCTCCCTTGAC
1 CTTTAACCTCCCTTGAC
45628728 CTTTAACCT
1 CTTTAACCT
45628737 TCTATCTTCC
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
14 11 0.37
17 19 0.63
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.46
Consensus pattern (17 bp):
CTTTAACCTCCCTTGAC
Found at i:45633611 original size:43 final size:42
Alignment explanation
Indices: 45633578--45633867 Score: 397
Period size: 43 Copynumber: 6.8 Consensus size: 42
45633568 AGAACATGGC
*
45633578 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGGCATGTT
1 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA-GCCATGTT
* *
45633621 CTTTAACGGCGCTTTTCCCACAAACGCCGCTAAATGCCATGTT
1 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA-GCCATGTT
* *
45633664 CTTTAGTGGCGCTTTAT-CCACAAGCGCCGCTAAAGGCATGTT
1 CTTTAGCGGCGCTTT-TCCCACAAGCGCCGCTAAAGCCATGTT
*
45633706 CTTTAGTGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTT
1 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA-GCCATGTT
*
45633749 CTTTAGCGGCGCTTTAT-CCACAAGCGCCGCTAAAGGCATGTT
1 CTTTAGCGGCGCTTT-TCCCACAAGCGCCGCTAAAGCCATGTT
* *
45633791 TTTTAGCGGCGCTTTTCTCCACAAGCGCCGCTAAAGCCCTTGTT
1 CTTTAGCGGCGCTTTTC-CCACAAGCGCCGCTAAAG-CCATGTT
*
45633835 CTTTAGCGGCGC-TTTCTCCAAAAGCGCCGCTAA
1 CTTTAGCGGCGCTTTTC-CCACAAGCGCCGCTAA
45633868 TATAACAGAT
Statistics
Matches: 224, Mismatches: 16, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
41 2 0.01
42 60 0.27
43 144 0.64
44 18 0.08
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGCCATGTT
Found at i:45633738 original size:85 final size:84
Alignment explanation
Indices: 45633578--45633867 Score: 447
Period size: 85 Copynumber: 3.4 Consensus size: 84
45633568 AGAACATGGC
*
45633578 CTTTAGCGGCGCTTT-TCCCACAAGCGCCGCTAAAGGGCATGTTCTTTAACGGCGCTTTTCCCAC
1 CTTTAGCGGCGCTTTAT-CCACAAGCGCCGCTAAA-GGCATGTTCTTTAGCGGCGCTTTTCCCAC
*
45633642 AAACGCCGCTAAATGCCATGTT
64 AAGCGCCGCTAAA-GCCATGTT
* *
45633664 CTTTAGTGGCGCTTTATCCACAAGCGCCGCTAAAGGCATGTTCTTTAGTGGCGCTTTTCCCACAA
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGGCATGTTCTTTAGCGGCGCTTTTCCCACAA
45633729 GCGCCGCTAAAGGCCATGTT
66 GCGCCGCTAAA-GCCATGTT
*
45633749 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGGCATGTTTTTTAGCGGCGCTTTTCTCCACA
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGGCATGTTCTTTAGCGGCGCTTTTC-CCACA
*
45633814 AGCGCCGCTAAAGCCCTTGTT
65 AGCGCCGCTAAAG-CCATGTT
* *
45633835 CTTTAGCGGCGCTTTCTCCAAAAGCGCCGCTAA
1 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAA
45633868 TATAACAGAT
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
85 104 0.55
86 85 0.45
87 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (84 bp):
CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGGCATGTTCTTTAGCGGCGCTTTTCCCACAA
GCGCCGCTAAAGCCATGTT
Found at i:45633812 original size:128 final size:129
Alignment explanation
Indices: 45633578--45633867 Score: 426
Period size: 128 Copynumber: 2.3 Consensus size: 129
45633568 AGAACATGGC
*
45633578 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGGCATGTTCTTTAACGGCGCTTTTCCCACA
1 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCGCTTTTCCCACA
* *
45633643 AACGCCGCTAAATGCCATGTTCTTTAGTGGCGCTTTATCCACAAGCGCCGCTAAAG-GCATGTT
66 AACGCCGCTAAATGCCATGTTCTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGCCCATGTT
* *
45633706 CTTTAGTGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTAT-CCAC
1 CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCGCTTT-TCCCAC
* * * * *
45633770 AAGCGCCGCTAAA-GGCATGTTTTTTAGCGGCGCTTTTCTCCACAAGCGCCGCTAAAGCCCTTGT
65 AAACGCCGCTAAATGCCATGTTCTTTAGCGGCGC-TTTATCCACAAGCGCCGCTAAAGCCCATGT
45633834 T
129 T
*
45633835 CTTTAGCGGCGC-TTTCTCCAAAAGCGCCGCTAA
1 CTTTAGCGGCGCTTTTC-CCACAAGCGCCGCTAA
45633868 TATAACAGAT
Statistics
Matches: 146, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
127 17 0.12
128 97 0.66
129 32 0.22
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGGCCATGTTCTTTAACGGCGCTTTTCCCACA
AACGCCGCTAAATGCCATGTTCTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGCCCATGTT
Found at i:45634175 original size:21 final size:21
Alignment explanation
Indices: 45634150--45634202 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
45634140 CTTGTAGCCT
*
45634150 CTGCTTCCTTCGCTTGCCTCG
1 CTGCTTCCTCCGCTTGCCTCG
45634171 CTGCTTCCTCCGCTTGCCTCG
1 CTGCTTCCTCCGCTTGCCTCG
* *
45634192 TTGCTGCCTCC
1 CTGCTTCCTCC
45634203 ACTTTAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.19, T:0.36
Consensus pattern (21 bp):
CTGCTTCCTCCGCTTGCCTCG
Found at i:45634274 original size:66 final size:66
Alignment explanation
Indices: 45634197--45634345 Score: 253
Period size: 66 Copynumber: 2.3 Consensus size: 66
45634187 CCTCGTTGCT
* *
45634197 GCCTCCACTTTAAGTTGTAGATGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
45634262 A
66 A
* * *
45634263 GCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
45634328 A
66 A
45634329 GCCTCCTCTTTAAGTTG
1 GCCTCCTCTTTAAGTTG
45634346 AGCAATTTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (66 bp):
GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
A
Found at i:45639880 original size:8 final size:8
Alignment explanation
Indices: 45639867--45639960 Score: 65
Period size: 8 Copynumber: 11.8 Consensus size: 8
45639857 CTGTTTTTAT
45639867 TAATTAAA
1 TAATTAAA
45639875 TAATTAAA
1 TAATTAAA
*
45639883 T-ATTTAA
1 TAATTAAA
45639890 T--TTAATA
1 TAATTAA-A
45639897 TAATTAAA
1 TAATTAAA
45639905 TAATTAAA
1 TAATTAAA
* *
45639913 T-CTT--T
1 TAATTAAA
45639918 TCAATTAAA
1 T-AATTAAA
45639927 TAATTAAA
1 TAATTAAA
45639935 TAAGCTTAAA
1 TAA--TTAAA
45639945 TAATTATATA
1 TAATTA-A-A
45639955 TAATTA
1 TAATTA
45639961 TTTACGACCA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 12 0.17
8 32 0.46
9 6 0.09
10 15 0.22
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (8 bp):
TAATTAAA
Found at i:45639901 original size:30 final size:29
Alignment explanation
Indices: 45639867--45639946 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 29
45639857 CTGTTTTTAT
45639867 TAATTAAATAATTAAATATTT-AATTTAATA
1 TAATTAAATAATTAAATATTTCAA-TTAA-A
*
45639897 TAATTAAATAATTAAATCTTTTCAATTAAA
1 TAATTAAATAATTAAAT-ATTTCAATTAAA
45639927 TAATTAAATAAGCTTAAATA
1 TAATTAAATAA--TTAAATA
45639947 ATTATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 29 0.66
31 7 0.16
32 8 0.18
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TAATTAAATAATTAAATATTTCAATTAAA
Found at i:45639902 original size:22 final size:20
Alignment explanation
Indices: 45639865--45639911 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
45639855 GGCTGTTTTT
45639865 ATTAATTAAATAATTAAATA
1 ATTAATTAAATAATTAAATA
*
45639885 TTTAATTTAATATAATTAAATA
1 ATTAA-TTAA-ATAATTAAATA
45639907 ATTAA
1 ATTAA
45639912 ATCTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAATTAAATAATTAAATA
Found at i:45639924 original size:44 final size:44
Alignment explanation
Indices: 45639876--45640170 Score: 168
Period size: 48 Copynumber: 6.4 Consensus size: 44
45639866 TTAATTAAAT
45639876 AATTAAATATTTAATTTAATATAATTAAATAATTAAATCTTTTC
1 AATTAAATATTTAATTTAATATAATTAAATAATTAAATCTTTTC
* * * * *
45639920 AATTAAATAATTAAATAAGCTTAA-ATAATTATAT-A-TAATTATTTAC
1 AATTAAAT-ATT---TAA-TTTAATATAATTAAATAATTAAATCTTTTC
* ** * * **
45639966 GACCACAT-TTTAAGTTAAATAGTTAATTAAATATAATTAAAAATTTT-
1 AATTAAATATTTAA-TTTAATA--TAATT-AA-ATAATTAAATCTTTTC
* ** * *
45640013 AATATAATTATTTACCTTAATATAATTAAATAATTAAATATTTAATTT
1 AAT-TAAATATTTAATTTAATATAATTAAATAATTAAAT-CTT--TTC
* * *
45640061 AATATAATTATTTACTTAAATATAATTAAATAATTAAATCTTTTAAC
1 AAT-TAAATATTTAATTTAATATAATTAAATAATTAAATCTTTT--C
* * *
45640108 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTA
1 --AAT-TAAATATTTAATTTAATATAATTAAATAATTAAATCTTTTC
45640155 AATTAAATATTTAATT
1 AATTAAATATTTAATT
45640171 AATCGATAGT
Statistics
Matches: 196, Mismatches: 33, Indels: 44
0.72 0.12 0.16
Matches are distributed among these distances:
41 7 0.04
42 1 0.01
44 35 0.18
45 13 0.07
46 19 0.10
47 7 0.04
48 63 0.32
49 51 0.26
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (44 bp):
AATTAAATATTTAATTTAATATAATTAAATAATTAAATCTTTTC
Found at i:45640032 original size:18 final size:17
Alignment explanation
Indices: 45640011--45640137 Score: 90
Period size: 18 Copynumber: 7.7 Consensus size: 17
45640001 ATTAAAAATT
45640011 TTAATATAATTATTTACC
1 TTAATATAATTATTTA-C
45640029 TTAATATAATTA---A-
1 TTAATATAATTATTTAC
* * *
45640042 ATAAT-TAAATATTTAAT
1 TTAATATAATTATTT-AC
45640059 TTAATATAATTATTTAC
1 TTAATATAATTATTTAC
** *
45640076 TTAAATATAATTAAATAA
1 TT-AATATAATTATTTAC
* *
45640094 TTAA-AT-CTT-TTAAC
1 TTAATATAATTATTTAC
45640108 TTAATATAATTATTTAC
1 TTAATATAATTATTTAC
45640125 TTTAATATAATTA
1 -TTAATATAATTA
45640138 AATAATTAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
12 5 0.06
13 4 0.05
14 5 0.06
15 5 0.06
16 5 0.06
17 13 0.16
18 46 0.55
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATAATTATTTAC
Found at i:45640123 original size:49 final size:48
Alignment explanation
Indices: 45640011--45640160 Score: 239
Period size: 49 Copynumber: 3.1 Consensus size: 48
45640001 ATTAAAAATT
* *
45640011 TTAATATAATTATTTACCTTAATATAATTAAATAATTAAAT-ATTTAAT
1 TTAATATAATTATTTA-CTTAATATAATTAAATAATTAAATCTTTTAAA
*
45640059 TTAATATAATTATTTACTTAAATATAATTAAATAATTAAATCTTTTAAC
1 TTAATATAATTATTTACTT-AATATAATTAAATAATTAAATCTTTTAAA
45640108 TTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAAA
1 TTAATATAATTATTTAC-TTAATATAATTAAATAATTAAATCTTTTAAA
45640157 TTAA
1 TTAA
45640161 ATATTTAATT
Statistics
Matches: 96, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
47 3 0.03
48 37 0.39
49 54 0.56
50 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (48 bp):
TTAATATAATTATTTACTTAATATAATTAAATAATTAAATCTTTTAAA
Found at i:45640231 original size:18 final size:18
Alignment explanation
Indices: 45640210--45640256 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
45640200 ATTAAACATG
45640210 ATTAAATAATTTAATATA
1 ATTAAATAATTTAATATA
** *
45640228 ATTATTTAGTTTAATATA
1 ATTAAATAATTTAATATA
45640246 ATTAAATAATT
1 ATTAAATAATT
45640257 ATATCTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTAAATAATTTAATATA
Found at i:45640266 original size:26 final size:27
Alignment explanation
Indices: 45640211--45640269 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
45640201 TTAAACATGA
*
45640211 TTAAATAATTTAATATAATTATTTAGT
1 TTAAATAATTTAATATAATTATATAGT
**
45640238 TTAATATAA-TTAA-ATAATTATATCTT
1 TTAA-ATAATTTAATATAATTATATAGT
45640264 TTAAAT
1 TTAAAT
45640270 TGAAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.07
26 14 0.50
27 8 0.29
28 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAAATAATTTAATATAATTATATAGT
Found at i:45640526 original size:14 final size:14
Alignment explanation
Indices: 45640507--45640536 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45640497 AAGATAGGTT
45640507 CAATTATATATTCC
1 CAATTATATATTCC
45640521 CAATTATATATTCC
1 CAATTATATATTCC
45640535 CA
1 CA
45640537 TTCAACAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (14 bp):
CAATTATATATTCC
Found at i:45641314 original size:12 final size:12
Alignment explanation
Indices: 45641297--45641334 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
45641287 TTACACTACC
45641297 AATGAAAGAAGT
1 AATGAAAGAAGT
45641309 AATGAAAGAAGT
1 AATGAAAGAAGT
45641321 AATGAAAGAAGT
1 AATGAAAGAAGT
45641333 AA
1 AA
45641335 CAGATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AATGAAAGAAGT
Found at i:45642459 original size:42 final size:41
Alignment explanation
Indices: 45642403--45642666 Score: 289
Period size: 41 Copynumber: 6.4 Consensus size: 41
45642393 AAATGATCCT
45642403 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* * * *
45642444 ACCTTTTAGTGGCGCTTTAGGGAAAGCGCCGCTAATGATCAT
1 ACC-TTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* ** * * *
45642486 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAAT
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
* **
45642527 ACCTTTAGCGGCGCATT-AGAGAAAGCGCCGCTAATGACTTG
1 ACCTTTAGCGGCGC-TTGAGGGAAAGCGCCGCTAATGACCAG
* * ** *
45642568 AACTTTAGCGGTGCTTGAGATAAAGCGCCGCTAATTA-CATG
1 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCA-G
* * *
45642609 ATCTTTAGCGGCGCTTGTGGGTAAAGCGCCGCTAATGACCCG
1 ACCTTTAGCGGCGCTTGAGGG-AAAGCGCCGCTAATGACCAG
45642651 ACCTTTAGCGGCGCTT
1 ACCTTTAGCGGCGCTT
45642667 TTGTTAAGCG
Statistics
Matches: 184, Mismatches: 33, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.01
41 111 0.60
42 70 0.38
43 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAG
Found at i:45642585 original size:82 final size:82
Alignment explanation
Indices: 45642403--45642745 Score: 333
Period size: 82 Copynumber: 4.2 Consensus size: 82
45642393 AAATGATCCT
** * * * * *
45642403 ACCTTTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCAGACCTTTTAGTGGCGCTTTAG-GGA
1 ACCTTTAGCGGCGCTTGAGTTAAAGCGCCGCTAATTA-CATACC-TTTAGCGGCGCATTAGAGAA
45642467 AAGCGCCGCTAATGATCAT-
64 AAGCGCCGCTAATGA-CATG
*
45642486 ACCTTTAGCGGCACTTGAGTTAAAGCGCCGCTAATTACAATACCTTTAGCGGCGCATTAGAG-AA
1 ACCTTTAGCGGCGCTTGAGTTAAAGCGCCGCTAATTAC-ATACCTTTAGCGGCGCATTAGAGAAA
*
45642550 AGCGCCGCTAATGACTTG
65 AGCGCCGCTAATGACATG
* * * * * * *
45642568 AACTTTAGCGGTGCTTGAGATAAAGCGCCGCTAATTACATGATCTTTAGCGGCGC-TTGTGGGTA
1 ACCTTTAGCGGCGCTTGAGTTAAAGCGCCGCTAATTACAT-ACCTTTAGCGGCGCATT-AGAGAA
**
45642632 AAGCGCCGCTAATGACCCG
64 AAGCGCCGCTAATGACATG
** * * *
45642651 ACCTTTAGCGGCGCTTTTGTT-AAGCGCCGCTAA-TGCTTTACCTTTTGCGGCGCATTA-AGAAA
1 ACCTTTAGCGGCGCTTGAGTTAAAGCGCCGCTAATTAC-ATACCTTTAGCGGCGCATTAGAGAAA
* *
45642713 AGCGCCGCTAATG-CTTT
65 AGCGCCGCTAATGACATG
*
45642730 ACCTTTTGCGGCGCTT
1 ACCTTTAGCGGCGCTT
45642746 TGTTTCCAAA
Statistics
Matches: 219, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
79 16 0.07
80 16 0.07
81 20 0.09
82 95 0.43
83 72 0.33
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (82 bp):
ACCTTTAGCGGCGCTTGAGTTAAAGCGCCGCTAATTACATACCTTTAGCGGCGCATTAGAGAAAA
GCGCCGCTAATGACATG
Found at i:45642999 original size:17 final size:17
Alignment explanation
Indices: 45642977--45643035 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
45642967 ATGTTCAACC
45642977 TTTAACCTCCATTGACT
1 TTTAACCTCCATTGACT
45642994 TTTAACCTTCCA-T--CT
1 TTTAACC-TCCATTGACT
* *
45643009 TCCTTAACCTCCCTTGACC
1 T--TTAACCTCCATTGACT
45643028 TTTAACCT
1 TTTAACCT
45643036 TCTATCTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 22 0.65
18 4 0.12
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAACCTCCATTGACT
Found at i:45643026 original size:34 final size:34
Alignment explanation
Indices: 45642978--45643052 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
45642968 TGTTCAACCT
*
45642978 TTAACCTCCATTGACTTTTAACCTTCCATCTTCC
1 TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
* *
45643012 TTAACCTCCCTTGACCTTTAACCTTCTATCTTCC
1 TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
45643046 TTAACCT
1 TTAACCT
45643053 TTCATATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.20, C:0.36, G:0.03, T:0.41
Consensus pattern (34 bp):
TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
Found at i:45643049 original size:17 final size:16
Alignment explanation
Indices: 45642995--45643053 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
45642985 CCATTGACTT
45642995 TTAACCTTCCATCTTCC
1 TTAACCTT-CATCTTCC
*
45643012 TTAACC-TC-CCTTGACC
1 TTAACCTTCATCTT--CC
45643028 TTTAACCTTCTATCTTCC
1 -TTAACCTTC-ATCTTCC
45643046 TTAACCTT
1 TTAACCTT
45643054 TCATATTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 3 0.09
17 20 0.59
18 4 0.12
20 3 0.09
ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAACCTTCATCTTCC
Found at i:45643492 original size:17 final size:18
Alignment explanation
Indices: 45643467--45643500 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
45643457 TAAAATTAAT
45643467 AAATAAATATTT-TTTTA
1 AAATAAATATTTATTTTA
*
45643484 AAATCAATATTTATTTT
1 AAATAAATATTTATTTT
45643501 TATCGAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATAAATATTTATTTTA
Found at i:45651948 original size:42 final size:42
Alignment explanation
Indices: 45651877--45651971 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
45651867 GTTACACGAC
* * ** *
45651877 CTAGATACACGGGCGTGGATGTGACCGTGTGCGATGCTCGGG
1 CTAGATACACGGGAGTGGATGTGACCGTGTGAGACACACGGG
* **
45651919 CTAGATACACGGGAGTGGGTGTGGTCGTGTGAGACACACGGG
1 CTAGATACACGGGAGTGGATGTGACCGTGTGAGACACACGGG
45651961 CTA-ATACACGG
1 CTAGATACACGG
45651972 TCGTGTGTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 8 0.18
42 37 0.82
ACGTcount: A:0.21, C:0.20, G:0.39, T:0.20
Consensus pattern (42 bp):
CTAGATACACGGGAGTGGATGTGACCGTGTGAGACACACGGG
Found at i:45652099 original size:78 final size:77
Alignment explanation
Indices: 45652009--45652192 Score: 210
Period size: 78 Copynumber: 2.4 Consensus size: 77
45651999 TGAGACTGTG
* * * *
45652009 ATACAATACTGAACTGACGGTGACACTGCGAACATCGTAATACT-GTA-CTGAACTGGCAGTGAC
1 ATACAACACTGAACTGACGGTGACACTGCAAACATCGTAATA-TGGTAGCAG-ACTAGCAGTGAC
* *
45652072 ATTGTAAACACTGC
64 AATGTAAACACTAC
* ** *
45652086 AATACAACACTGAACTGACGGTTACACTATAAACATCGTAATATGGTAGCAGATTAGCAGTGACA
1 -ATACAACACTGAACTGACGGTGACACTGCAAACATCGTAATATGGTAGCAGACTAGCAGTGACA
45652151 ATGTAAACACTAC
65 ATGTAAACACTAC
* *
45652164 ATTCTAACACTGAATTGACGGTGACACTG
1 ATAC-AACACTGAACTGACGGTGACACTG
45652193 TAAAACACCA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
77 4 0.04
78 83 0.93
79 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (77 bp):
ATACAACACTGAACTGACGGTGACACTGCAAACATCGTAATATGGTAGCAGACTAGCAGTGACAA
TGTAAACACTAC
Found at i:45656887 original size:15 final size:15
Alignment explanation
Indices: 45656867--45656900 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
45656857 ACGGTTTGAC
45656867 TTGGTTCAATTAGGT
1 TTGGTTCAATTAGGT
* *
45656882 TTGGTTCACTTTGGT
1 TTGGTTCAATTAGGT
45656897 TTGG
1 TTGG
45656901 GTTTAAAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.29, T:0.50
Consensus pattern (15 bp):
TTGGTTCAATTAGGT
Found at i:45663369 original size:2 final size:2
Alignment explanation
Indices: 45663362--45663386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45663352 ATGACCACAT
45663362 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
45663387 TACCTCAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45664069 original size:13 final size:13
Alignment explanation
Indices: 45664051--45664078 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45664041 TTTTTCAAAA
45664051 AAAGTCAACGATC
1 AAAGTCAACGATC
45664064 AAAGTCAACGATC
1 AAAGTCAACGATC
45664077 AA
1 AA
45664079 CGGCCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:45664105 original size:22 final size:22
Alignment explanation
Indices: 45664075--45664169 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
45664065 AAGTCAACGA
45664075 TCAACGGCCAATCAACGGTCGG
1 TCAACGGCCAATCAACGGTCGG
* * * *
45664097 TCAATGGCCGATCAATGGTCAG
1 TCAACGGCCAATCAACGGTCGG
* * * * *
45664119 TCAACGACCGATTAACGGTTGA
1 TCAACGGCCAATCAACGGTCGG
* *
45664141 TCAATGGCCAGTCAACGGTCGG
1 TCAACGGCCAATCAACGGTCGG
45664163 TCAACGG
1 TCAACGG
45664170 TTTGACTTGG
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (22 bp):
TCAACGGCCAATCAACGGTCGG
Found at i:45664170 original size:33 final size:33
Alignment explanation
Indices: 45664073--45664171 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
45664063 CAAAGTCAAC
* * * **
45664073 GATCAACGGCCAATCAACGGTCGGTCAATGGCC
1 GATCAATGGCCAGTCAACGGTCGGTCAACGGTT
* ** * *
45664106 GATCAATGGTCAGTCAACGACCGATTAACGGTT
1 GATCAATGGCCAGTCAACGGTCGGTCAACGGTT
45664139 GATCAATGGCCAGTCAACGGTCGGTCAACGGTT
1 GATCAATGGCCAGTCAACGGTCGGTCAACGGTT
45664172 TGACTTGGTT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (33 bp):
GATCAATGGCCAGTCAACGGTCGGTCAACGGTT
Found at i:45664266 original size:23 final size:23
Alignment explanation
Indices: 45664234--45664295 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
45664224 TTTTGGGTCC
45664234 AAAACGGTTTGGGTTTCTATAATT
1 AAAA-GGTTTGGGTTTCTATAATT
*
45664258 AAAAGGTTTGGGTTTTTATAATT
1 AAAAGGTTTGGGTTTCTATAATT
45664281 AAAAGGTTTGGGTTT
1 AAAAGGTTTGGGTTT
45664296 ATTGGGTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 33 0.89
24 4 0.11
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (23 bp):
AAAAGGTTTGGGTTTCTATAATT
Found at i:45676412 original size:110 final size:110
Alignment explanation
Indices: 45676219--45676439 Score: 442
Period size: 110 Copynumber: 2.0 Consensus size: 110
45676209 TGCACCTAAT
45676219 ATCATCTCAAACCCTTGCAATGAATCACCATACATGAGAAGCATTTGGTCGATTAATACTGGCTG
1 ATCATCTCAAACCCTTGCAATGAATCACCATACATGAGAAGCATTTGGTCGATTAATACTGGCTG
45676284 GACATGTTTCCACCATGTTATATTTAGAGCATAAAATTCGAACCC
66 GACATGTTTCCACCATGTTATATTTAGAGCATAAAATTCGAACCC
45676329 ATCATCTCAAACCCTTGCAATGAATCACCATACATGAGAAGCATTTGGTCGATTAATACTGGCTG
1 ATCATCTCAAACCCTTGCAATGAATCACCATACATGAGAAGCATTTGGTCGATTAATACTGGCTG
45676394 GACATGTTTCCACCATGTTATATTTAGAGCATAAAATTCGAACCC
66 GACATGTTTCCACCATGTTATATTTAGAGCATAAAATTCGAACCC
45676439 A
1 A
45676440 CAAAGTTTCT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (110 bp):
ATCATCTCAAACCCTTGCAATGAATCACCATACATGAGAAGCATTTGGTCGATTAATACTGGCTG
GACATGTTTCCACCATGTTATATTTAGAGCATAAAATTCGAACCC
Found at i:45678024 original size:19 final size:20
Alignment explanation
Indices: 45677989--45678030 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
45677979 ATGAGGATAT
*
45677989 TTTATTTTTAATTCATTT-A
1 TTTATTTTTAATACATTTGA
45678008 TTTATTTTGT-ATACATTTGA
1 TTTATTTT-TAATACATTTGA
45678028 TTT
1 TTT
45678031 GATTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTATTTTTAATACATTTGA
Found at i:45678573 original size:2 final size:2
Alignment explanation
Indices: 45678566--45678596 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45678556 AAAAGTTTTA
45678566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45678597 AGAGAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45678963 original size:16 final size:16
Alignment explanation
Indices: 45678942--45678975 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
45678932 AACCGCATGA
*
45678942 TTGAAAATTGTATGCT
1 TTGAAAATTGTATACT
45678958 TTGAAAATTGTATACT
1 TTGAAAATTGTATACT
45678974 TT
1 TT
45678976 TCAACATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (16 bp):
TTGAAAATTGTATACT
Found at i:45679209 original size:23 final size:23
Alignment explanation
Indices: 45679165--45679210 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
45679155 ATCACCATTT
* *
45679165 CCATTTTTTAAAATATTTTTTTA
1 CCATGTTTTAAAATATTCTTTTA
45679188 CCATGTTTTAATAAT-TTCTTTTA
1 CCATGTTTTAA-AATATTCTTTTA
45679211 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (23 bp):
CCATGTTTTAAAATATTCTTTTA
Found at i:45693887 original size:14 final size:14
Alignment explanation
Indices: 45693868--45693896 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45693858 TATGGAAGAA
45693868 TCACAACTATTATG
1 TCACAACTATTATG
45693882 TCACAACTATTATG
1 TCACAACTATTATG
45693896 T
1 T
45693897 TTTTGCTCAT
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:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (14 bp):
TCACAACTATTATG
Found at i:45696108 original size:30 final size:30
Alignment explanation
Indices: 45696074--45696134 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
45696064 CAAAAGTTCA
45696074 AAATCTACAAAATAAACGAAATAAGTAAGT
1 AAATCTACAAAATAAACGAAATAAGTAAGT
45696104 AAATCTACAAAATAAACGAAATAAGTAAGT
1 AAATCTACAAAATAAACGAAATAAGTAAGT
45696134 A
1 A
45696135 TAATGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
AAATCTACAAAATAAACGAAATAAGTAAGT
Found at i:45696388 original size:50 final size:51
Alignment explanation
Indices: 45696291--45696393 Score: 136
Period size: 50 Copynumber: 2.0 Consensus size: 51
45696281 TTCATTGCGT
* **
45696291 TTTACGCTCGTCAACTTGCACACATTTACGCTCATCAGTTTAAATATG-CA
1 TTTACGCTCGCCAACTTGCACACATTTACGCTCATCAACTTAAATATGTCA
* * * *
45696341 TTTACGCTCGCCAGCTTGCACACGTTTGCGCTCATCAACTTACATATGTCA
1 TTTACGCTCGCCAACTTGCACACATTTACGCTCATCAACTTAAATATGTCA
45696392 TT
1 TT
45696394 AATTTGACGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 41 0.91
51 4 0.09
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (51 bp):
TTTACGCTCGCCAACTTGCACACATTTACGCTCATCAACTTAAATATGTCA
Found at i:45699473 original size:28 final size:27
Alignment explanation
Indices: 45699442--45699500 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
45699432 ATAATGATGA
45699442 TTATAATTTT-AAAATAATTTTAATAATT
1 TTAT-ATTTTAAAAATAATTTT-ATAATT
*
45699470 TTATATTTTAAAAAATAATTTTATATTT
1 TTATATTTT-AAAAATAATTTTATAATT
45699498 TTA
1 TTA
45699501 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.18
28 12 0.43
29 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATTTTAAAAATAATTTTATAATT
Found at i:45699486 original size:20 final size:21
Alignment explanation
Indices: 45699463--45699505 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
45699453 AAATAATTTT
45699463 AATAATTTTATA-TTTTAAAA
1 AATAATTTTATATTTTTAAAA
45699483 AATAATTTTATATTTTTAAAA
1 AATAATTTTATATTTTTAAAA
45699504 AA
1 AA
45699506 AATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAATTTTATATTTTTAAAA
Found at i:45706700 original size:30 final size:29
Alignment explanation
Indices: 45706666--45706726 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
45706656 AAAAATGGGA
45706666 TTTTGGAAGGTTTAGGGGT-AAAATAGTAAT
1 TTTTGGAA-GTTTAGGGGTCAAAAT-GTAAT
*
45706696 TTTTGGAAGTTTTGGGGTCAAAATGTAAT
1 TTTTGGAAGTTTAGGGGTCAAAATGTAAT
45706725 TT
1 TT
45706727 CTGAACAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.41
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTCAAAATGTAAT
Found at i:45707722 original size:30 final size:30
Alignment explanation
Indices: 45707673--45707730 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
45707663 TTTCTTTTTT
45707673 TTATTATTAAAAATATTATTAATGATTATCA
1 TTATTATTAAAAATATTATTAAT-ATTATCA
45707704 TTATTA-TAAAACAT-TTATTAATATTAT
1 TTATTATTAAAA-ATATTATTAATATTAT
45707731 TAAAGCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 13 0.50
31 8 0.31
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TTATTATTAAAAATATTATTAATATTATCA
Found at i:45707739 original size:21 final size:21
Alignment explanation
Indices: 45707705--45707790 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
45707695 TGATTATCAT
45707705 TATTA-TAAAACATTTATTAA
1 TATTATTAAAACATTTATTAA
* *
45707725 TATTATTAAAGCATTTATTAT
1 TATTATTAAAACATTTATTAA
* * *
45707746 TATTACT-AAACATTAATTAC
1 TATTATTAAAACATTTATTAA
* * *
45707766 TATTATCAAAATAGTTATTAA
1 TATTATTAAAACATTTATTAA
45707787 TATT
1 TATT
45707791 TAATATTATT
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 20 0.38
21 32 0.62
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTATTAAAACATTTATTAA
Found at i:45707748 original size:18 final size:18
Alignment explanation
Indices: 45707703--45707770 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 18
45707693 AATGATTATC
45707703 ATTATTA-TAAAACATTT
1 ATTATTATTAAAACATTT
*
45707720 ATTAATATTATTAAAGCATTT
1 A-T--TATTATTAAAACATTT
*
45707741 ATTATTATTACTAAACATTA
1 ATTATTATTA--AAACATTT
*
45707761 ATTACTATTA
1 ATTATTATTA
45707771 TCAAAATAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.02
18 9 0.22
20 21 0.51
21 10 0.24
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTATTATTAAAACATTT
Found at i:45707757 original size:41 final size:39
Alignment explanation
Indices: 45707684--45707771 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 39
45707674 TATTATTAAA
* *
45707684 AATATTATTAATGATTATCATTATTATAAAACATTTATT
1 AATATTATTAAAGATTATCATTATTATAAAACATTAATT
*
45707723 AATATTATTAAAGCATTTATTATTATTACT-AAACATTAATT
1 AATATTATTAAAG-A-TTATCATTATTA-TAAAACATTAATT
*
45707764 ACTATTAT
1 AATATTAT
45707772 CAAAATAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 12 0.29
40 1 0.02
41 28 0.67
42 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (39 bp):
AATATTATTAAAGATTATCATTATTATAAAACATTAATT
Found at i:45707784 original size:41 final size:41
Alignment explanation
Indices: 45707698--45707811 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 41
45707688 TTATTAATGA
* * * * *
45707698 TTATCATTATTATAAAACATTTATTAATATTATTAAAGCAT
1 TTATTATTATTATAAAACATTAATTAATATTATCAAAACAG
* *
45707739 TTATTATTATTACT-AAACATTAATTACTATTATCAAAATAG
1 TTATTATTATTA-TAAAACATTAATTAATATTATCAAAACAG
* **
45707780 TTATTAATATT-TAATATTATTAA-TAATATTAT
1 TTATTATTATTATAA-AACATTAATTAATATTAT
45707812 TATTAAGGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
39 1 0.02
40 9 0.15
41 48 0.81
42 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (41 bp):
TTATTATTATTATAAAACATTAATTAATATTATCAAAACAG
Found at i:45708130 original size:26 final size:26
Alignment explanation
Indices: 45708101--45708161 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
45708091 TTTCAGAACT
*
45708101 GGGTTCGTATTTGGATTTCAAAAATA
1 GGGTTCGTATTTGAATTTCAAAAATA
* * * *
45708127 GGGTTTGTGTTTTAATTTCAAGAATA
1 GGGTTCGTATTTGAATTTCAAAAATA
*
45708153 GGGGTCGTA
1 GGGTTCGTA
45708162 ACCCTTACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (26 bp):
GGGTTCGTATTTGAATTTCAAAAATA
Found at i:45708619 original size:17 final size:16
Alignment explanation
Indices: 45708599--45708630 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
45708589 AATTTTGTGC
45708599 AAATTTAAATTTAAAAT
1 AAATTT-AATTTAAAAT
45708616 AAATTTAATTTAAAA
1 AAATTTAATTTAAAA
45708631 CCAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAATTTAAAAT
Found at i:45708636 original size:17 final size:16
Alignment explanation
Indices: 45708598--45708639 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
45708588 AAATTTTGTG
45708598 CAAATTTAAATTTAAAA
1 CAAATTT-AATTTAAAA
*
45708615 TAAATTTAATTTAAAA
1 CAAATTTAATTTAAAA
45708631 CCAAATTTA
1 -CAAATTTA
45708640 TCTCATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (16 bp):
CAAATTTAATTTAAAA
Found at i:45723294 original size:30 final size:30
Alignment explanation
Indices: 45723260--45723321 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
45723250 ACCTATTTTA
*
45723260 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
* *
45723290 TTGTTAATTTTGTTACTATTTTAGAGATAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
45723320 TT
1 TT
45723322 ATTTGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGACAT
Found at i:45733049 original size:13 final size:13
Alignment explanation
Indices: 45733031--45733067 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
45733021 CTGTACATAT
45733031 AATAAAATA-AATA
1 AATAAAATATAA-A
45733044 AATAAAATATAAA
1 AATAAAATATAAA
45733057 AATAAAA-ATAA
1 AATAAAATATAA
45733068 TTGGGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 17 0.74
14 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:45735863 original size:22 final size:22
Alignment explanation
Indices: 45735806--45735852 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
45735796 CGATTTGAGG
45735806 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
45735827 AAAAATAAAAGAAAACATAATT
1 AAAAATAAAAGAAAACAGAATT
45735849 AAAA
1 AAAA
45735853 GAAATAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:45750620 original size:16 final size:16
Alignment explanation
Indices: 45750599--45750642 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
45750589 AATGGGCTCA
45750599 ACTTGCCACTTTCGAG
1 ACTTGCCACTTTCGAG
45750615 ACTTGCCACTTTCGAG
1 ACTTGCCACTTTCGAG
*
45750631 ATTTGCCACTTT
1 ACTTGCCACTTT
45750643 ACTTTTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (16 bp):
ACTTGCCACTTTCGAG
Found at i:45752509 original size:16 final size:16
Alignment explanation
Indices: 45752454--45752512 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
45752444 TATTTTTTAA
*
45752454 AATATTTAAAATCATTT
1 AATA-TTAAAATTATTT
*
45752471 -ATATTAATATTATTT
1 AATATTAAAATTATTT
* *
45752486 GATTTTAAAATTATTT
1 AATATTAAAATTATTT
45752502 AATATTAAAAT
1 AATATTAAAAT
45752513 AATACAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
AATATTAAAATTATTT
Found at i:45753887 original size:16 final size:17
Alignment explanation
Indices: 45753863--45753895 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45753853 TAGCAATATA
45753863 AAACACATAA-AATTTT
1 AAACACATAATAATTTT
*
45753879 AAACGCATAATAATTTT
1 AAACACATAATAATTTT
45753896 TTGACCTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (17 bp):
AAACACATAATAATTTT
Found at i:45755707 original size:17 final size:17
Alignment explanation
Indices: 45755685--45755723 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
45755675 CTCCACCTTG
* *
45755685 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
45755702 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
45755719 ACAAG
1 ACAAG
45755724 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:45762429 original size:22 final size:23
Alignment explanation
Indices: 45762402--45762466 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
45762392 CTTAAAAATA
*
45762402 ATAAAATTTTAATTTAATTTTTT
1 ATAAAATTTTAATTTAATTTATT
* * * *
45762425 A-AAAATTATATTTTTA-CTATT
1 ATAAAATTTTAATTTAATTTATT
45762446 ATAAAATTTATAATTTAATTT
1 ATAAAATTT-TAATTTAATTT
45762467 CGACTCCCTA
Statistics
Matches: 30, Mismatches: 9, Indels: 5
0.68 0.20 0.11
Matches are distributed among these distances:
21 4 0.13
22 18 0.60
23 7 0.23
24 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATAAAATTTTAATTTAATTTATT
Found at i:45767354 original size:37 final size:38
Alignment explanation
Indices: 45767289--45767361 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
45767279 GGAGAGAAAG
45767289 CTTATAGTTTAAAAGTTATTTATATATTATTGATATGA
1 CTTATAGTTTAAAAGTTATTTATATATTATTGATATGA
* *
45767327 CTTATAGTTT-AAATTTATTTTTATATTATTGATAT
1 CTTATAGTTTAAAAGTTATTTATATATTATTGATAT
45767362 TATTGGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 23 0.70
38 10 0.30
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (38 bp):
CTTATAGTTTAAAAGTTATTTATATATTATTGATATGA
Found at i:45769923 original size:18 final size:19
Alignment explanation
Indices: 45769880--45769916 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45769870 TCACTGTTTG
*
45769880 ATACAATTATTTTTCTAAC
1 ATACAATCATTTTTCTAAC
45769899 ATACAATCATTTTTCTAA
1 ATACAATCATTTTTCTAA
45769917 TAACAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (19 bp):
ATACAATCATTTTTCTAAC
Found at i:45770950 original size:6 final size:6
Alignment explanation
Indices: 45770939--45770966 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
45770929 TACTCGTAGT
45770939 GCCAGC GCCAGC GCCAGC GCCAGC GCCA
1 GCCAGC GCCAGC GCCAGC GCCAGC GCCA
45770967 AATGGTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.50, G:0.32, T:0.00
Consensus pattern (6 bp):
GCCAGC
Found at i:45783163 original size:29 final size:30
Alignment explanation
Indices: 45783131--45783187 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
45783121 AAAACGGCCT
* * *
45783131 ATATCTCTAGTTATTT-TTAAAACTGGCGC
1 ATATCCCTAATTATTTATTAAAAATGGCGC
45783160 ATATCCCTAATTATTTATTAAAAATGGC
1 ATATCCCTAATTATTTATTAAAAATGGC
45783188 ATATACCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
ATATCCCTAATTATTTATTAAAAATGGCGC
Found at i:45784061 original size:20 final size:21
Alignment explanation
Indices: 45784030--45784069 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
45784020 ATATTTATTC
45784030 TATTTAAATATATATAATTAT
1 TATTTAAATATATATAATTAT
45784051 TATTT-AATATATATAATTA
1 TATTTAAATATATATAATTA
45784070 CACCAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAAATATATATAATTAT
Found at i:45786013 original size:4 final size:4
Alignment explanation
Indices: 45786004--45786029 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
45785994 TCTGAGTTGA
45786004 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
45786030 GCATGCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:45787419 original size:8 final size:8
Alignment explanation
Indices: 45787406--45787435 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
45787396 TCAATTACTT
*
45787406 TTAATTAA
1 TTAATTTA
45787414 TTAATTTA
1 TTAATTTA
45787422 TTAATTTA
1 TTAATTTA
45787430 TTAATT
1 TTAATT
45787436 GAAAATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAATTTA
Found at i:45787660 original size:29 final size:29
Alignment explanation
Indices: 45787618--45787674 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
45787608 ATTTAATAAA
* *
45787618 TTTAGGTACCAAATTGAGCCCAAAAAAAG
1 TTTAGGCACCAAATTGAACCCAAAAAAAG
*
45787647 TTTAGGCACCAAATTGAACCTAAAAAAA
1 TTTAGGCACCAAATTGAACCCAAAAAAA
45787675 ACTTAGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (29 bp):
TTTAGGCACCAAATTGAACCCAAAAAAAG
Found at i:45787686 original size:29 final size:29
Alignment explanation
Indices: 45787619--45787686 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
45787609 TTTAATAAAT
* **
45787619 TTAGGTACCAAATTGAGCCCAAAAAAAGT
1 TTAGGTACCAAATTGAACCCAAAAAAAAC
* *
45787648 TTAGGCACCAAATTGAACCTAAAAAAAAC
1 TTAGGTACCAAATTGAACCCAAAAAAAAC
*
45787677 TTAGTTACCA
1 TTAGGTACCA
45787687 GATTAAGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (29 bp):
TTAGGTACCAAATTGAACCCAAAAAAAAC
Found at i:45787755 original size:59 final size:57
Alignment explanation
Indices: 45787668--45787824 Score: 163
Period size: 59 Copynumber: 2.7 Consensus size: 57
45787658 AATTGAACCT
* * *
45787668 AAAAAAAACTT-AGTTACCAGATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTGGGCCC
1 AAAAAAAA-TTAAG-TACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAATTAGG--C
* * * * * *
45787728 AAAAAAATTTAAGTACCAAATTAAGAAAAAGTGTCAAATTTAGGTACCAATTTAGGT
1 AAAAAAAATTAAGTACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAATTAGGC
* * *
45787785 AAAAAAAATTAAATACCAAATTAAGAAAAAGTATCAAATT
1 AAAAAAAATTAAGTACCAAATTAAGAAAAAATGTCAAATT
45787825 TAGATATCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 37 0.44
59 38 0.45
60 9 0.11
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.24
Consensus pattern (57 bp):
AAAAAAAATTAAGTACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAATTAGGC
Found at i:45787775 original size:31 final size:30
Alignment explanation
Indices: 45787732--45787836 Score: 85
Period size: 31 Copynumber: 3.6 Consensus size: 30
45787722 GGGCCCAAAA
*
45787732 AAATTTAAGTACCAAATTAAGAAAAAGTGTC
1 AAATTTAAATACCAAATTAAGAAAAAGT-TC
** * *
45787763 AAATTTAGGTACCAATTTAGGTAAAAA----
1 AAATTTAAATACCAAATTAAG-AAAAAGTTC
45787790 AAA-TTAAATACCAAATTAAGAAAAAGTATC
1 AAATTTAAATACCAAATTAAGAAAAAGT-TC
* *
45787820 AAATTTAGATATCAAAT
1 AAATTTAAATACCAAAT
45787837 ATTATATTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
25 5 0.09
26 13 0.22
27 3 0.05
30 3 0.05
31 29 0.50
32 5 0.09
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (30 bp):
AAATTTAAATACCAAATTAAGAAAAAGTTC
Found at i:45787816 original size:57 final size:58
Alignment explanation
Indices: 45787647--45787836 Score: 184
Period size: 57 Copynumber: 3.2 Consensus size: 58
45787637 CCAAAAAAAG
* ** ** * * *
45787647 TTTAGGCACCAAATTGAACCTAAAAAAAACTTAGTTACCAGATTAAGAAAAAATGTCAAG
1 TTTAGGTACCAAATT-AGGCTAAAAAAAA-TTAAATACCAAATTAAGAAAAAGTGTCAAA
* * * * * *
45787707 TTCAAGTACCAAATTGGGCCCAAAAAAATTTAAGTACCAAATTAAGAAAAAGTGTCAAA
1 TTTAGGTACCAAATTAGG-CTAAAAAAAATTAAATACCAAATTAAGAAAAAGTGTCAAA
* *
45787766 TTTAGGTACCAATTTAGG-TAAAAAAAATTAAATACCAAATTAAGAAAAAGTATCAAA
1 TTTAGGTACCAAATTAGGCTAAAAAAAATTAAATACCAAATTAAGAAAAAGTGTCAAA
* *
45787823 TTTAGATATCAAAT
1 TTTAGGTACCAAAT
45787837 ATTATATTAA
Statistics
Matches: 105, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
57 46 0.44
59 39 0.37
60 20 0.19
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (58 bp):
TTTAGGTACCAAATTAGGCTAAAAAAAATTAAATACCAAATTAAGAAAAAGTGTCAAA
Found at i:45798834 original size:29 final size:27
Alignment explanation
Indices: 45798792--45798872 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 27
45798782 TATCATAAAT
*
45798792 CTTAAACCTTAAACTTGTAATCTCAAA
1 CTTAAACCATAAACTTGTAATCTCAAA
45798819 CCCTTAAACCATAAACATTG-AATCTCAAA
1 --CTTAAACCATAAAC-TTGTAATCTCAAA
*
45798848 CATAAACCATAAACTT-TAAATCTCA
1 CTTAAACCATAAACTTGT-AATCTCA
45798873 TGTCCAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.04
27 20 0.43
29 22 0.47
30 3 0.06
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.28
Consensus pattern (27 bp):
CTTAAACCATAAACTTGTAATCTCAAA
Found at i:45799473 original size:24 final size:22
Alignment explanation
Indices: 45799456--45799509 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
45799446 AAAAAAATTT
*
45799456 ATTGATA-ATTTA-TCAAAATA
1 ATTGATATATTTATTCAAAAAA
45799476 ATTGATATATTTATTCAAAAAA
1 ATTGATATATTTATTCAAAAAA
45799498 A-TGATATATTTA
1 ATTGATATATTTA
45799510 ATTATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 7 0.23
21 16 0.52
22 8 0.26
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
ATTGATATATTTATTCAAAAAA
Found at i:45799667 original size:6 final size:7
Alignment explanation
Indices: 45799652--45799678 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45799642 ATATTTCATT
45799652 AAAATAA
1 AAAATAA
45799659 AAAATAA
1 AAAATAA
45799666 AAAATAA
1 AAAATAA
45799673 AAAATA
1 AAAATA
45799679 TATTATTTAC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:45800329 original size:6 final size:6
Alignment explanation
Indices: 45800292--45800328 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
45800282 GCTCTAACAA
*
45800292 GTGTCG GTGTCG GTGTCG GTGTCG GTGTCG GCGTCG G
1 GTGTCG GTGTCG GTGTCG GTGTCG GTGTCG GTGTCG G
45800329 CTTGCCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.19, G:0.51, T:0.30
Consensus pattern (6 bp):
GTGTCG
Found at i:45807591 original size:4 final size:4
Alignment explanation
Indices: 45807551--45807608 Score: 55
Period size: 4 Copynumber: 13.5 Consensus size: 4
45807541 CAACCCAAAA
*
45807551 TTAT TTAT TCAT TTAACT TT-T TATAT TTCATT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TT-A-T TTAT T-TAT TT-A-T TTAT TTAT TTAT TTAT
45807599 TTAT TTAT TT
1 TTAT TTAT TT
45807609 CTAGCACCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 2 0.04
4 33 0.72
5 5 0.11
6 6 0.13
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:45815897 original size:6 final size:6
Alignment explanation
Indices: 45815872--45815910 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
45815862 ACAATTCATA
* * *
45815872 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
45815911 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:45816009 original size:20 final size:22
Alignment explanation
Indices: 45815974--45816016 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
45815964 CTTACCTTTG
45815974 TTTCATCAAATAAATC-CACAA
1 TTTCATCAAATAAATCACACAA
*
45815995 TTTCA-CAAATTAATCACACAA
1 TTTCATCAAATAAATCACACAA
45816016 T
1 T
45816017 AAATCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
TTTCATCAAATAAATCACACAA
Found at i:45817983 original size:26 final size:26
Alignment explanation
Indices: 45817918--45817984 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
45817908 ATTATAAGCC
* *
45817918 CTAAAAAATTATGCATTTTATAAAATT
1 CTAAAAAATTAT-TATATTATAAAATT
* *
45817945 ATAAAAAA--ATTATATTATTAAATT
1 CTAAAAAATTATTATATTATAAAATT
45817969 CTAAAAAATTATTATA
1 CTAAAAAATTATTATA
45817985 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 18 0.55
25 2 0.06
26 6 0.18
27 7 0.21
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (26 bp):
CTAAAAAATTATTATATTATAAAATT
Found at i:45820321 original size:2 final size:2
Alignment explanation
Indices: 45820314--45820363 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
45820304 TGGATGGGCA
45820314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45820356 AT AT AT AT
1 AT AT AT AT
45820364 TTGTGATTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45821870 original size:23 final size:23
Alignment explanation
Indices: 45821812--45821871 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
45821802 TATTATCAGG
* * *
45821812 TTTAAGTGTCAATTTAAATGGAT
1 TTTAAGTATCAATTCAAATAGAT
* *
45821835 TTTACGGGA-CAATTCAAATAGAT
1 TTTA-AGTATCAATTCAAATAGAT
45821858 TTTAAGTATCAATT
1 TTTAAGTATCAATT
45821872 TAGATGTTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
22 2 0.07
23 25 0.89
24 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (23 bp):
TTTAAGTATCAATTCAAATAGAT
Found at i:45824321 original size:24 final size:24
Alignment explanation
Indices: 45824270--45824324 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
45824260 TCTTGCAGTT
*
45824270 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
*
45824294 AAACTTTGTTTATTTGTTT-AAGTC
1 AAACTCTGTTTATTTGTTTCAA-TC
45824318 AAACTCT
1 AAACTCT
45824325 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:45826261 original size:24 final size:24
Alignment explanation
Indices: 45826233--45826295 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
45826223 ATAAATAATC
*
45826233 TTTCAGTTAAACTCTGCTTATTGG
1 TTTCAATTAAACTCTGCTTATTGG
* *
45826257 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGCTTATTGG
* *
45826281 TTTAAATCAAACTCT
1 TTTCAATTAAACTCT
45826296 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (24 bp):
TTTCAATTAAACTCTGCTTATTGG
Done.