Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 111 of 226
Found at i:34583319 original size:29 final size:30
Alignment explanation
Indices: 34583285--34583346 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
34583275 ATTTCACATG
*
34583285 TACAATT-ACACCAAA-CTAAAATTCATGTA
1 TACAATTCACACCAAATC-AAAACTCATGTA
*
34583314 TACAATTGCACATCAAATCAAAACTCATGTA
1 TACAATT-CACACCAAATCAAAACTCATGTA
34583345 TA
1 TA
34583347 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.25
31 20 0.71
32 1 0.04
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (30 bp):
TACAATTCACACCAAATCAAAACTCATGTA
Found at i:34587971 original size:11 final size:11
Alignment explanation
Indices: 34587957--34588056 Score: 51
Period size: 11 Copynumber: 9.9 Consensus size: 11
34587947 ATAAAAAATT
34587957 TATTTTAAAAA
1 TATTTTAAAAA
34587968 TATTTT--AAA
1 TATTTTAAAAA
34587977 -A--TTAAAAA
1 TATTTTAAAAA
** *
34587985 -AAATTAAAAG
1 TATTTTAAAAA
34587995 TATTTTAAAAA
1 TATTTTAAAAA
34588006 TATTTT--AAA
1 TATTTTAAAAA
34588015 -A--TTAAAAA
1 TATTTTAAAAA
* *
34588023 AATTTAAAAAAA
1 TATTT-TAAAAA
*
34588035 TTATTTTAAAAG
1 -TATTTTAAAAA
34588047 TATTTTAAAA
1 TATTTTAAAA
34588057 TTTAAAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
6 4 0.06
8 9 0.13
9 7 0.10
10 6 0.09
11 30 0.43
12 9 0.13
13 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:34588044 original size:79 final size:83
Alignment explanation
Indices: 34587925--34588074 Score: 227
Period size: 79 Copynumber: 1.9 Consensus size: 83
34587915 CCAAAAAATT
*
34587925 TATTTTAAAATTTAAAACAAAAATAAAAAATTTATTTTAAAAATATTTTAAAA-TTAAAAAA-AA
1 TATTTTAAAATTTAAAACAAAAATAAAAAAATTATTTTAAAAATATTTTAAAATTTAAAAAATAA
*
34587988 TTAAAAGTATTTTAAAAA
66 ATAAAAGTATTTTAAAAA
** *
34588006 TATTTTAAAA-TTAAAA-AAATTTAAAAAAATTATTTTAAAAGTATTTTAAAATTTAAAAAATAA
1 TATTTTAAAATTTAAAACAAAAATAAAAAAATTATTTTAAAAATATTTTAAAATTTAAAAAATAA
34588069 ATAAAA
66 ATAAAA
34588075 AATAAAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
79 31 0.50
80 14 0.23
81 17 0.27
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (83 bp):
TATTTTAAAATTTAAAACAAAAATAAAAAAATTATTTTAAAAATATTTTAAAATTTAAAAAATAA
ATAAAAGTATTTTAAAAA
Found at i:34591310 original size:27 final size:27
Alignment explanation
Indices: 34591280--34591662 Score: 396
Period size: 27 Copynumber: 14.2 Consensus size: 27
34591270 GGGTATAAAA
*
34591280 GTCATTTTATCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
34591307 GTCATTTTACCTTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
34591334 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
34591361 GTTACTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
34591388 ATCATGTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
34591415 ATCATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
34591442 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
34591469 ATTATTCTA-CCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
34591495 GTCATTCTACCCTATAGAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
34591522 GTCATTTTA-CCTTTGAGGGGGTATTTCA
1 GTCATTTTACCCTAT--GGGGGTATTTCG
* *
34591550 GTCATTCTACTCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
** *
34591577 GTCATTTTACCCTATTAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
34591604 GTCATTTTACCCT-TCGAGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
* * *
34591631 ATCATTTTACCCT-TCGAGGGTATTTTG
1 GTCATTTTACCCTAT-GGGGGTATTTCG
34591658 GTCAT
1 GTCAT
34591663 AACAGTGTAT
Statistics
Matches: 296, Mismatches: 55, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
26 26 0.09
27 250 0.84
28 17 0.06
29 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:34591726 original size:19 final size:19
Alignment explanation
Indices: 34591694--34591749 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
34591684 ACCATTGCTT
* *
34591694 GGCCCAATTAGGCCAATAC-
1 GGCCCATTTTGGCCAA-ACG
*
34591713 GGCCCATTTTGGCCTAACG
1 GGCCCATTTTGGCCAAACG
*
34591732 TGGCCCATTATGGCCAAA
1 -GGCCCATTTTGGCCAAA
34591750 GTCCATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 15 0.50
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.21
Consensus pattern (19 bp):
GGCCCATTTTGGCCAAACG
Found at i:34592775 original size:25 final size:24
Alignment explanation
Indices: 34592741--34592820 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
34592731 TCATGTACAA
*
34592741 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATTCGAGCTGT-AATCG
*
34592766 GTATGCTCATTTGAGCTGTAGATCG
1 GTATGCTCATTCGAGCTGTA-ATCG
* *
34592791 ATATGCTC-TCTCGAGCTATAAATCG
1 GTATGCTCAT-TCGAGCTGT-AATCG
34592816 GTATG
1 GTATG
34592821 TTTTCATGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
24 2 0.04
25 43 0.93
26 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (24 bp):
GTATGCTCATTCGAGCTGTAATCG
Found at i:34595460 original size:4 final size:4
Alignment explanation
Indices: 34595453--34595477 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34595443 AATATATATG
34595453 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
34595478 CTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:34596437 original size:6 final size:6
Alignment explanation
Indices: 34596426--34596511 Score: 59
Period size: 6 Copynumber: 14.0 Consensus size: 6
34596416 TGAAACAACC
* * * * * *
34596426 ATAAAA ATAAAA ATATAG TTCAAAA GATAAAA AT-GAA ATAAGA CTAAGAAA
1 ATAAAA ATAAAA ATAAAA AT-AAAA -ATAAAA ATAAAA ATAAAA ATAA--AA
*
34596477 ATAAAA ATAAAC ATAAAA ATAAAA AT-AAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
34596512 CGACGGTGGA
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
5 9 0.15
6 40 0.67
7 6 0.10
8 5 0.08
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:34596497 original size:18 final size:17
Alignment explanation
Indices: 34596474--34596511 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
34596464 TAAGACTAAG
34596474 AAAATAAAAATAAACATA
1 AAAATAAAAATAAA-ATA
34596492 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
34596509 AAA
1 AAA
34596512 CGACGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:34596756 original size:21 final size:21
Alignment explanation
Indices: 34596726--34596766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34596716 AGAGGGCGTG
34596726 GCTTGGGTGGCTGGT-CGAGGT
1 GCTTGGGTGG-TGGTGCGAGGT
*
34596747 GCTTGTGTGGTGGTGCGAGG
1 GCTTGGGTGGTGGTGCGAGG
34596767 GCTGGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.05, C:0.12, G:0.54, T:0.29
Consensus pattern (21 bp):
GCTTGGGTGGTGGTGCGAGGT
Found at i:34607043 original size:12 final size:12
Alignment explanation
Indices: 34607026--34607053 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
34607016 CCTCACACAT
34607026 CCGTGTGCTAGG
1 CCGTGTGCTAGG
34607038 CCGTGTGCTAGG
1 CCGTGTGCTAGG
34607050 CCGT
1 CCGT
34607054 CTAATAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.29, G:0.39, T:0.25
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:34608674 original size:43 final size:40
Alignment explanation
Indices: 34608612--34608737 Score: 105
Period size: 43 Copynumber: 3.0 Consensus size: 40
34608602 GGATTTCGTT
34608612 ATGTGTTATCGTGTAAGACCACGTCTAGGACGTTGGCATTA
1 ATGTGTTA-CGTGTAAGACCACGTCTAGGACGTTGGCATTA
* *
34608653 ACTTGTGTTTACGTGTAAGACC-C-TATATGGGACAG-TGGCATCGTT
1 A--TGTG-TTACGTGTAAGACCACGTCTA--GGAC-GTTGGCAT--TA
* *
34608698 ATGTGATTACATGTAAGACCACGTCTAGGACATTGGCATT
1 ATGTG-TTACGTGTAAGACCACGTCTAGGACGTTGGCATT
34608738 GTACGATATG
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
41 5 0.07
42 1 0.01
43 52 0.76
44 5 0.07
45 5 0.07
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (40 bp):
ATGTGTTACGTGTAAGACCACGTCTAGGACGTTGGCATTA
Found at i:34610665 original size:50 final size:50
Alignment explanation
Indices: 34610549--34610895 Score: 433
Period size: 50 Copynumber: 6.8 Consensus size: 50
34610539 GATAATAACA
* ** * *
34610549 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTTATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * ***
34610600 TGCCCATGCCATGTCTCAAACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
34610650 TGCCAATGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
34610700 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
34610750 TAACAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
34610800 TGGCAACACCATGTCCCAGACATGGTCTTACATGACCATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTC-T---T-A-CATGGGACCTCTCATCTCGG
34610856 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
34610896 ATTTACCCAA
Statistics
Matches: 258, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
50 179 0.69
51 32 0.12
52 1 0.00
54 1 0.00
55 2 0.01
56 43 0.17
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34612417 original size:23 final size:23
Alignment explanation
Indices: 34612385--34612726 Score: 423
Period size: 23 Copynumber: 14.6 Consensus size: 23
34612375 GATTCAAGTG
* * *
34612385 AATTTAGTGTATATATGTTGTCC
1 AATTTGGTGTATAAATGCTGTCC
34612408 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
34612431 AATTTTGGTGTATAAATGCTGTCC
1 AA-TTTGGTGTATAAATGCTGTCC
** * * *
34612455 AATTTGGAATATATATTCTGCCC
1 AATTTGGTGTATAAATGCTGTCC
34612478 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
*
34612501 AATTTGGTGTATATATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
34612524 AATTTTGGTGTATAAATGCTGTCC
1 AA-TTTGGTGTATAAATGCTGTCC
34612548 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
*
34612571 AATTTGGTGTATAAAATGTTGTCC
1 AATTTGGTGTAT-AAATGCTGTCC
* * * *
34612595 AATTTTGTATATATATATGCTATTC
1 AATTTGGTGTATA-A-ATGCTGTCC
34612620 AATTTGGTGTATAAAATGCTGTCC
1 AATTTGGTGTAT-AAATGCTGTCC
*
34612644 AATTTGGTGTATAAATGCTATCC
1 AATTTGGTGTATAAATGCTGTCC
* * *
34612667 AATTTGGTATATATATACTGTCC
1 AATTTGGTGTATAAATGCTGTCC
* * *
34612690 AATTGGGTGTATAAATGCTATTC
1 AATTTGGTGTATAAATGCTGTCC
* *
34612713 GATTTGATGTATAA
1 AATTTGGTGTATAA
34612727 GAGCTGCCCA
Statistics
Matches: 274, Mismatches: 39, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
23 171 0.62
24 85 0.31
25 17 0.06
26 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (23 bp):
AATTTGGTGTATAAATGCTGTCC
Found at i:34612454 original size:47 final size:46
Alignment explanation
Indices: 34612385--34612726 Score: 423
Period size: 47 Copynumber: 7.3 Consensus size: 46
34612375 GATTCAAGTG
* * *
34612385 AATTTAGTGTATATATGTTGTCCAATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
** * * *
34612431 AATTTTGGTGTATAAATGCTGTCCAATTTGGAATATATATTCTGCCC
1 AA-TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
*
34612478 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
34612524 AATTTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
1 AA-TTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
* * * * *
34612571 AATTTGGTGTATAAAATGTTGTCCAATTTTGTATATATATATGCTATTC
1 AATTTGGTGTAT-AAATGCTGTCCAATTTGGTGTATA-A-ATGCTGTCC
*
34612620 AATTTGGTGTATAAAATGCTGTCCAATTTGGTGTATAAATGCTATCC
1 AATTTGGTGTAT-AAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
* * * * * *
34612667 AATTTGGTATATATATACTGTCCAATTGGGTGTATAAATGCTATTC
1 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
* *
34612713 GATTTGATGTATAA
1 AATTTGGTGTATAA
34612727 GAGCTGCCCA
Statistics
Matches: 260, Mismatches: 31, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
46 94 0.36
47 123 0.47
48 2 0.01
49 41 0.16
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (46 bp):
AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCC
Found at i:34612480 original size:70 final size:70
Alignment explanation
Indices: 34612394--34612726 Score: 445
Period size: 70 Copynumber: 4.7 Consensus size: 70
34612384 GAATTTAGTG
*
34612394 TATATATGTTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTGGTGTATAAATGCTGTCCAA-T
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCTGTCCAATT
34612458 TTGGAA
65 TTGGAA
* * *
34612464 TATATATTCTGCCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTT
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTT
**
34612529 TGGTG
66 TGGAA
* *
34612534 TATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAAATGTTGTCCAATT
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTAT-AAATGCTGTCCAATT
*
34612599 TTGTATA
65 TTGGA-A
* * *
34612606 TATATATGCTATTCAATTTGGTGTATAAAATGCTGTCCAATTTGGTGTATAAATGCTATCCAA-T
1 TATATATGCTGTCCAATTTGGTGTAT-AAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATT
*
34612670 TTGGTA
65 TTGGAA
* * * * * *
34612676 TATATATACTGTCCAATTGGGTGTATAAATGCTATTCGATTTGATGTATAA
1 TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAA
34612727 GAGCTGCCCA
Statistics
Matches: 230, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
69 43 0.19
70 110 0.48
71 20 0.09
72 34 0.15
73 23 0.10
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (70 bp):
TATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTT
TGGAA
Found at i:34617564 original size:18 final size:18
Alignment explanation
Indices: 34617538--34617575 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34617528 TGCTATAATA
34617538 ATTAATTTT-ATCGTCACC
1 ATTAATTTTAATC-TCACC
*
34617556 ATTATTTTTAATCTCACC
1 ATTAATTTTAATCTCACC
34617574 AT
1 AT
34617576 AAATAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTTTAATCTCACC
Found at i:34628776 original size:12 final size:12
Alignment explanation
Indices: 34628751--34628783 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
34628741 TATGGAACAA
34628751 ATTTAAATAAATC
1 ATTTAAA-AAATC
34628764 ATTTAAAAAATC
1 ATTTAAAAAATC
34628776 ATTTAAAA
1 ATTTAAAA
34628784 TTACATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTTAAAAAATC
Found at i:34630104 original size:14 final size:13
Alignment explanation
Indices: 34630085--34630118 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
34630075 CTAATTTGGG
34630085 TTTTAGGCTTAGTA
1 TTTTAGGC-TAGTA
34630099 TTTTAGG-TAGTA
1 TTTTAGGCTAGTA
34630111 TTTTAGGC
1 TTTTAGGC
34630119 CTGCTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.63
14 7 0.37
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.50
Consensus pattern (13 bp):
TTTTAGGCTAGTA
Found at i:34631130 original size:48 final size:49
Alignment explanation
Indices: 34631037--34631130 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
34631027 CTCGCCCATA
* *
34631037 TTATTTTTTTATTTTTAAAAATATTTATAATATTTTATTTAGCATTTTT
1 TTATTTTTTTATTTTTAAAAATATTTATAATATGTCATTTAGCATTTTT
*
34631086 TTATTTTTTTATTTATTGAAAAT-TTTAT-ATA-GTCATCTTAGCATT
1 TTATTTTTTTATTT-TTAAAAATATTTATAATATGTCAT-TTAGCATT
34631131 ATTTGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 3 0.08
48 11 0.28
49 19 0.47
50 7 0.17
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (49 bp):
TTATTTTTTTATTTTTAAAAATATTTATAATATGTCATTTAGCATTTTT
Found at i:34631156 original size:137 final size:126
Alignment explanation
Indices: 34630991--34631303 Score: 398
Period size: 137 Copynumber: 2.4 Consensus size: 126
34630981 TAAGCCTGTC
*
34630991 CATT-TTTACAAAAGATTAACCCAAACCCATTTTAGGCTCGCCCATATTATTTTTTTATTTTTAA
1 CATTATTTGCAAAAGATTAACCCAAACCCATTTTAGGCTCGCCCATATTATTTTTTTATTTTTAA
*
34631055 AAATATTTATAATATTTTA-TTT-AGCATTTTTTTATTTTTTTATTTATTGAAAATTTTATATAG
66 AAATACTTATAATATTTTACTTTCA-CA-TTTTTTA-------A-TTA---AAAATTTTATATAG
*
34631118 TCATCTTAG
118 TCATCTTAA
* * * *
34631127 CATTATTTGCAAAAGATTAATCCAGACCCATTCTAGGCTCACCCATATTATTTTTTTATTTTTAA
1 CATTATTTGCAAAAGATTAACCCAAACCCATTTTAGGCTCGCCCATATTATTTTTTTATTTTTAA
34631192 AAATACTTATAATATTTTACTTTCACATTTTTTAATTAAAAATTTTATATAGTCATCTTAA
66 AAATACTTATAATATTTTACTTTCACATTTTTTAATTAAAAATTTTATATAGTCATCTTAA
* * *
34631253 CATTATTTGCAAACGATTAACCCAAACCCACTTTAGGCTCGCCCATTTTAT
1 CATTATTTGCAAAAGATTAACCCAAACCCATTTTAGGCTCGCCCATATTAT
34631304 GCTCACACGA
Statistics
Matches: 160, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
126 66 0.41
129 3 0.02
130 1 0.01
136 4 0.03
137 80 0.50
138 5 0.03
139 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (126 bp):
CATTATTTGCAAAAGATTAACCCAAACCCATTTTAGGCTCGCCCATATTATTTTTTTATTTTTAA
AAATACTTATAATATTTTACTTTCACATTTTTTAATTAAAAATTTTATATAGTCATCTTAA
Found at i:34634434 original size:11 final size:11
Alignment explanation
Indices: 34634418--34634442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34634408 CTTGCAGATA
34634418 CACAATATAGT
1 CACAATATAGT
34634429 CACAATATAGT
1 CACAATATAGT
34634440 CAC
1 CAC
34634443 TAGAAATTGT
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:0.24, G:0.08, T:0.24
Consensus pattern (11 bp):
CACAATATAGT
Found at i:34652119 original size:23 final size:22
Alignment explanation
Indices: 34652072--34652119 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
34652062 ATAAATAATG
34652072 AAAATGATAAAAAAAATCTATAA
1 AAAATGATAAAAAAAATCTA-AA
* *
34652095 AAATTGATAAAAAAAGT-TAAA
1 AAAATGATAAAAAAAATCTAAA
34652116 AAAA
1 AAAA
34652120 CTTATTAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 2 0.09
23 15 0.68
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAATGATAAAAAAAATCTAAA
Found at i:34653590 original size:20 final size:21
Alignment explanation
Indices: 34653551--34653590 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34653541 CTTCTTTTTG
34653551 ATTTTTGGCTTTTGTTATATT
1 ATTTTTGGCTTTTGTTATATT
34653572 ATTTATTGG-TTTT-TTATAT
1 ATTT-TTGGCTTTTGTTATAT
34653591 CCGATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.17, C:0.03, G:0.12, T:0.68
Consensus pattern (21 bp):
ATTTTTGGCTTTTGTTATATT
Found at i:34653923 original size:86 final size:85
Alignment explanation
Indices: 34653778--34654174 Score: 340
Period size: 88 Copynumber: 4.7 Consensus size: 85
34653768 TATTTGAAAA
* * * * * * *
34653778 TAAAAATTATATAAATTCTGTTTCGGGATTTATTTTCGCCGTTCAACAGATTTTATTCCATTTTT
1 TAAAAATTAAATAAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATTCCATTTTT
*
34653843 ATTATGTTTCCAAACGAGTAT
66 ATTTTGTTTCCAAACGAG-AT
* *
34653864 TAAAAATTAAATAAAATCTGTTTCAGGATTTATTCCCACCATTTAATAGATTTTATTCCATTTTT
1 TAAAAATTAAATAAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATTCCA-TTTT
* *
34653929 TATTTTGTTGCCAAAACGAGAA
65 TATTTTGTTTCC-AAACGAGAT
* * * *
34653951 AATAAAATTAAATAAAATATGTTTCGGGATTTATTCTCACCATTTAACAGATTTTATTCGATTTT
1 TA-AAAATTAAATAAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATTCCATTTT
* *
34654016 AATTTTGTTT-CTAA--A-A-
65 TATTTTGTTTCCAAACGAGAT
* * * * * **
34654032 T-AGAATTAAATTGAAAATCTGTTTCAGGATTTATTCTCGCCGTTTAGCAAATTTTATTTTATTT
1 TAAAAATTAAA-T-AAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATTCCATTT
* * *
34654096 TAATTTTTTTTCCAAACGAGAA
64 TTATTTTGTTTCCAAACGAGAT
* ** * * * * * * *
34654118 CACTTAATCAAAT-AATTCTATTTCAAGATTTATTCCCATCGTTTAACAGATTTTATT
1 TA-AAAATTAAATAAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATT
34654175 TTGATTTAAT
Statistics
Matches: 254, Mismatches: 45, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
79 8 0.03
80 1 0.00
81 53 0.21
82 4 0.02
83 1 0.00
84 1 0.00
85 39 0.15
86 52 0.20
87 29 0.11
88 66 0.26
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (85 bp):
TAAAAATTAAATAAAATCTGTTTCAGGATTTATTCTCACCATTTAACAGATTTTATTCCATTTTT
ATTTTGTTTCCAAACGAGAT
Found at i:34654055 original size:81 final size:79
Alignment explanation
Indices: 34653949--34654107 Score: 210
Period size: 81 Copynumber: 2.0 Consensus size: 79
34653939 CCAAAACGAG
* *
34653949 AAAATAAAATTAAATAAAATATGTTTCGGGATTTATTCTCACCATTTAACAGATTTTATTCGATT
1 AAAATAAAATTAAATAAAATATGTTTCAGGATTTATTCTCACCATTTAACAAATTTTATTCGATT
34654014 TTAATTTTGTTTCT
66 TTAATTTTGTTTCT
* * * * * **
34654028 AAAATAGAATTAAATTGAAAATCTGTTTCAGGATTTATTCTCGCCGTTTAGCAAATTTTATTTTA
1 AAAATAAAATTAAA-T-AAAATATGTTTCAGGATTTATTCTCACCATTTAACAAATTTTATTCGA
*
34654093 TTTTAATTTTTTTTC
64 TTTTAATTTTGTTTC
34654108 CAAACGAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 13 0.19
80 1 0.01
81 54 0.79
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.47
Consensus pattern (79 bp):
AAAATAAAATTAAATAAAATATGTTTCAGGATTTATTCTCACCATTTAACAAATTTTATTCGATT
TTAATTTTGTTTCT
Found at i:34669095 original size:41 final size:40
Alignment explanation
Indices: 34669050--34669176 Score: 123
Period size: 41 Copynumber: 3.2 Consensus size: 40
34669040 CTGCCAATCT
*
34669050 CAAAGCCTGATATAACACACCGGCACAAAGCCTACTAGGCA
1 CAAAGCCTGATATAA-ACACCGGCACAAAGCCTGCTAGGCA
* * ** *
34669091 CAAAGCTTGATATAATACACCGGTATGAAGCTTGCTAGGCA
1 CAAAGCCTGATATAA-ACACCGGCACAAAGCCTGCTAGGCA
* * * *
34669132 CAGAGCCCGA-AT-ATCACCGGCACAGAGCCTGCTAGGCA
1 CAAAGCCTGATATAAACACCGGCACAAAGCCTGCTAGGCA
*
34669170 CAGAGCC
1 CAAAGCC
34669177 CGAAGAACGT
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
38 26 0.37
39 1 0.01
40 2 0.03
41 41 0.59
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (40 bp):
CAAAGCCTGATATAAACACCGGCACAAAGCCTGCTAGGCA
Found at i:34674558 original size:15 final size:14
Alignment explanation
Indices: 34674538--34674594 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
34674528 TCTTGATTTT
34674538 ATTTGATTCTAATCC
1 ATTTGATT-TAATCC
* **
34674553 ATTTGATTTGATTTT
1 ATTTGATTT-AATCC
34674568 ATTTGATTCTAATCC
1 ATTTGATT-TAATCC
34674583 ATTTGATTTAAT
1 ATTTGATTTAAT
34674595 TGCCCCATGC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.15
15 28 0.82
16 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (14 bp):
ATTTGATTTAATCC
Found at i:34674566 original size:30 final size:30
Alignment explanation
Indices: 34674530--34674591 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
34674520 AAGTATTATC
34674530 TTGATTTTATTTGATTCTAATCCATTTGAT
1 TTGATTTTATTTGATTCTAATCCATTTGAT
34674560 TTGATTTTATTTGATTCTAATCCATTTGAT
1 TTGATTTTATTTGATTCTAATCCATTTGAT
34674590 TT
1 TT
34674592 AATTGCCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.58
Consensus pattern (30 bp):
TTGATTTTATTTGATTCTAATCCATTTGAT
Found at i:34681847 original size:21 final size:21
Alignment explanation
Indices: 34681821--34681861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34681811 ATCTGCTCAA
* *
34681821 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
34681842 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
34681862 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:34685194 original size:12 final size:12
Alignment explanation
Indices: 34685179--34685211 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34685169 TATATTAGAA
34685179 TTTTATTATATT
1 TTTTATTATATT
*
34685191 TTTTAATATATT
1 TTTTATTATATT
34685203 TTTT-TTATA
1 TTTTATTATA
34685212 AGTTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:34685862 original size:20 final size:19
Alignment explanation
Indices: 34685832--34685887 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
34685822 AATTTTGGGT
34685832 TTTATTAATTTTTTTCATATG
1 TTTA-TAATTTTTTT-ATATG
*
34685853 TTTATAATTTCTTTTATATT
1 TTTATAATTT-TTTTATATG
*
34685873 TTTATAATATTTTTA
1 TTTATAATTTTTTTA
34685888 GTTTTAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 19 0.59
21 8 0.25
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATAATTTTTTTATATG
Found at i:34689984 original size:2 final size:2
Alignment explanation
Indices: 34689977--34690019 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
34689967 CTGCCTAGCT
34689977 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34690019 G
1 G
34690020 CATTTGAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34690940 original size:19 final size:19
Alignment explanation
Indices: 34690918--34690976 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 19
34690908 AATTTTAATG
34690918 ATTTTTTATTTTTAAAAAT
1 ATTTTTTATTTTTAAAAAT
34690937 ATTTGTTATATTTTTTAAAAA-
1 ATTT-TT-TA-TTTTTAAAAAT
** *
34690958 ATTTTAAATTTTAAAAAAT
1 ATTTTTTATTTTTAAAAAT
34690977 TAATTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.27
19 5 0.15
20 3 0.09
21 6 0.18
22 10 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTTATTTTTAAAAAT
Found at i:34696476 original size:50 final size:49
Alignment explanation
Indices: 34696296--34696492 Score: 141
Period size: 50 Copynumber: 4.0 Consensus size: 49
34696286 AACCATGCAA
* * * * *
34696296 ATGTATTTGGATGAG-AAAATGTCTCCT-TTCATTGAAATCGTCCATGTTG
1 ATGTATTTGAATGAGAAAAATGTCT-CTATGCATTGAAACCATCCATG-TC
* * * * *
34696345 ATGTATTTGATTGAGGAAAAATGTCT-TCATGCATTTGAAATCGTCCAAGCC
1 ATGTATTTGAATGA-GAAAAATGTCTCT-ATGCA-TTGAAACCATCCATGTC
* * ** *
34696396 ATGTATGT-AGATGAGATAAACATCTTTATGCATTGAAACCATCCATGATC
1 ATGTATTTGA-ATGAGAAAAATGTCTCTATGCATTGAAACCATCCATG-TC
* * *
34696446 ATGTATTTGAATGTGAAAAATGTCTCTATGCAATGAAACTATCCATG
1 ATGTATTTGAATGAGAAAAATGTCTCTATGCATTGAAACCATCCATG
34696493 CTCCATACTT
Statistics
Matches: 116, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
49 25 0.22
50 53 0.46
51 24 0.21
52 14 0.12
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (49 bp):
ATGTATTTGAATGAGAAAAATGTCTCTATGCATTGAAACCATCCATGTC
Found at i:34700850 original size:20 final size:20
Alignment explanation
Indices: 34700827--34700865 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34700817 GGAGTACAGA
*
34700827 CAGAGGCACCGACGTGCAAG
1 CAGAGGCACCGAAGTGCAAG
34700847 CAGAGGCACCGAAGTGCAA
1 CAGAGGCACCGAAGTGCAA
34700866 TCTCGTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.33, T:0.05
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAG
Found at i:34711459 original size:50 final size:50
Alignment explanation
Indices: 34711396--34711578 Score: 152
Period size: 50 Copynumber: 3.5 Consensus size: 50
34711386 CTGTACTACA
* * * ** *
34711396 AATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTACC
* * * * *
34711446 CATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGGTACC
1 AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTACC
* * * **
34711496 AACGCCATGCCCCAGACATGGTCTTAC-GTGGGACCTCTCATAACCTCAATAATGCC
1 AATGCCATGTCCCAGACATGGTCTTACAG-GAGACCTCTCAT-A--TCGGT-A--CC
34711552 AATGCCATGTCCCAGACATGGTCTTAC
1 AATGCCATGTCCCAGACATGGTCTTAC
34711579 GTGGGATATG
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 74 0.70
53 3 0.03
54 1 0.01
56 27 0.25
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTACC
Found at i:34711566 original size:56 final size:52
Alignment explanation
Indices: 34711442--34711584 Score: 173
Period size: 50 Copynumber: 2.7 Consensus size: 52
34711432 CTCATATCGG
* * * **
34711442 TGCCCATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
* *
34711494 --CCAACGCCATGCCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A
34711548 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
34711585 TATGGCATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
50 38 0.50
53 4 0.05
54 1 0.01
56 33 0.43
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
Found at i:34711788 original size:50 final size:50
Alignment explanation
Indices: 34711725--34711907 Score: 168
Period size: 50 Copynumber: 3.5 Consensus size: 50
34711715 CTGTACTACA
* * ** *
34711725 AATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTACC
* * * * *
34711775 CATGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATCTCGGTACC
1 AATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTACC
* * * * **
34711825 AACGCCATGCCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TCGGT-A--CC
34711881 AATGCCATGTCCCAGACATGGTCTTAC
1 AATGCCATGTCCCAGACATGGTCTTAC
34711908 GTGGGATATG
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 77 0.71
53 3 0.03
54 1 0.01
56 27 0.25
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTACC
Found at i:34711863 original size:329 final size:329
Alignment explanation
Indices: 34711265--34712854 Score: 2815
Period size: 329 Copynumber: 4.8 Consensus size: 329
34711255 TGAACTTTCA
*
34711265 TGTAACATAGTCTATTTACTAGCCCATTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
1 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
* *
34711330 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTATTATATGAGATGTTTCCTGTACTAC
66 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
*
34711395 AAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
131 AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
34711460 GACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
196 GACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
34711525 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
261 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
34711590 CATT
326 CATT
34711594 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
1 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
*
34711659 TATGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
66 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
*
34711724 AAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
131 AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
*
34711789 GACATAGTCTTACGTGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
196 GACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
34711854 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
261 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
34711919 CATT
326 CATT
34711923 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
1 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
* *
34711988 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCATATATTGGG-TGTTTCTTGTACTA
66 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATA-TGGGATGTTTCCTGTACTA
*
34712052 CAAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTACCCATGCCATGTCCC
130 CAAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCC
*
34712117 AGACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACA
195 AGACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACG
* *
34712182 TGGGACCTCTCATAACCTCAATGATGCCAATGCCATGTCCCAAACATGGTCTTACGTGGGATATG
260 TGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATG
34712247 GCATT
325 GCATT
*
34712252 TGTAACATAGTCTATTTACTAGCCCATTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
1 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
34712317 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
66 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
34712382 AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
131 AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
* *
34712447 GACATAGCCTTATGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
196 GACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
34712512 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
261 GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
34712577 CATT
326 CATT
*
34712581 TGTGACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
1 TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
34712646 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
66 TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
* * * ** ** *
34712711 AAATGCTATATCCCAGATATGGTCTTACATGGGAGTTCTCATCTCGGTACGAACACCATGCCCCA
131 AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
* * ** * *
34712776 GACATGGTC-TACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTC
196 GACATAGTCTTACGGGGGACCTCTCAT---CTCGGT-A--CCAACGCCATGCCCCAGACATGGTC
*
34712840 TTACGTGGGATCTCT
255 TTACGTGGGACCTCT
34712855 TCCCCCTAAT
Statistics
Matches: 1211, Mismatches: 42, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
328 19 0.02
329 1146 0.95
330 4 0.00
331 4 0.00
332 1 0.00
334 37 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (329 bp):
TGTAACATAGTCTATTTACTAGCCCGTTGAACCACTTGGAATACTAAGGATACTCGGGTCTCCTA
TCTGATAATAACATGCCAAAGCCATGTCCCGGACATGGTCTTATATGGGATGTTTCCTGTACTAC
AAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCA
GACATAGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGT
GGGACCTCTCATAACCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATATGG
CATT
Found at i:34711895 original size:56 final size:52
Alignment explanation
Indices: 34711771--34711913 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 52
34711761 CTCATATCGG
* * **
34711771 TGCCCATGCCATGTCCCAGACATAGTCTTACGTGGGACCTCTCATCTCGGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
* *
34711823 --CCAACGCCATGCCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A
34711877 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
34711914 TATGGCATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
50 39 0.51
53 4 0.05
54 1 0.01
56 33 0.43
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCAATA
Found at i:34712117 original size:50 final size:50
Alignment explanation
Indices: 34712054--34712242 Score: 189
Period size: 50 Copynumber: 3.7 Consensus size: 50
34712044 TTGTACTACA
* * **
34712054 AATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTACC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACC
* * ** *
34712104 CATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGGTACC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACC
* * * *
34712154 AACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTACC
* *
34712210 AATGCCATGTCCCAAACATGGTCTTACGTGGGA
1 AATGCCATGTCCCAGACATGGTCTTACATGGGA
34712243 TATGGCATTT
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 76 0.68
53 2 0.02
56 33 0.30
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTACC
Found at i:34712472 original size:50 final size:50
Alignment explanation
Indices: 34712418--34712524 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
34712408 ACATGGGAGT
* * * * *
34712418 TCTCATATCGGTGCCCATGCCATGTCCCAGACATAGCCTTATGGGGGACC
1 TCTCATATCGGTACCAACGCCATGCCCCAGACATAGCCTTACGGGGGACC
* * * *
34712468 TCTCATCTCGGTACCAACGCCATGCCCCAGACATGGTCTTACGTGGGACC
1 TCTCATATCGGTACCAACGCCATGCCCCAGACATAGCCTTACGGGGGACC
34712518 TCTCATA
1 TCTCATA
34712525 ACCTCAATAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (50 bp):
TCTCATATCGGTACCAACGCCATGCCCCAGACATAGCCTTACGGGGGACC
Found at i:34714672 original size:20 final size:20
Alignment explanation
Indices: 34714645--34714694 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
34714635 ATAGAGGAAC
* *
34714645 CAAAGTGCAAGCAGAGGCAT
1 CAAAGTGCAACCAAAGGCAT
34714665 -AAATGTGCAACCAAAGGCAT
1 CAAA-GTGCAACCAAAGGCAT
34714685 CAAAGTGCAA
1 CAAAGTGCAA
34714695 ATAGAGACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 20 0.77
21 3 0.12
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (20 bp):
CAAAGTGCAACCAAAGGCAT
Found at i:34715762 original size:21 final size:21
Alignment explanation
Indices: 34715721--34715759 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
34715711 CTTTTGTTTT
* *
34715721 ATTAATATTATTACATTAATA
1 ATTAATATTAATACATAAATA
34715742 ATTAA-ATTAATACATAAA
1 ATTAATATTAATACATAAA
34715760 ATATGCTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATATTAATACATAAATA
Found at i:34726306 original size:29 final size:29
Alignment explanation
Indices: 34726262--34726476 Score: 159
Period size: 29 Copynumber: 7.4 Consensus size: 29
34726252 TCAATGGCTA
* *
34726262 ATGAAAAGGGATAGCTTCAGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* * *
34726291 GTGAAAAGAGAAAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
34726320 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* ** * * *
34726349 ATGAAAAGGGAT-GGTGAT-AACCATCAACT
1 ATGAAAAGGGATAGCT--TCGGCTATCGATT
* * * * * *
34726378 ATTG-AAAGGGAT-GGTGACGACCATCAAAT
1 A-TGAAAAGGGATAGCT-TCGGCTATCGATT
* *
34726407 ATGAAAAGGGATAGCTCCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
* *
34726436 ATGAAAAGGGATAACTTCGGCTATCTATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATT
*
34726465 ATGAAAGGGGAT
1 ATGAAAAGGGAT
34726477 GGTGACGACC
Statistics
Matches: 151, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.03
29 142 0.94
30 5 0.03
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATT
Found at i:34726470 original size:116 final size:117
Alignment explanation
Indices: 34726292--34726535 Score: 357
Period size: 116 Copynumber: 2.1 Consensus size: 117
34726282 CTATCGAATG
* * * * * *
34726292 TGAAAAGAGAAAGCTTCGGCTATCGATTATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAG
1 TGAAAAGGGATAGCTCCGACTATCGATTATGAAAAGGGATAACTTCGGCTATCGATTATGAAAAG
*
34726357 GGATGGTGATAACCATCAACTATTG-AAAGGGATGGTGACGACCATCAAAT-A
66 GGATGGTGACAACCATCAACTA-TGAAAAGGGATGGTGACGACCATCAAATAA
* *
34726408 TGAAAAGGGATAGCTCCGACTATCGATTATGAAAAGGGATAACTTCGGCTATCTATTATGAAAGG
1 TGAAAAGGGATAGCTCCGACTATCGATTATGAAAAGGGATAACTTCGGCTATCGATTATGAAAAG
* * *
34726473 GGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACGACTATCAATTAA
66 GGATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAATAA
34726525 TGAAAAGGGAT
1 TGAAAAGGGAT
34726536 GGTTTCAACC
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
115 2 0.02
116 100 0.88
117 12 0.11
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (117 bp):
TGAAAAGGGATAGCTCCGACTATCGATTATGAAAAGGGATAACTTCGGCTATCGATTATGAAAAG
GGATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAATAA
Found at i:34726496 original size:29 final size:29
Alignment explanation
Indices: 34726346--34726538 Score: 176
Period size: 29 Copynumber: 6.6 Consensus size: 29
34726336 TTGGCTATCG
**
34726346 ATTATGAAAAGGGATGGTGATAACCATCA
1 ATTATGAAAAGGGATGGTGACGACCATCA
*
34726375 ACTATTG-AAAGGGATGGTGACGACCATCA
1 ATTA-TGAAAAGGGATGGTGACGACCATCA
* * * * *
34726404 AATATGAAAAGGGATAGCT-CCGACTATCG
1 ATTATGAAAAGGGAT-GGTGACGACCATCA
** * * * *
34726433 ATTATGAAAAGGGATAACT-TCGGCTATCT
1 ATTATGAAAAGGGAT-GGTGACGACCATCA
*
34726462 ATTATGAAAGGGGATGGTGACGACCATCA
1 ATTATGAAAAGGGATGGTGACGACCATCA
* *
34726491 ACTATGAAAAGGGATGGTGACGACTATCA
1 ATTATGAAAAGGGATGGTGACGACCATCA
34726520 ATTAATGAAAAGGGATGGT
1 ATT-ATGAAAAGGGATGGT
34726539 TTCAACCATC
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
28 3 0.02
29 113 0.84
30 19 0.14
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (29 bp):
ATTATGAAAAGGGATGGTGACGACCATCA
Found at i:34728047 original size:33 final size:33
Alignment explanation
Indices: 34728010--34728077 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
34728000 TTGGACCTAA
*
34728010 ATTTGGTATGTATATATATTGGATGTTGGAACC
1 ATTTGGTATGTATATATATTGGATGTTGAAACC
34728043 ATTTGGTATGTATATATATTGGATGTTGAAACC
1 ATTTGGTATGTATATATATTGGATGTTGAAACC
34728076 AT
1 AT
34728078 GTTACACGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (33 bp):
ATTTGGTATGTATATATATTGGATGTTGAAACC
Found at i:34729446 original size:32 final size:32
Alignment explanation
Indices: 34729409--34729592 Score: 236
Period size: 32 Copynumber: 5.8 Consensus size: 32
34729399 CCAGAAATAC
* *
34729409 AGTAATATGATTGGCACA-AAGCCATCAGTAGT
1 AGTAATATGATCGGCACACAA-CCATCAGTAAT
34729441 AGTAATATGATCGGCACACAACCATCAGTAAT
1 AGTAATATGATCGGCACACAACCATCAGTAAT
*
34729473 AGTAGTATGATCGGCACA-AAGCCATCAG---T
1 AGTAATATGATCGGCACACAA-CCATCAGTAAT
* *
34729502 AGTAATATGATTGACACACAACCATCAGTAAT
1 AGTAATATGATCGGCACACAACCATCAGTAAT
*
34729534 GGTAATATGATCGGCACACAACCATCAGTAAT
1 AGTAATATGATCGGCACACAACCATCAGTAAT
*
34729566 GGTAATATGATCGGCACA-AAGCCATCA
1 AGTAATATGATCGGCACACAA-CCATCA
34729593 ATAGCATCGA
Statistics
Matches: 136, Mismatches: 9, Indels: 14
0.86 0.06 0.09
Matches are distributed among these distances:
29 23 0.17
30 2 0.01
31 4 0.03
32 105 0.77
33 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (32 bp):
AGTAATATGATCGGCACACAACCATCAGTAAT
Found at i:34729528 original size:61 final size:61
Alignment explanation
Indices: 34729409--34729592 Score: 228
Period size: 61 Copynumber: 2.9 Consensus size: 61
34729399 CCAGAAATAC
* *
34729409 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATC---AGTAGTAATATGATCGACACACAACCATCAGTAAT
* *
34729473 AGTAGTATGATCGGCACAAAGCCATCAGTAGTAATATGATTGACACACAACCATCAGTAAT
1 AGTAATATGATCGGCACAAAGCCATCAGTAGTAATATGATCGACACACAACCATCAGTAAT
* *
34729534 GGTAATATGATCGGCACACAA-CCATCAGTAATGGTAATATGATCGGCACA-AAGCCATCA
1 AGTAATATGATCGGCACA-AAGCCATCAGT-A--GTAATATGATCGACACACAA-CCATCA
34729593 ATAGCATCGA
Statistics
Matches: 107, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
61 57 0.53
62 3 0.03
63 2 0.02
64 45 0.42
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (61 bp):
AGTAATATGATCGGCACAAAGCCATCAGTAGTAATATGATCGACACACAACCATCAGTAAT
Found at i:34729575 original size:93 final size:93
Alignment explanation
Indices: 34729409--34729592 Score: 307
Period size: 93 Copynumber: 2.0 Consensus size: 93
34729399 CCAGAAATAC
* *
34729409 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAGTAATA
1 AGTAATATGATTGACACAAAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAATA
*
34729474 GTAGTATGATCGGCACAAAGCCATCAGT
66 GTAATATGATCGGCACAAAGCCATCAGT
*
34729502 AGTAATATGATTGACACACAA-CCATCAGTAATGGTAATATGATCGGCACACAACCATCAGTAAT
1 AGTAATATGATTGACACA-AAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAAT
*
34729566 GGTAATATGATCGGCACAAAGCCATCA
65 AGTAATATGATCGGCACAAAGCCATCA
34729593 ATAGCATCGA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
93 83 0.98
94 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (93 bp):
AGTAATATGATTGACACAAAGCCATCAGTAATAGTAATATGATCGGCACACAACCATCAGTAATA
GTAATATGATCGGCACAAAGCCATCAGT
Found at i:34729698 original size:27 final size:27
Alignment explanation
Indices: 34729639--34729703 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
34729629 AGTAAAGCTG
*
34729639 CCAGTAACAGTATATGTGGTCAAGCTA
1 CCAGTAACAGTATATGTGGTCAAGCCA
*
34729666 CTAGTAACAGTGAT-TGTGG-CAGAGCCA
1 CCAGTAACAGT-ATATGTGGTCA-AGCCA
34729693 CCAGT-ACAGTA
1 CCAGTAACAGTA
34729704 CTTCCTCCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 23 0.70
28 2 0.06
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGTCAAGCCA
Found at i:34729799 original size:24 final size:24
Alignment explanation
Indices: 34729767--34729900 Score: 144
Period size: 24 Copynumber: 5.6 Consensus size: 24
34729757 TCATGCACGG
**
34729767 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATTTAAATCACAAACA
34729791 AATCAGTCATTTAAATCA-AAGACA
1 AATCAGTCATTTAAATCACAA-ACA
*
34729815 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAAACA
* * * *
34729839 AATTAGTCATTTACATCTCAGACA
1 AATCAGTCATTTAAATCACAAACA
* * **
34729863 AATCATTCATTTACATCACAGTCA
1 AATCAGTCATTTAAATCACAAACA
*
34729887 AATCAATCATTTAA
1 AATCAGTCATTTAA
34729901 CCTCGAGGGG
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
23 2 0.02
24 93 0.97
25 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.28
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAAACA
Found at i:34729840 original size:48 final size:48
Alignment explanation
Indices: 34729767--34729900 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
34729757 TCATGCACGG
** *
34729767 AATCAGTCATACAAATCACAAACAAATCAGTCATTTAAATCAAAGACA
1 AATCAGTCATTTAAATCACAGACAAATCAGTCATTTAAATCAAAGACA
* * **
34729815 AATCAGTCATTTAAATCACAGACAAATTAGTCATTTACATCTCAGACA
1 AATCAGTCATTTAAATCACAGACAAATCAGTCATTTAAATCAAAGACA
* * * *
34729863 AATCATTCATTTACATCACAGTCAAATCAATCATTTAA
1 AATCAGTCATTTAAATCACAGACAAATCAGTCATTTAA
34729901 CCTCGAGGGG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.28
Consensus pattern (48 bp):
AATCAGTCATTTAAATCACAGACAAATCAGTCATTTAAATCAAAGACA
Found at i:34729926 original size:27 final size:27
Alignment explanation
Indices: 34729896--34729963 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
34729886 AAATCAATCA
*
34729896 TTTAACCTCGAGGGGCAAAATAGTCAT
1 TTTAACCTAGAGGGGCAAAATAGTCAT
* * ** *
34729923 TTTACCCTATAGGGGCATTATGGTCAT
1 TTTAACCTAGAGGGGCAAAATAGTCAT
* *
34729950 TTTACCCTACAGGG
1 TTTAACCTAGAGGG
34729964 CATTACGATC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTAACCTAGAGGGGCAAAATAGTCAT
Found at i:34729975 original size:26 final size:26
Alignment explanation
Indices: 34729919--34729991 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
34729909 GGCAAAATAG
* *
34729919 TCATTTTACCCTATAGGGGCATTATGG
1 TCATTTTACCCTATA-GGGCATTACGA
*
34729946 TCATTTTACCCTACAGGGCATTACGA
1 TCATTTTACCCTATAGGGCATTACGA
*
34729972 TCATTTTATCCTATAGGGCA
1 TCATTTTACCCTATAGGGCA
34729992 GATACCCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 27 0.66
27 14 0.34
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (26 bp):
TCATTTTACCCTATAGGGCATTACGA
Found at i:34730011 original size:42 final size:42
Alignment explanation
Indices: 34729952--34730031 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
34729942 ATGGTCATTT
*
34729952 TACCCTACAGGGCATTACGATCATTTTATCC-TATAGGGCAGA
1 TACCCTACAAGGCATTACGATCATTTTA-CCATATAGGGCAGA
* *
34729994 TACCCTATAAGGCATTACGGTCATTTTACCATATAGGG
1 TACCCTACAAGGCATTACGATCATTTTACCATATAGGG
34730032 GTATTACGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
TACCCTACAAGGCATTACGATCATTTTACCATATAGGGCAGA
Found at i:34730078 original size:27 final size:27
Alignment explanation
Indices: 34730005--34730078 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
34729995 ACCCTATAAG
* * *
34730005 GCATTACGGTCATTTTACCATATAGGG
1 GCATTACGGTCATTTTACCCTACAGGA
*
34730032 GTATTACGGTCATTTTACCCTACAGGA
1 GCATTACGGTCATTTTACCCTACAGGA
34730059 GCATTACGGTCATTTTACCC
1 GCATTACGGTCATTTTACCC
34730079 ATCGAGGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (27 bp):
GCATTACGGTCATTTTACCCTACAGGA
Found at i:34730099 original size:27 final size:26
Alignment explanation
Indices: 34730070--34730210 Score: 129
Period size: 27 Copynumber: 5.2 Consensus size: 26
34730060 CATTACGGTC
*
34730070 ATTTTACCCATCGAGGGTATTTCGAA
1 ATTTTACCCTTCGAGGGTATTTCGAA
* * * *
34730096 CATTTTACGCTTCAAGGGTATTTTAGTA
1 -ATTTTACCCTTCGAGGGTA-TTTCGAA
**
34730124 ATTTTACCCTTCGAGGGTATTTTTATA
1 ATTTTACCCTTCGAGGGTATTTCGA-A
* *
34730151 ATTTTACCTTTCGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTC-GAA
* * *
34730178 ATTTTACCCATCAAGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGA-A
34730205 ATTTTA
1 ATTTTA
34730211 TAACATTTTT
Statistics
Matches: 91, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
26 4 0.04
27 82 0.90
28 5 0.05
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTTCGAGGGTATTTCGAA
Found at i:34730100 original size:54 final size:54
Alignment explanation
Indices: 34730004--34730199 Score: 155
Period size: 54 Copynumber: 3.6 Consensus size: 54
34729994 TACCCTATAA
* ** * ** *
34730004 GGCATTACGGTCATTTTA-CCATATAGGGGTATTACGGTCATTTTACCCTAC-AG
1 GGCATTACGGTAATTTTACCCATCGA-GGGTATTTCGAACATTTTACCCTTCAAG
* *
34730057 GAGCATTACGGTCATTTTACCCATCGAGGGTATTTCGAACATTTTACGCTTCAAG
1 G-GCATTACGGTAATTTTACCCATCGAGGGTATTTCGAACATTTTACCCTTCAAG
* *** * ** * *
34730112 GGTATTTTAGTAATTTTACCCTTCGAGGGTATTTTTATA-ATTTTACCTTTCGAG
1 GGCATTACGGTAATTTTACCCATCGAGGGTATTTCGA-ACATTTTACCCTTCAAG
* * *
34730166 GGTATTTCGGTAATTTTACCCATCAAGGGTATTT
1 GGCATTACGGTAATTTTACCCATCGAGGGTATTT
34730200 TGATAATTTT
Statistics
Matches: 117, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 107 0.91
55 9 0.08
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (54 bp):
GGCATTACGGTAATTTTACCCATCGAGGGTATTTCGAACATTTTACCCTTCAAG
Found at i:34730200 original size:54 final size:54
Alignment explanation
Indices: 34730065--34730210 Score: 188
Period size: 54 Copynumber: 2.7 Consensus size: 54
34730055 AGGAGCATTA
* *
34730065 CGGTCATTTTACCCATCGAGGGTATTTCGA-ACATTTTACGCTTCAAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTTTGATA-ATTTTACGCTTCAAGGGTATTT
** * * *
34730119 TAGTAATTTTACCCTTCGAGGGTATTTTTATAATTTTAC-CTTTCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTTTGATAATTTTACGC-TTCAAGGGTATTT
*
34730173 CGGTAATTTTACCCATCAAGGGTATTTTGATAATTTTA
1 CGGTAATTTTACCCATCGAGGGTATTTTGATAATTTTA
34730211 TAACATTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 76 0.97
55 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (54 bp):
CGGTAATTTTACCCATCGAGGGTATTTTGATAATTTTACGCTTCAAGGGTATTT
Found at i:34736388 original size:23 final size:23
Alignment explanation
Indices: 34736357--34736416 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
34736347 GCAAAAAATT
* *
34736357 CTACTAGTAAAAATACAGACAAG
1 CTACCAGTAAAAATACAAACAAG
* * * *
34736380 TTGCCAGTAAAAATGCAAATAAG
1 CTACCAGTAAAAATACAAACAAG
34736403 CTACCAGTAAAAAT
1 CTACCAGTAAAAAT
34736417 GCGATAAATC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (23 bp):
CTACCAGTAAAAATACAAACAAG
Found at i:34746303 original size:40 final size:41
Alignment explanation
Indices: 34746240--34746344 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 41
34746230 AGTAAGAATT
* * * *
34746240 ATTACACCGGCTTGAAGCTTGCTAGGCACTAAGCTCTATA-
1 ATTACACCGGCATGAAGCCTGCTAGGCACTAAGCCCGATAG
*
34746280 ATTACACCGGCACT-AAGCCTGCTAGGCATTAAGCCCGATAG
1 ATTACACCGGCA-TGAAGCCTGCTAGGCACTAAGCCCGATAG
*
34746321 A-TACACTGGCATGAAGCCTGCTAG
1 ATTACACCGGCATGAAGCCTGCTAG
34746345 ACTCAAAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 1 0.02
40 53 0.95
41 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (41 bp):
ATTACACCGGCATGAAGCCTGCTAGGCACTAAGCCCGATAG
Found at i:34747077 original size:16 final size:16
Alignment explanation
Indices: 34747056--34747090 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34747046 AGTCCTTGTA
34747056 ATTTTA-TCACTTTAAC
1 ATTTTAGTCA-TTTAAC
34747072 ATTTTAGTCATTTAAC
1 ATTTTAGTCATTTAAC
34747088 ATT
1 ATT
34747091 AAAATTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCATTTAAC
Found at i:34752328 original size:24 final size:24
Alignment explanation
Indices: 34752301--34752347 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
34752291 CACACGGTCG
*
34752301 TGTGACAACCCGTGTCCTAGGCCA
1 TGTGACAACCCATGTCCTAGGCCA
* *
34752325 TGTGATATCCCATGTCCTAGGCC
1 TGTGACAACCCATGTCCTAGGCC
34752348 GGGTGCAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (24 bp):
TGTGACAACCCATGTCCTAGGCCA
Found at i:34761275 original size:24 final size:25
Alignment explanation
Indices: 34761214--34761275 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 25
34761204 TTTGCAACAC
* *
34761214 ATATTAATCTATCAACATTTATTAA
1 ATATCAATCTATCAACATTTATAAA
* * *
34761239 TTTTCCATC-ATCAACATTTA-AAA
1 ATATCAATCTATCAACATTTATAAA
34761262 ATATCAATCTATCA
1 ATATCAATCTATCA
34761276 TCAATGGAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
23 8 0.29
24 15 0.54
25 5 0.18
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATCAATCTATCAACATTTATAAA
Found at i:34766930 original size:26 final size:26
Alignment explanation
Indices: 34766899--34766951 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
34766889 ACATCAAACA
34766899 TACCATGTCTAATAACGTTCAATTCC
1 TACCATGTCTAATAACGTTCAATTCC
*
34766925 TACCATGTCTAATAACGTTCGATTCC
1 TACCATGTCTAATAACGTTCAATTCC
34766951 T
1 T
34766952 TCTCTCTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (26 bp):
TACCATGTCTAATAACGTTCAATTCC
Found at i:34769254 original size:21 final size:22
Alignment explanation
Indices: 34769228--34769268 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34769218 AATAAATACC
*
34769228 TATTG-TTTTCCAGTATTTTGT
1 TATTGTTTTTCCACTATTTTGT
34769249 TATTGTTTTTCCACTATTTT
1 TATTGTTTTTCCACTATTTT
34769269 CCTATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.15, C:0.12, G:0.10, T:0.63
Consensus pattern (22 bp):
TATTGTTTTTCCACTATTTTGT
Found at i:34769278 original size:22 final size:22
Alignment explanation
Indices: 34769233--34769279 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
34769223 ATACCTATTG
* ** *
34769233 TTTTCCAGTATTTTGTTATTGT
1 TTTTCCACTATTTTCCTATGGT
34769255 TTTTCCACTATTTTCCTATGGT
1 TTTTCCACTATTTTCCTATGGT
34769277 TTT
1 TTT
34769280 GCTTCCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.62
Consensus pattern (22 bp):
TTTTCCACTATTTTCCTATGGT
Found at i:34769995 original size:26 final size:27
Alignment explanation
Indices: 34769966--34770022 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
34769956 ATTTAATAAA
* *
34769966 AATAAGAAATATT-TTAATTATATTTT
1 AATAAGAAATATTATTAAATATAATTT
* *
34769992 AAT-ATAATTATTATTAAATATAATTT
1 AATAAGAAATATTATTAAATATAATTT
34770018 AATAA
1 AATAA
34770023 TATATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 7 0.28
26 17 0.68
27 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AATAAGAAATATTATTAAATATAATTT
Found at i:34770027 original size:15 final size:15
Alignment explanation
Indices: 34770009--34770037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34769999 TTATTATTAA
34770009 ATATAATTTAATAAT
1 ATATAATTTAATAAT
34770024 ATATAATTTAATAA
1 ATATAATTTAATAA
34770038 CATTCTTAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATTTAATAAT
Found at i:34774870 original size:25 final size:27
Alignment explanation
Indices: 34774815--34774870 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
34774805 CAAATTATGG
*
34774815 CTTCAAACACAAACATACATTTATATA
1 CTTCAAACACAAACATACACTTATATA
34774842 -TTCAAAC-C-AACATTACACTTATA-A
1 CTTCAAACACAAACA-TACACTTATATA
34774866 CTTCA
1 CTTCA
34774871 CTTACAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 7 0.27
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (27 bp):
CTTCAAACACAAACATACACTTATATA
Found at i:34776477 original size:15 final size:16
Alignment explanation
Indices: 34776451--34776490 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
34776441 TTGTCATAAC
*
34776451 TTCTTCTCTCTTTTCT
1 TTCTTCTTTCTTTTCT
34776467 TT-TTCTTTCTTTTCT
1 TTCTTCTTTCTTTTCT
34776482 TTCTTCTTT
1 TTCTTCTTT
34776491 TTACTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTTCTTTCTTTTCT
Found at i:34777948 original size:17 final size:17
Alignment explanation
Indices: 34777926--34777965 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
34777916 TTCGTGAAGT
34777926 ATAAACTCTTTTAATTC
1 ATAAACTCTTTTAATTC
34777943 ATAAACTCTTTTAATTC
1 ATAAACTCTTTTAATTC
*
34777960 AGAAAC
1 ATAAAC
34777966 ATCCGGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (17 bp):
ATAAACTCTTTTAATTC
Found at i:34783945 original size:14 final size:14
Alignment explanation
Indices: 34783916--34783961 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
34783906 TTGCTGTAAC
34783916 TTCTTGTCTCTTTTCT
1 TTCTT-TCT-TTTTCT
34783932 TTCTTTCTTTTTCT
1 TTCTTTCTTTTTCT
34783946 TTC-TTCTTTTTACT
1 TTCTTTCTTTTT-CT
34783960 TT
1 TT
34783962 AATTTGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.28
14 13 0.45
15 3 0.10
16 5 0.17
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (14 bp):
TTCTTTCTTTTTCT
Found at i:34784785 original size:20 final size:20
Alignment explanation
Indices: 34784742--34784783 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
34784732 TAAAGAAAGT
34784742 AAATAAAATGGAAAGTAATG
1 AAATAAAATGGAAAGTAATG
34784762 AAATACAAAT-GAAAGTAA-G
1 AAATA-AAATGGAAAGTAATG
34784781 AAA
1 AAA
34784784 ATTTGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.64, C:0.02, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATAAAATGGAAAGTAATG
Found at i:34785249 original size:15 final size:16
Alignment explanation
Indices: 34785229--34785258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34785219 TGGTGCCTTG
34785229 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
34785244 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
34785259 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:34786251 original size:20 final size:21
Alignment explanation
Indices: 34786219--34786257 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34786209 CTGAAGTTTG
*
34786219 AAAATTTTCATATTTTTCCTA
1 AAAATTTTCATATGTTTCCTA
34786240 AAAATTTT-ATATGTTTCC
1 AAAATTTTCATATGTTTCC
34786258 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (21 bp):
AAAATTTTCATATGTTTCCTA
Found at i:34787629 original size:38 final size:38
Alignment explanation
Indices: 34787573--34787658 Score: 147
Period size: 38 Copynumber: 2.3 Consensus size: 38
34787563 TGTTCGTTTC
34787573 AATCTTTTAATTCATGTTTTGTGCCGATTTCATTATCT
1 AATCTTTTAATTCATGTTTTGTGCCGATTTCATTATCT
*
34787611 AATCTTTTAATTCCTGTTTTGTGCCGATTTCATTATCT
1 AATCTTTTAATTCATGTTTTGTGCCGATTTCATTATCT
34787649 AA-CTTGTTAA
1 AATCTT-TTAA
34787659 GATTTCTTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 3 0.07
38 43 0.93
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.51
Consensus pattern (38 bp):
AATCTTTTAATTCATGTTTTGTGCCGATTTCATTATCT
Found at i:34791734 original size:50 final size:50
Alignment explanation
Indices: 34791618--34791860 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
34791608 GATAATGACA
* * ** * *
34791618 TGCCAAAGCCATGTCCCAGACTTGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTTGG
* * **
34791669 TGCCCATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* *
34791719 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
*
34791769 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
*
34791819 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34791861 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
50 139 0.81
51 32 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:34798853 original size:50 final size:50
Alignment explanation
Indices: 34798731--34798973 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
34798721 GATAATAACC
* * ** *
34798731 TGCCAAAGCCATGTCCCAGACTTGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* ** *
34798782 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34798832 TGCCAATGTCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34798882 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
34798932 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34798974 TTACCCAAAT
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
50 138 0.81
51 33 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34808294 original size:16 final size:16
Alignment explanation
Indices: 34808273--34808306 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
34808263 ATTACCTCTG
34808273 AATATTATAATATATT
1 AATATTATAATATATT
34808289 AATATTATAATATATT
1 AATATTATAATATATT
34808305 AA
1 AA
34808307 AAAATCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTATAATATATT
Found at i:34809253 original size:11 final size:11
Alignment explanation
Indices: 34809202--34809248 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
34809192 AACAAATCCT
34809202 CTCTCATATTTC
1 CTCTCA-ATTTC
34809214 CTCTCAATTTC
1 CTCTCAATTTC
*
34809225 CTCTCAATTTT
1 CTCTCAATTTC
*
34809236 CTCCCAATTTC
1 CTCTCAATTTC
34809247 CT
1 CT
34809249 TCCAAAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 26 0.81
12 6 0.19
ACGTcount: A:0.17, C:0.36, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:34809285 original size:51 final size:51
Alignment explanation
Indices: 34809228--34809415 Score: 189
Period size: 51 Copynumber: 3.4 Consensus size: 51
34809218 CAATTTCCTC
*
34809228 TCAATTTTCTCCCAATTTCCTTCCAAAATTCTCATAAATCCATATTTAATT
1 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCATAAATCCATATTTAATT
34809279 TCAATTTTCTCTCAATTTCCTTCCAAAATTTCCTTCCAAAATTCTCATAAATCCATATTTAATT
1 TCAATTTTCTCTCAATTTCCTTCCAAAA------T------T-CTCATAAATCCATATTTAATT
* * * *
34809343 TCAATTTCCTCTCAATTTCATTCCAAAAATCTC-TCAAAGCCATATTTAATT
1 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATT
*
34809394 TCAATTTGCTCTCAATTTCCTT
1 TCAATTTTCTCTCAATTTCCTT
34809416 TTTTAAAATA
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
50 1 0.01
51 65 0.56
52 1 0.01
57 1 0.01
63 1 0.01
64 47 0.41
ACGTcount: A:0.30, C:0.26, G:0.01, T:0.43
Consensus pattern (51 bp):
TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCATAAATCCATATTTAATT
Found at i:34809310 original size:13 final size:13
Alignment explanation
Indices: 34809292--34809321 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
34809282 ATTTTCTCTC
34809292 AATTTCCTTCCAA
1 AATTTCCTTCCAA
34809305 AATTTCCTTCCAA
1 AATTTCCTTCCAA
34809318 AATT
1 AATT
34809322 CTCATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTCCTTCCAA
Found at i:34811764 original size:25 final size:25
Alignment explanation
Indices: 34811729--34811917 Score: 176
Period size: 25 Copynumber: 7.7 Consensus size: 25
34811719 TATTTTGATA
*
34811729 TTATTTGATGTAATAAAATAGAAGT
1 TTATATGATGTAATAAAATAGAAGT
*
34811754 TTATATAATGTAATAAAATAGAAGT
1 TTATATGATGTAATAAAATAGAAGT
** *
34811779 TT-TATTGATGTAATAAAAATTTAAAT
1 TTATA-TGATGTAAT-AAAATAGAAGT
* * ** *
34811805 TT-T-T-TTG-AATTATTTTG-A-T
1 TTATATGATGTAATAAAATAGAAGT
*
34811824 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATATGATGTAATAAAATAGAAGT
*
34811850 TTATTTGATGTAATAAAATAGAAGT
1 TTATATGATGTAATAAAATAGAAGT
34811875 TTATATGATGTAATAAAATAGAAGT
1 TTATATGATGTAATAAAATAGAAGT
* *
34811900 TTATTTGATGTGATAAAA
1 TTATATGATGTAATAAAA
34811918 ATTGAAAACC
Statistics
Matches: 136, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 4 0.03
22 4 0.03
23 4 0.03
24 9 0.07
25 99 0.73
26 12 0.09
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATATGATGTAATAAAATAGAAGT
Found at i:34811847 original size:96 final size:96
Alignment explanation
Indices: 34811666--34811892 Score: 377
Period size: 96 Copynumber: 2.4 Consensus size: 96
34811656 AGTTCGTTTG
* *
34811666 ATGTAATAAAATAGAAGTTTTACTGATGTAA-AAAAAATTAAAATTTTTTGAGTTATTTTGATAT
1 ATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAAATTAAAATTTTTTGAATTATTTTGATAT
34811730 TATTTGATGTAATAAAATAGAAGTTTATATA
66 TATTTGATGTAATAAAATAGAAGTTTATATA
* *
34811761 ATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAATTTAAATTTTTTTGAATTATTTTGATAT
1 ATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAAATTAAAATTTTTTGAATTATTTTGATAT
* *
34811826 TATTTGATGTAATAAAATAGAAGTTTATTTG
66 TATTTGATGTAATAAAATAGAAGTTTATATA
34811857 ATGTAATAAAATAGAAG-TTTATATGATGTAATAAAA
1 ATGTAATAAAATAGAAGTTTTAT-TGATGTAATAAAA
34811893 TAGAAGTTTA
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
95 35 0.28
96 89 0.72
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (96 bp):
ATGTAATAAAATAGAAGTTTTATTGATGTAATAAAAAATTAAAATTTTTTGAATTATTTTGATAT
TATTTGATGTAATAAAATAGAAGTTTATATA
Found at i:34811949 original size:23 final size:23
Alignment explanation
Indices: 34811919--34812094 Score: 298
Period size: 23 Copynumber: 7.7 Consensus size: 23
34811909 GTGATAAAAA
34811919 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
34811942 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
34811965 TTGAAAACCCAAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
34811988 TTGAAAACCCTAACCTAATTAAA
1 TTGAAAACCCTAACCTAATTAAG
* * *
34812011 TTAAAAACCCAAACCTATTTAAG
1 TTGAAAACCCTAACCTAATTAAG
*
34812034 TTGAAAACCCAAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
34812057 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAG
34812080 TTGAAAACCCTAACC
1 TTGAAAACCCTAACC
34812095 CTAAACTTAA
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 143 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.24
Consensus pattern (23 bp):
TTGAAAACCCTAACCTAATTAAG
Found at i:34814689 original size:124 final size:124
Alignment explanation
Indices: 34814463--34814694 Score: 340
Period size: 124 Copynumber: 1.9 Consensus size: 124
34814453 CTCAAACAAG
* * * *
34814463 CTACTGTAGCAAAAGCGCGTCCCCAAGGGCGGGATTTTCACAAATTCTTCTCAAATAGCATCATG
1 CTACTATAGCAAAAGCGCGTCCACAAGGGCGAGAATTTCACAAATTCTTCTCAAATAGCATCATG
*
34814528 CTAGAAGCAAATTTATACTATTTGCTCAGAAGCGTCAAAAAAAATATTTCATCCATGAC
66 CTAGAAGCAAATTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTCATCCATGAC
* * * *
34814587 CTACTATAGCAAGAGCGCGTCCACGAGGGCTAGAATTTCA-AAATTTCTTCTCAAATAGCATCCT
1 CTACTATAGCAAAAGCGCGTCCACAAGGGCGAGAATTTCACAAA-TTCTTCTCAAATAGCATCAT
* * *
34814651 GCTAGAAGCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAA
65 GCTAGAAGCAAATTTATACTATTTGCTCAGAAACGTCAAAAAAA
34814695 TTTATTTCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 3 0.03
124 92 0.97
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (124 bp):
CTACTATAGCAAAAGCGCGTCCACAAGGGCGAGAATTTCACAAATTCTTCTCAAATAGCATCATG
CTAGAAGCAAATTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTCATCCATGAC
Found at i:34815149 original size:33 final size:33
Alignment explanation
Indices: 34815112--34815186 Score: 77
Period size: 33 Copynumber: 2.3 Consensus size: 33
34815102 AATATTTAAA
34815112 TAATTTAATATAGAT-A-TACATAAAATATATTT-T
1 TAATTTAATATA-ATAATTA-ATAAAAT-TATTTAT
34815145 TAA-TTAATTATAATAATTAATAAAATTATTTAT
1 TAATTTAA-TATAATAATTAATAAAATTATTTAT
*
34815178 AAATTTAAT
1 TAATTTAAT
34815187 TATACATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
32 11 0.31
33 19 0.53
34 6 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TAATTTAATATAATAATTAATAAAATTATTTAT
Found at i:34815247 original size:28 final size:26
Alignment explanation
Indices: 34815158--34815248 Score: 71
Period size: 28 Copynumber: 3.3 Consensus size: 26
34815148 TTAATTATAA
*
34815158 TAAT-TAATAAA-ATTATTTATAAATT
1 TAATATAATAAATA-TATTTAAAAATT
*
34815183 TAATTATACATGAAATAT-TTTAAAATTT
1 TAA-TATA-AT-AAATATATTTAAAAATT
*
34815211 TAAAAATAATAAATAGTATTTAAATAATT
1 T-AATATAATAAATA-TATTTAAA-AATT
34815240 TAATATAAT
1 TAATATAAT
34815249 GCATAAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
25 3 0.06
26 6 0.12
27 5 0.10
28 27 0.52
29 10 0.19
30 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATAATAAATATATTTAAAAATT
Found at i:34817325 original size:26 final size:26
Alignment explanation
Indices: 34817296--34817358 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
34817286 TTTATCGAGG
*
34817296 TTATTAGTTTAT-GAT-AAATGAATATT
1 TTATTAATTTATCGATAAAAT-AATA-T
34817322 TTATTAATTTATCGATAAAATAATAT
1 TTATTAATTTATCGATAAAATAATAT
34817348 TTATTAATTTA
1 TTATTAATTTA
34817359 GAGAATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 23 0.68
27 7 0.21
28 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (26 bp):
TTATTAATTTATCGATAAAATAATAT
Found at i:34817485 original size:38 final size:38
Alignment explanation
Indices: 34817437--34817513 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
34817427 TGAATCAAAG
* * *
34817437 TTAATTGGTTCATGTAACACACAAA-AACAAAGAGTTAA
1 TTAATAGGTTCATGTAAC-CAAAAAGAAAAAAGAGTTAA
34817475 TTAATAGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
1 TTAATAGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
34817513 T
1 T
34817514 GATTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 5 0.14
38 30 0.86
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.26
Consensus pattern (38 bp):
TTAATAGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
Found at i:34819873 original size:15 final size:15
Alignment explanation
Indices: 34819853--34819883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34819843 CCTACACACC
34819853 ATGATAGTGGATCTA
1 ATGATAGTGGATCTA
34819868 ATGATAGTGGATCTA
1 ATGATAGTGGATCTA
34819883 A
1 A
34819884 GTCACTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (15 bp):
ATGATAGTGGATCTA
Found at i:34820599 original size:42 final size:42
Alignment explanation
Indices: 34820544--34820649 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
34820534 AGTGACGACT
* * * * * *
34820544 GTGTGACTAAAACACATGCCCGTGTGGTTGAGATACAAGGTC
1 GTGTGGCTGAAACACACGCCCGTGTGATGGAGATACAAGATC
* ** *
34820586 GTGTGGCTGAAACACACACTTGTGTGATGGAGATACATGATC
1 GTGTGGCTGAAACACACGCCCGTGTGATGGAGATACAAGATC
*
34820628 GTGTGGATGAAACACACGCCCG
1 GTGTGGCTGAAACACACGCCCG
34820650 AGCACGACCG
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (42 bp):
GTGTGGCTGAAACACACGCCCGTGTGATGGAGATACAAGATC
Found at i:34822046 original size:44 final size:44
Alignment explanation
Indices: 34821997--34822085 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
34821987 ATTACATCTT
34821997 TACCCAAACGAAGAACAAACAATTAAATTAATTATTTGTAATGA
1 TACCCAAACGAAGAACAAACAATTAAATTAATTATTTGTAATGA
* *
34822041 TACCCAAATGAAGAACAAACAATTAATTTAATTATTTGTAATGA
1 TACCCAAACGAAGAACAAACAATTAAATTAATTATTTGTAATGA
34822085 T
1 T
34822086 TTTCTTTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (44 bp):
TACCCAAACGAAGAACAAACAATTAAATTAATTATTTGTAATGA
Found at i:34822460 original size:21 final size:19
Alignment explanation
Indices: 34822428--34822467 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
34822418 ACTTTAATCC
34822428 TTAATATTTTTTACAGTGAT
1 TTAATATTTTTTA-AGTGAT
34822448 TTAATATTTTTTTAAGTGAT
1 TTAATA-TTTTTTAAGTGAT
34822468 AAAAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATATTTTTTAAGTGAT
Found at i:34827137 original size:19 final size:20
Alignment explanation
Indices: 34827096--34827147 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
34827086 AGCCTTGTGG
**
34827096 TATCAATATTTTTACACGGA
1 TATCAATATTTTTACACAAA
*
34827116 TATCAATATTTTTATA-AAA
1 TATCAATATTTTTACACAAA
*
34827135 TATCGATATTTTT
1 TATCAATATTTTT
34827148 CAGTTGGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (20 bp):
TATCAATATTTTTACACAAA
Found at i:34842585 original size:42 final size:42
Alignment explanation
Indices: 34842533--34842618 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
34842523 GATGATAAAT
34842533 TTACTTTATTTTACTTAATTTATCATTTATTTACTAATTTAC
1 TTACTTTATTTTACTTAATTTATCATTTATTTACTAATTTAC
34842575 TTACTTTATTTTACTTAATTTATCATTTATTTACTAATTTAC
1 TTACTTTATTTTACTTAATTTATCATTTATTTACTAATTTAC
34842617 TT
1 TT
34842619 TTATAACCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (42 bp):
TTACTTTATTTTACTTAATTTATCATTTATTTACTAATTTAC
Found at i:34842589 original size:14 final size:14
Alignment explanation
Indices: 34842533--34842597 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
34842523 GATGATAAAT
34842533 TTACTTTATTTTAC
1 TTACTTTATTTTAC
* *
34842547 TTAATTTATCATTTAT
1 TTACTTTAT--TTTAC
*
34842563 TTAC--TAATTTAC
1 TTACTTTATTTTAC
34842575 TTACTTTATTTTAC
1 TTACTTTATTTTAC
*
34842589 TTAATTTAT
1 TTACTTTAT
34842598 CATTTATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
12 8 0.20
14 25 0.62
16 7 0.17
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.62
Consensus pattern (14 bp):
TTACTTTATTTTAC
Found at i:34847270 original size:31 final size:31
Alignment explanation
Indices: 34847249--34847358 Score: 177
Period size: 31 Copynumber: 3.6 Consensus size: 31
34847239 ATAAATATCA
*
34847249 ACATATTCATACCATGTAATCATTCATATTT
1 ACATATTCATACCCTGTAATCATTCATATTT
34847280 ACATATTCATACCCTGTAATCATTCATATTT
1 ACATATTCATACCCTGTAATCATTCATATTT
* **
34847311 ACATATTCATACCCTGTAATCATTCACACAT
1 ACATATTCATACCCTGTAATCATTCATATTT
34847342 ACATATT-ATACCCTGTA
1 ACATATTCATACCCTGTA
34847359 CTTGATGACA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 10 0.13
31 65 0.87
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (31 bp):
ACATATTCATACCCTGTAATCATTCATATTT
Found at i:34847275 original size:17 final size:17
Alignment explanation
Indices: 34847253--34847336 Score: 58
Period size: 17 Copynumber: 5.3 Consensus size: 17
34847243 ATATCAACAT
34847253 ATTCATACCATGTAATC
1 ATTCATACCATGTAATC
*
34847270 ATTCAT---ATTTACAT-
1 ATTCATACCATGTA-ATC
*
34847284 ATTCATACCCTGTAATC
1 ATTCATACCATGTAATC
*
34847301 ATTCAT---ATTTACAT-
1 ATTCATACCATGTA-ATC
*
34847315 ATTCATACCCTGTAATC
1 ATTCATACCATGTAATC
34847332 ATTCA
1 ATTCA
34847337 CACATACATA
Statistics
Matches: 50, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
14 19 0.38
15 4 0.08
16 4 0.08
17 23 0.46
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (17 bp):
ATTCATACCATGTAATC
Found at i:34847289 original size:14 final size:14
Alignment explanation
Indices: 34847270--34847321 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
34847260 CCATGTAATC
34847270 ATTCATATTTACAT
1 ATTCATATTTACAT
*
34847284 ATTCATACCCTGTA-AT
1 ATTCATA---TTTACAT
34847300 CATTCATATTTACAT
1 -ATTCATATTTACAT
34847315 ATTCATA
1 ATTCATA
34847322 CCCTGTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
16 2 0.06
17 10 0.32
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (14 bp):
ATTCATATTTACAT
Found at i:34849105 original size:22 final size:22
Alignment explanation
Indices: 34849071--34849122 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
34849061 TTTATAATAA
34849071 AAATTA-TAAAATA-TAATTATT
1 AAATTATTAAAATATTAA-TATT
34849092 AAATTATTAAAATATTAATATT
1 AAATTATTAAAATATTAATATT
*
34849114 AAAATATTA
1 AAATTATTA
34849123 GTTTCCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATTATTAAAATATTAATATT
Found at i:34849113 original size:14 final size:14
Alignment explanation
Indices: 34849096--34849122 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34849086 ATTATTAAAT
34849096 TATTAAAATATTAA
1 TATTAAAATATTAA
34849110 TATTAAAATATTA
1 TATTAAAATATTA
34849123 GTTTCCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTAAAATATTAA
Found at i:34849516 original size:33 final size:35
Alignment explanation
Indices: 34849474--34849539 Score: 109
Period size: 33 Copynumber: 1.9 Consensus size: 35
34849464 TGTGTCCTGC
34849474 GGTTAGGGTTTTGG-GTTATT-GGTTTAGGGTTAA
1 GGTTAGGGTTTTGGTGTTATTAGGTTTAGGGTTAA
*
34849507 GGTTAGGGTTTTGGTGTTTTTAGGTTTAGGGTT
1 GGTTAGGGTTTTGGTGTTATTAGGTTTAGGGTT
34849540 TTAGAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 14 0.47
34 5 0.17
35 11 0.37
ACGTcount: A:0.12, C:0.00, G:0.39, T:0.48
Consensus pattern (35 bp):
GGTTAGGGTTTTGGTGTTATTAGGTTTAGGGTTAA
Found at i:34849694 original size:95 final size:95
Alignment explanation
Indices: 34849567--34849857 Score: 289
Period size: 94 Copynumber: 3.0 Consensus size: 95
34849557 TAAATAAAGG
** ** * ** * *
34849567 ATTAGGGTTTAGGGTTTGTCAATTAAATTAATTATAAATTTTTCAAAATTGGATT-AGGTTTCGT
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTCAAAATCAGATTAAGGTTTAGA
* * *
34849631 GTTTATTGTTTTTTAAGAAAAAATCAATTAA
66 GTTAAGTG-TTTTTAAGAAAAAATCAAATAA
* ** *
34849662 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTA-ATTTTTTTTAAAATCAGATTAAGGTTTAGA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTCAAAATCAGATTAAGGTTTAGA
34849726 GTTAAGTGTTTTTAAGAAAAAATCAAATAA
66 GTTAAGTGTTTTTAAGAAAAAATCAAATAA
* * ** * *
34849756 ATTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAGAATTAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT-TCAA-AATCAGATTAAGGTTTA
* * * * *
34849821 GTGTTTAGGGTTTTTAAGTAGAAACTCAAATAA
64 GAGTTAAGTGTTTTTAAG-AAAAAATCAAATAA
34849854 ATTA
1 ATTA
34849858 TGTAAGATAT
Statistics
Matches: 161, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
94 67 0.42
95 46 0.29
96 2 0.01
97 30 0.19
98 16 0.10
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTCAAAATCAGATTAAGGTTTAGA
GTTAAGTGTTTTTAAGAAAAAATCAAATAA
Found at i:34849870 original size:9 final size:9
Alignment explanation
Indices: 34849855--34849966 Score: 101
Period size: 9 Copynumber: 13.1 Consensus size: 9
34849845 CTCAAATAAA
34849855 TTATGTAAG
1 TTATGTAAG
*
34849864 ATATGTAAG
1 TTATGTAAG
*
34849873 ATATGTAAG
1 TTATGTAAG
**
34849882 -T-TGTATT
1 TTATGTAAG
34849889 TTATGTAAG
1 TTATGTAAG
*
34849898 TTCTGT-A-
1 TTATGTAAG
*
34849905 TTATGTATG
1 TTATGTAAG
34849914 TTATGTAAG
1 TTATGTAAG
*
34849923 TTGTGT-AG
1 TTATGTAAG
*
34849931 -AATGTAAG
1 TTATGTAAG
*
34849939 CTATGTAAG
1 TTATGTAAG
34849948 TTATGTAAG
1 TTATGTAAG
34849957 TTATGTAAG
1 TTATGTAAG
34849966 T
1 T
34849967 GGTGTATTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
7 12 0.14
8 7 0.08
9 64 0.77
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:34849904 original size:25 final size:26
Alignment explanation
Indices: 34849856--34849963 Score: 96
Period size: 25 Copynumber: 4.2 Consensus size: 26
34849846 TCAAATAAAT
* * *
34849856 TATGTAAGATATGTAAGATATGTAAG
1 TATGTATGTTATGTAAGTTATGTAAG
* * *
34849882 T-TGTATTTTATGTAAGTTCTGT-AT
1 TATGTATGTTATGTAAGTTATGTAAG
*
34849906 TATGTATGTTATGTAAGTTGTGT-AG
1 TATGTATGTTATGTAAGTTATGTAAG
* * *
34849931 AATGTAAGCTATGTAAGTTATGTAAG
1 TATGTATGTTATGTAAGTTATGTAAG
34849957 TTATGTA
1 -TATGTA
34849964 AGTGGTGTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
24 2 0.03
25 55 0.85
26 3 0.05
27 5 0.08
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.44
Consensus pattern (26 bp):
TATGTATGTTATGTAAGTTATGTAAG
Found at i:34849920 original size:16 final size:16
Alignment explanation
Indices: 34849854--34850041 Score: 58
Period size: 16 Copynumber: 10.9 Consensus size: 16
34849844 ACTCAAATAA
*
34849854 ATTATGTAAGATATGT
1 ATTATGTAAGTTATGT
* * *
34849870 AAGATATGTAAGTTGTAT
1 -A-TTATGTAAGTTATGT
* *
34849888 TTTATGTAAGTTCTGT
1 ATTATGTAAGTTATGT
*
34849904 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
* *
34849920 AAGTTGTGT-AG-AATGT
1 -A-TTATGTAAGTTATGT
*
34849936 AAGCTATGTAAGTTATGT
1 -A-TTATGTAAGTTATGT
**
34849954 AAGTTATGTAAGTGGTGT
1 -A-TTATGTAAGTTATGT
** *
34849972 ATTATGT-TCTTCGGTGT
1 ATTATGTAAGTT--ATGT
* *
34849989 AAGTTATGTAGGCTATGT
1 -A-TTATGTAAGTTATGT
34850007 ATTATGTAAGTTATTATGTT
1 ATTATGTAAG---TTATG-T
34850027 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
34850042 CAAGTTTATA
Statistics
Matches: 128, Mismatches: 29, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
15 1 0.01
16 50 0.39
17 16 0.12
18 39 0.30
19 10 0.08
20 12 0.09
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.46
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:34849972 original size:18 final size:18
Alignment explanation
Indices: 34849933--34849998 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
34849923 TTGTGTAGAA
* **
34849933 TGTAAGCTATGTAAGTTA
1 TGTAAGTTATGTAAGTGG
34849951 TGTAAGTTATGTAAGTGG
1 TGTAAGTTATGTAAGTGG
***
34849969 TGT-A-TTATGTTCTTCGG
1 TGTAAGTTATGTAAGT-GG
34849986 TGTAAGTTATGTA
1 TGTAAGTTATGTA
34849999 GGCTATGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 7 0.18
17 6 0.16
18 19 0.50
19 6 0.16
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (18 bp):
TGTAAGTTATGTAAGTGG
Found at i:34849978 original size:34 final size:33
Alignment explanation
Indices: 34849889--34850028 Score: 88
Period size: 34 Copynumber: 4.1 Consensus size: 33
34849879 AAGTTGTATT
* *
34849889 TTATGTAAGTTCTGTATTATGTATGTTATGTAAG
1 TTATGTAAG-TGTGTATTATGTAAGTTATGTAAG
* * * *
34849923 TTGTGTAGAATGT-AAGCTATGTAAGTTATGTAAG
1 TTATGTA-AGTGTGTA-TTATGTAAGTTATGTAAG
** *
34849957 TTATGTAAGTGGTGTATTATGT-TCTTCGGTGTAAG
1 TTATGTAAGT-GTGTATTATGTAAGTT--ATGTAAG
* * *
34849992 TTATGTAGGCTATGTATTATGTAAGTTAT-TATG
1 TTATGTAAG-TGTGTATTATGTAAGTTATGTAAG
34850025 TTAT
1 TTAT
34850029 TATGTAAGTT
Statistics
Matches: 79, Mismatches: 19, Indels: 17
0.69 0.17 0.15
Matches are distributed among these distances:
33 12 0.15
34 38 0.48
35 26 0.33
36 3 0.04
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (33 bp):
TTATGTAAGTGTGTATTATGTAAGTTATGTAAG
Found at i:34850070 original size:33 final size:32
Alignment explanation
Indices: 34850024--34850105 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
34850014 AAGTTATTAT
*
34850024 GTTATTATGTAAGTTATGCAAGTT-TATATATAA
1 GTTA-TATATAAGTTATGCAAGTTAT-TATATAA
* * *
34850057 GTTTCTATATAAGTTATGTAAGTTATTATGTAA
1 G-TTATATATAAGTTATGCAAGTTATTATATAA
*
34850090 GTTATGTATAAGTTAT
1 GTTATATATAAGTTAT
34850106 CATATGATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
32 13 0.32
33 25 0.61
34 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (32 bp):
GTTATATATAAGTTATGCAAGTTATTATATAA
Found at i:34850078 original size:21 final size:21
Alignment explanation
Indices: 34850054--34850097 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34850044 AGTTTATATA
34850054 TAAGTT-TCTATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
34850075 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
34850096 TA
1 TA
34850098 TAAGTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:34850137 original size:34 final size:36
Alignment explanation
Indices: 34850089--34850157 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 36
34850079 TTATTATGTA
34850089 AGTTATGTATAAGTTATCATATGATTGATAAATTTG
1 AGTTATGTATAAGTTATCATATGATTGATAAATTTG
*
34850125 AGTTAT-T-TAAGTTATGATATGATTGATAAATTT
1 AGTTATGTATAAGTTATCATATGATTGATAAATTT
34850158 TGAAATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 25 0.78
35 1 0.03
36 6 0.19
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.46
Consensus pattern (36 bp):
AGTTATGTATAAGTTATCATATGATTGATAAATTTG
Found at i:34850186 original size:17 final size:19
Alignment explanation
Indices: 34850150--34850188 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
34850140 GATATGATTG
34850150 ATAAATTTTGAAATAATAT
1 ATAAATTTTGAAATAATAT
34850169 ATAAATTTT-AAA-AATAT
1 ATAAATTTTGAAATAATAT
34850186 ATA
1 ATA
34850189 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
ATAAATTTTGAAATAATAT
Found at i:34850272 original size:15 final size:15
Alignment explanation
Indices: 34850252--34850392 Score: 89
Period size: 15 Copynumber: 9.4 Consensus size: 15
34850242 TTTGGTTATG
34850252 TATATTAAAACTATA
1 TATATTAAAACTATA
34850267 TATATTTTAAAACTATA
1 TATA--TTAAAACTATA
34850284 -ATA-TATAAACTATA
1 TATATTA-AAACTATA
*
34850298 TAGATATTAAAACAATA
1 T--ATATTAAAACTATA
*
34850315 TATATT-ATA-TATA
1 TATATTAAAACTATA
* *
34850328 -AAATATATATA-TATA
1 TATAT-TA-AAACTATA
* * *
34850343 AATTTTAAAAATATA
1 TATATTAAAACTATA
*
34850358 TTTATTAAAACTATA
1 TATATTAAAACTATA
34850373 TATATTAAAAC-ATA
1 TATATTAAAACTATA
*
34850387 TGTATT
1 TATATT
34850393 TTTAATATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
12 3 0.03
13 6 0.06
14 20 0.20
15 43 0.43
16 5 0.05
17 22 0.22
18 2 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (15 bp):
TATATTAAAACTATA
Found at i:34850289 original size:18 final size:17
Alignment explanation
Indices: 34850256--34850339 Score: 75
Period size: 17 Copynumber: 4.9 Consensus size: 17
34850246 GTTATGTATA
34850256 TTAAAACTATATATATT
1 TTAAAACTATATATATT
34850273 TTAAAACTATA-ATA-T
1 TTAAAACTATATATATT
* * *
34850288 AT-AAACTATATAGATA
1 TTAAAACTATATATATT
*
34850304 TTAAAACAATATATATT
1 TTAAAACTATATATATT
*
34850321 ATATATAAAATATATATAT
1 -T-TA-AAACTATATATAT
34850340 ATAAATTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
14 8 0.15
15 4 0.08
16 4 0.08
17 22 0.42
18 1 0.02
19 2 0.04
20 11 0.21
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAAACTATATATATT
Found at i:34850297 original size:31 final size:30
Alignment explanation
Indices: 34850259--34850319 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
34850249 ATGTATATTA
* * *
34850259 AAACTATATATATTTTAAAACTATAATATAT
1 AAACTATATAGATATTAAAACAAT-ATATAT
34850290 AAACTATATAGATATTAAAACAATATATAT
1 AAACTATATAGATATTAAAACAATATATAT
34850320 TATATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (30 bp):
AAACTATATAGATATTAAAACAATATATAT
Done.