Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 14 of 206
Found at i:4275719 original size:9 final size:9
Alignment explanation
Indices: 4275677--4275819 Score: 64
Period size: 9 Copynumber: 15.7 Consensus size: 9
4275667 TTTTTTTACG
4275677 ATTTTTATAA
1 ATTTTTAT-A
* *
4275687 AATTTTACA
1 ATTTTTATA
4275696 ATTATTTATA
1 ATT-TTTATA
* *
4275706 TTTTTTATG
1 ATTTTTATA
4275715 ATTTTTATA
1 ATTTTTATA
4275724 ATCTTTTTATA
1 A--TTTTTATA
4275735 ATTTTTAATA
1 ATTTTT-ATA
*** *
4275745 AAAATTAAA
1 ATTTTTATA
4275754 TATTTCTTAT-
1 -ATTT-TTATA
4275764 A-TTTT-T-
1 ATTTTTATA
4275770 -TTTTTA-A
1 ATTTTTATA
* *
4275777 AATTTAATA
1 ATTTTTATA
4275786 ATTTTTATA
1 ATTTTTATA
*
4275795 ATTTTTATTT
1 ATTTTTA-TA
*
4275805 ATTTTTATC
1 ATTTTTATA
4275814 ATTTTT
1 ATTTTT
4275820 TGCTACATCT
Statistics
Matches: 99, Mismatches: 22, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
6 5 0.05
7 2 0.02
8 6 0.06
9 46 0.46
10 28 0.28
11 12 0.12
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4275730 original size:11 final size:10
Alignment explanation
Indices: 4275678--4275745 Score: 59
Period size: 10 Copynumber: 6.9 Consensus size: 10
4275668 TTTTTTACGA
*
4275678 TTTTTATAAA
1 TTTTTATAAT
* *
4275688 ATTTTACAAT
1 TTTTTATAAT
*
4275698 TATTTAT-AT
1 TTTTTATAAT
*
4275707 TTTTTATGA-
1 TTTTTATAAT
4275716 TTTTTATAAT
1 TTTTTATAAT
4275726 CTTTTTATAAT
1 -TTTTTATAAT
*
4275737 TTTTAATAA
1 TTTTTATAA
4275746 AAATTAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
9 16 0.35
10 20 0.43
11 10 0.22
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:4275778 original size:31 final size:31
Alignment explanation
Indices: 4275727--4275805 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
4275717 TTTTATAATC
*
4275727 TTTTTATAATTTTTA-ATAAAAATTAAAT-A
1 TTTTTATAATTTTTATTTAAAAATTAAATAA
* * *
4275756 TTTCTTAT-ATTTTTTTTTTAAAATTTAATAA
1 TTT-TTATAATTTTTATTTAAAAATTAAATAA
4275787 TTTTTATAATTTTTATTTA
1 TTTTTATAATTTTTATTTA
4275806 TTTTTATCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
29 9 0.22
30 18 0.45
31 13 0.32
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTATAATTTTTATTTAAAAATTAAATAA
Found at i:4277473 original size:22 final size:22
Alignment explanation
Indices: 4277428--4277473 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
4277418 ATATAATAAT
* **
4277428 AAAATAGTAGCAAAACAGTTAG
1 AAAATAGCAGCAAAACAGCAAG
*
4277450 AAAATAGCAGCAAAATAGCAAG
1 AAAATAGCAGCAAAACAGCAAG
4277472 AA
1 AA
4277474 GTTTTTGCCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.17, T:0.13
Consensus pattern (22 bp):
AAAATAGCAGCAAAACAGCAAG
Found at i:4281772 original size:13 final size:13
Alignment explanation
Indices: 4281747--4281782 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4281737 AATTAAGATA
4281747 TTTTATA-TTTAT
1 TTTTATATTTTAT
4281759 TTTTATATTTTAT
1 TTTTATATTTTAT
*
4281772 TTATATATTTT
1 TTTTATATTTT
4281783 CAGGTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATATTTTAT
Found at i:4283639 original size:4 final size:4
Alignment explanation
Indices: 4283630--4283674 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
4283620 ACTACTACTA
**
4283630 TTAT TTAT TTAT TTAT TTAT TTAT TTAT CCAT TTAT TTA- TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
4283675 GGTTTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:4289853 original size:55 final size:57
Alignment explanation
Indices: 4289783--4289890 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 57
4289773 GTATCAGATT
* *
4289783 AAAAAAATGACAAGTTCA-ACTGTGAAATTAAA-AAAAATTAAGTACCAAATTAGAAA
1 AAAAAAATGACAAGTTCAGA-TATGAAATTAAACAAAAATTAAATACCAAATTAGAAA
* * *
4289839 AAAAAAAT-TCAAGTTCAGATATTAAATTAAACCAAAACTTAAATACCAAATT
1 AAAAAAATGACAAGTTCAGATATGAAATTAAA-CAAAAATTAAATACCAAATT
4289891 TTGTAAACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
55 18 0.41
56 9 0.20
57 17 0.39
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.24
Consensus pattern (57 bp):
AAAAAAATGACAAGTTCAGATATGAAATTAAACAAAAATTAAATACCAAATTAGAAA
Found at i:4292075 original size:25 final size:24
Alignment explanation
Indices: 4292020--4292081 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
4292010 TAATTAATTT
*
4292020 TATATTATATATATAATTTAACAAA
1 TATA-TATATATATAATCTAACAAA
* *
4292045 TAATATATTTATATAATCTAATCTAA
1 T-ATATATATATATAATCTAA-CAAA
*
4292071 TATATTTATAT
1 TATATATATAT
4292082 TATATTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATATATATATAATCTAACAAA
Found at i:4292087 original size:11 final size:11
Alignment explanation
Indices: 4292071--4292098 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4292061 TCTAATCTAA
4292071 TATATTTATAT
1 TATATTTATAT
4292082 TATATTTATAT
1 TATATTTATAT
4292093 TATATT
1 TATATT
4292099 ATCTACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:4306686 original size:5 final size:5
Alignment explanation
Indices: 4306676--4306704 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4306666 TGTTTCATGC
4306676 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
4306705 TTAATTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:4309304 original size:15 final size:14
Alignment explanation
Indices: 4309279--4309324 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
4309269 AACTCTATTT
4309279 TAATTATATTAGGA
1 TAATTATATTAGGA
*
4309293 TAATTAATATTAAGA
1 TAATT-ATATTAGGA
*
4309308 TAATTAT-TAAGGA
1 TAATTATATTAGGA
4309321 TAAT
1 TAAT
4309325 CTAATTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 8 0.29
14 7 0.25
15 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (14 bp):
TAATTATATTAGGA
Found at i:4311297 original size:11 final size:13
Alignment explanation
Indices: 4311266--4311297 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4311256 TTTATGGTCT
4311266 ATAATTTCATAGA
1 ATAATTTCATAGA
4311279 ATAATTTCAT-GA
1 ATAATTTCATAGA
4311291 A-AATTTC
1 ATAATTTC
4311298 GTTCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.32
12 3 0.16
13 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATAATTTCATAGA
Found at i:4319325 original size:22 final size:23
Alignment explanation
Indices: 4319295--4319337 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
4319285 AGCTAGAAAA
4319295 ATAGAACCAAATAGCC-CTATCT
1 ATAGAACCAAATAGCCTCTATCT
*
4319317 ATAGTACCAAATAGCCTCTAT
1 ATAGAACCAAATAGCCTCTAT
4319338 TCCAGATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (23 bp):
ATAGAACCAAATAGCCTCTATCT
Found at i:4327940 original size:16 final size:15
Alignment explanation
Indices: 4327906--4327941 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
4327896 ATGTTATTTC
4327906 AAAATTAAAACAATGA
1 AAAATTAAAACAAT-A
*
4327922 AAACTTAAAACAATA
1 AAAATTAAAACAATA
4327937 AAAAT
1 AAAAT
4327942 ATTATCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATTAAAACAATA
Found at i:4328832 original size:50 final size:52
Alignment explanation
Indices: 4328705--4328845 Score: 214
Period size: 52 Copynumber: 2.8 Consensus size: 52
4328695 ATTAATAATG
* * *
4328705 TTAACAGCATAATAATTCACTAATTAAAATTAAATAATTTAATAACATTTTC
1 TTAACAACATAATAATTAACTAATTAAAATTAAATAATTAAATAACATTTTC
* *
4328757 TTAACAACATAACAATTAACTAATTAAAATTAAATAATTAAATAATA-TTT-
1 TTAACAACATAATAATTAACTAATTAAAATTAAATAATTAAATAACATTTTC
*
4328807 TTAACAACATAATAGTTAACTAATTAAAATTAAATAATT
1 TTAACAACATAATAATTAACTAATTAAAATTAAATAATT
4328846 TATAAATATT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 37 0.45
51 3 0.04
52 42 0.51
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.37
Consensus pattern (52 bp):
TTAACAACATAATAATTAACTAATTAAAATTAAATAATTAAATAACATTTTC
Found at i:4328854 original size:50 final size:50
Alignment explanation
Indices: 4328705--4328857 Score: 211
Period size: 50 Copynumber: 3.0 Consensus size: 50
4328695 ATTAATAATG
* *
4328705 TTAACAGCATAATAATTCACTAATTAAAATTAAATAATTTAATAACAT-TTT
1 TTAACAACATAATAATTAACTAATTAAAATTAAATAATTT-ATAA-ATATTT
* *
4328756 CTTAACAACATAACAATTAACTAATTAAAATTAAATAA-TTAAATAATATTT
1 -TTAACAACATAATAATTAACTAATTAAAATTAAATAATTTATA-AATATTT
*
4328807 TTAACAACATAATAGTTAACTAATTAAAATTAAATAATTTATAAATATTT
1 TTAACAACATAATAATTAACTAATTAAAATTAAATAATTTATAAATATTT
4328857 T
1 T
4328858 GTTACCATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
50 47 0.52
51 10 0.11
52 34 0.37
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (50 bp):
TTAACAACATAATAATTAACTAATTAAAATTAAATAATTTATAAATATTT
Found at i:4332896 original size:18 final size:18
Alignment explanation
Indices: 4332859--4332895 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4332849 AATAAATATA
*
4332859 TAATTAAAAACTAATTTT
1 TAATTAAAAAATAATTTT
4332877 TAATTAAAAAATAGATTTT
1 TAATTAAAAAATA-ATTTT
4332896 AGTAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTAAAAAATAATTTT
Found at i:4340007 original size:13 final size:14
Alignment explanation
Indices: 4339982--4340010 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4339972 TGACAAAATC
4339982 AAAATGTATTTAAA
1 AAAATGTATTTAAA
4339996 AAAATGTA-TTAAA
1 AAAATGTATTTAAA
4340009 AA
1 AA
4340011 TGTCAATGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAATGTATTTAAA
Found at i:4340494 original size:3 final size:3
Alignment explanation
Indices: 4340486--4340525 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
4340476 ATATAAATAC
* *
4340486 AAT AAT AAT -AT TAT AAT AAT AAT AAT AAT TAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4340526 ACAATATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:4340533 original size:15 final size:15
Alignment explanation
Indices: 4340478--4340525 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4340468 GCGCACACAT
*
4340478 ATAAATACAATAATA
1 ATAAATATAATAATA
*
4340493 ATATTATAATAATAATA
1 ATA-AAT-ATAATAATA
*
4340510 ATAATTATAATAATA
1 ATAAATATAATAATA
4340525 A
1 A
4340526 ACAATATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 13 0.48
16 3 0.11
17 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATATAATAATA
Found at i:4341677 original size:23 final size:24
Alignment explanation
Indices: 4341621--4341678 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
4341611 TAAGATAACT
4341621 ATATAAAAAATTCAATAAATAGAA
1 ATATAAAAAATTCAATAAATAGAA
* * * **
4341645 AAATATAAAATT-ATTAAATATTA
1 ATATAAAAAATTCAATAAATAGAA
4341668 ATATAAAAAAT
1 ATATAAAAAAT
4341679 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
ATATAAAAAATTCAATAAATAGAA
Found at i:4345647 original size:25 final size:25
Alignment explanation
Indices: 4345587--4345675 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
4345577 AGAGCACATA
* **
4345587 AACGGGAAGCTCTCTCTCGAGCCATAT
1 AACGGGAAG--CTCTATCGAGCTGTAT
**
4345614 AACAAGAAGCTCGTAT-GAGCTGTAT
1 AACGGGAAGCTC-TATCGAGCTGTAT
*
4345639 AACGGGAAGCT-TATCCGGGCTGTAT
1 AACGGGAAGCTCTAT-CGAGCTGTAT
4345664 AACGGGAAGCTC
1 AACGGGAAGCTC
4345676 ATAAGAGCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 3 0.06
25 38 0.76
26 2 0.04
27 7 0.14
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (25 bp):
AACGGGAAGCTCTATCGAGCTGTAT
Found at i:4345819 original size:73 final size:73
Alignment explanation
Indices: 4345681--4345820 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
4345671 AGCTCATAAG
* * * * ***
4345681 AGCCATAATTAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCTGAAGAGCCATTAATTGGGAAG
1 AGCCATAATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCCGAAGAGCCATTAATCAAGAAG
4345746 CTTCGGAT
66 CTTCGGAT
* **
4345754 AGCCATATATCAGGAAGTTCAAGCGAGCC-ATATTGGGAAGCTCCGAAGAGCCATTAATCAAGAA
1 AGCCATA-ATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCCGAAGAGCCATTAATCAAGAA
4345818 GCT
65 GCT
4345821 CACAAAGAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
73 38 0.68
74 18 0.32
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (73 bp):
AGCCATAATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCCGAAGAGCCATTAATCAAGAAG
CTTCGGAT
Found at i:4345821 original size:25 final size:25
Alignment explanation
Indices: 4345790--4345858 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
4345780 GCCATATTGG
4345790 GAAGCTCCGAAGAGCCATTAATCAA
1 GAAGCTCCGAAGAGCCATTAATCAA
* ** **
4345815 GAAGCTCACAAAGAGCTTTTAATCGG
1 GAAGCTC-CGAAGAGCCATTAATCAA
*
4345841 GAAGCTTCGAAGAGCCAT
1 GAAGCTCCGAAGAGCCAT
4345859 ATATCGAGAC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (25 bp):
GAAGCTCCGAAGAGCCATTAATCAA
Found at i:4345864 original size:25 final size:25
Alignment explanation
Indices: 4345704--4345864 Score: 79
Period size: 25 Copynumber: 6.5 Consensus size: 25
4345694 AAGCTCATGC
* *
4345704 GAGCCA-ATAACGGGTAGC-TCTGAA
1 GAGCCATATATCGGGAAGCTTC-GAA
* *
4345728 GAGCCAT-TAATTGGGAAGCTTCGGA
1 GAGCCATAT-ATCGGGAAGCTTCGAA
* *
4345753 TAGCCATATATCAGGAAG-TTC-AA
1 GAGCCATATATCGGGAAGCTTCGAA
*
4345776 GCGAGCCATAT-T-GGGAAGCTCCGAA
1 --GAGCCATATATCGGGAAGCTTCGAA
** * *
4345801 GAGCCAT-TAATCAAGAAGCTCACAAA
1 GAGCCATAT-ATCGGGAAGCT-TCGAA
* *
4345827 GAG-CTTTTAATCGGGAAGCTTCGAA
1 GAGCCATAT-ATCGGGAAGCTTCGAA
4345852 GAGCCATATATCG
1 GAGCCATATATCG
4345865 AGACGCTCAT
Statistics
Matches: 101, Mismatches: 22, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
22 1 0.01
23 13 0.13
24 14 0.14
25 50 0.50
26 23 0.23
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTTCGAA
Found at i:4347426 original size:10 final size:11
Alignment explanation
Indices: 4347396--4347427 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
4347386 TGCGTGTATA
4347396 ATATATATA-T
1 ATATATATATT
4347406 ATATATATATT
1 ATATATATATT
4347417 ATAT-TATATT
1 ATATATATATT
4347427 A
1 A
4347428 GATACTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:4354811 original size:10 final size:10
Alignment explanation
Indices: 4354796--4354830 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
4354786 AATGTCATAT
4354796 ATATAGATAG
1 ATATAGATAG
4354806 ATATAGATATAG
1 ATATAG--ATAG
4354818 ATATAGATAG
1 ATATAGATAG
4354828 ATA
1 ATA
4354831 GATAGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (10 bp):
ATATAGATAG
Found at i:4354813 original size:6 final size:6
Alignment explanation
Indices: 4354802--4354826 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4354792 ATATATATAG
4354802 ATAGAT ATAGAT ATAGAT ATAGAT A
1 ATAGAT ATAGAT ATAGAT ATAGAT A
4354827 GATAGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATAGAT
Found at i:4354817 original size:16 final size:16
Alignment explanation
Indices: 4354796--4354830 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4354786 AATGTCATAT
*
4354796 ATATAGATAGATATAG
1 ATATAGATAGAGATAG
*
4354812 ATATAGATATAGATAG
1 ATATAGATAGAGATAG
4354828 ATA
1 ATA
4354831 GATAGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATATAGATAGAGATAG
Found at i:4362207 original size:20 final size:20
Alignment explanation
Indices: 4362178--4362217 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4362168 TTCACCTCAT
*
4362178 GCATCGCATCATATGTATTA
1 GCATCACATCATATGTATTA
4362198 GCATCACATCATATGTATTA
1 GCATCACATCATATGTATTA
4362218 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
GCATCACATCATATGTATTA
Found at i:4372544 original size:3 final size:3
Alignment explanation
Indices: 4372533--4372608 Score: 107
Period size: 3 Copynumber: 25.3 Consensus size: 3
4372523 TTTTAAATAT
* * * *
4372533 TTA TCA TTA TTA TTT TTA TTA TTA TTA TTG CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
4372581 TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4372609 ACATATACAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4372779 original size:12 final size:12
Alignment explanation
Indices: 4372762--4372790 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4372752 TATGCATACC
4372762 TACATATTTTAA
1 TACATATTTTAA
4372774 TACATATTTTAA
1 TACATATTTTAA
4372786 TACAT
1 TACAT
4372791 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:4378899 original size:12 final size:12
Alignment explanation
Indices: 4378869--4378901 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4378859 TATATATTTT
4378869 AAAATT-ATATA
1 AAAATTAATATA
4378880 AAAA-TAATATA
1 AAAATTAATATA
4378891 AAAATTAATAT
1 AAAATTAATAT
4378902 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:4383857 original size:161 final size:161
Alignment explanation
Indices: 4383592--4383882 Score: 485
Period size: 161 Copynumber: 1.8 Consensus size: 161
4383582 ATATACGAAT
* * *
4383592 TTTTTAATTAATTAAATGTCATACTTTATTTTGTTGAGTAAATTTATATGTAGAATTTGTAAATC
1 TTTTTAATTAACTAAATGTAATACTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAATC
* *
4383657 AAGTATTGATTTATCTATCTATAAGAAAAATATTAATTTGACTTAAGTTAAAGTCTTGCCTCTAC
66 AAGTATTAATTTATCTATCTATAAGAAAAATATTAATTTGACTGAAGTTAAAGTCTTGCCTCTAC
4383722 CTCATCTTTTTTTTTTCTAGAGTGCTAATTA
131 CTCATCTTTTTTTTTTCTAGAGTGCTAATTA
*
4383753 TTTTTAATTAACTAAATGTAATGCTTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAA-
1 TTTTTAATTAACTAAATGTAATAC-TTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAAT
* * *
4383817 CAAGTATTAATTTTTCTATCTATAAGAAAAATATTAATTTGACTGAATTTAATGTCTTGCCTCTA
65 CAAGTATTAATTTATCTATCTATAAGAAAAATATTAATTTGACTGAAGTTAAAGTCTTGCCTCTA
4383882 C
130 C
4383883 TTTCTCTCTT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
161 82 0.68
162 38 0.32
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (161 bp):
TTTTTAATTAACTAAATGTAATACTTTATTTTGTTGAATAAATTTATATGTAGAATTTGTAAATC
AAGTATTAATTTATCTATCTATAAGAAAAATATTAATTTGACTGAAGTTAAAGTCTTGCCTCTAC
CTCATCTTTTTTTTTTCTAGAGTGCTAATTA
Found at i:4388093 original size:23 final size:22
Alignment explanation
Indices: 4388049--4388120 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
4388039 AAATTGACTA
4388049 TTTTTTATATATTTTTTAATTT
1 TTTTTTATATATTTTTTAATTT
4388071 TTTTGTTATATA-TTTTTAGATTT
1 TTTT-TTATATATTTTTTA-ATTT
*
4388094 TAAATTTTT-T-TATTTTTTTATTT
1 T---TTTTTATATATTTTTTAATTT
4388117 TTTT
1 TTTT
4388121 AAGTTGAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
20 3 0.07
22 10 0.23
23 19 0.44
24 6 0.14
25 2 0.05
26 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (22 bp):
TTTTTTATATATTTTTTAATTT
Found at i:4388120 original size:8 final size:8
Alignment explanation
Indices: 4388097--4388121 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4388087 TAGATTTTAA
4388097 ATTTTTTT
1 ATTTTTTT
4388105 ATTTTTTT
1 ATTTTTTT
4388113 ATTTTTTT
1 ATTTTTTT
4388121 A
1 A
4388122 AGTTGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:4389072 original size:26 final size:26
Alignment explanation
Indices: 4389033--4389089 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
4389023 ATGACAACAT
* *
4389033 CTTTGATTTGTTTGAGCTCTAGAAAA
1 CTTTGATTTATTTGAGCTCAAGAAAA
4389059 CTTTGATTTATTTGAGCTCAAGAAAA
1 CTTTGATTTATTTGAGCTCAAGAAAA
4389085 CTTTG
1 CTTTG
4389090 GAGCTAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (26 bp):
CTTTGATTTATTTGAGCTCAAGAAAA
Found at i:4392202 original size:18 final size:19
Alignment explanation
Indices: 4392179--4392217 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4392169 AATTTTACTA
*
4392179 ATTAAAAAT-AATAATTAT
1 ATTAAAAATAAATAATAAT
4392197 ATTAAAAATAAATAATAAT
1 ATTAAAAATAAATAATAAT
4392216 AT
1 AT
4392218 AATATATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAATAAATAATAAT
Found at i:4396723 original size:19 final size:19
Alignment explanation
Indices: 4396694--4396738 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4396684 ATTGGAATTT
*
4396694 TAATAAT-TAAAAAAT-AA
1 TAATAATATTAAAAATAAA
*
4396711 TAATTATATTAAAAATAAA
1 TAATAATATTAAAAATAAA
4396730 TAATAATAT
1 TAATAATAT
4396739 AATATATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAATATTAAAAATAAA
Found at i:4400109 original size:12 final size:12
Alignment explanation
Indices: 4400092--4400119 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4400082 TTTTTTTTAT
4400092 ATTTATCATCAA
1 ATTTATCATCAA
4400104 ATTTATCATCAA
1 ATTTATCATCAA
4400116 ATTT
1 ATTT
4400120 GTTGTTAGGT
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:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTTATCATCAA
Found at i:4405468 original size:19 final size:20
Alignment explanation
Indices: 4405446--4405483 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4405436 TTTAAAAACC
4405446 TTAAAATTT-TGAAAAAAAA
1 TTAAAATTTGTGAAAAAAAA
*
4405465 TTAAAATTTGTTAAAAAAA
1 TTAAAATTTGTGAAAAAAA
4405484 TAAGAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAAATTTGTGAAAAAAAA
Found at i:4405551 original size:31 final size:31
Alignment explanation
Indices: 4405515--4405574 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
4405505 AACTTCAAAT
*
4405515 ATATATAAATTGAAATTGAAAATAA-AAAAGA
1 ATATATAAATTGAAAAT-AAAATAACAAAAGA
4405546 ATATATAAATTGAAAATAAAATAACAAAA
1 ATATATAAATTGAAAATAAAATAACAAAA
4405575 TTAGTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (31 bp):
ATATATAAATTGAAAATAAAATAACAAAAGA
Found at i:4405825 original size:8 final size:8
Alignment explanation
Indices: 4405812--4405875 Score: 57
Period size: 8 Copynumber: 8.4 Consensus size: 8
4405802 AAATTGAATA
4405812 TTTATATT
1 TTTATATT
4405820 TTTATATT
1 TTTATATT
4405828 TTTA-A-T
1 TTTATATT
4405834 TTTAT-TT
1 TTTATATT
4405841 GTTATATATT
1 -TT-TATATT
*
4405851 TTTAGA-T
1 TTTATATT
*
4405858 TTTAGATT
1 TTTATATT
4405866 TTT-TATT
1 TTTATATT
4405873 TTT
1 TTT
4405876 TAAGTTGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
6 5 0.10
7 15 0.31
8 21 0.44
9 5 0.10
10 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (8 bp):
TTTATATT
Found at i:4405875 original size:23 final size:21
Alignment explanation
Indices: 4405812--4405903 Score: 78
Period size: 23 Copynumber: 4.1 Consensus size: 21
4405802 AAATTGAATA
4405812 TTTATATTTTTATATTTTTAAT
1 TTTAT-TTTTTATATTTTTAAT
4405834 TTTATTTGTTATATATTTTTAGAT
1 TTTATTT-TT-TATATTTTTA-AT
*
4405858 TTTAGATTTTTTAT-TTTTTAAG
1 TTT--ATTTTTTATATTTTTAAT
* * * *
4405880 TTGAATTTTTATATATTTAGT
1 TTTATTTTTTATATTTTTAAT
4405901 TTT
1 TTT
4405904 TGAAGTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.14
21 9 0.16
22 10 0.18
23 16 0.28
24 8 0.14
25 2 0.04
26 4 0.07
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTATTTTTTATATTTTTAAT
Found at i:4419532 original size:46 final size:45
Alignment explanation
Indices: 4419465--4419731 Score: 311
Period size: 46 Copynumber: 5.6 Consensus size: 45
4419455 TTTGAGTACT
* *
4419465 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
4419511 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
4419557 TTTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
4419603 TCTGATCAGTGACAAGTGGAAAGTGATGAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
4419654 TCTGATCAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCAGTTACACTTA
1 TCTGATCAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
4419705 TCTGATCAGGGAC-AAGTGATAAGTGAT
1 TCTGATCAGTGACAAAGTGATAAGTGAT
4419732 CATACGCAAG
Statistics
Matches: 204, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
44 14 0.07
45 6 0.03
46 94 0.46
51 90 0.44
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTGATCAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:4419639 original size:51 final size:49
Alignment explanation
Indices: 4419479--4419731 Score: 297
Period size: 51 Copynumber: 5.2 Consensus size: 49
4419469 ATCAAGTGAC
* *
4419479 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAC----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC-AGTGACAAGT
* * *
4419525 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAAGTGAC----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC-AGTGACAAGT
*
4419571 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAGTGACAAGT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGT
*
4419620 GGAAAGTGATGAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGT
1 --AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGT
* *
4419671 GAAAAGTGATAAGTGATAGCTTCAGTTACACTTATCTGATCAGGGACAAGT
1 --AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGT
4419722 GATAAGTGAT
1 -A-AAGTGAT
4419732 CATACGCAAG
Statistics
Matches: 188, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
45 6 0.03
46 80 0.43
50 1 0.01
51 101 0.54
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (49 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGT
Found at i:4420849 original size:18 final size:17
Alignment explanation
Indices: 4420822--4420855 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4420812 GACCTAAGTG
*
4420822 GGGGGTGTTATTGTTGTT
1 GGGGGAGTTATT-TTGTT
4420840 GGGGGAGTTATTTTGT
1 GGGGGAGTTATTTTGT
4420856 GAACTACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.00, G:0.44, T:0.47
Consensus pattern (17 bp):
GGGGGAGTTATTTTGTT
Found at i:4422353 original size:26 final size:26
Alignment explanation
Indices: 4422324--4422385 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
4422314 CCCATTTTTT
* * *
4422324 AAATAAACACCAAAAAATTATTTTAA
1 AAATAAAAACAAAAAAAGTATTTTAA
*
4422350 AAATAAAAAATAAAAAAAGTATTTTAA
1 AAAT-AAAAACAAAAAAAGTATTTTAA
*
4422377 AATTAAAAA
1 AAATAAAAA
4422386 ATATATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATAAAAACAAAAAAAGTATTTTAA
Found at i:4422373 original size:27 final size:27
Alignment explanation
Indices: 4422335--4422388 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
4422325 AATAAACACC
*
4422335 AAAAAATTATTTTAAAAATAAAAAATA
1 AAAAAAGTATTTTAAAAATAAAAAATA
*
4422362 AAAAAAGTATTTTAAAATTAAAAAATA
1 AAAAAAGTATTTTAAAAATAAAAAATA
4422389 TATTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAAGTATTTTAAAAATAAAAAATA
Found at i:4422765 original size:12 final size:12
Alignment explanation
Indices: 4422748--4422787 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
4422738 CTCCTTTCCT
4422748 ATTTTCTCTTTA
1 ATTTTCTCTTTA
4422760 A-TTT-TCTTT-
1 ATTTTCTCTTTA
*
4422769 CTTTTCTCTTTA
1 ATTTTCTCTTTA
4422781 ATTTTCT
1 ATTTTCT
4422788 TTCTCTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 8 0.35
11 8 0.35
12 7 0.30
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTCTCTTTA
Found at i:4422774 original size:21 final size:21
Alignment explanation
Indices: 4422749--4422797 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
4422739 TCCTTTCCTA
4422749 TTTTCTCTTTAATTTTCTTTC
1 TTTTCTCTTTAATTTTCTTTC
4422770 TTTTCTCTTTAATTTTCTTTC
1 TTTTCTCTTTAATTTTCTTTC
4422791 TCTTTCT
1 T-TTTCT
4422798 TTCTTTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTCTTTAATTTTCTTTC
Found at i:4430447 original size:21 final size:21
Alignment explanation
Indices: 4430423--4430465 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4430413 TCAGCTCTCT
4430423 GGCCATCTTCCAT-CAAACATG
1 GGCCAT-TTCCATCCAAACATG
* *
4430444 GGCCCTTTCCTTCCAAACATG
1 GGCCATTTCCATCCAAACATG
4430465 G
1 G
4430466 AGCAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (21 bp):
GGCCATTTCCATCCAAACATG
Found at i:4434336 original size:28 final size:28
Alignment explanation
Indices: 4434280--4434336 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
4434270 TCTTGAATTT
* * *
4434280 TTTTTATGCCTTAATAGTGTCAACCAAA
1 TTTTTATCCCTTAATAGTATCAACAAAA
*
4434308 TTTTTATCCCTTAATAGTATCATCAAAA
1 TTTTTATCCCTTAATAGTATCAACAAAA
4434336 T
1 T
4434337 CAATGATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (28 bp):
TTTTTATCCCTTAATAGTATCAACAAAA
Found at i:4435813 original size:15 final size:15
Alignment explanation
Indices: 4435793--4435970 Score: 56
Period size: 16 Copynumber: 11.8 Consensus size: 15
4435783 TTTTACATAC
4435793 TTTTAAAT-TTTTTAA
1 TTTTAAATATTTTT-A
4435808 TTTTAAATATTTTTA
1 TTTTAAATATTTTTA
* **
4435823 TTTTTTTAAT-TTAAATA
1 --TTTTAAATATT-TTTA
**
4435840 TTTTAAA-A-TACT-
1 TTTTAAATATTTTTA
*
4435852 TTTT-AAT-TTTTAA
1 TTTTAAATATTTTTA
4435865 TT-TAAATATTTTTA
1 TTTTAAATATTTTTA
* **
4435879 TTTTTTAATATTAAATA
1 -TTTTAAATATT-TTTA
*
4435896 TTTTAAATA--CTT-
1 TTTTAAATATTTTTA
4435908 TTTTAAA-ATTTTTAA
1 TTTTAAATATTTTT-A
4435923 TTTTAAAATATTTTAAATA
1 TTTT-AAATATTTT---TA
4435942 TTTTAAATACTTTTTAA
1 TTTTAAATA-TTTTT-A
*
4435959 TTTTAAAAATTT
1 TTTTAAATATTT
4435971 AAAATAAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 47
0.66 0.09 0.25
Matches are distributed among these distances:
11 3 0.02
12 13 0.11
13 10 0.08
14 6 0.05
15 21 0.17
16 29 0.24
17 25 0.20
18 5 0.04
19 9 0.07
20 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAAATATTTTTA
Found at i:4435835 original size:23 final size:23
Alignment explanation
Indices: 4435800--4435899 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
4435790 TACTTTTAAA
4435800 TTTTTTAATTTTAAATATTTTTAT
1 TTTTTTAA-TTTAAATATTTTTAT
4435824 TTTTTTAATTTAAATATTTTAAAATACTTT
1 TTTTTTAATTTAAATATTTT----TA---T
4435854 TTAATTTTTAATTTAAATATTTTTA-
1 T---TTTTTAATTTAAATATTTTTAT
4435879 TTTTTTAATATTAAATATTTT
1 TTTTTTAAT-TTAAATATTTT
4435900 AAATACTTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 23
0.74 0.00 0.26
Matches are distributed among these distances:
22 8 0.12
23 23 0.35
24 8 0.12
25 1 0.02
27 2 0.03
29 2 0.03
30 2 0.03
33 19 0.29
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTAATTTAAATATTTTTAT
Found at i:4435844 original size:9 final size:9
Alignment explanation
Indices: 4435832--4435976 Score: 73
Period size: 9 Copynumber: 16.9 Consensus size: 9
4435822 ATTTTTTTAA
4435832 TTTAAATAT
1 TTTAAATAT
4435841 TTTAAAATACT
1 TTT-AAATA-T
*
4435852 TTTTAAT-T
1 TTTAAATAT
4435860 TTT--A-A-
1 TTTAAATAT
4435865 TTTAAATAT
1 TTTAAATAT
*
4435874 TTT-TAT-T
1 TTTAAATAT
*
4435881 TTTTAATA-
1 TTTAAATAT
4435889 -TTAAATAT
1 TTTAAATAT
4435897 TTTAAATACTTT
1 TTTAAATA---T
4435909 TTTAAA-AT
1 TTTAAATAT
*
4435917 TTTTAAT-T
1 TTTAAATAT
*
4435925 TTAAAATAT
1 TTTAAATAT
4435934 TTTAAATAT
1 TTTAAATAT
4435943 TTTAAATACT
1 TTTAAATA-T
*
4435953 TTT-TA-AT
1 TTTAAATAT
*
4435960 TTTAAAAAT
1 TTTAAATAT
*
4435969 TTAAAATA
1 TTTAAATA
4435977 AAAATGGGCC
Statistics
Matches: 105, Mismatches: 12, Indels: 38
0.68 0.08 0.25
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 15 0.14
8 23 0.22
9 39 0.37
10 12 0.11
11 5 0.05
12 7 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAAATAT
Found at i:4435849 original size:33 final size:32
Alignment explanation
Indices: 4435807--4435945 Score: 120
Period size: 33 Copynumber: 4.5 Consensus size: 32
4435797 AAATTTTTTA
*
4435807 ATTTTAAATA-TTTTTATTTTTTTAATTTAAAT
1 ATTTTAAATACTTTTTA-ATTTTTAATTTAAAT
4435839 ATTTTAAAATACTTTTTAATTTTTAATTTAAAT
1 ATTTT-AAATACTTTTTAATTTTTAATTTAAAT
*
4435872 ATTTT---TATTTTTTAA----T-A-TTAAAT
1 ATTTTAAATACTTTTTAATTTTTAATTTAAAT
4435895 ATTTTAAATACTTTTTTAAAATTTTTAATTTTAAAAT
1 ATTTTAAATAC-TTTTT--AATTTTTAA-TTT-AAAT
4435932 ATTTTAAATA-TTTT
1 ATTTTAAATACTTTT
4435946 AAATACTTTT
Statistics
Matches: 88, Mismatches: 3, Indels: 29
0.73 0.03 0.24
Matches are distributed among these distances:
23 11 0.12
24 1 0.01
25 1 0.01
26 2 0.02
27 5 0.06
29 11 0.12
32 5 0.06
33 25 0.28
34 7 0.08
35 4 0.05
36 2 0.02
37 14 0.16
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTTTAAATACTTTTTAATTTTTAATTTAAAT
Found at i:4435851 original size:58 final size:56
Alignment explanation
Indices: 4435762--4435936 Score: 228
Period size: 56 Copynumber: 3.0 Consensus size: 56
4435752 ATAATAAATA
* *
4435762 TATTTTTTTATTTTAAAATATTTTTACATACTTTTAAATTTTTTAATTTTAAATATTTT
1 TATTTTTTTAATTT-AAATA-TTTTAAATACTTTTAAA-TTTTTAATTTTAAATATTTT
*
4435821 TATTTTTTTAATTTAAATATTTTAAAATACTTTTTAATTTTTAA-TTTAAATATTTT
1 TATTTTTTTAATTTAAATATTTT-AAATACTTTTAAATTTTTAATTTTAAATATTTT
4435877 TA-TTTTTTAATATTAAATATTTTAAATACTTTTTTAAAATTTTTAATTTTAAAATATTTT
1 TATTTTTTTAAT-TTAAATATTTTAAATAC--TTTT-AAATTTTTAATTTT-AAATATTTT
4435937 AAATATTTTA
Statistics
Matches: 105, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
55 15 0.14
56 25 0.24
57 15 0.14
58 25 0.24
59 16 0.15
60 9 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (56 bp):
TATTTTTTTAATTTAAATATTTTAAATACTTTTAAATTTTTAATTTTAAATATTTT
Found at i:4435883 original size:22 final size:23
Alignment explanation
Indices: 4435860--4435945 Score: 65
Period size: 23 Copynumber: 3.8 Consensus size: 23
4435850 CTTTTTAATT
*
4435860 TTTAAT-TTAAATATTTTTATTT
1 TTTAATATTAAATATTTTTAATT
* *
4435882 TTTAATATTAAATATTTTAAATAC
1 TTTAATATTAAATATTTTTAAT-T
4435906 TTT--T-TTAAA-ATTTTTAATT
1 TTTAATATTAAATATTTTTAATT
*
4435925 TTAAAATATTTTAAATATTTT
1 TT-TAATA--TTAAATATTTT
4435946 AAATACTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
19 2 0.04
20 8 0.16
21 5 0.10
22 8 0.16
23 13 0.27
24 3 0.06
25 5 0.10
26 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAATATTAAATATTTTTAATT
Found at i:4436265 original size:20 final size:20
Alignment explanation
Indices: 4436240--4436279 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4436230 CGTAAAATAA
*
4436240 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
4436260 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
4436280 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4436269 original size:34 final size:35
Alignment explanation
Indices: 4436225--4436291 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
4436215 CAGTAAAATG
* *
4436225 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
* *
4436259 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTT
4436292 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:4438022 original size:12 final size:11
Alignment explanation
Indices: 4437996--4438152 Score: 55
Period size: 11 Copynumber: 15.5 Consensus size: 11
4437986 TATTTTTTTA
4437996 TTTTAAATATT
1 TTTTAAATATT
*
4438007 TTTTACATACTT
1 TTTTAAATA-TT
4438019 TTTT-AAT-TT
1 TTTTAAATATT
*
4438028 TTTT---TAAT
1 TTTTAAATATT
*
4438036 TTTAAAATATT
1 TTTTAAATATT
**
4438047 TTCAAAATACTT
1 TTTTAAATA-TT
4438059 TTTT-AAT-TT
1 TTTTAAATATT
4438068 TTTT--A-A-T
1 TTTTAAATATT
*
4438075 TTTAAAATA-T
1 TTTTAAATATT
*
4438085 TTTTAAAAATAT
1 TTTTAAATAT-T
4438097 TTTT-AATA-T
1 TTTTAAATATT
4438106 TTTT--A-A-T
1 TTTTAAATATT
*
4438113 TTTAAAATATT
1 TTTTAAATATT
*
4438124 TTTAAAATACTTT
1 TTTTAAATA--TT
4438137 TTTTAAAT-TT
1 TTTTAAATATT
4438147 TTTTAA
1 TTTTAA
4438153 TTTTTAAAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 37
0.69 0.08 0.22
Matches are distributed among these distances:
7 10 0.09
8 6 0.05
9 19 0.17
10 18 0.16
11 37 0.32
12 15 0.13
13 9 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:4438044 original size:40 final size:39
Alignment explanation
Indices: 4437987--4438163 Score: 245
Period size: 38 Copynumber: 4.5 Consensus size: 39
4437977 NNNNNNNNNT
* *
4437987 ATTTTTTT-ATTTT-AAATATTTTTTACATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
4438024 ATTTTTTTTAATTTTAAAATATTTTCAAAATACTTTTTTA
1 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
4438064 ATTTTTTTAATTTTAAAATATTTTTAAAA-A-TATTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACT-TTTTTA
*
4438102 ATATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTT-A
4438143 ATTTTTTTAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
4438164 AAAATGGGCC
Statistics
Matches: 125, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
37 2 0.02
38 42 0.34
39 33 0.26
40 27 0.22
41 11 0.09
42 10 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:4438106 original size:9 final size:9
Alignment explanation
Indices: 4438058--4438128 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
4438048 TCAAAATACT
*
4438058 TTTTTAATT
1 TTTTTAATA
4438067 TTTTTAAT-
1 TTTTTAATA
**
4438075 TTTAAAATA
1 TTTTTAATA
4438084 TTTTTAAAAATA
1 TTTTT---AATA
4438096 TTTTTAATA
1 TTTTTAATA
4438105 TTTTTAAT-
1 TTTTTAATA
**
4438113 TTTAAAATA
1 TTTTTAATA
4438122 TTTTTAA
1 TTTTTAA
4438129 AATACTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 12 0.24
9 28 0.57
12 9 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAATA
Found at i:4438862 original size:21 final size:23
Alignment explanation
Indices: 4438838--4438879 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4438828 TTCGCCCCTG
4438838 TTTAGAT-TA-ATTAGAGTTTTA
1 TTTAGATGTACATTAGAGTTTTA
*
4438859 TTTAGATGTACTTTAGAGTTT
1 TTTAGATGTACATTAGAGTTT
4438880 AGAGTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (23 bp):
TTTAGATGTACATTAGAGTTTTA
Found at i:4449754 original size:30 final size:29
Alignment explanation
Indices: 4449714--4449780 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
4449704 ACCAATAAAA
4449714 GCCGTTTTTTTT-TTAATTTACCGAAATGG
1 GCCGTTTTTTTTATT-ATTTACCGAAATGG
* *
4449743 GCCGATTTTTTTTATTATTTATCGGAATGG
1 GCCG-TTTTTTTTATTATTTACCGAAATGG
4449773 GCCGTTTT
1 GCCGTTTT
4449781 CCGCGAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.24
30 24 0.71
31 2 0.06
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.49
Consensus pattern (29 bp):
GCCGTTTTTTTTATTATTTACCGAAATGG
Found at i:4449874 original size:40 final size:40
Alignment explanation
Indices: 4449785--4449903 Score: 111
Period size: 40 Copynumber: 2.9 Consensus size: 40
4449775 CGTTTTCCGC
* * **
4449785 GAAATCGCGTCCACGTCAGCGCGATGT-CAGGGTACGTGTCAG
1 GAAATCGCGTCCACGTCAGCGCGATTTGC--TG-ACGTGGAAG
*
4449827 GACATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
1 GAAATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
4449867 GAAATCGCG-CC-C-TCTAGGACGCGATTTGCTGACGTGG
1 GAAATCGCGTCCACGTC-A-G-CGCGATTTGCTGACGTGG
4449904 CATGAACAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
37 2 0.03
38 2 0.03
39 3 0.04
40 33 0.49
41 1 0.01
42 25 0.37
43 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (40 bp):
GAAATCGCGTCCACGTCAGCGCGATTTGCTGACGTGGAAG
Found at i:4455557 original size:14 final size:14
Alignment explanation
Indices: 4455538--4455564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4455528 CTTTTAAATA
4455538 TTTTGAATTTTTAT
1 TTTTGAATTTTTAT
4455552 TTTTGAATTTTTA
1 TTTTGAATTTTTA
4455565 AGAAGTAAAA
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:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTGAATTTTTAT
Found at i:4459669 original size:30 final size:30
Alignment explanation
Indices: 4459634--4459789 Score: 97
Period size: 30 Copynumber: 5.2 Consensus size: 30
4459624 AAAAAAAATG
*
4459634 CATTTTAGCCCCCAAATTTTTCAAAAATTA
1 CATTTTAGACCCCAAATTTTTCAAAAATTA
* * * * *
4459664 TATTTTA-ACCCTTAAGTTTTTCTAAATTTA
1 CATTTTAGACCC-CAAATTTTTCAAAAATTA
* * *
4459694 CATCTT-GACCCCTAATATTTT-ATAAATTA
1 CATTTTAGACCCCAAAT-TTTTCAAAAATTA
* *
4459723 CA-TTTAGACCCCTAATATTTCTAAAAATTA
1 CATTTTAGACCCCAAATTTTTC-AAAAATTA
* * * * *
4459753 TATTTT-GGCCCCATATTTTTCTAAAATTG
1 CATTTTAGACCCCAAATTTTTCAAAAATTA
4459782 CACTTTTA
1 CA-TTTTA
4459790 CCCCAGAAAT
Statistics
Matches: 92, Mismatches: 25, Indels: 17
0.69 0.19 0.13
Matches are distributed among these distances:
28 5 0.05
29 29 0.32
30 55 0.60
31 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (30 bp):
CATTTTAGACCCCAAATTTTTCAAAAATTA
Found at i:4459732 original size:29 final size:28
Alignment explanation
Indices: 4459681--4459757 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
4459671 ACCCTTAAGT
*
4459681 TTTTCTAAATTTACATCTTGACCCCTAATA
1 TTTTATAAA-TTACAT-TTGACCCCTAATA
4459711 TTTTATAAATTACATTTAGACCCCTAATA
1 TTTTATAAATTACATTT-GACCCCTAATA
* *
4459740 TTTCTAAAAATTATATTT
1 TTT-TATAAATTACATTT
4459758 TGGCCCCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 2 0.05
29 20 0.48
30 20 0.48
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (28 bp):
TTTTATAAATTACATTTGACCCCTAATA
Found at i:4460378 original size:6 final size:6
Alignment explanation
Indices: 4460322--4460366 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
4460312 TATGCCTAAA
4460322 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA- AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
4460367 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:4461467 original size:157 final size:152
Alignment explanation
Indices: 4461235--4461767 Score: 671
Period size: 157 Copynumber: 3.4 Consensus size: 152
4461225 CAAGAAATAG
* *
4461235 TTTTCAATTTCTGCTTTTTTAATAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGCA
1 TTTTCAATTTCTG-TTTTTCAAAAAAATCAACTCATAATGCGAG-AGTGAGTTGAGCCTC-GGCA
*
4461300 CACGCTGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
63 CACGCCGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
4461365 GAGCCTCGGGTCAAATGCCGAGGTATTT
128 GAGCCTCGGGTCAAAT-CCGAGGTA--T
* *
4461393 CTTTTAAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGGACA
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGA-GTGAGTTGAGCCTCGG-CA
*
4461457 CACGCCGAGGTATTTTTT-AATTTCTA-TTTTTCGAAAAGTCAACTCATATTGCGAGAGGTGAGT
63 CACGCCGAGGTATTTTTTAAATTTCTATTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGT
*
4461520 TGAGCCTCGGGTCACATCCTGAGGTAT
127 TGAGCCTCGGGTCAAATCC-GAGGTAT
* *
4461547 TTTTCAATTTCTATTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGAG
1 TTTTCAATTTC--TGTTTTTC-AAAAAAATCAACTCATAATGCGAGAG-TGAGTTGAGCCTC--G
* * * *
4461612 GCGCATGCCGATGTATTTCTTTTAAATTTCTATTTTTT-AAAAATCAACTCATATTGTGAGAGGT
60 GCACACGCCGAGGTA-TT-TTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGT
*
4461676 GAGTTGAGCATCGGGTCACACAT-CGAGGTAT
123 GAGTTGAGCCTCGGGTCA-A-ATCCGAGGTAT
* ** *
4461707 TTTCCAATTTCTGTTTTTCAAAAAAAAAAACTCATAATGCGAGAGGTGAGTTGAGCTTCGG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGA-GTGAGTTGAGCCTCGG
4461768 GTCGCACGTT
Statistics
Matches: 334, Mismatches: 22, Indels: 40
0.84 0.06 0.10
Matches are distributed among these distances:
153 10 0.03
154 1 0.00
155 17 0.05
156 63 0.19
157 125 0.37
158 24 0.07
159 16 0.05
160 62 0.19
161 9 0.03
162 7 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (152 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGTGAGTTGAGCCTCGGCACAC
GCCGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
CCTCGGGTCAAATCCGAGGTAT
Found at i:4461518 original size:76 final size:78
Alignment explanation
Indices: 4461235--4461775 Score: 596
Period size: 79 Copynumber: 6.9 Consensus size: 78
4461225 CAAGAAATAG
* * * * * *
4461235 TTTTCAATTTCTGCTTTTTTAATAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGG-C
1 TTTTAAATTTCT-ATTTTTCAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
4461299 ACACGCTGAGGTATT
64 ACACGCCGAGGTATT
4461314 TTTTAAATTTCTATTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTAAATTTCTA-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
4461378 AATGCCGAGGTATTT
65 CACGCCGAGGTA-TT
* * *
4461393 CTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTC-GGACA
1 -TTTTAAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
4461457 CACGCCGAGGTATT
65 CACGCCGAGGTATT
* *
4461471 TTTT-AATTTCTATTTTTCGAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTAAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
4461535 ATC-CTGAGGTA-T
66 A-CGCCGAGGTATT
* *
4461547 TTTTCAATTTCTATTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGAG
1 TTTTAAATTTCTA--TTTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-G
* * *
4461612 G-CGCATGCCGATGTATTT
61 GTCACACGCCGAGGTA-TT
* * *
4461630 CTTTTAAATTTCTATTTTT-TAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCATCGGGTCA
1 -TTTTAAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
**
4461694 CACATCGAGGTA-T
65 CACGCCGAGGTATT
** * ** * * *
4461707 TTTCCAATTTCTGTTTTTCAAAAAAAAAAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCG
1 TTTTAAATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
4461772 CACG
65 CACG
4461776 TTGAGCTTTT
Statistics
Matches: 394, Mismatches: 48, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
76 69 0.18
77 63 0.16
78 58 0.15
79 89 0.23
80 49 0.12
81 46 0.12
82 7 0.02
83 1 0.00
84 12 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (78 bp):
TTTTAAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ACGCCGAGGTATT
Found at i:4461679 original size:79 final size:77
Alignment explanation
Indices: 4461235--4461768 Score: 583
Period size: 76 Copynumber: 6.8 Consensus size: 77
4461225 CAAGAAATAG
* * * * *
4461235 TTTTCAATTTCTGCTTTTTTAATAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGGCA
1 TTTTAAATTTCT-ATTTTTTAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCA
* *
4461300 CACGCTGAGGTATT
64 CATGCCGAGGTATT
* *
4461314 TTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAA
1 TTTTAAATTTCTATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
4461379 ATGCCGAGGTATTT
65 ATGCCGAGGTA-TT
* * * *
4461393 CTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGGACAC
1 -TTTTAAATTTCTATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC
*
4461458 ACGCCGAGGTATT
65 ATGCCGAGGTATT
** *
4461471 TTTT-AATTTCTATTTTTCGAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTTAAATTTCTATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CAC
4461535 AT-CCTGAGGTA-T
65 ATGCC-GAGGTATT
* *
4461547 TTTTCAATTTCTATTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGAG
1 TTTTAAATTTCTA-TTTTTT---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-G
* *
4461612 GCGCATGCCGATGTATTT
61 GCACATGCCGAGGTA-TT
* *
4461630 CTTTTAAATTTCTATTTTTT-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCATCGGGTCA
1 -TTTTAAATTTCTATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CA
***
4461694 CACATCGAGGTA-T
64 CATGCCGAGGTATT
** * * ** * *
4461707 TTTCCAATTTCTGTTTTTCAAAAAAAAAAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGG
1 TTTTAAATTTCTATTTTT-TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
4461769 TCGCACGTTG
Statistics
Matches: 391, Mismatches: 46, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
76 73 0.19
77 60 0.15
78 63 0.16
79 70 0.18
80 56 0.14
81 46 0.12
82 4 0.01
83 7 0.02
84 12 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (77 bp):
TTTTAAATTTCTATTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACA
TGCCGAGGTATT
Found at i:4461705 original size:237 final size:234
Alignment explanation
Indices: 4461235--4461780 Score: 708
Period size: 237 Copynumber: 2.3 Consensus size: 234
4461225 CAAGAAATAG
* * * *
4461235 TTTT-CAATTTCTGCTTTTTTAATAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCAGG-
1 TTTTCCAATTTCT-ATTTTTCAA-AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
*
4461298 CACACGCTGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
64 CACACGCTGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGATGAG
*
4461363 TTGAGCCTCGGGTCAAATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAAATCAACTCAT
129 TTGAGCCTCGGGTCAAATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAAATCAACTCAT
* * *
4461428 ATTGCGAGATGTGAGTTGAGCCTCGGACACACGCCGAGGTA
194 ATTGCGAGAGGTGAGTTGAGCATCGGACACACACCGAGGTA
** * * *
4461469 TTTTTTAATTTCTATTTTTCGAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCCAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
4461534 CATC-CTGAGGTA-TTTTTCAATTTCTATTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGAT
66 CA-CGCTGAGGTATTTTTTAAATTTCTA-TTTTTTC---AAAAATCAACTCATATTGCGAGAGAT
** * *
4461597 GAGTTGAGCCTCGAGG-CGCATGCCGATGTATTTCTTTTAAATTTCTATTTTT-TAAAAATCAAC
126 GAGTTGAGCCTCG-GGTCAAATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAAATCAAC
* * *
4461660 TCATATTGTGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGGTA
190 TCATATTGCGAGAGGTGAGTTGAGCATC-GGACACACACCGAGGTA
* ** *
4461706 TTTTCCAATTTCTGTTTTTCAAAAAAAAAAACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTC
1 TTTTCCAATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
4461771 GCACGTTGAG
65 ACACGCTGAG
4461781 CTTTTCTCGA
Statistics
Matches: 269, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
233 49 0.18
234 29 0.11
235 8 0.03
236 35 0.13
237 102 0.38
238 46 0.17
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (234 bp):
TTTTCCAATTTCTATTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
CACGCTGAGGTATTTTTTAAATTTCTATTTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTT
GAGCCTCGGGTCAAATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAAATCAACTCATAT
TGCGAGAGGTGAGTTGAGCATCGGACACACACCGAGGTA
Found at i:4461811 original size:78 final size:78
Alignment explanation
Indices: 4461264--4461811 Score: 291
Period size: 77 Copynumber: 7.0 Consensus size: 78
4461254 TAATAAAATC
* * * * * **
4461264 AACTCATAATGCGAGAAGTGAGTTGAGCCTCAGG-CACAC-GCTGAGGTATTTTTTAAATTTCTA
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACATC-GAGCTA-TTTTCCAATTTCTA
**
4461327 TTTTTTC--AAAAATC
64 -TTTTTCAAAAAAAAA
* * * **
4461341 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA-A-ATGCCGAGGTATTTCTTTTAAATTT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACAT--CGAGCTA--T-TTTCCAATTT
* **
4461404 CTGTTTTTC-AAAAAATC
61 CTATTTTTCAAAAAAAAA
* * * * ** * **
4461421 AACTCATATTGCGAGATGTGAGTTGAGCCTC-GGACACACGCCGAGGTATTTTTTAATTTCTATT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGCTATTTTCCAATTTCTATT
* ***
4461485 TTTC-GAAAAGTC
66 TTTCAAAAAAAAA
* * * * *
4461497 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATCCT-GAGGTATTTTTCAATTTCTAT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACA-CATCGAGCTATTTTCCAATTTCTA-
*
4461561 TTTTTTCAAAAAAAATC
64 -TTTTTCAAAAAAAA-A
* * * * *** **
4461578 AACTCATATTGCGAGAGATGAGTTGAGCCTCGAGG-CGCATGCCGATG-TATTTCTTTTAAATTT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCG-GGTCACACATCGA-GCTA--T-TTTCCAATTT
* **
4461641 CTATTTTT--TAAAAATC
61 CTATTTTTCAAAAAAAAA
* * * *
4461657 AACTCATATTGTGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGGTATTTTCCAATTTCTGTT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGCTATTTTCCAATTTCTATT
4461722 TTTCAAAAAAAAA
66 TTTCAAAAAAAAA
* * * * * *
4461735 AACTCATAATGCGAGAGGTGAGTTGAGCTTCGGGTCGCACGTTGAGC--TTTTCTCGATTTTTAT
1 AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGCTATTTTC-CAATTTCTAT
*
4461798 TTTTCAAATAAAAA
65 TTTTCAAAAAAAAA
4461812 GAAAATTTTG
Statistics
Matches: 392, Mismatches: 53, Indels: 52
0.79 0.11 0.10
Matches are distributed among these distances:
76 73 0.19
77 79 0.20
78 57 0.15
79 64 0.16
80 59 0.15
81 39 0.10
82 8 0.02
83 1 0.00
84 12 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (78 bp):
AACTCATAATGCGAGAGGTGAGTTGAGCATCGGGTCACACATCGAGCTATTTTCCAATTTCTATT
TTTCAAAAAAAAA
Found at i:4461975 original size:31 final size:30
Alignment explanation
Indices: 4461932--4462051 Score: 118
Period size: 30 Copynumber: 4.0 Consensus size: 30
4461922 ACGAATTTGC
*
4461932 GTTTTTTAAAAAAATTACATTTT-AGCCCCTA
1 GTTTTTT-CAAAAATTACATTTTGA-CCCCTA
4461963 GTTTTTTCAAAAATTACATTTTGACCCCTA
1 GTTTTTTCAAAAATTACATTTTGACCCCTA
* * * **
4461993 GATTTTTCTAAATTTACACCTTGACCCCTA
1 GTTTTTTCAAAAATTACATTTTGACCCCTA
* * * *
4462023 ATATTTT-ATAAATTACATTTAGACCCCTA
1 GTTTTTTCAAAAATTACATTTTGACCCCTA
4462052 AAATTTCTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
29 16 0.22
30 49 0.67
31 8 0.11
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.42
Consensus pattern (30 bp):
GTTTTTTCAAAAATTACATTTTGACCCCTA
Found at i:4462048 original size:29 final size:29
Alignment explanation
Indices: 4461941--4462072 Score: 108
Period size: 30 Copynumber: 4.4 Consensus size: 29
4461931 CGTTTTTTAA
* *
4461941 AAAAATTACATTTTAG-CCCCTAGTTTTTT
1 AAAAATTACA-TTTAGACCCCTAATATTTT
*
4461970 CAAAAATTACATTTTGACCCCTAGAT-TTTT
1 -AAAAATTACATTTAGACCCCTA-ATATTTT
* * *
4462000 CTAAATTTACACCTT-GACCCCTAATATTTT
1 -AAAAATTACA-TTTAGACCCCTAATATTTT
* *
4462030 ATAAATTACATTTAGACCCCTAAAATTTCT
1 AAAAATTACATTTAGACCCCTAATATTT-T
*
4462060 AAAAATTATATTT
1 AAAAATTACATTT
4462073 TGGCCCCATA
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.02
29 26 0.31
30 53 0.63
31 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAAATTACATTTAGACCCCTAATATTTT
Found at i:4462095 original size:59 final size:59
Alignment explanation
Indices: 4461941--4462116 Score: 146
Period size: 59 Copynumber: 3.0 Consensus size: 59
4461931 CGTTTTTTAA
* * * **
4461941 AAAAATTACATTTTAGCCCCTAGTTTTTTCAAAAATTACATTTTGACCCCTAGATTTTTCT
1 AAAAATTACATTTTGGCCCCTA--TTTTTCTAAAATTACATTTAGACCCCTAGAAATTTCT
* ** * *
4462002 -AAATTTACACCTTGACCCCTAATATTT-TATAAATTACATTTAGACCCCTA-AAATTTCT
1 AAAAATTACATTTTGGCCCCT-ATTTTTCTA-AAATTACATTTAGACCCCTAGAAATTTCT
* * *
4462060 AAAAATTATATTTTGGCCCCATATTTTTCTAAAATTGCACTTT-TA-CCCTAGAAATTT
1 AAAAATTACATTTTGGCCCC-TATTTTTCTAAAATTACA-TTTAGACCCCTAGAAATTT
4462117 TACAACTTCT
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
58 12 0.13
59 56 0.62
60 21 0.23
61 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (59 bp):
AAAAATTACATTTTGGCCCCTATTTTTCTAAAATTACATTTAGACCCCTAGAAATTTCT
Found at i:4462635 original size:19 final size:19
Alignment explanation
Indices: 4462608--4462656 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
4462598 AACCAAGAGG
4462608 CAAGAAAAAAGAAAAAAAA
1 CAAGAAAAAAGAAAAAAAA
*
4462627 CAAGCAAAAAGAAAAAAAAA
1 CAAGAAAAAAG-AAAAAAAA
*
4462647 GAAGAAAAAA
1 CAAGAAAAAA
4462657 AAGAGCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (19 bp):
CAAGAAAAAAGAAAAAAAA
Found at i:4462657 original size:32 final size:31
Alignment explanation
Indices: 4462612--4462681 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
4462602 AAGAGGCAAG
4462612 AAAAAAGAAAAAAAACAAGCAAA-AAGAAAAA
1 AAAAAAGAAAAAAAA-AAGCAAAGAAGAAAAA
*
4462643 AAAAGAAGAAAAAAAAGAGCAAAGAAGAAAAA
1 AAAA-AAGAAAAAAAAAAGCAAAGAAGAAAAA
4462675 AAGAAAA
1 AA-AAAA
4462682 AGGGGGAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 10 0.29
32 23 0.66
33 2 0.06
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.00
Consensus pattern (31 bp):
AAAAAAGAAAAAAAAAAGCAAAGAAGAAAAA
Found at i:4462801 original size:21 final size:20
Alignment explanation
Indices: 4462776--4462881 Score: 92
Period size: 21 Copynumber: 5.0 Consensus size: 20
4462766 GTTGATCGGG
4462776 GAAGAAAGAAAGGAAGAAAAA
1 GAAGAAAGAAA-GAAGAAAAA
4462797 GAAGAAAGAAAGAAGAAAAAA
1 GAAGAAAGAAAGAAG-AAAAA
*
4462818 GAAAGGAGAAAGAAAGAAGAAAATGG
1 G--A--AGAAAGAAAGAAGAAAA--A
4462844 GAAG-AAGAAAGAAGAAAAAA
1 GAAGAAAGAAAGAAG-AAAAA
4462864 GAA-AAAGGAAA-AAGAAAA
1 GAAGAAA-GAAAGAAGAAAA
4462882 CAATTTTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
19 4 0.05
20 12 0.16
21 31 0.42
22 6 0.08
23 1 0.01
24 5 0.07
25 13 0.18
26 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (20 bp):
GAAGAAAGAAAGAAGAAAAA
Found at i:4462805 original size:25 final size:26
Alignment explanation
Indices: 4462777--4462880 Score: 90
Period size: 25 Copynumber: 4.1 Consensus size: 26
4462767 TTGATCGGGG
* *
4462777 AAGAAAGAAAGGAAGAA-AAAGAAGA
1 AAGAAAGAAAGAAAAAAGAAAGAAGA
*
4462802 AAGAAAG-AAGAAAAAAGAAAGGAGA
1 AAGAAAGAAAGAAAAAAGAAAGAAGA
** *
4462827 AAGAAAG-AAGAAAATGGGAAGAAGA
1 AAGAAAGAAAGAAAAAAGAAAGAAGA
* *
4462852 AAGAAGAAAAAAGAAAAAGGAAA-AAGA
1 AAG-A-AAGAAAGAAAAAAGAAAGAAGA
4462879 AA
1 AA
4462881 ACAATTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
24 7 0.11
25 38 0.58
26 1 0.02
27 8 0.12
28 11 0.17
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (26 bp):
AAGAAAGAAAGAAAAAAGAAAGAAGA
Found at i:4462806 original size:7 final size:7
Alignment explanation
Indices: 4462781--4462880 Score: 64
Period size: 7 Copynumber: 13.9 Consensus size: 7
4462771 TCGGGGAAGA
4462781 AAGAAAGG
1 AAGAAA-G
4462789 AAGAAA-
1 AAGAAAG
4462795 AAG-AAG
1 AAGAAAG
4462801 AAAGAAAG
1 -AAGAAAG
*
4462809 AAGAAAA
1 AAGAAAG
4462816 AAGAAAG
1 AAGAAAG
*
4462823 GAGAAAG
1 AAGAAAG
*
4462830 AAAGAAGAA
1 -AAGAA-AG
*
4462839 AATGGGAAG
1 AA--GAAAG
4462848 AAGAAAG
1 AAGAAAG
*
4462855 AAGAAAA
1 AAGAAAG
4462862 AAGAAA-
1 AAGAAAG
4462868 AAGGAAA-
1 AA-GAAAG
4462875 AAGAAA
1 AAGAAA
4462881 ACAATTTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
5 2 0.03
6 9 0.12
7 43 0.57
8 15 0.20
9 4 0.05
10 2 0.03
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (7 bp):
AAGAAAG
Found at i:4462852 original size:46 final size:46
Alignment explanation
Indices: 4462778--4462867 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
4462768 TGATCGGGGA
4462778 AGAAAGAAAGGAAGAAAAAGAAGAAAGAAAGAAGAAAAAAGAAAGG
1 AGAAAGAAAGGAAGAAAAAGAAGAAAGAAAGAAGAAAAAAGAAAGG
*
4462824 AGAAAGAAA-GAAGAAAATGGGAAG-AAGAAAGAAGAAAAAAGAAA
1 AGAAAGAAAGGAAGAAAA--AGAAGAAAGAAAGAAGAAAAAAGAAA
4462868 AAGGAAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 8 0.20
46 29 0.71
47 4 0.10
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (46 bp):
AGAAAGAAAGGAAGAAAAAGAAGAAAGAAAGAAGAAAAAAGAAAGG
Found at i:4463028 original size:14 final size:14
Alignment explanation
Indices: 4463011--4463044 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4463001 AACAAAATAG
4463011 CAGCAGCAAAAAAA
1 CAGCAGCAAAAAAA
*
4463025 CAGCAGTAAAAAAA
1 CAGCAGCAAAAAAA
*
4463039 TAGCAG
1 CAGCAG
4463045 GCCTTTCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.18, T:0.06
Consensus pattern (14 bp):
CAGCAGCAAAAAAA
Found at i:4463173 original size:13 final size:12
Alignment explanation
Indices: 4463146--4463211 Score: 78
Period size: 13 Copynumber: 5.2 Consensus size: 12
4463136 AGCAGGCCAG
4463146 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
4463158 AAAAAGAGAAGGA
1 AAAAAGAGAA-AA
4463171 AAAAAGAGAAAAA
1 AAAAAGAG-AAAA
4463184 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
4463196 AGGAAAAAAGAAAA
1 A--AAAAGAGAAAA
4463210 AA
1 AA
4463212 GGTTCAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 16 0.34
13 18 0.38
14 13 0.28
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:4463183 original size:26 final size:27
Alignment explanation
Indices: 4463146--4463211 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 27
4463136 AGCAGGCCAG
4463146 AAAAAGAG-AAAAAAAAAGAG-AAGGA
1 AAAAAGAGAAAAAAAAAAGAGAAAGGA
4463171 AAAAAGAGAAAAAAAAAAGAGAAAAAGGA
1 AAAAAGAGAAAAAAAAAAGAG--AAAGGA
4463200 AAAAAGA-AAAAA
1 AAAAAGAGAAAAA
4463212 GGTTCAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.22
26 12 0.32
28 5 0.14
29 12 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAAAAGAGAAAGGA
Found at i:4463346 original size:9 final size:9
Alignment explanation
Indices: 4463332--4463356 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4463322 AATATTATTA
4463332 GCATTTTAT
1 GCATTTTAT
4463341 GCATTTTAT
1 GCATTTTAT
4463350 GCATTTT
1 GCATTTT
4463357 TAATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.56
Consensus pattern (9 bp):
GCATTTTAT
Found at i:4463543 original size:19 final size:19
Alignment explanation
Indices: 4463521--4463561 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4463511 AAAAGTATTC
4463521 AAAAAATTTCATGT-TTTCG
1 AAAAAA-TTCATGTGTTTCG
*
4463540 AAAAAATTCCTGTGTTTCG
1 AAAAAATTCATGTGTTTCG
4463559 AAA
1 AAA
4463562 TTTTCGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (19 bp):
AAAAAATTCATGTGTTTCG
Found at i:4463615 original size:19 final size:19
Alignment explanation
Indices: 4463518--4463618 Score: 59
Period size: 18 Copynumber: 5.4 Consensus size: 19
4463508 ACCAAAAGTA
*
4463518 TTCAAAAAAT-TTCATGTT
1 TTCAAAAAATATTCGTGTT
* *
4463536 TTCGAAAAA-ATTCCTGTGT
1 TTCAAAAAATATTCGTGT-T
* * *
4463555 TTC--GAAATTTTCGTGTC
1 TTCAAAAAATATTCGTGTT
* * *
4463572 TTCAAATATTTTTC-TCGTGT
1 TTCAAAAAATATTCGT-GT-T
4463592 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTGTT
4463611 TTCAAAAA
1 TTCAAAAA
4463619 TAAGGCAACG
Statistics
Matches: 62, Mismatches: 13, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
17 6 0.10
18 21 0.34
19 21 0.34
20 13 0.21
21 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (19 bp):
TTCAAAAAATATTCGTGTT
Found at i:4463776 original size:18 final size:19
Alignment explanation
Indices: 4463750--4463785 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4463740 AAAATCTTTC
4463750 CGTGGTTTCA-AAAATAAT
1 CGTGGTTTCACAAAATAAT
*
4463768 CGTGTTTTCACAAAATAA
1 CGTGGTTTCACAAAATAA
4463786 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (19 bp):
CGTGGTTTCACAAAATAAT
Found at i:4463845 original size:16 final size:19
Alignment explanation
Indices: 4463809--4463866 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
4463799 TCCGTTCTTC
4463809 AAAATTCTAATGTTTTCAA
1 AAAATTCTAATGTTTTCAA
4463828 AAAATTCT-AT-TTTT-AA
1 AAAATTCTAATGTTTTCAA
* **
4463844 AAAATTTTCGTGTTTTCAA
1 AAAATTCTAATGTTTTCAA
4463863 AAAA
1 AAAA
4463867 AATAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 6 0.18
19 14 0.41
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTCTAATGTTTTCAA
Found at i:4466305 original size:31 final size:29
Alignment explanation
Indices: 4466235--4466308 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
4466225 GGCTCAGGTT
* *
4466235 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
4466264 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
4466295 ACATTTTAGTCACT
1 ACATTTTAGTCACT
4466309 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:4467239 original size:20 final size:19
Alignment explanation
Indices: 4467214--4467254 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
4467204 ATTTAAAAAA
4467214 TAAAAATTATTAAATTATTT
1 TAAAAATTATTAAATT-TTT
4467234 TAAAAATTATTAAATTTTT
1 TAAAAATTATTAAATTTTT
4467253 TA
1 TA
4467255 GAATATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAAAATTATTAAATTTTT
Found at i:4475077 original size:18 final size:18
Alignment explanation
Indices: 4475038--4475079 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4475028 TAAATAAGTG
*
4475038 TAATAATAGTACCAATAA
1 TAATAATAGTAACAATAA
* *
4475056 TAATAATAGTAACAGTAC
1 TAATAATAGTAACAATAA
4475074 TAATAA
1 TAATAA
4475080 CAATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.29
Consensus pattern (18 bp):
TAATAATAGTAACAATAA
Found at i:4476813 original size:27 final size:27
Alignment explanation
Indices: 4476775--4476829 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4476765 AAAATAGTCA
4476775 AAGCTATTACTAAGTCAGTTAGCAGTT
1 AAGCTATTACTAAGTCAGTTAGCAGTT
4476802 AAGCTATTACTAAGTCAGTTAGCAGTT
1 AAGCTATTACTAAGTCAGTTAGCAGTT
4476829 A
1 A
4476830 GAAAGTTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
AAGCTATTACTAAGTCAGTTAGCAGTT
Found at i:4480175 original size:27 final size:27
Alignment explanation
Indices: 4480144--4480198 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
4480134 AAAATAGTCA
4480144 AAGCTGTTACTAAGTCAGTTAGCAGTT
1 AAGCTGTTACTAAGTCAGTTAGCAGTT
4480171 AAGCTGTTACTAAGTCAGTTAGCAGTT
1 AAGCTGTTACTAAGTCAGTTAGCAGTT
4480198 A
1 A
4480199 GAAAGTTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
AAGCTGTTACTAAGTCAGTTAGCAGTT
Found at i:4480206 original size:27 final size:27
Alignment explanation
Indices: 4480149--4480206 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
4480139 AGTCAAAGCT
**
4480149 GTTACTAAGTCAGTTAGCAGTTAAGCT
1 GTTACTAAGTCAGTTAGCAGTTAAGAA
4480176 GTTACTAAGTCAGTTAGCAGTT-AGAAA
1 GTTACTAAGTCAGTTAGCAGTTAAG-AA
4480203 GTTA
1 GTTA
4480207 GCTACAACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (27 bp):
GTTACTAAGTCAGTTAGCAGTTAAGAA
Found at i:4484417 original size:15 final size:15
Alignment explanation
Indices: 4484397--4484425 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4484387 CTTAAATAAC
4484397 TTTGATACTGTGAAA
1 TTTGATACTGTGAAA
4484412 TTTGATACTGTGAA
1 TTTGATACTGTGAA
4484426 TTTTTAATAT
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:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (15 bp):
TTTGATACTGTGAAA
Found at i:4485299 original size:13 final size:13
Alignment explanation
Indices: 4485281--4485307 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4485271 CTTTTATCTG
4485281 TTTATATGGCTTT
1 TTTATATGGCTTT
4485294 TTTATATGGCTTT
1 TTTATATGGCTTT
4485307 T
1 T
4485308 CTTGATGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (13 bp):
TTTATATGGCTTT
Found at i:4490215 original size:84 final size:86
Alignment explanation
Indices: 4490116--4490280 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 86
4490106 ATAGTAAAAA
* *
4490116 TGTAATTTCACCATTTTAATAACTTATATCTTTAT-AATTTTTAAAGGGT-TAAATCAAATTTTT
1 TGTAATTTCACCA-TTTAATAACTTAAAT-TTTATAAAATTTTAAAGGGTCTAAAT-AAATTTTT
*
4490179 ATT-ATTTTTAGGG-GTCATAAAG
63 ATTCATTTTAAGGGAGTCATAAAG
* * * * * *
4490201 TGTAATTTTA-CATTTATTAATTTAAATTTTTTAAAATTTTAAAGGGTCTAAATGAATTTTTTTT
1 TGTAATTTCACCATTTAATAACTTAAATTTTATAAAATTTTAAAGGGTCTAAATAAATTTTTATT
4490265 CATTTTAAGGGAGTCA
66 CATTTTAAGGGAGTCA
4490281 ATGCCTTGTC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
82 4 0.06
83 34 0.51
84 16 0.24
85 13 0.19
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (86 bp):
TGTAATTTCACCATTTAATAACTTAAATTTTATAAAATTTTAAAGGGTCTAAATAAATTTTTATT
CATTTTAAGGGAGTCATAAAG
Found at i:4498497 original size:16 final size:16
Alignment explanation
Indices: 4498476--4498506 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4498466 AGAGATCAAG
4498476 AATTTTAAATTTAAAA
1 AATTTTAAATTTAAAA
4498492 AATTTTAAATTTAAA
1 AATTTTAAATTTAAA
4498507 TCATAACAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTAAATTTAAAA
Found at i:4499022 original size:22 final size:22
Alignment explanation
Indices: 4498994--4499041 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
4498984 AATCCTATCT
4498994 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
4499016 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
4499038 TCAA
1 TCAA
4499042 ACCCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCTC
Found at i:4499077 original size:51 final size:51
Alignment explanation
Indices: 4499013--4499124 Score: 197
Period size: 51 Copynumber: 2.2 Consensus size: 51
4499003 TTCCAAAATT
*
4499013 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTAC
*
4499064 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTAC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTAC
*
4499115 CCCTCAATTT
1 CTCTCAATTT
4499125 TATTTTTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTAC
Found at i:4499182 original size:30 final size:29
Alignment explanation
Indices: 4499125--4499181 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4499115 CCCTCAATTT
*
4499125 TATTTTTTAAAATAATTTTTATATTTTTA
1 TATTTTTTAAAATAATTTTAATATTTTTA
4499154 TATTTTTTAAAAATAATTTTAA-ATTTTT
1 TATTTTTT-AAAATAATTTTAATATTTTT
4499182 TTATAATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TATTTTTTAAAATAATTTTAATATTTTTA
Found at i:4500284 original size:7 final size:7
Alignment explanation
Indices: 4500272--4500296 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4500262 AGTCGATTGA
4500272 TATTTAG
1 TATTTAG
4500279 TATTTAG
1 TATTTAG
4500286 TATTTAG
1 TATTTAG
4500293 TATT
1 TATT
4500297 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:4500973 original size:18 final size:18
Alignment explanation
Indices: 4500947--4500981 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4500937 AGGTGTGTTT
* *
4500947 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
4500965 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
4500982 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:4501414 original size:25 final size:25
Alignment explanation
Indices: 4501385--4501570 Score: 85
Period size: 25 Copynumber: 7.7 Consensus size: 25
4501375 TTTAAATTTA
4501385 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
** *
4501410 TTATTTGATGTAATACGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
4501436 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
4501455 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
* ** *
4501481 TTATTTGATATAATAGGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
4501507 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
*
4501526 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
4501552 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
4501571 ACCATAATTT
Statistics
Matches: 116, Mismatches: 24, Indels: 41
0.64 0.13 0.23
Matches are distributed among these distances:
19 2 0.02
20 10 0.09
21 13 0.11
23 4 0.03
24 6 0.05
25 41 0.35
26 40 0.34
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:4501471 original size:71 final size:71
Alignment explanation
Indices: 4501383--4501567 Score: 334
Period size: 71 Copynumber: 2.6 Consensus size: 71
4501373 TATTTAAATT
4501383 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
4501448 TTTTGA
66 TTTTGA
* *
4501454 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
4501519 TTTTGA
66 TTTTGA
*
4501525 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
4501568 AAAACCATAA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
71 96 0.88
72 13 0.12
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
TTTTGA
Found at i:4501621 original size:29 final size:29
Alignment explanation
Indices: 4501570--4501750 Score: 310
Period size: 29 Copynumber: 6.2 Consensus size: 29
4501560 ATGTAATAAA
* *
4501570 AACCATAATTTAATTAAAAACCCTAACCAT
1 AACC-TAACTTAATTAAAAACCCTAACCCT
4501600 AACCTAACTTAATTAAAAACCCTAACCCT
1 AACCTAACTTAATTAAAAACCCTAACCCT
4501629 AACCTAACTTAATT-AAAACCCTAACCCT
1 AACCTAACTTAATTAAAAACCCTAACCCT
4501657 AACCTAACTTAATTAAAAACCCTAACCCT
1 AACCTAACTTAATTAAAAACCCTAACCCT
*
4501686 AACCAAACTTAATTAAAAACCCTAACCCT
1 AACCTAACTTAATTAAAAACCCTAACCCT
*
4501715 AACCTAACTTAATTAAAAACCCTAGCCCT
1 AACCTAACTTAATTAAAAACCCTAACCCT
4501744 AACCTAA
1 AACCTAA
4501751 TTTTACATAA
Statistics
Matches: 145, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
28 28 0.19
29 113 0.78
30 4 0.03
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (29 bp):
AACCTAACTTAATTAAAAACCCTAACCCT
Found at i:4501724 original size:86 final size:87
Alignment explanation
Indices: 4501570--4501750 Score: 310
Period size: 86 Copynumber: 2.1 Consensus size: 87
4501560 ATGTAATAAA
* *
4501570 AACCATAATTTAATTAAAAACCCTAACCATAACCTAACTTAATTAAAAACCCTAACCCTAACCTA
1 AACC-TAACTTAATTAAAAACCCTAACCATAACCAAACTTAATTAAAAACCCTAACCCTAACCTA
4501635 ACTTAATT-AAAACCCTAACCCT
65 ACTTAATTAAAAACCCTAACCCT
*
4501657 AACCTAACTTAATTAAAAACCCTAACCCTAACCAAACTTAATTAAAAACCCTAACCCTAACCTAA
1 AACCTAACTTAATTAAAAACCCTAACCATAACCAAACTTAATTAAAAACCCTAACCCTAACCTAA
*
4501722 CTTAATTAAAAACCCTAGCCCT
66 CTTAATTAAAAACCCTAACCCT
4501744 AACCTAA
1 AACCTAA
4501751 TTTTACATAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 65 0.73
87 24 0.27
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.24
Consensus pattern (87 bp):
AACCTAACTTAATTAAAAACCCTAACCATAACCAAACTTAATTAAAAACCCTAACCCTAACCTAA
CTTAATTAAAAACCCTAACCCT
Found at i:4501809 original size:55 final size:55
Alignment explanation
Indices: 4501748--4501927 Score: 317
Period size: 55 Copynumber: 3.2 Consensus size: 55
4501738 AGCCCTAACC
4501748 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
4501803 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
*
4501858 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAAAAATTTTTGG-CTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAAC---ACAATTTTTGGACTTAA
4501915 TAATTTTACATAA
1 TAATTTTACATAA
4501928 ATTTACATAA
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
55 93 0.77
57 18 0.15
58 10 0.08
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:4505240 original size:124 final size:124
Alignment explanation
Indices: 4505020--4505368 Score: 621
Period size: 123 Copynumber: 2.8 Consensus size: 124
4505010 CTCAAACTTG
* *
4505020 CTACTGCAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
4505085 TACAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATGAC
66 TACAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
*
4505144 CTACTGTAGCAAAATCGCGTCCACGAAGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
4505209 TACAAGCGATTTTATACTATTTGCTCAGAAACGT-AAAAAAAATTATTTCTTACATGAC
66 TACAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
*
4505267 CTACTATAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
4505332 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TACAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
4505369 CTCGAAATAA
Statistics
Matches: 216, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
123 117 0.54
124 99 0.46
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TACAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
Found at i:4507576 original size:17 final size:15
Alignment explanation
Indices: 4507546--4507592 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
4507536 GTTTGTGAGG
4507546 TTTTTTTAAAAAATA
1 TTTTTTTAAAAAATA
4507561 TTTTATTTATAAAAATA
1 TTTT-TTTA-AAAAATA
* *
4507578 TTATTTTAAGAAATA
1 TTTTTTTAAAAAATA
4507593 AATGTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.36
16 8 0.29
17 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTTTTTAAAAAATA
Found at i:4507585 original size:16 final size:15
Alignment explanation
Indices: 4507549--4507592 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
4507539 TGTGAGGTTT
*
4507549 TTTTAAAAAATATTT
1 TTTTAAAAAATATTA
4507564 TATTTATAAAAATATTA
1 T-TTTA-AAAAATATTA
*
4507581 TTTTAAGAAATA
1 TTTTAAAAAATA
4507593 AATGTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATATTA
Found at i:4507672 original size:20 final size:20
Alignment explanation
Indices: 4507647--4507685 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4507637 TATAATTGTG
4507647 TTATGTATTGTTATAAAAAC
1 TTATGTATTGTTATAAAAAC
* *
4507667 TTATGTGTTTTTATAAAAA
1 TTATGTATTGTTATAAAAA
4507686 AAAAACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (20 bp):
TTATGTATTGTTATAAAAAC
Found at i:4508610 original size:16 final size:15
Alignment explanation
Indices: 4508589--4508618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4508579 CATAATTTAT
4508589 TAAAAAATATTAAAAA
1 TAAAAAAT-TTAAAAA
4508605 TAAAAAATTTAAAA
1 TAAAAAATTTAAAA
4508619 TTTATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAAATTTAAAAA
Found at i:4533210 original size:25 final size:26
Alignment explanation
Indices: 4533163--4533212 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4533153 ATAAAAATTA
4533163 TTTTAAAAAACTTTAAAAATTATTTTT
1 TTTTAAAAAAC-TTAAAAATTATTTTT
* *
4533190 TTTTAAAAAA-TTGAAATTTATTT
1 TTTTAAAAAACTTAAAAATTATTT
4533213 AATTGCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
27 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTAAAAAACTTAAAAATTATTTTT
Found at i:4534531 original size:40 final size:38
Alignment explanation
Indices: 4534484--4534593 Score: 130
Period size: 40 Copynumber: 2.8 Consensus size: 38
4534474 TAAAAAATGC
**
4534484 CGCTATAGATCGATTATTAGCGGCGCTTTCTGAAAAACG
1 CGCTATAGATCGAACATTAGCGGCGCTTT-TGAAAAACG
* *
4534523 CTGCTATAGATCGAGCATTAGCGGCACATTTTGAAAAACG
1 C-GCTATAGATCGAACATTAGCGGCGC-TTTTGAAAAACG
* *
4534563 ACGCTATAGGTCAAACATTAGCGGCGCTTTT
1 -CGCTATAGATCGAACATTAGCGGCGCTTTT
4534594 TGATAACACC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
39 5 0.08
40 52 0.85
41 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (38 bp):
CGCTATAGATCGAACATTAGCGGCGCTTTTGAAAAACG
Done.