Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 16 of 113
Found at i:5309032 original size:55 final size:56
Alignment explanation
Indices: 5308966--5309081 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 56
5308956 AGATGTATTC
* * ** *
5308966 TAAAATTTTATCCCAATACGATAAAT-CAGGATAGAAAGAGTCATCGGTATATCCA
1 TAAAATTTTATCCCAATACGATAAATCCAGGATAAAAAAAACCACCGGTATATCCA
** * *
5309021 TAAAATTTTATCCTGATATGATAAATCCAGGATAAAAAAAACCACCGGTGTATCCA
1 TAAAATTTTATCCCAATACGATAAATCCAGGATAAAAAAAACCACCGGTATATCCA
5309077 TAAAA
1 TAAAA
5309082 GTGTCGAGCG
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
55 23 0.45
56 28 0.55
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (56 bp):
TAAAATTTTATCCCAATACGATAAATCCAGGATAAAAAAAACCACCGGTATATCCA
Found at i:5312845 original size:16 final size:15
Alignment explanation
Indices: 5312834--5312876 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
5312824 TCATAATTAG
5312834 TTAAATTTATAAATA
1 TTAAATTTATAAATA
5312849 TCATAAATTTATAAATAA
1 T--TAAATTTATAAAT-A
5312867 TTAAATTTAT
1 TTAAATTTAT
5312877 GTAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 13 0.52
18 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAATTTATAAATA
Found at i:5312904 original size:23 final size:24
Alignment explanation
Indices: 5312854--5312919 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
5312844 AAATATCATA
** *
5312854 AATTTATAAATAATTAAATTTATGT
1 AATTTA-AAATAAAAAAATTAATGT
5312879 AATTTAAAATAAAAAAATTAAT-T
1 AATTTAAAATAAAAAAATTAATGT
*
5312902 AA-TTAATAGTAAAAAAAT
1 AATTTAA-AATAAAAAAAT
5312920 ATATTCATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.11
23 13 0.36
24 13 0.36
25 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
AATTTAAAATAAAAAAATTAATGT
Found at i:5314780 original size:64 final size:65
Alignment explanation
Indices: 5314660--5314787 Score: 149
Period size: 64 Copynumber: 2.0 Consensus size: 65
5314650 AATAATTAAA
*
5314660 AAAAAAATTTGAAATTGATTATTCAATACGTTTTTTATAAAAAAATTACTTAAATAATCTCTTAG
1 AAAAAAATTTGAAATTAATTATTCAATA-GTTTTTTATAAAAAAATTACTTAAATAATCTCTTAG
5314725 T
65 T
* *
5314726 AAAAAAA-TTG-AATTAAATTATTCAAT-GTGTTTTTA-ACAAAAAA-TACATTGAATAATTTCT
1 AAAAAAATTTGAAATT-AATTATTCAATAGT-TTTTTATA-AAAAAATTAC-TTAAATAATCTCT
5314786 TA
62 TA
5314788 CAAAAAATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
63 6 0.11
64 29 0.53
65 13 0.24
66 7 0.13
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (65 bp):
AAAAAAATTTGAAATTAATTATTCAATAGTTTTTTATAAAAAAATTACTTAAATAATCTCTTAGT
Found at i:5325166 original size:13 final size:13
Alignment explanation
Indices: 5325141--5325175 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
5325131 GCAGTCAAAG
5325141 AATAATATACTAGT
1 AATAAT-TACTAGT
5325155 AATAATTACTAGT
1 AATAATTACTAGT
*
5325168 AGTAATTA
1 AATAATTA
5325176 AAGCTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (13 bp):
AATAATTACTAGT
Found at i:5330820 original size:150 final size:150
Alignment explanation
Indices: 5330548--5330828 Score: 323
Period size: 150 Copynumber: 1.9 Consensus size: 150
5330538 GGGGATGAAG
** * * * *
5330548 AATCCTTGTTAGCTATACTGTTCATATGAGTTGTCAATCCCCCTTCATTAGACTCTGTAAAACCA
1 AATCCTTGTTAGCTATACCATCCATATGAGTCGTCAATCCCCCTGCATTAGACTCTATAAAACCA
* * * *
5330613 TCAACTTTATTAGTTCCATGAATTCTTAAAGTGAAGTCCTTCCTCAAGACATGCTCATGATGACT
66 TCAACTTCATTAGTTCCATGAACTCTTAAAGTCAAGTCCTTCCTCAAGACATGCTCATGATCACT
5330678 AAGGATTGATCCTCCTGATA
131 AAGGATTGATCCTCCTGATA
* * ** * *
5330698 AATCCTTGTTAGCTGTACCATCCTTATGAGTCGTCAATTGCCCTGCATTAGCCTCTATAACACCA
1 AATCCTTGTTAGCTATACCATCCATATGAGTCGTCAATCCCCCTGCATTAGACTCTATAAAACCA
* * * * * * *
5330763 TCAATCTTCGTT-GTTCCCTGTACTCTTAGAGTCAAGTCCTTCCTTAATGA-GTTCTCATGATCA
66 TCAA-CTTCATTAGTTCCATGAACTCTTAAAGTCAAGTCCTTCCTCAA-GACATGCTCATGATCA
5330826 CTA
129 CTA
5330829 GCAACTGATC
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
150 99 0.93
151 7 0.07
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (150 bp):
AATCCTTGTTAGCTATACCATCCATATGAGTCGTCAATCCCCCTGCATTAGACTCTATAAAACCA
TCAACTTCATTAGTTCCATGAACTCTTAAAGTCAAGTCCTTCCTCAAGACATGCTCATGATCACT
AAGGATTGATCCTCCTGATA
Found at i:5333586 original size:16 final size:17
Alignment explanation
Indices: 5333560--5333591 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5333550 TTTCAATGGT
5333560 AAAATACAAAAAAAATA
1 AAAATACAAAAAAAATA
5333577 AAAATA-AAAAAAAAT
1 AAAATACAAAAAAAAT
5333592 CAATGGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAATACAAAAAAAATA
Found at i:5335092 original size:20 final size:20
Alignment explanation
Indices: 5335032--5335092 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
5335022 GCACACGCTG
5335032 CAGATGAAAGGAATAAACTA
1 CAGATGAAAGGAATAAACTA
** * * *
5335052 TCA-ATCTAA-GCACACACTA
1 -CAGATGAAAGGAATAAACTA
5335071 CAGATGAAAGGAATAAACTA
1 CAGATGAAAGGAATAAACTA
5335091 CA
1 CA
5335093 ATCTAAGCAC
Statistics
Matches: 28, Mismatches: 10, Indels: 5
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.07
19 11 0.39
20 13 0.46
21 2 0.07
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.16
Consensus pattern (20 bp):
CAGATGAAAGGAATAAACTA
Found at i:5335110 original size:38 final size:39
Alignment explanation
Indices: 5335005--5335117 Score: 165
Period size: 39 Copynumber: 2.9 Consensus size: 39
5334995 AAAAGAAATG
* * *
5335005 ATAAACCATAAATCTAAGCACACGCTGCAGATGAAAGGA
1 ATAAACTATCAATCTAAGCACACGCTACAGATGAAAGGA
*
5335044 ATAAACTATCAATCTAAGCACACACTACAGATGAAAGGA
1 ATAAACTATCAATCTAAGCACACGCTACAGATGAAAGGA
**
5335083 ATAAACTA-CAATCTAAGCACGTGCTACAGATGAAA
1 ATAAACTATCAATCTAAGCACACGCTACAGATGAAA
5335118 TGCATAGTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
38 24 0.36
39 43 0.64
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATAAACTATCAATCTAAGCACACGCTACAGATGAAAGGA
Found at i:5353349 original size:2 final size:2
Alignment explanation
Indices: 5353342--5353369 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5353332 TGTCATTAGA
5353342 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5353370 GTGTACCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5368796 original size:30 final size:29
Alignment explanation
Indices: 5368722--5368797 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
5368712 ACTTGATTAC
* *
5368722 AAATAAAAAATAAAAAACTTATTTAAGTA
1 AAATAAAAAATTAAAAACTTATTTAAATA
*
5368751 TAAT-AAAAATATAAAAACTTATTTAAATA
1 AAATAAAAAAT-TAAAAACTTATTTAAATA
5368780 AAATAATAAAATTAAAAA
1 AAATAA-AAAATTAAAAA
5368798 TCTCTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.15
29 22 0.55
30 7 0.17
31 5 0.12
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (29 bp):
AAATAAAAAATTAAAAACTTATTTAAATA
Found at i:5378324 original size:2 final size:2
Alignment explanation
Indices: 5378319--5378349 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5378309 TTTTGTTTTG
5378319 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5378350 GGAGTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5382445 original size:2 final size:2
Alignment explanation
Indices: 5382401--5382432 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5382391 TATCTGAGTT
5382401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5382433 ATCTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5386315 original size:2 final size:2
Alignment explanation
Indices: 5386308--5386334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5386298 CAACTTACTT
5386308 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5386335 TGCTTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5386883 original size:2 final size:2
Alignment explanation
Indices: 5386876--5386903 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5386866 CTTTTCTATG
5386876 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
5386904 TCAGGGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5388592 original size:23 final size:23
Alignment explanation
Indices: 5388544--5388596 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5388534 ACATTAAAAC
* **
5388544 TTAAAAATATTTGTATAATATTT
1 TTAAATATATTTGTATAATAAAT
5388567 TTAAATATATTT-TATAATTAAAT
1 TTAAATATATTTGTATAA-TAAAT
5388590 TTAAATA
1 TTAAATA
5388597 AAATAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAATATATTTGTATAATAAAT
Found at i:5388938 original size:45 final size:45
Alignment explanation
Indices: 5388874--5388965 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
5388864 CAACGAACAT
* *
5388874 GTCCATAATTAATTTTATGAGATTACAGACCACCTTGAAGGGTTG
1 GTCCATAATTAATTTTATGAGATCACAGACCACCTTGAAGGATTG
* * * *
5388919 GTCCATGATTGATTTTATGAGATCACGGACCACCTTTAAGGATTG
1 GTCCATAATTAATTTTATGAGATCACAGACCACCTTGAAGGATTG
5388964 GT
1 GT
5388966 TCATTGCGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (45 bp):
GTCCATAATTAATTTTATGAGATCACAGACCACCTTGAAGGATTG
Found at i:5391624 original size:2 final size:2
Alignment explanation
Indices: 5391617--5391674 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
5391607 ATTGTTTATC
* * * *
5391617 TA TA TA TA CA TA TA TA TA TA TA TA TG TG TA TA TA -A TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5391658 TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
5391675 GTCTTATTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5396185 original size:15 final size:16
Alignment explanation
Indices: 5396167--5396196 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5396157 TCATCCAACC
5396167 AATAATGA-ATAATTA
1 AATAATGATATAATTA
5396182 AATAATGATATAATT
1 AATAATGATATAATT
5396197 TATTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (16 bp):
AATAATGATATAATTA
Found at i:5396913 original size:13 final size:13
Alignment explanation
Indices: 5396895--5396921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5396885 TTTTTTAAAA
5396895 AATTTTACAAGTT
1 AATTTTACAAGTT
5396908 AATTTTACAAGTT
1 AATTTTACAAGTT
5396921 A
1 A
5396922 GATTAGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTTTACAAGTT
Found at i:5397812 original size:14 final size:14
Alignment explanation
Indices: 5397770--5397814 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5397760 GTGATTGAAC
5397770 AATAATAATATTAT
1 AATAATAATATTAT
* * *
5397784 AATAAAAAGAATAT
1 AATAATAATATTAT
5397798 AATAATAATATTAT
1 AATAATAATATTAT
5397812 AAT
1 AAT
5397815 TTTTTTATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AATAATAATATTAT
Found at i:5405259 original size:14 final size:14
Alignment explanation
Indices: 5405240--5405266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5405230 ACCACCTTTT
5405240 TGTACCCGCCGGTC
1 TGTACCCGCCGGTC
5405254 TGTACCCGCCGGT
1 TGTACCCGCCGGT
5405267 GCCCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.41, G:0.30, T:0.22
Consensus pattern (14 bp):
TGTACCCGCCGGTC
Found at i:5414282 original size:5 final size:5
Alignment explanation
Indices: 5414274--5414316 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
5414264 ATTCACAGTC
5414274 AATAT AATAT AATAT AATAT AATAT AATAT ATATAT ATATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT A
5414317 TATTTGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:5414307 original size:2 final size:2
Alignment explanation
Indices: 5414275--5414319 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
5414265 TTCACAGTCA
5414275 AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- 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
5414312 AT AT AT AT
1 AT AT AT AT
5414320 TTGAGTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.13
2 33 0.87
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5414616 original size:20 final size:20
Alignment explanation
Indices: 5414574--5414617 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5414564 CATTTGCATG
* *
5414574 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTAT
5414594 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAATTTAT
5414614 TATT
1 TATT
5414618 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:5414658 original size:18 final size:19
Alignment explanation
Indices: 5414623--5414659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5414613 TTATTTTAAA
5414623 TTAATTAAAATTAATATATT
1 TTAATTAAAA-TAATATATT
5414643 TTAATTAAAA-AATATAT
1 TTAATTAAAATAATATAT
5414660 ATTAGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATTAAAATAATATATT
Found at i:5414663 original size:28 final size:28
Alignment explanation
Indices: 5414632--5414685 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
5414622 ATTAATTAAA
* *
5414632 ATTAATATAT-TTTAATTAAAAAATATAT
1 ATTAATACATATTT-ATAAAAAAATATAT
*
5414660 ATTAGTACATATTTATAAAAAAATAT
1 ATTAATACATATTTATAAAAAAATAT
5414686 TTAAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 19 0.86
29 3 0.14
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTAATACATATTTATAAAAAAATATAT
Found at i:5414816 original size:18 final size:18
Alignment explanation
Indices: 5414763--5414823 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 18
5414753 AAAATTATCT
5414763 ATATTTATTAAATATTAATA
1 ATATTTATTAAAT-TTAA-A
5414783 ATAAATTTAAATTTAAATTTAAA
1 AT--ATTT--A-TTAAATTTAAA
*
5414806 ATATTTATTAAATATAAA
1 ATATTTATTAAATTTAAA
5414824 TACGAGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
18 10 0.29
19 1 0.03
20 2 0.06
21 4 0.11
22 4 0.11
23 3 0.09
24 5 0.14
25 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTTATTAAATTTAAA
Found at i:5421593 original size:21 final size:21
Alignment explanation
Indices: 5421569--5421613 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5421559 GAATTAAAAA
*
5421569 AATTAACTTATATCA-TTTTTT
1 AATTAAATTAT-TCACTTTTTT
*
5421590 AATTAAATTATTTACTTTTTT
1 AATTAAATTATTCACTTTTTT
5421611 AAT
1 AAT
5421614 ATATCTCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTAAATTATTCACTTTTTT
Found at i:5423183 original size:13 final size:13
Alignment explanation
Indices: 5423165--5423189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5423155 CCATGATTAT
5423165 TATAATAATATAA
1 TATAATAATATAA
5423178 TATAATAATATA
1 TATAATAATATA
5423190 GTATGTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:5423575 original size:20 final size:20
Alignment explanation
Indices: 5423533--5423576 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5423523 TATTTATATG
* *
5423533 TATTTAATAAATAAATTTTT
1 TATTAAATAAATAAATTTAT
5423553 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAATTTAT
5423573 TATT
1 TATT
5423577 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:5435509 original size:28 final size:28
Alignment explanation
Indices: 5435478--5435533 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5435468 AGAAGAAATA
* *
5435478 TTTTTCTATAA-AATCTCATGTACTTCAT
1 TTTTTCTA-AATAAACTCAAGTACTTCAT
*
5435506 TTTTTTTAAATAAACTCAAGTACTTCAT
1 TTTTTCTAAATAAACTCAAGTACTTCAT
5435534 AAATACATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (28 bp):
TTTTTCTAAATAAACTCAAGTACTTCAT
Found at i:5436075 original size:13 final size:12
Alignment explanation
Indices: 5436057--5436086 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
5436047 GGAGACGTCT
5436057 GAGAGTGAGAGGA
1 GAGAGTGAGA-GA
5436070 GAGAGTGAGAGA
1 GAGAGTGAGAGA
5436082 GAGAG
1 GAGAG
5436087 AAAAGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.53, T:0.07
Consensus pattern (12 bp):
GAGAGTGAGAGA
Found at i:5442249 original size:27 final size:27
Alignment explanation
Indices: 5442195--5442250 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
5442185 AGTTATATGT
* ***
5442195 ATTTTTTAATTATATATTAAATTTTTA
1 ATTTTTTAAGTATATATTAAAAAGTTA
*
5442222 ATTTTTTTAGTATATATTAAAAAGTTA
1 ATTTTTTAAGTATATATTAAAAAGTTA
5442249 AT
1 AT
5442251 GCCATGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
ATTTTTTAAGTATATATTAAAAAGTTA
Found at i:5442338 original size:37 final size:38
Alignment explanation
Indices: 5442264--5442338 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
5442254 ATGATTAGTC
* **
5442264 ATTGAATTTTAATCAATTGTTTAATATGATATTTGAATA
1 ATTGAATTTTAA-CAATTGTTTAATATAATACATGAATA
*
5442303 ATTGAATTTTAA-AATTTTTTAATATAATACATGAAT
1 ATTGAATTTTAACAATTGTTTAATATAATACATGAAT
5442339 TATAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 20 0.62
39 12 0.38
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (38 bp):
ATTGAATTTTAACAATTGTTTAATATAATACATGAATA
Found at i:5442748 original size:32 final size:31
Alignment explanation
Indices: 5442693--5442753 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
5442683 AGCCATTGAT
* *
5442693 TTTTAATTTGTATACAAATAAACCCCTTAAAC
1 TTTTAATTTATATACAAACAAA-CCCTTAAAC
5442725 TTTTAATTTATAT-CTAAACAAACCCTTAA
1 TTTTAATTTATATAC-AAACAAACCCTTAA
5442754 CATAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (31 bp):
TTTTAATTTATATACAAACAAACCCTTAAAC
Found at i:5442857 original size:29 final size:28
Alignment explanation
Indices: 5442774--5442858 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
5442764 TATTTCATTT
*
5442774 AAAATAAAAT-TTTATTTGAACAAA-AATT
1 AAAATAAAATATTTATTT-AA-AAATAATA
* * * *
5442802 AAAGTACAAAAATTTATTTGAATATAATA
1 AAAATA-AAATATTTATTTAAAAATAATA
5442831 AAAATATAAATATTTATTTAAAAATAAT
1 AAAATA-AAATATTTATTTAAAAATAAT
5442859 TTAAAATTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
28 7 0.16
29 30 0.68
30 7 0.16
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATAAAATATTTATTTAAAAATAATA
Found at i:5455521 original size:17 final size:18
Alignment explanation
Indices: 5455500--5455549 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5455490 ATAATTTTAT
5455500 TAATATAATACATACATA
1 TAATATAATACATACATA
* * *
5455518 -AATATAAAAAATATATA
1 TAATATAATACATACATA
*
5455535 TAATAAAATACATAC
1 TAATATAATACATAC
5455550 TTTTATATAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATATAATACATACATA
Found at i:5455763 original size:15 final size:15
Alignment explanation
Indices: 5455739--5455800 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
5455729 TGTTTTAATT
*
5455739 TTAATGATAATATTA
1 TTAATAATAATATTA
*
5455754 TTAATAATAATAATA
1 TTAATAATAATATTA
*
5455769 TTTAAAAATAATTATTAA
1 -TTAATAATAA-TATT-A
*
5455787 TTATATAAAAATAT
1 TTA-ATAATAATAT
5455801 AAAAAAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.35
16 9 0.24
17 9 0.24
18 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TTAATAATAATATTA
Found at i:5455803 original size:29 final size:29
Alignment explanation
Indices: 5455750--5455807 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
5455740 TAATGATAAT
*
5455750 ATTATTAATAATAATAATATTTAAAAATA
1 ATTATTAATAATAATAATATATAAAAATA
* *
5455779 ATTATTAATTATATAAAAATATAAAAAAA
1 ATTATTAA-TA-ATAATAATATATAAAAA
5455808 CAAAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 2 0.08
31 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTATTAATAATAATAATATATAAAAATA
Found at i:5456584 original size:1 final size:1
Alignment explanation
Indices: 5456580--5456610 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5456570 TCCCCCCCCC
5456580 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5456611 CTGAAAACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5457357 original size:17 final size:18
Alignment explanation
Indices: 5457332--5457370 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5457322 ACCTTAAACA
*
5457332 CTAATTTTTTCAAAA-TC
1 CTAAGTTTTTCAAAACTC
*
5457349 CTAAGTTTTTTAAAACTC
1 CTAAGTTTTTCAAAACTC
5457367 CTAA
1 CTAA
5457371 AAATTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (18 bp):
CTAAGTTTTTCAAAACTC
Found at i:5457359 original size:18 final size:17
Alignment explanation
Indices: 5457332--5457370 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5457322 ACCTTAAACA
5457332 CTAATTTTTTCAAAA-TC
1 CTAATTTTTT-AAAACTC
5457349 CTAAGTTTTTTAAAACTC
1 CTAA-TTTTTTAAAACTC
5457367 CTAA
1 CTAA
5457371 AAATTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (17 bp):
CTAATTTTTTAAAACTC
Found at i:5457441 original size:14 final size:14
Alignment explanation
Indices: 5457386--5457456 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
5457376 CAAAACCCCA
5457386 TAAAATCCCAAACTCT
1 TAAAAT-CCAAAC-CT
* *
5457402 T-AAATCCAATCAT
1 TAAAATCCAAACCT
*
5457415 CAAAATCCAAAACCT
1 TAAAATCC-AAACCT
*
5457430 TAAAATCCAAACTT
1 TAAAATCCAAACCT
* *
5457444 TTAAATCAAAACC
1 TAAAATCCAAACC
5457457 CCAAAACACA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
13 1 0.02
14 26 0.60
15 15 0.35
16 1 0.02
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATCCAAACCT
Found at i:5457462 original size:43 final size:44
Alignment explanation
Indices: 5457386--5457471 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 44
5457376 CAAAACCCCA
* * *
5457386 TAAAATCCCAAACTCTTAAATCCAATCATCAAAATC-CAAAACCT
1 TAAAATCCCAAACTCTTAAATCAAAACACCAAAA-CACAAAACCT
* *
5457430 TAAAAT-CCAAACTTTTAAATCAAAACCCCAAAACACAAAACC
1 TAAAATCCCAAACTCTTAAATCAAAACACCAAAACACAAAACC
5457472 CAAACCCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.03
43 29 0.81
44 6 0.17
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (44 bp):
TAAAATCCCAAACTCTTAAATCAAAACACCAAAACACAAAACCT
Found at i:5458804 original size:24 final size:24
Alignment explanation
Indices: 5458763--5458808 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5458753 AATTTATCTA
* *
5458763 AAAAAATAACAAACAAAAAAAGGC
1 AAAAAATAAAAAAAAAAAAAAGGC
*
5458787 AAAAATTAAAAAAAAAAAAAAG
1 AAAAAATAAAAAAAAAAAAAAG
5458809 AGAGAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (24 bp):
AAAAAATAAAAAAAAAAAAAAGGC
Found at i:5460118 original size:18 final size:19
Alignment explanation
Indices: 5460095--5460130 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5460085 CACCTTTCAC
5460095 TTTTATTT-TTTTTTATTT
1 TTTTATTTGTTTTTTATTT
5460113 TTTTATTTGTTTTTTATT
1 TTTTATTTGTTTTTTATT
5460131 GGATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (19 bp):
TTTTATTTGTTTTTTATTT
Found at i:5460190 original size:15 final size:15
Alignment explanation
Indices: 5460170--5460199 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5460160 TTGTTTTAAA
5460170 TTTTTTCTCTCTTTT
1 TTTTTTCTCTCTTTT
*
5460185 TTTTTTTTCTCTTTT
1 TTTTTTCTCTCTTTT
5460200 CCATCTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTCTCTTTT
Found at i:5467578 original size:9 final size:9
Alignment explanation
Indices: 5467564--5467588 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5467554 AGATTAGTAT
5467564 TTTTTTTAA
1 TTTTTTTAA
5467573 TTTTTTTAA
1 TTTTTTTAA
5467582 TTTTTTT
1 TTTTTTT
5467589 TGCGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:5473160 original size:2 final size:2
Alignment explanation
Indices: 5473153--5473179 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5473143 GAGGATCCTG
5473153 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5473180 ATGCATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5479320 original size:3 final size:3
Alignment explanation
Indices: 5479305--5479336 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5479295 TCCATAAATC
*
5479305 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5479337 ATCAATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5489667 original size:12 final size:12
Alignment explanation
Indices: 5489643--5489690 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
5489633 CACCAACCAT
5489643 AAAAAA-AAA-A
1 AAAAAACAAACA
5489653 AAAAAACAAACA
1 AAAAAACAAACA
5489665 AAAAAACAGAAACA
1 AAAAAAC--AAACA
*
5489679 AAAAGACAAACA
1 AAAAAACAAACA
5489691 CAGTTCTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
12 13 0.39
14 11 0.33
ACGTcount: A:0.83, C:0.12, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAACAAACA
Found at i:5489669 original size:18 final size:18
Alignment explanation
Indices: 5489646--5489680 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5489636 CAACCATAAA
5489646 AAAAAAAAAAAAACAAAC
1 AAAAAAAAAAAAACAAAC
* *
5489664 AAAAAAACAGAAACAAA
1 AAAAAAAAAAAAACAAA
5489681 AAGACAAACA
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:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAACAAAC
Found at i:5490396 original size:18 final size:17
Alignment explanation
Indices: 5490351--5490397 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
5490341 TAAAAAAATT
* *
5490351 TTTTTTATATATTATTA
1 TTTTTTATATTTTAGTA
5490368 TTTTTGT-TATTTTGAGTA
1 TTTTT-TATATTTT-AGTA
5490386 TTTTTTATATTT
1 TTTTTTATATTT
5490398 ATGCATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTTATATTTTAGTA
Found at i:5490774 original size:14 final size:14
Alignment explanation
Indices: 5490758--5490936 Score: 58
Period size: 14 Copynumber: 12.2 Consensus size: 14
5490748 ACTAATTCTT
5490758 AAATCCAAACCTCTA
1 AAATCCAAACC-CTA
*
5490773 AAATCTAAACCCCTA
1 AAATCCAAA-CCCTA
* *
5490788 AAATTCAAACCCTT
1 AAATCCAAACCCTA
*
5490802 AAATCAAAACCGC--
1 AAATCCAAACC-CTA
* ***
5490815 AAACCTCAAATTTTA
1 AAATC-CAAACCCTA
* *
5490830 AAATCAAAACTCTA
1 AAATCCAAACCCTA
*
5490844 AAATCTCCAAACTCTA
1 AAA--TCCAAACCCTA
* * *
5490860 AAATCAAAATCATA
1 AAATCCAAACCCTA
* *
5490874 AACCTTCCATACCCTA
1 AA--ATCCAAACCCTA
* *
5490890 AAATCCAAGCCTTA
1 AAATCCAAACCCTA
* *
5490904 AGAACCTCTAAACCTTA
1 A-AA--TCCAAACCCTA
5490921 AAAT-CAAACCCTA
1 AAATCCAAACCCTA
5490934 AAA
1 AAA
5490937 CCCTTAAAAC
Statistics
Matches: 119, Mismatches: 33, Indels: 26
0.67 0.19 0.15
Matches are distributed among these distances:
13 14 0.12
14 44 0.37
15 25 0.21
16 26 0.22
17 10 0.08
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (14 bp):
AAATCCAAACCCTA
Found at i:5490944 original size:22 final size:20
Alignment explanation
Indices: 5490916--5490967 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
5490906 AACCTCTAAA
5490916 CCTTAAAATCAAACCCTAAAAC
1 CCTTAAAATC-AACCC-AAAAC
*
5490938 CCTTAAAACTCAACCCAAAAT
1 CCTTAAAA-TCAACCCAAAAC
5490959 CC-TAAAATC
1 CCTTAAAATC
5490968 TGAATTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 5 0.18
21 6 0.21
22 13 0.46
23 2 0.07
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (20 bp):
CCTTAAAATCAACCCAAAAC
Found at i:5492985 original size:13 final size:13
Alignment explanation
Indices: 5492967--5492992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5492957 AGAGAGATTG
5492967 TTTTTATTTTTAT
1 TTTTTATTTTTAT
5492980 TTTTTATTTTTAT
1 TTTTTATTTTTAT
5492993 AAAAATCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:5508332 original size:25 final size:23
Alignment explanation
Indices: 5508292--5508341 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
5508282 ATATTTAACT
*
5508292 AAAAATATAAATAATGTATAATTA
1 AAAAATATAAATAATGT-TAAATA
5508316 AAAAATCATATAA-AATGTTAAATA
1 AAAAAT-ATA-AATAATGTTAAATA
5508340 AA
1 AA
5508342 TAAGTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 13 0.57
25 8 0.35
26 2 0.09
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAATATAAATAATGTTAAATA
Found at i:5508965 original size:12 final size:12
Alignment explanation
Indices: 5508948--5508975 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5508938 AACAGACCTT
5508948 TATAAAAAAGTA
1 TATAAAAAAGTA
5508960 TATAAAAAAGTA
1 TATAAAAAAGTA
5508972 TATA
1 TATA
5508976 TGGTCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (12 bp):
TATAAAAAAGTA
Found at i:5509624 original size:21 final size:21
Alignment explanation
Indices: 5509566--5509629 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
5509556 CTTTCATATA
* *
5509566 TATTATTATTAATTTTAACTTTAC
1 TATTATAATTAA-TTTAA-TTT-T
5509590 TATTATAA-T-ATTTAATTTT
1 TATTATAATTAATTTAATTTT
*
5509609 TATTATAATTAATTTACTTTT
1 TATTATAATTAATTTAATTTT
5509630 AATCTCGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 8 0.23
20 4 0.11
21 14 0.40
22 1 0.03
23 1 0.03
24 7 0.20
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATAATTAATTTAATTTT
Found at i:5523038 original size:2 final size:2
Alignment explanation
Indices: 5523031--5523055 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5523021 TATTTCTAAG
5523031 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5523056 AGATCAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5525088 original size:8 final size:8
Alignment explanation
Indices: 5525064--5525096 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5525054 ATGGAATTTC
5525064 ATAA-AAA
1 ATAATAAA
5525071 ATATATAAA
1 ATA-ATAAA
5525080 ATAATAAA
1 ATAATAAA
5525088 ATAATAAA
1 ATAATAAA
5525096 A
1 A
5525097 ATTTCAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 3 0.12
8 15 0.62
9 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAATAAA
Found at i:5532563 original size:24 final size:24
Alignment explanation
Indices: 5532531--5532578 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5532521 CATGGGGTTG
5532531 TTGTGGCCGT-AGCTGTGGTGGCAT
1 TTGTGGCCGTGA-CTGTGGTGGCAT
*
5532555 TTGTGGCCGTGACTGTGTTGGCAT
1 TTGTGGCCGTGACTGTGGTGGCAT
5532579 CAAGGGAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.08, C:0.17, G:0.40, T:0.35
Consensus pattern (24 bp):
TTGTGGCCGTGACTGTGGTGGCAT
Found at i:5540504 original size:17 final size:17
Alignment explanation
Indices: 5540478--5540512 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5540468 AATTCCTAAC
5540478 AATATAAAAAATTAAAA
1 AATATAAAAAATTAAAA
*
5540495 AATATGAAAAATTAAAA
1 AATATAAAAAATTAAAA
5540512 A
1 A
5540513 CTCTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AATATAAAAAATTAAAA
Found at i:5541366 original size:74 final size:73
Alignment explanation
Indices: 5541246--5541385 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 73
5541236 GCACAAAGCC
* * * * * *
5541246 ATCATCAAACTTGCTATCATTTTCTCTTAATACTTGGTTTAAGACACGACTCATAGCTTTGTACA
1 ATCATCAAACTTGCTACCATATTCTCCTAATACTTGGTTTAAGACACAACTCATAACTTTGCACA
5541311 CGAATCCA
66 CGAATCCA
* * *
5541319 ATCATCGAACTTTGCTACCATATTCTCCTAATACTTGGTTTGAGACACAACTTATAACTTTGCAC
1 ATCATCAAAC-TTGCTACCATATTCTCCTAATACTTGGTTTAAGACACAACTCATAACTTTGCAC
5541384 AC
65 AC
5541386 ATGGCCATCA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
73 9 0.16
74 48 0.84
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (73 bp):
ATCATCAAACTTGCTACCATATTCTCCTAATACTTGGTTTAAGACACAACTCATAACTTTGCACA
CGAATCCA
Found at i:5542912 original size:10 final size:10
Alignment explanation
Indices: 5542899--5542931 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5542889 AAATAAATTT
5542899 AAAAAAATCA
1 AAAAAAATCA
5542909 AAAAATAA-CA
1 AAAAA-AATCA
5542919 AAAAAAATCA
1 AAAAAAATCA
5542929 AAA
1 AAA
5542932 TAGATGGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.10
10 17 0.81
11 2 0.10
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:5544334 original size:69 final size:68
Alignment explanation
Indices: 5544234--5544366 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 68
5544224 TTTTTCCGTT
* ** * * *
5544234 AAAAAAGTTTTTTGCGTTCTTTCTTGTTGTTGTATTTTGATTTCTGCTTTTGTGTTTGTTTTTTA
1 AAAAAAATTTTTTGCGTTCTTTCTTACTGTTGTATCTTGATTTCTGCTTGTCTGTTTGTTTTTTA
5544299 TCA
66 TCA
* * *
5544302 AAAAAAATTTTCTTGCGTTCTTTGTTACTGTTGTATCTTGGTTTTTGCTTGTCTGTTTGTTTTTT
1 AAAAAAATTTT-TTGCGTTCTTTCTTACTGTTGTATCTTGATTTCTGCTTGTCTGTTTGTTTTTT
5544367 CTGCGTATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
68 10 0.18
69 45 0.82
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.59
Consensus pattern (68 bp):
AAAAAAATTTTTTGCGTTCTTTCTTACTGTTGTATCTTGATTTCTGCTTGTCTGTTTGTTTTTTA
TCA
Found at i:5558430 original size:12 final size:12
Alignment explanation
Indices: 5558413--5558443 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5558403 ACCTCCAGTG
*
5558413 GCATCTGTTTTA
1 GCATCTGGTTTA
5558425 GCATCTGGTTTA
1 GCATCTGGTTTA
5558437 GCATCTG
1 GCATCTG
5558444 AGCGACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (12 bp):
GCATCTGGTTTA
Found at i:5559177 original size:21 final size:21
Alignment explanation
Indices: 5559153--5559194 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5559143 GGAAGCAAGG
5559153 TTTTGATTTAAGCGAACCAGA
1 TTTTGATTTAAGCGAACCAGA
* *
5559174 TTTTGATTTACGTGAACCAGA
1 TTTTGATTTAAGCGAACCAGA
5559195 AACCTTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (21 bp):
TTTTGATTTAAGCGAACCAGA
Found at i:5563630 original size:73 final size:73
Alignment explanation
Indices: 5563507--5563649 Score: 250
Period size: 73 Copynumber: 2.0 Consensus size: 73
5563497 TAAAAAGTAA
*
5563507 AACACCAATCCAGATCTTATATTTCTATATGCAACACAATTAAACAGTAAACAAATTTAAATTGA
1 AACACCAATCCAGATCTTATATTTCTATATGCAACACAATTAAACAGTAAACAAATTTAAATGGA
5563572 AGTTATAT
66 AGTTATAT
* * *
5563580 AACACCAATCCATATCTTATATTTCTATATGCAACACAATTAAACTGTAAACACATTTAAATGGA
1 AACACCAATCCAGATCTTATATTTCTATATGCAACACAATTAAACAGTAAACAAATTTAAATGGA
5563645 AGTTA
66 AGTTA
5563650 CAACATCCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (73 bp):
AACACCAATCCAGATCTTATATTTCTATATGCAACACAATTAAACAGTAAACAAATTTAAATGGA
AGTTATAT
Found at i:5564339 original size:6 final size:6
Alignment explanation
Indices: 5564326--5564386 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
5564316 CGATTAGCAC
* * * *
5564326 AGAGAG AAAGAG AAAGAA AGAGAG AGAGAG AGAGAG AGAGAG AGATAG
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG
*
5564374 AGAGAG AAAGAG A
1 AGAGAG AGAGAG A
5564387 CGGACTCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (6 bp):
AGAGAG
Found at i:5564345 original size:10 final size:10
Alignment explanation
Indices: 5564326--5564386 Score: 81
Period size: 10 Copynumber: 6.3 Consensus size: 10
5564316 CGATTAGCAC
5564326 AGAGAGAAAG
1 AGAGAGAAAG
*
5564336 AGAAAGAAAG
1 AGAGAGAAAG
5564346 AGAGAG--AG
1 AGAGAGAAAG
*
5564354 AGAGAGAGAG
1 AGAGAGAAAG
*
5564364 AGAGAGATAG
1 AGAGAGAAAG
5564374 AGAGAGAAAG
1 AGAGAGAAAG
5564384 AGA
1 AGA
5564387 CGGACTCTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.18
10 37 0.82
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (10 bp):
AGAGAGAAAG
Found at i:5564351 original size:4 final size:4
Alignment explanation
Indices: 5564326--5564386 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
5564316 CGATTAGCAC
* * * *
5564326 AGAG AGAA AGAG AAAG AAAG AGAG AGAG AGAG AGAG AGAG AGAG ATAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
*
5564374 AGAG AGAA AGAG A
1 AGAG AGAG AGAG A
5564387 CGGACTCTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (4 bp):
AGAG
Found at i:5566052 original size:7 final size:7
Alignment explanation
Indices: 5566040--5566074 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5566030 TAATCATAAA
5566040 TTAAATT
1 TTAAATT
5566047 TTAAATT
1 TTAAATT
5566054 TTAAATTT
1 TTAAA-TT
*
5566062 TTATATT
1 TTAAATT
5566069 TTAAAT
1 TTAAAT
5566075 AAATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAAATT
Found at i:5566069 original size:15 final size:15
Alignment explanation
Indices: 5566040--5566074 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5566030 TAATCATAAA
5566040 TTAAA-TTTTAAATT
1 TTAAATTTTTAAATT
*
5566054 TTAAATTTTTATATT
1 TTAAATTTTTAAATT
5566069 TTAAAT
1 TTAAAT
5566075 AAATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAATTTTTAAATT
Found at i:5566609 original size:17 final size:17
Alignment explanation
Indices: 5566589--5566622 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5566579 ACATATTTAG
5566589 ATATTTAAATTTTAAAA
1 ATATTTAAATTTTAAAA
**
5566606 ATATTTATTTTTTAAAA
1 ATATTTAAATTTTAAAA
5566623 TTCTAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAAATTTTAAAA
Found at i:5567579 original size:23 final size:22
Alignment explanation
Indices: 5567565--5567607 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5567555 AAATAAGTTC
*
5567565 ATTTGTAAATATTAAAAAAAAAT
1 ATTTGTAAATATT-AAATAAAAT
*
5567588 ATTTGTAAATAATAAATAAA
1 ATTTGTAAATATTAAATAAA
5567608 TTATAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
ATTTGTAAATATTAAATAAAAT
Found at i:5575641 original size:40 final size:40
Alignment explanation
Indices: 5575586--5575663 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
5575576 TCGTCCACAG
5575586 AAGTTAACTTGGGATCTGAAATCTCATTTTTGTCCTTCCA
1 AAGTTAACTTGGGATCTGAAATCTCATTTTTGTCCTTCCA
5575626 AAGTTAACTTGGGATCTGAAATCTCATTTTTGTCCTTC
1 AAGTTAACTTGGGATCTGAAATCTCATTTTTGTCCTTC
5575664 GAAAACTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (40 bp):
AAGTTAACTTGGGATCTGAAATCTCATTTTTGTCCTTCCA
Found at i:5578650 original size:16 final size:16
Alignment explanation
Indices: 5578629--5578659 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5578619 GAGGAAGTGC
5578629 TTAAATTATATATATT
1 TTAAATTATATATATT
5578645 TTAAATTATATATAT
1 TTAAATTATATATAT
5578660 AATAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTATATATATT
Found at i:5578975 original size:15 final size:15
Alignment explanation
Indices: 5578952--5578982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5578942 TGCAATTAAT
5578952 ATTTAAAATAATTTA
1 ATTTAAAATAATTTA
*
5578967 ATTTGAAATAATTTA
1 ATTTAAAATAATTTA
5578982 A
1 A
5578983 CATTATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTTAAAATAATTTA
Found at i:5579449 original size:36 final size:38
Alignment explanation
Indices: 5579402--5579474 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
5579392 TTCTTTATAT
*
5579402 TGTCGAAAATCTT-TAAAAAA-ATCATATTATGAGAAC
1 TGTCGAAAATCTTAAAAAAAATATCATATTATGAGAAC
5579438 TGTCGAAAATCTTAAAAAAAATTATCATATTATGAGA
1 TGTCGAAAATCTTAAAAAAAA-TATCATATTATGAGA
5579475 TCGGAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 13 0.39
37 6 0.18
39 14 0.42
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (38 bp):
TGTCGAAAATCTTAAAAAAAATATCATATTATGAGAAC
Found at i:5589192 original size:2 final size:2
Alignment explanation
Indices: 5589187--5589220 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5589177 ATATGTGCAA
5589187 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
5589221 GTTGGGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5589447 original size:2 final size:2
Alignment explanation
Indices: 5589442--5589472 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5589432 ATGATGTCTG
5589442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5589473 CATAAGGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5596291 original size:22 final size:22
Alignment explanation
Indices: 5596229--5596292 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
5596219 TTTTTATGTG
5596229 TAATTTTAT-AA-AAAATTATT
1 TAATTTTATAAATAAAATTATT
* *
5596249 TAATATATTA-ACAGTAAAATTTTT
1 TAAT-T-TTATA-AATAAAATTATT
5596273 TAATTTTATAAATAAAATTA
1 TAATTTTATAAATAAAATTA
5596293 AAACGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 14 0.41
23 3 0.09
24 12 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATTTTATAAATAAAATTATT
Found at i:5596501 original size:32 final size:33
Alignment explanation
Indices: 5596427--5596502 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
5596417 ATTTTATAAC
*
5596427 TATTAATT-GAAATAAAAATTTATATAAAAAAT
1 TATTAATTATAAATAAAAATTTATATAAAAAAT
* * *
5596459 TATTATTTATAAATATAAATTT-TATATAAAAT
1 TATTAATTATAAATAAAAATTTATATAAAAAAT
5596491 T-TTAAATTATAA
1 TATT-AATTATAA
5596503 TTAATTATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.05
32 24 0.65
33 11 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
TATTAATTATAAATAAAAATTTATATAAAAAAT
Found at i:5603598 original size:2 final size:2
Alignment explanation
Indices: 5603591--5603616 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5603581 TTAAATAGTA
5603591 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
5603617 TAAGGCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5623597 original size:18 final size:18
Alignment explanation
Indices: 5623574--5623608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5623564 GTAACTTTCG
*
5623574 TTTCTCGCGTTTTTATTA
1 TTTCTCACGTTTTTATTA
*
5623592 TTTCTCACTTTTTTATT
1 TTTCTCACGTTTTTATT
5623609 TTGTCAAAGG
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:0.11, C:0.17, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTCTCACGTTTTTATTA
Found at i:5634654 original size:280 final size:280
Alignment explanation
Indices: 5634147--5634710 Score: 1101
Period size: 280 Copynumber: 2.0 Consensus size: 280
5634137 CATTTGAATA
*
5634147 ACATTGATTTAACCACAATGTTCATGTATGTGAACAGAACAGGCCTCTTATTTTCGTTTGATGAT
1 ACATTCATTTAACCACAATGTTCATGTATGTGAACAGAACAGGCCTCTTATTTTCGTTTGATGAT
* *
5634212 ACCATTCTGCGTGGAGAAAAGGGCTGATGTTGGCCACTGTATATGAACTCATATATGTATGGGGC
66 ACCAATCTGCGTGGAGAAAAGGGCTGATGTTGGCCACTATATATGAACTCATATATGTATGGGGC
5634277 ATGTTTGTGAATGTTCATAAGGAACAAATTTGAATTTAAAATGTATTTAATAATGCTCCTCCCCT
131 ATGTTTGTGAATGTTCATAAGGAACAAATTTGAATTTAAAATGTATTTAATAATGCTCCTCCCCT
5634342 GCAACAACTGTCTGAGTTAATGGATTCTTTGTATATTTTCAGACAAAACAGTCGCACCAAAGTCA
196 GCAACAACTGTCTGAGTTAATGGATTCTTTGTATATTTTCAGACAAAACAGTCGCACCAAAGTCA
5634407 ATAAATGATTTGAAACTTAT
261 ATAAATGATTTGAAACTTAT
5634427 ACATTCATTTAACCACAATGTTCATGTATGTGAACAGAACAGGCCTCTTATTTTCGTTTGATGAT
1 ACATTCATTTAACCACAATGTTCATGTATGTGAACAGAACAGGCCTCTTATTTTCGTTTGATGAT
5634492 ACCAATCTGCGTGGAGAAAAGGGCTGATGTTGGCCACTATATATGAACTCATATATGTATGGGGC
66 ACCAATCTGCGTGGAGAAAAGGGCTGATGTTGGCCACTATATATGAACTCATATATGTATGGGGC
5634557 ATGTTTGTGAATGTTCATAAGGAACAAATTTGAATTTAAAATGTATTTAATAATGCTCCTCCCCT
131 ATGTTTGTGAATGTTCATAAGGAACAAATTTGAATTTAAAATGTATTTAATAATGCTCCTCCCCT
5634622 GCAACAACTGTCTGAGTTAATGGATTCTTTGTATATTTTCAGACAAAACAGTCGCACCAAAGTCA
196 GCAACAACTGTCTGAGTTAATGGATTCTTTGTATATTTTCAGACAAAACAGTCGCACCAAAGTCA
5634687 ATAAATGATTTGAAACTTAT
261 ATAAATGATTTGAAACTTAT
5634707 ACAT
1 ACAT
5634711 GCTGGTAAAG
Statistics
Matches: 281, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 281 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (280 bp):
ACATTCATTTAACCACAATGTTCATGTATGTGAACAGAACAGGCCTCTTATTTTCGTTTGATGAT
ACCAATCTGCGTGGAGAAAAGGGCTGATGTTGGCCACTATATATGAACTCATATATGTATGGGGC
ATGTTTGTGAATGTTCATAAGGAACAAATTTGAATTTAAAATGTATTTAATAATGCTCCTCCCCT
GCAACAACTGTCTGAGTTAATGGATTCTTTGTATATTTTCAGACAAAACAGTCGCACCAAAGTCA
ATAAATGATTTGAAACTTAT
Found at i:5636312 original size:2 final size:2
Alignment explanation
Indices: 5636305--5636340 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5636295 TCCTAAATAC
* *
5636305 AT AT AT AT AT AT AC AT AA 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
5636341 TTTATTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5637850 original size:16 final size:18
Alignment explanation
Indices: 5637809--5637852 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
5637799 AACATGGGTA
*
5637809 TTTTTTATTTTCTCTCTT
1 TTTTTTGTTTTCTCTCTT
*
5637827 TCTTTTGTTTTCT-T-TT
1 TTTTTTGTTTTCTCTCTT
5637843 TTTTTTGTTT
1 TTTTTTGTTT
5637853 CAATTATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 11 0.48
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTGTTTTCTCTCTT
Found at i:5652953 original size:18 final size:17
Alignment explanation
Indices: 5652920--5652953 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5652910 TAAAATTTAA
*
5652920 TGATCAAAATAAAATTG
1 TGATCAAAACAAAATTG
5652937 TGATCAATAACAAAATT
1 TGATCAA-AACAAAATT
5652954 TACTCTCTTT
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:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
TGATCAAAACAAAATTG
Found at i:5665439 original size:18 final size:18
Alignment explanation
Indices: 5665416--5665452 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5665406 GCACAACACT
5665416 GATATCATGAGCATGAGC
1 GATATCATGAGCATGAGC
5665434 GATATCATGAGCATGAGC
1 GATATCATGAGCATGAGC
5665452 G
1 G
5665453 TGATCGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (18 bp):
GATATCATGAGCATGAGC
Found at i:5669215 original size:12 final size:12
Alignment explanation
Indices: 5669198--5669222 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5669188 CGTGTGAAAG
5669198 GAAGGAGGAGGA
1 GAAGGAGGAGGA
5669210 GAAGGAGGAGGA
1 GAAGGAGGAGGA
5669222 G
1 G
5669223 TTTCAATGGA
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:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (12 bp):
GAAGGAGGAGGA
Found at i:5670903 original size:7 final size:7
Alignment explanation
Indices: 5670887--5670916 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5670877 TAATAAAAAA
5670887 AATT-AT
1 AATTAAT
5670893 AATTAAT
1 AATTAAT
5670900 AATTAAT
1 AATTAAT
5670907 AATTAAT
1 AATTAAT
5670914 AAT
1 AAT
5670917 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTAAT
Found at i:5672739 original size:42 final size:40
Alignment explanation
Indices: 5672675--5672810 Score: 100
Period size: 42 Copynumber: 3.3 Consensus size: 40
5672665 TAATTTATAT
** * *
5672675 ATATT-ATATTAATAAATTTATTATTTAATAATTTCATTTAAG
1 ATATTAAT-TTAATAAAAATATTATTTAAT-ATAT-AATTAAG
*
5672717 ATATTAATTTAATAAAAATATTATATTTATATATAATTAAG
1 ATATTAATTTAATAAAAATATTAT-TTAATATATAATTAAG
* *
5672758 ATA-TAATTTATATTAAAAATAATATTTTAAAATATTATATTAA-
1 ATATTAATTTA-A-TAAAAATATTA-TTTAATATA-TA-ATTAAG
5672801 A-ATTAATTTA
1 ATATTAATTTA
5672811 TAGTATGATC
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
40 7 0.09
41 10 0.13
42 39 0.50
43 17 0.22
44 5 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (40 bp):
ATATTAATTTAATAAAAATATTATTTAATATATAATTAAG
Found at i:5676460 original size:18 final size:18
Alignment explanation
Indices: 5676417--5676460 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5676407 TACGTATATA
5676417 ATTTTTATTTTTAATAAT
1 ATTTTTATTTTTAATAAT
* *
5676435 ATTATTATTTTATAATTAT
1 ATTTTTATTTT-TAATAAT
5676454 -TTTTTAT
1 ATTTTTAT
5676461 CTCGTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTATTTTTAATAAT
Found at i:5680682 original size:30 final size:30
Alignment explanation
Indices: 5680646--5680713 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
5680636 GTTAGCCATG
*
5680646 GGACCTGGCGGACCTGGAGGAGGACCAGGA
1 GGACCTGGCGGACCGGGAGGAGGACCAGGA
* ***
5680676 GGACCTGGTGGTTGGGGAGGAGGACCAGGA
1 GGACCTGGCGGACCGGGAGGAGGACCAGGA
*
5680706 GGGCCTGG
1 GGACCTGG
5680714 TGGATTTGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.51, T:0.10
Consensus pattern (30 bp):
GGACCTGGCGGACCGGGAGGAGGACCAGGA
Found at i:5682606 original size:2 final size:2
Alignment explanation
Indices: 5682599--5682637 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5682589 AGATACAGAA
5682599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5682638 CTTTCACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5685852 original size:19 final size:19
Alignment explanation
Indices: 5685809--5685852 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5685799 TGTGTTTGGT
*
5685809 ATATAAAATTATAATAAAA
1 ATATAAAATAATAATAAAA
* * *
5685828 AAATAAAATAATATTATAA
1 ATATAAAATAATAATAAAA
5685847 ATATAA
1 ATATAA
5685853 TTAAATAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAAATAATAATAAAA
Found at i:5685975 original size:20 final size:19
Alignment explanation
Indices: 5685943--5685982 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5685933 TTTCTTAAAG
5685943 TTTATATAATTT-AAATTA
1 TTTATATAATTTAAAATTA
5685961 TTTATATAAATTTTAAAATTA
1 TTTATAT-AA-TTTAAAATTA
5685982 T
1 T
5685983 AATAAGACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 3 0.16
21 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATATAATTTAAAATTA
Found at i:5686925 original size:25 final size:25
Alignment explanation
Indices: 5686883--5686930 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5686873 GCATTAAAAA
5686883 TTAAAAATTAAAACCAATAAAAATT
1 TTAAAAATTAAAACCAATAAAAATT
*
5686908 TTAAAATTTACAAA-CAATAAAAA
1 TTAAAAATTA-AAACCAATAAAAA
5686931 ACATTAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
TTAAAAATTAAAACCAATAAAAATT
Found at i:5688450 original size:17 final size:18
Alignment explanation
Indices: 5688430--5688483 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 18
5688420 TCCATAAACA
*
5688430 TATTTAAATAATAA-ATT
1 TATTTATATAATAATATT
5688447 TATTTATA-AATAATATT
1 TATTTATATAATAATATT
*
5688464 TATTCATATAATAATATT
1 TATTTATATAATAATATT
5688482 TA
1 TA
5688484 AATTTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 5 0.15
17 17 0.52
18 11 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTATATAATAATATT
Found at i:5688458 original size:19 final size:18
Alignment explanation
Indices: 5688434--5688483 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
5688424 TAAACATATT
*
5688434 TAAATAATAAATTTATTTA
1 TAAATAAT-AATTTATTCA
5688453 TAAATAAT-ATTTATTCA
1 TAAATAATAATTTATTCA
5688470 TATAATAAT-ATTTA
1 TA-AATAATAATTTA
5688484 AATTTTAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 10 0.34
18 11 0.38
19 8 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATAATAATTTATTCA
Found at i:5688967 original size:11 final size:11
Alignment explanation
Indices: 5688951--5688975 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5688941 CATGTATTTA
5688951 TTTATTTATAT
1 TTTATTTATAT
5688962 TTTATTTATAT
1 TTTATTTATAT
5688973 TTT
1 TTT
5688976 TTGTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATAT
Found at i:5689212 original size:51 final size:51
Alignment explanation
Indices: 5689157--5689254 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
5689147 TGGGATAAAA
* *
5689157 ATAATTTCATTAAAATTTAAATTA-AT-TTTTTATTAA-AATTTAAAATTTTAG
1 ATAATTT-AATAAAATTTAAAATATATATTTTTA--AATAATTTAAAATTTTAG
5689208 ATAATTTAATAAAATTTAAAATATATATTTTTAAATAATTTAAAATT
1 ATAATTTAATAAAATTTAAAATATATATTTTTAAATAATTTAAAATT
5689255 AATAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 16 0.38
51 20 0.48
52 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (51 bp):
ATAATTTAATAAAATTTAAAATATATATTTTTAAATAATTTAAAATTTTAG
Found at i:5702312 original size:22 final size:22
Alignment explanation
Indices: 5702266--5702312 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5702256 GAGTGATCTG
* * *
5702266 TTTTTATTATTTGTTTCTTTGA
1 TTTTTATTATTCGTTTCCTTAA
*
5702288 TTTTTATTCTTCGTTTCCTTAA
1 TTTTTATTATTCGTTTCCTTAA
5702310 TTT
1 TTT
5702313 GACAGAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.11, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTTTATTATTCGTTTCCTTAA
Found at i:5704173 original size:26 final size:27
Alignment explanation
Indices: 5704144--5704195 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
5704134 GATTAAACAA
5704144 TAAAAAAATTCTTC-T-TTTTTATTTTT
1 TAAAAAAATT-TTCATATTTTTATTTTT
*
5704170 TAAATAAATTTTCATATTTTTATTTT
1 TAAAAAAATTTTCATATTTTTATTTT
5704196 ACCCAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 3 0.13
26 10 0.43
27 10 0.43
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (27 bp):
TAAAAAAATTTTCATATTTTTATTTTT
Found at i:5704460 original size:26 final size:26
Alignment explanation
Indices: 5704428--5704486 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
5704418 TTTTAACAAT
5704428 AAAAATTGTGAAACTTTAATTTTATA
1 AAAAATTGTGAAACTTTAATTTTATA
5704454 AAAAATTGTGAAACTTTAATTTTATA
1 AAAAATTGTGAAACTTTAATTTTATA
5704480 AAAAATT
1 AAAAATT
5704487 AAAGATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (26 bp):
AAAAATTGTGAAACTTTAATTTTATA
Found at i:5704630 original size:30 final size:29
Alignment explanation
Indices: 5704594--5704671 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
5704584 AAAGTTAAAG
* *
5704594 ATTTATTTGAATATAGGTAAAAAT-TTAAGA
1 ATTTATTTGAATATA-ATAAAAATATGAA-A
*
5704624 ATTTATTTGAATGTAATAAAAATATGAAA
1 ATTTATTTGAATATAATAAAAATATGAAA
* *
5704653 ATTTATTTAAATAAAATAA
1 ATTTATTTGAATATAATAA
5704672 TAAAATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (29 bp):
ATTTATTTGAATATAATAAAAATATGAAA
Found at i:5709582 original size:18 final size:19
Alignment explanation
Indices: 5709559--5709594 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5709549 CTAAAAATAA
*
5709559 TTAAATAA-AATTTAAAAT
1 TTAAATAATAAATTAAAAT
5709577 TTAAATAATAAATTAAAA
1 TTAAATAATAAATTAAAA
5709595 AATCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAATAATAAATTAAAAT
Found at i:5720973 original size:3 final size:3
Alignment explanation
Indices: 5720967--5720993 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5720957 AACAACAACA
5720967 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
5720994 TAGTATGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5728441 original size:36 final size:36
Alignment explanation
Indices: 5728394--5728499 Score: 189
Period size: 36 Copynumber: 3.0 Consensus size: 36
5728384 AAGAAAAGCC
5728394 CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
1 CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
5728430 CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
1 CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
*
5728466 CTTAGTTTATTGCTAATGAAA--ATCAAGTTCTTGG
1 CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
5728500 TTTAAGTTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 12 0.17
36 57 0.83
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (36 bp):
CTTAGTTTATTGCTAATGAAATTATCACGTTCTTGG
Found at i:5733087 original size:19 final size:18
Alignment explanation
Indices: 5733063--5733120 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
5733053 CTTCTACAAG
5733063 ATTTTGCAGGTGCTCTAAA
1 ATTTTGCAGGT-CTCTAAA
*
5733082 ATTTTGCA-ATC-CTAAAA
1 ATTTTGCAGGTCTCT-AAA
5733099 ATTTTGCAGGTACTCTAAA
1 ATTTTGCAGGT-CTCTAAA
5733118 ATT
1 ATT
5733121 GACTTCTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 2 0.06
17 12 0.36
18 2 0.06
19 15 0.45
20 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (18 bp):
ATTTTGCAGGTCTCTAAA
Found at i:5734520 original size:15 final size:16
Alignment explanation
Indices: 5734487--5734527 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5734477 ATATATTTTT
5734487 ATTTTTTA-AGTATGAA
1 ATTTTTTATAGTAT-AA
5734503 ATTTTTTATAGTAT-A
1 ATTTTTTATAGTATAA
5734518 ATTTTATTAT
1 ATTTT-TTAT
5734528 TTATCACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
ATTTTTTATAGTATAA
Found at i:5736944 original size:2 final size:2
Alignment explanation
Indices: 5736934--5736966 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5736924 TCACACACAC
5736934 AT AT A- 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
5736967 GTTTGAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5745362 original size:15 final size:15
Alignment explanation
Indices: 5745344--5745376 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5745334 ATTATGAACT
5745344 AAACAACCAGATAAA
1 AAACAACCAGATAAA
5745359 AAACAACCAGATAAA
1 AAACAACCAGATAAA
5745374 AAA
1 AAA
5745377 TAATGGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (15 bp):
AAACAACCAGATAAA
Found at i:5750080 original size:31 final size:31
Alignment explanation
Indices: 5750042--5750109 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
5750032 TTTAATTGGT
*
5750042 ATAATTTTATCCTTACATTTTTAATTTTAAA
1 ATAATTTTATCCTTACATTTTAAATTTTAAA
**
5750073 ATAATTTTATTGTTACATTTTAAATTTTAAA
1 ATAATTTTATCCTTACATTTTAAATTTTAAA
5750104 ATAATT
1 ATAATT
5750110 AAAGAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.54
Consensus pattern (31 bp):
ATAATTTTATCCTTACATTTTAAATTTTAAA
Found at i:5758639 original size:3 final size:3
Alignment explanation
Indices: 5758633--5758658 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5758623 TTTGATCATC
5758633 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5758659 GCTCATAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5760538 original size:28 final size:29
Alignment explanation
Indices: 5760507--5760581 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
5760497 ATAAAAATTA
*
5760507 TTATATTA-T-AATTTTTATTAGAATTTTT
1 TTATATTATTAAATTTATA-TAGAATTTTT
* *
5760535 TTATTTTATTAAATTTATATATAATTTTT
1 TTATATTATTAAATTTATATAGAATTTTT
5760564 TTCA-ATT-TTAAA-TTATAT
1 TT-ATATTATTAAATTTATAT
5760582 TATTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 6 0.15
28 12 0.30
29 14 0.35
30 8 0.20
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATATTATTAAATTTATATAGAATTTTT
Found at i:5760539 original size:31 final size:29
Alignment explanation
Indices: 5760504--5760565 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5760494 CATATAAAAA
*
5760504 TTATTATATTATAATTTTTATTAGAATTTTT
1 TTATTATATTA-AATTTATA-TAGAATTTTT
* *
5760535 TTATTTTATTAAATTTATATATAATTTTT
1 TTATTATATTAAATTTATATAGAATTTTT
5760564 TT
1 TT
5760566 CAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
30 7 0.25
31 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TTATTATATTAAATTTATATAGAATTTTT
Done.