Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 173 of 208
Found at i:52702364 original size:19 final size:20
Alignment explanation
Indices: 52702336--52702378 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
52702326 ATTGACTTAA
*
52702336 TTTAATATATATTT-TAATT
1 TTTAAAATATATTTATAATT
52702355 TTTAAAATATATTTATAATT
1 TTTAAAATATATTTATAATT
52702375 TTTA
1 TTTA
52702379 TATAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAAAATATATTTATAATT
Found at i:52705805 original size:21 final size:21
Alignment explanation
Indices: 52705765--52705979 Score: 177
Period size: 21 Copynumber: 10.3 Consensus size: 21
52705755 GTACATCGTT
* *
52705765 AACAGAAGATCA-AA-AGCTA
1 AACAGAAGCTCATAAGAGCTG
* *
52705784 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* * * * * *
52705805 AACAAAAACCCATAAGGGTTT
1 AACAGAAGCTCATAAGAGCTG
52705826 AACAGAAGCTCGA-AAGAGCTG
1 AACAGAAGCTC-ATAAGAGCTG
* *
52705847 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
*
52705868 AACGGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
52705889 AA-TGAAAACTCATAAGAGTTG
1 AACAG-AAGCTCATAAGAGCTG
*
52705910 AACAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * * * *
52705931 AACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTG
*
52705952 AACAGAAGCTCATTAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
52705973 AACAGAA
1 AACAGAA
52705980 AGTAAAACAC
Statistics
Matches: 151, Mismatches: 39, Indels: 10
0.75 0.19 0.05
Matches are distributed among these distances:
19 11 0.07
20 3 0.02
21 135 0.89
22 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:52705844 original size:42 final size:42
Alignment explanation
Indices: 52705784--52705976 Score: 235
Period size: 42 Copynumber: 4.6 Consensus size: 42
52705774 TCAAAAGCTA
* * * * *
52705784 AACAGAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTT
1 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
*
52705826 AACAGAAGCTCGA-AAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTC-ATAAGAGCTGAACAAAAACTCATAAGAGTTG
* **
52705868 AACGGAAGCTCATAAGAGCTGAATGAAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
* ** * *
52705910 AACAGAAGCTCAAAAGAGCTGAACGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
*
52705952 AACAGAAGCTCATTAGAGCTGAACA
1 AACAGAAGCTCATAAGAGCTGAACA
52705977 GAAAGTAAAA
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 128 0.98
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAAAAACTCATAAGAGTTG
Found at i:52705929 original size:84 final size:84
Alignment explanation
Indices: 52705782--52705976 Score: 273
Period size: 84 Copynumber: 2.3 Consensus size: 84
52705772 GATCAAAAGC
* * * * *
52705782 TAAACAGAAGCTCATGAGAGCTAAACAAAAACCCATAAGGGTTTAACAGAAGCTCGAAAGAGCTG
1 TAAACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTG
52705847 AACAGAAACTCATAAGAGT
66 AACAGAAACTCATAAGAGT
* * ** *
52705866 TGAACGGAAGCTCATAAGAGCTGAATGAAAACTCATAAGAGTTGAACAGAAGCTCAAAAGAGCTG
1 TAAACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTG
* *
52705931 AACGGAAACTCATATGAGT
66 AACAGAAACTCATAAGAGT
*
52705950 TAAACAGAAGCTCATTAGAGCTGAACA
1 TAAACAGAAGCTCATAAGAGCTGAACA
52705977 GAAAGTAAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.17
Consensus pattern (84 bp):
TAAACAGAAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTG
AACAGAAACTCATAAGAGT
Found at i:52707886 original size:20 final size:20
Alignment explanation
Indices: 52707844--52707886 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
52707834 AATTAAACTA
*
52707844 AATTAAACTAAGACTAATCT
1 AATTAAACTAAGACTAATAT
*
52707864 AATT-AACTAAGATTAATTAT
1 AATTAAACTAAGACTAA-TAT
52707884 AAT
1 AAT
52707887 CCAACCTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (20 bp):
AATTAAACTAAGACTAATAT
Found at i:52709566 original size:147 final size:147
Alignment explanation
Indices: 52709299--52709584 Score: 493
Period size: 147 Copynumber: 1.9 Consensus size: 147
52709289 TTCTATTTTG
*
52709299 ATCATCAATTGAAACGGTGTAAAAGTATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTG
1 ATCATCAATTGAAACGGAGTAAAAGTATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTG
*
52709364 AATTGTGGCATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATGAAA
66 AATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATGAAA
52709429 GTACCACTGCTAGTTTA
131 GTACCACTGCTAGTTTA
* * * *
52709446 ATCATCAATTGAAATGGAGTAAAAGTATGATATTTGAGTATTGAATATGCAAATTTATTTGGTTG
1 ATCATCAATTGAAACGGAGTAAAAGTATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTG
*
52709511 AATTGTGACATATATTGATTGAATTTCTATATTGAA-TATGCTTATTTGTTACTTGAATCATGAA
66 AATTGTGACATATATTGATTGAATTTCTATATT-AAGTATGCTTATTTGTGACTTGAATCATGAA
52709575 AGTACCACTG
130 AGTACCACTG
52709585 AGCTTTATTG
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 129 0.98
148 2 0.02
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.39
Consensus pattern (147 bp):
ATCATCAATTGAAACGGAGTAAAAGTATGATATTTGAGTATTGAATATGCAAAGTGATCTGGTTG
AATTGTGACATATATTGATTGAATTTCTATATTAAGTATGCTTATTTGTGACTTGAATCATGAAA
GTACCACTGCTAGTTTA
Found at i:52711271 original size:22 final size:22
Alignment explanation
Indices: 52711246--52711287 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
52711236 AATTTTATCC
52711246 AAATTCAT-TTATATTATTTTTT
1 AAATT-ATATTATATTATTTTTT
52711268 AAATTATATTATATTATTTT
1 AAATTATATTATATTATTTT
52711288 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AAATTATATTATATTATTTTTT
Found at i:52728722 original size:2 final size:2
Alignment explanation
Indices: 52728715--52728762 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
52728705 CATCTCAAAT
52728715 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
52728757 CA CA CA
1 CA CA CA
52728763 TTTACAAACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:52729445 original size:40 final size:40
Alignment explanation
Indices: 52729388--52729494 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
52729378 TAATGCAAAC
* *
52729388 AGGAGCATGAATA-TGCTATCAGGAGCAAAGTGGTGCTAAA
1 AGGAGCACGAA-AGTGCTATCAGGAGCAAAGTAGTGCTAAA
* * ** *
52729428 AGGAGCAC-AAATGTGCTATTAAGAGCACCGTAGTGCTAAC
1 AGGAGCACGAAA-GTGCTATCAGGAGCAAAGTAGTGCTAAA
* *
52729468 AGGAGGACGAAAGTACTATCAGGAGCA
1 AGGAGCACGAAAGTGCTATCAGGAGCA
52729495 CTTATTCAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 47 0.89
41 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (40 bp):
AGGAGCACGAAAGTGCTATCAGGAGCAAAGTAGTGCTAAA
Found at i:52731952 original size:257 final size:256
Alignment explanation
Indices: 52731572--52732082 Score: 959
Period size: 257 Copynumber: 2.0 Consensus size: 256
52731562 TAAATATTGA
*
52731572 AGGCATAATACCAAAAACAGCCCCTAAAGTTTGGTTGTTTGGTCACTTTGGCCATTTTTTTTTGA
1 AGGCATAATACCAAAAACAGCCCCTAAAGTTTGGTTGTTTGATCACTTTGGCCATTTTTTTTTGA
*
52731637 GCACTTTAACACCTAAGTTTTTTAGTCAAATTGGTCTGTTTTTAACGGACATGCTGACGTGATAG
66 GCACTTTAACACCTAAGTTTTTTAGTCAAATTGGTCTGATTTTAACGGACATGCTGACGTGATAG
52731702 TTAGTTGACTAATGGTCAACATAAACCGCTGACGTGGCAGTCCAAATATTTTTAAATGGTGACAT
131 TTAGTTGACTAATGGTCAACATAAACCGCTGACGTGGCAGTCCAAATATTTTTAAATGGTGACAT
52731767 GGCACTATTTTGTCTTATATGCCACGTCAGCAAATGATTTTAAAATTATTAATTTTTTTGT
196 GGCACTATTTTGTCTTATATGCCACGTCAGCAAATGATTTTAAAATTATTAATTTTTTTGT
* *
52731828 AGGCATAATACTAAAAACATCCCCTAAAGTTTGGTTGTTTGATCACTTTGGCCATTTTTTTTTTG
1 AGGCATAATACCAAAAACAGCCCCTAAAGTTTGGTTGTTTGATCACTTTGGCCA-TTTTTTTTTG
52731893 AGCACTTTAACACCTAAGTTTTTTAGTCAAATTGGTCTGATTTTAACGGACATGCTGACGTGATA
65 AGCACTTTAACACCTAAGTTTTTTAGTCAAATTGGTCTGATTTTAACGGACATGCTGACGTGATA
*
52731958 GTTAGTTGACTAATGGTCAACATAAACCGCTGACGTGGCAGTCTAAATATTTTTAAATGGTGACA
130 GTTAGTTGACTAATGGTCAACATAAACCGCTGACGTGGCAGTCCAAATATTTTTAAATGGTGACA
*
52732023 TGGCACTATTTTGTCTTATATGCCACGTCAGTAAATGATTTTAAAATTATTAATTTTTTT
195 TGGCACTATTTTGTCTTATATGCCACGTCAGCAAATGATTTTAAAATTATTAATTTTTTT
52732083 AAATTATTTA
Statistics
Matches: 248, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
256 51 0.21
257 197 0.79
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (256 bp):
AGGCATAATACCAAAAACAGCCCCTAAAGTTTGGTTGTTTGATCACTTTGGCCATTTTTTTTTGA
GCACTTTAACACCTAAGTTTTTTAGTCAAATTGGTCTGATTTTAACGGACATGCTGACGTGATAG
TTAGTTGACTAATGGTCAACATAAACCGCTGACGTGGCAGTCCAAATATTTTTAAATGGTGACAT
GGCACTATTTTGTCTTATATGCCACGTCAGCAAATGATTTTAAAATTATTAATTTTTTTGT
Found at i:52735363 original size:27 final size:27
Alignment explanation
Indices: 52735333--52735385 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
52735323 CTGAGTGTAG
* *
52735333 TGTCCTGGCAAACTATCTCGTGTTTAT
1 TGTCCCGGCAAACTATCCCGTGTTTAT
* *
52735360 TGTCCCGTCGAACTATCCCGTGTTTA
1 TGTCCCGGCAAACTATCCCGTGTTTA
52735386 ATGTGTCATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (27 bp):
TGTCCCGGCAAACTATCCCGTGTTTAT
Found at i:52735724 original size:45 final size:45
Alignment explanation
Indices: 52735631--52735745 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 45
52735621 GTCATAGCGC
* * * *
52735631 CTTTCAGCTATGGTCTTACTCATTTCTATCACGATGCTATAACAT
1 CTTTCAACTATGGTCTTACTCATTTCAATCACGATACCATAACAT
* ***
52735676 CTTTCAACTATGGTCTTACTCATCTT-AATCATGATACCATAGTGT
1 CTTTCAACTATGGTCTTACTCAT-TTCAATCACGATACCATAACAT
*
52735721 CTTTTAACTA-GGTTCTTACTCATTT
1 CTTTCAACTATGG-TCTTACTCATTT
52735746 TAGGCGTATA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 4 0.07
45 53 0.90
46 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (45 bp):
CTTTCAACTATGGTCTTACTCATTTCAATCACGATACCATAACAT
Found at i:52746519 original size:72 final size:72
Alignment explanation
Indices: 52746383--52746519 Score: 157
Period size: 72 Copynumber: 1.9 Consensus size: 72
52746373 GGCATCATGA
* ** * * **
52746383 TAAAATATGTAATACCATAGCTAAAAGATGTTATGGCATCATAGATAGTCCGCCGATATGATAAA
1 TAAAATATGTAAGACCATAGCTAAAAGACATTATGGCATCATAGATAGTCCACCGAGACAATAAA
52746448 CACGAGT
66 CACGAGT
* * * * * *
52746455 TAAACTATGTAAGACCATAGTTGAAAGACATTATGGTATCATAGATAGTCTATCGAGACAATAAA
1 TAAAATATGTAAGACCATAGCTAAAAGACATTATGGCATCATAGATAGTCCACCGAGACAATAAA
52746520 TATGGGATAG
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
72 52 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (72 bp):
TAAAATATGTAAGACCATAGCTAAAAGACATTATGGCATCATAGATAGTCCACCGAGACAATAAA
CACGAGT
Found at i:52747016 original size:19 final size:19
Alignment explanation
Indices: 52746976--52747019 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
52746966 ATTAACGTTC
* *
52746976 TTTCTTATTTTTGTTTTTT
1 TTTCTTATTTTTGATTTAT
52746995 TTTCTTATTTCTT-ATTTAT
1 TTTCTTATTT-TTGATTTAT
52747014 TTTCTT
1 TTTCTT
52747020 TGTTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTCTTATTTTTGATTTAT
Found at i:52757331 original size:3 final size:3
Alignment explanation
Indices: 52757323--52757383 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
52757313 ATTGTGGATG
52757323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52757371 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
52757384 AAAGTTGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52760172 original size:45 final size:45
Alignment explanation
Indices: 52760103--52760188 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
52760093 AGATACTCGA
* * *
52760103 TGGATTCAGCACATAGTAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
52760148 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
52760189 TCAGTTCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
Found at i:52760257 original size:51 final size:50
Alignment explanation
Indices: 52760199--52760385 Score: 214
Period size: 51 Copynumber: 3.7 Consensus size: 50
52760189 TCAGTTCACA
* *
52760199 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGGTACACG
* * * * * *
52760250 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCGGTACACG
* * * *
52760301 TAGTAGCTTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGGTACACG
* *
52760351 TAGTAGTCTGCACATAGTACTACACAGGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
52760386 CACTTTCACT
Statistics
Matches: 110, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 68 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGGTACACG
Found at i:52760373 original size:101 final size:101
Alignment explanation
Indices: 52760197--52760381 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
52760187 GTTCAGTTCA
* * *
52760197 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
52760262 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
52760299 CATAGTAGCTTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGTCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
*
52760363 CATAGTACTACACAGGTGA
65 CATAGTACTACACACGTGA
52760382 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 32 0.43
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:52761666 original size:3 final size:3
Alignment explanation
Indices: 52761658--52761697 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52761648 TAGAATCAAG
52761658 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
52761698 TGCTTTGACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52763515 original size:19 final size:19
Alignment explanation
Indices: 52763493--52763541 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
52763483 ATTACAAAAT
52763493 AATTCAAAATCATTTTT-AA
1 AATTCAAAAT-ATTTTTAAA
*
52763512 AATTAAAAATATTTTTAAA
1 AATTCAAAATATTTTTAAA
52763531 AATTTCAAAAT
1 AA-TTCAAAAT
52763542 TTATATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 7 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATATTTTTAAA
Found at i:52763543 original size:18 final size:18
Alignment explanation
Indices: 52763493--52763531 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
52763483 ATTACAAAAT
*
52763493 AATTCAAAATCATTTTTAA
1 AATTAAAAAT-ATTTTTAA
52763512 AATTAAAAATATTTTTAA
1 AATTAAAAATATTTTTAA
52763530 AA
1 AA
52763532 ATTTCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAAAATATTTTTAA
Found at i:52763571 original size:25 final size:24
Alignment explanation
Indices: 52763516--52763571 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
52763506 TTTTAAAATT
52763516 AAAA-ATATTTTTAAAAATTTCAA
1 AAAATATATTTTTAAAAATTTCAA
**
52763539 AATTTATATTTTTAAAAAATTAT-AA
1 AAAATATATTTTT-AAAAATT-TCAA
52763564 AAAATATA
1 AAAATATA
52763572 AAAAAAGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.08
24 8 0.31
25 15 0.58
26 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATATATTTTTAAAAATTTCAA
Found at i:52772745 original size:204 final size:201
Alignment explanation
Indices: 52772375--52772786 Score: 506
Period size: 204 Copynumber: 2.0 Consensus size: 201
52772365 TCATATGTTT
* * *
52772375 TTTTATTTTTTTAATTTGGTTATGCCAACTTTAACTGTTTTGTCACGCATCTGTTCTTCTCATTC
1 TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACGCATCTGTTCTTCTCATGC
** * * * * * **
52772440 TGATTGGGATACAAAATTGTAATTTCTTTTCCATAGTCTCCCTCCTGTTTCTTCCTCATGCTATC
66 TGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTTTCTTCCACACACTATC
* * * *
52772505 AGTCAAGAACTAGAATTTCTAACTGAATTGGGGAGAACATAACATGTTTTAACTTCCATTGCTGA
131 AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACATGTGTTAACTTCCATTGCTAA
52772570 TATTGA
196 TATTGA
* * ** *
52772576 TTTTCTTTTTTT-ATTCGGTTATGCCATCTGTAACTGTTTTGTCATTCTTCTGTTCTTCCTCATG
1 TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACGCATCTGTTCTT-CTCATG
* *
52772640 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTTCTTCCT-TTCTCTTCTTCACACAC
65 CTGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTT-TCTTC--CACACAC
* * * *
52772704 TCATCAGTCAAGAACTAGAGTTTCTAACTGATTTAGGGAGAACACAACTTGTGTTAGCTTCCATT
127 T-ATCAGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACATGTGTTAACTTCCATT
*
52772769 GCTAATATTTA
191 GCTAATATTGA
52772780 -TTTATTT
1 TTTTATTT
52772787 ACATACTAAC
Statistics
Matches: 177, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
200 41 0.23
201 60 0.34
203 11 0.06
204 65 0.37
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (201 bp):
TTTTATTTTTTTAATTCGGTTATGCCAACTGTAACTGTTTTGTCACGCATCTGTTCTTCTCATGC
TGAAAGGGATACAAAAATGAAATTTCTTTTCCACAGACTCCCTCCTGTTTCTTCCACACACTATC
AGTCAAGAACTAGAATTTCTAACTGAATTAGGGAGAACACAACATGTGTTAACTTCCATTGCTAA
TATTGA
Found at i:52773251 original size:13 final size:12
Alignment explanation
Indices: 52773228--52773271 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
52773218 AAAAAGCTTG
*
52773228 GTTTGGAAAAGT
1 GTTTTGAAAAGT
52773240 GCTTTTGAAAAGT
1 G-TTTTGAAAAGT
*
52773253 GTTGTGGAAAAGT
1 GTT-TTGAAAAGT
52773266 GTTTTG
1 GTTTTG
52773272 TTAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.27, C:0.02, G:0.32, T:0.39
Consensus pattern (12 bp):
GTTTTGAAAAGT
Found at i:52775873 original size:34 final size:34
Alignment explanation
Indices: 52775835--52775906 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
52775825 TAAAAAAATG
*
52775835 TAAA-TATATATACTATA-AAAATGA-ATGTATATTT
1 TAAATTATA-ATA-TATAGAAAAT-ATATGTATATTC
52775869 TAAATTATAATATATAGAAAATATATGTATATTC
1 TAAATTATAATATATAGAAAATATATGTATATTC
52775903 TAAA
1 TAAA
52775907 ATGTACATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 5 0.15
34 25 0.74
35 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (34 bp):
TAAATTATAATATATAGAAAATATATGTATATTC
Found at i:52776765 original size:6 final size:6
Alignment explanation
Indices: 52776756--52776784 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52776746 AAAAAAGGGA
52776756 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
52776785 CGAAACTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:52777965 original size:132 final size:132
Alignment explanation
Indices: 52777602--52778797 Score: 1638
Period size: 132 Copynumber: 8.9 Consensus size: 132
52777592 CAGCAACTTC
* * * * **
52777602 AGGGAGATAAGACCTGTAATCTTCAATCCATTCCACTATTGCCCAGGG-AGATAGAATTACTGGC
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGC
* * * * * *
52777666 TTCAATATACTTCACTGTAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTG
*
52777731 TTT
130 CTT
* **
52777734 AGGGAGATAAGATCTGAAATCTTCAATCTTCAATCTATTCCACTGCTGCTTAGGGAAGTAGAATT
1 AGGGAGACAAGATCTG--A-----AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
52777799 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCA
59 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCA
52777864 CTACTGCTT
124 CTACTGCTT
*
52777873 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTTA-TGGC
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA-TTACTGGC
*
52777937 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACT
65 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACT
52778001 GCTT
129 GCTT
* * * *
52778005 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAATTATTGGCT
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
*
52778070 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGTCTA
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGC-TC-C--ACTA
52778135 -TGC--
127 CTGCTT
* * * * *
52778138 AGGAAGGCAATATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
52778203 TCAATGTACTCCGCTGTAACCACAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACCGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGC
52778268 TT
131 TT
* * * * * *
52778270 AGGGAGACAATATCTGAAATCTTCAATCTACTCCACTACTGCTCAGAGAAGTAGAATTACTGTCT
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
52778335 TCAATGTACTCTACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACCG
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTG
52778399 CTT
130 CTT
52778402 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* *
52778467 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACCG
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTG
52778531 CTT
130 CTT
52778534 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* *
52778599 TCAATGTACTCCGCTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACTG
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTG
52778663 CTT
130 CTT
* * *
52778666 GGGGAGACAAGATCTGAAATCTTTAAACTTCAATCTATTCCACTGCTGTCCAGAG-AGATAGAAT
1 AGGGAGACAAGATCTGAAA----T---CTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAAT
* * * *
52778730 TACTGGCTTCAATATACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTC
58 TACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCC
52778795 ACT
123 ACT
52778798 GTCTATGTAG
Statistics
Matches: 966, Mismatches: 69, Indels: 51
0.89 0.06 0.05
Matches are distributed among these distances:
129 3 0.00
130 2 0.00
131 6 0.01
132 620 0.64
133 114 0.12
134 1 0.00
135 3 0.00
136 4 0.00
137 1 0.00
138 2 0.00
139 207 0.21
140 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGC
TT
Found at i:52778624 original size:529 final size:532
Alignment explanation
Indices: 52777610--52778797 Score: 1775
Period size: 529 Copynumber: 2.2 Consensus size: 532
52777600 TCAGGGAGAT
* * * ** *
52777610 AAGACCTGTAATCTTCAATCCATTCCACTATTGCCCAGGGAGATAGAATTACTGGCTTCAATATA
1 AAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAGATAGAATTACTGGCTTCAATATA
* * * * *
52777675 CTTCACTGTAACCTCAGGAAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGTTTAGGGAG
66 CTCCACTGTAACCTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACCGCTTAGGGAG
* * * *
52777740 ATAAGATCTGAAATCTTCAATCTTCAATCTATTCCACTGCTGCTTAGGGAAGTAGAATTACTGGC
131 ACAAGATCTGAAATCTTCAATCTT-AATC--TTCCACTACTGCTCAGAGAAGTAGAATTACTGGC
* *
52777805 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTG
193 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACCG
*
52777870 CTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTTATG
258 CTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTATG
52777935 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTAC
323 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTAC
* * * *
52778000 TGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCTAGGGAAGTAGAATTAT
388 CGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTAC
* * *
52778065 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTGCCATCTTTGATCTGCTTCGC
453 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACCATCTTTGATCTGCTCCAC
* *
52778129 T-GT-CTATGCAGGAAGGC
517 TACTGCT-TG--GGAAGAC
* * *
52778146 AATATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGA-AGTAGAATTACTGGCTTCAATGT
1 AAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAGA-TAGAATTACTGGCTTCAATAT
* *
52778210 ACTCCGCTGTAACCACAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACCGCTTAGGGA
65 ACTCCACTGTAACCTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACCGCTTAGGGA
* *
52778275 GACAATATCTGAAATCTTCAATC-T-A-C-TCCACTACTGCTCAGAGAAGTAGAATTACTGTCTT
130 GACAAGATCTGAAATCTTCAATCTTAATCTTCCACTACTGCTCAGAGAAGTAGAATTACTGGCTT
*
52778336 CAATGTACTCTACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACCGC
195 CAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-ACCATCTTTGATCTGCTCCACTACCGC
52778400 TTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA-TTACTG
259 TTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTA-TG
52778464 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTAC
323 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTAC
*
52778529 CGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTAC
388 CGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTAC
*
52778594 TGGCTTCAATGTACTCCGCTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
453 TGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACT
*
52778659 ACTGCTTGGGGAGAC
518 ACTGCTTGGGAAGAC
*
52778674 AAGATCTGAAATCTTTAAACTTCAATCTATTCCACTGCTGTCCAGAGAGATAGAATTACTGGCTT
1 AAGATCTGAAA----T---CTTCAATCTATTCCACTGCTGTCCAGGGAGATAGAATTACTGGCTT
* * *
52778739 CAATATACTCCACTGTAATCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCACT
59 CAATATACTCCACTGTAACCTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACT
52778798 GTCTATGTAG
Statistics
Matches: 591, Mismatches: 47, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
528 19 0.03
529 332 0.56
530 5 0.01
531 2 0.00
532 2 0.00
533 1 0.00
535 97 0.16
536 133 0.23
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (532 bp):
AAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAGATAGAATTACTGGCTTCAATATA
CTCCACTGTAACCTCAGGAAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACCGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTTAATCTTCCACTACTGCTCAGAGAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACCGCTT
AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTTATGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTACCGC
TTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGG
CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCACTACT
GCTTGGGAAGAC
Found at i:52784598 original size:3 final size:3
Alignment explanation
Indices: 52784578--52784663 Score: 124
Period size: 3 Copynumber: 29.7 Consensus size: 3
52784568 AATATAAATG
* * *
52784578 ATA ATG ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52784626 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52784664 TAAACAGTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 6 0.08
3 69 0.92
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52788295 original size:27 final size:27
Alignment explanation
Indices: 52788253--52788322 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
52788243 ACAAACGTAT
*
52788253 GAAAGATTGAAACCTTTTGAAAGAAAA
1 GAAAGATTGACACCTTTTGAAAGAAAA
*
52788280 GAAAGATTGACGCCTTTTGAAAGAAAA
1 GAAAGATTGACACCTTTTGAAAGAAAA
52788307 GAAAGATTGACACCTT
1 GAAAGATTGACACCTT
52788323 GAATTTATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (27 bp):
GAAAGATTGACACCTTTTGAAAGAAAA
Found at i:52791873 original size:24 final size:24
Alignment explanation
Indices: 52791846--52791897 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
52791836 ATTTGAGAAG
*
52791846 ATTTAGTATTTATT-AGTATAATAT
1 ATTTAGCATTTATTGA-TATAATAT
*
52791870 ATTTAGCATTTATTGATATAATTT
1 ATTTAGCATTTATTGATATAATAT
52791894 ATTT
1 ATTT
52791898 GACCTACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTGATATAATAT
Found at i:52800142 original size:18 final size:17
Alignment explanation
Indices: 52800119--52800179 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
52800109 CTACATTTGT
*
52800119 GAGCTCACCAAAAGTTGC
1 GAGCTCACAAAAAG-TGC
*
52800137 GAGCTCAACTAAAAGTGC
1 GAGCTC-ACAAAAAGTGC
*
52800155 GAGCTCATAAAAAGATGC
1 GAGCTCACAAAAAG-TGC
52800173 GAGCTCA
1 GAGCTCA
52800180 ACTTAAATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 6 0.16
18 25 0.66
19 7 0.18
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (17 bp):
GAGCTCACAAAAAGTGC
Found at i:52803885 original size:3 final size:3
Alignment explanation
Indices: 52803877--52803940 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
52803867 ACAGTAACAT
52803877 TAA TAA TAA 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 TAA TAA TAA
52803925 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
52803941 TAAAGAGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52804573 original size:15 final size:16
Alignment explanation
Indices: 52804549--52804582 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52804539 CTTAGTTTAT
*
52804549 GAAAACAAATTA-AAA
1 GAAAAAAAATTATAAA
52804564 GAAAAAAAATTATAAA
1 GAAAAAAAATTATAAA
52804580 GAA
1 GAA
52804583 GAGAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
GAAAAAAAATTATAAA
Found at i:52807422 original size:29 final size:29
Alignment explanation
Indices: 52807386--52807443 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
52807376 TTCTGAATTA
52807386 ACTAAAATTGTGATTTCGATAGAAATTCG
1 ACTAAAATTGTGATTTCGATAGAAATTCG
*
52807415 ACTAAAATTGTGATTTTGATAGAAATTCG
1 ACTAAAATTGTGATTTCGATAGAAATTCG
52807444 TTAGGGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (29 bp):
ACTAAAATTGTGATTTCGATAGAAATTCG
Found at i:52808513 original size:30 final size:29
Alignment explanation
Indices: 52808474--52808554 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
52808464 GATTTAATCA
* *
52808474 AAATTAAAGTTTCATGTATATAATTG-CATT
1 AAATCAAAG-TTCATGTATA-AAATGACATT
*
52808504 AAATCAAAGTTCATGGATCAAAATGCACATT
1 AAATCAAAGTTCATGTAT-AAAATG-ACATT
*
52808535 AAATCAAAATTCATGTATAA
1 AAATCAAAGTTCATGTATAA
52808555 TTTTGAGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 12 0.28
30 11 0.26
31 20 0.47
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATGACATT
Found at i:52813821 original size:55 final size:55
Alignment explanation
Indices: 52813709--52813813 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
52813699 TAAGCAACTC
* * *
52813709 TTTTTTTTAGCAAATACCGACTTTCATAATGAAATGGATTTGAAAGATGACCATT
1 TTTTTTTTAGCAAATACCAACTTTCATAATGAAATGAATTTGAAAGATAACCATT
* * * *
52813764 TTTTTTTTAGCAAATA-CAATTTTTTATAATTAAATGAATTTGACAGATAA
1 TTTTTTTTAGCAAATACCAA-CTTTCATAATGAAATGAATTTGAAAGATAA
52813814 TTATTTTTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 2 0.05
55 40 0.95
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (55 bp):
TTTTTTTTAGCAAATACCAACTTTCATAATGAAATGAATTTGAAAGATAACCATT
Found at i:52817135 original size:27 final size:27
Alignment explanation
Indices: 52817082--52817142 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
52817072 TAAACTATTA
*
52817082 CCACAAAGGCTATCATTGCAGGGTTTG
1 CCACAAAGGCTATCATTGCAGGATTTG
* *
52817109 CCACAAAGGCTATCCCTT-CATGATTTG
1 CCACAAAGGCTAT-CATTGCAGGATTTG
52817136 CCACAAA
1 CCACAAA
52817143 AGCGTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTATCATTGCAGGATTTG
Found at i:52817165 original size:27 final size:27
Alignment explanation
Indices: 52817135--52817260 Score: 74
Period size: 27 Copynumber: 4.7 Consensus size: 27
52817125 TTCATGATTT
*
52817135 GCCACAAAAGCGTTCCTTTTATATTGC
1 GCCACAAAAGCGTTCCTTTCATATTGC
* * * *
52817162 GCCATAAAGGCTTTCCTTTCATATTGT
1 GCCACAAAAGCGTTCCTTTCATATTGC
* * * **
52817189 GCTAGAAAGGCGTTATTTTCATAATT-C
1 GCCACAAAAGCGTTCCTTTCAT-ATTGC
* * * * *
52817216 ACCACAAATGCTTTACTTTCATATTGT
1 GCCACAAAAGCGTTCCTTTCATATTGC
* * *
52817243 GTCACAAAGGCTTTCCTT
1 GCCACAAAAGCGTTCCTT
52817261 AGGCGTTATT
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
26 3 0.04
27 69 0.92
28 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (27 bp):
GCCACAAAAGCGTTCCTTTCATATTGC
Found at i:52817202 original size:54 final size:55
Alignment explanation
Indices: 52817108--52817260 Score: 145
Period size: 54 Copynumber: 2.8 Consensus size: 55
52817098 TGCAGGGTTT
* * * *
52817108 GCCACAAAGGCTATCCCTTCATGATT-TGCCACAAAAGCGTTCCTTTT-AT-ATTGC
1 GCCACAAAGGCTTTCCTTTCAT-ATTGTGCTACAAAGGCGTTCCTTTTCATAATT-C
* * *
52817162 GCCATAAAGGCTTTCCTTTCATATTGTGCTAGAAAGGCGTT-ATTTTCATAATTC
1 GCCACAAAGGCTTTCCTTTCATATTGTGCTACAAAGGCGTTCCTTTTCATAATTC
* * * *
52817216 ACCACAAATGCTTTACTTTCATATTGTG-TCACAAAGGCTTTCCTT
1 GCCACAAAGGCTTTCCTTTCATATTGTGCT-ACAAAGGCGTTCCTT
52817261 AGGCGTTATT
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
53 8 0.10
54 67 0.84
55 5 0.06
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (55 bp):
GCCACAAAGGCTTTCCTTTCATATTGTGCTACAAAGGCGTTCCTTTTCATAATTC
Found at i:52817300 original size:65 final size:65
Alignment explanation
Indices: 52817196--52817325 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
52817186 TGTGCTAGAA
52817196 AGGCGTTATTTTCATAATTCACCACAAATGCTTTACTTTCATATTGTGTCACAAAGGCTTTCCTT
1 AGGCGTTATTTTCATAATTCACCACAAATGCTTTACTTTCATATTGTGTCACAAAGGCTTTCCTT
52817261 AGGCGTTATTTTCATAATTCACCACAAATGCTTTACTTTCATATTGTGTCACAAAGGCTTTCCTT
1 AGGCGTTATTTTCATAATTCACCACAAATGCTTTACTTTCATATTGTGTCACAAAGGCTTTCCTT
52817326 TCTTGACATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (65 bp):
AGGCGTTATTTTCATAATTCACCACAAATGCTTTACTTTCATATTGTGTCACAAAGGCTTTCCTT
Found at i:52821453 original size:30 final size:30
Alignment explanation
Indices: 52821414--52821481 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
52821404 ACCAAAAAAA
*
52821414 GCCGTTTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
* ** *
52821444 GCCGA-TTTTTTGATTATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
52821473 GCC-ATTTTT
1 GCCGATTTTT
52821482 CGCGAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.84
30 4 0.12
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (30 bp):
GCCGATTTTTTTCAAAATTTACCGAAATGG
Found at i:52823082 original size:63 final size:63
Alignment explanation
Indices: 52822962--52823086 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
52822952 CTACAATCCA
* * * *
52822962 GACATTCAAAAAAACTTAGTTTCATCAATTGAAACATAAAAATCTTTGTCATTAGATGAACCG
1 GACATTCAAAAAAACTTAGTTTCATCAATAGAAACATAAAAACCTTTATCATCAGATGAACCG
* * * *
52823025 GACATTCAAACAAAACTTGGTTTCAT-TATAGAAATATACAAACCTTTATCATCAGATGAACC
1 GACATTCAAA-AAAACTTAGTTTCATCAATAGAAACATAAAAACCTTTATCATCAGATGAACC
52823087 AGACTAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 39 0.74
64 14 0.26
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (63 bp):
GACATTCAAAAAAACTTAGTTTCATCAATAGAAACATAAAAACCTTTATCATCAGATGAACCG
Found at i:52831474 original size:19 final size:20
Alignment explanation
Indices: 52831450--52831493 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
52831440 GTTTTGTATT
52831450 TTTTTTA-CT-TTTACTTTTA
1 TTTTTTATCTATTTA-TTTTA
*
52831469 TTTTTTATTTATTTATTTTA
1 TTTTTTATCTATTTATTTTA
52831489 TTTTT
1 TTTTT
52831494 ATTAATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTATCTATTTATTTTA
Found at i:52831483 original size:15 final size:15
Alignment explanation
Indices: 52831446--52831496 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
52831436 TTTTGTTTTG
* *
52831446 TATTTTTTTTACTTT
1 TATTTATTTTATTTT
52831461 TACTTTTATTTT-TTATT
1 TA--TTTATTTTATT-TT
52831478 TATTTATTTTATTTT
1 TATTTATTTTATTTT
52831493 TATT
1 TATT
52831497 AATCTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 16 0.53
16 3 0.10
17 11 0.37
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTATTTTATTTT
Found at i:52831774 original size:19 final size:19
Alignment explanation
Indices: 52831750--52831789 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52831740 ATATTTCATA
*
52831750 TTTCTTGTCGTAGTATTTT
1 TTTCTTGTCATAGTATTTT
52831769 TTTCTTGTCATAGTATTTT
1 TTTCTTGTCATAGTATTTT
52831788 TT
1 TT
52831790 AGGTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTCTTGTCATAGTATTTT
Found at i:52836080 original size:45 final size:44
Alignment explanation
Indices: 52836018--52836271 Score: 240
Period size: 45 Copynumber: 5.7 Consensus size: 44
52836008 TTTGACATGA
* * *
52836018 TGCCATAGTGCTTTTCAACTATGGTCTTATTCATTTCCATCATAT
1 TGCCATAGTGTTTTTCAACTATGGTCTTATTCATTTCCGT-ATAG
* * * **
52836063 TGCCACAATGTTTTTCAACTGTGGTCTTATTCGATTTTGGTATAG
1 TGCCATAGTGTTTTTCAACTATGGTCTTATTC-ATTTCCGTATAG
* *
52836108 TGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTCCGGTATAG
1 TGCCATAGTGTTTTTCAACTATGGTCTTATTCATTTCC-GTATAG
* * **
52836153 TGTCATAGTGTCTTTT-AACTATGATCTTATTCATTTTTGATATAG
1 TGCCATAGTGT-TTTTCAACTATGGTCTTATTCATTTCCG-TATAG
* * * * * *
52836198 TGCCATTGTGTCTTTCAATTATCGTCTTTTTCATTTCTGGTATAG
1 TGCCATAGTGTTTTTCAACTATGGTCTTATTCATTTC-CGTATAG
* * *
52836243 TGCTATAGTGTCTTTCAATTATGGTCTTA
1 TGCCATAGTGTTTTTCAACTATGGTCTTA
52836272 CTCGTATTTC
Statistics
Matches: 169, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
44 8 0.05
45 152 0.90
46 9 0.05
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (44 bp):
TGCCATAGTGTTTTTCAACTATGGTCTTATTCATTTCCGTATAG
Found at i:52836214 original size:135 final size:135
Alignment explanation
Indices: 52836021--52836271 Score: 319
Period size: 135 Copynumber: 1.9 Consensus size: 135
52836011 GACATGATGC
* * * * *
52836021 CATAGTGCTTTTCAACTATGGTCTTATTCATTTCCATCATATTGCCACAATGTTTTTCAACTGTG
1 CATAGTGCTTTTCAACTATGATCTTATTCATTTCCATCATAGTGCCACAATGTCTTTCAACTATC
*
52836086 GTCTTATTCGATTT-TGGTATAGTGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTCCGGTA
66 GTCTTATTC-ATTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGGTA
52836150 TAGTGT
130 TAGTGT
** *** *
52836156 CATAGTGTCTTTT-AACTATGATCTTATTCATTTTTGAT-ATAGTGCCATTGTGTCTTTCAATTA
1 CATAGTG-CTTTTCAACTATGATCTTATTCA-TTTCCATCATAGTGCCACAATGTCTTTCAACTA
* * *
52836219 TCGTCTTTTTCATTTCTGGTATAGTGCTATAGTGTCTTTCAATTATGGTCTTA
64 TCGTCTTATTCATTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTA
52836272 CTCGTATTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
134 4 0.04
135 84 0.86
136 10 0.10
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (135 bp):
CATAGTGCTTTTCAACTATGATCTTATTCATTTCCATCATAGTGCCACAATGTCTTTCAACTATC
GTCTTATTCATTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGGTAT
AGTGT
Found at i:52836251 original size:90 final size:90
Alignment explanation
Indices: 52836018--52836280 Score: 273
Period size: 90 Copynumber: 2.9 Consensus size: 90
52836008 TTTGACATGA
* * * * * * *
52836018 TGCCATAGTG-CTTTTCAACTATGGTCTTATTCATTTCC-ATCATATTGCCACAATGTTTTTCAA
1 TGCCATAGTGTC-TTTCAACTATCGTCTTATTCATTTCCGGT-ATAGTGTCATAGTGTCTTTCAA
* * *
52836081 CTGTGGTCTTATTCGATTTTGGTATAG
64 CTATGATCTTATTCGATTTTGATATAG
* * *
52836108 TGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTCCGGTATAGTGTCATAGTGTCTTTTAACT
1 TGCCATAGTGTCTTTCAACTATCGTCTTATTCATTTCCGGTATAGTGTCATAGTGTCTTTCAACT
52836173 ATGATCTTATTC-ATTTTTGATATAG
66 ATGATCTTATTCGA-TTTTGATATAG
* * * * *
52836198 TGCCATTGTGTCTTTCAATTATCGTCTTTTTCATTTCTGGTATAGTG-CTATAGTGTCTTTCAAT
1 TGCCATAGTGTCTTTCAACTATCGTCTTATTCATTTCCGGTATAGTGTC-ATAGTGTCTTTCAAC
* *
52836262 TATGGTCTTACTCGTATTT
65 TATGATCTTATTCG-ATTT
52836281 CAACCAATAA
Statistics
Matches: 146, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
89 2 0.01
90 138 0.95
91 5 0.03
92 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (90 bp):
TGCCATAGTGTCTTTCAACTATCGTCTTATTCATTTCCGGTATAGTGTCATAGTGTCTTTCAACT
ATGATCTTATTCGATTTTGATATAG
Found at i:52844572 original size:42 final size:42
Alignment explanation
Indices: 52844453--52844560 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
52844443 ACGGTCTATG
* * *
52844453 ACACGACCGTGTGTATCAAGTTAGTGAGTCACACGGTTTGGC
1 ACACGGCCGTGTGTATCAAGTCAGTGAGTCACACGGTCTGGC
* *
52844495 ACACGGCCGTCTGTATCAAGTCAGTGAGCCACACGGTCTGGC
1 ACACGGCCGTGTGTATCAAGTCAGTGAGTCACACGGTCTGGC
52844537 ACACGGCCGTGTGTATCAAGTCAG
1 ACACGGCCGTGTGTATCAAGTCAG
52844561 AAAGTTACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.22
Consensus pattern (42 bp):
ACACGGCCGTGTGTATCAAGTCAGTGAGTCACACGGTCTGGC
Found at i:52844578 original size:30 final size:30
Alignment explanation
Indices: 52844537--52844600 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
52844527 ACGGTCTGGC
52844537 ACACGGCCGTGTGTATC-AAGTCAGAAAGTT
1 ACACGGCCGTGTG-ATCTAAGTCAGAAAGTT
* **
52844567 ACACGGGCGTGTGATCTAAGTCAGTGAGTT
1 ACACGGCCGTGTGATCTAAGTCAGAAAGTT
52844597 ACAC
1 ACAC
52844601 AATTTAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (30 bp):
ACACGGCCGTGTGATCTAAGTCAGAAAGTT
Found at i:52847279 original size:27 final size:27
Alignment explanation
Indices: 52847240--52847303 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
52847230 AAATATTCTT
* *
52847240 TAAATTAAT-AAATATTAATTTATTGA
1 TAAACTAATAAAATATTAATTTAGTGA
*
52847266 TAAACTAATAAAATATTCATTTAGTGA
1 TAAACTAATAAAATATTAATTTAGTGA
52847293 TAAACTAATAA
1 TAAACTAATAA
52847304 CCTCAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.24
27 26 0.76
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (27 bp):
TAAACTAATAAAATATTAATTTAGTGA
Found at i:52849402 original size:45 final size:45
Alignment explanation
Indices: 52849299--52849414 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 45
52849289 TCAAAGATGT
* * * *
52849299 CATAGTGTCTTTCAACTATGTTCTTATTCATTTTCGTCATATTGT
1 CATAGTGTCTTTCAACTATGGTCTTATTCATTCTCGTCATAGTGC
* * * * *
52849344 CATAATTTTTTTCAACTATGGTCTTATTTGATTCTGGT-ATAGTGC
1 CATAGTGTCTTTCAACTATGGTCTTA-TTCATTCTCGTCATAGTGC
*
52849389 CATAGTGTCTTTCATCTATGGTCTTA
1 CATAGTGTCTTTCAACTATGGTCTTA
52849415 CTTGTTTGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
45 49 0.86
46 8 0.14
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (45 bp):
CATAGTGTCTTTCAACTATGGTCTTATTCATTCTCGTCATAGTGC
Found at i:52849512 original size:5 final size:5
Alignment explanation
Indices: 52849502--52849532 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
52849492 CCAAAATAGT
*
52849502 AATTA AATTA AATTA AATTA AATTA ATTTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
52849533 GAACTTACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:52850280 original size:17 final size:17
Alignment explanation
Indices: 52850258--52850292 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52850248 ATTTAATAAA
52850258 ATTTCATAAAACATATC
1 ATTTCATAAAACATATC
52850275 ATTTCATAAAACATATC
1 ATTTCATAAAACATATC
52850292 A
1 A
52850293 CCTAATCCGT
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:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTCATAAAACATATC
Found at i:52858126 original size:13 final size:13
Alignment explanation
Indices: 52858108--52858152 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
52858098 ACTCCACCCC
52858108 AAATACAGATACA
1 AAATACAGATACA
*
52858121 AAATACAGAAACA
1 AAATACAGATACA
**
52858134 GTATACAGATACA
1 AAATACAGATACA
52858147 GAAATA
1 -AAATA
52858153 TCATGCTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (13 bp):
AAATACAGATACA
Found at i:52859500 original size:69 final size:69
Alignment explanation
Indices: 52859389--52859519 Score: 246
Period size: 69 Copynumber: 1.9 Consensus size: 69
52859379 TATCATCTTC
52859389 TCAGGAAAGTCACTTTATGATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
1 TCAGGAAAGTCACTTTATGATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
52859454 AAAG
66 AAAG
52859458 TCAGGAAAGTCACTTTATGATTTTTCTCTCAAC-GAGAAGAGCAATTGTTATACTAAATTCAA
1 TCAGGAAAGTCACTTTATGATTTTTCTCTC-ACTGAGAAGAGCAATTGTTATACTAAATTCAA
52859520 TGTAGCTCTG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 59 0.97
70 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (69 bp):
TCAGGAAAGTCACTTTATGATTTTTCTCTCACTGAGAAGAGCAATTGTTATACTAAATTCAACCT
AAAG
Found at i:52860830 original size:31 final size:32
Alignment explanation
Indices: 52860795--52860856 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
52860785 CTTTTTAGTT
* *
52860795 AAATTTAACTTTTAACCTTTT-AAAAAGAGTG
1 AAATTTAACTATCAACCTTTTGAAAAAGAGTG
* *
52860826 AAATTTGACTATCAACTTTTTGAAAAAGAGT
1 AAATTTAACTATCAACCTTTTGAAAAAGAGT
52860857 CTAATTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (32 bp):
AAATTTAACTATCAACCTTTTGAAAAAGAGTG
Found at i:52861282 original size:27 final size:28
Alignment explanation
Indices: 52861251--52861312 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
52861241 TGTATTTTTT
52861251 TTATTTTATAAATAATTTT-AAAAAAAA
1 TTATTTTATAAATAATTTTAAAAAAAAA
* * ** *
52861278 TTATTATGTGTATATTTTTAAAAAAAAA
1 TTATTTTATAAATAATTTTAAAAAAAAA
52861306 TTATTTT
1 TTATTTT
52861313 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TTATTTTATAAATAATTTTAAAAAAAAA
Found at i:52862642 original size:129 final size:129
Alignment explanation
Indices: 52862484--52862746 Score: 490
Period size: 129 Copynumber: 2.0 Consensus size: 129
52862474 TTTTGTAACA
* *
52862484 GTTGAACTGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGAGAGCTCAAAAATTCTGGT
1 GTTGAAATGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
*
52862549 GAAGATGAATAACTTAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTAAT
66 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTAAT
52862613 GTTGAAATGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
1 GTTGAAATGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
*
52862678 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTGAT
66 GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTAAT
52862742 GTTGA
1 GTTGA
52862747 TTGTGTATTC
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (129 bp):
GTTGAAATGAAGAGAAGAAAAGAGAGAAATTGTTGTGTTTAGTAGGACAGCTCAAAAATTCTGGT
GAAGATGAATAACTCAGTGTTTTTAGTGTACATTCTTTTTTATGGTGAAATTGTAAAAGGTAAT
Found at i:52866118 original size:20 final size:20
Alignment explanation
Indices: 52866095--52866133 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52866085 AAGAAATTTG
52866095 ATAACAAAGA-AAAAATAAAA
1 ATAA-AAAGAGAAAAATAAAA
*
52866115 ATAAAAATAGAAAAATAAA
1 ATAAAAAGAGAAAAATAAA
52866134 TAGAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (20 bp):
ATAAAAAGAGAAAAATAAAA
Found at i:52882964 original size:33 final size:31
Alignment explanation
Indices: 52882897--52882964 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 31
52882887 TACCTACAAC
* *
52882897 AAAAGAAAGAAATAAAACTAATTACTTCAAT
1 AAAAGAAAGAAATAAAACAAATTAATTCAAT
*
52882928 AAAAGAGAGAAATAAAAAACAAATTAATT-AACT
1 AAAAGAAAGAAAT--AAAACAAATTAATTCAA-T
52882961 AAAA
1 AAAA
52882965 CCAAGCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 12 0.39
32 2 0.06
33 17 0.55
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.19
Consensus pattern (31 bp):
AAAAGAAAGAAATAAAACAAATTAATTCAAT
Found at i:52904907 original size:25 final size:25
Alignment explanation
Indices: 52904873--52904926 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
52904863 TGAGCTACAT
*
52904873 GGCCTGGCACATGGGCGCATGACAC
1 GGCCTGGCACACGGGCGCATGACAC
* **
52904898 GGCCTGGCACACGGGTGTGTGACAC
1 GGCCTGGCACACGGGCGCATGACAC
52904923 GGCC
1 GGCC
52904927 GTGTGACCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.17, C:0.31, G:0.39, T:0.13
Consensus pattern (25 bp):
GGCCTGGCACACGGGCGCATGACAC
Found at i:52906773 original size:27 final size:27
Alignment explanation
Indices: 52906742--52906796 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
52906732 CTACTTGGAT
*
52906742 TCATTTCA-AGTTTCACATCTCATTTCA
1 TCATTTCATA-TTTCACATCTCATCTCA
*
52906769 TCATTTCATATTTCACTTCTCATCTCA
1 TCATTTCATATTTCACATCTCATCTCA
52906796 T
1 T
52906797 ATACATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (27 bp):
TCATTTCATATTTCACATCTCATCTCA
Found at i:52906808 original size:18 final size:19
Alignment explanation
Indices: 52906762--52906811 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
52906752 TTTCACATCT
* *
52906762 CATTTCATCATTTCATATTT
1 CATTTC-TCATCTCATATTA
*
52906782 CACTTCTCATCTCATA-TA
1 CATTTCTCATCTCATATTA
52906800 CATTTCTCATCT
1 CATTTCTCATCT
52906812 TTGCCATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 12 0.46
19 9 0.35
20 5 0.19
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (19 bp):
CATTTCTCATCTCATATTA
Found at i:52906834 original size:43 final size:43
Alignment explanation
Indices: 52906785--52906869 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
52906775 CATATTTCAC
52906785 TTCTCATCTCATATACATTTCTCATCTTTGCCATTTCAATATT
1 TTCTCATCTCATATACATTTCTCATCTTTGCCATTTCAATATT
* *
52906828 TTCTCATCTCATATGCATTTCTCATCTTTTCCATTTCAATAT
1 TTCTCATCTCATATACATTTCTCATCTTTGCCATTTCAATAT
52906870 CAATCACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.22, C:0.26, G:0.02, T:0.49
Consensus pattern (43 bp):
TTCTCATCTCATATACATTTCTCATCTTTGCCATTTCAATATT
Found at i:52907235 original size:22 final size:24
Alignment explanation
Indices: 52907191--52907235 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
52907181 TCACATATAA
*
52907191 ATATATATTCAATTCAATCTCATT
1 ATATATATTCAATTAAATCTCATT
52907215 ATATATATTC-ATTAAAT-TCAT
1 ATATATATTCAATTAAATCTCAT
52907236 AATTTACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATATTCAATTAAATCTCATT
Found at i:52916162 original size:13 final size:14
Alignment explanation
Indices: 52916144--52916174 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
52916134 ATTAGAGGTA
52916144 GTCAAAGTCATT-T
1 GTCAAAGTCATTCT
52916157 GTCAAAGTCATTCT
1 GTCAAAGTCATTCT
52916171 GTCA
1 GTCA
52916175 GACAATCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (14 bp):
GTCAAAGTCATTCT
Found at i:52916323 original size:31 final size:29
Alignment explanation
Indices: 52916265--52916323 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
52916255 TTAGTTAGGC
**
52916265 CCTTTAAAATTTTAAAAATTATTATTAAG
1 CCTTTAAAATTTTAAAAATTACAATTAAG
52916294 CCTTTGAAAATTTTTAAAAATTACAATTAA
1 CCTTT-AAAA-TTTTAAAAATTACAATTAA
52916324 ACTCTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 17 0.65
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (29 bp):
CCTTTAAAATTTTAAAAATTACAATTAAG
Found at i:52924556 original size:29 final size:30
Alignment explanation
Indices: 52924524--52924582 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
52924514 TATGGTTTAA
*
52924524 TGTGCAATTGTATATATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* * *
52924553 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
52924583 GATCCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:52931596 original size:20 final size:22
Alignment explanation
Indices: 52931556--52931596 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52931546 ATTTGGTTTT
*
52931556 AAAAGTATTGAAAATATTAAAG
1 AAAAGTAATGAAAATATTAAAG
52931578 AAAAGTAAT-AAAA-ATTAAA
1 AAAAGTAATGAAAATATTAAA
52931597 TTGAAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (22 bp):
AAAAGTAATGAAAATATTAAAG
Found at i:52935039 original size:3 final size:3
Alignment explanation
Indices: 52935028--52935073 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
52935018 CCCAAAACCC
52935028 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCTT CT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CT
52935074 ACAGCTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:52938878 original size:24 final size:24
Alignment explanation
Indices: 52938815--52938866 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52938805 TTTCTAGAAG
* * *
52938815 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
52938839 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
52938863 ATTT
1 ATTT
52938867 GCCTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:52943272 original size:10 final size:10
Alignment explanation
Indices: 52943257--52943294 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
52943247 TATGTTTAGT
52943257 TTTAATTAAG
1 TTTAATTAAG
52943267 TTTAATTAA-
1 TTTAATTAAG
52943276 TTTAATTAAG
1 TTTAATTAAG
*
52943286 ATTAATTAA
1 TTTAATTAA
52943295 TTACTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (10 bp):
TTTAATTAAG
Found at i:52943281 original size:19 final size:19
Alignment explanation
Indices: 52943257--52943296 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52943247 TATGTTTAGT
*
52943257 TTTAATTAAGTTTAATTAA
1 TTTAATTAAGATTAATTAA
52943276 TTTAATTAAGATTAATTAA
1 TTTAATTAAGATTAATTAA
52943295 TT
1 TT
52943297 ACTATGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTTAATTAAGATTAATTAA
Found at i:52944497 original size:119 final size:120
Alignment explanation
Indices: 52944369--52944686 Score: 324
Period size: 120 Copynumber: 2.7 Consensus size: 120
52944359 AGATATTTGT
* *
52944369 GACACAGGTTTAG-CTCGGACGAGTAACCTGATGTCAATTTAAAGGTTTAGACT-GAAC-ATGTA
1 GACATAGGTTTAGCCT-GGACGAGTAACCTGATGTCATTTTAAAGGTTTAG-CTCGAACGA-GTA
* ** * *
52944431 ACCTGACATGTATATA-TTTCAGCTCGGATGAGCAATTGATGTGTCGAGGATACTTAG
63 ACCTGACATGTATATATTTTCAGCTAGGACAAACAATTGATGTGTCGAGAATACTTAG
** * * *
52944488 GACATAGGTTTAGCCTGGATTAGTAACCTGATGTCGTTTTAAAGATTTAGCTCGAACGAGTAATC
1 GACATAGGTTTAGCCTGGACGAGTAACCTGATGTCATTTTAAAGGTTTAGCTCGAACGAGTAACC
** ** * *
52944553 TGTTATGTATATATTTTCAGCTAGGACAAATGATTGATGTTTCGAGAATACTTGG
66 TGACATGTATATATTTTCAGCTAGGACAAACAATTGATGTGTCGAGAATACTTAG
* ** * *
52944608 GACATAAGTTTAGCCTAAACTG-GTAACCTGATGTCATTTTAAAGGTTTAG-TCCGGACGAATAA
1 GACATAGGTTTAGCCTGGAC-GAGTAACCTGATGTCATTTTAAAGGTTTAGCT-CGAACGAGTAA
* *
52944671 CTTGACATGTGTATAT
64 CCTGACATGTATATAT
52944687 ATATTAAACT
Statistics
Matches: 161, Mismatches: 32, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
118 2 0.01
119 62 0.39
120 97 0.60
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (120 bp):
GACATAGGTTTAGCCTGGACGAGTAACCTGATGTCATTTTAAAGGTTTAGCTCGAACGAGTAACC
TGACATGTATATATTTTCAGCTAGGACAAACAATTGATGTGTCGAGAATACTTAG
Found at i:52962268 original size:8 final size:7
Alignment explanation
Indices: 52962243--52962327 Score: 53
Period size: 7 Copynumber: 11.4 Consensus size: 7
52962233 AAATAAAATA
52962243 AAAATTC
1 AAAATTC
52962250 AAAATTC
1 AAAATTC
52962257 AAAATTC
1 AAAATTC
* *
52962264 AAAAATA
1 AAAATTC
**
52962271 AAAATAA
1 AAAATTC
**
52962278 AAAATAA
1 AAAATTC
52962285 AAAATCTC
1 AAAAT-TC
*
52962293 AAAATTTT
1 AAAA-TTC
*
52962301 AAAATATA
1 AAAAT-TC
52962309 AAAATCCTC
1 AAAAT--TC
52962318 AAAATTC
1 AAAATTC
52962325 AAA
1 AAA
52962328 GTTATCAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
7 42 0.66
8 15 0.23
9 7 0.11
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTC
Found at i:52962309 original size:25 final size:25
Alignment explanation
Indices: 52962275--52962323 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
52962265 AAAATAAAAA
52962275 TAAAAAATAAAAAAT-CTCAAAATTT
1 TAAAAAAT-AAAAATCCTCAAAATTT
*
52962300 TAAAATATAAAAATCCTCAAAATT
1 TAAAAAATAAAAATCCTCAAAATT
52962324 CAAAGTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAAATAAAAATCCTCAAAATTT
Found at i:52969349 original size:20 final size:20
Alignment explanation
Indices: 52969303--52969342 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52969293 TTTCCCTTTT
*
52969303 ATATAAAAATTAATTGATTG
1 ATATAAAAATTAATTGAGTG
*
52969323 ATATAAAAATTAATTTAGTG
1 ATATAAAAATTAATTGAGTG
52969343 TAATAAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
ATATAAAAATTAATTGAGTG
Found at i:52969362 original size:7 final size:7
Alignment explanation
Indices: 52969350--52969390 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
52969340 GTGTAATAAA
52969350 CTCTTTT
1 CTCTTTT
52969357 CTCTTTT
1 CTCTTTT
52969364 CTCTTTT
1 CTCTTTT
*
52969371 CTCTTTG
1 CTCTTTT
52969378 CTCTTTT
1 CTCTTTT
52969385 CTCTTT
1 CTCTTT
52969391 ATCTTCTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (7 bp):
CTCTTTT
Found at i:52969376 original size:21 final size:22
Alignment explanation
Indices: 52969350--52969400 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 22
52969340 GTGTAATAAA
*
52969350 CTCTTTTCTCTTTTCTCTTT-T
1 CTCTTTGCTCTTTTCTCTTTAT
52969371 CTCTTTGCTCTTTTCTCTTTAT
1 CTCTTTGCTCTTTTCTCTTTAT
52969393 CTTCTTTG
1 C-TCTTTG
52969401 TATTTTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 19 0.70
22 2 0.07
23 6 0.22
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (22 bp):
CTCTTTGCTCTTTTCTCTTTAT
Found at i:52979800 original size:57 final size:56
Alignment explanation
Indices: 52979730--52979845 Score: 162
Period size: 57 Copynumber: 2.1 Consensus size: 56
52979720 CACTGTCGCA
52979730 ATTATGGATTGACTTTTA-ATCTTTTCTCGGTTTAACAAAAGTATTTTAATTGGTTAT
1 ATTATGGATTGACTTTTAGATCTTTTCTCGGTTTAACAAAAG--TTTTAATTGGTTAT
* * * * *
52979787 ATTATGGATTGACTTTTAGGTTTTTTCTCGGTTTGAGAGAAGTTTTAATTGGTTAT
1 ATTATGGATTGACTTTTAGATCTTTTCTCGGTTTAACAAAAGTTTTAATTGGTTAT
52979843 ATT
1 ATT
52979846 TAATTTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 17 0.32
57 18 0.34
58 18 0.34
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (56 bp):
ATTATGGATTGACTTTTAGATCTTTTCTCGGTTTAACAAAAGTTTTAATTGGTTAT
Found at i:52980803 original size:25 final size:26
Alignment explanation
Indices: 52980752--52980803 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
52980742 TTATTATTGT
*
52980752 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATATATAACAATAA
*
52980778 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATTAAAATATATATAACAATAA
52980803 T
1 T
52980804 CATCTACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATTAAAATATATATAACAATAA
Found at i:52980980 original size:16 final size:16
Alignment explanation
Indices: 52980961--52981004 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
52980951 ATTATAGCTA
*
52980961 TATTCCATTACAACTC
1 TATTCCATTACAACCC
* * *
52980977 TATTCAATTATAGCCC
1 TATTCCATTACAACCC
52980993 TATTCCATTACA
1 TATTCCATTACA
52981005 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (16 bp):
TATTCCATTACAACCC
Found at i:52985749 original size:16 final size:16
Alignment explanation
Indices: 52985730--52985776 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
52985720 TAATAAATTC
52985730 AAAATCCAACAAGTTT
1 AAAATCCAACAAGTTT
* * *
52985746 AAAA-CATAATAATTTT
1 AAAATC-CAACAAGTTT
52985762 AAAATCCAACAAGTT
1 AAAATCCAACAAGTT
52985777 AATTTCAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAATCCAACAAGTTT
Found at i:52985774 original size:32 final size:32
Alignment explanation
Indices: 52985695--52985776 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
52985685 TGTCAATCAT
* **
52985695 TTCAATATCCAACAAACTTAAAACATAATAAA
1 TTCAAAATCCAACAAGTTTAAAACATAATAAA
*
52985727 TTCAAAATCCAACAAGTTTAAAACATAATAAT
1 TTCAAAATCCAACAAGTTTAAAACATAATAAA
*
52985759 TTTAAAATCCAACAAGTT
1 TTCAAAATCCAACAAGTT
52985777 AATTTCAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (32 bp):
TTCAAAATCCAACAAGTTTAAAACATAATAAA
Found at i:52989335 original size:5 final size:5
Alignment explanation
Indices: 52989325--52989350 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52989315 GCTTGACATA
52989325 TCATC TCATC TCATC TCATC TCATC T
1 TCATC TCATC TCATC TCATC TCATC T
52989351 TTGTCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.42
Consensus pattern (5 bp):
TCATC
Found at i:53010968 original size:20 final size:21
Alignment explanation
Indices: 53010926--53010970 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
53010916 AATTTATTAA
**
53010926 AAATTATAAAAAAATATTTTT
1 AAATTATAAAAAAATATAATT
*
53010947 AAATTTTAAAAAAAT-TAATT
1 AAATTATAAAAAAATATAATT
53010967 AAAT
1 AAAT
53010971 GTTGATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTATAAAAAAATATAATT
Found at i:53014298 original size:21 final size:21
Alignment explanation
Indices: 53014274--53014314 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53014264 CCTCCATTAT
53014274 TTATTT-ATTTATATCTTGTAA
1 TTATTTAATTT-TATCTTGTAA
*
53014295 TTATTTAATTTTATTTTGTA
1 TTATTTAATTTTATCTTGTA
53014315 TTTGGATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TTATTTAATTTTATCTTGTAA
Found at i:53022428 original size:44 final size:44
Alignment explanation
Indices: 53022362--53022475 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
53022352 CTAATCCACT
* * * * *
53022362 CCACTACAACTTTAAGGAGATAAGA-TTTGTTCATTCAGTCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTTTCTT-AGTCAGTCTGCC
* * * * *
53022406 CCACTGTAATTTCAGGGGGATAAGACTTTCTTAGTCAGTTTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTTCTTAGTCAGTCTGCC
53022450 CCACTGCAACTTCAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
53022476 CAGATGCGAC
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 51 0.91
45 5 0.09
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTTTCTTAGTCAGTCTGCC
Found at i:53022642 original size:44 final size:44
Alignment explanation
Indices: 53022594--53022863 Score: 201
Period size: 44 Copynumber: 6.2 Consensus size: 44
53022584 GCAACTTTAA
* *
53022594 GGAGATAAGATTCTCAATCTTCAACCTATTCCCCTGCTGACCAG
1 GGAGATAAGATTCTCAATCTTCAACCTATTCCACTACTGACCAG
* *
53022638 GGAGATAGGATTCAT-AATCTTCAACCTATTCCACTGCTGACCAG
1 GGAGATAAGATTC-TCAATCTTCAACCTATTCCACTACTGACCAG
** **** * * ** ***
53022682 GGAGATAAGGCTGGGGA-CTTCGATCTGCTCCACTACTGTTTAG
1 GGAGATAAGATTCTCAATCTTCAACCTATTCCACTACTGACCAG
* * *
53022725 GGAGATAAGA-TCTGTAATTTTCAACCTACTCCACTACTG-CTCAG
1 GGAGATAAGATTCT-CAATCTTCAACCTATTCCACTACTGAC-CAG
* * * * *
53022769 GGAGACAGGATTCACAATCTTTAACCTATTCCACTGCTGACCAG
1 GGAGATAAGATTCTCAATCTTCAACCTATTCCACTACTGACCAG
* * *
53022813 GGAGAT-AGAATTCACAAACTTAAACCTATTCCACTACTG-CCTAG
1 GGAGATAAG-ATTCTCAATCTTCAACCTATTCCACTACTGACC-AG
53022857 GGAGATA
1 GGAGATA
53022864 GGGCTGAGTC
Statistics
Matches: 176, Mismatches: 40, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.01
43 31 0.18
44 140 0.80
45 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
GGAGATAAGATTCTCAATCTTCAACCTATTCCACTACTGACCAG
Found at i:53022912 original size:175 final size:175
Alignment explanation
Indices: 53022602--53022936 Score: 397
Period size: 175 Copynumber: 1.9 Consensus size: 175
53022592 AAGGAGATAA
* * * * * *
53022602 GATTCTCAATCTTCAACCTATTCCCCTGCTGACCAGGGAGATAGGATTCATAATCTTCAACCTAT
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAAACTTAAACCTAT
* * * * ** ** *
53022667 TCCACTGCTGACCAGGGAGATAAGGCTGGGGACTTCGATCTGCTCCACTACTGTTTAGGGAGATA
66 TCCACTACTGACCAGGGAGATAAGGCTGGAGACATCGATCTGCTCCACTACGGTGCAGAAAGACA
53022732 AGATCTG-TAATTTTCAACCTACTCCACTACTGCTCAGGGAGACAG
131 AGATCTGCT-ATTTTCAACCTACTCCACTACTGCTCAGGGAGACAG
*
53022777 GATTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAAACTTAAACCTAT
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAAACTTAAACCTAT
* * * * * *
53022842 TCCACTACTG-CCTAGGGAGATAGGGCT-GAGTCATCGATCTGCTTCGCTGTCGGTGCAGAAAGG
66 TCCACTACTGACC-AGGGAGATAAGGCTGGAGACATCGATCTGCTCCACT-ACGGTGCAGAAAGA
* * *
53022905 CAAGATCTGCTATTTTTAACCTGCTCCGCTAC
129 CAAGATCTGCTATTTTCAACCTACTCCACTAC
53022937 AACCCAGGGA
Statistics
Matches: 132, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
174 18 0.14
175 113 0.86
176 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (175 bp):
GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAAACTTAAACCTAT
TCCACTACTGACCAGGGAGATAAGGCTGGAGACATCGATCTGCTCCACTACGGTGCAGAAAGACA
AGATCTGCTATTTTCAACCTACTCCACTACTGCTCAGGGAGACAG
Found at i:53022952 original size:44 final size:44
Alignment explanation
Indices: 53022902--53023040 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
53022892 CGGTGCAGAA
53022902 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
* * * * ** * * * **** *
53022946 AGGCAAGGT-TGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCT-ACAACCCAGGG
*
53022990 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGAG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
53023034 AGGCAAG
1 AGGCAAG
53023041 GCTGGTGTCT
Statistics
Matches: 64, Mismatches: 29, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 16 0.25
44 32 0.50
45 16 0.25
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
Found at i:53022984 original size:88 final size:88
Alignment explanation
Indices: 53022875--53023088 Score: 401
Period size: 88 Copynumber: 2.4 Consensus size: 88
53022865 GGCTGAGTCA
53022875 TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
* *
53022940 CCAGGGAGGCAAGGTTGGTGTCT
66 CCAGAGAGGCAAGGCTGGTGTCT
*
53022963 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
53023028 CCAGAGAGGCAAGGCTGGTGTCT
66 CCAGAGAGGCAAGGCTGGTGTCT
53023051 TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCT
1 TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCT
53023089 ATTATCTTCA
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 122 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGAAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
CCAGAGAGGCAAGGCTGGTGTCT
Found at i:53023082 original size:44 final size:44
Alignment explanation
Indices: 53022946--53023084 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
53022936 CAACCCAGGG
* *
53022946 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAA
* * * * ** * * * **** *
53022990 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCT-ACAACCCAGAG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAA
53023034 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAA
53023078 AGGCAAG
1 AGGCAAG
53023085 ATCTATTATC
Statistics
Matches: 63, Mismatches: 30, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
43 17 0.27
44 30 0.48
45 16 0.25
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGAA
Found at i:53026671 original size:19 final size:20
Alignment explanation
Indices: 53026634--53026671 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
53026624 TTTAAGAAAA
*
53026634 CTTTACTATAAATTAAATTT
1 CTTTACTATAAAGTAAATTT
*
53026654 CTTTAC-ATAAAGTGAATT
1 CTTTACTATAAAGTAAATT
53026672 ACAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (20 bp):
CTTTACTATAAAGTAAATTT
Found at i:53030689 original size:25 final size:24
Alignment explanation
Indices: 53030660--53030716 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
53030650 ATATTTTTTA
*
53030660 AAAAATAATTAAATATGAAAAATAAT
1 AAAAA-AACTAAATATGAAAAA-AAT
* *
53030686 AAAAAAACTAATTATTAAAAAAAT
1 AAAAAAACTAAATATGAAAAAAAT
53030710 AAAAAAA
1 AAAAAAA
53030717 TGAAAAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
25 13 0.46
26 5 0.18
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAAAAACTAAATATGAAAAAAAT
Found at i:53037824 original size:2 final size:2
Alignment explanation
Indices: 53037817--53037844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53037807 TAGAGTCTTA
53037817 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
53037845 CAAACTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53045427 original size:14 final size:14
Alignment explanation
Indices: 53045404--53045434 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53045394 ATTCACAAAT
*
53045404 TAAAATAATAATGA
1 TAAAACAATAATGA
53045418 TAAAACAATAATGA
1 TAAAACAATAATGA
53045432 TAA
1 TAA
53045435 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (14 bp):
TAAAACAATAATGA
Found at i:53052156 original size:20 final size:20
Alignment explanation
Indices: 53052131--53052171 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53052121 TTAATTTTTT
53052131 AAAATTATAAA-ATTATAAAA
1 AAAATT-TAAATATTATAAAA
*
53052151 AAAATTTAAATTTTATAAAA
1 AAAATTTAAATATTATAAAA
53052171 A
1 A
53052172 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTTAAATATTATAAAA
Found at i:53052206 original size:19 final size:19
Alignment explanation
Indices: 53052150--53052213 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 19
53052140 AAATTATAAA
53052150 AAAAATTTAAA--TTTTAT
1 AAAAATTTAAATTTTTTAT
53052167 AAAAA--T--ATTTTTT-T
1 AAAAATTTAAATTTTTTAT
*
53052181 -AATATTTAAATTTTTTAT
1 AAAAATTTAAATTTTTTAT
53052199 AAAAATTTAATATTT
1 AAAAATTTAA-ATTT
53052214 AAATATTCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
13 4 0.11
14 1 0.03
15 6 0.17
17 12 0.33
18 1 0.03
19 8 0.22
20 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAAATTTAAATTTTTTAT
Found at i:53055031 original size:19 final size:19
Alignment explanation
Indices: 53054998--53055045 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
53054988 ATGGCAATGT
53054998 TGAGAAATG-AATATGAGA
1 TGAGAAATGAAATATGAGA
*
53055016 TGAGAAATGAAATATGGGA
1 TGAGAAATGAAATATGAGA
53055035 TGATGAAATGA
1 TGA-GAAATGA
53055046 GATGTGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.33
19 11 0.41
20 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (19 bp):
TGAGAAATGAAATATGAGA
Found at i:53055174 original size:30 final size:30
Alignment explanation
Indices: 53055130--53055188 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53055120 ATGCTATATT
* *
53055130 TATGGAATAACATTG-ATATGTGCTTAAACA
1 TATGAAATAACATTGCA-ATGTGCTAAAACA
*
53055160 TATGAAATATCATTGCAATGTGCTAAAAC
1 TATGAAATAACATTGCAATGTGCTAAAAC
53055189 TTGTGAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (30 bp):
TATGAAATAACATTGCAATGTGCTAAAACA
Found at i:53056028 original size:42 final size:42
Alignment explanation
Indices: 53055964--53056044 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
53055954 CACGGCCTGG
* *
53055964 GATACGGTCATGTGACCTAAGTTAGTGAGTTACATGGGCAGA
1 GATACGGTCATGTGACCTAAGTTAGTAAGTTACACGGGCAGA
*
53056006 GATACGGTCATGTG-TCTCAAGTTAGTAAGTTACACGGGC
1 GATACGGTCATGTGACCT-AAGTTAGTAAGTTACACGGGC
53056045 TGGGACACGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (42 bp):
GATACGGTCATGTGACCTAAGTTAGTAAGTTACACGGGCAGA
Found at i:53082247 original size:17 final size:17
Alignment explanation
Indices: 53082225--53082262 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
53082215 TACAATTTGA
*
53082225 ATTTATTCCTTGAGATT
1 ATTTATTACTTGAGATT
*
53082242 ATTTATTATTTGAGATT
1 ATTTATTACTTGAGATT
53082259 ATTT
1 ATTT
53082263 GTTGATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (17 bp):
ATTTATTACTTGAGATT
Found at i:53087654 original size:21 final size:21
Alignment explanation
Indices: 53087615--53087654 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53087605 ATATATTCTG
*
53087615 AAATTATAAAAAGACATTAAA
1 AAATTATAAAAAAACATTAAA
*
53087636 AAATTATAAAAAAATATTA
1 AAATTATAAAAAAACATTA
53087655 GAAGTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATTATAAAAAAACATTAAA
Found at i:53098752 original size:35 final size:36
Alignment explanation
Indices: 53098667--53098739 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
53098657 CCATCAATTA
*
53098667 CACCATCATAAAAACTTTAATTTGAATATCAAAGTT
1 CACCATCATAAAAACCTTAATTTGAATATCAAAGTT
53098703 CACCATCATAAAAACCTTAATTTGAATATC-AAGTT
1 CACCATCATAAAAACCTTAATTTGAATATCAAAGTT
53098738 CA
1 CA
53098740 GTCGGTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
CACCATCATAAAAACCTTAATTTGAATATCAAAGTT
Found at i:53113952 original size:16 final size:16
Alignment explanation
Indices: 53113931--53113963 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53113921 TTCCATGTTG
53113931 TCAATTAGTTTTTGGA
1 TCAATTAGTTTTTGGA
53113947 TCAATTAGTTTTTGGA
1 TCAATTAGTTTTTGGA
53113963 T
1 T
53113964 TGGGGATTTA
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:0.06, G:0.18, T:0.52
Consensus pattern (16 bp):
TCAATTAGTTTTTGGA
Found at i:53125186 original size:13 final size:13
Alignment explanation
Indices: 53125168--53125192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53125158 TAATTTATAT
53125168 GTGTGAAAATTTC
1 GTGTGAAAATTTC
53125181 GTGTGAAAATTT
1 GTGTGAAAATTT
53125193 TTATCATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:53126399 original size:42 final size:43
Alignment explanation
Indices: 53126326--53126442 Score: 121
Period size: 43 Copynumber: 2.7 Consensus size: 43
53126316 AATTGAGATT
* * * * **
53126326 TACATGTAAGACCATCTCTGGGAAATAGGCATCG-TATATGTT
1 TACATGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGAA
* * * *
53126368 TTCGTGTAAGACCCTGTCCGGGACATTGGCATCGTTATTTGAA
1 TACATGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGAA
53126411 TACATGTAAGACCAC-GTCTGGGACATTGGCAT
1 TACATGTAAGACC-CTGTCTGGGACATTGGCAT
53126443 TGTACGAGCT
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 27 0.45
43 32 0.53
44 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
TACATGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGAA
Found at i:53130222 original size:40 final size:39
Alignment explanation
Indices: 53130152--53130286 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 39
53130142 ACCAGTTTGG
* *
53130152 CACCCAGTGCCTCATCGGAC-AATTCAAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGG-CTAATCCGAAGT-ATAAATTGA
* * *
53130192 CACCCAGTGTCTCATCGGCTAAACCGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGCTAATCCGAAGTATAAATTGA
* * ** *
53130229 CACCTAGTGCCTCATTGAATTAATCTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCG-GCTAATCCGAAGTA-TAAATTGA
*
53130270 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
53130287 ACTCGAAGCT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
39 1 0.01
40 23 0.31
41 21 0.28
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGCTAATCCGAAGTATAAATTGA
Found at i:53130490 original size:24 final size:24
Alignment explanation
Indices: 53130445--53130501 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
53130435 TATATATACC
53130445 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
53130469 AATTC-ATCACATACTAAA-TCAATCA
1 AATTCAATCA-ATA-TAAATTCAAT-A
*
53130494 ATTTCAAT
1 AATTCAAT
53130502 TGAAAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 4 0.14
24 13 0.46
25 9 0.32
26 2 0.07
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:53131175 original size:9 final size:9
Alignment explanation
Indices: 53131161--53131200 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
53131151 GGCTTTCTCC
53131161 TTCATTTCT
1 TTCATTTCT
53131170 TTCA-TT-T
1 TTCATTTCT
*
53131177 TTCTTTTCT
1 TTCATTTCT
53131186 TTC-TTTCT
1 TTCATTTCT
53131194 TTCATTT
1 TTCATTT
53131201 TCATTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
7 4 0.15
8 12 0.44
9 11 0.41
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (9 bp):
TTCATTTCT
Found at i:53131193 original size:24 final size:24
Alignment explanation
Indices: 53131165--53131213 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
53131155 TTCTCCTTCA
53131165 TTTCTTTCATTTTTC-TTTTCTTTC
1 TTTCTTTCA-TTTTCATTTTCTTTC
53131189 TTTCTTTCATTTTCATTTTCTTTC
1 TTTCTTTCATTTTCATTTTCTTTC
53131213 T
1 T
53131214 GTTTCGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTCTTTCATTTTCATTTTCTTTC
Found at i:53131205 original size:30 final size:32
Alignment explanation
Indices: 53131169--53131244 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
53131159 CCTTCATTTC
*
53131169 TTTCATTTTTCTTT-TCTTTC-TTTCTTTCAT
1 TTTCATTTTTCTTTCTCTTTCGTTTCTATCAT
* *
53131199 TTTCA-TTTTCTTTCTGTTTCGTTTCTATCTT
1 TTTCATTTTTCTTTCTCTTTCGTTTCTATCAT
*
53131230 TTTTATTTATTCTTT
1 TTTCATTT-TTCTTT
53131245 ATTTTATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 8 0.21
30 10 0.26
31 12 0.32
32 2 0.05
33 6 0.16
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (32 bp):
TTTCATTTTTCTTTCTCTTTCGTTTCTATCAT
Found at i:53135192 original size:28 final size:28
Alignment explanation
Indices: 53135160--53135218 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
53135150 AATTGAAAAG
53135160 CATGTGAAAGTTTTACGTGTTATTATTT
1 CATGTGAAAGTTTTACGTGTTATTATTT
53135188 CATGTGAAAGTTTTACGTGTTATTATTT
1 CATGTGAAAGTTTTACGTGTTATTATTT
53135216 CAT
1 CAT
53135219 AAGTGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.49
Consensus pattern (28 bp):
CATGTGAAAGTTTTACGTGTTATTATTT
Found at i:53137370 original size:101 final size:102
Alignment explanation
Indices: 53137255--53137439 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
53137245 AAAGTGACGG
* * * *
53137255 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGAGTACT
53137318 ACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
* *
53137356 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGAGTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGAGTACTA
*
53137421 CTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
53137440 TGAATCCGCA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 39 0.52
102 32 0.43
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGAGTACTA
CTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
Found at i:53137398 original size:51 final size:50
Alignment explanation
Indices: 53137255--53137437 Score: 172
Period size: 51 Copynumber: 3.6 Consensus size: 50
53137245 AAAGTGACGG
* * *
53137255 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GATAGA
* * * ** * *
53137305 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-ATAGA
* *
53137356 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAT-A-GA
* * * *
53137407 TCACATGAGTACTACTATGTGCATGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
53137438 TGTGAATCCG
Statistics
Matches: 107, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 36 0.34
51 70 0.65
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGATAGA
Found at i:53137528 original size:43 final size:43
Alignment explanation
Indices: 53137449--53137576 Score: 163
Period size: 42 Copynumber: 3.0 Consensus size: 43
53137439 GTGAATCCGC
*
53137449 ATCATTGAATATAAAGATGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
* * * * *
53137492 ATCCTT-AACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-TCGC
1 ATCATTGAA-TAT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGT
53137534 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
53137577 GTAACGATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
41 5 0.07
42 30 0.43
43 30 0.43
44 4 0.06
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (43 bp):
ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGT
Found at i:53137565 original size:42 final size:43
Alignment explanation
Indices: 53137445--53137575 Score: 169
Period size: 43 Copynumber: 3.1 Consensus size: 43
53137435 CTATGTGAAT
*
53137445 CCGCATCATTGAATATAAAGATGGTTGCTAAGTGCTGATTCCA
1 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
* * * *
53137488 CCGTATCCTT-AACTGTGAAAGG-GGTTGCTATGTGCTGATTCC-
1 CCGCATCATTGAA-TAT-AAAGGTGGTTGCTAAGTGCTGATTCCA
*
53137530 TCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
1 CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
53137573 CCG
1 CCG
53137576 TGTAACGATT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
41 5 0.07
42 30 0.42
43 33 0.46
44 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (43 bp):
CCGCATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCA
Done.