Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 20 of 168
Found at i:5277702 original size:51 final size:53
Alignment explanation
Indices: 5277639--5277742 Score: 131
Period size: 55 Copynumber: 2.0 Consensus size: 53
5277629 TACCCGGTAA
* *
5277639 ACATAGTAGCCTGCACATAGTAC-T-ACACATGTGACCATTACTCTCACTTTC
1 ACATAGTAGCCTGCACACAGTACGTCACACATGTGACCATTACTATCACTTTC
* * *
5277690 ACATAGTGGCCTGCACACAGTTCGTGCCACACATGTGATCATTACTATCACTT
1 ACATAGTAGCCTGCACACAGTACGT--CACACATGTGACCATTACTATCACTT
5277743 CATTCGTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
51 20 0.45
52 1 0.02
55 23 0.52
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (53 bp):
ACATAGTAGCCTGCACACAGTACGTCACACATGTGACCATTACTATCACTTTC
Found at i:5279561 original size:18 final size:19
Alignment explanation
Indices: 5279527--5279566 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
5279517 TTGTGCTTGC
*
5279527 AAAATAAATTAAGTGAATT
1 AAAATAAACTAAGTGAATT
5279546 AAAATAAACT-AGTGAATT
1 AAAATAAACTAAGTGAATT
5279564 AAA
1 AAA
5279567 TTTATTAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (19 bp):
AAAATAAACTAAGTGAATT
Found at i:5281406 original size:12 final size:12
Alignment explanation
Indices: 5281389--5281414 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5281379 CTTTTTTCTC
5281389 TATATTTATGCT
1 TATATTTATGCT
5281401 TATATTTATGCT
1 TATATTTATGCT
5281413 TA
1 TA
5281415 GAGTTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (12 bp):
TATATTTATGCT
Found at i:5281561 original size:44 final size:45
Alignment explanation
Indices: 5281481--5281565 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 45
5281471 TAATTGTAAT
* * * *
5281481 TTAAATTATAATTATTTTTTAAATGTGTAGTTATCACAACTTCTC
1 TTAAATTATAATTATCTTGTAAATGTATAATTATCACAACTTCTC
5281526 TTAAATTATAATTA-CTTGTAAATGTATAATTATCACAACT
1 TTAAATTATAATTATCTTGTAAATGTATAATTATCACAACT
5281566 ATTTTATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.61
45 14 0.39
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (45 bp):
TTAAATTATAATTATCTTGTAAATGTATAATTATCACAACTTCTC
Found at i:5285631 original size:25 final size:22
Alignment explanation
Indices: 5285577--5285634 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 22
5285567 AAACAACCAT
5285577 AAAAATATATTTAAAAAATAATA
1 AAAAATA-ATTTAAAAAATAATA
5285600 ATTAAAATAAGTTTAAGAAAATAAATA
1 A--AAAATAA-TTTAA-AAAAT-AATA
5285627 AAAAATAA
1 AAAAATAA
5285635 AGCAACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 18 0.60
26 5 0.17
27 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (22 bp):
AAAAATAATTTAAAAAATAATA
Found at i:5285683 original size:5 final size:5
Alignment explanation
Indices: 5285641--5285728 Score: 52
Period size: 6 Copynumber: 15.8 Consensus size: 5
5285631 ATAAAGCAAC
* * *
5285641 TAAAA CAAAA TTAAAA TGAAAAA TGAAA -AAAA TAAAA TGAAA TAATAA
1 TAAAA TAAAA -TAAAA T--AAAA TAAAA TAAAA TAAAA TAAAA TAA-AA
5285689 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAAA
1 TAA-AA TAA-AA TAA-AA TAA-AA TAA-AA TAA-AA TAAA
5285729 CTCAATGATA
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
4 3 0.04
5 19 0.26
6 45 0.62
7 5 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:5285687 original size:3 final size:3
Alignment explanation
Indices: 5285681--5285727 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5285671 AATAAAATGA
5285681 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5285728 ACTCAATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5285906 original size:30 final size:29
Alignment explanation
Indices: 5285840--5285911 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
5285830 AAGAATAATA
5285840 AATAAATAAAATAAAAAATAGGAAAATAAA-
1 AATAAATAAAATAAAAAATA--AAAATAAAT
* * *
5285870 AATAAATAATATAACAAATAACAATAAAT
1 AATAAATAAAATAAAAAATAAAAATAAAT
*
5285899 AATTAAATTAAAT
1 AA-TAAATAAAAT
5285912 TAAATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.20
29 2 0.06
30 26 0.74
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (29 bp):
AATAAATAAAATAAAAAATAAAAATAAAT
Found at i:5299660 original size:5 final size:5
Alignment explanation
Indices: 5299652--5299685 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5299642 ACTTTACTCA
5299652 TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
5299686 CATGTAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:5312781 original size:15 final size:15
Alignment explanation
Indices: 5312761--5312789 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5312751 AAAAATATGG
5312761 ATGAATTGAAATTGT
1 ATGAATTGAAATTGT
5312776 ATGAATTGAAATTG
1 ATGAATTGAAATTG
5312790 AAATTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
ATGAATTGAAATTGT
Found at i:5315329 original size:11 final size:11
Alignment explanation
Indices: 5315314--5315347 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5315304 ATAAAGTACC
5315314 AATAAAATATA
1 AATAAAATATA
*
5315325 TATAAAATATA
1 AATAAAATATA
5315336 AATAAAA-ATA
1 AATAAAATATA
5315346 AA
1 AA
5315348 ACTGGGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATATA
Found at i:5324911 original size:46 final size:46
Alignment explanation
Indices: 5324849--5324943 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
5324839 AGCCTATTGG
5324849 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGA
1 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGA
5324895 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGA
1 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGA
5324941 AGG
1 AGG
5324944 GATGTGACCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (46 bp):
AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGA
Found at i:5325011 original size:118 final size:118
Alignment explanation
Indices: 5324803--5325015 Score: 399
Period size: 118 Copynumber: 1.8 Consensus size: 118
5324793 TTCCAATTTT
*
5324803 GTTAACTGACCTAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGACCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
5324868 CAAATTCGTTAACTGGCCCAGAGAGGAAGGATAGATCCAATTCAACCAAATTC
66 CAAATTCGTTAACTGGCCCAGAGAGGAAGGATAGATCCAATTCAACCAAATTC
* *
5324921 GTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGCTTATTGGAGGATAGATCCAATTCAAC
1 GTTAACTGACCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
5324986 CAAATTCGTTAACTGGCCCAGAGAGGAAGG
66 CAAATTCGTTAACTGGCCCAGAGAGGAAGG
5325016 GATGTGACCT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 92 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (118 bp):
GTTAACTGACCCAGAGAGGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAAC
CAAATTCGTTAACTGGCCCAGAGAGGAAGGATAGATCCAATTCAACCAAATTC
Found at i:5325012 original size:72 final size:72
Alignment explanation
Indices: 5324895--5325140 Score: 429
Period size: 72 Copynumber: 3.4 Consensus size: 72
5324885 CCAGAGAGGA
5324895 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
1 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
*
5324960 TTATTGG
66 CTATTGG
5324967 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
1 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
5325032 CTATTGG
66 CTATTGG
* *
5325039 AGGATAGATCCAATTCAACCAAATTCGTTAAATGGCCCAGAGAGGAAGGGATGTGACCTAAAAGC
1 AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
*
5325104 CCATTGG
66 CTATTGG
* * *
5325111 AGGATAGTTTCAATTCAACCAAATCCGTTA
1 AGGATAGATCCAATTCAACCAAATTCGTTA
5325141 GTCCCCCAAT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 167 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (72 bp):
AGGATAGATCCAATTCAACCAAATTCGTTAACTGGCCCAGAGAGGAAGGGATGTGACCTGAAAGC
CTATTGG
Found at i:5325213 original size:144 final size:144
Alignment explanation
Indices: 5325065--5325386 Score: 396
Period size: 144 Copynumber: 2.2 Consensus size: 144
5325055 AACCAAATTC
* * * * * *
5325065 GTTAAATGGCCCAGAGAGGAAGGGA-TGTGACCTAA-AAGCCCATTGGAGGATAGTTTCAATTCA
1 GTTAAATGGCCCACAGAAGAAGGGATTG-GACC-AACAAGACAATTGGAGGATAGATTCAATGCA
*
5325128 ACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATTAAGTTGATTGCTTTGAAGGAA
64 ACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAA
5325193 CAAAGAGGAAAGATTG
129 CAAAGAGGAAAGATTG
* * ** *
5325209 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
1 GTTAAATGGCCCACAGAAGAAGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
* * * *
5325274 CAAATTCGTTAGTCTCCCAATATCTTTTGGAATGGATCCATCAAGTTGGTTGCTTTGAAGGAACA
66 CAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAACA
* **
5325339 ACGAGTCAAGATTG
131 AAGAGGAAAGATTG
* * ** *
5325353 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAA
1 GTTAAATGGCCCACAGAAGAAGGGATTGGACCAA
5325387 TAAACCAATT
Statistics
Matches: 157, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
143 2 0.01
144 153 0.97
145 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (144 bp):
GTTAAATGGCCCACAGAAGAAGGGATTGGACCAACAAGACAATTGGAGGATAGATTCAATGCAAC
CAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCATCAAGTTGATTGCTTTGAAGGAACA
AAGAGGAAAGATTG
Found at i:5325397 original size:144 final size:144
Alignment explanation
Indices: 5325106--5325386 Score: 472
Period size: 144 Copynumber: 2.0 Consensus size: 144
5325096 CTAAAAGCCC
* *
5325106 ATTGGAGGATAGTTTCAATTCAACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
1 ATTGGAGGATAGATTCAATGCAACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
*
5325171 TAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
66 CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
5325236 GGACCAACAAGACA
131 GGACCAACAAGACA
* * *
5325250 ATTGGAGGATAGATTCAATGCAACCAAATTCGTTAGTCTCCCAATATCTTTTGGAATGGATCCAT
1 ATTGGAGGATAGATTCAATGCAACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
* * **
5325315 CAAGTTGGTTGCTTTGAAGGAACAACGAGTCAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
66 CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
5325380 GGACCAA
131 GGACCAA
5325387 TAAACCAATT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 127 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (144 bp):
ATTGGAGGATAGATTCAATGCAACCAAATCCGTTAGTCCCCCAATATCTTCTGGAATGGATCCAT
CAAGTTGATTGCTTTGAAGGAACAAAGAGGAAAGATTGGTTAAGTTGCTGACAGAAGATGGGATT
GGACCAACAAGACA
Found at i:5327285 original size:27 final size:28
Alignment explanation
Indices: 5327251--5327303 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5327241 CCATTTTCTC
*
5327251 TCACTCTAT-TTATTTTTT-ATTTTTAT
1 TCACTCTATATGATTTTTTAATTTTTAT
5327277 TCACTTCTATATGATTTTTTAATTTTT
1 TCAC-TCTATATGATTTTTTAATTTTT
5327304 TGAATTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 5 0.22
28 8 0.35
29 6 0.26
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (28 bp):
TCACTCTATATGATTTTTTAATTTTTAT
Found at i:5328693 original size:15 final size:17
Alignment explanation
Indices: 5328664--5328696 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5328654 GTTCCATCAC
5328664 TTTTTTCTAATTTTATT
1 TTTTTTCTAATTTTATT
5328681 TTTTTTC-AA-TTTATT
1 TTTTTTCTAATTTTATT
5328696 T
1 T
5328697 AAAAAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCTAATTTTATT
Found at i:5334290 original size:22 final size:22
Alignment explanation
Indices: 5334259--5334309 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5334249 CTCTCTAATC
*
5334259 CTCTCTATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
5334281 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
5334303 CTCTCAA
1 CTCTCAA
5334310 ACCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:5334385 original size:28 final size:30
Alignment explanation
Indices: 5334353--5334416 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 30
5334343 CTCTCAAATC
5334353 TATTTTTTAAAATAATTAT-AA-TTTTTTA
1 TATTTTTTAAAATAATTATAAATTTTTTTA
*
5334381 TATTTTTTAAAATAATTTTAAATTTTTTTA
1 TATTTTTTAAAATAATTATAAATTTTTTTA
5334411 TATTTT
1 TATTTT
5334417 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 18 0.55
29 2 0.06
30 13 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTTTAAAATAATTATAAATTTTTTTA
Found at i:5336202 original size:18 final size:18
Alignment explanation
Indices: 5336181--5336215 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5336171 AGGTATGTTT
* *
5336181 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
5336199 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
5336216 TCCTTTTTCC
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:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:5336496 original size:21 final size:21
Alignment explanation
Indices: 5336472--5336521 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5336462 AAGATGCCGA
* *
5336472 ACCGGAAGAACCACAATCACC
1 ACCGGAAGAACAACAACCACC
* *
5336493 ACCGGAGGAAGAACAACCACC
1 ACCGGAAGAACAACAACCACC
5336514 ACCGGAAG
1 ACCGGAAG
5336522 CTAGAGGAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.34, G:0.22, T:0.02
Consensus pattern (21 bp):
ACCGGAAGAACAACAACCACC
Found at i:5336743 original size:29 final size:29
Alignment explanation
Indices: 5336710--5336925 Score: 206
Period size: 29 Copynumber: 7.0 Consensus size: 29
5336700 ATAAAATAAA
* *
5336710 AACCCTAATTTAATTGAAAACCCTAACCT
1 AACCCTAAATTAATTAAAAACCCTAACCT
5336739 AACCCTAACCTAAATTAATTAAAAACCCTAAACCT
1 AA--C---CCTAAATTAATTAAAAACCCT-AACCT
5336774 AA-CCTAAATTAATT-AAAACCCTAACCT
1 AACCCTAAATTAATTAAAAACCCTAACCT
5336801 AA-CCTAAATTAATTAAAAACCCTAAACCT
1 AACCCTAAATTAATTAAAAACCCT-AACCT
* *
5336830 -AGCCTAAATTAATTAAAAACCCTAATCT
1 AACCCTAAATTAATTAAAAACCCTAACCT
5336858 AACCCTAACCTAGCTTAATTAAAAACCCTAACCCT
1 AACCCTAA---A--TTAATTAAAAACCCTAA-CCT
5336893 AACCCTAACCTAGCTTAATTAAAAACCCTAACC
1 AACCCTAA---A--TTAATTAAAAACCCTAACC
5336926 ATTAAATTTT
Statistics
Matches: 166, Mismatches: 5, Indels: 27
0.84 0.03 0.14
Matches are distributed among these distances:
27 19 0.11
28 21 0.13
29 46 0.28
31 1 0.01
32 1 0.01
34 38 0.23
35 40 0.24
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.25
Consensus pattern (29 bp):
AACCCTAAATTAATTAAAAACCCTAACCT
Found at i:5336751 original size:34 final size:33
Alignment explanation
Indices: 5336713--5336925 Score: 220
Period size: 34 Copynumber: 6.8 Consensus size: 33
5336703 AAATAAAAAC
* *
5336713 CCTAATTTAATTGAAAACCCTAACCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAA-CCTAA
5336747 CCTAAATTAATTAAAAACCCT-A---AACCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACCTAA
5336776 CCTAAATTAATT-AAAA--C---CCTAACCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACCTAA
*
5336803 CCTAAATTAATTAAAAACCCT-A---AACCTAG
1 CCTAAATTAATTAAAAACCCTAACCTAACCTAA
*
5336832 CCTAAATTAATTAAAAACCCTAATCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAA-CCTAA
**
5336866 CCTAGCTTAATTAAAAACCCTAACCCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAA-CCTAA-CCTAA
**
5336901 CCTAGCTTAATTAAAAACCCTAACC
1 CCTAAATTAATTAAAAACCCTAACC
5336926 ATTAAATTTT
Statistics
Matches: 158, Mismatches: 7, Indels: 28
0.82 0.04 0.15
Matches are distributed among these distances:
26 1 0.01
27 19 0.12
28 8 0.05
29 44 0.28
30 4 0.03
33 3 0.02
34 46 0.29
35 33 0.21
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.25
Consensus pattern (33 bp):
CCTAAATTAATTAAAAACCCTAACCTAACCTAA
Found at i:5336810 original size:56 final size:57
Alignment explanation
Indices: 5336736--5336925 Score: 229
Period size: 56 Copynumber: 3.1 Consensus size: 57
5336726 AAAACCCTAA
5336736 CCTAACCCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATT-AAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAAC
*
5336793 CCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAGCCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAAC
* *
5336850 CCTAATCTAACCCTAACCTAGCTTAATTAAAAACCCTAACCCTAACCCTAACCTAGCTTAATTAA
1 CCTAACCTAA-CCTAA---A--TTAATTAAAAACCCTAAACCTAA-CCTAA---A--TTAATTAA
5336915 AAAC
54 AAAC
5336919 CCTAACC
1 CCTAACC
5336926 ATTAAATTTT
Statistics
Matches: 115, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
56 45 0.39
57 19 0.17
58 5 0.04
61 1 0.01
63 21 0.18
64 5 0.04
67 1 0.01
69 18 0.16
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (57 bp):
CCTAACCTAACCTAAATTAATTAAAAACCCTAAACCTAACCTAAATTAATTAAAAAC
Found at i:5336821 original size:22 final size:23
Alignment explanation
Indices: 5336768--5336830 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 23
5336758 TAAAAACCCT
5336768 AAACCTAACCTAAATTAATTAAA
1 AAACCTAACCTAAATTAATTAAA
5336791 ACCCTAACCTAACCTAAATTAATTAAA
1 A----AACCTAACCTAAATTAATTAAA
*
5336818 AACCCTAAACCTA
1 AAACCT-AACCTA
5336831 GCCTAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
23 5 0.15
24 6 0.18
27 23 0.68
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (23 bp):
AAACCTAACCTAAATTAATTAAA
Found at i:5336898 original size:35 final size:35
Alignment explanation
Indices: 5336790--5336925 Score: 171
Period size: 35 Copynumber: 4.1 Consensus size: 35
5336780 AATTAATTAA
**
5336790 AACCCTAA-CCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
* *
5336824 AAACCT-AGCCTAA---A--TTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
*
5336853 AA-TCTAACCCTAACCTAGCTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
5336887 AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
5336922 AACC
1 AACC
5336926 ATTAAATTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
28 2 0.02
29 23 0.26
31 1 0.01
32 1 0.01
33 1 0.01
34 27 0.30
35 35 0.39
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (35 bp):
AACCCTAACCCTAACCTAGCTTAATTAAAAACCCT
Found at i:5337084 original size:10 final size:10
Alignment explanation
Indices: 5337069--5337093 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5337059 TTTTGGCTTA
5337069 ATAATTTTAC
1 ATAATTTTAC
5337079 ATAATTTTAC
1 ATAATTTTAC
5337089 ATAAT
1 ATAAT
5337094 GTTAGATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:5344924 original size:288 final size:288
Alignment explanation
Indices: 5344504--5345311 Score: 1388
Period size: 288 Copynumber: 2.8 Consensus size: 288
5344494 CAAACTTGGA
* * * * * *
5344504 GGGATGACACTACTAATTTGATTATGG-GAGAGGTTA-AGATATTCTAATTTTGTTAACTGGCCC
1 GGGATGAAACTATTAATTTGATTATGGTG-GAGG-TAGAGAGATTCCAGTTTTGTTAACTGACCC
* * *
5344567 AGAGAAGAAGGGATGTGACCTGAAAGCCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAG
64 AAAGAGGAAGGGATGTGACCTGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAG
*
5344632 TCCCCCAGA-ATCTTCTGGAATGGATCCATTAAGTTGATTGCTTTGAAGGAACAACGAGGAAAGA
129 TCCCCCA-ATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAACGAGGAAAGA
* * *
5344696 TTGGTTAAGTTGTTAACAGAAGATGGGATTGGACCAATAAACCAATTGTTTGAGAGATCCAAATA
193 TTGGTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAACCAATTGTTTGAGAGATCCAAATA
5344761 TTTTAAATCCTTCAACCTCTCAATTTCATGG
258 TTTTAAATCCTTCAACCTCTCAATTTCATGG
5344792 GGGATGAAACTATTAATTTGATTATGGTGGAGGTAGAGAGATTCCAGTTTTGTTAACTGACCCAA
1 GGGATGAAACTATTAATTTGATTATGGTGGAGGTAGAGAGATTCCAGTTTTGTTAACTGACCCAA
* *
5344857 AGAGGAAGGGATTTGACCCGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAGTC
66 AGAGGAAGGGATGTGACCTGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAGTC
*
5344922 CCCCAATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAACGAGGAAAGATTA
131 CCCCAATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAACGAGGAAAGATTG
5344987 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAACCAATTGTTTGAGAGATCCAAATATTT
196 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAACCAATTGTTTGAGAGATCCAAATATTT
5345052 TAAATCCTTCAACCTCTCAATTTCATGG
261 TAAATCCTTCAACCTCTCAATTTCATGG
* *
5345080 GGGATGAAACCATTAATTTGATTATGGTAGAGGTAGAGAGATTCCAGTTTTGTTAACTGACCCAA
1 GGGATGAAACTATTAATTTGATTATGGTGGAGGTAGAGAGATTCCAGTTTTGTTAACTGACCCAA
5345145 AGAGGAAGGGATGTGACCTGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAGTC
66 AGAGGAAGGGATGTGACCTGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAGTC
*
5345210 CCCCAATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAATGAGGAAAGATTG
131 CCCCAATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAACGAGGAAAGATTG
*
5345275 GTTAAGCTGCTGACAGAAGATGGGATTGGACCAACAA
196 GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAA
5345312 GTCCGTTCTG
Statistics
Matches: 494, Mismatches: 23, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
287 3 0.01
288 490 0.99
289 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (288 bp):
GGGATGAAACTATTAATTTGATTATGGTGGAGGTAGAGAGATTCCAGTTTTGTTAACTGACCCAA
AGAGGAAGGGATGTGACCTGAAAGTCTATTGGAGGATAGATCCAATTCAACCAAATTCGTTAGTC
CCCCAATATCTTCTGGAATGGATCCATTAAGTTGGTTGCTTTGAAGGAACAACGAGGAAAGATTG
GTTAAGTTGCTGACAGAAGATGGGATTGGACCAACAAACCAATTGTTTGAGAGATCCAAATATTT
TAAATCCTTCAACCTCTCAATTTCATGG
Found at i:5346569 original size:27 final size:27
Alignment explanation
Indices: 5346512--5346569 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
5346502 CCTTTCCCCA
*
5346512 TTTTATCTCACTCTATTTATTTTTTAT
1 TTTTATCTCACTCTATTTATTTTTTAG
*
5346539 TTTTAT-TCACTTTTATATTATTTTTT-G
1 TTTTATCTCAC-TCTAT-TTATTTTTTAG
5346566 TTTT
1 TTTT
5346570 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 14 0.52
28 9 0.33
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTATCTCACTCTATTTATTTTTTAG
Found at i:5346569 original size:28 final size:27
Alignment explanation
Indices: 5346512--5346570 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
5346502 CCTTTCCCCA
5346512 TTTTATCTCACTCTATTTATTTTTTAT
1 TTTTATCTCACTCTATTTATTTTTTAT
* *
5346539 TTTTAT-TCACTTTTATATTATTTTTTGT
1 TTTTATCTCAC-TCTAT-TTATTTTTTAT
5346567 TTTT
1 TTTT
5346571 TTTAATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 10 0.36
28 14 0.50
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTATCTCACTCTATTTATTTTTTAT
Found at i:5348067 original size:13 final size:13
Alignment explanation
Indices: 5348035--5348085 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
5348025 ATATGTTCTT
*
5348035 TATATTTTAAAATA
1 TATATTTT-ATATA
*
5348049 TATATTTTATATG
1 TATATTTTATATA
*
5348062 TATATTTTTTATA
1 TATATTTTATATA
5348075 TATATTTTATA
1 TATATTTTATA
5348086 ATTCACATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 24 0.75
14 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATATTTTATATA
Found at i:5348071 original size:15 final size:15
Alignment explanation
Indices: 5348047--5348085 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 15
5348037 TATTTTAAAA
5348047 TATATATTTTATATG
1 TATATATTTTATATG
5348062 TATAT-TTTT-TA--
1 TATATATTTTATATG
5348073 TATATATTTTATA
1 TATATATTTTATA
5348086 ATTCACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.23
12 4 0.18
13 4 0.18
14 4 0.18
15 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
TATATATTTTATATG
Found at i:5348105 original size:28 final size:29
Alignment explanation
Indices: 5348074--5348135 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
5348064 TATTTTTTAT
*
5348074 ATATATTTTA-TAAT-TCACATATACATAC
1 ATATATTTAATTAATATC-CATATACATAC
* *
5348102 ATAT-TTTAATTTATATCTATATACATAC
1 ATATATTTAATTAATATCCATATACATAC
5348130 ATATAT
1 ATATAT
5348136 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 4 0.14
28 21 0.75
29 3 0.11
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATTTAATTAATATCCATATACATAC
Found at i:5348135 original size:2 final size:2
Alignment explanation
Indices: 5348113--5348153 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5348103 TATTTTAATT
* * *
5348113 TA TA TC TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5348154 CTCTTTACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5348144 original size:28 final size:28
Alignment explanation
Indices: 5348092--5348153 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
5348082 TATAATTCAC
* * *
5348092 ATATACATACATATTTTAATTTATATCT
1 ATATACATACATATTATAATATATATAT
5348120 ATATACATACATATATATATATATATATAT
1 ATATACATACATAT-TATA-ATATATATAT
5348150 ATAT
1 ATAT
5348154 CTCTTTACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 3 0.10
30 12 0.41
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATACATACATATTATAATATATATAT
Found at i:5350549 original size:12 final size:12
Alignment explanation
Indices: 5350533--5350566 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5350523 TTGCAAAAGG
5350533 AGATGCAAGATC
1 AGATGCAAGATC
* *
5350545 GGATGCAAGATT
1 AGATGCAAGATC
5350557 AGATGCAAGA
1 AGATGCAAGA
5350567 AAAACTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (12 bp):
AGATGCAAGATC
Found at i:5353287 original size:19 final size:19
Alignment explanation
Indices: 5353265--5353324 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
5353255 TAAAAAATAT
5353265 AAAAAAAGAGAAAAAGAGA
1 AAAAAAAGAGAAAAAGAGA
*
5353284 AAAAAAAAAGAAAAA-AGA
1 AAAAAAAGAGAAAAAGAGA
*
5353302 AAGAAGAAGAG-AAAAGA-A
1 AA-AAAAAGAGAAAAAGAGA
5353320 AAAAA
1 AAAAA
5353325 TAAAAAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 12 0.34
19 21 0.60
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAGAAAAAGAGA
Found at i:5353291 original size:30 final size:30
Alignment explanation
Indices: 5353256--5353330 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
5353246 TAGATTCAAT
* *
5353256 AAAAAATATAAAAAA-AGAGAAAAAGAGAA
1 AAAAAAAATAAAAAAGAAAGAAAAAGAGAA
* *
5353285 AAAAAAAAGAAAAAAGAAAGAAGAAGAGAAA
1 AAAAAAAATAAAAAAGAAAGAAAAAGAG-AA
5353316 AGAAAAAAATAAAAA
1 A-AAAAAAATAAAAA
5353331 GGAGAGGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 13 0.34
30 10 0.26
31 3 0.08
32 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (30 bp):
AAAAAAAATAAAAAAGAAAGAAAAAGAGAA
Found at i:5353304 original size:24 final size:24
Alignment explanation
Indices: 5353265--5353323 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
5353255 TAAAAAATAT
5353265 AAAAAAAGAGAAAAAG--AG-A-AA
1 AAAAAAAGA-AAAAAGAAAGAAGAA
5353286 AAAAAAAGAAAAAAGAAAGAAGAA
1 AAAAAAAGAAAAAAGAAAGAAGAA
* *
5353310 GAGAAAAGAAAAAA
1 AAAAAAAGAAAAAA
5353324 ATAAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 9 0.28
22 2 0.06
23 1 0.03
24 14 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAAAGAAAGAAGAA
Found at i:5353319 original size:10 final size:9
Alignment explanation
Indices: 5353266--5353316 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
5353256 AAAAAATATA
5353266 AAAAAAGAG
1 AAAAAAGAG
*
5353275 AAAAAGAGAA
1 AAAAA-AGAG
*
5353285 AAAAAAAAG
1 AAAAAAGAG
5353294 AAAAAAGA-
1 AAAAAAGAG
5353302 AAGAAGAAGAG
1 AA-AA-AAGAG
5353313 AAAA
1 AAAA
5353317 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 2 0.06
9 16 0.47
10 14 0.41
11 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:5353323 original size:7 final size:7
Alignment explanation
Indices: 5353266--5353323 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
5353256 AAAAAATATA
5353266 AAAAAAG
1 AAAAAAG
5353273 AGAAAAAG
1 A-AAAAAG
*
5353281 AGAAAA-
1 AAAAAAG
5353287 AAAAAAG
1 AAAAAAG
5353294 AAAAAAG
1 AAAAAAG
5353301 AAAGAAGAAG
1 -AA-AA-AAG
*
5353311 AGAAAAG
1 AAAAAAG
5353318 AAAAAA
1 AAAAAA
5353324 ATAAAAAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 5 0.12
7 20 0.48
8 11 0.26
9 3 0.07
10 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5353336 original size:24 final size:24
Alignment explanation
Indices: 5353289--5353336 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5353279 AGAGAAAAAA
*
5353289 AAAAGAAAAAAGAAAGAAGAAGAG
1 AAAAGAAAAAAGAAAAAAGAAGAG
*
5353313 AAAAGAAAAAA-ATAAAAAGGAGAG
1 AAAAGAAAAAAGA-AAAAAGAAGAG
5353337 GCCAAGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAAAGAAAAAAGAAGAG
Found at i:5354772 original size:88 final size:87
Alignment explanation
Indices: 5354628--5354832 Score: 320
Period size: 88 Copynumber: 2.3 Consensus size: 87
5354618 GTTGTCATAC
* * *
5354628 CAGTCCTATCTCCCTAGGCAGTAGTGGAGTAGGTCGAAGATGGTGAATCTTATCTTCCCAAGATA
1 CAGTCCTATCT-CCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATA
* *
5354693 GTGGAGAAGTAGATTTAAGCCAT
65 ATGGAGAAGCAGATTTAAGCCAT
5354716 CAGTCCTATCTCCGTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATA
1 CAGTCCTATCTCC-TAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATA
*
5354781 ATGGAGAAGCAGATTTAAGGCAT
65 ATGGAGAAGCAGATTTAAGCCAT
*
5354804 TAGTCCTATCTCTCTAAGCAGTAGTGGAG
1 CAGTCCTATCTC-CTAAGCAGTAGTGGAG
5354833 TAGGACGAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
87 2 0.02
88 105 0.97
89 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (87 bp):
CAGTCCTATCTCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAA
TGGAGAAGCAGATTTAAGCCAT
Found at i:5354884 original size:132 final size:132
Alignment explanation
Indices: 5354724--5354963 Score: 419
Period size: 132 Copynumber: 1.8 Consensus size: 132
5354714 ATCAGTCCTA
*
5354724 TCTCCGTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAGAA
* *
5354789 GCAGATTTAAGGCATTAGTCCTATCTCTC-TAAGCAGTAGTGGAGTAGGACGAATATTTCAGATT
66 GCAGATTTAAGCCATCAGTCCTATCTC-CGTAAGCAGTAGTGGAGTAGGACGAATATTTCAGATT
5354853 CTG
130 CTG
* *
5354856 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAGAA
5354921 GCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGA
66 GCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGA
5354964 ACAGATCGAA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
131 1 0.01
132 101 0.99
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAATGGAGAA
GCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAGTAGGACGAATATTTCAGATTC
TG
Found at i:5354958 original size:88 final size:88
Alignment explanation
Indices: 5354856--5355314 Score: 349
Period size: 88 Copynumber: 5.2 Consensus size: 88
5354846 TCAGATTCTG
5354856 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
5354921 GCAGATTTAAGCCATCAGTCCTA
66 GCAGATTTAAGCCATCAGTCCTA
* ** *
5354944 TCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
** *
5355009 GCAGATTTAAGGTATTAGTCCTA
66 GCAGATTTAAGCCATCAGTCCTA
* * * * ** *
5355032 TCTCCTTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC-TATC-TCCCTAAGCA-A-TAGG
1 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGA-TGGTGAATCTTATCTTCCC-AAG-ATAGT-GG
** *** * * *
5355093 -GAAGCAGATCGAAGATGGTGAATCTTA
62 AGAAGCAGATTTAAG-CCATCAGTCCTA
* * ** * *
5355120 TTTTTCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCAT--T-AGTCCTATC-TCCCTAAGTAGT
1 -TCTCCCTAAGCAGTAGTGG-G--GCAGATCGAAG--ATGGTGAATCTTATCTTCCC-AAG-A-T
** *
5355178 AGTGGAGAAG--G-TCGAAG--ATTGCAGATTCTA
57 AGTGGAGAAGCAGATTTAAGCCA-T-CAG-TCCTA
*
5355208 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
*
5355273 GCAGATTTAAGCCATTAGTCCTA
66 GCAGATTTAAGCCATCAGTCCTA
5355296 TCTCCCTAAGCAGTAGTGG
1 TCTCCCTAAGCAGTAGTGG
5355315 AACAGGTTGA
Statistics
Matches: 292, Mismatches: 48, Indels: 62
0.73 0.12 0.15
Matches are distributed among these distances:
85 2 0.01
86 18 0.06
87 37 0.13
88 186 0.64
89 31 0.11
90 11 0.04
91 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (88 bp):
TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
GCAGATTTAAGCCATCAGTCCTA
Found at i:5354962 original size:46 final size:43
Alignment explanation
Indices: 5354691--5355052 Score: 110
Period size: 44 Copynumber: 8.2 Consensus size: 43
5354681 CTTCCCAAGA
*
5354691 TAGTGGAGAAGTAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAG
1 TAGTGGAGAAGCAGATTTAAG--ATCAGTCCTATCTCC-TAAGCAG
** * * * *
5354737 TAGT-G-G-AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAG-A-
1 TAGTGGAGAAGCAGATTTAAGA---TCAGTCCTATC-TCCTAAGCAG
* *
5354779 TAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCTCTCTAAGCAG
1 TAGTGGAGAAGCAGATTTAA-G-ATCAGTCCTATCTC-CTAAGCAG
* * * ** * *
5354825 TAGTGGAGTAGGACGA-AT-ATTTCAGATTCTGTCTCCCTAAGCAG
1 TAGTGGAGAAGCA-GATTTAAGATCAG-TCCTATCT-CCTAAGCAG
** * * * *
5354869 TAGTGG-G--GCAGATCGAAGATGGTGAATCTTATCTTCCCAAG-A-
1 TAGTGGAGAAGCAGATTTAAGA---TCAGTCCTATC-TCCTAAGCAG
5354911 TAGTGGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAG
1 TAGTGGAGAAGCAGATTTAAG--ATCAGTCCTATCTCC-TAAGCAG
** * * *
5354957 TAGT-G-GAA-CAGATCGAAGATGGAGAATCTTATCTTCCCAAG-A-
1 TAGTGGAGAAGCAGATTTAAGAT-CAG--TCCTATC-TCCTAAGCAG
*
5354999 TAGTGGAGAAGCAGATTTAAGGTATTAGTCCTATCTCCTTAAGCAG
1 TAGTGGAGAAGCAGATTTAA-G-ATCAGTCCTATCTCC-TAAGCAG
5355045 TAGTGGAG
1 TAGTGGAG
5355053 TAGGTCGAAG
Statistics
Matches: 225, Mismatches: 50, Indels: 82
0.63 0.14 0.23
Matches are distributed among these distances:
40 2 0.01
41 5 0.02
42 16 0.07
43 35 0.16
44 89 0.40
45 41 0.18
46 31 0.14
47 6 0.03
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TAGTGGAGAAGCAGATTTAAGATCAGTCCTATCTCCTAAGCAG
Found at i:5355018 original size:220 final size:220
Alignment explanation
Indices: 5354633--5355196 Score: 900
Period size: 220 Copynumber: 2.6 Consensus size: 220
5354623 CATACCAGTC
* * *
5354633 CTATCTCCCTAGGCAGTAGTGGAGTAGGTCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGA
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGA
* * *
5354698 GAAGTAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAA
66 GAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAA
5354763 TCTTATCTTCCCAAGATAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCT-CTCTAAGCAGTA
131 TCTTATCTTCCCAAGATAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCTCCT-TAAGCAGTA
* *
5354827 GTGGAGTAGGACGAATATTTCAGATT
195 GTGGAGTAGGACGAAGATTGCAGATT
* *
5354853 CTGTCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGA
1 CTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGA
5354918 GAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAA
66 GAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAA
* *
5354983 TCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGGTATTAGTCCTATCTCCTTAAGCAGTAG
131 TCTTATCTTCCCAAGATAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCTCCTTAAGCAGTAG
*
5355048 TGGAGTAGGTCGAAGATTGCAGATT
196 TGGAGTAGGACGAAGATTGCAGATT
* * *
5355073 CTATCTCCCTAAGCAATAG-GGAAGCAGATCGAAGATGGTGAATCTTATTTTTCCAAGATAGTGG
1 CTATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGG
* * * *
5355137 AGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGA-AGGTCGAAGAT
65 AGAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGA-ACAGATCGAAGAT
5355197 TGCAGATTCT
Statistics
Matches: 319, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
219 2 0.01
220 314 0.98
221 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (220 bp):
CTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGA
GAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAA
TCTTATCTTCCCAAGATAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCTCCTTAAGCAGTAG
TGGAGTAGGACGAAGATTGCAGATT
Found at i:5355077 original size:44 final size:44
Alignment explanation
Indices: 5354809--5355636 Score: 214
Period size: 44 Copynumber: 18.8 Consensus size: 44
5354799 GGCATTAGTC
* * * * *
5354809 CTATCTCTCTAAGCAGTAGTGGAGTAGGACGAATATTTCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* * * * ** *
5354853 CTGTCTCCCTAAGCAGTAGTGGGGCAGATCGAAGA-TGGTGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
** *
5354896 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCA-T-CAG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TCGAAG--ATTGCAGATT
* * * *
5354941 CTATCTCCGTAAGCAGTAGTGGA-ACAGATCGAAGA-TGGAGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGA-AGGTCGAAGATTGCAGATT
** *
5354984 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGGTATT--AG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TCGAA-G-ATTGCAGATT
* *
5355029 CTATCTCCTTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* * * ** *
5355073 CTATCTCCCTAAGCAATAG-GGAAGCAGATCGAAGA-TGGTGAAT
1 CTATCTCCCTAAGCAGTAGTGG-AGAAGGTCGAAGATTGCAGATT
* * ** *
5355116 CTTATTTTTCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TA-TCTCCCTAAGCAGTAGTGGAGAAG--G-TCGAAG--ATTGCAGATT
*
5355161 CTATCTCCCTAAGTAGTAGTGGAGAAGGTCGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* * * ** *
5355205 CTATCTCCCTAAGCAGTAGTGGGGCAGATCGAAGA-TGGTGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* ** *
5355248 CTTATCTTCCC-AA-TA-TAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TCGAAG--ATTGCAGATT
*
5355293 CTATCTCCCTAAGCAGTAGTGGA-ACAGGTTGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGA-AGGTCGAAGATTGCAGATT
* * * * * ** *
5355337 CTGTCTCCCTAAGTAGTAGTAGAGCAGATCGAAGA-TGGTGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
** *
5355380 CTTATCTTCCC-AAG-A-TAGTGGAGAAGTAGATTTAAGTCATT--AG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TCGAAG--ATTGCAGATT
* *
5355425 CTATCTCCCTAAGCAGCAGTGGAGTAGGTCGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* * * * * ** *
5355469 CTGTCTCCCTAAGTAGTAGTGGGGCAGATCGAAGA-TGGTGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* * ** **** **
5355512 CTTATCTTTCC-AAG-A-TAGTGGTGAAGCAGATTTAAGCCACCAG-CC
1 C-TATC-TCCCTAAGCAGTAGTGGAGAAG--G-TCGAAGATTGCAGATT
* *
5355557 CTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
* *
5355601 CTGTCTCCCTAAGCAGTAGTGGA-ACAGATCGAAGAT
1 CTATCTCCCTAAGCAGTAGTGGAGA-AGGTCGAAGAT
5355637 GGTGAATCTT
Statistics
Matches: 559, Mismatches: 140, Indels: 170
0.64 0.16 0.20
Matches are distributed among these distances:
41 14 0.03
42 55 0.10
43 97 0.17
44 259 0.46
45 59 0.11
46 65 0.12
47 6 0.01
48 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
CTATCTCCCTAAGCAGTAGTGGAGAAGGTCGAAGATTGCAGATT
Found at i:5355299 original size:220 final size:219
Alignment explanation
Indices: 5354631--5355316 Score: 734
Period size: 220 Copynumber: 3.1 Consensus size: 219
5354621 GTCATACCAG
* * *
5354631 TCCTATCTCCCTAGGCAGTAGTGG-AGTAGGTCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
1 TCCTATCTCCCTAAGCAGTAGTGGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
* * * **
5354695 GGAGAAGTAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAGCAGATCGAAGATGGT
66 GGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGATGCA
* ** ** * *
5354760 GAATCTTATCTTCCCAAGATAATGGAGAAGCAGATTTAAGGCATTAGTCCTATCT-CTCTAAGCA
131 GAATCTTATCTTCCCAAGATAGTGGAG-AGCAGATCGAAGATATGAATCCTATCTCCTC-AAGCA
* * *
5354824 GTAGTGGAGTAGGACGAATATTTCAGA
194 GTAGTGGAGAAGGTCGAAGA-TTCAGA
* * *
5354851 TTCTGTCTCCCTAAGCAGTAGTGG-GGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
1 TCCTATCTCCCTAAGCAGTAGTGGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
* *
5354915 GGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGA
66 GGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGATGCA
** * * * *
5354980 GAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGGTATTAGTCCTATCTCCTTAAGCAG
131 GAATCTTATCTTCCCAAGATAGTGGAG-AGCAGATCGAAGATATGAATCCTATCTCCTCAAGCAG
*
5355045 TAGTGGAGTAGGTCGAAGATTGCAGA
195 TAGTGGAGAAGGTCGAAGATT-CAGA
* * * *
5355071 TTCTATCTCCCTAAGCAATAG-GGAAGCAGATCGAAGATGGTGAATCTTATTTTTCCAAGATAGT
1 TCCTATCTCCCTAAGCAGTAGTGGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
* * *
5355135 GGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGA-AGGTCGAAGATTG
66 GGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCCTAAGCAGTAGTGGA-ACAGATCGAAGA-TG
* * *
5355199 CAGATTC-TATC-TCCCTAAGCAGTAGTGG-G-GCAGATCGAAGATGGTGAATCTTATCTTCC-C
129 CAGAATCTTATCTTCCC-AAG-A-TAGTGGAGAGCAGATCGAAGAT-ATGAATCCTATC-TCCTC
* **
5355259 AA-TA-TAGTGGAGAAGCAGATTTAAGCCATT-AG-
189 AAGCAGTAGTGGAGAAG--G-TCGAAG--ATTCAGA
5355291 TCCTATCTCCCTAAGCAGTAGTGGAA
1 TCCTATCTCCCTAAGCAGTAGTGGAA
5355317 CAGGTTGAAG
Statistics
Matches: 411, Mismatches: 39, Indels: 31
0.85 0.08 0.06
Matches are distributed among these distances:
218 10 0.02
219 19 0.05
220 348 0.85
221 25 0.06
222 6 0.01
223 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (219 bp):
TCCTATCTCCCTAAGCAGTAGTGGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGT
GGAGAAGCAGATTTAAGCCATCAGTCCTATCTCCCTAAGCAGTAGTGGAACAGATCGAAGATGCA
GAATCTTATCTTCCCAAGATAGTGGAGAGCAGATCGAAGATATGAATCCTATCTCCTCAAGCAGT
AGTGGAGAAGGTCGAAGATTCAGA
Found at i:5355815 original size:132 final size:132
Alignment explanation
Indices: 5354944--5355777 Score: 1213
Period size: 132 Copynumber: 6.3 Consensus size: 132
5354934 ATCAGTCCTA
* * * *
5354944 TCTCCGTAAGCAGTAGTGGAACAGATCGAAGATGGAGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
** * *
5355009 GCAGATTTAAGGTATTAGTCCTATCTCCTTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
66 GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
*
5355074 TA
131 TG
* * * *
5355076 TCTCCCTAAGCAATAG-GGAAGCAGATCGAAGATGGTGAATCTTATTTTTCCAAGATAGTGGAGA
1 TCTCCCTAAGTAGTAGTGG-AGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGA
* * *
5355140 AGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGTAGTAGTGGAGAAGGTCGAAGATTGCAGATT
65 AGCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
*
5355205 CTA
130 CTG
* * *
5355208 TCTCCCTAAGCAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAA
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* ** *
5355273 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAACAGGTTGAAGATTGCAGATTC
66 GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
5355338 TG
131 TG
*
5355340 TCTCCCTAAGTAGTAGTAGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * * *
5355405 GTAGATTTAAGTCATTAGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTCGAAGATTGCAGATTC
66 GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
5355470 TG
131 TG
* * *
5355472 TCTCCCTAAGTAGTAGTGGGGCAGATCGAAGATGGTGAATCTTATCTTTCCAAGATAGTGGTGAA
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * *
5355537 GCAGATTTAAGCCACCAGCCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTC
66 GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
5355602 TG
131 TG
* *
5355604 TCTCCCTAAGCAGTAGTGGAACAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * * * * * *
5355669 GCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAGATCGTAGA-TC
66 GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
*
5355733 TTA
131 -TG
* *
5355736 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGTAAATCT
1 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCT
5355778 CGTTTCCCCG
Statistics
Matches: 639, Mismatches: 60, Indels: 6
0.91 0.09 0.01
Matches are distributed among these distances:
131 4 0.01
132 633 0.99
133 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
GCAGATTTAAGCCACTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
TG
Found at i:5355857 original size:50 final size:49
Alignment explanation
Indices: 5355803--5356134 Score: 247
Period size: 50 Copynumber: 6.7 Consensus size: 49
5355793 GTAATTAAAA
* * * *
5355803 AGATTGAAGCCACAACGACGAATCTTACTTCCCTTGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC-AGCAGTGCAGTGGAAC
* * * * * * *
5355853 AGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGCAAT-TAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCAG-CAGTGCAGTGGAAC
* * * *
5355902 AGATTGAGGCCACAACGGTGAATCTTACTTCCCTAGCAGTCCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC-AGCAGTGCAGTGGAAC
* * * ** *
5355952 AGATTGAAGCTACGACGGTGAATCTTACTTCTCC-GACATTGCAGTTAAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTC-CCAG-CAGTGCAGTGGAAC
* * *
5356002 AGATTGAAGCTACAACAGCAAATCTTACTTCCCGAGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC-AGCAGTGCAGTGGAAC
* * * ** * * ** *
5356052 AGATTGAAGTTATAACGGCAAATCTTGTTTCCTC-GACATTGCAATTAAAT
1 AGATTGAAGCTACAACGGCGAATCTTACTTCC-CAG-CAGTGCAGTGGAAC
**
5356102 AGATTGAAGCTACAACAACGAATCTTACTTCCC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC
5356135 TAGTGAATAG
Statistics
Matches: 217, Mismatches: 56, Indels: 19
0.74 0.19 0.07
Matches are distributed among these distances:
49 42 0.19
50 171 0.79
51 4 0.02
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (49 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCAGCAGTGCAGTGGAAC
Found at i:5355899 original size:100 final size:100
Alignment explanation
Indices: 5355781--5356137 Score: 475
Period size: 100 Copynumber: 3.6 Consensus size: 100
5355771 TAAATCTCGT
* *
5355781 TTCCCCGACATTGTAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTTGCGGTGCA
1 TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCGGTGCA
*
5355846 GTGGAACAGATTGAAGCTACAATGGCGAATCTTGC
66 GTGGAACAGATTGAAGCTACAACGGCGAATCTTGC
* ** * *
5355881 TTCCCCGACATTGCAATT-AAAAGATTGAGGCCACAACGGTGAATCTTACTTCCCTAGCAGTCCA
1 TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCGGTGCA
* * *
5355945 GTGGAACAGATTGAAGCTACGACGGTGAATCTTAC
66 GTGGAACAGATTGAAGCTACAACGGCGAATCTTGC
* * * * *
5355980 TTCTCCGACATTGCAGTTAAAAAGATTGAAGCTACAAC-AGCAAATCTTACTTCCCGAGCGGTGC
1 TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGA-CGAATCTTACTTCCCTAGCGGTGC
* * * *
5356044 AGTGGAACAGATTGAAGTTATAACGGCAAATCTTGT
65 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTGC
* * * *
5356080 TTCCTCGACATTGCAATTAAATAGATTGAAGCTACAACAACGAATCTTACTTCCCTAG
1 TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAG
5356138 TGAATAGATT
Statistics
Matches: 220, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
99 87 0.40
100 132 0.60
101 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (100 bp):
TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCGGTGCA
GTGGAACAGATTGAAGCTACAACGGCGAATCTTGC
Found at i:5357971 original size:13 final size:13
Alignment explanation
Indices: 5357939--5357991 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
5357929 ATATATTCTT
*
5357939 TATATTTTAAAATA
1 TATATTTT-ATATA
5357953 TATATTTTATATGTA
1 TATATTTTATA--TA
*
5357968 TATTTTTTATATA
1 TATATTTTATATA
5357981 TATATTTTATA
1 TATATTTTATA
5357992 ATTCACATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 14 0.41
14 8 0.24
15 12 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATATTTTATATA
Found at i:5357975 original size:15 final size:15
Alignment explanation
Indices: 5357950--5357988 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5357940 ATATTTTAAA
*
5357950 ATATATATTTTATAT
1 ATATATTTTTTATAT
*
5357965 GTATATTTTTTATAT
1 ATATATTTTTTATAT
5357980 ATATATTTT
1 ATATATTTT
5357989 ATAATTCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
ATATATTTTTTATAT
Found at i:5363136 original size:12 final size:12
Alignment explanation
Indices: 5363119--5363143 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5363109 AAGTATATCA
5363119 GCTTTAGTTTTT
1 GCTTTAGTTTTT
5363131 GCTTTAGTTTTT
1 GCTTTAGTTTTT
5363143 G
1 G
5363144 AGGTATAGAG
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:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (12 bp):
GCTTTAGTTTTT
Found at i:5364172 original size:22 final size:24
Alignment explanation
Indices: 5364111--5364179 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 24
5364101 CTCGACTTTC
5364111 ATTTTCATATGCTTATCAAATATA
1 ATTTTCATATGCTTATCAAATATA
* *
5364135 AGTATT-ATAT--TAATCAAAT-T-
1 A-TTTTCATATGCTTATCAAATATA
5364155 ATTTTCATATGCTTATCAAATATA
1 ATTTTCATATGCTTATCAAATATA
5364179 A
1 A
5364180 GTATGCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 5 0.14
21 1 0.03
22 16 0.46
23 1 0.03
24 6 0.17
25 3 0.09
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTTCATATGCTTATCAAATATA
Found at i:5364538 original size:21 final size:21
Alignment explanation
Indices: 5364514--5364553 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5364504 CGTGTCAATA
5364514 TTTA-ATTACAAATATTTAATT
1 TTTATATT-CAAATATTTAATT
*
5364535 TTTATATTTAAATATTTAA
1 TTTATATTCAAATATTTAA
5364554 ATATAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATTCAAATATTTAATT
Found at i:5364833 original size:13 final size:13
Alignment explanation
Indices: 5364815--5364875 Score: 104
Period size: 13 Copynumber: 4.7 Consensus size: 13
5364805 CTCAAATTTT
5364815 TCAAAAGCACTTC
1 TCAAAAGCACTTC
5364828 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
5364841 TGAAAAGTACTTC
1 TCAAAAGCACTTC
5364854 TCAAAAGCACTTC
1 TCAAAAGCACTTC
5364867 TCAAAAGCA
1 TCAAAAGCA
5364876 ATGAAGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:5367352 original size:40 final size:39
Alignment explanation
Indices: 5367260--5367395 Score: 114
Period size: 39 Copynumber: 3.5 Consensus size: 39
5367250 GGCGTTTGGA
* * * * *
5367260 TAAAAAACACCACTAAAAATCAATCATTAGCGGCGC-TT-
1 TAAAAAACGCCGCTAAAAAT-GAGCACTAGCGGCGCTTTC
* *
5367298 TAAAAAACGCCGCTAAAGATCGAGTACTAGCGGCGCTTTC
1 TAAAAAACGCCGCTAAAAAT-GAGCACTAGCGGCGCTTTC
* * * *
5367338 TGAAAAATGCCGCTAAAAATGAGCATTAGCGGCGTTTTC
1 TAAAAAACGCCGCTAAAAATGAGCACTAGCGGCGCTTTC
* * *
5367377 TAATAAGCGCCGCAAAAAA
1 TAAAAAACGCCGCTAAAAA
5367396 CCTAAGCCCA
Statistics
Matches: 78, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
38 29 0.37
39 32 0.41
40 17 0.22
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (39 bp):
TAAAAAACGCCGCTAAAAATGAGCACTAGCGGCGCTTTC
Found at i:5367389 original size:39 final size:38
Alignment explanation
Indices: 5367262--5367395 Score: 110
Period size: 38 Copynumber: 3.4 Consensus size: 38
5367252 CGTTTGGATA
* * * * *
5367262 AAAAACACCACTAAAAATCAATCATTAGCGGCGCTTT-A
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTCT
* * *
5367300 AAAAACGCCGCTAAAGATCGAGTACTAGCGGCGCTTTCT
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTCT
*
5367339 GAAAAATGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTCT
1 -AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTCT
* *
5367378 AATAAGCGCCGCAAAAAA
1 AA-AAACGCCGCTAAAAA
5367396 CCTAAGCCCA
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
38 32 0.42
39 29 0.38
40 16 0.21
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTCT
Found at i:5367495 original size:41 final size:41
Alignment explanation
Indices: 5367433--5367715 Score: 365
Period size: 41 Copynumber: 6.9 Consensus size: 41
5367423 GTTTTCAAGG
* * * *
5367433 CTTTAGTGGCGTTTTTTAAAAAGTGCCGCTAATTCTCGGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGT
*
5367474 CTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCAGGG-
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGGT
* *
5367515 CTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGT
* * *
5367556 CTATAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGT
** * *
5367597 CTTTAGAAGTGTTTTT-AGAAAAGCGCCGCTAATGCTAGGGT
1 CTTTAGCGGCGTTTTTGA-AAAAGCGCCGCTAATGCTCGGGT
*
5367638 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGGG-
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-GGGT
* *
5367679 CTTTAGCGGCGTTTTTGAAGAAGCGCTGCTAATGCTC
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
5367716 TATTTTAGCT
Statistics
Matches: 213, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
40 3 0.01
41 204 0.96
42 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGT
Found at i:5371250 original size:24 final size:24
Alignment explanation
Indices: 5371223--5371280 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
5371213 TATAATGTAA
*
5371223 GACTAACATGCTTGTATAGAATAT
1 GACTAACATGCTTGTATAGAATAC
*
5371247 GACTAACATACTTGTATAGAATAC
1 GACTAACATGCTTGTATAGAATAC
5371271 GACTAACATG
1 GACTAACATG
5371281 GTAAAACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
GACTAACATGCTTGTATAGAATAC
Found at i:5372264 original size:47 final size:47
Alignment explanation
Indices: 5372195--5372287 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
5372185 TCTAGTATGA
5372195 TTGTTCACGACCAGCTTGTTGTGAAAGCATTTATTTGCTATATCCCG
1 TTGTTCACGACCAGCTTGTTGTGAAAGCATTTATTTGCTATATCCCG
5372242 TTGTTCACGACCAGCTTGTTGTGAAAGCATTTATTTGCTATATCCC
1 TTGTTCACGACCAGCTTGTTGTGAAAGCATTTATTTGCTATATCCC
5372288 CGTTCATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (47 bp):
TTGTTCACGACCAGCTTGTTGTGAAAGCATTTATTTGCTATATCCCG
Found at i:5372924 original size:34 final size:35
Alignment explanation
Indices: 5372859--5372924 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5372849 TAATTGTGTT
*
5372859 ATTAATTTATTATTTTAAATTTTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTTTAAAGTTAAATTC
*
5372894 ATTAATTT-TTATATTT-AGTTTTAAAGTTAAA
1 ATTAATTTATTAT-TTTAAATTTTAAAGTTAAA
5372925 ATTTTCGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTTTAAAGTTAAATTC
Found at i:5372927 original size:35 final size:35
Alignment explanation
Indices: 5372859--5372927 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
5372849 TAATTGTGTT
*
5372859 ATTAATTTATTATTTTAAATTTTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTTTAAATTAAAATTC
*
5372894 ATTAATTT-TTATATTT-AGTTTTAAAGTTAAAATT
1 ATTAATTTATTAT-TTTAAATTTTAAA-TTAAAATT
5372928 TTCGTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTTTAAATTAAAATTC
Found at i:5373132 original size:43 final size:43
Alignment explanation
Indices: 5373031--5373386 Score: 444
Period size: 43 Copynumber: 8.3 Consensus size: 43
5373021 AAGATATGTT
* * *
5373031 TTTAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTC-TGATA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * * *
5373073 TATAGCGGCATTTGTGGGAAAAGTGCCGCTAACGGTCGTGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
5373116 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTTATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
5373159 TTTAGTGGTGTTTGTGGGAAAAGGGCTGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
5373202 TTTAGCGGTGTTTCTGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
5373245 TTTAGCGGCATTTGTGGTAAAAGTGCTGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
5373288 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
5373331 TTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
5373374 TTTAGCGACGTTT
1 TTTAGCGGCGTTT
5373387 TAGAAAAAAA
Statistics
Matches: 271, Mismatches: 42, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
42 32 0.12
43 239 0.88
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:5373507 original size:22 final size:22
Alignment explanation
Indices: 5373479--5373521 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5373469 TAGCGGCGCT
*
5373479 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
5373501 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
5373522 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:5381612 original size:9 final size:9
Alignment explanation
Indices: 5381598--5381628 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5381588 GTTAAACGAA
5381598 TCGAGTTAT
1 TCGAGTTAT
*
5381607 TCGAGTTAA
1 TCGAGTTAT
5381616 TCGAGTTAT
1 TCGAGTTAT
5381625 TCGA
1 TCGA
5381629 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:5381699 original size:9 final size:9
Alignment explanation
Indices: 5381682--5381718 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5381672 TGAGTTTTCG
5381682 AATTCGAAT
1 AATTCGAAT
*
5381691 AACTCGAAT
1 AATTCGAAT
5381700 AATTCGAAT
1 AATTCGAAT
5381709 AATTCGAAT
1 AATTCGAAT
5381718 A
1 A
5381719 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5381801 original size:30 final size:31
Alignment explanation
Indices: 5381767--5381827 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
5381757 AAACTTTATT
* *
5381767 ACTTTTCCCTCAAAACTTTTACT-CCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
*
5381797 ACTTTCCCCCCAAAACTTTTGCTCCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
5381828 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.18, C:0.44, G:0.02, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
Found at i:5384362 original size:72 final size:72
Alignment explanation
Indices: 5384242--5384756 Score: 405
Period size: 72 Copynumber: 7.2 Consensus size: 72
5384232 TTACTGGTAT
* * * *
5384242 TATCCCTTCTA-CCTTGGGCAAATTAACTAACTTGGAATTGTTGAACCTATTTGAAAACCAATTT
1 TATCCCTTCTATCC-TGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAAAACCAAATT
** *
5384306 ATTGGTCC
65 ACCGGTCA
* * * * * * * * *
5384314 TATTCCTTTTAACCTGGGCAACTTAATCAACTTGAAACTGTTGGACCTATCTGATAATCAAATTA
1 TATCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAAAACCAAATTA
5384379 -CGAGTCA
66 CCG-GTCA
* ** * **
5384386 TGTCCCTTCTATCCTGGTTAACTTAACCAACTTGAAATTGCTGAACCTATGTAAAAAACCAAATT
1 TATCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTAT-TTGAAAACCAAATT
*
5384451 ACGGGTCA
65 ACCGGTCA
* * * *
5384459 TATCCCTTCTATCATAGGAAACTTAACCAACTTGAACTTGTTGAACCTATTTGAAAACCAAATTA
1 TATCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAAAACCAAATTA
* *
5384524 CCAGTCC
66 CCGGTCA
* * * * * * * * *
5384531 TATCCCTTCTACCCTGGGCAGCTTAATCAACTTGAATTTGTTGGACCAATCT-AATAATCAAATA
1 TATCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAA-AACCAAATT
**
5384595 ACAAGTCA
65 ACCGGTCA
* * * * * *
5384603 TGT-CTTTCT-TCCCTGGGCAGCTTAACCAATTTGAAATTGTTGGACCTATCTT-AAAATCAAAT
1 TATCCCTTCTAT-CCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTAT-TTGAAAACCAAAT
* *
5384665 AACGGGTCA
64 TACCGGTCA
** * * **
5384674 TATCCCTTCTA-CCATGGGCAACTTAACCAGTTTGAAATTGTTAAACTTATCCGAAAACCAAATT
1 TATCCCTTCTATCC-TGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAAAACCAAATT
* *
5384738 ACTGGTCC
65 ACCGGTCA
*
5384746 TACCCCTTCTA
1 TATCCCTTCTA
5384757 CCTTAGGTAA
Statistics
Matches: 352, Mismatches: 80, Indels: 22
0.78 0.18 0.05
Matches are distributed among these distances:
71 61 0.17
72 231 0.66
73 59 0.17
74 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (72 bp):
TATCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGTTGAACCTATTTGAAAACCAAATTA
CCGGTCA
Found at i:5384791 original size:215 final size:217
Alignment explanation
Indices: 5384242--5384791 Score: 516
Period size: 217 Copynumber: 2.5 Consensus size: 217
5384232 TTACTGGTAT
* * * * * ** *
5384242 TATCCCTTCTACCTTGGGCAAA-TTAACTAACTTGGAATTGTTGAACCTATTTGAAAACCAATTT
1 TATCCCTTCTACCATAGG-AAACTTAACCAACTTGAAATTGTTAAACCTATCCGAAAACCAAATT
*** ** * * * * * ** * *
5384306 ATTGGTCCTATTCCTTTTAACCTGGGCAACTTAATCAACTTGAAACTGTTGGACCTATCTGATAA
65 ACCAGTCCTACCCCTTCTACCCTAGGCAAATTAAGCAACTTGAAAGAGTTGGACCAATCTAATAA
* * **
5384371 TCAAATTACGAGTCATGTCCCTTCTATCCTGGTTAACTTAACCAACTTGAAATTGCTGAACCTAT
130 TCAAATAACAAGTCATGTCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGCTGAACCTAT
* *
5384436 GTAAAAAACCAAATTACGGGTCA
195 CTAAAAAACCAAATAACGGGTCA
* * * **
5384459 TATCCCTTCTATCATAGGAAACTTAACCAACTTGAACTTGTTGAACCTATTTGAAAACCAAATTA
1 TATCCCTTCTACCATAGGAAACTTAACCAACTTGAAATTGTTAAACCTATCCGAAAACCAAATTA
* * ** * ***
5384524 CCAGTCCTATCCCTTCTACCCTGGGCAGCTTAATCAACTTGAATTTGTTGGACCAATCTAATAAT
66 CCAGTCCTACCCCTTCTACCCTAGGCAAATTAAGCAACTTGAAAGAGTTGGACCAATCTAATAAT
* * * * *
5384589 CAAATAACAAGTCATGT-CTTTCT-TCCCTGGGCAGCTTAACCAATTTGAAATTGTTGGACCTAT
131 CAAATAACAAGTCATGTCCCTTCTAT-CCTGGGCAACTTAACCAACTTGAAATTGCTGAACCTAT
* *
5384652 CT-TAAAATCAAATAACGGGTCA
195 CTAAAAAACCAAATAACGGGTCA
* * ** *
5384674 TATCCCTTCTACCATGGGCAACTTAACCAGTTTGAAATTGTTAAACTTATCCGAAAACCAAATTA
1 TATCCCTTCTACCATAGGAAACTTAACCAACTTGAAATTGTTAAACCTATCCGAAAACCAAATTA
** * * *
5384739 CTGGTCCTACCCCTTCTACCTTAGGTAAATTAAGCAA-TTTACAAGAGTTGGAC
66 CCAGTCCTACCCCTTCTACCCTAGGCAAATTAAGCAACTTGA-AAGAGTTGGAC
5384792 TTATCCTTTA
Statistics
Matches: 276, Mismatches: 54, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
214 3 0.01
215 109 0.39
216 41 0.15
217 123 0.45
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (217 bp):
TATCCCTTCTACCATAGGAAACTTAACCAACTTGAAATTGTTAAACCTATCCGAAAACCAAATTA
CCAGTCCTACCCCTTCTACCCTAGGCAAATTAAGCAACTTGAAAGAGTTGGACCAATCTAATAAT
CAAATAACAAGTCATGTCCCTTCTATCCTGGGCAACTTAACCAACTTGAAATTGCTGAACCTATC
TAAAAAACCAAATAACGGGTCA
Found at i:5389807 original size:26 final size:26
Alignment explanation
Indices: 5389771--5389822 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5389761 AGGAAGGAAA
5389771 GAAAGAATATTAGAATTTGTTAGTGT
1 GAAAGAATATTAGAATTTGTTAGTGT
5389797 GAAAGAATATTAGAATTTGTTAGTGT
1 GAAAGAATATTAGAATTTGTTAGTGT
5389823 AATTTCCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (26 bp):
GAAAGAATATTAGAATTTGTTAGTGT
Found at i:5398940 original size:50 final size:50
Alignment explanation
Indices: 5398825--5399123 Score: 391
Period size: 50 Copynumber: 5.8 Consensus size: 50
5398815 GATAATAACA
* ** *
5398825 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
5398876 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5398926 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5398976 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
5399026 TGCCCATGCCATGTCTCAGACATGGTCTTACAGGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
5399081 ATGCCAATGCCATGTCACAAACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5399124 TTACCCAAAT
Statistics
Matches: 218, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
50 142 0.65
51 33 0.15
53 5 0.02
55 1 0.00
56 37 0.17
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5404104 original size:31 final size:28
Alignment explanation
Indices: 5404062--5404118 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 28
5404052 TTGATTTAAT
5404062 GTGTAATTATATGTATAAACTGTAATTTA
1 GTGTAATTATATGTA-AAACTGTAATTTA
*
5404091 GTGTAATTATATATGTAAAACTTTAATT
1 GTGTAA-T-TATATGTAAAACTGTAATT
5404119 GTAATTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (28 bp):
GTGTAATTATATGTAAAACTGTAATTTA
Found at i:5404109 original size:29 final size:30
Alignment explanation
Indices: 5404062--5404118 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5404052 TTGATTTAAT
*
5404062 GTGTAATTATATGTAT-AAACTGTAATTTA
1 GTGTAATTATATATATAAAACTGTAATTTA
* *
5404091 GTGTAATTATATATGTAAAACTTTAATT
1 GTGTAATTATATATATAAAACTGTAATT
5404119 GTAATTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (30 bp):
GTGTAATTATATATATAAAACTGTAATTTA
Found at i:5405085 original size:12 final size:12
Alignment explanation
Indices: 5405066--5405098 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5405056 TTAAACGTTC
5405066 TTTTCTTTT-CT
1 TTTTCTTTTACT
5405077 TTTTACTTTTACT
1 TTTT-CTTTTACT
5405090 TTTTCTTTT
1 TTTTCTTTT
5405099 TCTTGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 10 0.50
13 6 0.30
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTACT
Found at i:5410928 original size:26 final size:26
Alignment explanation
Indices: 5410899--5410949 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5410889 GATTTTGCAT
5410899 TTTATGGT-TAAATTATGATTATATGA
1 TTTATGGTATAAATTATGA-TATATGA
**
5410925 TTTATTTTATAAATTATGATATATG
1 TTTATGGTATAAATTATGATATATG
5410950 TCAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (26 bp):
TTTATGGTATAAATTATGATATATGA
Found at i:5413680 original size:15 final size:15
Alignment explanation
Indices: 5413660--5413693 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5413650 ATACAAGGAT
5413660 ATATAAA-TATATAAG
1 ATATAAATTATAT-AG
5413675 ATATAAATTATATAG
1 ATATAAATTATATAG
5413690 ATAT
1 ATAT
5413694 GGAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
ATATAAATTATATAG
Found at i:5413889 original size:15 final size:16
Alignment explanation
Indices: 5413852--5413890 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5413842 ATAATTATTC
*
5413852 TAAATTTATTAGTATA
1 TAAATTTAGTAGTATA
*
5413868 AAAATTTAGTAGTAT-
1 TAAATTTAGTAGTATA
5413883 TAAATTTA
1 TAAATTTA
5413891 TAAGTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAATTTAGTAGTATA
Found at i:5413959 original size:61 final size:61
Alignment explanation
Indices: 5413849--5413964 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 61
5413839 NAAATAATTA
* *
5413849 TTCTAAATTTATTAGTATAAAAATTTAGTAGTATTAAATTTATAAGTTTTCTAAAAAAGTG
1 TTCTAAATTTATTAGTATAAAAATTTAGTAGTATCAAATTTACAAGTTTTCTAAAAAAGTG
* * * * *
5413910 TTCTAGATTTATTATTA-ATAAAATTTA-TAAGTATCAATTTTACACGTTTTGTAAA
1 TTCTAAATTTATTAGTATA-AAAATTTAGT-AGTATCAAATTTACAAGTTTTCTAAA
5413965 TAATTATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 2 0.04
61 44 0.96
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TTCTAAATTTATTAGTATAAAAATTTAGTAGTATCAAATTTACAAGTTTTCTAAAAAAGTG
Found at i:5414205 original size:8 final size:7
Alignment explanation
Indices: 5414192--5414237 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
5414182 TAACGTATAT
5414192 ATAATAAC
1 ATAAT-AC
5414200 ATAATA-
1 ATAATAC
*
5414206 A-ATTAC
1 ATAATAC
5414212 ATAATAC
1 ATAATAC
5414219 ATAATAAC
1 ATAAT-AC
5414227 ATAATAC
1 ATAATAC
5414234 ATAA
1 ATAA
5414238 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:5414215 original size:52 final size:51
Alignment explanation
Indices: 5414156--5414333 Score: 158
Period size: 52 Copynumber: 3.6 Consensus size: 51
5414146 GTATATAAGT
5414156 TTGCATAACTTACATAATAACTTCCATAACGTATATATAATAACATAATAAA
1 TTGCATAACTTACATAATAACTTCCATAAC-TATATATAATAACATAATAAA
* * * * * *
5414208 TTACATAA--TACATAATAA----CATAA-TACATA-ACTTATAT-ATAAGC
1 TTGCATAACTTACATAATAACTTCCATAACTATATATAATAACATAATAA-A
* * *** *
5414251 TTGTATAACTTACATAATAACTTTCATAACTTATATATAATCTGATAATACA
1 TTGCATAACTTACATAATAACTTCCATAAC-TATATATAATAACATAATAAA
5414303 TTGCATAACTTACATAATAACTTCCATAACT
1 TTGCATAACTTACATAATAACTTCCATAACT
5414334 TAATACACCA
Statistics
Matches: 98, Mismatches: 17, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
42 4 0.04
43 11 0.11
44 5 0.05
45 10 0.10
46 5 0.05
49 5 0.05
50 10 0.10
51 6 0.06
52 39 0.40
53 3 0.03
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (51 bp):
TTGCATAACTTACATAATAACTTCCATAACTATATATAATAACATAATAAA
Found at i:5414223 original size:95 final size:95
Alignment explanation
Indices: 5414113--5414323 Score: 271
Period size: 95 Copynumber: 2.2 Consensus size: 95
5414103 AATCATTTGC
* * * *
5414113 TTACTTAATACATAATAACACAATGCATAA-TTGGTATATAAGTTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACACAATACATAACTT-ATATATAAGCTTGCATAACTTACATAATAAC
5414177 TTCCATAACGTATATATAATAACATAATAAA
65 TTCCATAACGTATATATAATAACATAATAAA
* *
5414208 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACATAATAACT
1 TTACATAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
* * *** *
5414273 TTCATAACTTATATATAATCTGATAATACA
66 TCCATAACGTATATATAATAACATAATAAA
*
5414303 TTGCATAACTTACATAATAAC
1 TTACATAA--TACATAATAAC
5414324 TTCCATAACT
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
95 87 0.87
96 2 0.02
97 11 0.11
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (95 bp):
TTACATAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
TCCATAACGTATATATAATAACATAATAAA
Found at i:5414230 original size:15 final size:15
Alignment explanation
Indices: 5414192--5414237 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
5414182 TAACGTATAT
5414192 ATAATAACATAAT--
1 ATAATAACATAATAC
*
5414205 A-AATTACATAATAC
1 ATAATAACATAATAC
5414219 ATAATAACATAATAC
1 ATAATAACATAATAC
5414234 ATAA
1 ATAA
5414238 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:5414259 original size:21 final size:20
Alignment explanation
Indices: 5414233--5414290 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
5414223 TAACATAATA
5414233 CATAACTTATATATAAGCTTGT
1 CATAACTTATATATAA-CTT-T
*
5414255 -ATAACTTACATAATAACTTT
1 CATAACTTATAT-ATAACTTT
5414275 CATAACTTATATATAA
1 CATAACTTATATATAA
5414291 TCTGATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 23 0.72
22 4 0.12
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (20 bp):
CATAACTTATATATAACTTT
Found at i:5414434 original size:9 final size:9
Alignment explanation
Indices: 5414406--5414577 Score: 82
Period size: 9 Copynumber: 20.2 Consensus size: 9
5414396 CATATATAGA
*
5414406 AACTGACAT
1 AACTTACAT
* *
5414415 AAATTAAAT
1 AACTTACAT
5414424 AACTTACAT
1 AACTTACAT
5414433 AACTTACAT
1 AACTTACAT
* *
5414442 AAATTAAAT
1 AACTTACAT
*
5414451 TACTTACAT
1 AACTTACAT
5414460 AACTTACAT
1 AACTTACAT
*
5414469 TA--TACAT
1 AACTTACAT
*
5414476 AACCTT-CTT
1 AA-CTTACAT
5414485 AACTTACAT
1 AACTTACAT
* *
5414494 TA--TACAC
1 AACTTACAT
* *
5414501 GACTCACAT
1 AACTTACAT
5414510 AA-TTA-AT
1 AACTTACAT
* *
5414517 -ATTATACAC
1 AACT-TACAT
5414526 AACTTACAT
1 AACTTACAT
* *
5414535 TACTTGCAGT
1 AACTTACA-T
5414545 -ACTTACAT
1 AACTTACAT
5414553 AA--TACAT
1 AACTTACAT
5414560 AA--TACAT
1 AACTTACAT
5414567 AACTTACAT
1 AACTTACAT
5414576 AA
1 AA
5414578 TACATAAAAA
Statistics
Matches: 121, Mismatches: 28, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
6 1 0.01
7 28 0.23
8 8 0.07
9 80 0.66
10 4 0.03
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:5414436 original size:27 final size:27
Alignment explanation
Indices: 5414406--5414468 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
5414396 CATATATAGA
*
5414406 AACTGACATAAATTAAATAACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
*
5414433 AACTTACATAAATTAAATTACTTACAT
1 AACTTACATAAATTAAATAACTTACAT
5414460 AACTTACAT
1 AACTTACAT
5414469 TATACATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (27 bp):
AACTTACATAAATTAAATAACTTACAT
Found at i:5414560 original size:7 final size:7
Alignment explanation
Indices: 5414548--5414584 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
5414538 TTGCAGTACT
5414548 TACATAA
1 TACATAA
5414555 TACATAA
1 TACATAA
5414562 TACATAA
1 TACATAA
5414569 CTTACATAA
1 --TACATAA
5414578 TACATAA
1 TACATAA
5414585 AAATATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:5420225 original size:21 final size:20
Alignment explanation
Indices: 5420178--5420229 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5420168 ACTTAAAGAA
* *
5420178 GAGGCGGCAGCGAGGGAAGC
1 GAGGCTGCAGCAAGGGAAGC
*
5420198 AACGGCTGCAGCAAGGGAAGC
1 GA-GGCTGCAGCAAGGGAAGC
5420219 GGAGGCTGCAG
1 -GAGGCTGCAG
5420230 TGAGAGAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.27, C:0.21, G:0.48, T:0.04
Consensus pattern (20 bp):
GAGGCTGCAGCAAGGGAAGC
Found at i:5420615 original size:42 final size:41
Alignment explanation
Indices: 5420557--5420844 Score: 279
Period size: 42 Copynumber: 6.9 Consensus size: 41
5420547 GCGTTTTTGT
*
5420557 AAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* *
5420598 AAAACAACGCCGCTAAAGAACATGTTCTTTAGAGGCGTTTAG
1 AAAA-AACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * *
5420640 AAAAAAACGCCGCTAAATACCATGTTCTTTAGCGGCACTTAG
1 -AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * *
5420682 AGAAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAG
1 A-AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * * **
5420724 AAGAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTT
1 AA-AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-CTTAG
*** * * * * * **
5420767 CTTAAGCGCCGCTAAAGAACATGGTCTTTGGCGACGTTTTTT
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-CTTAG
** *
5420809 ACTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
5420845 TTTTTGTTTG
Statistics
Matches: 206, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
41 6 0.03
42 194 0.94
43 6 0.03
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
Found at i:5420655 original size:84 final size:84
Alignment explanation
Indices: 5420557--5420760 Score: 311
Period size: 84 Copynumber: 2.4 Consensus size: 84
5420547 GCGTTTTTGT
* *
5420557 AAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-AAACAACGCCGCTAAAGAACAT
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAGAAA-AACGCCGCTAAAGAACAT
* * *
5420621 GTTCTTTAGAGGCGTTTAGA
65 ATTCTTTAGAGACGCTTAGA
* *
5420641 AAAAAACGCCGCTAAATACCATGTTCTTTAGCGGCACTTAGAGAAAAACGCCGCTAAAGAACATA
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAGAAAAACGCCGCTAAAGAACATA
5420706 TTCTTTAGAGACGCTTAGA
66 TTCTTTAGAGACGCTTAGA
* *
5420725 AGAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
5420761 TTTTTTCTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 105 0.97
85 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAGAAAAACGCCGCTAAAGAACATA
TTCTTTAGAGACGCTTAGA
Found at i:5420795 original size:126 final size:126
Alignment explanation
Indices: 5420558--5420795 Score: 307
Period size: 126 Copynumber: 1.9 Consensus size: 126
5420548 CGTTTTTGTA
* * * *
5420558 AAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAACAACGCCGCTAAAGAACATGT
1 AAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAGAAAACAACGCCGCTAAAGAACATGT
* * *
5420623 TCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAATACCATGTTCTTTAGCGGCACTTAGAG
66 TCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTAGAG
* *
5420684 AAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAGAAGAA-AATGCCGCTAAAGACCATG
1 AAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAGAA-AACAACGCCGCTAAAGAACATG
* ****** *
5420748 TTCTTTAGCGGCGTTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTT
65 TTCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAAGAACATGGTCTTT
5420796 GGCGACGTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
126 92 0.98
127 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAGAAAACAACGCCGCTAAAGAACATGT
TCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCACTTAGAG
Found at i:5420961 original size:22 final size:22
Alignment explanation
Indices: 5420930--5420974 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5420920 TACATTTAGT
* * *
5420930 GGCCTTAAAAAGCGCCGCTAAA
1 GGCCTAAAAAAACACCGCTAAA
5420952 GGCCTAAAAAAACACCGCTAAA
1 GGCCTAAAAAAACACCGCTAAA
5420974 G
1 G
5420975 ACCTGTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.27, G:0.20, T:0.11
Consensus pattern (22 bp):
GGCCTAAAAAAACACCGCTAAA
Found at i:5421180 original size:3 final size:3
Alignment explanation
Indices: 5421172--5421266 Score: 109
Period size: 3 Copynumber: 30.7 Consensus size: 3
5421162 TGATAAGGCA
* * *
5421172 AAT AAT AAT AAT AAAT GCAAT AAC AAG AAT AAT AAT AAT AAT AAT AAG
1 AAT AAT AAT AAT -AAT --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** *
5421220 CTT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5421267 AGGATTAGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
3 72 0.92
4 3 0.04
5 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5422044 original size:11 final size:11
Alignment explanation
Indices: 5422028--5422062 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5422018 TGAAAGAAAG
*
5422028 AATAAAAATGA
1 AATAAAAATAA
5422039 AATAAAAATAA
1 AATAAAAATAA
*
5422050 AATAAAAACAA
1 AATAAAAATAA
5422061 AA
1 AA
5422063 ACAGTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:5422048 original size:17 final size:18
Alignment explanation
Indices: 5422013--5422051 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5422003 CATATGTAAA
5422013 AAAAATGAAAGAAAGAAT
1 AAAAATGAAAGAAAGAAT
*
5422031 AAAAATGAAATAAA-AAT
1 AAAAATGAAAGAAAGAAT
5422048 AAAA
1 AAAA
5422052 TAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAGAAAGAAT
Found at i:5422844 original size:46 final size:46
Alignment explanation
Indices: 5422782--5423587 Score: 1153
Period size: 46 Copynumber: 17.4 Consensus size: 46
5422772 TCCTTGCCAG
* *
5422782 TACAAGAAGACAAGATCTGCAATCTTCGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
5422828 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
*
5422874 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCTAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* * * **
5422920 TACAGGAAGACAAGATATGTTATCTTCGATCTCCTCTACTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* *
5422966 TACAGGAAGACAAGATCTGCTATCTTTGATCTCCTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
**
5423012 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGTAAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
** * *
5423058 TACAATAAGACAAGATCTGCTATCTTTGATCTACTCCACTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* *
5423104 TACAGGAAGACAAGATCTGTTATCTTCGATCTACTCTGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* *
5423150 TACAGGAAGACAAGACCTGCTATATCTTTGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGC--TATCTTCGATCTACTCCGCTGCCAAA
* * **
5423198 TACAGGAAGGCAAGATCTGCTATCTTCGATCTACTCCACTGTAAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
** * * * *
5423244 TACAATAAGACAATATATGCTATCTTTGATCTACTCCACTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* * *
5423290 TACAGGAAGACAAGATCTGTTATCTTCAATCTACTCTGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
*
5423336 TACAGGAAGACAAGATCTGCTATATCTTCGATCTACTCTGCTGCCAAA
1 TACAGGAAGACAAGATCTGC--TATCTTCGATCTACTCCGCTGCCAAA
* * *
5423384 TATAGGAAGACAAGATCTGCTATATCTTCGATCTACTCTGCTACCAAA
1 TACAGGAAGACAAGATCTGC--TATCTTCGATCTACTCCGCTGCCAAA
* * *
5423432 TACAGGAAGACAAGGTCTGCTATCTTTGATCTACTCCGCTACCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
* * *
5423478 TATAGGAAGACAAGGTCTGCTATCTTTGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
*
5423524 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCACTGCCAAA
1 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
*
5423570 TATAGGAAGACAAGATCT
1 TACAGGAAGACAAGATCT
5423588 ACTGCTTTTA
Statistics
Matches: 684, Mismatches: 72, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
46 553 0.81
48 131 0.19
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (46 bp):
TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
Found at i:5424632 original size:108 final size:106
Alignment explanation
Indices: 5424484--5424909 Score: 496
Period size: 108 Copynumber: 4.1 Consensus size: 106
5424474 GAAAAATGCT
* * * * * * * *
5424484 TGAAAAAGATTACCAAAATAGACAAGATGGAATTTTATTGAGAATAAGGCTCAAAATGAATAAAT
1 TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAACAA-GCTCGAAATGAATAAAT
*
5424549 TAATCAGGATAGCAAATTTTGCTAATATTCAAAATGAATAAGA
65 TAATCAAGATAGCAAATTTTGCTAATA-TCAAAATGAATAAGA
* * * *
5424592 TGAAAAGGATTATCACAATGGATAAGATAAAATTTTATTGAGAGCAAAGCTCGGAA-CAAGTAAA
1 TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAAC-AAGCTCGAAATGAA-TAAA
* * *
5424656 TTAATCAGGATAGCCAATTTTGCTAAGATCAAAAATGAATAAGA
64 TTAATCAAGATAGCAAATTTTGCTAATATC-AAAATGAATAAGA
*
5424700 TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCAAGCTCGAAATGAATAAATT
1 TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAACAAGCTCGAAATGAATAAATT
5424765 AATCAAGATAGCAAATTTTGC-----T---AA-G-ATAAGA
66 AATCAAGATAGCAAATTTTGCTAATATCAAAATGAATAAGA
* * * *
5424796 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCATAGCTTGAAATGAATAAAT
1 TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAACA-AGCTCGAAATGAATAAAT
* *
5424861 TAATCAAGATAGAAAATTTTGCTAATATACGAAATGAATAAGA
65 TAATCAAGATAGCAAATTTTGCTAATAT-CAAAATGAATAAGA
*
5424904 TAAAAA
1 TGAAAA
5424910 CAGGTGTCCC
Statistics
Matches: 278, Mismatches: 24, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
96 50 0.18
97 39 0.14
98 2 0.01
102 2 0.01
106 2 0.01
107 39 0.14
108 142 0.51
109 2 0.01
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (106 bp):
TGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAACAAGCTCGAAATGAATAAATT
AATCAAGATAGCAAATTTTGCTAATATCAAAATGAATAAGA
Found at i:5424880 original size:97 final size:96
Alignment explanation
Indices: 5424694--5424885 Score: 339
Period size: 96 Copynumber: 2.0 Consensus size: 96
5424684 TCAAAAATGA
* *
5424694 ATAAGATGAAAAGGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCAAGCTCGAAATGAA
1 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCAAGCTCGAAATGAA
*
5424759 TAAATTAATCAAGATAGCAAATTTTGCTAAG
66 TAAATTAATCAAGATAGAAAATTTTGCTAAG
*
5424790 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCATAGCTTGAAATGA
1 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCA-AGCTCGAAATGA
5424855 ATAAATTAATCAAGATAGAAAATTTTGCTAA
65 ATAAATTAATCAAGATAGAAAATTTTGCTAA
5424886 TATACGAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
96 50 0.55
97 41 0.45
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (96 bp):
ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAGCAAGCTCGAAATGAA
TAAATTAATCAAGATAGAAAATTTTGCTAAG
Found at i:5425213 original size:12 final size:11
Alignment explanation
Indices: 5425181--5425236 Score: 62
Period size: 12 Copynumber: 4.9 Consensus size: 11
5425171 CCTTTTTCTT
5425181 TTTCTTCTTTTC
1 TTTCTT-TTTTC
5425193 TTT-TTTTTTC
1 TTTCTTTTTTC
5425203 TATTCTTTTTTC
1 T-TTCTTTTTTC
5425215 TTTTCTTTTTTC
1 -TTTCTTTTTTC
5425227 TCTT-TTTTTT
1 T-TTCTTTTTT
5425237 GGACATTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.15
11 11 0.28
12 22 0.55
13 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:5430051 original size:15 final size:15
Alignment explanation
Indices: 5430031--5430064 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5430021 ATACAAGGAT
5430031 ATATAAA-TATATAAG
1 ATATAAATTATAT-AG
5430046 ATATAAATTATATAG
1 ATATAAATTATATAG
5430061 ATAT
1 ATAT
5430065 GGAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
ATATAAATTATATAG
Found at i:5438471 original size:21 final size:20
Alignment explanation
Indices: 5438424--5438475 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5438414 ACTTAAAGAA
* *
5438424 GAGGCGGCAGCGAGGGAAGC
1 GAGGCTGCAGCAAGGGAAGC
*
5438444 AACGGCTGCAGCAAGGGAAGC
1 GA-GGCTGCAGCAAGGGAAGC
5438465 GGAGGCTGCAG
1 -GAGGCTGCAG
5438476 TGAGAGAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.27, C:0.21, G:0.48, T:0.04
Consensus pattern (20 bp):
GAGGCTGCAGCAAGGGAAGC
Found at i:5438861 original size:42 final size:41
Alignment explanation
Indices: 5438803--5439048 Score: 314
Period size: 42 Copynumber: 5.9 Consensus size: 41
5438793 GCGTTTTTGT
*
5438803 AAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* *
5438844 AAAACAACGCCGCTAAAGAACATGTTCTTTAGAGGCGTTTAG
1 AAAA-AACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * *
5438886 AAAAAAACGCCGCTAAATACCATGTTCTTTAGCGGCGCTTAAT
1 -AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT-AG
* * *
5438929 AAAAAACGCCGCTAAAGACCATGTTCTTTGGCGGCACTTAG
1 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
* * *
5438970 AGAAAAACGCCGCTAAAGAACATATTCTTTAGAGACGCTTAG
1 A-AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
*
5439012 AAGAAAATGCCGCTAAAG-ACGATGTTCTTTAGCGGCG
1 AA-AAAACGCCGCTAAAGAAC-ATGTTCTTTAGCGGCG
5439049 TTTTGACCTA
Statistics
Matches: 177, Mismatches: 22, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
41 9 0.05
42 163 0.92
43 5 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
Found at i:5438984 original size:126 final size:126
Alignment explanation
Indices: 5438802--5439048 Score: 379
Period size: 126 Copynumber: 2.0 Consensus size: 126
5438792 GGCGTTTTTG
* *
5438802 TAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAACAACGCCGCTAAAGAACAT
1 TAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTTAGAAAACAACGCCGCTAAAGAACAT
* * * *
5438867 GTTCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAATACCATGTTCTTTAGCGGCGCTTAA
66 ATTCTTTAGAGACGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAA
* *
5438928 TAAAAAACGCCGCTAAAGACCATGTTCTTTGGCGGCACTTAGAGAAA-AACGCCGCTAAAGAACA
1 TAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTTAGA-AAACAACGCCGCTAAAGAACA
* * *
5438992 TATTCTTTAGAGACGCTTAGAAGAAAATGCCGCTAAAGACGATGTTCTTTAGCGGCG
65 TATTCTTTAGAGACGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
5439049 TTTTGACCTA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
126 106 0.97
127 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (126 bp):
TAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTTAGAAAACAACGCCGCTAAAGAACAT
ATTCTTTAGAGACGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAA
Found at i:5441471 original size:11 final size:11
Alignment explanation
Indices: 5441455--5441489 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5441445 TGAAAGAAAG
*
5441455 AATAAAAATGA
1 AATAAAAATAA
5441466 AATAAAAATAA
1 AATAAAAATAA
*
5441477 AATAAAAACAA
1 AATAAAAATAA
5441488 AA
1 AA
5441490 ACAGTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:5441475 original size:17 final size:18
Alignment explanation
Indices: 5441440--5441478 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5441430 CCATATGTAA
5441440 AAAAATGAAAGAAAGAAT
1 AAAAATGAAAGAAAGAAT
*
5441458 AAAAATGAAATAAA-AAT
1 AAAAATGAAAGAAAGAAT
5441475 AAAA
1 AAAA
5441479 TAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAGAAAGAAT
Found at i:5441897 original size:19 final size:19
Alignment explanation
Indices: 5441875--5441918 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
5441865 AAATTTTAGT
5441875 TTTTTATTTCATTTTT-ATA
1 TTTTT-TTTCATTTTTCATA
*
5441894 TTTTTTTTTATTTTTCATA
1 TTTTTTTTCATTTTTCATA
5441913 TATTTT
1 T-TTTT
5441919 GATCCTATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTTCATTTTTCATA
Found at i:5442546 original size:22 final size:21
Alignment explanation
Indices: 5442515--5442556 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
5442505 TAACACCTTA
5442515 AACCCTAAATCCCTAACCCCT
1 AACCCTAAATCCCTAACCCCT
5442536 AACCCATAAATCTCCTAACCC
1 AACCC-TAAATC-CCTAACCC
5442557 TTAAATTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCTAAATCCCTAACCCCT
Found at i:5442557 original size:22 final size:21
Alignment explanation
Indices: 5442515--5442615 Score: 88
Period size: 22 Copynumber: 4.9 Consensus size: 21
5442505 TAACACCTTA
5442515 AACCCTAAATCCCTAACCCCT
1 AACCCTAAATCCCTAACCCCT
5442536 AACCCATAAAT--CT----CCT
1 AACCC-TAAATCCCTAACCCCT
*
5442552 AACCCTTAAATTCCTAACCCCT
1 AACCC-TAAATCCCTAACCCCT
5442574 AACTCCTAAATCCCTAACCCCT
1 AAC-CCTAAATCCCTAACCCCT
* * *
5442596 AAACCTTATATCCCAAACCC
1 -AACCCTAAATCCCTAACCC
5442616 TAATCCATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
16 13 0.20
18 2 0.03
20 2 0.03
21 5 0.08
22 39 0.59
23 5 0.08
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCTAAATCCCTAACCCCT
Found at i:5442573 original size:16 final size:16
Alignment explanation
Indices: 5442533--5442571 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5442523 ATCCCTAACC
*
5442533 CCTAACCCATAAATCT
1 CCTAACCCTTAAATCT
5442549 CCTAACCCTTAAAT-T
1 CCTAACCCTTAAATCT
5442564 CCTAACCC
1 CCTAACCC
5442572 CTAACTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (16 bp):
CCTAACCCTTAAATCT
Found at i:5443700 original size:41 final size:40
Alignment explanation
Indices: 5443545--5443723 Score: 141
Period size: 41 Copynumber: 4.3 Consensus size: 40
5443535 GCTTCAACAA
* *
5443545 AAACGCCGCTAAAAGACCATATA-TTAGCGACGCTTATCATAA-
1 AAACGCCGCTAAAA-ACCTTA-ACTTAGCGGCGCTTAT-A-AAG
* * *
5443587 AAACGCCGCTAAAAATCTTAACTTTAGCAGCGCTTATATAG
1 AAACGCCGCTAAAAACCTTAAC-TTAGCGGCGCTTATAAAG
* * *
5443628 AAACGCCGCTAAAAGACCATATCTTAACGGCGCTT-TAAAG
1 AAACGCCGCTAAAA-ACCTTAACTTAGCGGCGCTTATAAAG
* * *
5443668 AAATCGCCGCTAAATACCTTAACGTTAGCGGCGGTTGATTAA-
1 AAA-CGCCGCTAAAAACCTTAAC-TTAGCGGCGCTT-ATAAAG
*
5443710 AAACGCCACTAAAA
1 AAACGCCGCTAAAA
5443724 CCCTCGACCA
Statistics
Matches: 110, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
40 15 0.14
41 58 0.53
42 34 0.31
43 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (40 bp):
AAACGCCGCTAAAAACCTTAACTTAGCGGCGCTTATAAAG
Found at i:5443715 original size:82 final size:83
Alignment explanation
Indices: 5443543--5443723 Score: 217
Period size: 82 Copynumber: 2.2 Consensus size: 83
5443533 GCGCTTCAAC
* *
5443543 AAAAACGCCGCTAAAAGACCATATATTAGCGACGCTTATCATAAAAACGCCGCTAAAAATCTTAA
1 AAAAACGCCGCTAAAAGACCATATATTAACGACGCTTATCATAAAAACGCCGCTAAAAACCTTAA
*
5443608 CTTTAGCAGCGCTTATAT
66 CGTTAGCAGCGCTTATAT
* * * *
5443626 AGAAACGCCGCTAAAAGACCATATCTTAACGGCGCTT-T-A-AAGAAATCGCCGCTAAATACCTT
1 AAAAACGCCGCTAAAAGACCATATATTAACGACGCTTATCATAA-AAA-CGCCGCTAAAAACCTT
* *
5443688 AACGTTAGCGGCGGTTGAT-T
64 AACGTTAGCAGCGCTT-ATAT
*
5443708 AAAAACGCCACTAAAA
1 AAAAACGCCGCTAAAA
5443724 CCCTCGACCA
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
80 2 0.02
81 4 0.05
82 43 0.51
83 35 0.42
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (83 bp):
AAAAACGCCGCTAAAAGACCATATATTAACGACGCTTATCATAAAAACGCCGCTAAAAACCTTAA
CGTTAGCAGCGCTTATAT
Found at i:5446944 original size:11 final size:11
Alignment explanation
Indices: 5446925--5446954 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5446915 TCAAGTTTTG
*
5446925 TTCTTGATTTA
1 TTCTCGATTTA
5446936 TTCTCGATTTA
1 TTCTCGATTTA
5446947 TTCTCGAT
1 TTCTCGAT
5446955 GATTTGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.57
Consensus pattern (11 bp):
TTCTCGATTTA
Found at i:5449938 original size:18 final size:18
Alignment explanation
Indices: 5449917--5449971 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
5449907 CTGTTTTTGT
* *
5449917 TATGATTTTCTGTTGGGA
1 TATGATTTTCTATTGAGA
*
5449935 TATGATTTCCTATTGAGA
1 TATGATTTTCTATTGAGA
*
5449953 TATGATTTTCTATTAAGA
1 TATGATTTTCTATTGAGA
5449971 T
1 T
5449972 TTGTTGCTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTATTGAGA
Found at i:5450878 original size:18 final size:18
Alignment explanation
Indices: 5450857--5450902 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5450847 TGGCCACATA
5450857 CAGAAGAGGTTATCGTGG
1 CAGAAGAGGTTATCGTGG
*
5450875 CAGAAGTGGTTATCGTGG
1 CAGAAGAGGTTATCGTGG
* *
5450893 TAGAGGAGGT
1 CAGAAGAGGT
5450903 CGTGGCAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.24
Consensus pattern (18 bp):
CAGAAGAGGTTATCGTGG
Found at i:5454283 original size:18 final size:18
Alignment explanation
Indices: 5454262--5454316 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
5454252 CTGTTTTTGT
* *
5454262 TATGGTTTTCTATTGGGA
1 TATGATTTTCTATTGAGA
*
5454280 TATGATTTCCTATTGAGA
1 TATGATTTTCTATTGAGA
*
5454298 TATGATTTTCTATTAAGA
1 TATGATTTTCTATTGAGA
5454316 T
1 T
5454317 TTGTTGCTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (18 bp):
TATGATTTTCTATTGAGA
Found at i:5455498 original size:16 final size:16
Alignment explanation
Indices: 5455477--5455509 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5455467 TACTTTCTTC
5455477 TATTTTTTATTTATTT
1 TATTTTTTATTTATTT
*
5455493 TATTTTTTGTTTATTT
1 TATTTTTTATTTATTT
5455509 T
1 T
5455510 CTACAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TATTTTTTATTTATTT
Found at i:5468325 original size:46 final size:46
Alignment explanation
Indices: 5468258--5468500 Score: 127
Period size: 46 Copynumber: 5.5 Consensus size: 46
5468248 ATTATACAGG
*
5468258 TCTTATTTCCCTGAGATTACAGTGGAATAGACCGAATAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAATAATTTCAGA
* ** ** *
5468304 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-A-GT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAA--TAATTTCAGA
* * * * **
5468348 TCCTATCTCCCTGAGATTACAGTGG---AG-CGGATTAAAATGAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAT-AATTTCA-GA
* *** * * ** *
5468392 TCTTATCTCTCTGA-AGTTACAACAGAGTAGATCG-----CGTCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGACCGAATAATTTCAGA
* *
5468433 TCTTATTTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAATAATTTCAGA
5468479 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
5468501 CGGAGCAGAT
Statistics
Matches: 141, Mismatches: 37, Indels: 38
0.65 0.17 0.18
Matches are distributed among these distances:
38 1 0.01
40 3 0.02
41 28 0.20
42 3 0.02
43 1 0.01
44 43 0.30
45 1 0.01
46 56 0.40
47 3 0.02
48 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAATAATTTCAGA
Done.