Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 107 of 160
Found at i:20237842 original size:18 final size:18
Alignment explanation
Indices: 20237747--20237842 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 18
20237737 TTTTCCCTCA
* * *
20237747 TTTTATATTTTTCCATTT
1 TTTTATTTTTTTTCTTTT
* *
20237765 TTTTATATTTTTCTCTTAT
1 TTTTAT-TTTTTTTCTTTT
* * *
20237784 TTCTCTTATTTTTCTTATT
1 TTTTATTTTTTTTCTT-TT
20237803 TTTTATTTTTTTAT-TTCATT
1 TTTTATTTTTTT-TCTT--TT
20237823 TTTTATTTTTTTTCTTTT
1 TTTTATTTTTTTTCTTTT
20237841 TT
1 TT
20237843 CATTTTTTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
18 18 0.30
19 24 0.40
20 18 0.30
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTTTTCTTTT
Found at i:20237849 original size:17 final size:17
Alignment explanation
Indices: 20237747--20237850 Score: 68
Period size: 18 Copynumber: 5.6 Consensus size: 17
20237737 TTTTCCCTCA
* *
20237747 TTTTATATTTTTCCATTT
1 TTTTATTTTTTTTCA-TT
*
20237765 TTTTATATTTTTCTCTTATT
1 TTTTAT-TTTTT-T-TCATT
*
20237785 TCTCTTATTTTTCTT-ATT
1 T-T-TTATTTTTTTTCATT
20237803 TTTTATTTTTTTATTTCATT
1 TTTTA--TTTTT-TTTCATT
20237823 TTTTATTTTTTTTC-TT
1 TTTTATTTTTTTTCATT
20237839 TTTTCATTTTTT
1 TTTT-ATTTTTT
20237851 CATCCATTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
16 9 0.13
17 12 0.17
18 20 0.28
19 7 0.10
20 13 0.18
21 6 0.08
22 4 0.06
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTTTTCATT
Found at i:20242593 original size:205 final size:203
Alignment explanation
Indices: 20242192--20242573 Score: 462
Period size: 205 Copynumber: 1.9 Consensus size: 203
20242182 AAAGTTACTT
* * *
20242192 TTATTGAAATTTCATCTAAATTATTCAATCATTTGGGACAAATTTAGAAAAATTTCTCACCTAGA
1 TTATTAAAATTTCATCTAAATTATTCAATCATTTGAGACAAATTTAGAAAAATTTCTCACATAGA
*
20242257 GATTTCTTAAGAAATTTATCATTTGAAATTTCTAAAATTCTCATCATTGGATAATTGATATTTAA
66 GATTTCTTAAGAAATTTACCATTTGAAATTTCTAAAATTCTCATCATTGGATAATTGATATTTAA
** * * * *
20242322 TTCCCAAATTTTTATTAAAATTCATGTTTTTTATTTTTTATTCTTTTTAAAAATGAAAATAAATA
131 TTCAAAAAATATTATT--AATTCATGTTTTATATTTTTTATTCTTTCTAAAAATGAAAATAAATA
20242387 TTAATTATTA
194 TTAATTATTA
* * *
20242397 TTATTAAAATTTTATCTAAATTATTCCATCATTTGAGATAAATTTAGAAAAAATTT-TCACATAG
1 TTATTAAAATTTCATCTAAATTATTCAATCATTTGAGACAAATTTAG-AAAAATTTCTCACATAG
*
20242461 -GAATTT-TATAA-AAATTTACCATTTGAAATTTTTAAAAATT-TCATCATTGGATAATT-ATTA
65 AG-ATTTCT-TAAGAAATTTACCATTTGAAATTTCT-AAAATTCTCATCATTGGATAATTGA-TA
*
20242521 TTT-ATTCTAAAAAATATT-TT-ATT-TTGTTTTATATTTTTTTATT-TTTCCTAAAA
126 TTTAATTC-AAAAAATATTATTAATTCATGTTTTATA-TTTTTTATTCTTT-CTAAAA
20242574 TTTGATCAGG
Statistics
Matches: 154, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
199 11 0.07
200 17 0.11
203 7 0.05
204 49 0.32
205 62 0.40
206 8 0.05
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (203 bp):
TTATTAAAATTTCATCTAAATTATTCAATCATTTGAGACAAATTTAGAAAAATTTCTCACATAGA
GATTTCTTAAGAAATTTACCATTTGAAATTTCTAAAATTCTCATCATTGGATAATTGATATTTAA
TTCAAAAAATATTATTAATTCATGTTTTATATTTTTTATTCTTTCTAAAAATGAAAATAAATATT
AATTATTA
Found at i:20242644 original size:22 final size:22
Alignment explanation
Indices: 20242597--20242647 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
20242587 AAATATTTTG
* *
20242597 AAAATAATCAAAAAAATATAAT
1 AAAATAATCAAAAAAAAATAAC
*
20242619 AAAATAAT-AAAATAAAAATACC
1 AAAATAATCAAAA-AAAAATAAC
20242641 AAAATAA
1 AAAATAA
20242648 GAAGCGACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATAATCAAAAAAAAATAAC
Found at i:20243517 original size:25 final size:27
Alignment explanation
Indices: 20243489--20243540 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
20243479 GATTTGATAA
*
20243489 TTATATAATATATTATTT-T-TTATAT
1 TTATATAATATATAATTTATGTTATAT
*
20243514 TTATATATTATATAATTTATGTTATAT
1 TTATATAATATATAATTTATGTTATAT
20243541 AAAGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 16 0.70
26 1 0.04
27 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTATATAATATATAATTTATGTTATAT
Found at i:20243740 original size:2 final size:2
Alignment explanation
Indices: 20243733--20243766 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20243723 GACATATCCA
20243733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20243767 ACAACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20261947 original size:20 final size:21
Alignment explanation
Indices: 20261895--20261949 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
20261885 TATATGATAA
*
20261895 TTTAATAATA-AA-TATTTAT
1 TTTAATAATATAATTAATTAT
20261914 TTTAATAA-ATTAATTAATT-T
1 TTTAATAATA-TAATTAATTAT
20261934 TTTAATAATATAATTA
1 TTTAATAATATAATTA
20261950 TATAACATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.03
19 8 0.26
20 17 0.55
21 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATAATATAATTAATTAT
Found at i:20262958 original size:17 final size:18
Alignment explanation
Indices: 20262936--20262972 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20262926 GGACTAAAAT
*
20262936 TTTTTTATTT-TTTATTA
1 TTTTTTATTTGTTAATTA
20262953 TTTTTTATTTGTTAATTA
1 TTTTTTATTTGTTAATTA
20262971 TT
1 TT
20262973 ATTCCATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTTATTTGTTAATTA
Found at i:20263437 original size:9 final size:9
Alignment explanation
Indices: 20263428--20263472 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
20263418 TTTATTATTT
20263428 TTTTTGTT-
1 TTTTTGTTC
20263436 TTCTTT-TTC
1 TT-TTTGTTC
*
20263445 TTTTT-CTC
1 TTTTTGTTC
20263453 TTTTTGTTC
1 TTTTTGTTC
20263462 TTTTTGTTC
1 TTTTTGTTC
20263471 TT
1 TT
20263473 CATTGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (9 bp):
TTTTTGTTC
Found at i:20264507 original size:11 final size:11
Alignment explanation
Indices: 20264493--20264517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20264483 TTTTATTTTT
20264493 ATTTTATAATA
1 ATTTTATAATA
20264504 ATTTTATAATA
1 ATTTTATAATA
20264515 ATT
1 ATT
20264518 AAGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTTATAATA
Found at i:20264865 original size:16 final size:18
Alignment explanation
Indices: 20264834--20264879 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
20264824 AATATTTTTA
* *
20264834 AAAATAATTAATAAC-TT
1 AAAATAATAAAAAACATT
20264851 -AAATAATAAAAAACTATT
1 AAAATAATAAAAAAC-ATT
20264869 AAAATAATAAA
1 AAAATAATAAA
20264880 CATTAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 12 0.50
18 2 0.08
19 10 0.42
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATAATAAAAAACATT
Found at i:20266392 original size:19 final size:21
Alignment explanation
Indices: 20266351--20266400 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
20266341 ATTAAAATGG
*
20266351 TTTTAATTTTTTATATTACTA
1 TTTTAATTTTTTATAATACTA
20266372 TTTTAATTTTTTA-AATA-TA
1 TTTTAATTTTTTATAATACTA
20266391 TTTTAGATTT
1 TTTTA-ATTT
20266401 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.26
20 7 0.26
21 13 0.48
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTTTATAATACTA
Found at i:20266542 original size:24 final size:24
Alignment explanation
Indices: 20266497--20266542 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20266487 ATCGTTAATG
*
20266497 ATAATAAAATTAATTATATAATAT
1 ATAATAAAATTAATAATATAATAT
*
20266521 ATAATAAATTTTAATAAT-TAAT
1 ATAATAAA-ATTAATAATATAAT
20266543 TGTATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATAAAATTAATAATATAATAT
Found at i:20266659 original size:66 final size:65
Alignment explanation
Indices: 20266579--20266747 Score: 236
Period size: 66 Copynumber: 2.6 Consensus size: 65
20266569 CAATTTTTTG
* *
20266579 TTTTTAATTTAAAAATAATATTTATCTATTAATTGTGT-TTTTTTTTACTCTCTTTACCTTTTC-
1 TTTTTATTTTAAAAATAATATTTATCTATTAATTGTGTATTTTTGTT--T-TCTTTACCTTTTCA
20266642 ATT
63 ATT
* *
20266645 TTTTTATTTTAAAAATAATATTTAT-TAATTAATTATGTATTTTTGTTTTCTTTATCTTTTCAAT
1 TTTTTATTTTAAAAATAATATTTATCT-ATTAATTGTGTATTTTTGTTTTCTTTACCTTTTCAAT
20266709 T
65 T
20266710 TTTTTGATTTTAAAAATAATATTTATCTATTAATTGTG
1 TTTTT-ATTTTAAAAATAATATTTATCTATTAATTGTG
20266748 ATCATTAGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
64 12 0.13
65 10 0.11
66 63 0.68
67 8 0.09
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (65 bp):
TTTTTATTTTAAAAATAATATTTATCTATTAATTGTGTATTTTTGTTTTCTTTACCTTTTCAATT
Found at i:20268434 original size:17 final size:16
Alignment explanation
Indices: 20268400--20268446 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
20268390 AAATAAATAC
20268400 TTTTA-TTTAG-TA-T
1 TTTTATTTTAGTTATT
20268413 TTTTATTTTATGTTATT
1 TTTTATTTTA-GTTATT
20268430 TTTTATTTTAGTTATT
1 TTTTATTTTAGTTATT
20268446 T
1 T
20268447 AGATAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.17
14 4 0.13
15 1 0.03
16 9 0.30
17 11 0.37
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTATTTTAGTTATT
Found at i:20269911 original size:22 final size:23
Alignment explanation
Indices: 20269886--20269938 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
20269876 AAACTTTAGG
20269886 GAAAGAAG-GAAAAAAAAAAAGA
1 GAAAGAAGAGAAAAAAAAAAAGA
*
20269908 GAAAGAGAGAGAAAAAAGAAAAGA
1 GAAAGA-AGAGAAAAAAAAAAAGA
*
20269932 AAAAGAA
1 GAAAGAA
20269939 AAAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 18 0.67
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (23 bp):
GAAAGAAGAGAAAAAAAAAAAGA
Found at i:20269930 original size:18 final size:19
Alignment explanation
Indices: 20269889--20269942 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
20269879 CTTTAGGGAA
*
20269889 AGAAGGAAAAA-AAAAAAG
1 AGAAAGAAAAAGAAAAAAG
* *
20269907 AGAAAGAGAGAGAAAAAAG
1 AGAAAGAAAAAGAAAAAAG
20269926 A-AAAGAAAAAGAAAAAA
1 AGAAAGAAAAAGAAAAAA
20269943 TAATAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 22 0.73
19 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAAAGAAAAAAG
Found at i:20269958 original size:15 final size:16
Alignment explanation
Indices: 20269938--20269974 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
20269928 AAGAAAAAGA
*
20269938 AAAAATAATAAT-AAT
1 AAAAATAAAAATAAAT
20269953 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
20269969 AAAAAT
1 AAAAAT
20269975 TTAAAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:20270644 original size:35 final size:34
Alignment explanation
Indices: 20270600--20270720 Score: 138
Period size: 34 Copynumber: 3.6 Consensus size: 34
20270590 GCGATACTTG
* * *
20270600 AAAATCTTCTCTAACCAGAGGTAATAAGACTTTA
1 AAAAACTTCTCTAACCAGAGGCAATAAAACTTTA
* *
20270634 AAAGAACTTCTCTAGCTAGAGGCAATAAAACTTTA
1 AAA-AACTTCTCTAACCAGAGGCAATAAAACTTTA
* * *
20270669 AAAAATTTCTCTAACTAGAGGCGATAAAACTTT-
1 AAAAACTTCTCTAACCAGAGGCAATAAAACTTTA
20270702 AAAAAC-TCTTCTAACCAGA
1 AAAAACTTC-TCTAACCAGA
20270721 AGCTATTAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 14 0.19
34 30 0.40
35 29 0.39
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (34 bp):
AAAAACTTCTCTAACCAGAGGCAATAAAACTTTA
Found at i:20270687 original size:34 final size:34
Alignment explanation
Indices: 20270600--20270706 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
20270590 GCGATACTTG
* * *
20270600 AAAATCTTCTCTAACCAGAGGTAATAAGACTTTAA
1 AAAAT-TTCTCTAACTAGAGGCAATAAAACTTTAA
* *
20270635 AAGAACTTCTCTAGCTAGAGGCAATAAAACTTTAA
1 AA-AATTTCTCTAACTAGAGGCAATAAAACTTTAA
*
20270670 AAAATTTCTCTAACTAGAGGCGATAAAACTTTAA
1 AAAATTTCTCTAACTAGAGGCAATAAAACTTTAA
20270704 AAA
1 AAA
20270707 CTCTTCTAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
34 32 0.51
35 29 0.46
36 2 0.03
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (34 bp):
AAAATTTCTCTAACTAGAGGCAATAAAACTTTAA
Found at i:20270792 original size:22 final size:22
Alignment explanation
Indices: 20270757--20270802 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20270747 TTCAACAATT
* *
20270757 CTCGAAGCTCTTATAGATTATG
1 CTCGAAGCTCTTATAAATAATG
* *
20270779 CTCGAAGGTTTTATAAATAATG
1 CTCGAAGCTCTTATAAATAATG
20270801 CT
1 CT
20270803 TATATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
CTCGAAGCTCTTATAAATAATG
Found at i:20270822 original size:18 final size:20
Alignment explanation
Indices: 20270787--20270825 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
20270777 TGCTCGAAGG
*
20270787 TTTTATAAATAATGCTTATA
1 TTTTATAAAGAATGCTTATA
20270807 TTTTA-AAAGAAT-CTTATA
1 TTTTATAAAGAATGCTTATA
20270825 T
1 T
20270826 CTAAAGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTATAAAGAATGCTTATA
Found at i:20270956 original size:103 final size:101
Alignment explanation
Indices: 20270849--20271046 Score: 220
Period size: 103 Copynumber: 1.9 Consensus size: 101
20270839 AAATTTTTAA
* * * *
20270849 AAAAAAATTCCTTTAACTA-AAGGCTATAACACTTGAAAAACTCTTCTAACCA-GAGACAATAAG
1 AAAAAAACTCCTCTAACCAGAA-GCTATAACACTTGAAAAACTCCTCTAA-CATGAGACAATAAG
* *
20270912 ACTTTAAAAGAGCTTTTCTAACTAAAGGCTATGATACTTT
64 A-TTCAAAAGA-CTTTTCTAACTAAAGGCAATGATACTTT
** * * * *
20270952 AAAAAAACTCCTCTAACCAGAAGCTATAGGATTTGAAAGACTCCTCTAACATGAGGCAATGAGAT
1 AAAAAAACTCCTCTAACCAGAAGCTATAACACTTGAAAAACTCCTCTAACATGAGACAATAAGAT
* *
20271017 TCAAAAGATTTTTCTAACTAGAGGCAATGA
66 TCAAAAGACTTTTCTAACTAAAGGCAATGA
20271047 GATTTGAAAG
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
101 19 0.24
102 10 0.13
103 48 0.61
104 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (101 bp):
AAAAAAACTCCTCTAACCAGAAGCTATAACACTTGAAAAACTCCTCTAACATGAGACAATAAGAT
TCAAAAGACTTTTCTAACTAAAGGCAATGATACTTT
Found at i:20270967 original size:35 final size:35
Alignment explanation
Indices: 20270849--20270968 Score: 91
Period size: 35 Copynumber: 3.5 Consensus size: 35
20270839 AAATTTTTAA
* *
20270849 AAAAAAATTCCTTTAACTAAAGGCTATAACAC-TT
1 AAAAAAACTCCTCTAACTAAAGGCTATAACACTTT
* * * * * * *
20270883 -GAAAAACTCTTCTAACCAGAGACAATAAGACTTT
1 AAAAAAACTCCTCTAACTAAAGGCTATAACACTTT
* * ** * *
20270917 AAAAGAGCTTTTCTAACTAAAGGCTATGATACTTT
1 AAAAAAACTCCTCTAACTAAAGGCTATAACACTTT
20270952 AAAAAAACTCCTCTAAC
1 AAAAAAACTCCTCTAAC
20270969 CAGAAGCTAT
Statistics
Matches: 61, Mismatches: 23, Indels: 3
0.70 0.26 0.03
Matches are distributed among these distances:
33 22 0.36
34 2 0.03
35 37 0.61
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (35 bp):
AAAAAAACTCCTCTAACTAAAGGCTATAACACTTT
Found at i:20271000 original size:68 final size:68
Alignment explanation
Indices: 20270857--20271001 Score: 152
Period size: 68 Copynumber: 2.1 Consensus size: 68
20270847 AAAAAAAAAT
* * *
20270857 TCCTTTAACTAAAGGCTATAACACTTGAAAAACTCTTCTAACCAGAGACAATAAGACTTTAAAAG
1 TCCTCTAACTAAAGGCTATAACACTTAAAAAACTCCTCTAACCAGAGACAATAAGACTTTAAAAG
20270922 AGC
66 AGC
** * * * * *
20270925 TTTTCTAACTAAAGGCTATGATACTTTAAAAAAACTCCTCTAACCAGA-AGCTATAGGA-TTTGA
1 TCCTCTAACTAAAGGCTATAACAC-TT-AAAAAACTCCTCTAACCAGAGA-CAATAAGACTTTAA
20270988 AAGA-C
63 AAGAGC
20270993 TCCTCTAAC
1 TCCTCTAAC
20271002 ATGAGGCAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
68 27 0.44
69 11 0.18
70 24 0.39
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (68 bp):
TCCTCTAACTAAAGGCTATAACACTTAAAAAACTCCTCTAACCAGAGACAATAAGACTTTAAAAG
AGC
Found at i:20271057 original size:33 final size:33
Alignment explanation
Indices: 20270981--20271067 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
20270971 GAAGCTATAG
* *
20270981 GATTTGAAAGACTCCTCTAACATGAGGCAATGA
1 GATTTGAAAGATTTCTCTAACATGAGGCAATGA
** *
20271014 GATTCAAAAGATTTTTCTAAC-TAGAGGCAATGA
1 GATTTGAAAGATTTCTCTAACAT-GAGGCAATGA
20271047 GATTTGAAAGATTTCTCTAAC
1 GATTTGAAAGATTTCTCTAAC
20271068 CAAATGCTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
32 1 0.02
33 44 0.98
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (33 bp):
GATTTGAAAGATTTCTCTAACATGAGGCAATGA
Found at i:20277021 original size:18 final size:18
Alignment explanation
Indices: 20276995--20277075 Score: 71
Period size: 18 Copynumber: 4.6 Consensus size: 18
20276985 CTAAAATTTA
*
20276995 TTATTATTTTTTTATTAT
1 TTATAATTTTTTTATTAT
*
20277013 TTATAATTTTTATATTAT
1 TTATAATTTTTTTATTAT
*
20277031 TT-T-A-TTTTTAATTATT
1 TTATAATTTTTTTATTA-T
*
20277047 TTAGTAA-TTTTTTATTTT
1 TTA-TAATTTTTTTATTAT
*
20277065 TTTTAATTTTT
1 TTATAATTTTT
20277076 ATTTCAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 8 0.16
16 4 0.08
17 4 0.08
18 26 0.51
19 9 0.18
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (18 bp):
TTATAATTTTTTTATTAT
Found at i:20277028 original size:26 final size:26
Alignment explanation
Indices: 20276989--20277076 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
20276979 TTTAGGCTAA
*
20276989 AATTTATTATTATTTTTTTATTATTTAT
1 AATTT-TTAGTATTTTTTTATT-TTTAT
*
20277017 AATTTTTA-TATTATTTTATTTTTA-
1 AATTTTTAGTATTTTTTTATTTTTAT
* * *
20277041 ATTATTTTAGTAATTTTTTATTTTTTTT
1 AAT-TTTTAGTATTTTTTTA-TTTTTAT
20277069 AATTTTTA
1 AATTTTTA
20277077 TTTCAAGATT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.04
25 9 0.18
26 19 0.38
27 13 0.26
28 7 0.14
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (26 bp):
AATTTTTAGTATTTTTTTATTTTTAT
Found at i:20277079 original size:16 final size:16
Alignment explanation
Indices: 20277003--20277079 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 16
20276993 TATTATTATT
* *
20277003 TTTTTATTATTTATAA
1 TTTTTATTTTTTTTAA
*
20277019 TTTTTATATTATTTT-A
1 TTTTTAT-TTTTTTTAA
*
20277035 TTTTTAATTATTTTAGTAA
1 TTTTT-ATT-TTTT-TTAA
20277054 TTTTTTATTTTTTTTAA
1 -TTTTTATTTTTTTTAA
20277071 TTTTTATTT
1 TTTTTATTT
20277080 CAAGATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 23 0.47
17 12 0.24
18 5 0.10
19 4 0.08
20 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTTTTTAA
Found at i:20277184 original size:25 final size:24
Alignment explanation
Indices: 20277132--20277184 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
20277122 GTAAACTCAT
* *
20277132 TTTTTCTATTTTTTTAAATTGAAT
1 TTTTTCTATTTTTTTAAATTAAAA
**
20277156 TTTTTCTATTTTATTTTTATTAAAA
1 TTTTTCTATTTT-TTTAAATTAAAA
20277181 TTTT
1 TTTT
20277185 ATTCTTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTTCTATTTTTTTAAATTAAAA
Found at i:20278124 original size:9 final size:9
Alignment explanation
Indices: 20278110--20278157 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
20278100 TTTTTTACTA
20278110 TTTATAATT
1 TTTATAATT
20278119 TTTAT-ATT
1 TTTATAATT
20278127 TTTATAATTT
1 TTTATAA-TT
*
20278137 TTTATAGTT
1 TTTATAATT
20278146 TTTATAATT
1 TTTATAATT
20278155 TTT
1 TTT
20278158 TTTTGTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 8 0.23
9 19 0.54
10 8 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATAATT
Found at i:20278147 original size:27 final size:26
Alignment explanation
Indices: 20278110--20278187 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 26
20278100 TTTTTTACTA
*
20278110 TTTATAATTTTTATATTTTTATAATTT-
1 TTTATAGTTTTTATATTTTTAT--TTTG
20278137 TTTATAGTTTTTATAATTTTT-TTTTG
1 TTTATAGTTTTTAT-ATTTTTATTTTG
20278163 TTTA-AGGATTTTTATATTTTTATTT
1 TTTATA-G-TTTTTATATTTTTATTT
20278188 GGCTTTTCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
25 4 0.09
26 11 0.24
27 24 0.53
28 6 0.13
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (26 bp):
TTTATAGTTTTTATATTTTTATTTTG
Found at i:20278165 original size:19 final size:19
Alignment explanation
Indices: 20278110--20278158 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
20278100 TTTTTTACTA
20278110 TTTATAA-TTTTTATA-TT
1 TTTATAATTTTTTATAGTT
20278127 TTTATAATTTTTTATAGTT
1 TTTATAATTTTTTATAGTT
20278146 TTTATAATTTTTT
1 TTTATAATTTTTT
20278159 TTTGTTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 15 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATAATTTTTTATAGTT
Found at i:20278616 original size:33 final size:31
Alignment explanation
Indices: 20278573--20278687 Score: 122
Period size: 32 Copynumber: 3.5 Consensus size: 31
20278563 GCTGAACTGA
20278573 GCTTAAATTTTCATTGGGATCAACTAAACTAG
1 GCTTAAATTTTCATTGGG-TCAACTAAACTAG
* * *
20278605 GCTTAAAATTTTCATTAGGTGCTAGCTAATCTAG
1 GCTT-AAATTTTCATTGGGT-C-AACTAAACTAG
* * * *
20278639 ACTTAAATTTTCATTGTGGCCAACTAAATTAA
1 GCTTAAATTTTCATTG-GGTCAACTAAACTAG
20278671 GCTTAAATTTTCATTGG
1 GCTTAAATTTTCATTGG
20278688 TGTGATATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
31 1 0.01
32 27 0.40
33 26 0.38
34 14 0.21
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (31 bp):
GCTTAAATTTTCATTGGGTCAACTAAACTAG
Found at i:20278681 original size:32 final size:31
Alignment explanation
Indices: 20278572--20278687 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 31
20278562 AGCTGAACTG
* *
20278572 AGCTTAAATTTTCATTGGGATCAACTAAACTA
1 AGCTTAAATTTTCATTGGG-CCAACTAAATTA
* * *
20278604 GGCTTAAAATTTTCATTAGGTGCTAGCT-AATCT-
1 AGCTT-AAATTTTCATT-GG-GCCAACTAAAT-TA
20278637 AGACTTAAATTTTCATTGTGGCCAACTAAATTA
1 AG-CTTAAATTTTCATTG-GGCCAACTAAATTA
20278670 AGCTTAAATTTTCATTGG
1 AGCTTAAATTTTCATTGG
20278688 TGTGATATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
31 1 0.01
32 26 0.38
33 31 0.46
34 9 0.13
35 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (31 bp):
AGCTTAAATTTTCATTGGGCCAACTAAATTA
Found at i:20280004 original size:19 final size:21
Alignment explanation
Indices: 20279974--20280019 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
20279964 GTTCTTTTTC
20279974 TCTTTT-CTTTTTT-ACCTTT
1 TCTTTTCCTTTTTTCACCTTT
*
20279993 T-TTTTCCTTTTTTCACTTTT
1 TCTTTTCCTTTTTTCACCTTT
20280013 TCTTTTC
1 TCTTTTC
20280020 TTTAAGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 6 0.26
21 5 0.22
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (21 bp):
TCTTTTCCTTTTTTCACCTTT
Found at i:20284329 original size:25 final size:27
Alignment explanation
Indices: 20284296--20284347 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
20284286 ATTATTGTCT
*
20284296 ATATATATGTTTA-T-TTTAATTATTG
1 ATATATATGGTTACTATTTAATTATTG
*
20284321 ATATTTATGGTTAGCTATTTAATTATT
1 ATATATATGGTTA-CTATTTAATTATT
20284348 TAATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
27 1 0.05
28 10 0.45
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (27 bp):
ATATATATGGTTACTATTTAATTATTG
Found at i:20285981 original size:12 final size:12
Alignment explanation
Indices: 20285951--20285981 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20285941 TTGTTTTGCA
*
20285951 TTTTTTGCTTTT
1 TTTTTTTCTTTT
20285963 TTTTTTTCTTTT
1 TTTTTTTCTTTT
20285975 TTTTTTT
1 TTTTTTT
20285982 AACTTGCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:20286446 original size:20 final size:20
Alignment explanation
Indices: 20286421--20286519 Score: 66
Period size: 20 Copynumber: 5.0 Consensus size: 20
20286411 TTGCTTATTT
20286421 TATTTTATTTATATATTTTA
1 TATTTTATTTATATATTTTA
20286441 TATTTTATATTATTATTATATTT-
1 TATTTTAT-TTA-TA-TAT-TTTA
* *
20286464 T-TTTTCTTTTTAT-TGTTTA
1 TATTTTATTTATATAT-TTTA
**
20286483 TATTTTATTT-GGT-TTTTA
1 TATTTTATTTATATATTTTA
20286501 TATATTT-TTTATATATTTT
1 TAT-TTTATTTATATATTTT
20286520 TTTTGTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
18 14 0.23
19 8 0.13
20 21 0.34
21 5 0.08
22 7 0.11
23 4 0.06
24 3 0.05
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (20 bp):
TATTTTATTTATATATTTTA
Found at i:20286473 original size:27 final size:26
Alignment explanation
Indices: 20286418--20286477 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
20286408 GTTTTGCTTA
20286418 TTTTATTTTATTTATATATTTTATAT
1 TTTTATTTTATTTATATATTTTATAT
* * *
20286444 TTTATATTATTA-TTATATTTTTTTTCT
1 TTT-TATT-TTATTTATATATTTTATAT
20286471 TTTTATT
1 TTTTATT
20286478 GTTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.24
27 19 0.66
28 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTATTTTATTTATATATTTTATAT
Found at i:20286509 original size:11 final size:11
Alignment explanation
Indices: 20286495--20286521 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20286485 TTTTATTTGG
20286495 TTTTTATATAT
1 TTTTTATATAT
20286506 TTTTTATATAT
1 TTTTTATATAT
20286517 TTTTT
1 TTTTT
20286522 TTGTTTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTATATAT
Found at i:20291596 original size:10 final size:10
Alignment explanation
Indices: 20291581--20291624 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
20291571 AGTTTAGAAC
*
20291581 TATGTATTTA
1 TATGTATATA
20291591 TATGTATATA
1 TATGTATATA
*
20291601 TATATATATA
1 TATGTATATA
*
20291611 TATATATATA
1 TATGTATATA
20291621 TATG
1 TATG
20291625 AAATTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:20291602 original size:2 final size:2
Alignment explanation
Indices: 20291589--20291623 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20291579 ACTATGTATT
*
20291589 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20291624 GAAATTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20293797 original size:97 final size:99
Alignment explanation
Indices: 20293624--20293823 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 99
20293614 CAACCTTGAT
* * * *
20293624 ATCTCTCATGAGGACTCACATCAATGAAGAGTTGGATCTGCTTTGATACCACTTATCACGCATCC
1 ATCTCTCATGAGGACTCACATCAATGAAGA---GGATCAGCTTGGATACCACTAATCACACATCC
** *
20293689 ACATTTCCAACCCCAAAAGACATAGTTGTTGGGTGAAA
63 ACATTTCCAA-CCCAAAAGACATAAATGTTAGGTGAAA
* **
20293727 ATCTCTCATGAGGACTCACATCAGTG-A-A-GATCAGCTTGGATACCACTAATCACATGTCCACA
1 ATCTCTCATGAGGACTCACATCAATGAAGAGGATCAGCTTGGATACCACTAATCACACATCCACA
*
20293789 TTTCCAACCTAAAAGACATAAATGTTAGGTGAAA
66 TTTCCAACCCAAAAGACATAAATGTTAGGTGAAA
20293823 A
1 A
20293824 AAGTGAAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
96 24 0.28
97 35 0.41
101 1 0.01
102 1 0.01
103 25 0.29
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (99 bp):
ATCTCTCATGAGGACTCACATCAATGAAGAGGATCAGCTTGGATACCACTAATCACACATCCACA
TTTCCAACCCAAAAGACATAAATGTTAGGTGAAA
Found at i:20295967 original size:22 final size:22
Alignment explanation
Indices: 20295941--20295984 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20295931 ATTTTTTGTC
*
20295941 CTTAATTCTATGAATACAAATA
1 CTTAATTCTAGGAATACAAATA
*
20295963 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGGAATACAAATA
20295985 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGGAATACAAATA
Found at i:20311287 original size:31 final size:30
Alignment explanation
Indices: 20311266--20311378 Score: 110
Period size: 31 Copynumber: 3.8 Consensus size: 30
20311256 TAACCTAGAC
*
20311266 CCCCAAACCCACCTTAAACCCTAACTCAAAA
1 CCCCAAACCAACC-TAAACCCTAACTCAAAA
*
20311297 CCCCAAACCAACCTAAACCCTAAGCT--GAA
1 CCCCAAACCAACCTAAACCCTAA-CTCAAAA
* *
20311326 -CCCAAACCAACCAAAACCTTAAGC-C-AAA
1 CCCCAAACCAACCTAAACCCTAA-CTCAAAA
20311354 CCCCAAATCCAAACCTAAACCCTAA
1 CCCCAAA-CC-AACCTAAACCCTAA
20311379 ACCTACCCCA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
28 24 0.34
29 8 0.11
30 12 0.17
31 26 0.37
ACGTcount: A:0.44, C:0.42, G:0.03, T:0.11
Consensus pattern (30 bp):
CCCCAAACCAACCTAAACCCTAACTCAAAA
Found at i:20311343 original size:58 final size:60
Alignment explanation
Indices: 20311267--20311378 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
20311257 AACCTAGACC
* *
20311267 CCCAAACCCACCTTAAACCCTAA-CTCAAAACCCCAAA-CC-AACCTAAACCCTAAGCTGAA
1 CCCAAACCAACCTAAAACCCTAAGC-C-AAACCCCAAATCCAAACCTAAACCCTAAGCTGAA
*
20311326 CCCAAACCAACC-AAAACCTTAAGCCAAACCCCAAATCCAAACCTAAACCCTAA
1 CCCAAACCAACCTAAAACCCTAAGCCAAACCCCAAATCCAAACCTAAACCCTAA
20311379 ACCTACCCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 10 0.21
58 11 0.23
59 26 0.55
ACGTcount: A:0.45, C:0.42, G:0.03, T:0.11
Consensus pattern (60 bp):
CCCAAACCAACCTAAAACCCTAAGCCAAACCCCAAATCCAAACCTAAACCCTAAGCTGAA
Found at i:20311531 original size:35 final size:35
Alignment explanation
Indices: 20311486--20311554 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
20311476 TGCATTCTTA
*
20311486 AATTGTCATGCATTCAT-ACT-TTATCATTCATGTTT
1 AATTATCATGCATTCATCA-TGTTATCATT-ATGTTT
20311521 AATTATCATGCATTCATCATGTTATCATTATGTT
1 AATTATCATGCATTCATCATGTTATCATTATGTT
20311555 CATGCATGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.48
Consensus pattern (35 bp):
AATTATCATGCATTCATCATGTTATCATTATGTTT
Found at i:20311573 original size:21 final size:20
Alignment explanation
Indices: 20311533--20311575 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
20311523 TTATCATGCA
*
20311533 TTCATCATGTTATCATTATG
1 TTCATCATGTCATCATTATG
20311553 TTCATGCATGTCATGCA-TATG
1 TTCAT-CATGTCAT-CATTATG
20311574 TT
1 TT
20311576 TTCAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 13 0.65
22 2 0.10
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (20 bp):
TTCATCATGTCATCATTATG
Found at i:20311852 original size:26 final size:27
Alignment explanation
Indices: 20311819--20311875 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
20311809 ATCTTAATCC
*
20311819 AAAA-ATAAAATATTTTACTTTCAAA-
1 AAAATATAAAATAATTTACTTTCAAAG
* *
20311844 AAAATATAAATTAATTTGCTTTCAAAG
1 AAAATATAAAATAATTTACTTTCAAAG
20311871 AAAAT
1 AAAAT
20311876 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 18 0.67
27 5 0.19
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
AAAATATAAAATAATTTACTTTCAAAG
Found at i:20318038 original size:16 final size:16
Alignment explanation
Indices: 20318017--20318048 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20318007 GTTTTGCCTC
20318017 TAGTTTTGATAATACT
1 TAGTTTTGATAATACT
20318033 TAGTTTTGATAATACT
1 TAGTTTTGATAATACT
20318049 AATAGAACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TAGTTTTGATAATACT
Found at i:20322563 original size:49 final size:49
Alignment explanation
Indices: 20322477--20322858 Score: 237
Period size: 49 Copynumber: 7.8 Consensus size: 49
20322467 ACCAAACTTA
* * * * *
20322477 TTTTTGAAAAAGAAATTTTTAAAGTTCCCTGCTTATATTTATATGAGCC
1 TTTTTCAAAGAGAAATTTTTAAAGTTCCCTACCTATATTTATAAGAGCC
* * * * *
20322526 TTTTCCAAAGAGAAACTTTTAAAGTTCGCTACCTATATTTATAAGGGCT
1 TTTTTCAAAGAGAAATTTTTAAAGTTCCCTACCTATATTTATAAGAGCC
* * * **
20322575 TTTTTTAAAGA-AAAGTTTTTAAAGCTCCCAACCTACGTTTAT-AGAAGCC
1 TTTTTCAAAGAGAAA-TTTTTAAAGTTCCCTACCTATATTTATAAG-AGCC
* * * * * * *
20322624 TTTTTCAAAGAAAAAGTTTTAAACTTCCTTGCCTATGTTTATAAAAGCC
1 TTTTTCAAAGAGAAATTTTTAAAGTTCCCTACCTATATTTATAAGAGCC
* * * *
20322673 -TTTTCAAA-ATGAGATTTTTAAAGTTCTCT-CCTTATGTTTGTAAGAGCC
1 TTTTTCAAAGA-GAAATTTTTAAAGTTCCCTACC-TATATTTATAAGAGCC
* * * *
20322721 -TTTACAAA-ATGAGATTTTCAAAGTTCCCCTACCTATGTTTATAAGAG-C
1 TTTTTCAAAGA-GAAATTTTTAAAGTT-CCCTACCTATATTTATAAGAGCC
* * * * *
20322769 TTTCTTCAAAAAGAGAGTTTTAAAGTTCTCCGT--CTATGTTTATAGGAGCC
1 TTT-TTCAAAGAGAAATTTTTAAAGTTC-CC-TACCTATATTTATAAGAGCC
* * * * * *
20322819 TTTTTTAACGTGATATTTTTAAAGTTCTC-ACCTATGTTTA
1 TTTTTCAAAGAGAAATTTTTAAAGTTCCCTACCTATATTTA
20322859 CCGAAGCCCT
Statistics
Matches: 265, Mismatches: 52, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
47 3 0.01
48 74 0.28
49 156 0.59
50 30 0.11
51 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (49 bp):
TTTTTCAAAGAGAAATTTTTAAAGTTCCCTACCTATATTTATAAGAGCC
Found at i:20322579 original size:98 final size:95
Alignment explanation
Indices: 20322477--20322858 Score: 274
Period size: 98 Copynumber: 3.9 Consensus size: 95
20322467 ACCAAACTTA
* * *
20322477 TTTTTGAAAAAGAAATTTTTAAAGTTCCCTGCTTATATTTATATGAGCCTTTTCCAAAGAGAAAC
1 TTTTTCAAAAAGAAATTTTTAAAGTTCCCTGCTTATGTTTATA-GAGCCTTTTACAAAGAGAAA-
* *
20322542 TTTTAAAGTTCGCTACCTATATTTATAAGGGCT
64 TTTTAAAGTTC-CTACCTATGTTTATAAGAGCT
* * * ** * * * *
20322575 TTTTTTAAAGAA-AAGTTTTTAAAGCTCCCAACCTACGTTTATAGAAGCCTTTTTCAAAGAAAAA
1 TTTTTCAAA-AAGAAATTTTTAAAGTTCCCTGCTTATGTTTATAG-AGCCTTTTACAAAGAGAAA
* * *
20322639 GTTTTAAACTTCCTTGCCTATGTTTATAAAAGC-
64 -TTTTAAAGTTCC-TACCTATGTTTATAAGAGCT
* * * * * * *
20322672 CTTTTCAAAATGAGATTTTTAAAGTTCTCTCCTTATGTTTGTAAGAGCC-TTTACAAA-ATGAGA
1 TTTTTCAAAAAGAAATTTTTAAAGTTCCCTGCTTATGTTTAT-AGAGCCTTTTACAAAGA-GAAA
20322735 TTTTCAAAGTTCCCCTACCTATGTTTATAAGAGCT
64 TTTT-AAAGTT--CCTACCTATGTTTATAAGAGCT
* * * ** * *
20322770 TTCTTCAAAAAGAGAGTTTTAAAGTTCTCC-G-TCTATGTTTATAGGAGCCTTTTTTAACGTGAT
1 TTTTTCAAAAAGAAATTTTTAAAGTTC-CCTGCT-TATGTTTATA-GAGCCTTTTACAAAGAGA-
*
20322833 ATTTTTAAAGTT-CTCACCTATGTTTA
62 AATTTTAAAGTTCCT-ACCTATGTTTA
20322859 CCGAAGCCCT
Statistics
Matches: 220, Mismatches: 47, Indels: 35
0.73 0.16 0.12
Matches are distributed among these distances:
95 5 0.02
96 17 0.08
97 64 0.29
98 114 0.52
99 16 0.07
100 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (95 bp):
TTTTTCAAAAAGAAATTTTTAAAGTTCCCTGCTTATGTTTATAGAGCCTTTTACAAAGAGAAATT
TTAAAGTTCCTACCTATGTTTATAAGAGCT
Found at i:20325333 original size:37 final size:38
Alignment explanation
Indices: 20325253--20325334 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 38
20325243 CCTTCAAATT
* *
20325253 CTAAAA-CCTAACCAAGCTCTAAACCCTAAACTTAACA
1 CTAAAACCCTAACCAAACTCTAAACCCTAAACTTAAAA
20325290 CT-AAACCCTAACCAAAC-CTAAACCCTAAAC-TAAAA
1 CTAAAACCCTAACCAAACTCTAAACCCTAAACTTAAAA
20325325 CTTAAAACCC
1 C-TAAAACCC
20325335 AACTTAAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
35 5 0.12
36 17 0.43
37 18 0.45
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.17
Consensus pattern (38 bp):
CTAAAACCCTAACCAAACTCTAAACCCTAAACTTAAAA
Found at i:20325363 original size:17 final size:18
Alignment explanation
Indices: 20325341--20325377 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20325331 ACCCAACTTA
*
20325341 AACCCTAAA-CTAACCCT
1 AACCCTAAACCAAACCCT
20325358 AACCCTAAACCAAACCCT
1 AACCCTAAACCAAACCCT
20325376 AA
1 AA
20325378 AGCTCAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.41, G:0.00, T:0.14
Consensus pattern (18 bp):
AACCCTAAACCAAACCCT
Found at i:20326412 original size:23 final size:24
Alignment explanation
Indices: 20326386--20326433 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
20326376 TCTTCACTTC
*
20326386 TCTTCCTTCTTTTA-GTTTTTAGT
1 TCTTACTTCTTTTATGTTTTTAGT
* *
20326409 TCTTAGTTCTTTTATTTTTTTAGT
1 TCTTACTTCTTTTATGTTTTTAGT
20326433 T
1 T
20326434 ACGTTATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.10, C:0.12, G:0.08, T:0.69
Consensus pattern (24 bp):
TCTTACTTCTTTTATGTTTTTAGT
Found at i:20326609 original size:21 final size:21
Alignment explanation
Indices: 20326576--20326615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20326566 TAAATTTGAC
* *
20326576 AAAAGCAATTTTTATTTTTCA
1 AAAACCAAGTTTTATTTTTCA
*
20326597 AAAACCAAGTTTTTTTTTT
1 AAAACCAAGTTTTATTTTT
20326616 TTTGCAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
AAAACCAAGTTTTATTTTTCA
Found at i:20326609 original size:22 final size:21
Alignment explanation
Indices: 20326576--20326616 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20326566 TAAATTTGAC
*
20326576 AAAAGCAATTTTTATTTTTCA
1 AAAACCAATTTTTATTTTTCA
*
20326597 AAAACCAAGTTTTTTTTTTT
1 AAAACCAA-TTTTTATTTTT
20326617 TTGCAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (21 bp):
AAAACCAATTTTTATTTTTCA
Found at i:20329717 original size:16 final size:17
Alignment explanation
Indices: 20329696--20329729 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20329686 TTTCTCTTCT
20329696 TTCTTTTA-GTCTTTAG
1 TTCTTTTATGTCTTTAG
*
20329712 TTCTTTTATTTCTTTAG
1 TTCTTTTATGTCTTTAG
20329729 T
1 T
20329730 AAAATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (17 bp):
TTCTTTTATGTCTTTAG
Found at i:20336932 original size:11 final size:11
Alignment explanation
Indices: 20336906--20336962 Score: 78
Period size: 11 Copynumber: 5.0 Consensus size: 11
20336896 AAAGCCCAAA
*
20336906 ATTTTAATTTTA
1 ATTTT-ATTTTG
20336918 ATTTTATTTTG
1 ATTTTATTTTG
20336929 ATTTTGATTTTG
1 ATTTT-ATTTTG
20336941 ATTTTATTTTG
1 ATTTTATTTTG
*
20336952 ATTTGATTTTG
1 ATTTTATTTTG
20336963 TTTGGGGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
11 26 0.62
12 16 0.38
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (11 bp):
ATTTTATTTTG
Found at i:20336938 original size:23 final size:23
Alignment explanation
Indices: 20336906--20336961 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
20336896 AAAGCCCAAA
*
20336906 ATTTTAATTTTAATTTTATTTTG
1 ATTTTGATTTTAATTTTATTTTG
*
20336929 ATTTTGATTTTGATTTTATTTTG
1 ATTTTGATTTTAATTTTATTTTG
20336952 A-TTTGATTTT
1 ATTTTGATTTT
20336962 GTTTGGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (23 bp):
ATTTTGATTTTAATTTTATTTTG
Found at i:20336956 original size:5 final size:6
Alignment explanation
Indices: 20336906--20336962 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
20336896 AAAGCCCAAA
* *
20336906 ATTTTA ATTTTA ATTTT- ATTTTG ATTTTG ATTTTG ATTTT- ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
20336952 A-TTTG ATTTTG
1 ATTTTG ATTTTG
20336963 TTTGGGGTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:20337002 original size:18 final size:19
Alignment explanation
Indices: 20336979--20337022 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
20336969 GTCTAATTTG
20336979 GTCAAAAGTC-AAAAAAAA
1 GTCAAAAGTCTAAAAAAAA
20336997 GTCAAAAGTCTAAAAAAAA
1 GTCAAAAGTCTAAAAAAAA
*
20337016 GTTAAAA
1 GTCAAAA
20337023 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (19 bp):
GTCAAAAGTCTAAAAAAAA
Found at i:20337030 original size:19 final size:20
Alignment explanation
Indices: 20337008--20337046 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20336998 TCAAAAGTCT
*
20337008 AAAAAAAAGTTAAA-AAAAA
1 AAAAAAAAGATAAACAAAAA
20337027 AAAAAAAAGATAAACAAAAA
1 AAAAAAAAGATAAACAAAAA
20337047 TGTGGGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAAAAAAGATAAACAAAAA
Found at i:20337382 original size:21 final size:22
Alignment explanation
Indices: 20337347--20337387 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20337337 TCTAGTTTTA
*
20337347 TGATTTTATTTTGTTTTTGGAT
1 TGATTTGATTTTGTTTTTGGAT
20337369 TGATTTGA-TTTGTTTTTGG
1 TGATTTGATTTTGTTTTTGG
20337388 GTTTTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.66
Consensus pattern (22 bp):
TGATTTGATTTTGTTTTTGGAT
Found at i:20337837 original size:27 final size:27
Alignment explanation
Indices: 20337773--20337840 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
20337763 TAAAGGTGCC
20337773 CAAATTCTTACCAATTTGAAACAAAAT
1 CAAATTCTTACCAATTTGAAACAAAAT
** * *
20337800 TTAATAT-TTACCAGTTTGAATA-AATAT
1 CAAAT-TCTTACCAATTTGAA-ACAAAAT
20337827 CAAATTCTTACCAA
1 CAAATTCTTACCAA
20337841 CAAATAGTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (27 bp):
CAAATTCTTACCAATTTGAAACAAAAT
Found at i:20338523 original size:19 final size:22
Alignment explanation
Indices: 20338501--20338543 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
20338491 TAGTTTTTTG
20338501 AAAATTTT-A-TTATT-TTAAA
1 AAAATTTTCATTTATTGTTAAA
20338520 AAAATTTTCATTTATTGTTAAA
1 AAAATTTTCATTTATTGTTAAA
20338542 AA
1 AA
20338544 TAACATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 1 0.05
21 5 0.24
22 7 0.33
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AAAATTTTCATTTATTGTTAAA
Found at i:20339048 original size:21 final size:22
Alignment explanation
Indices: 20339009--20339059 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
20338999 TCAAAAGGAA
* *
20339009 AAATTATAAATTTATTTATCAAT
1 AAATT-TAAATATATTTATAAAT
20339032 AAATTTAAATAT-TTTATAAAT
1 AAATTTAAATATATTTATAAAT
*
20339053 ATATTTA
1 AAATTTA
20339060 TTTAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 6 0.24
23 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTAAATATATTTATAAAT
Found at i:20339053 original size:11 final size:12
Alignment explanation
Indices: 20339012--20339060 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
20339002 AAAGGAAAAA
*
20339012 TTATAAATTTAT
1 TTATAAATATAT
* *
20339024 TTATCAATA-AA
1 TTATAAATATAT
20339035 TT-TAAATAT-T
1 TTATAAATATAT
20339045 TTATAAATATAT
1 TTATAAATATAT
20339057 TTAT
1 TTAT
20339061 TTAATATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
10 7 0.24
11 10 0.34
12 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
TTATAAATATAT
Found at i:20347847 original size:348 final size:347
Alignment explanation
Indices: 20346874--20347918 Score: 2036
Period size: 347 Copynumber: 3.0 Consensus size: 347
20346864 GTTTGCTTTT
20346874 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
1 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
20346939 TAAAATCATATTCATGAGAAATACTACTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTTC
66 TAAAATCATATTCATGAGAAATACTACTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTTC
20347004 CATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCTT
131 CATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCTT
20347069 TCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAGA
196 TCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAGA
20347134 AACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATCT
261 AACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATCT
20347199 GCACACCCAGATAAAGGTTTCA
326 GCACACCCAGATAAAGGTTTCA
20347221 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
1 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
20347286 TAAAATCATATTCATGAGAAATACTACTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTTC
66 TAAAATCATATTCATGAGAAATACTACTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTTC
* *
20347351 CATGCCTTGTTAGATTTTATTAGCATAATGACTGTTTTCCACTTAATAGAGGAAACTAATTGCTT
131 CATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCTT
20347416 TCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAGA
196 TCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAGA
*
20347481 AACCAAGATGTTAAGGGAGAAAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATCT
261 AACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATCT
20347546 GCACACCCAGATAAAGGTTTCA
326 GCACACCCAGATAAAGGTTTCA
20347568 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
1 ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
*
20347633 TAAAATCATATTTATGAGAAATACTACTTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTT
66 TAAAATCATATTCATGAGAAATACTAC-TTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTT
20347698 CCATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCT
130 CCATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCT
20347763 TTCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAG
195 TTCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAG
*
20347828 AAACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGAAATTAGAGATC
260 AAACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATC
20347893 TGCACACCCAGATAAAGGTTTCA
325 TGCACACCCAGATAAAGGTTTCA
20347916 ATT
1 ATT
20347919 CATTCAGTTG
Statistics
Matches: 689, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
347 435 0.63
348 254 0.37
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (347 bp):
ATTATCTTTTCTTCCTATAGGAGATATATGCTCCTTGTCTTTAAAAATTTACTGCCATTGATTCT
TAAAATCATATTCATGAGAAATACTACTTTTTTCCCTGAAAAGAAGTATTACTCCTTGGATTTTC
CATGCCTTGCTAGATTTTATTAGCATAATGACTGTTTTCCAGTTAATAGAGGAAACTAATTGCTT
TCCTTTCTGAACAGTCTAGAGAAAAGGTTTGAATTGCTTTTGAGAAGAAAAGCAGGCAACTCAGA
AACCAAGATGTTAAGGGAGATAACCCGTATGCAGTAGATAAAACGAGGGCAGCAATTAGAGATCT
GCACACCCAGATAAAGGTTTCA
Found at i:20354827 original size:9 final size:9
Alignment explanation
Indices: 20354813--20354844 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20354803 CAAAGAGTTC
20354813 GAGAAGAAG
1 GAGAAGAAG
20354822 GAGAAGAAG
1 GAGAAGAAG
20354831 GAGAAGAAG
1 GAGAAGAAG
*
20354840 AAGAA
1 GAGAA
20354845 AATAAGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (9 bp):
GAGAAGAAG
Found at i:20355167 original size:29 final size:30
Alignment explanation
Indices: 20355116--20355188 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
20355106 ATAAAAAATT
* * *
20355116 ATATATTTATTTTTAAAATAATTTT-TTA-G
1 ATATATTTA-TGTCAAAATAATTTTAATATG
20355145 ATATATTTATGTCAAAATAAATTTTAATATG
1 ATATATTTATGTCAAAAT-AATTTTAATATG
20355176 ATATAATTTATGT
1 ATAT-ATTTATGT
20355189 TTTATATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 15 0.41
30 2 0.05
31 5 0.14
32 8 0.22
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (30 bp):
ATATATTTATGTCAAAATAATTTTAATATG
Found at i:20355830 original size:27 final size:29
Alignment explanation
Indices: 20355795--20355887 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
20355785 TAATTATTTA
* *
20355795 TTATTTTAGTCATAT-T-TTTGTATATAT
1 TTATATTAGTCATATCTATTTATATATAT
*
20355822 TTATATTAGTCATGTCTATTTATATATAT
1 TTATATTAGTCATATCTATTTATATATAT
* * * * *
20355851 TTATGTTAGTCGTGTCTATTTGTATAGAT
1 TTATATTAGTCATATCTATTTATATATAT
*
20355880 TCATATTA
1 TTATATTA
20355888 TTTGTATTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.24
28 1 0.02
29 41 0.75
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (29 bp):
TTATATTAGTCATATCTATTTATATATAT
Found at i:20355848 original size:29 final size:29
Alignment explanation
Indices: 20355815--20355887 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
20355805 CATATTTTTG
20355815 TATATATTTATATTAGTCATGTCTATTTA
1 TATATATTTATATTAGTCATGTCTATTTA
* * *
20355844 TATATATTTATGTTAGTCGTGTCTATTTG
1 TATATATTTATATTAGTCATGTCTATTTA
* *
20355873 TATAGATTCATATTA
1 TATATATTTATATTA
20355888 TTTGTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (29 bp):
TATATATTTATATTAGTCATGTCTATTTA
Found at i:20359914 original size:14 final size:15
Alignment explanation
Indices: 20359883--20359918 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
20359873 CATGAACAAT
*
20359883 AAACAAATAATAACC
1 AAACAAATAATAAAC
20359898 AAACAAAT-ATAAAC
1 AAACAAATAATAAAC
20359912 AAACAAA
1 AAACAAA
20359919 CCCAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.72, C:0.17, G:0.00, T:0.11
Consensus pattern (15 bp):
AAACAAATAATAAAC
Found at i:20362773 original size:6 final size:7
Alignment explanation
Indices: 20362753--20362782 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
20362743 AAGTCTAATC
20362753 TAATTTT
1 TAATTTT
20362760 TAATTTT
1 TAATTTT
20362767 TAATTTT
1 TAATTTT
20362774 TAATATTT
1 TAAT-TTT
20362782 T
1 T
20362783 TATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TAATTTT
Found at i:20362791 original size:17 final size:16
Alignment explanation
Indices: 20362753--20362794 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
20362743 AAGTCTAATC
20362753 TAATTTTT-A-ATTTT
1 TAATTTTTAATATTTT
20362767 TAATTTTTAATATTTT
1 TAATTTTTAATATTTT
*
20362783 TATTATTTTAAT
1 TAAT-TTTTAAT
20362795 TAAAATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 1 0.04
16 8 0.33
17 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTTAATATTTT
Found at i:20369019 original size:60 final size:61
Alignment explanation
Indices: 20368947--20369067 Score: 158
Period size: 60 Copynumber: 2.0 Consensus size: 61
20368937 TTGGAACAAT
** * * *
20368947 CTTATACACCTTAAGTGTATACCAAGTCT-TAAACAGTCTT-ATTTA-TGCTTTCACTTTTCC
1 CTTATACACCTTAAGCATATACCAAGTATGAAAACAAT-TTCATTTACT-CTTTCACTTTTCC
20369007 CTTATACACCTTAAGCATATACCAAGTATGAAAACAATTTCATTTACTCTTTCACTTTTCC
1 CTTATACACCTTAAGCATATACCAAGTATGAAAACAATTTCATTTACTCTTTCACTTTTCC
20369068 TACCTACATC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 28 0.53
61 24 0.45
62 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (61 bp):
CTTATACACCTTAAGCATATACCAAGTATGAAAACAATTTCATTTACTCTTTCACTTTTCC
Found at i:20375269 original size:22 final size:23
Alignment explanation
Indices: 20375242--20375289 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
20375232 CCTAAAATTA
20375242 ATAAAATATTATTTTTT-AAAAT
1 ATAAAATATTATTTTTTAAAAAT
20375264 ATAAAATATTATTTTTTAAAAAT
1 ATAAAATATTATTTTTTAAAAAT
20375287 ATA
1 ATA
20375290 TTATATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTTTTTAAAAAT
Found at i:20378566 original size:18 final size:18
Alignment explanation
Indices: 20378532--20378573 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20378522 TGATGCATGA
20378532 GTTAAAATAATTGTATTT
1 GTTAAAATAATTGTATTT
*
20378550 GTTATAATAATAT-TATTT
1 GTTAAAATAAT-TGTATTT
*
20378568 ATTAAA
1 GTTAAA
20378574 TTCATTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
GTTAAAATAATTGTATTT
Found at i:20379985 original size:25 final size:24
Alignment explanation
Indices: 20379942--20379990 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
20379932 ATTTATTTAG
*
20379942 TTATTTAATATATAATAAATAAAT
1 TTATATAATATATAATAAATAAAT
*
20379966 TTATATAATTATATATTAAATAAAT
1 TTATATAA-TATATAATAAATAAAT
20379991 ATGTAACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATATAATATATAATAAATAAAT
Found at i:20381917 original size:15 final size:15
Alignment explanation
Indices: 20381897--20381925 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20381887 AATCTAATAT
20381897 ATATATATATTATAG
1 ATATATATATTATAG
20381912 ATATATATATTATA
1 ATATATATATTATA
20381926 TTATATTACA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATATATATTATAG
Found at i:20382094 original size:27 final size:26
Alignment explanation
Indices: 20382035--20382096 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
20382025 TTTATTTATC
* *
20382035 AAATAAAATTTTTTAATAAATTATTT
1 AAATGAAATATTTTAATAAATTATTT
20382061 AAATGAAATATTTTAGAT-AATTATTT
1 AAATGAAATATTTTA-ATAAATTATTT
20382087 AAATTGAAAT
1 AAA-TGAAAT
20382097 CAAAATCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
AAATGAAATATTTTAATAAATTATTT
Found at i:20383080 original size:2 final size:2
Alignment explanation
Indices: 20383073--20383099 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20383063 TCAATCAAAC
20383073 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20383100 CACACACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20389215 original size:19 final size:19
Alignment explanation
Indices: 20389173--20389301 Score: 82
Period size: 20 Copynumber: 6.6 Consensus size: 19
20389163 TAAGGTTGTG
*
20389173 CTTAGGG-TTTAGGATTTTA
1 CTTAGGGTTTTAGG-TTTCA
*
20389192 TTTAGGGTTTTAGGTTTCA
1 CTTAGGGTTTTAGGTTTCA
* *
20389211 CTTAGGATTTAAGGTTTTCA
1 CTTAGGGTTTTAGG-TTTCA
*** *
20389231 CTTATATTTTTAGGGTTCA
1 CTTAGGGTTTTAGGTTTCA
* *
20389250 CCTAGGGTTTT-GAGTTTTA
1 CTTAGGGTTTTAG-GTTTCA
* *
20389269 TTTTAGGGTTTTAGCATTTCA
1 -CTTAGGGTTTTAG-GTTTCA
*
20389290 CTTAAGGTTTTA
1 CTTAGGGTTTTA
20389302 AAAATTTACA
Statistics
Matches: 82, Mismatches: 23, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
18 1 0.01
19 36 0.44
20 40 0.49
21 5 0.06
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.50
Consensus pattern (19 bp):
CTTAGGGTTTTAGGTTTCA
Found at i:20389231 original size:20 final size:19
Alignment explanation
Indices: 20389193--20389234 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
20389183 AGGATTTTAT
* *
20389193 TTAGGGTTTTAGGTTTCAC
1 TTAGGATTTAAGGTTTCAC
20389212 TTAGGATTTAAGGTTTTCAC
1 TTAGGATTTAAGG-TTTCAC
20389232 TTA
1 TTA
20389235 TATTTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (19 bp):
TTAGGATTTAAGGTTTCAC
Found at i:20389480 original size:3 final size:3
Alignment explanation
Indices: 20389431--20389456 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20389421 TATTAAAATT
20389431 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20389457 TATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20389681 original size:13 final size:14
Alignment explanation
Indices: 20389635--20389686 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
20389625 TAGGGATTTA
20389635 AATTTT-TTATTAT
1 AATTTTATTATTAT
20389648 --TTTTATTATTAT
1 AATTTTATTATTAT
*
20389660 AAATTTATTATT-T
1 AATTTTATTATTAT
*
20389673 ACTTTTATTATTAT
1 AATTTTATTATTAT
20389687 TTTTAAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 11 0.34
14 10 0.31
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTTATTATTAT
Found at i:20389686 original size:27 final size:26
Alignment explanation
Indices: 20389633--20389686 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
20389623 AATAGGGATT
* *
20389633 TAAATTTTTTATTATTTTTATTATTA
1 TAAATTTATTATTACTTTTATTATTA
20389659 TAAATTTATTATTTACTTTTATTATTA
1 TAAATTTATTA-TTACTTTTATTATTA
20389686 T
1 T
20389687 TTTTAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TAAATTTATTATTACTTTTATTATTA
Found at i:20390493 original size:16 final size:17
Alignment explanation
Indices: 20390474--20390512 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
20390464 CTGCATTCTT
*
20390474 TTTTTTTTTGC-CATAG
1 TTTTTTTTTACACATAG
*
20390490 TTTTTTTTTACACTTAG
1 TTTTTTTTTACACATAG
20390507 TTTTTT
1 TTTTTT
20390513 CATGCTACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTTTTTTTACACATAG
Found at i:20391102 original size:31 final size:31
Alignment explanation
Indices: 20390991--20391109 Score: 86
Period size: 31 Copynumber: 3.9 Consensus size: 31
20390981 GATGACCATA
*
20390991 ACTAAA-CTGCAAGTCAAATGAAGTGA-TCAAG
1 ACTAAATC-GCAAGTCAAATGAGGTGACT-AAG
*** **
20391022 ACTAAATCGCAAGTTGCATGAGGTGAC-GGG
1 ACTAAATCGCAAGTCAAATGAGGTGACTAAG
*
20391052 ACTAAATCG-TAGATCAAATGAGGTGACTAAG
1 ACTAAATCGCAAG-TCAAATGAGGTGACTAAG
* *
20391083 ACTAAA-CTGTAAGTTAAATGAGGTGAC
1 ACTAAATC-GCAAGTCAAATGAGGTGAC
20391110 CACTAATCTG
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
29 2 0.03
30 22 0.32
31 41 0.60
32 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (31 bp):
ACTAAATCGCAAGTCAAATGAGGTGACTAAG
Found at i:20391212 original size:32 final size:31
Alignment explanation
Indices: 20391176--20391244 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
20391166 ATAATCTGGA
*
20391176 CTTAAAATCTCATTGGTGTCAGGTAAATTGAG
1 CTTAAAATCTCATTGGTATCA-GTAAATTGAG
* * * * *
20391208 CTTAAATTTTTATTGGTATTAGTTAATTGAG
1 CTTAAAATCTCATTGGTATCAGTAAATTGAG
20391239 CTTAAA
1 CTTAAA
20391245 TTTCATAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (31 bp):
CTTAAAATCTCATTGGTATCAGTAAATTGAG
Found at i:20391471 original size:33 final size:32
Alignment explanation
Indices: 20391434--20391511 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
20391424 AAATTGGACT
* * * *
20391434 TTAAATTTTCATTAGATTACAGCTAAATTGTGC
1 TTAAATTTTCATTAGATGACAACT-AATCGGGC
* * *
20391467 TTAAATTTTTATTGGATGCCAACTAATCGGGC
1 TTAAATTTTCATTAGATGACAACTAATCGGGC
20391499 TTAAATTTTCATT
1 TTAAATTTTCATT
20391512 GAGTGTTAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 18 0.49
33 19 0.51
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (32 bp):
TTAAATTTTCATTAGATGACAACTAATCGGGC
Found at i:20391532 original size:32 final size:32
Alignment explanation
Indices: 20391496--20391605 Score: 109
Period size: 32 Copynumber: 3.4 Consensus size: 32
20391486 CAACTAATCG
* *
20391496 GGCTTAAATTTTCATTGAGTGTTAGTTAAACT
1 GGCTTAAATTTTCATTGAGTGCTAGATAAACT
* *
20391528 GGCTTAAATTTTCATTG-GTGCCAGATAATCT
1 GGCTTAAATTTTCATTGAGTGCTAGATAAACT
* *
20391559 GAGCTTAAA-TTTCATT-AGGTGCTAGCTAGACT
1 G-GCTTAAATTTTCATTGA-GTGCTAGATAAACT
*
20391591 AGGCTTAGATTTTCA
1 -GGCTTAAATTTTCA
20391606 CAAGAGTCAG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
31 18 0.28
32 40 0.62
33 6 0.09
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
GGCTTAAATTTTCATTGAGTGCTAGATAAACT
Found at i:20391545 original size:64 final size:64
Alignment explanation
Indices: 20391465--20391605 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
20391455 GCTAAATTGT
* * * *
20391465 GCTTAAATTTTTATTGGATGCCA-ACTAATC-GGGCTTAAATTTTCATT-GAGTGTTAGTTAAAC
1 GCTTAAATTTTCATTGG-TGCCAGA-TAATCTGAGCTTAAA-TTTCATTAG-GTGCTAGCTAAAC
20391527 T-G
62 TAG
*
20391529 GCTTAAATTTTCATTGGTGCCAGATAATCTGAGCTTAAATTTCATTAGGTGCTAGCTAGACTAG
1 GCTTAAATTTTCATTGGTGCCAGATAATCTGAGCTTAAATTTCATTAGGTGCTAGCTAAACTAG
*
20391593 GCTTAGATTTTCA
1 GCTTAAATTTTCA
20391606 CAAGAGTCAG
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 28 0.42
64 39 0.58
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (64 bp):
GCTTAAATTTTCATTGGTGCCAGATAATCTGAGCTTAAATTTCATTAGGTGCTAGCTAAACTAG
Found at i:20395239 original size:18 final size:19
Alignment explanation
Indices: 20395203--20395241 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20395193 GAGAGGAAGG
*
20395203 AAAAAGTAAAAGAAGAGAA
1 AAAAAGTAAAAGAAAAGAA
*
20395222 AAAAAG-AAAGGAAAAGAA
1 AAAAAGTAAAAGAAAAGAA
20395240 AA
1 AA
20395242 CCCTGGTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (19 bp):
AAAAAGTAAAAGAAAAGAA
Found at i:20399748 original size:61 final size:60
Alignment explanation
Indices: 20399646--20400132 Score: 575
Period size: 61 Copynumber: 8.2 Consensus size: 60
20399636 TCTTGTGCAG
* * * *
20399646 GGAAAATTGATACTTTCAACTTTTCCCCAAGAAATA-TTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTT-GAAATTTT-ATTTTTAA
20399707 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTGAAATTTTATTTTTAA
* * *
20399767 GGAAAATTGATGCTTTCAACTTTTTCTCAAAAAAACCTTTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAC--TTTTTTTGAAATTTTATTTTTAA
* * *** * *
20399829 GGAAAATTGATACTTTCAACTTTTCCT-TAAAAATA-TTTTTGAAAAATTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTGAAATTTTATTTTTAA
*
20399887 GGAAAATTGATACTTTCAACTTTTTCTC-AAAAAAACTTTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAC--TTTTTTTGAAATTTTATTTTTAA
* *
20399948 GGAAAATTGATACTTTCAACTTTTTCTCAAAACAAACCTTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAA-AAAACTTTTTTTGAAATTTTATTTTTAA
* * *
20400009 GAAAAATT-ATTACTTTCAACTTTTTCTC--AAAAAAC-CTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGA-TACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTGAAATTTTATTTTTAA
* * * * *
20400066 AGAAAATTGATGCTTTCAACTTTTCCCCAAAAATATA-TTTTTTT--AATTTT-TATTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-AAACTTTTTTTGAAATTTTATTTTTAA
*
20400123 AGAAAATTGA
1 GGAAAATTGA
20400133 ATAATAAAAC
Statistics
Matches: 375, Mismatches: 36, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
57 58 0.15
58 61 0.16
59 5 0.01
60 49 0.13
61 140 0.37
62 58 0.15
63 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTGAAATTTTATTTTTAA
Found at i:20399992 original size:180 final size:179
Alignment explanation
Indices: 20399646--20400132 Score: 661
Period size: 180 Copynumber: 2.7 Consensus size: 179
20399636 TCTTGTGCAG
* * *
20399646 GGAAAATTGATACTTTCAACTTTTCCCCAAGAAATATTTTTTTGGAAATTTTGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAA-AAATA-CTTTTT-GAAAATTTGATTTTCAAGGAA
20399711 AATTGATACTTTCAACTTTTCCTCAAAAAAAAC-TTTTTTTGAAATTTTATTTTTAAGGAAAATT
63 AATTGATACTTTCAACTTTTCCTC-AAAAAAACTTTTTTTTGAAATTTTATTTTTAAGGAAAATT
*
20399775 GATGCTTTCAACTTTTTCTCAAAAAAACCTTTTTTTTTGAAATTTTATTTTTAA
127 GATACTTTCAACTTTTTCTCAAAAAAACC-TTTTTTTTGAAATTTTATTTTTAA
*
20399829 GGAAAATTGATACTTTCAACTTTTCCTTAAAAATA-TTTTTGAAAAATTTGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTG-AAAATTTGATTTTCAAGGAAAA
*
20399893 TTGATACTTTCAACTTTTTCTCAAAAAAACTTTTTTTTTGAAATTTTATTTTTAAGGAAAATTGA
65 TTGATACTTTCAACTTTTCCTCAAAAAAAC-TTTTTTTTGAAATTTTATTTTTAAGGAAAATTGA
20399958 TACTTTCAACTTTTTCTCAAAACAAACC-TTTTTTTGAAATTTTATTTTTAA
129 TACTTTCAACTTTTTCTCAAAA-AAACCTTTTTTTTGAAATTTTATTTTTAA
* * * * *
20400009 GAAAAATT-ATTACTTTCAACTTTTTCTCAAAAA-ACCTTTTTG-AAATTTTATTTTTAAAGAAA
1 GGAAAATTGA-TACTTTCAACTTTTCCTCAAAAATA-CTTTTTGAAAATTTGATTTTCAAGGAAA
* * * * *
20400071 ATTGATGCTTTCAACTTTTCCCCAAAAATA-TATTTTTTT--AATTTT-TATTTAAAGAAAATTG
64 ATTGATACTTTCAACTTTTCCTCAAAAAAACT-TTTTTTTGAAATTTTATTTTTAAGGAAAATTG
20400132 A
128 A
20400133 ATAATAAAAC
Statistics
Matches: 279, Mismatches: 17, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
175 15 0.05
176 6 0.02
177 1 0.00
178 7 0.03
179 54 0.19
180 98 0.35
181 60 0.22
182 10 0.04
183 28 0.10
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (179 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTGAAAATTTGATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATA
CTTTCAACTTTTTCTCAAAAAAACCTTTTTTTTGAAATTTTATTTTTAA
Found at i:20400158 original size:6 final size:5
Alignment explanation
Indices: 20400135--20400218 Score: 50
Period size: 5 Copynumber: 16.4 Consensus size: 5
20400125 AAAATTGAAT
*
20400135 AATAA AACAA AATAAA AATGAA AAT-A AA-AA AATAA AATAA AGA-AA
1 AATAA AATAA AAT-AA AAT-AA AATAA AATAA AATAA AATAA A-ATAA
* * *
20400180 AGTAA AACAAA AACAAA AATAA AATAA AGATAA AA-AA AA
1 AATAA AA-TAA AA-TAA AATAA AATAA A-ATAA AATAA AA
20400219 CATTAACTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
4 10 0.15
5 29 0.45
6 26 0.40
ACGTcount: A:0.80, C:0.04, G:0.05, T:0.12
Consensus pattern (5 bp):
AATAA
Found at i:20400167 original size:14 final size:13
Alignment explanation
Indices: 20400148--20400203 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
20400138 AAAACAAAAT
20400148 AAAAATGAAAATAA
1 AAAAAT-AAAATAA
20400162 AAAAATAAAATAA
1 AAAAATAAAATAA
*
20400175 AGAAAAGTAAAACAA
1 A-AAAA-TAAAATAA
*
20400190 AAACA-AAAATAA
1 AAAAATAAAATAA
20400202 AA
1 AA
20400204 TAAAGATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.22
13 8 0.22
14 13 0.35
15 8 0.22
ACGTcount: A:0.80, C:0.04, G:0.05, T:0.11
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:20401279 original size:11 final size:11
Alignment explanation
Indices: 20401264--20401364 Score: 56
Period size: 11 Copynumber: 9.5 Consensus size: 11
20401254 ATAAAAGAAG
20401264 AAAAAAAA-AT
1 AAAAAAAATAT
* *
20401274 ATAAAATA-AT
1 AAAAAAAATAT
*
20401284 AATAAAAATA-
1 AAAAAAAATAT
*
20401294 AAATAAAAATAG
1 AAA-AAAAATAT
*
20401306 AATAAAAATA-
1 AAAAAAAATAT
20401316 AAAAATAAA-AT
1 AAAAA-AAATAT
20401327 AAAATAAAATA-
1 AAAA-AAAATAT
*
20401338 AAATAAAAT-T
1 AAAAAAAATAT
20401348 AAAATAAAAT-T
1 AAAA-AAAATAT
20401359 AAAAAA
1 AAAAAA
20401365 TAAAACATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
10 30 0.42
11 38 0.53
12 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.01, T:0.20
Consensus pattern (11 bp):
AAAAAAAATAT
Found at i:20401284 original size:28 final size:26
Alignment explanation
Indices: 20401249--20401369 Score: 102
Period size: 29 Copynumber: 4.4 Consensus size: 26
20401239 TAGCTAAAAT
*
20401249 AAAAAATAAAAGAAGAAAAAAAAATATA
1 AAAAAATAAAA-AATAAAAAAAAATA-A
*
20401277 AAATAATAATAAAAATAAAATAAAAATAGA
1 AAAAAAT-A-AAAAATAAAA-AAAAATA-A
*
20401307 ATAAAAATAAAAAATAAAATAAAATAA
1 A-AAAAATAAAAAATAAAAAAAAATAA
* * *
20401334 AATAAAAT-AAAATTAAAATAAAAT-T
1 AA-AAAATAAAAAATAAAAAAAAATAA
20401359 AAAAAATAAAA
1 AAAAAATAAAA
20401370 CATATACCTA
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.06
25 5 0.06
26 16 0.20
27 7 0.09
28 12 0.15
29 17 0.21
30 13 0.16
31 5 0.06
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.18
Consensus pattern (26 bp):
AAAAAATAAAAAATAAAAAAAAATAA
Found at i:20401341 original size:44 final size:45
Alignment explanation
Indices: 20401243--20401369 Score: 163
Period size: 44 Copynumber: 2.9 Consensus size: 45
20401233 AGTAAATAGC
* *
20401243 TAAAATAAAA-AATAAA-AGAAGAAAAA-AAAATATAAAATAATAA
1 TAAAATAAAATAA-AAATAGAATAAAAATAAAAAATAAAATAATAA
20401286 TAAAAATAAAATAAAAATAGAATAAAAATAAAAAATAAAATAA-AA
1 T-AAAATAAAATAAAAATAGAATAAAAATAAAAAATAAAATAATAA
* * *
20401331 TAAAATAAAATAAAATTAAAATAAAATTAAAAAATAAAA
1 TAAAATAAAATAAAAATAGAATAAAAATAAAAAATAAAA
20401370 CATATACCTA
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.01
44 47 0.63
45 14 0.19
46 13 0.17
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (45 bp):
TAAAATAAAATAAAAATAGAATAAAAATAAAAAATAAAATAATAA
Found at i:20401369 original size:5 final size:5
Alignment explanation
Indices: 20401251--20401362 Score: 106
Period size: 5 Copynumber: 21.8 Consensus size: 5
20401241 GCTAAAATAA
*
20401251 AAAAT AAAAG AAGAA- AAAA- AAATAT AAAAT AATAAT AAAAAT AAAAT
1 AAAAT AAAAT AA-AAT AAAAT AAA-AT AAAAT AA-AAT -AAAAT AAAAT
* *
20401298 AAAAAT AGAAT AAAA- ATAA- AAAAT AAAAT AAAAT AAAAT AAAAT AAAATT
1 -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
20401348 AAAAT AAAATT AAAA
1 AAAAT AAAA-T AAAA
20401363 AATAAAACAT
Statistics
Matches: 93, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
4 11 0.12
5 54 0.58
6 26 0.28
7 2 0.02
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20401530 original size:8 final size:8
Alignment explanation
Indices: 20401519--20401583 Score: 60
Period size: 9 Copynumber: 7.6 Consensus size: 8
20401509 ACATTTTCAT
20401519 TTTTTTTA
1 TTTTTTTA
20401527 TTTTTTT-
1 TTTTTTTA
*
20401534 TTGGTTTTTT
1 TT--TTTTTA
20401544 TGTTTTTTA
1 T-TTTTTTA
20401553 TATTTTTTA
1 T-TTTTTTA
*
20401562 TATTTTTA
1 TTTTTTTA
20401570 TATTTTTTA
1 T-TTTTTTA
20401579 TTTTT
1 TTTTT
20401584 GACCAAAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
7 2 0.04
8 18 0.38
9 26 0.54
10 1 0.02
11 1 0.02
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:20401541 original size:17 final size:17
Alignment explanation
Indices: 20401520--20401583 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
20401510 CATTTTCATT
*
20401520 TTTTTTATTTTTTTTTGG
1 TTTTTTATTTTTTTTT-A
*
20401538 TTTTTT-TGTTTTTTATA
1 TTTTTTAT-TTTTTTTTA
* *
20401555 TTTTTTATATTTTTATA
1 TTTTTTATTTTTTTTTA
20401572 TTTTTTATTTTT
1 TTTTTTATTTTT
20401584 GACCAAAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTATTTTTTTTTA
Found at i:20403781 original size:22 final size:19
Alignment explanation
Indices: 20403749--20403793 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
20403739 TTTTTTTAGC
20403749 AAAAAAAAAAATCGTAAATAAT
1 AAAAAAAAAAAT--TAAA-AAT
*
20403771 AAAAAATAAAATTAAAAAT
1 AAAAAAAAAAATTAAAAAT
20403790 AAAA
1 AAAA
20403794 CCAAAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 4 0.18
22 11 0.50
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAAAAAAATTAAAAAT
Found at i:20408202 original size:15 final size:16
Alignment explanation
Indices: 20408182--20408224 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20408172 GTTTATCAAT
20408182 AATTTTTTACCTTA-A
1 AATTTTTTACCTTAGA
*
20408197 AATTTTTT-TCTTAGA
1 AATTTTTTACCTTAGA
20408212 AATTTTCTTACCT
1 AATTTT-TTACCT
20408225 ATCAAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 2 0.09
17 2 0.09
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.56
Consensus pattern (16 bp):
AATTTTTTACCTTAGA
Found at i:20410587 original size:5 final size:5
Alignment explanation
Indices: 20410577--20410635 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
20410567 GAAAGAATAC
* * * *
20410577 AAAAG AAAAG AAAAG AAAA- AAAATG AAAGG AAAGG AAAGG AAGAAT AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAA-G AAAAG AAAAG AAAAG AA-AAG AAAAG
20410628 -AAAG AAAA
1 AAAAG AAAA
20410636 AGACAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.17
5 32 0.70
6 6 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:20411835 original size:5 final size:5
Alignment explanation
Indices: 20411822--20411859 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
20411812 ATGGGGACGT
*
20411822 AAAAA AAAAG AAAA- AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
20411860 ATGGTTATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:20413682 original size:33 final size:32
Alignment explanation
Indices: 20413630--20413948 Score: 162
Period size: 33 Copynumber: 9.7 Consensus size: 32
20413620 AGTCAAGCTC
* * *
20413630 AGTTTACCTGGCATCAATGAAAGTTTAAGCCT
1 AGTTTAGCTAGCACCAATGAAAGTTTAAGCCT
* *
20413662 AGCTTAGCTAGCACCTAATGAAATTTTAAGCCT
1 AGTTTAGCTAGCACC-AATGAAAGTTTAAGCCT
* * **
20413695 AGTTTATCTGGCACCAAAAAAAGATTTTAAG-CT
1 AGTTTAGCTAGCACCAATGAAAG--TTTAAGCCT
* *
20413728 CAGTTTA-CTTGGCACCAATGAAAGTTTAAGCAT
1 -AGTTTAGC-TAGCACCAATGAAAGTTTAAGCCT
* * ** *
20413761 GGTTTAG-TTGCCACTTGATGAAAATTTAAAGCCT
1 AGTTTAGCTAG-CAC-CAATGAAAGTTT-AAGCCT
* * *
20413795 AGTTTACCTAGTACCAATGAAAGTTTAAGCTT
1 AGTTTAGCTAGCACCAATGAAAGTTTAAGCCT
** * ** *
20413827 AACTTAGTTATTACCCAATGAAATTTTAAG-CT
1 AGTTTAGCTAGCA-CCAATGAAAGTTTAAGCCT
* ** * * *
20413859 CAATTTATATTGCACCAAAGAAAGGTTTCAAGCAT
1 -AGTTTAGCTAGCACCAATGAAA-GTTT-AAGCCT
* * * *
20413894 AGTTTACCTAGCATCAGTGAAAGTTTAAGCCC
1 AGTTTAGCTAGCACCAATGAAAGTTTAAGCCT
*
20413926 AGTTTACCTAGCACCCAAT-AAAG
1 AGTTTAGCTAGCA-CCAATGAAAG
20413949 ATTTTAAGTA
Statistics
Matches: 215, Mismatches: 55, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
31 2 0.01
32 73 0.34
33 82 0.38
34 55 0.26
35 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (32 bp):
AGTTTAGCTAGCACCAATGAAAGTTTAAGCCT
Found at i:20414190 original size:34 final size:32
Alignment explanation
Indices: 20414146--20414212 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 32
20414136 ACCTTCGATG
*
20414146 AAATTTTAAGCCTAGTTTATCTAGTCCCTAATGA
1 AAATTGTAAGCCTAGTTTATCTAG--CCTAATGA
*
20414180 AAATTGTAAGCTTAGTTTATCTAGCCTAATGA
1 AAATTGTAAGCCTAGTTTATCTAGCCTAATGA
20414212 A
1 A
20414213 TTTTTAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 9 0.29
34 22 0.71
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
AAATTGTAAGCCTAGTTTATCTAGCCTAATGA
Found at i:20414452 original size:23 final size:22
Alignment explanation
Indices: 20414415--20414457 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
20414405 CCAGTTTAAC
* *
20414415 TGGCACATAAGCCTAAGATTAGT
1 TGGCACAAAAACCT-AGATTAGT
20414438 TGGCACAAAAACCTAGATTA
1 TGGCACAAAAACCTAGATTA
20414458 ATGGTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (22 bp):
TGGCACAAAAACCTAGATTAGT
Found at i:20414663 original size:20 final size:20
Alignment explanation
Indices: 20414596--20414666 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
20414586 AACCAAAAAA
* *
20414596 AAAAAAAAAAACATAAACAAAC
1 AAAAAAAATAACA-AAA-ACAC
*
20414618 AAACAAAAATAACAATAACA-
1 AAA-AAAAATAACAAAAACAC
*
20414638 ATAAAAAGATAACAAAAACAC
1 A-AAAAAAATAACAAAAACAC
20414659 AAAAAAAA
1 AAAAAAAA
20414667 GGAAAGAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 21 0.52
21 5 0.12
22 5 0.12
23 9 0.22
ACGTcount: A:0.79, C:0.13, G:0.01, T:0.07
Consensus pattern (20 bp):
AAAAAAAATAACAAAAACAC
Found at i:20415504 original size:143 final size:149
Alignment explanation
Indices: 20415174--20415517 Score: 381
Period size: 152 Copynumber: 2.3 Consensus size: 149
20415164 CTGAGCTTGA
*
20415174 ATTTTCATGAAACTTTTT-AGATCTTAATTTCATAATATTTCATGATTTTTCATGTATTTAAAAA
1 ATTTTTATGAAA-TTTTTCAGATCTTAATTTCATAATATTTCATGATTTTTCATGTATTTAAAAA
**
20415238 TCATAGTAATACCTTGAGAAGTGTGAAATTATCAAAATACCTTTATAAGAGTATTTTCGTAATTT
65 TCATAGTAATACCTCAAGAAGTGTGAAATTATCAAAATACCTTTATAAGAGTATTTTCGTAATTT
*
20415303 GGCCTTGGCCTTCTCGAGCTAGG
130 GGACTT---CTTCTCGAGCTAGG
* * * * * * *
20415326 ACTTTTATGAAACTTTTCATATATTAATTTCATAATATTTTATGATTTTTTATGTATTT-GAAAT
1 ATTTTTATGAAATTTTTCAGATCTTAATTTCATAATATTTCATGATTTTTCATGTATTTAAAAAT
* *
20415390 CA-AGGTAGTATCC-CAAGAGGTGTGAAATTA-CTAAAATACCTTT-T-AGAGGTATTTT-GTAA
66 CATA-GTAATA-CCTCAAGAAGTGTGAAATTATC-AAAATACCTTTATAAGA-GTATTTTCGTAA
*
20415449 TTT-GACTT-TT-TCGAGCTCA-T
127 TTTGGACTTCTTCTCGAGCT-AGG
*
20415469 ATTTTTATGAAATTTTTCAGATCTTAATTTTATAATATTTCAT-ATTTTT
1 ATTTTTATGAAATTTTTCAGATCTTAATTTCATAATATTTCATGATTTTT
20415518 GGTGTTTTAA
Statistics
Matches: 166, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
142 6 0.04
143 44 0.27
144 3 0.02
148 4 0.02
149 10 0.06
150 10 0.06
151 40 0.24
152 49 0.30
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (149 bp):
ATTTTTATGAAATTTTTCAGATCTTAATTTCATAATATTTCATGATTTTTCATGTATTTAAAAAT
CATAGTAATACCTCAAGAAGTGTGAAATTATCAAAATACCTTTATAAGAGTATTTTCGTAATTTG
GACTTCTTCTCGAGCTAGG
Found at i:20415684 original size:12 final size:12
Alignment explanation
Indices: 20415667--20415699 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
20415657 AATGTAGACT
20415667 ATTGAATCTCTC
1 ATTGAATCTCTC
20415679 ATTGAATCTCTC
1 ATTGAATCTCTC
20415691 ATTGAATCT
1 ATTGAATCT
20415700 TAATCTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (12 bp):
ATTGAATCTCTC
Found at i:20417083 original size:3 final size:3
Alignment explanation
Indices: 20417075--20417108 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
20417065 TGTATTTTAT
*
20417075 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
20417109 TTTAAAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:20423749 original size:20 final size:20
Alignment explanation
Indices: 20423724--20423761 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20423714 CAATAAAGTA
* *
20423724 ATAATGATTATGTTCACTTG
1 ATAATGATCATATTCACTTG
20423744 ATAATGATCATATTCACT
1 ATAATGATCATATTCACT
20423762 ACTAGTCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
ATAATGATCATATTCACTTG
Found at i:20424305 original size:11 final size:11
Alignment explanation
Indices: 20424276--20424308 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
20424266 TGACCTCATC
20424276 TTTAAGCAAAAA
1 TTTAA-CAAAAA
20424288 TTT-ACAAAAA
1 TTTAACAAAAA
20424298 TTTAACAAAAA
1 TTTAACAAAAA
20424309 AAAAAAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 8 0.40
12 3 0.15
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (11 bp):
TTTAACAAAAA
Found at i:20440345 original size:28 final size:27
Alignment explanation
Indices: 20440288--20440346 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
20440278 GATATATTTT
*
20440288 ATTTTATATTTTAAAATTTTAAATATA
1 ATTTTATATTTTAAAATTTTAAATAAA
*
20440315 ATTTTAT-TTTTATAAATTTTCTAATAAA
1 ATTTTATATTTTA-AAATTTT-AAATAAA
20440343 ATTT
1 ATTT
20440347 AAAAGACCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.18
27 14 0.50
28 9 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATTTTAAAATTTTAAATAAA
Done.