Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 105 of 130
Found at i:20601611 original size:9 final size:9
Alignment explanation
Indices: 20601548--20601595 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
20601538 AAACTCAAAA
20601548 TTTTTTCTT
1 TTTTTTCTT
20601557 TTTTTT-TT
1 TTTTTTCTT
20601565 TTTTTTGCTT
1 TTTTTT-CTT
**
20601575 TTTTCCCTT
1 TTTTTTCTT
*
20601584 TTTTTTGTT
1 TTTTTTCTT
20601593 TTT
1 TTT
20601596 GCTTTTTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 8 0.25
9 18 0.56
10 6 0.19
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:20603292 original size:30 final size:30
Alignment explanation
Indices: 20603256--20603321 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
20603246 CATAAAATAA
*
20603256 GATGCATATACTATCCATTAAT-TTGAATGG
1 GATGCATATACTATCCATTAATGTAG-ATGG
*
20603286 GATGCATGTACTATCCATTAATGTAGATGG
1 GATGCATATACTATCCATTAATGTAGATGG
20603316 GATGCA
1 GATGCA
20603322 AAGCATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (30 bp):
GATGCATATACTATCCATTAATGTAGATGG
Found at i:20608186 original size:145 final size:144
Alignment explanation
Indices: 20607839--20608235 Score: 351
Period size: 145 Copynumber: 2.7 Consensus size: 144
20607829 CTTTAAAACC
* * * * * *** * * *
20607839 CCAAAAATCATGAAATATTATAAGA-TTATGAATTGAAAAGTTTCGTGAAATTTCGAGCTTGAAA
1 CCAAAAATCATGAAATATTACAAAAGTGA-GATTTGGAAAGTTTCACAAAAATTCAAGCTCGAAA
* * * *
20607903 AG-CTAGATTACAAAATATCCCTATGAGGGTATTTTGGTAATTTCACACTTTTCGGGATACTATT
65 AGACCAAATTACAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTTTCGGGATACTATT
*
20607967 ATGATTTTGAACTCA
130 ATGATTTTGAAATCA
* * * **
20607982 TCAAAAATCATGAAATGTTACAAAAGTGAGATTTGGAAAGTTTCACAAAATTTTGAGCTCGAAAA
1 CCAAAAATCATGAAATATTACAAAAGTGAGATTTGGAAAGTTTCACAAAAATTCAAGCTCGAAAA
* * * *
20608047 GGCCAATTTACAAAAGTACCCCTATAAGGGTATTTTGATAATTTCACA-TTTGTCAGGG-TACTG
66 GACCAAATTACAAAA-TACCCCTATAAGGGTATTTTGGTAATTTCACACTTT-TC-GGGATACTA
*
20608110 TTGTGATTTT-AAATGCA
128 TTATGATTTTGAAAT-CA
* ** * *
20608127 CCAAAAATCATGAAATATTATAGGA-TTA-ATGTCT-GAAAGGTTTTACAAAAATTCAAGCTCGA
1 CCAAAAATCATGAAATATTACAAAAGTGAGAT-T-TGGAAA-GTTTCACAAAAATTCAAGCTCGA
**
20608189 AAAGATTAAATTACGAAAATACCCCCTATAAGGGTATTTTGGTAATT
63 AAAGACCAAATTAC-AAAATA-CCCCTATAAGGGTATTTTGGTAATT
20608236 CGACCTTTCT
Statistics
Matches: 207, Mismatches: 36, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
143 53 0.26
144 25 0.12
145 98 0.47
146 31 0.15
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (144 bp):
CCAAAAATCATGAAATATTACAAAAGTGAGATTTGGAAAGTTTCACAAAAATTCAAGCTCGAAAA
GACCAAATTACAAAATACCCCTATAAGGGTATTTTGGTAATTTCACACTTTTCGGGATACTATTA
TGATTTTGAAATCA
Found at i:20612206 original size:24 final size:24
Alignment explanation
Indices: 20612162--20612240 Score: 63
Period size: 26 Copynumber: 3.2 Consensus size: 24
20612152 TAAATAATTC
*
20612162 AAAATTTGA-GTTTT-AATAAAGAT
1 AAAATTTGATATTTTGAA-AAAGAT
*
20612185 AAAATTTGATATTTTGAAAAAGAC
1 AAAATTTGATATTTTGAAAAAGAT
* * *
20612209 AAGATATATGATTTTTTGAAAAAAAT
1 AA-A-ATTTGATATTTTGAAAAAGAT
*
20612235 TAAATT
1 AAAATT
20612241 AAAATTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
23 9 0.20
24 13 0.30
25 4 0.09
26 18 0.41
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (24 bp):
AAAATTTGATATTTTGAAAAAGAT
Found at i:20613034 original size:379 final size:379
Alignment explanation
Indices: 20612336--20613091 Score: 1030
Period size: 379 Copynumber: 2.0 Consensus size: 379
20612326 AAATTTTTAG
* * *
20612336 CTTTTAGATGTTTTTCTAAAAATTCAAATGCCATGTTAACAAAGTTAATGGAGAGTAATTTATCA
1 CTTTTAGATGTCTTTCTAAAAATTCAAAGGCCATGTCAACAAAGTTAATGGAGAGTAATTTATCA
* *
20612401 CATTAATAATTGGACCAACATTAATAAATTCAACTTGTATGAGAGCGAAATTTTAATAAATGATA
66 CATTAATAATTGGACCAACATTAATAAATTCAACTTGTATAAGAGCAAAATTTTAATAAATGATA
* * * *
20612466 CTAAATGAACAAAAATTCATATTTCATATTTGTACAAGGATCACTTGCAAAATTTGCCAACTAAT
131 CTAAAGGAACAAAAATTCAAATTTCATATTAGTACAAGGATCACTTGCAAAATTTGACAACTAAT
* ** * ** **
20612531 TTCATCATTCGGGTTGCTATTAAGCAAAATTAACTTTATGTCAGCAAAGTCAACACAAAGCACTC
196 TTCATCATCCAAGTTGATATTAAGCAAAATTAACGCTACATCAGCAAAGTCAACACAAAGCACTC
* * *
20612596 CAACTTGACCATAGGGACTCTCGACTTAGGCCATTCCCATGCTTAGCCAAGACC-TTTTTTTTCT
261 CAACTTGACCATAAGGACTCTCAACCTAGGCCATTCCCATGCTTAGCCAAGACCTTTTTTTTTCT
* * * *
20612660 TTTTCCTCTTGCATTTCTTTGTTTGTTTGTTTATGCATGGTTAGTTTATCAAAA
326 TTTTCCTCTTGCATTACTTTGGTTGTTTGCTTATGCATGGGTAGTTTATCAAAA
*
20612714 CTTTTAGATGTCTTTCTAAAAATTCAACGGCCATGTCAACAAAGTTAATGGAGAGTAATTTATCA
1 CTTTTAGATGTCTTTCTAAAAATTCAAAGGCCATGTCAACAAAGTTAATGGAGAGTAATTTATCA
* * * * *
20612779 CATTAATAATTGGACCAATATTAGTAAATTCAACTTGTATAAGGGCTAAAATTTTTATGAATGAT
66 CATTAATAATTGGACCAACATTAATAAATTCAACTTGTATAAGAGC-AAAATTTTAATAAATGAT
* * * * * *
20612844 ACTAAGGGAACAAAAATTCAAATTTCGTGTTAGTACAGGGATTATTTGCAAAATTTGACAACTAA
130 ACTAAAGGAACAAAAATTCAAATTTCATATTAGTACAAGGATCACTTGCAAAATTTGACAACTAA
* * * *
20612909 TTTCATTATCCAAGTTGATATTCAGCAAAATTAACGCTACATCAGTAAAGTCAATACAAAGCACT
195 TTTCATCATCCAAGTTGATATTAAGCAAAATTAACGCTACATCAGCAAAGTCAACACAAAGCACT
* * ** * **
20612974 CCAACTTGGCCATAAGGACTTTCAACCTAGGCTTTTCCCATGCTTGGTTTAA-ACCTTTTTTTTT
260 CCAACTTGACCATAAGGACTCTCAACCTAGGCCATTCCCATGCTTAG-CCAAGACCTTTTTTTTT
* * *
20613038 TTTTTTCCTTTTGCATTAGTTTGGTTGTTTGCTTATGCATGGGTAGTTTATCAA
324 CTTTTTCCTCTTGCATTACTTTGGTTGTTTGCTTATGCATGGGTAGTTTATCAA
20613092 GTGTTTGTAA
Statistics
Matches: 325, Mismatches: 50, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
378 103 0.32
379 165 0.51
380 57 0.18
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (379 bp):
CTTTTAGATGTCTTTCTAAAAATTCAAAGGCCATGTCAACAAAGTTAATGGAGAGTAATTTATCA
CATTAATAATTGGACCAACATTAATAAATTCAACTTGTATAAGAGCAAAATTTTAATAAATGATA
CTAAAGGAACAAAAATTCAAATTTCATATTAGTACAAGGATCACTTGCAAAATTTGACAACTAAT
TTCATCATCCAAGTTGATATTAAGCAAAATTAACGCTACATCAGCAAAGTCAACACAAAGCACTC
CAACTTGACCATAAGGACTCTCAACCTAGGCCATTCCCATGCTTAGCCAAGACCTTTTTTTTTCT
TTTTCCTCTTGCATTACTTTGGTTGTTTGCTTATGCATGGGTAGTTTATCAAAA
Found at i:20613380 original size:24 final size:24
Alignment explanation
Indices: 20613353--20613428 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
20613343 AGCTTTAAAA
20613353 AAACCTAAACCATGTCCAAACCCT
1 AAACCTAAACCATGTCCAAACCCT
*
20613377 AAACCTTAA--AT-T-CAAACCCT
1 AAACCTAAACCATGTCCAAACCCT
* *
20613397 AAAAAAACCTAAACCATGTCCGAACCCC
1 ----AAACCTAAACCATGTCCAAACCCT
20613425 AAAC
1 AAAC
20613429 ATTAAAACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
20 8 0.20
21 1 0.03
22 2 0.05
24 20 0.50
26 2 0.05
27 1 0.03
28 6 0.15
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
AAACCTAAACCATGTCCAAACCCT
Found at i:20614071 original size:17 final size:17
Alignment explanation
Indices: 20614049--20614083 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20614039 TTTGTAAAAT
20614049 AAAATTAAAATCACTAC
1 AAAATTAAAATCACTAC
20614066 AAAATTAAAATCACTAC
1 AAAATTAAAATCACTAC
20614083 A
1 A
20614084 GAAAAATGGG
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:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATTAAAATCACTAC
Found at i:20614955 original size:17 final size:19
Alignment explanation
Indices: 20614935--20614973 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
20614925 AGTTCAGCTC
*
20614935 TTTTTTTTTTA-ATTT-TA
1 TTTTTTTTCTAGATTTGTA
20614952 TTTTTTTTCTAGATTTGTA
1 TTTTTTTTCTAGATTTGTA
20614971 TTT
1 TTT
20614974 ATACAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 4 0.21
19 5 0.26
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTTTCTAGATTTGTA
Found at i:20616786 original size:236 final size:236
Alignment explanation
Indices: 20616275--20616987 Score: 939
Period size: 236 Copynumber: 3.0 Consensus size: 236
20616265 GTTGCCAAAA
*
20616275 TTTACCACCAAATTTATTTGGTGGAAAATTTTTCTTGTGACATTTTTTTTATTTTAGGTGATGTT
1 TTTACCACCAAATTTATTTGGTGAAAAATTTTT-TTGTGACA--TTTTTTATTTTAGGTGATGTT
* * * * *
20616340 ATAATTTTGTCACTAACTTAAAATTTTATTTGT-AAAAAGTTTTTCTAATAAATTTTAGGTGATG
63 ATAATTTTGTCACAAATTTAAAATTTTATTTGTGACAAAGTTTTTCTAATAGATTTTAGGTGACG
* * ** * * *
20616404 TTATTAATTCTTGTCGCAAAGTGAACGCTTTAGTTAATTATTAATAACATTATAATTTTATCGCG
128 TTATTAATTTTTGTCGCAAATTGAATACTTTAGTTAACTATTAATGACATTATAATTTTATCACG
* * *
20616469 TCAATGTATAGT-TTATATGCCGATAACATAAATGTCACAAACT
193 TTAATGTATGGTGTTATATGACGATAACATAAATGTCACAAACT
* *
20616512 TTTACCACCAAATTTATTTGGTGAAAAATTTATTTGTGACATTTTTTATTTTTGGTGATGTTATA
1 TTTACCACCAAATTTATTTGGTGAAAAATTTTTTTGTGACATTTTTTATTTTAGGTGATGTTATA
* *
20616577 ATTTTTGTCACAAATTTAAAATTTTATTTGTGACAAA-TTTTTCTGATAGATTTTAGGTGAGGTT
66 A-TTTTGTCACAAATTTAAAATTTTATTTGTGACAAAGTTTTTCTAATAGATTTTAGGTGACGTT
* * * * *
20616641 ATTAATTTTTGTCGTAAATTGAATACTTTGGTTGACTATTAATGACATTATAATTTCATCACATT
130 ATTAATTTTTGTCGCAAATTGAATACTTTAGTTAACTATTAATGACATTATAATTTTATCACGTT
*
20616706 AATGTATGGTGTTATATGACGATAATATAAATGTCACAAACT
195 AATGTATGGTGTTATATGACGATAACATAAATGTCACAAACT
** ** *
20616748 TTTACTGCCAAATTTATTTGGTGAAAAATTTTTTTGTGATGTTTTTTATTTTAGGTGACGTTATA
1 TTTACCACCAAATTTATTTGGTGAAAAATTTTTTTGTGACATTTTTTATTTTAGGTGATGTTATA
* ** * * *
20616813 ATTTTATCA-ATAATTTAAAATTTTAACTATGACAAATTTTTTCTAATAGATTTAAGGTGACGTT
66 ATTTTGTCACA-AATTTAAAATTTTATTTGTGACAAAGTTTTTCTAATAGATTTTAGGTGACGTT
* * ** * *
20616877 ATGAATTTTTGTCACAAATTGAATACTTTAGTTAACTATTAATGACATTGCAATTTTGTCATGTT
130 ATTAATTTTTGTCGCAAATTGAATACTTTAGTTAACTATTAATGACATTATAATTTTATCACGTT
* * *
20616942 AATGTATGATGGTATATGACGATAACATAAATGCCACAAACT
195 AATGTATGGTGTTATATGACGATAACATAAATGTCACAAACT
20616984 TTTA
1 TTTA
20616988 AATATTGTTA
Statistics
Matches: 417, Mismatches: 54, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
234 25 0.06
235 141 0.34
236 220 0.53
237 31 0.07
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (236 bp):
TTTACCACCAAATTTATTTGGTGAAAAATTTTTTTGTGACATTTTTTATTTTAGGTGATGTTATA
ATTTTGTCACAAATTTAAAATTTTATTTGTGACAAAGTTTTTCTAATAGATTTTAGGTGACGTTA
TTAATTTTTGTCGCAAATTGAATACTTTAGTTAACTATTAATGACATTATAATTTTATCACGTTA
ATGTATGGTGTTATATGACGATAACATAAATGTCACAAACT
Found at i:20619626 original size:203 final size:200
Alignment explanation
Indices: 20619007--20619692 Score: 705
Period size: 202 Copynumber: 3.4 Consensus size: 200
20618997 TTAATTATGT
* *
20619007 TAATTATGTCACCAATATTGTGATGATTTACCTTTCATCACTAATATATCAT-ATTTATCATTTA
1 TAATTGTGTCACCAATATTGTGACGATTTACCTTTCATCACTAATATAT-ATGATTTATCATTTA
* * * * ** ** *
20619071 TTTTGTGACGATTATAGCTTTTAATGACATTTTTTTTAATAAATACCTAATGAAAACTATTGTCA
65 TTTTGTGACGATTATAGCCTTTAATGACGTTTTTCTTAATAAATAACTAACAAAAACTAACGTTA
* ** * * *
20619136 CAAAAAAAAGCATAATGCAAATTTTGATTTTATTGTCACGTTTGACATTATTTTACAATCATTTG
130 CAAAAAAAAGCATAAGGTGAAGTTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATTCG
20619201 TGATGA
195 TGATGA
* ** * * ** * *
20619207 TAATTGTGTTACCAATACCGTGACTACTTACCTTTTGTCATTAATATATTTGATTTTATCATTTA
1 TAATTGTGTCACCAATATTGTGACGATTTACCTTTCATCACTAATATATATGA-TTTATCATTTA
* * * * * *
20619272 TTTTGTGACAATTATAACCTTCAATGAAGTTTTTCTTTATAAATAGCTAACAAAAACTAACGTTA
65 TTTTGTGACGATTATAGCCTTTAATGACGTTTTTCTTAATAAATAACTAACAAAAACTAACGTTA
* * * * *
20619337 CAAAAAAAAAGCATAAGGTGATGTTTGATTTTATTGTCACATTTGATATTATCTTATAATTATTC
130 C-AAAAAAAAGCATAAGGTGAAGTTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATTC
*
20619402 ATGATGA
194 GTGATGA
* * * * *
20619409 TAATTGTGTCACTAATATTATAACGATTTATCTTTCATCACTAATATATATGATTTCATTATTTA
1 TAATTGTGTCACCAATATTGTGACGATTTACCTTTCATCACTAATATATATGATTT-ATCATTTA
* * * *
20619474 TTTTGTGACGATTATAGCCTTTAATGACGTTTTTGTTCATAAATAACTAACCAAAGCTAACGTTA
65 TTTTGTGACGATTATAGCCTTTAATGACGTTTTTCTTAATAAATAACTAACAAAAACTAACGTTA
* * * * *
20619539 CAAAAATTAAAGTATAAGGTGACGTTTGATTTTATTGTCATGGTAGACATTATCTTACAATCATT
130 CAAAAA--AAAGCATAAGGTGAAGTTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATT
*
20619604 GGTGA-GAA
193 CGTGATG-A
* * * ** * *
20619612 TAATTTTGTCACTAATATTGTGACAATTTACCTTTTGTCACTAATAT-TTTGAATTTTCTCATTT
1 TAATTGTGTCACCAATATTGTGACGATTTACCTTTCATCACTAATATATATG-A-TTTATCATTT
* *
20619676 TTTTTGT-ATGATTATAG
64 ATTTTGTGACGATTATAG
20619693 ATTTCAATAA
Statistics
Matches: 394, Mismatches: 83, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
199 1 0.00
200 40 0.10
201 71 0.18
202 175 0.44
203 104 0.26
204 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (200 bp):
TAATTGTGTCACCAATATTGTGACGATTTACCTTTCATCACTAATATATATGATTTATCATTTAT
TTTGTGACGATTATAGCCTTTAATGACGTTTTTCTTAATAAATAACTAACAAAAACTAACGTTAC
AAAAAAAAGCATAAGGTGAAGTTTGATTTTATTGTCACGTTTGACATTATCTTACAATCATTCGT
GATGA
Found at i:20621215 original size:92 final size:91
Alignment explanation
Indices: 20621056--20621232 Score: 203
Period size: 92 Copynumber: 1.9 Consensus size: 91
20621046 ACATGTTTTA
* * * * * * ** * * ***
20621056 GAATTTTGAAATTCTTTCTTAATTGGTTTAATTGAGGAATAATTATGTAGTTTTTGGCTATTTTT
1 GAATTTTGAAATTCTTGCTTAACTAGTTCAATTAAAGAATAATTATACAATTTTAGGCTA-CCCT
20621121 TTTTTAGA-TCTTTATTTTTTTCCAATT
65 TTTTTAGATTC-TTATTTTTTTCCAATT
*
20621148 GAATTTTGAAATTCTTGCTTAACTAGTTCAATTAAAGAATAATTATACAATTTTAGGTTACCCTT
1 GAATTTTGAAATTCTTGCTTAACTAGTTCAATTAAAGAATAATTATACAATTTTAGGCTACCCTT
20621213 TTTTAGATTCTTATTTTTTT
66 TTTTAGATTCTTATTTTTTT
20621233 TTTATAAATA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
91 19 0.27
92 51 0.73
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.53
Consensus pattern (91 bp):
GAATTTTGAAATTCTTGCTTAACTAGTTCAATTAAAGAATAATTATACAATTTTAGGCTACCCTT
TTTTAGATTCTTATTTTTTTCCAATT
Found at i:20626106 original size:13 final size:13
Alignment explanation
Indices: 20626088--20626112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20626078 CTTCTCAATG
20626088 TCTTTATATATAC
1 TCTTTATATATAC
20626101 TCTTTATATATA
1 TCTTTATATATA
20626113 GTTACTTATA
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:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TCTTTATATATAC
Found at i:20626575 original size:21 final size:21
Alignment explanation
Indices: 20626533--20626574 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
20626523 CAAAGCCTAA
20626533 ATTTATTTTTATCGTTTTATT
1 ATTTATTTTTATCGTTTTATT
20626554 ATTT-TTTTTATC-TTTT-TT
1 ATTTATTTTTATCGTTTTATT
20626572 ATT
1 ATT
20626575 AATTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 8 0.38
21 4 0.19
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTATTTTTATCGTTTTATT
Found at i:20628862 original size:17 final size:17
Alignment explanation
Indices: 20628842--20628881 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20628832 TCCCTTACAA
*
20628842 AAAATTCACACTTTTTT
1 AAAATTCACACTTTCTT
* *
20628859 AAAAATCACTCTTTCTT
1 AAAATTCACACTTTCTT
20628876 AAAATT
1 AAAATT
20628882 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTCACACTTTCTT
Found at i:20629560 original size:30 final size:29
Alignment explanation
Indices: 20629503--20629560 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
20629493 GTCCGTCCGT
20629503 TTAAAGATTTGAATAAAAATATTAAATTTG
1 TTAAAGATTTGAATAAAAATA-TAAATTTG
*
20629533 TTAAAGAATTTGAGCTAAAAATA-AAATT
1 TTAAAG-ATTTGA-ATAAAAATATAAATT
20629561 CATTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 11 0.44
31 6 0.24
32 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (29 bp):
TTAAAGATTTGAATAAAAATATAAATTTG
Found at i:20630210 original size:20 final size:20
Alignment explanation
Indices: 20630170--20630225 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
20630160 TTGGTAATTG
20630170 ATATATT-TATTTCGTAT-AAA
1 ATATATTATATTT--TATAAAA
20630190 ATATATTATATTTTATAAAA
1 ATATATTATATTTTATAAAA
*
20630210 A-AT-TTATATATTATAA
1 ATATATTATATTTTATAA
20630226 TTTATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 11 0.33
21 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATATTATATTTTATAAAA
Found at i:20630218 original size:18 final size:19
Alignment explanation
Indices: 20630184--20630225 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
20630174 ATTTATTTCG
* *
20630184 TATAAAATATATTATATTT
1 TATAAAAAATATTATATAT
20630203 TATAAAAAAT-TTATATAT
1 TATAAAAAATATTATATAT
20630221 TATAA
1 TATAA
20630226 TTTATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATAAAAAATATTATATAT
Found at i:20630334 original size:18 final size:19
Alignment explanation
Indices: 20630290--20630327 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20630280 AAATTTTAAA
*
20630290 TTATATTAATTTTATATTT
1 TTATATCAATTTTATATTT
20630309 TTATATCAATTTT-TATTT
1 TTATATCAATTTTATATTT
20630327 T
1 T
20630328 ATTATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATCAATTTTATATTT
Found at i:20630774 original size:25 final size:25
Alignment explanation
Indices: 20630734--20630814 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
20630724 TAGCCTTTGT
20630734 TTTTATTAGTTTAATATTATAATTA
1 TTTTATTAGTTTAATATTATAATTA
* *
20630759 TTTTATTCGTTCAATA-TA-AA-TA
1 TTTTATTAGTTTAATATTATAATTA
* *
20630781 TTTTTATTTGTTTAATATAATAATTA
1 -TTTTATTAGTTTAATATTATAATTA
20630807 TTTTATTA
1 TTTTATTA
20630815 ATTTTAACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.04
23 16 0.35
24 3 0.07
25 23 0.50
26 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTTATTAGTTTAATATTATAATTA
Found at i:20630782 original size:22 final size:23
Alignment explanation
Indices: 20630733--20630800 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
20630723 CTAGCCTTTG
* *
20630733 TTTTTATTAGTTTAATATTATAAT-
1 TTTTTATTCGTTCAATA-TA-AATA
20630757 TATTTTATTCGTTCAATATAAATA
1 T-TTTTATTCGTTCAATATAAATA
* *
20630781 TTTTTATTTGTTTAATATAA
1 TTTTTATTCGTTCAATATAA
20630801 TAATTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 20 0.53
24 4 0.11
25 14 0.37
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (23 bp):
TTTTTATTCGTTCAATATAAATA
Found at i:20630924 original size:27 final size:27
Alignment explanation
Indices: 20630859--20630932 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
20630849 AGCAAAACTA
*
20630859 TTAATTTATTTTA-AAATAATTTAATAAT
1 TTAATTT-TTTTATAAAT-ATTAAATAAT
*
20630887 TT-ATTAATTTTATAAATATTAAATAAT
1 TTAATT-TTTTTATAAATATTAAATAAT
*
20630914 TTAATTTTTTTATTAATAT
1 TTAATTTTTTTATAAATAT
20630933 AATTTTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 30 0.77
28 9 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTAATTTTTTTATAAATATTAAATAAT
Found at i:20631253 original size:22 final size:21
Alignment explanation
Indices: 20631201--20631253 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
20631191 ATAAATTTTT
20631201 TATTAAAAT-TTTTTTAATTA
1 TATTAAAATATTTTTTAATTA
* *
20631221 CAGTTACAATATTTTTTAATTA
1 TA-TTAAAATATTTTTTAATTA
20631243 TATTAATAATA
1 TATTAA-AATA
20631254 AATTTTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 9 0.35
22 16 0.62
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTAAAATATTTTTTAATTA
Found at i:20632322 original size:12 final size:12
Alignment explanation
Indices: 20632305--20632329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20632295 TGTGGTACCT
20632305 CTTCAATATCTA
1 CTTCAATATCTA
20632317 CTTCAATATCTA
1 CTTCAATATCTA
20632329 C
1 C
20632330 AACAAACAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CTTCAATATCTA
Found at i:20639818 original size:23 final size:22
Alignment explanation
Indices: 20639768--20639811 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20639758 TAATGATTTA
* *
20639768 AAATTTAATAAAAATCATAAAT
1 AAATTTAACAAAAATCAAAAAT
20639790 AAATTTAACAAAAAT-AAAAAT
1 AAATTTAACAAAAATCAAAAAT
20639811 A
1 A
20639812 TATATTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATTTAACAAAAATCAAAAAT
Found at i:20650142 original size:31 final size:31
Alignment explanation
Indices: 20650107--20650166 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
20650097 ATATATTATC
20650107 AATTAAT-TAAATAATATCATTTCATTAATAA
1 AATTAATATAAA-AATATCATTTCATTAATAA
* *
20650138 AATTAATATGAAAATATCATTTTATTAAT
1 AATTAATATAAAAATATCATTTCATTAAT
20650167 GAATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (31 bp):
AATTAATATAAAAATATCATTTCATTAATAA
Found at i:20650425 original size:42 final size:42
Alignment explanation
Indices: 20650376--20650458 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
20650366 CATCAATAAA
*
20650376 GTTAGATTTGTTAAGATTATATTAATTATTTATTCATTTCTG
1 GTTAGATTCGTTAAGATTATATTAATTATTTATTCATTTCTG
20650418 GTTAGATTCGTTAAGATTATATTAATTATTTATTCATTTCT
1 GTTAGATTCGTTAAGATTATATTAATTATTTATTCATTTCT
20650459 TGTGCATCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (42 bp):
GTTAGATTCGTTAAGATTATATTAATTATTTATTCATTTCTG
Found at i:20651105 original size:114 final size:115
Alignment explanation
Indices: 20650895--20651600 Score: 721
Period size: 114 Copynumber: 6.2 Consensus size: 115
20650885 TATAAAAACG
* * * * * * * * *
20650895 GAGTCGAGATCGTAAATAAATTATTGGTCTAATGTCGCAAGTCTGACAATGATCTGACTTAAGTC
1 GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
* * * * * * * *
20650960 AAGATTAAATGATTGAAATAAT-ACCGCGAGTCGAAAGGTGACCAAGACC
66 GAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
* * * *
20651009 GAGTCGAGGTCGTAAATAAATAACTAGACTGATATCATAAGTCTGACAATGATCTGACCTAAGTC
1 GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
* * *
20651074 GAGATCAAATGACTGAGATGAT-TCCGTGAGTCAAAAGGCGACTAAGATC
66 GAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
* * * * *
20651123 -AGTCGAGGTCATAAATAAATGATTTGACTGATGTCGCAAGTCTGACGATGATCTAACCTAAGTC
1 GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
* ** *
20651187 GAGATCAAATGACTGGGATGATG-CCACGAGTCAAAAGGTGACCAAGATC
66 GAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
* * * * * * ** * *
20651236 AAGTCGAGGTCGTAAATAAATGATTGGACTAATATCACAAGTTTGATTATGATTTGACTTAAGTC
1 GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
* * * * *
20651301 GAGATCAAATGACTGGGACGATATCAC--GAGTCAAAAGGTGACAAAGATC
66 GAGATCAAATGACTGAGATGATGTC-CGTGAGTCAAAAGGTGACCAAGACC
* * * *
20651350 GAGTCGAGGTCATAAATAAATGACTAGATTGATGTCACAAGTTTGATGATGATCTGACCTAAGTC
1 GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
* * * *
20651415 GAGATCAAATGACTGAGACGATGT-CGTAAGCCAGAAGGTGACCAAGACC
66 GAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
* * * * * * * *
20651464 GAGTCAAAGTCAG-AAATAAATGGCTGGACTGATGTCGCAAGTTTGACGAT-AACTTAACCTAAG
1 GAGTCGAGGTC-GTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATC-TGACCTAAG
*
20651527 TCGAGATCAAATGACTGGGATGATGT-CGTGAGTCAAAAGGTGACCAAGACC
64 TCGAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
*
20651578 GAGTCAAGGTCGTAAATAAATGA
1 GAGTCGAGGTCGTAAATAAATGA
20651601 TTGGATTGAT
Statistics
Matches: 500, Mismatches: 83, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
112 1 0.00
113 101 0.20
114 396 0.79
115 1 0.00
116 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (115 bp):
GAGTCGAGGTCGTAAATAAATGACTAGACTGATGTCACAAGTCTGACGATGATCTGACCTAAGTC
GAGATCAAATGACTGAGATGATGTCCGTGAGTCAAAAGGTGACCAAGACC
Found at i:20651803 original size:41 final size:38
Alignment explanation
Indices: 20651758--20651874 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 38
20651748 TTTATTAGCA
*
20651758 TGAAGGCATATTTTTGACAAAGAAACCATCTTTCATCAGCC
1 TGAAGGCATATTTTTGA-AAAGAAACC-TTTTTCATCA-CC
* *
20651799 TGAAGGCATGTTTTTGGAAAAGAAACTTTTTTCATCCACC
1 TGAAGGCATATTTTT-GAAAAGAAACCTTTTTCAT-CACC
* * *
20651839 TGGAGGCACATTTTTTGTAAAGAAACCTTTTTCATC
1 TGAAGGCATA-TTTTTGAAAAGAAACCTTTTTCATC
20651875 CACTTGTTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
39 1 0.02
40 33 0.51
41 29 0.45
42 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (38 bp):
TGAAGGCATATTTTTGAAAAGAAACCTTTTTCATCACC
Found at i:20653733 original size:20 final size:20
Alignment explanation
Indices: 20653710--20653753 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20653700 TGCCCAGTTT
*
20653710 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
20653730 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
20653750 CCGG
1 CCGG
20653754 TGAATTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.25, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Found at i:20653788 original size:62 final size:63
Alignment explanation
Indices: 20653708--20653825 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 63
20653698 ACTGCCCAGT
* *
20653708 TTCCGGCGAAGAATCCCAGAAACCGGC-AAAGAATCCCAGAAACCGGTGAAT-TTCCGGCCAAC
1 TTCCGGCGAAAAAACCCAGAAACCGGCGAAA-AATCCCAGAAACCGGTGAATCTTCCGGCCAAC
** * * *
20653770 TTCCGGCGAAAAAACCCAGATTCCGGCGAAAATTTCCAGAATCCGGTGAATCTTCC
1 TTCCGGCGAAAAAACCCAGAAACCGGCGAAAAATCCCAGAAACCGGTGAATCTTCC
20653826 ACCGGAGTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
62 40 0.85
63 7 0.15
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (63 bp):
TTCCGGCGAAAAAACCCAGAAACCGGCGAAAAATCCCAGAAACCGGTGAATCTTCCGGCCAAC
Found at i:20653814 original size:20 final size:20
Alignment explanation
Indices: 20653771--20653815 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20653761 CCGGCCAACT
*
20653771 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
20653791 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
20653811 TCCGG
1 TCCGG
20653816 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:20654081 original size:14 final size:15
Alignment explanation
Indices: 20654062--20654103 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
20654052 CCGAGCCGAG
20654062 CCGAGCCGTTCTTC-
1 CCGAGCCGTTCTTCT
20654076 CCGAGCCG--CTTCT
1 CCGAGCCGTTCTTCT
20654089 CCGAGCCGTT-TTCT
1 CCGAGCCGTTCTTCT
20654103 C
1 C
20654104 TTCCTTGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 13 0.52
ACGTcount: A:0.07, C:0.43, G:0.21, T:0.29
Consensus pattern (15 bp):
CCGAGCCGTTCTTCT
Found at i:20654094 original size:13 final size:14
Alignment explanation
Indices: 20654062--20654098 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
20654052 CCGAGCCGAG
20654062 CCGAGCCGTTCTTC
1 CCGAGCCGTTCTTC
20654076 CCGAGCCG--CTTC
1 CCGAGCCGTTCTTC
20654088 TCCGAGCCGTT
1 -CCGAGCCGTT
20654099 TTCTCTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.08, C:0.43, G:0.24, T:0.24
Consensus pattern (14 bp):
CCGAGCCGTTCTTC
Found at i:20660569 original size:4 final size:4
Alignment explanation
Indices: 20660560--20660591 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
20660550 TTGTTATGAT
*
20660560 AATG AATG AATG AATG AATG AATG AATA AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG
20660592 TGATGCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:20670496 original size:27 final size:25
Alignment explanation
Indices: 20670459--20670508 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
20670449 TGTTTATGTA
*
20670459 ATTTTTTATAAATATATATTAATAC
1 ATTTTTTATAAAAATATATTAATAC
20670484 ATTTTTTCAATAAAAATATATTAAT
1 ATTTTTT--ATAAAAATATATTAAT
20670509 TCTAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTTTATAAAAATATATTAATAC
Found at i:20675755 original size:25 final size:25
Alignment explanation
Indices: 20675706--20675755 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20675696 CACAAATAGA
** * *
20675706 GTTAAATTATTTATTTAATATTTTT
1 GTTAAATTATTTAAGTAAAAATTTT
20675731 GTTAAATTATTTAAGTAAAAATTTT
1 GTTAAATTATTTAAGTAAAAATTTT
20675756 AGGTTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (25 bp):
GTTAAATTATTTAAGTAAAAATTTT
Found at i:20676496 original size:2 final size:2
Alignment explanation
Indices: 20676489--20676531 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20676479 GTAAAACGAA
20676489 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
20676531 A
1 A
20676532 CTACCATTCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20678487 original size:11 final size:10
Alignment explanation
Indices: 20678451--20678492 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
20678441 GTAAATTCCG
*
20678451 TATAAAATTT
1 TATATAATTT
*
20678461 TATAAAATTT
1 TATATAATTT
20678471 TA-ATAATTT
1 TATATAATTT
20678480 TCATATAATTT
1 T-ATATAATTT
20678491 TA
1 TA
20678493 AATTATAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 7 0.24
10 14 0.48
11 8 0.28
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATAATTT
Found at i:20678491 original size:20 final size:19
Alignment explanation
Indices: 20678456--20678493 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20678446 TTCCGTATAA
20678456 AATTTTATAAAATTTTAAT
1 AATTTTATAAAATTTTAAT
*
20678475 AATTTTCATATAATTTTAA
1 AATTTT-ATAAAATTTTAA
20678494 ATTATAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTTATAAAATTTTAAT
Found at i:20684672 original size:21 final size:21
Alignment explanation
Indices: 20684632--20684674 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20684622 AATTGAAGAA
* *
20684632 AAAAAATTTATAAGTACTAAG
1 AAAAAATTTACAAATACTAAG
*
20684653 AAAAAATTTACAAATGCTAAG
1 AAAAAATTTACAAATACTAAG
20684674 A
1 A
20684675 TCAAATCTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAAAATTTACAAATACTAAG
Found at i:20686416 original size:29 final size:28
Alignment explanation
Indices: 20686370--20686424 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
20686360 TTTAATCTAT
*
20686370 TAATAAAACAAAAGATAAAGAGTTTTAGA
1 TAATAAAACAAAAGAT-AAGACTTTTAGA
* **
20686399 TAATTAAACAAACTATAAGACTTTTA
1 TAATAAAACAAAAGATAAGACTTTTA
20686425 ACTATATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (28 bp):
TAATAAAACAAAAGATAAGACTTTTAGA
Found at i:20687058 original size:29 final size:27
Alignment explanation
Indices: 20687011--20687070 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
20687001 TTATAATTAT
** *
20687011 TTATTTTAAATTATCAAATATAACATATC
1 TTATTTTAAATTAAAAAAT-TAA-ATAAC
*
20687040 TTATTTTAATTTAAAAAATTAAATAAC
1 TTATTTTAAATTAAAAAATTAAATAAC
20687067 TTAT
1 TTAT
20687071 CTGCTACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
28 3 0.11
29 16 0.59
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATTTTAAATTAAAAAATTAAATAAC
Found at i:20688590 original size:17 final size:16
Alignment explanation
Indices: 20688558--20688597 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
20688548 AAGTTCATAC
*
20688558 ATATTTAAATATAAAA
1 ATATATAAATATAAAA
*
20688574 CTATATAAATAATAAAA
1 ATATATAAAT-ATAAAA
20688591 ATATATA
1 ATATATA
20688598 TTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATAAATATAAAA
Found at i:20689328 original size:18 final size:18
Alignment explanation
Indices: 20689307--20689341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20689297 ATTTTACCCA
*
20689307 AAAAAAAATATTAAAAGC
1 AAAAAAAATAGTAAAAGC
*
20689325 AAAAAAACTAGTAAAAG
1 AAAAAAAATAGTAAAAG
20689342 AAAGGGTCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAAAAATAGTAAAAGC
Found at i:20689542 original size:14 final size:13
Alignment explanation
Indices: 20689512--20689579 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 13
20689502 ATTATTCATT
*
20689512 AAATATGAAAAAGA
1 AAATA-GAAAAAAA
20689526 AAATAGAAATAAAA
1 AAATAGAAA-AAAA
*
20689540 AAAAAGAAAAAAA
1 AAATAGAAAAAAA
**
20689553 GAAA-AGGAAAATGA
1 -AAATA-GAAAAAAA
20689567 AAAT-GAAAAAAA
1 AAATAGAAAAAAA
20689579 A
1 A
20689580 TAGTTTCGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 7 0.16
13 12 0.27
14 25 0.57
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (13 bp):
AAATAGAAAAAAA
Found at i:20689616 original size:4 final size:4
Alignment explanation
Indices: 20689607--20689655 Score: 80
Period size: 4 Copynumber: 12.2 Consensus size: 4
20689597 TGACACAAAA
* *
20689607 ATAG ATAG ATAA AGAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
20689655 A
1 A
20689656 CAAAAGTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (4 bp):
ATAG
Found at i:20690833 original size:3 final size:3
Alignment explanation
Indices: 20690827--20690876 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
20690817 GCTAGTAGTT
20690827 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
20690875 TT
1 TT
20690877 GTGTAATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20692775 original size:31 final size:29
Alignment explanation
Indices: 20692716--20692779 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
20692706 ATCAAAGTCT
*
20692716 AGTGACAAAATTCACTCAAATTAAAATAG
1 AGTGACAAAATTCACTCAAACTAAAATAG
**
20692745 AGTGACAAAATTCAACATTGAACTAAAATAG
1 AGTGACAAAATTC-AC-TCAAACTAAAATAG
20692776 AGTG
1 AGTG
20692780 GCGAATTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
30 2 0.07
31 15 0.50
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (29 bp):
AGTGACAAAATTCACTCAAACTAAAATAG
Found at i:20692860 original size:24 final size:24
Alignment explanation
Indices: 20692832--20692878 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20692822 AAACTAGCAA
* * *
20692832 CATTAGTTTATTGTGTAGCATCAC
1 CATTAGTTGATTGGGCAGCATCAC
20692856 CATTAGTTGATTGGGCAGCATCA
1 CATTAGTTGATTGGGCAGCATCA
20692879 GAGACATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
CATTAGTTGATTGGGCAGCATCAC
Found at i:20692995 original size:2 final size:2
Alignment explanation
Indices: 20692988--20693036 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
20692978 CTTCCCTTAA
* *
20692988 AT AT AT AT AT AG AT AT AT AT AG 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
*
20693030 AG AT AT A
1 AT AT AT A
20693037 GATAAGAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:20699457 original size:16 final size:17
Alignment explanation
Indices: 20699423--20699460 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
20699413 TCAAACTTCA
20699423 TTATCACGTGCATTTTT
1 TTATCACGTGCATTTTT
20699440 TTATCACGTGCATTTTT
1 TTATCACGTGCATTTTT
20699457 TTAT
1 TTAT
20699461 GAACATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (17 bp):
TTATCACGTGCATTTTT
Found at i:20706856 original size:20 final size:19
Alignment explanation
Indices: 20706826--20706882 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
20706816 AAAAGCTTTA
20706826 AAAATAATTATTTTTAGAAAT
1 AAAA-AATTATTTTTA-AAAT
*
20706847 AAAAAATTATTTTT-AAGT
1 AAAAAATTATTTTTAAAAT
*
20706865 AAAAAATAATTTTTAAAA
1 AAAAAATTATTTTTAAAA
20706883 CTTTACCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 10 0.31
21 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAAAATTATTTTTAAAAT
Found at i:20707925 original size:23 final size:22
Alignment explanation
Indices: 20707898--20707940 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
20707888 ACACGTATTA
*
20707898 TATTTCTTGCTTTCTTTTTTTTC
1 TATTTCTTCCTTT-TTTTTTTTC
20707921 TATTTCTTCCTTTTTTTTTT
1 TATTTCTTCCTTTTTTTTTT
20707941 CTTGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTTCTTCCTTTTTTTTTTTC
Found at i:20709362 original size:22 final size:22
Alignment explanation
Indices: 20709319--20709362 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20709309 TTCTTAAAAT
*
20709319 TAATTGTTATTATTTTATATTA
1 TAATTGTTATTATTTTAAATTA
*
20709341 TAATTTTTA-TATTTTCAAATTA
1 TAATTGTTATTATTTT-AAATTA
20709363 ATATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TAATTGTTATTATTTTAAATTA
Found at i:20710505 original size:7 final size:7
Alignment explanation
Indices: 20710488--20710534 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
20710478 TCTTAAAAAA
20710488 TATATATC
1 TATA-ATC
20710496 TATAATC
1 TATAATC
20710503 TATAATC
1 TATAATC
*
20710510 CATAATC
1 TATAATC
*
20710517 CATAATC
1 TATAATC
*
20710524 TATAATT
1 TATAATC
20710531 TATA
1 TATA
20710535 TTAAAACTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
7 32 0.89
8 4 0.11
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (7 bp):
TATAATC
Found at i:20714193 original size:25 final size:25
Alignment explanation
Indices: 20714145--20714193 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
20714135 TTAATTAAGG
*
20714145 TTTTTGTTTTTTTAAATTGGTTTTT
1 TTTTTGTTTTTTTAAATTGATTTTT
*
20714170 TTTTTGTGTTTTTTACATT-ATTTT
1 TTTTTGT-TTTTTTAAATTGATTTT
20714194 AAATACCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (25 bp):
TTTTTGTTTTTTTAAATTGATTTTT
Found at i:20714972 original size:14 final size:14
Alignment explanation
Indices: 20714949--20714978 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20714939 AAAAATTTAG
20714949 TCAATACCACATCA
1 TCAATACCACATCA
*
20714963 TCAATGCCACATCA
1 TCAATACCACATCA
20714977 TC
1 TC
20714979 TTTAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (14 bp):
TCAATACCACATCA
Found at i:20715075 original size:9 final size:9
Alignment explanation
Indices: 20715063--20715123 Score: 68
Period size: 9 Copynumber: 6.4 Consensus size: 9
20715053 TTTTTTTCAC
20715063 AATTCTAAA
1 AATTCTAAA
*
20715072 AATTATAAA
1 AATTCTAAA
*
20715081 AATTTTAATAA
1 AATTCT-A-AA
*
20715092 AATTTTAAA
1 AATTCTAAA
20715101 AATTCTAAAA
1 AATTCT-AAA
20715111 AATTCTAAA
1 AATTCTAAA
20715120 AATT
1 AATT
20715124 TTTGAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 27 0.59
10 11 0.24
11 8 0.17
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (9 bp):
AATTCTAAA
Found at i:20715087 original size:39 final size:40
Alignment explanation
Indices: 20715029--20715136 Score: 114
Period size: 39 Copynumber: 2.7 Consensus size: 40
20715019 AAAATTTTTA
** * * *
20715029 AAAAAATTCTAAATTTTTTAAAAATTTTTTTCACAATTCT
1 AAAAAATTCTAAAAATTTTAAAAATTATTTTAAAAATTCT
*
20715069 -AAAAATTATAAAAATTTTAATAAA--ATTTTAAAAATTCT
1 AAAAAATTCTAAAAATTTTAA-AAATTATTTTAAAAATTCT
20715107 AAAAAATTCTAAAAATTTTTGAAAAATTAT
1 AAAAAATTCTAAAAA-TTTT-AAAAATTAT
20715137 AAAAAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 11 0.20
39 30 0.55
40 10 0.18
41 2 0.04
42 2 0.04
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.42
Consensus pattern (40 bp):
AAAAAATTCTAAAAATTTTAAAAATTATTTTAAAAATTCT
Found at i:20715093 original size:12 final size:11
Alignment explanation
Indices: 20715079--20715150 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
20715069 AAAAATTATA
20715079 AAAATTTTAAT
1 AAAATTTTAAT
20715090 AAAATTTT-A-
1 AAAATTTTAAT
*
20715099 AAAATTCTAA-
1 AAAATTTTAAT
*
20715109 AAAATTCTAA-
1 AAAATTTTAAT
* *
20715119 AAATTTTTGA-
1 AAAATTTTAAT
*
20715129 AAAATTATAA-
1 AAAATTTTAAT
20715139 AAAATTTTAAT
1 AAAATTTTAAT
20715150 A
1 A
20715151 TTTATCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
9 7 0.14
10 35 0.69
11 9 0.18
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (11 bp):
AAAATTTTAAT
Found at i:20715095 original size:20 final size:19
Alignment explanation
Indices: 20715069--20715148 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 19
20715059 TCACAATTCT
20715069 AAAAATTATAAAAATTTTA
1 AAAAATTATAAAAATTTTA
* *
20715088 ATAAAATTTTAAAAATTCTA
1 A-AAAATTATAAAAATTTTA
* *
20715108 AAAAATTCTAAAAATTTTTG
1 AAAAATTATAAAAA-TTTTA
20715128 AAAAATTATAAAAAATTTTA
1 AAAAATTAT-AAAAATTTTA
20715148 A
1 A
20715149 TATTTATCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 13 0.25
20 33 0.65
21 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAAATTATAAAAATTTTA
Found at i:20715140 original size:9 final size:9
Alignment explanation
Indices: 20715063--20715199 Score: 62
Period size: 9 Copynumber: 14.4 Consensus size: 9
20715053 TTTTTTTCAC
*
20715063 AATTCTAAA
1 AATTATAAA
20715072 AATTATAAA
1 AATTATAAA
*
20715081 AATTTTAATAA
1 AATTAT-A-AA
*
20715092 AATTTTAAA
1 AATTATAAA
*
20715101 AATTCTAAAA
1 AATTAT-AAA
*
20715111 AATTCTAAA
1 AATTATAAA
*
20715120 AATTTTTGAAA
1 AA-TTAT-AAA
20715131 AATTATAAAA
1 AATTAT-AAA
* *
20715141 AATTTTAAT
1 AATTATAAA
*
20715150 ATTTATCAAA
1 AATTAT-AAA
*
20715160 AA-AATAAA
1 AATTATAAA
20715168 AA-TATGAAA
1 AATTAT-AAA
* * *
20715177 CATTTTTATA
1 -AATTATAAA
20715187 AATTATAAA
1 AATTATAAA
20715196 AATT
1 AATT
20715200 CCAATGATAT
Statistics
Matches: 99, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
8 7 0.07
9 46 0.46
10 31 0.31
11 15 0.15
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (9 bp):
AATTATAAA
Found at i:20715162 original size:30 final size:27
Alignment explanation
Indices: 20715068--20715153 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 27
20715058 TTCACAATTC
20715068 TAAAAATTAT-AAAAATTTTAATAAAATTT
1 TAAAAATTATAAAAAATTTTAAT---ATTT
* * *
20715097 TAAAAATTCTAAAAAATTCTAAAAATTTT
1 TAAAAATTATAAAAAATT-TTAATA-TTT
20715126 TGAAAAATTATAAAAAATTTTAATATTT
1 T-AAAAATTATAAAAAATTTTAATATTT
20715154 ATCAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 4 0.09
29 17 0.36
30 23 0.49
31 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (27 bp):
TAAAAATTATAAAAAATTTTAATATTT
Found at i:20715639 original size:20 final size:18
Alignment explanation
Indices: 20715614--20715693 Score: 79
Period size: 20 Copynumber: 4.2 Consensus size: 18
20715604 TGTTTAAAAG
20715614 AAAATTTCAAAAAACTTCTA
1 AAAATTTCAAAAAA-TT-TA
** *
20715634 AAAATTTTTAAAAATTTT
1 AAAATTTCAAAAAATTTA
20715652 AAAATTTCAAAAAAAATTTA
1 AAAATTTC--AAAAAATTTA
* *
20715672 AAATTTTCAAAAAATTCA
1 AAAATTTCAAAAAATTTA
20715690 AAAA
1 AAAA
20715694 ATTATAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 20 0.41
19 2 0.04
20 27 0.55
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTTCAAAAAATTTA
Found at i:20715654 original size:19 final size:19
Alignment explanation
Indices: 20715632--20715907 Score: 82
Period size: 19 Copynumber: 14.4 Consensus size: 19
20715622 AAAAAACTTC
20715632 TAAAAATTTTTAAAAATTT
1 TAAAAATTTTTAAAAATTT
** *
20715651 T-AAAATTTCAAAAAAAATT
1 TAAAAATTT-TTAAAAATTT
* *
20715670 T-AAAATTTTCAAAAAATT
1 TAAAAATTTTTAAAAATTT
* * * *
20715688 CAAAAAATTATAAAATTTT
1 TAAAAATTTTTAAAAATTT
* * ***
20715707 TAAAAAAAATTCTAATTTTTTT
1 T--AAAAATTTTTAA-AAATTT
* * *
20715729 TAAAAATTTTTTCACAATTC
1 TAAAAA-TTTTTAAAAATTT
*
20715749 TAAAAA-TTTTAAAATTTT
1 TAAAAATTTTTAAAAATTT
**
20715767 CTATAAAA-TTTTAAAAGCTT
1 -TA-AAAATTTTTAAAAATTT
*** *
20715787 TAAAAAAAATT-AAAACTT
1 TAAAAATTTTTAAAAATTT
* * *
20715805 AAAAAATTCTAAAAAATTT
1 TAAAAATTTTTAAAAATTT
* *
20715824 TAAAAATTCTTGAAAAATTA
1 TAAAAATT-TTTAAAAATTT
* * *
20715844 TAAAAAATTTTAATATTTAT
1 TAAAAATTTTTAAAAATT-T
*
20715864 TCAAAAA---TTAAAAATAT
1 T-AAAAATTTTTAAAAATTT
* * *
20715881 GAAACATTTTTAAAAATTA
1 TAAAAATTTTTAAAAATTT
20715900 TAAAAATT
1 TAAAAATT
20715908 CCAATGATAA
Statistics
Matches: 186, Mismatches: 55, Indels: 32
0.68 0.20 0.12
Matches are distributed among these distances:
16 4 0.02
17 1 0.01
18 45 0.24
19 68 0.37
20 43 0.23
21 20 0.11
22 5 0.03
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (19 bp):
TAAAAATTTTTAAAAATTT
Found at i:20715664 original size:28 final size:27
Alignment explanation
Indices: 20715614--20715856 Score: 76
Period size: 30 Copynumber: 8.4 Consensus size: 27
20715604 TGTTTAAAAG
* * *
20715614 AAAATTTCAAAAAACTTCTAAAAATTTTT
1 AAAATTT-TAAAAA-TTCAAAAAATTTTA
* *
20715643 AAAAATTTTAAAATTTCAAAAAAAATTT-
1 AAA-ATTTTAAAAATTC-AAAAAATTTTA
*
20715671 AAAATTTTCAAAAAATTCAAAAAATTATA
1 AAAATTTT--AAAAATTCAAAAAATTTTA
* ****
20715700 AAATTTTTAAAAAAAATTCTAATTTTTTTTA
1 AAAATTTT---AAAAATTC-AAAAAATTTTA
* * *
20715731 AAAATTTTTTCACAATTCTAAAAATTTTA
1 AAAA--TTTTAAAAATTCAAAAAATTTTA
* * ** *
20715760 AAATTTTCTATAAAATTTTAAAAGCTTTAA
1 AAAATTT-TA-AAAA-TTCAAAAAATTTTA
** * *
20715790 AAAAAATTAAAACTT-AAAAAATTCTAA
1 AAAATTTTAAAAATTCAAAAAATT-TTA
* *
20715817 AAAATTTTAAAAATTCTTGAAAAATTATAA
1 AAAATTTTAAAAATTC--AAAAAATT-TTA
20715847 AAAATTTTAA
1 AAAATTTTAA
20715857 TATTTATTCA
Statistics
Matches: 157, Mismatches: 41, Indels: 31
0.69 0.18 0.14
Matches are distributed among these distances:
26 6 0.04
27 25 0.16
28 18 0.11
29 43 0.27
30 52 0.33
31 9 0.06
33 4 0.03
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (27 bp):
AAAATTTTAAAAATTCAAAAAATTTTA
Found at i:20715828 original size:20 final size:21
Alignment explanation
Indices: 20715803--20715856 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
20715793 AAATTAAAAC
20715803 TTAAAAAATTC-TAAAAAATT
1 TTAAAAAATTCTTAAAAAATT
*
20715823 TT-AAAAATTCTTGAAAAATT
1 TTAAAAAATTCTTAAAAAATT
*
20715843 ATAAAAAATT-TTAA
1 TTAAAAAATTCTTAA
20715857 TATTTATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 8 0.28
20 14 0.48
21 7 0.24
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAAAAATTCTTAAAAAATT
Found at i:20715829 original size:11 final size:10
Alignment explanation
Indices: 20715804--20715852 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
20715794 AATTAAAACT
20715804 TAAAAAATTC
1 TAAAAAATTC
20715814 TAAAAAATT-
1 TAAAAAATTC
*
20715823 TTAAAAATTC
1 TAAAAAATTC
* *
20715833 TTGAAAAATTA
1 -TAAAAAATTC
20715844 TAAAAAATT
1 TAAAAAATT
20715853 TTAATATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.24
10 17 0.52
11 8 0.24
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:20715870 original size:30 final size:30
Alignment explanation
Indices: 20715806--20715877 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
20715796 TTAAAACTTA
* * *
20715806 AAAAATTCTAAAAAATTTTAAAAATTCTTG
1 AAAAATTATAAAAAATTTTAAAAATTATTC
* *
20715836 AAAAATTATAAAAAATTTTAATATTTATTC
1 AAAAATTATAAAAAATTTTAAAAATTATTC
20715866 AAAAATTA-AAAA
1 AAAAATTATAAAA
20715878 TATGAAACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATTATAAAAAATTTTAAAAATTATTC
Found at i:20716460 original size:20 final size:19
Alignment explanation
Indices: 20716415--20716541 Score: 73
Period size: 20 Copynumber: 6.6 Consensus size: 19
20716405 TCACAATTCT
** *
20716415 AAAAATTTTAAATTTTCTA
1 AAAAATTTTAAAAATTCAA
*
20716434 TAAAATTTTAAAAACTTCAA
1 AAAAATTTTAAAAA-TTCAA
20716454 AAAAATTTTCAAAACA-TC--
1 AAAAATTTT-AAAA-ATTCAA
*
20716472 AAAAATTCTAGAAAATTCAA
1 AAAAATTTTA-AAAATTCAA
* * *
20716492 AACAATTCTAAAAAATTCTA
1 AAAAATT-TTAAAAATTCAA
** *
20716512 AAACTTTTTGAAAAATT-AT
1 AAAAATTTT-AAAAATTCAA
20716531 AAAAATTTTAA
1 AAAAATTTTAA
20716542 TATTTATCAA
Statistics
Matches: 81, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
17 2 0.02
18 15 0.19
19 19 0.23
20 39 0.48
21 5 0.06
22 1 0.01
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTTTAAAAATTCAA
Found at i:20716486 original size:10 final size:10
Alignment explanation
Indices: 20716472--20716514 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
20716462 TCAAAACATC
20716472 AAAAATTCTA
1 AAAAATTCTA
*
20716482 GAAAATTC-A
1 AAAAATTCTA
20716491 AAACAATTCTA
1 AAA-AATTCTA
20716502 AAAAATTCTA
1 AAAAATTCTA
20716512 AAA
1 AAA
20716515 CTTTTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 3 0.10
10 22 0.76
11 4 0.14
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:20716593 original size:715 final size:707
Alignment explanation
Indices: 20715089--20716593 Score: 1667
Period size: 708 Copynumber: 2.1 Consensus size: 707
20715079 AAAATTTTAA
* * * * * * * * * *
20715089 TAAAATTTTAAAAATTCTAAAAAATTCTAAAAATTTTTGAAAAATTATAAAAAATTTTAATATTT
1 TAAAACTTAAAAAATTATAAAAAATTTTAAAAATTCTTCAAAAATAATAAAAAATATGAACATTT
* * *
20715154 A-TCAAAAAAATAAAAATATGAAACATTTTTATAAATTATAAAAATTCCAATGATATATTAAAAA
66 ATTCAAAAATATAAAAATATGAAACATTTTTAAAAATTATAAAAATTCCAATGATAAATTAAAAA
* * **
20715218 TATGAAACATTTTTACAAATTATAAATATTTTCACAATTCCAATGATAGGTGCGCTTTTTTTTAA
131 TATGAAACATTTTTACAAATTATAAACATTTTCACAATTCCAATGATAGGTGCGCCTTTTTAAAA
* *
20715283 ATTCGAGGTTCAATAAAAAAAAATTATAATAAATTTGAATAAGACTAGAAGTAGGTTTAGAATGT
196 ATTCGAGGTTCAATAAAAAAAAATTATAATAAATTTGAATAAAACTAGAAGTAGGTTTAGAACGT
* * *
20715348 TCCACCTTTCTTTGAGTATGTAAAAACTTATATATTTGGTTAAATATATATTTGGTCCCTAACCT
261 TCCACCTTTCTTTGAGTATATAAAAAATTATATATTTGGTTAAATATATATTTAGTCCCTAACCT
* * * * * *
20715413 TTATGATTTCTATCATATTGACATCTAAATAATTTTTCTGTCACATTATACTTAATCGTTCAAAT
326 TTATGATTTCTATCACATTGACACCTAAACAAATTTTCTGTCACATTATACTTAACCATTCAAAT
* * **
20715478 TTGTTATCACTTTGATTATTCAGATTAACAATGTTAGTTAATTTTGCTAACGCAGTATGAATATT
391 TTGTTATCACTTTGATTACTCAGATTAACAATGTTAGTCAACCTTGCTAACGCAGTATGAATATT
* * * *
20715543 CAACAAGATATTAACACATATAAAAAAATTTAGTCAATGCTATATCATCAATGACACGTCATGTT
456 CAACAAGATACTAACACATATAAAAAAATTCAGTCAATGCCATATCATCAATGACACGTCATCTT
*
20715608 TAAAAGAAAATTTCAAAAAACTTCTAAAAATTTTTAAAAATTTTAAAATTTCAAAAAAAATTTAA
521 TAAAAGAAAATTTCAAAAAAATTCTAAAAATTTTTAAAAATTTTAAAATTTCAAAAAAAATTTAA
* *** *
20715673 AATTTTCAAAAAATTCAAAAAATTATAAAATTTTTAAAAAAAATTCTAATTTTTTTTAAAAATTT
586 AATTTTCAAAAAATTCAAAAAATTATAAAAATTTT--AAAAAATTCTAATAAATTTTAAAAACTT
**** * ** * * * *
20715738 TTTCACAATTCTAAAAATTTTAAAATTTTCTATAAAATTTTAAAAGCTTTAAAAAAAAT
649 CAAAAAAATTCTAAAAACATCAAAATATTCTAGAAAATTTCAAAAGCTTTAAAAAAAAT
* * * * * *
20715797 TAAAACTTAAAAAATTCTAAAAAATTTTAAAAATTCTTGAAAAATTATAAAAAATTTTAATATTT
1 TAAAACTTAAAAAATTATAAAAAATTTTAAAAATTCTTCAAAAATAATAAAAAATATGAACATTT
20715862 ATTCAAAAAT-TAAAAATATGAAACATTTTTAAAAATTATAAAAATTCCAATGATAAATTAAAAA
66 ATTCAAAAATATAAAAATATGAAACATTTTTAAAAATTATAAAAATTCCAATGATAAATTAAAAA
*
20715926 TATGAAACATTTTTACAAATTATAAACATTTTCACAATTCCAATTATAGGTGCGCCTTTTTAAAA
131 TATGAAACATTTTTACAAATTATAAACATTTTCACAATTCCAATGATAGGTGCGCCTTTTTAAAA
*** *
20715991 ATTCGAGGTTCAATAAAAATTTTTATTTTTTTATAATAAATTTGACTAAAACTAGAAGTAGGTTT
196 ATTCGAGGTTCAATAAAAA-----A--AAATTATAATAAATTTGAATAAAACTAGAAGTAGGTTT
20716056 AGAACGTTCCACCTTTCTTTGAGTATATAAAAAATTATATATTTGGTT-AATATATATTTAG-CC
254 AGAACGTTCCACCTTTCTTTGAGTATATAAAAAATTATATATTTGGTTAAATATATATTTAGTCC
* *
20716119 TCTAACCTTTATGATTTCTGTCACATTGATACCTAAACAAATTTTCTGTCACATTAGTA-TCTAA
319 -CTAACCTTTATGATTTCTATCACATTGACACCTAAACAAATTTTCTGTCACATTA-TACT-TAA
* * * * *
20716183 CCATTCAAATTTGTTATCACTTTGGTTCCTC-GAATT-ACCATTTCTAGTCAACCTTGCTAATGC
381 CCATTCAAATTTGTTATCACTTTGATTACTCAG-ATTAACAATGT-TAGTCAACCTTGCTAACGC
* * * *
20716246 AGTATGAA-ATTCAATAAGATACTGACACATA-GAAAAAATTCAGTCAGTGCCATATCATCAATG
444 AGTATGAATATTCAACAAGATACTAACACATATAAAAAAATTCAGTCAATGCCATATCATCAATG
*
20716309 -CTACGTCATCTTTAAAAGAAAATTTCAAAAAAAATT-T-AAAATTTTT-GAAATTTTCAAAATA
509 AC-ACGTCATCTTTAAAAGAAAATTTC-AAAAAAATTCTAAAAATTTTTAAAAATTTT-AAAAT-
* * * ** *** * * **
20716370 TT-ATTAAAAAATTCTAAATTTTTTTAAAATTTTTTTCACAATTCTAAAAATTTT-AAATTTTCT
570 TTCA-AAAAAAATT-TAAA-ATTTTCAAAA-AATTCAAAAAATTATAAAAATTTTAAAAAATTCT
* *
20716433 -ATAAAATTTTAAAAACTTCAAAAAAATTTTCAAAACATCAAAA-ATTCTAGAAAA-TTCAAAA-
631 AAT-AAATTTTAAAAACTTCAAAAAAATTCTAAAAACATCAAAATATTCTAGAAAATTTCAAAAG
*
20716494 CAATTCT-AAAAAATT
695 C--TT-TAAAAAAAAT
* * *
20716509 CTAAAACTTTTTGAAAAATTAT-AAAAATTTT-AATATT-TATCAAAACA-AATTAAAAATATGA
1 -TAAAAC---TTAAAAAATTATAAAAAATTTTAAAAATTCT-TCAAAA-ATAATAAAAAATATGA
*
20716570 TACATTT-TT-ATAAATTATAAAAAT
60 -ACATTTATTCA-AAAATATAAAAAT
20716594 TATCATTATT
Statistics
Matches: 674, Mismatches: 89, Indels: 61
0.82 0.11 0.07
Matches are distributed among these distances:
708 193 0.29
709 7 0.01
710 1 0.00
711 13 0.02
712 36 0.05
713 107 0.16
714 126 0.19
715 165 0.24
716 26 0.04
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (707 bp):
TAAAACTTAAAAAATTATAAAAAATTTTAAAAATTCTTCAAAAATAATAAAAAATATGAACATTT
ATTCAAAAATATAAAAATATGAAACATTTTTAAAAATTATAAAAATTCCAATGATAAATTAAAAA
TATGAAACATTTTTACAAATTATAAACATTTTCACAATTCCAATGATAGGTGCGCCTTTTTAAAA
ATTCGAGGTTCAATAAAAAAAAATTATAATAAATTTGAATAAAACTAGAAGTAGGTTTAGAACGT
TCCACCTTTCTTTGAGTATATAAAAAATTATATATTTGGTTAAATATATATTTAGTCCCTAACCT
TTATGATTTCTATCACATTGACACCTAAACAAATTTTCTGTCACATTATACTTAACCATTCAAAT
TTGTTATCACTTTGATTACTCAGATTAACAATGTTAGTCAACCTTGCTAACGCAGTATGAATATT
CAACAAGATACTAACACATATAAAAAAATTCAGTCAATGCCATATCATCAATGACACGTCATCTT
TAAAAGAAAATTTCAAAAAAATTCTAAAAATTTTTAAAAATTTTAAAATTTCAAAAAAAATTTAA
AATTTTCAAAAAATTCAAAAAATTATAAAAATTTTAAAAAATTCTAATAAATTTTAAAAACTTCA
AAAAAATTCTAAAAACATCAAAATATTCTAGAAAATTTCAAAAGCTTTAAAAAAAAT
Found at i:20716955 original size:10 final size:10
Alignment explanation
Indices: 20716942--20716994 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
20716932 AATTTTAGAC
20716942 TTTTTTTAAA
1 TTTTTTTAAA
20716952 TTTTTTTAAA
1 TTTTTTTAAA
* * *
20716962 ATTTATTATA
1 TTTTTTTAAA
*
20716972 -TTTTTCAAA
1 TTTTTTTAAA
*
20716981 TTTTTTAAAA
1 TTTTTTTAAA
20716991 TTTT
1 TTTT
20716995 AACAAAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 6 0.17
10 29 0.83
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:20717009 original size:28 final size:27
Alignment explanation
Indices: 20716945--20717017 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
20716935 TTTAGACTTT
** * *
20716945 TTTTAAATTTTTTTAAAATTTATTATAT
1 TTTTAAA-TTTTTTAAAATTTAACAAAA
20716973 TTTTCAAATTTTTTAAAATTTTAACAAAA
1 TTTT-AAATTTTTTAAAA-TTTAACAAAA
20717002 TTTTAAATTTTATTAA
1 TTTTAAATTTT-TTAA
20717018 CATCATCAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTAAATTTTTTAAAATTTAACAAAA
Found at i:20717551 original size:18 final size:17
Alignment explanation
Indices: 20717519--20717552 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20717509 CAAAATCTAC
*
20717519 TTTTTTATTTTTTTTTG
1 TTTTTTATTTATTTTTG
20717536 TTTTTTAGTTTATTTTT
1 TTTTTTA-TTTATTTTT
20717553 ATTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTTATTTATTTTTG
Found at i:20717877 original size:14 final size:15
Alignment explanation
Indices: 20717846--20717881 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20717836 TTTTTAAAAG
20717846 CTTTTT-TTTTTCAT
1 CTTTTTATTTTTCAT
20717860 -TTTTTATTTTT-AT
1 CTTTTTATTTTTCAT
20717873 CTTTTTATT
1 CTTTTTATT
20717882 AGATAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTTTATTTTTCAT
Found at i:20718161 original size:175 final size:175
Alignment explanation
Indices: 20717961--20718315 Score: 577
Period size: 180 Copynumber: 2.0 Consensus size: 175
20717951 GTTCACTCCA
20717961 ATTCAATTAATGCATTTTCTTTTAATTCGAGGTAATTGGCTTCA-TTTTTTTTTTTAATTGAGTT
1 ATTCAATTAATGCATTTTCTTTTAATTCGAGGTAATTGGCTTCATTTTTTTTTTTTAATTGAGTT
*
20718025 CAGGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATATATAAAAAAAATTATTATTG
66 CAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATATATAAAAAAAATTATTATTG
20718090 ATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
131 ATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
* * *
20718135 ATTCAATTAATGCGTTTTTTTTTTAATTCGAGGTAATTGGCTTTATTTTTTTTTTTTTTTTAATT
1 ATTCAATTAATGC-ATTTTCTTTTAATTCGAGGTAATTGGCTTCA----TTTTTTTTTTTTAATT
* * **
20718200 GAGTTCAAGTAAGAGCAAGATTTTGGATGTTAGGCCTCGAACCTGGTATATATTAAAAATTTTAT
61 GAGTTCAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATATATAAAAAAAATTAT
*
20718265 TATTGATTTAATTCTATATTAGATATGTATTTTATTAAAAAATATTATTT
126 TATTGATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
20718315 A
1 A
20718316 ATATTTTAAT
Statistics
Matches: 166, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
174 13 0.08
175 28 0.17
180 125 0.75
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.47
Consensus pattern (175 bp):
ATTCAATTAATGCATTTTCTTTTAATTCGAGGTAATTGGCTTCATTTTTTTTTTTTAATTGAGTT
CAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATATATAAAAAAAATTATTATTG
ATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
Found at i:20718357 original size:180 final size:177
Alignment explanation
Indices: 20718005--20718367 Score: 478
Period size: 180 Copynumber: 2.0 Consensus size: 177
20717995 ATTGGCTTCA
*
20718005 TTTTTTTTTTTAATTGAGTTCAGGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATA
1 TTTTTTTTTTTAATTGAGTTCAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATA
20718070 TATAAAAAAAATTATTATTGATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
66 TATAAAAAAAATTATTATTGATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
* ** *** * * *
20718135 ATTCAATTAATGCGTTTTTTTTTTAATTCGAGGTAATTGGCTTTATTTTT
131 AATCAATTAAT--GTTAATAAATTAATTCCACGTAATTGGCTTT-TTTAT
*
20718185 TTTTTTTTTTTAATTGAGTTCAAGTAAGAGCAAGATTTTGGATGTTAGGCCTCGAACCTGGTATA
1 TTTTTTTTTTTAATTGAGTTCAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATA
* ** *
20718250 TATTAAAAATTTTATTATTGATTTAATTCTATATTAGATATGTATTTTATTAAAAAATATTATTT
66 TATAAAAAAAATTATTATTGATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
* * * *
20718315 AAT-ATTTTAAT-TTAATAAATTCATGTACCATCTTATTTGGCTTTTTTAT
131 AATCA-ATTAATGTTAATAAATTAAT-T-CCA-CGTAATTGGCTTTTTTAT
20718364 TTTT
1 TTTT
20718368 ATCATTTTCT
Statistics
Matches: 160, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 7 0.04
178 1 0.01
179 11 0.07
180 141 0.88
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (177 bp):
TTTTTTTTTTTAATTGAGTTCAAGTAAGAGCAAGATTTTGGATATTAGGCCTCGAACCTGGTATA
TATAAAAAAAATTATTATTGATTTAATTCTATATTAGATATGTAATTTATTAAAAAATATTATTT
AATCAATTAATGTTAATAAATTAATTCCACGTAATTGGCTTTTTTAT
Found at i:20718918 original size:6 final size:6
Alignment explanation
Indices: 20718907--20719004 Score: 124
Period size: 6 Copynumber: 16.3 Consensus size: 6
20718897 TCTAGCCATT
* * * * *
20718907 ATAATA ATAATA ACAATA ATAATA ACAATA ACAATA ACAACA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * *
20718955 ATAACA ATAATA ACAATA ACAATA ATAATA ATAATA ATAATA ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
20719003 AT
1 AT
20719005 TATTATTGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (6 bp):
ATAATA
Found at i:20719004 original size:15 final size:15
Alignment explanation
Indices: 20718907--20719004 Score: 124
Period size: 15 Copynumber: 6.5 Consensus size: 15
20718897 TCTAGCCATT
*
20718907 ATAATAATAATAACA
1 ATAATAATAATAATA
*
20718922 ATAATAATAACAATA
1 ATAATAATAATAATA
* * *
20718937 ACAATAACAACAATA
1 ATAATAATAATAATA
*
20718952 ATAATAACAATAATA
1 ATAATAATAATAATA
* *
20718967 ACAATAACAATAATA
1 ATAATAATAATAATA
20718982 ATAATAATAATAATA
1 ATAATAATAATAATA
20718997 ATAATAAT
1 ATAATAAT
20719005 TATTATTGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 74 1.00
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAATAATAATAATA
Found at i:20719009 original size:3 final size:3
Alignment explanation
Indices: 20719003--20719048 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
20718993 AATAATAATA
* *
20719003 ATT ATT ATT GTT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
20719049 CTAATACTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20719026 original size:18 final size:18
Alignment explanation
Indices: 20719003--20719047 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
20718993 AATAATAATA
20719003 ATTATTATTGTTATTATT
1 ATTATTATTGTTATTATT
20719021 ATTATTATTGTTATTATT
1 ATTATTATTGTTATTATT
20719039 ATTATTATT
1 ATTATTATT
20719048 ACTAATACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTATTATTGTTATTATT
Found at i:20719822 original size:18 final size:19
Alignment explanation
Indices: 20719778--20719822 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
20719768 ATGTTTTTTC
20719778 TTTTTTAATATTTGATAAA
1 TTTTTTAATATTTGATAAA
20719797 TATTTTTAATA-TT-ATACAA
1 T-TTTTTAATATTTGATA-AA
20719816 TTTTTTA
1 TTTTTTA
20719823 TTGATGCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTTAATATTTGATAAA
Found at i:20720033 original size:20 final size:21
Alignment explanation
Indices: 20719991--20720034 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20719981 TCCGATGATC
* *
20719991 TTTCTTTTTTTTTTTTCTATT
1 TTTCTTTATTTATTTTCTATT
20720012 TTTCTTTATTTATTTT-TATT
1 TTTCTTTATTTATTTTCTATT
20720032 TTT
1 TTT
20720035 TTCTCTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTCTTTATTTATTTTCTATT
Found at i:20720035 original size:21 final size:21
Alignment explanation
Indices: 20719991--20720038 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
20719981 TCCGATGATC
* *
20719991 TTTCTTTTTTTTTTTTCTATT
1 TTTCTTTTTTATTTTTATATT
*
20720012 TTTCTTTATTTATTTTTATTTT
1 TTTCTTT-TTTATTTTTATATT
20720034 TTTCT
1 TTTCT
20720039 CTGTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTCTTTTTTATTTTTATATT
Found at i:20720163 original size:159 final size:159
Alignment explanation
Indices: 20719905--20720196 Score: 346
Period size: 159 Copynumber: 1.8 Consensus size: 159
20719895 TGTGTACAAT
*
20719905 ATTAATAAAATTATTATTTTATAACTTAATTTAAAATATTAACATTTTAAACTCAATTTGGATGT
1 ATTAATAAAATTATTATTTAATAACTTAATTTAAAATATTAACATTTTAAACTCAATTTGGATGT
* * * * * *
20719970 TCATATGGCAATCCGATGATCTTTCTTTT-TTTTTTTTCTATTTTTCTTTATT-TATTTTTATTT
66 TCATATGGCAATCCAATAAGCTCTATTTTCTTTTTTTT-T-TTTCTCTTTATTGTATTTTTATTT
20720033 TTTTCTCTGTATTATTTTTTTTAGATTTTTA
129 TTTTCTCTGTATTATTTTTTTTAGATTTTTA
* * * *
20720064 ATTAATAAAATTATTATTTAATACCTTAATTTAACATATTAATATTTTAAACTTAA-TTGGAATG
1 ATTAATAAAATTATTATTTAATAACTTAATTTAAAATATTAACATTTTAAACTCAATTTGG-ATG
* * *
20720128 -TCATGTTAT-GC-A-CCAATAAGCTCTATTTTCCTTTTTTTTTTTTCTTTTTGTTGTTTTTTTA
65 TTCA---TATGGCAATCCAATAAGCTCTATTTT-CTTTTTTTTTTTTCTCTTTATTGTATTTTTA
20720189 TTTTTTTC
126 TTTTTTTC
20720197 ATCTTTTGTT
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
158 28 0.25
159 71 0.63
160 10 0.09
161 3 0.03
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (159 bp):
ATTAATAAAATTATTATTTAATAACTTAATTTAAAATATTAACATTTTAAACTCAATTTGGATGT
TCATATGGCAATCCAATAAGCTCTATTTTCTTTTTTTTTTTTCTCTTTATTGTATTTTTATTTTT
TTCTCTGTATTATTTTTTTTAGATTTTTA
Found at i:20720203 original size:27 final size:24
Alignment explanation
Indices: 20720153--20720227 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 24
20720143 ATAAGCTCTA
20720153 TTTTCCTTTTTTTTTTTTCTTTTTG
1 TTTT-CTTTTTTTTTTTTCTTTTTG
20720178 TTGTT-TTTTTATTTTTTTCATCTTTTG
1 TT-TTCTTTTT-TTTTTTTC-T-TTTTG
* *
20720205 TTTTCTTTTTCTTTTTTGTTTTT
1 TTTTCTTTTTTTTTTTTCTTTTT
20720228 ATGGTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
24 9 0.21
25 11 0.26
26 11 0.26
27 12 0.28
ACGTcount: A:0.03, C:0.09, G:0.05, T:0.83
Consensus pattern (24 bp):
TTTTCTTTTTTTTTTTTCTTTTTG
Found at i:20720213 original size:18 final size:18
Alignment explanation
Indices: 20720191--20720226 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20720181 TTTTTTTATT
20720191 TTTTTCATCTTTTGTTTTC
1 TTTTTC-TCTTTTGTTTTC
*
20720210 TTTTTCTTTTTTGTTTT
1 TTTTTCTCTTTTGTTTT
20720227 TATGGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.03, C:0.11, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTCTCTTTTGTTTTC
Found at i:20720954 original size:8 final size:9
Alignment explanation
Indices: 20720928--20720953 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20720918 CATATATCCC
20720928 ATTTTTTTT
1 ATTTTTTTT
20720937 ATTTTTTTT
1 ATTTTTTTT
20720946 ATTTTTTT
1 ATTTTTTT
20720954 AAAAGTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:20721411 original size:12 final size:12
Alignment explanation
Indices: 20721396--20721429 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20721386 TTTGTTTAAA
20721396 TATATTAAAAAT
1 TATATTAAAAAT
20721408 TATATT-AAAAT
1 TATATTAAAAAT
*
20721419 AATATTAAAAA
1 TATATTAAAAA
20721430 ATTAAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:20726739 original size:92 final size:90
Alignment explanation
Indices: 20726578--20726828 Score: 254
Period size: 92 Copynumber: 2.8 Consensus size: 90
20726568 ATTTTCTTTC
* * ** * *
20726578 CTTTTGGCAACCCTAAGAGTTGAATCC-AATTCTAGCTATAAATGGCTAATCAATTTAGACATTT
1 CTTTTGGCAACTCTAAAAAATGAA-CCTAATTCTAGCAATAAATGGCTAATCAACTTAGACATTT
* * * *
20726642 CATAAATTCAAGTCTTACCCTTACTTTT
65 AATAAACTCAAGTATTACCC-T-CATTT
* * * *
20726670 TTTTTGGCAACTCTAAAAAATGAACCTAATTCTAACAATAAATGGCTAATCAACATAGAGATTTA
1 CTTTTGGCAACTCTAAAAAATGAACCTAATTCTAGCAATAAATGGCTAATCAACTTAGACATTTA
* *
20726735 ATAAACTCAGGTATTATCCTCATTT
66 ATAAACTCAAGTATTACCCTCATTT
* * * * * * *
20726760 CTTTTGACAACTCTAAAAAATG-ATCTAGTACTAGCCATAAATGGCTAATCAACTTAGACCTTTG
1 CTTTTGGCAACTCTAAAAAATGAACCTAATTCTAGCAATAAATGGCTAATCAACTTAGACATTTA
20726824 ATAAA
66 ATAAA
20726829 ATTACTTTTA
Statistics
Matches: 131, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
89 38 0.29
90 24 0.18
91 3 0.02
92 66 0.50
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (90 bp):
CTTTTGGCAACTCTAAAAAATGAACCTAATTCTAGCAATAAATGGCTAATCAACTTAGACATTTA
ATAAACTCAAGTATTACCCTCATTT
Found at i:20727246 original size:91 final size:91
Alignment explanation
Indices: 20727017--20727250 Score: 213
Period size: 91 Copynumber: 2.6 Consensus size: 91
20727007 AGGTCTTAAT
* * ** * * * * * * *
20727017 CTCACCTTTTCTTGGCAAAACTAAAATTTGAATCTAATTTTAGCCATAAATGACCAATCAACTTT
1 CTCACATTCTCTTGGCAATCCTAAGAGTTGAATCAAATTTCAGCCATAAATGACAAATCAACATA
*
20727082 AACCTTGAATAAACTCAGATTTTACC
66 AACCTTGAATAAACTCAGATTGTACC
* * ** *
20727108 CTCACTTTCTCTTGGTAATCCTAAGAGTCAAATCCAA-TTCTAGCCATAAATGACAAATCAACAT
1 CTCACATTCTCTTGGCAATCCTAAGAGTTGAATCAAATTTC-AGCCATAAATGACAAATCAACAT
* * *
20727172 AAACTTTTG-GTAAACTCAGGTTGTACC
65 AAAC-CTTGAATAAACTCAGATTGTACC
* * *
20727199 CTTACATTCTCTTTGCAA-CTCTAAGAGTTGAATCAAATTTCAACCATAAATG
1 CTCACATTCTCTTGGCAATC-CTAAGAGTTGAATCAAATTTCAGCCATAAATG
20727251 GTTAATCTAT
Statistics
Matches: 113, Mismatches: 26, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
90 3 0.03
91 104 0.92
92 6 0.05
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (91 bp):
CTCACATTCTCTTGGCAATCCTAAGAGTTGAATCAAATTTCAGCCATAAATGACAAATCAACATA
AACCTTGAATAAACTCAGATTGTACC
Found at i:20733938 original size:45 final size:45
Alignment explanation
Indices: 20733878--20734009 Score: 203
Period size: 44 Copynumber: 3.0 Consensus size: 45
20733868 TGCTGCAGTA
* * * *
20733878 AGTTGGTAGATATGAAATAGAAGGTGGGGAACTAAAAAAAAAAAC
1 AGTTGCTAGAGATGAAATGGAAGATGGGGAACTAAAAAAAAAAAC
20733923 AGTTGCTAGAGATGAAATGGAAGATGGGGAACT-AAAAAAAAAAC
1 AGTTGCTAGAGATGAAATGGAAGATGGGGAACTAAAAAAAAAAAC
* *
20733967 AGCTGCTAGAGACGAAATGGAAGATGGGGAACTAAAAAAAAAA
1 AGTTGCTAGAGATGAAATGGAAGATGGGGAACTAAAAAAAAAA
20734010 CTATATAGAG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 42 0.52
45 38 0.47
ACGTcount: A:0.51, C:0.07, G:0.27, T:0.15
Consensus pattern (45 bp):
AGTTGCTAGAGATGAAATGGAAGATGGGGAACTAAAAAAAAAAAC
Found at i:20735722 original size:10 final size:10
Alignment explanation
Indices: 20735709--20735734 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20735699 ATTAAATTTT
20735709 AATATATATA
1 AATATATATA
20735719 AATATATATA
1 AATATATATA
20735729 AATATA
1 AATATA
20735735 AAATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATATATATA
Found at i:20735770 original size:9 final size:10
Alignment explanation
Indices: 20735751--20735796 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
20735741 TTATTTTTAT
20735751 TTTATAAAAA
1 TTTATAAAAA
20735761 TTTA-AAAAA
1 TTTATAAAAA
*
20735770 TATATAAAAA
1 TTTATAAAAA
*
20735780 TTAATAAAAA
1 TTTATAAAAA
*
20735790 TGTATAA
1 TTTATAA
20735797 TTTGATTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:20735777 original size:19 final size:20
Alignment explanation
Indices: 20735753--20735796 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
20735743 ATTTTTATTT
*
20735753 TATAAAAATTTA-AAAAATA
1 TATAAAAATTAATAAAAATA
*
20735772 TATAAAAATTAATAAAAATG
1 TATAAAAATTAATAAAAATA
20735792 TATAA
1 TATAA
20735797 TTTGATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:20735955 original size:14 final size:14
Alignment explanation
Indices: 20735932--20735962 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20735922 GATATTATAA
20735932 TTTTTATTTAATTT
1 TTTTTATTTAATTT
*
20735946 TTTTTTTTTAATTT
1 TTTTTATTTAATTT
20735960 TTT
1 TTT
20735963 GTATCCCCAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTAATTT
Found at i:20736059 original size:56 final size:57
Alignment explanation
Indices: 20735999--20736113 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 57
20735989 AGGATACAAT
* * * *
20735999 GCAATGGCTTTTTGAAATCAAATTGGGTTCTA-GTGATGTAACGAGAATGAATCCCC
1 GCAATGGCTTTTTGAAATCAAATCGGGTTCTACGTAATCTAACGAGAATAAATCCCC
* * *
20736055 GCAATGGCTTTTTGGAATCAAATCGGTTTCTACTGTAATCTAATGAGAATAAATCCCC
1 GCAATGGCTTTTTGAAATCAAATCGGGTTCTAC-GTAATCTAACGAGAATAAATCCCC
20736113 G
1 G
20736114 TCACATTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
56 29 0.58
58 21 0.42
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (57 bp):
GCAATGGCTTTTTGAAATCAAATCGGGTTCTACGTAATCTAACGAGAATAAATCCCC
Found at i:20744405 original size:2 final size:2
Alignment explanation
Indices: 20744398--20744432 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20744388 AAGTGGATCC
20744398 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
20744433 ATATATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:20744438 original size:2 final size:2
Alignment explanation
Indices: 20744433--20744467 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20744423 TCTCTCTCTC
* *
20744433 AT AT AT AT AA AT AA 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 AT AT A
20744468 CACATATGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:20756041 original size:41 final size:41
Alignment explanation
Indices: 20755984--20756065 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
20755974 TTTTCAAATC
* *
20755984 GAATCAACTAAATTGATCAATTACTCA-CTCTTAAATAGAAA
1 GAATCAACCAAATTGATCAATTACTCACCT-TTAAACAGAAA
* *
20756025 GAATCGACCAAATTGATCAATTGCTCACCTTTAAACAGAAA
1 GAATCAACCAAATTGATCAATTACTCACCTTTAAACAGAAA
20756066 CTTTAGCAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (41 bp):
GAATCAACCAAATTGATCAATTACTCACCTTTAAACAGAAA
Found at i:20764158 original size:17 final size:18
Alignment explanation
Indices: 20764127--20764160 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20764117 ACATATATTA
20764127 TTTTATTATAATTATAAC
1 TTTTATTATAATTATAAC
*
20764145 TTTT-TTATATTTATAA
1 TTTTATTATAATTATAA
20764161 ATTTATTAAA
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:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTATAATTATAAC
Found at i:20765360 original size:19 final size:19
Alignment explanation
Indices: 20765336--20765373 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20765326 TCGAATGCTC
*
20765336 TGAGTTAGTTTAACTATAA
1 TGAGTTACTTTAACTATAA
*
20765355 TGAGTTACTTTAATTATAA
1 TGAGTTACTTTAACTATAA
20765374 GGGAAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
TGAGTTACTTTAACTATAA
Found at i:20768332 original size:29 final size:30
Alignment explanation
Indices: 20768289--20768349 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
20768279 TTATTAGTTT
*
20768289 TTTATTTAGAAACAAATTAAAA-A-ATAAAC
1 TTTATTTAGAAAC-AATAAAAATATATAAAC
20768318 TTTATTTA-AATACAATAAAAATATATAAAC
1 TTTATTTAGAA-ACAATAAAAATATATAAAC
20768348 TT
1 TT
20768350 ACTTAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.32
29 11 0.39
30 8 0.29
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTATTTAGAAACAATAAAAATATATAAAC
Found at i:20770948 original size:34 final size:35
Alignment explanation
Indices: 20770905--20770972 Score: 111
Period size: 34 Copynumber: 1.9 Consensus size: 35
20770895 TCATTAAACT
20770905 TAAATTATTAAAGCATAAT-ATTTGTCGTACCATG
1 TAAATTATTAAAGCATAATGATTTGTCGTACCATG
*
20770939 TAAATTATTAAAGCATAATGGATTTGTGGTACCA
1 TAAATTATTAAAGCATAAT-GATTTGTCGTACCA
20770973 CGTTAATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 19 0.61
36 12 0.39
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (35 bp):
TAAATTATTAAAGCATAATGATTTGTCGTACCATG
Found at i:20771639 original size:5 final size:5
Alignment explanation
Indices: 20771629--20771693 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
20771619 CATTGTATTA
* * * *
20771629 TATAT TATAT TATAT TATAT TATAT TACTAT TTTAT GATGT TAT-T AATATT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T
20771680 TATAT TATTAT TAT
1 TATAT TA-TAT TAT
20771694 TATTTATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 3 0.06
5 33 0.67
6 13 0.27
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:20771681 original size:18 final size:18
Alignment explanation
Indices: 20771624--20771700 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
20771614 GCTATCATTG
20771624 TATTATATATTA-TATT-A
1 TATT-TATATTATTATTAA
*
20771641 TA-TTATATTA-TATTAC
1 TATTTATATTATTATTAA
*
20771657 TATTT-TATGATGTTATTAA
1 TATTTATAT--TATTATTAA
*
20771676 TATTTATATTATTATTAT
1 TATTTATATTATTATTAA
20771694 TATTTAT
1 TATTTAT
20771701 TTTTTCGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 11 0.22
16 6 0.12
17 4 0.08
18 15 0.31
19 10 0.20
20 3 0.06
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (18 bp):
TATTTATATTATTATTAA
Found at i:20771697 original size:12 final size:11
Alignment explanation
Indices: 20771624--20771701 Score: 60
Period size: 10 Copynumber: 7.4 Consensus size: 11
20771614 GCTATCATTG
20771624 TATTATATATTA
1 TATTAT-TATTA
20771636 TATTA-TATTA
1 TATTATTATTA
20771646 TATTA-TATTA
1 TATTATTATTA
*
20771656 CTATT-TTATGA
1 -TATTATTATTA
* *
20771667 TGTTATTAATA
1 TATTATTATTA
20771678 T-TTA-TATTA
1 TATTATTATTA
20771687 TTATTATTATT-
1 -TATTATTATTA
20771698 TATT
1 TATT
20771702 TTTTCGCATA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
9 4 0.07
10 26 0.47
11 16 0.29
12 9 0.16
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTATTATTA
Found at i:20775345 original size:120 final size:119
Alignment explanation
Indices: 20775131--20775348 Score: 274
Period size: 120 Copynumber: 1.8 Consensus size: 119
20775121 ATCAATCTCA
* * * * * * * * *
20775131 GCTCAATCCAGATCATTTTTTAACTTACGATTTCATTTCGATCATTTTTTTTTACCTTAACTTGA
1 GCTCAATCCAGATCATTTCTTAACTCACGACTTCATCTCAATAATTATTTTTAACCTCAACTTGA
* *
20775196 TCCTGGTCACTTTATTTTTTAGACTCATGATTTTGTCCCCTTCATCCGATTTTG
66 TCATGGTCACTTTATCTTTTAGACTCATGATTTTGTCCCCTTCATCCGATTTTG
* *
20775250 GCTCAGTCCAGATCATTTCTTAACTCGCGACTTCATCTCAATAATTCATTTTTAACCTCAACTTG
1 GCTCAATCCAGATCATTTCTTAACTCACGACTTCATCTCAATAATT-ATTTTTAACCTCAACTTG
* ** *
20775315 GTCATGGTCGTTTTATCTTTTAGATTCATGATTT
65 ATCATGGTCACTTTATCTTTTAGACTCATGATTT
20775349 CATCTCGATT
Statistics
Matches: 81, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
119 38 0.47
120 43 0.53
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (119 bp):
GCTCAATCCAGATCATTTCTTAACTCACGACTTCATCTCAATAATTATTTTTAACCTCAACTTGA
TCATGGTCACTTTATCTTTTAGACTCATGATTTTGTCCCCTTCATCCGATTTTG
Found at i:20775472 original size:121 final size:119
Alignment explanation
Indices: 20775189--20775664 Score: 336
Period size: 120 Copynumber: 3.9 Consensus size: 119
20775179 TTTTTACCTT
* * ** ** * ***
20775189 AACTTGATCCTGGTCACTTTATTTTTTAGACTCATGATTTTGTC-CCCTTCATCCGATTTTGGCT
1 AACTTGATCATGGTCACTTTATCTTTTAGACTCATGATTTCATCTCGATT-ATCCGA-TCTCATT
* * * * * * * * *
20775253 CAGTCCAGATCATTTCTTAACTCGCGACTTCATCTCAATAATTCATTTTTAACCTC
64 CAGTCCAAATAATTTCTTGACTCACGATTTCATCCCAGTCATTCATTTTTAATCTC
* ** * *
20775309 AACTTGGTCATGGTCGTTTTATCTTTTAGATTCATGATTTCATCTCGATTATTCGATCTCTATTC
1 AACTTGATCATGGTCACTTTATCTTTTAGACTCATGATTTCATCTCGATTATCCGATCTC-ATTC
*
20775374 AGTCCAAATAATTTCTTGACTCATGATTTCATCCCAGTCATTCATTTTTCAATCTC
65 AGTCCAAATAATTTCTTGACTCACGATTTCATCCCAGTCATTCATTTTT-AATCTC
* * * *
20775430 AACTTGATCTTGGTTACTTTATCTTTTAGACT-AGTGATTTCATC-CTAGTCATCCGATCTCAAT
1 AACTTGATCATGGTCACTTTATCTTTTAGACTCA-TGATTTCATCTCGA-TTATCCGATCTC-AT
* * * ** * *
20775493 TCAATCCTAGTCATTCATTT-TTGACTTGCGATTTCATCCCGGTCATTCATTTTTTATCTC
63 TCAGTCC-A---AATAATTTCTTGACTCACGATTTCATCCCAGTCATTCATTTTTAATCTC
** * ** * *
20775553 AACTCAATCCTGGTCACTTTAT-TTTCT-GACTCAT-AGTTTTGTTTTGATTATCCGATCTCATT
1 AACTTGATCATGGTCACTTTATCTTT-TAGACTCATGA-TTTCATCTCGATTATCCGATCTCATT
* * * * * *
20775615 TAGTCCATATCATTTTCTTGACTCATGATTTCAGCCCAGTTATTCATTTT
64 CAGTCCAAAT-AATTTCTTGACTCACGATTTCATCCCAGTCATTCATTTT
20775665 CAACCTTGAT
Statistics
Matches: 276, Mismatches: 65, Indels: 31
0.74 0.17 0.08
Matches are distributed among these distances:
117 1 0.00
118 3 0.01
119 29 0.11
120 87 0.32
121 70 0.25
122 24 0.09
123 26 0.09
124 30 0.11
125 6 0.02
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (119 bp):
AACTTGATCATGGTCACTTTATCTTTTAGACTCATGATTTCATCTCGATTATCCGATCTCATTCA
GTCCAAATAATTTCTTGACTCACGATTTCATCCCAGTCATTCATTTTTAATCTC
Found at i:20775873 original size:66 final size:66
Alignment explanation
Indices: 20775782--20776028 Score: 219
Period size: 66 Copynumber: 3.8 Consensus size: 66
20775772 TTGGTCATCC
* *
20775782 GATCTTGGCTCAGTTTAAATCATTTTATTTTTCCTGACTTATAGCTCAATCCCAGTCACCTGTTT
1 GATCTTGGCTCAATCTAAATCATTTTATTTTTCCTGACTTATAGCTCAATCCCAGTCACCTGTTT
20775847 T
66 T
* * * * * * ** * *
20775848 GATCTTGGCCCAATCTAGATCATTTTATTTTTCTTGACTTGTAGCTTAGTCCTGGTCATCTATTT
1 GATCTTGGCTCAATCTAAATCATTTTATTTTTCCTGACTTATAGCTCAATCCCAGTCACCTGTTT
*
20775913 C
66 T
* * * * * ** ** * *
20775914 AATATTGGCTTAGTCCAAATCATTTTATTTTTCCTGACTTACGGCTCAATTTCTGTTACCTG-TT
1 GATCTTGGCTCAATCTAAATCATTTTATTTTTCCTGACTTATAGCTCAATCCCAGTCACCTGTTT
20775978 T
66 T
* * * * *
20775979 GATCTCGACTCAATATAGATCATTTTATTTTT-CTGACTTATGGCTCAATC
1 GATCTTGGCTCAATCTAAATCATTTTATTTTTCCTGACTTATAGCTCAATC
20776029 ATTATCACTT
Statistics
Matches: 136, Mismatches: 45, Indels: 2
0.74 0.25 0.01
Matches are distributed among these distances:
64 16 0.12
65 25 0.18
66 95 0.70
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (66 bp):
GATCTTGGCTCAATCTAAATCATTTTATTTTTCCTGACTTATAGCTCAATCCCAGTCACCTGTTT
T
Found at i:20776931 original size:19 final size:19
Alignment explanation
Indices: 20776909--20776947 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20776899 TTTTATTTTA
20776909 TATTTTAAATTTTTTTATT
1 TATTTTAAATTTTTTTATT
* *
20776928 TATTTTTACTTTTTTTATT
1 TATTTTAAATTTTTTTATT
20776947 T
1 T
20776948 TGCTGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (19 bp):
TATTTTAAATTTTTTTATT
Found at i:20776947 original size:27 final size:27
Alignment explanation
Indices: 20776885--20776969 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
20776875 TAGATTTTTC
20776885 TTTTTATTTTTTGATTTTATTTTATAT
1 TTTTTATTTTTTGATTTTATTTTATAT
** *
20776912 TTTAAATTTTTTTA-TTTATTTT-TACTT
1 TTTTTATTTTTTGATTTTATTTTATA--T
* *
20776939 TTTTTATTTTGCTGATTTTTATTATATAT
1 TTTTTATTTT-TTGA-TTTTATTTTATAT
20776968 TT
1 TT
20776970 ATTTTTACTG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
25 2 0.05
26 8 0.18
27 20 0.45
28 2 0.05
29 3 0.07
30 7 0.16
31 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTTTATTTTTTGATTTTATTTTATAT
Found at i:20777057 original size:25 final size:26
Alignment explanation
Indices: 20777029--20777086 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
20777019 TTTTATAAAA
* *
20777029 AAATAA-AAATAAAAAAAATCTTTTT
1 AAATAAGAAAGAAAAAAAATCTTTTC
*
20777054 AAATAAGTAAGAAAAAAAATCTTTTC
1 AAATAAGAAAGAAAAAAAATCTTTTC
20777080 AAATAAG
1 AAATAAG
20777087 TTTGTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
AAATAAGAAAGAAAAAAAATCTTTTC
Found at i:20777157 original size:6 final size:6
Alignment explanation
Indices: 20777146--20777204 Score: 82
Period size: 6 Copynumber: 9.7 Consensus size: 6
20777136 CAAAAAGAAT
* * *
20777146 ATAAAA ATAAAA ATAAAAA ATAAAA GTAAAA ATAACA ACAAAA ATAAAA
1 ATAAAA ATAAAA AT-AAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
20777195 ATAAAA ATAA
1 ATAAAA ATAA
20777205 TTTTTACCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 40 0.87
7 6 0.13
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:20781067 original size:61 final size:58
Alignment explanation
Indices: 20780878--20781099 Score: 324
Period size: 58 Copynumber: 3.8 Consensus size: 58
20780868 TCTTGTATAG
* *
20780878 GAAAAATTGATACTTTCAA-TTTTTCTCCAAAAATAC-TTTTTTGGAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAAAT-CTTTTTTTGAAAATTTA-TTTTTAA
20780937 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
20780995 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATC---TTTTTTTGAAAATTTATTTTTAA
* *
20781056 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGA
1 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATCTTTTTTTGA
20781100 TTTTTTTATT
Statistics
Matches: 153, Mismatches: 4, Indels: 13
0.90 0.02 0.08
Matches are distributed among these distances:
58 52 0.34
59 40 0.26
60 6 0.04
61 49 0.32
62 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
Found at i:20781118 original size:119 final size:116
Alignment explanation
Indices: 20780878--20781099 Score: 317
Period size: 119 Copynumber: 1.9 Consensus size: 116
20780868 TCTTGTATAG
* *
20780878 GAAAAATTGATACTTTCAATTTTTCTCCAAAAATACTTTTTTGGAAATTTATTTTTTAAGAAAAA
1 GAAAAATTGATACTTTCAATTTTCCTCCAAAAATACTTTTTTGAAAATTTATTTTTTAAGAAAAA
*
20780943 TTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAATTTATTTTTAA
66 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTG-AAATTTATTTTTAA
20780995 GAAAAATTGATACTTTCAACTTTTCCT-CAAAAAT-CTTTTTTTTTTGAAAATTTA-TTTTTAAG
1 GAAAAATTGATACTTTCAA-TTTTCCTCCAAAAATAC----TTTTTTGAAAATTTATTTTTTAAG
*
20781057 GAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGA
61 AAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGA
20781100 TTTTTTTATT
Statistics
Matches: 95, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
116 1 0.01
117 26 0.27
118 7 0.07
119 41 0.43
120 20 0.21
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (116 bp):
GAAAAATTGATACTTTCAATTTTCCTCCAAAAATACTTTTTTGAAAATTTATTTTTTAAGAAAAA
TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAA
Found at i:20781151 original size:9 final size:9
Alignment explanation
Indices: 20781137--20781242 Score: 52
Period size: 9 Copynumber: 10.9 Consensus size: 9
20781127 AATAAAAGTG
20781137 AAAATAAAA
1 AAAATAAAA
20781146 AAAATAAAGA
1 AAAATAAA-A
*
20781156 AAAGTAAAA
1 AAAATAAAA
* *
20781165 CAAA-AATA
1 AAAATAAAA
20781173 AAAATAAGATA
1 AAAATAA-A-A
*
20781184 AAGATAAAA
1 AAAATAAAA
20781193 AAAGATTAAATA
1 AAA-A-TAAA-A
**
20781205 AATCTAATCTAA
1 AA---AATAAAA
*
20781217 TAAATAAAA
1 AAAATAAAA
20781226 AAAATAAAA
1 AAAATAAAA
*
20781235 CAAATAAA
1 AAAATAAA
20781243 TAAAGAAATT
Statistics
Matches: 72, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
8 6 0.08
9 36 0.50
10 10 0.14
11 11 0.15
12 5 0.07
13 2 0.03
14 1 0.01
15 1 0.01
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:20782252 original size:4 final size:4
Alignment explanation
Indices: 20782237--20782377 Score: 80
Period size: 4 Copynumber: 34.5 Consensus size: 4
20782227 GAAAAATAAT
* * *
20782237 AATA AA-A AATA AATA AATA AAT- TATA ATATA TAATA AATA TATA ACTA
1 AATA AATA AATA AATA AATA AATA AATA A-ATA -AATA AATA AATA AATA
* *
20782285 TATA AATAA AATA CATATA AATA TTAACA GAA-A AATA AATA AATA AATA
1 AATA AAT-A AATA -A-ATA AATA --AATA -AATA AATA AATA AATA AATA
* *
20782334 AATA AATA AGTA AA-A ATATA CATA TAAT- AAT- AATA AAT- AATA AA
1 AATA AATA AATA AATA A-ATA AATA -AATA AATA AATA AATA AATA AA
20782378 ATACATAAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
3 18 0.17
4 66 0.61
5 17 0.16
6 7 0.06
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:20782471 original size:20 final size:21
Alignment explanation
Indices: 20782446--20782485 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
20782436 GGGCTTACCC
20782446 ATTTGGGCCAGG-CCCAATTG
1 ATTTGGGCCAGGACCCAATTG
20782466 ATTTGGGCCAGGACCCAATT
1 ATTTGGGCCAGGACCCAATT
20782486 AGGTGTCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
ATTTGGGCCAGGACCCAATTG
Done.