Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 17 of 144
Found at i:4247859 original size:17 final size:17
Alignment explanation
Indices: 4247824--4247865 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4247814 GGAAAAAGTA
*
4247824 GTTACAAGAATATGAAAG
1 GTTA-AAGAAAATGAAAG
*
4247842 GTTAAAGAAAATGGAAG
1 GTTAAAGAAAATGAAAG
4247859 GTTAAAG
1 GTTAAAG
4247866 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAAATGAAAG
Found at i:4260368 original size:6 final size:6
Alignment explanation
Indices: 4260343--4260381 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4260333 ACAATTCATA
* * *
4260343 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
4260382 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:4287828 original size:31 final size:30
Alignment explanation
Indices: 4287775--4287852 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
4287765 TTTCTTTTAG
* *
4287775 CTTTTAAGGGTTT--AAAATTTTTTTACCAA
1 CTTTTAAGGATTTAAAAAATTTTTCT-CCAA
4287804 CTTTTAATGGATTTAAAAAATTTTTCTCCAA
1 CTTTTAA-GGATTTAAAAAATTTTTCTCCAA
4287835 CTTTTAAGGAATTTAAAA
1 CTTTTAAGG-ATTTAAAA
4287853 CCCCATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 7 0.16
30 7 0.16
31 19 0.44
32 10 0.23
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (30 bp):
CTTTTAAGGATTTAAAAAATTTTTCTCCAA
Found at i:4289472 original size:25 final size:25
Alignment explanation
Indices: 4289408--4289479 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
4289398 CATTAAGCTT
* * * *
4289408 AATTAGTTAATAATTAAGTAAACTA
1 AATTAATTATTAATTAACTTAACTA
*
4289433 AATTAA-AATTAAATTAA-TTAACTA
1 AATTAATTATT-AATTAACTTAACTA
4289457 AGATTAATTATTAATTAACTTAA
1 A-ATTAATTATTAATTAACTTAA
4289480 GTATAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 9 0.24
25 22 0.58
26 7 0.18
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
AATTAATTATTAATTAACTTAACTA
Found at i:4292488 original size:27 final size:27
Alignment explanation
Indices: 4292434--4292485 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
4292424 TAATTATTTA
* *
4292434 AATTCTTTTTGAATTTTTCTTTTCAAG
1 AATTCTTTTTAAATTTTTCTTTTAAAG
*
4292461 AATTGTTTTTAAATTTTT-TTTTAAA
1 AATTCTTTTTAAATTTTTCTTTTAAA
4292486 AGAGTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (27 bp):
AATTCTTTTTAAATTTTTCTTTTAAAG
Found at i:4292695 original size:8 final size:8
Alignment explanation
Indices: 4292682--4292706 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4292672 ATTTTATTCC
4292682 TATTTAAT
1 TATTTAAT
4292690 TATTTAAT
1 TATTTAAT
4292698 TATTTAAT
1 TATTTAAT
4292706 T
1 T
4292707 TCTTTTTATC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTAAT
Found at i:4296881 original size:17 final size:17
Alignment explanation
Indices: 4296856--4296889 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4296846 ATCCTAGTTT
* *
4296856 TTCCTTTTTCTTTTTCC
1 TTCCCTTTTCTTCTTCC
4296873 TTCCCTTTTCTTCTTCC
1 TTCCCTTTTCTTCTTCC
4296890 CCTGTTTCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCCCTTTTCTTCTTCC
Found at i:4303964 original size:18 final size:18
Alignment explanation
Indices: 4303941--4303976 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4303931 AATCCTAGTT
4303941 TTCCCTTTTTCTT-TTTCC
1 TTCCC-TTTTCTTCTTTCC
4303959 TTCCCTTTTCTTCTTTCC
1 TTCCCTTTTCTTCTTTCC
4303977 CTGTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TTCCCTTTTCTTCTTTCC
Found at i:4312570 original size:8 final size:7
Alignment explanation
Indices: 4312538--4312567 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
4312528 GCGTCCTAAT
4312538 AATAAAA
1 AATAAAA
4312545 AATAAAA
1 AATAAAA
4312552 AATAAAA
1 AATAAAA
4312559 AATAAAA
1 AATAAAA
4312566 AA
1 AA
4312568 ATATAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:4314637 original size:16 final size:16
Alignment explanation
Indices: 4314605--4314638 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4314595 TGTTCAAATT
*
4314605 AAAGAATTATTAGAAA
1 AAAGAATTAATAGAAA
4314621 AAAG-ATTAATAGAAA
1 AAAGAATTAATAGAAA
4314636 AAA
1 AAA
4314639 CTAATAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAGAATTAATAGAAA
Found at i:4323475 original size:23 final size:23
Alignment explanation
Indices: 4323430--4323479 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4323420 TTAACATTCG
*
4323430 CGAACATGTTCACGAACGTTAAA
1 CGAACATGTTCACGAACGCTAAA
** *
4323453 CGAACATGTTCGTGAATGCTAAA
1 CGAACATGTTCACGAACGCTAAA
4323476 CGAA
1 CGAA
4323480 TCGAGCTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (23 bp):
CGAACATGTTCACGAACGCTAAA
Found at i:4336016 original size:33 final size:33
Alignment explanation
Indices: 4335978--4336046 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
4335968 GGGTGGTGTA
4335978 GGTTCATATGG-GAGACTAGGAACCATGACTGGT
1 GGTTCATATGGAG-GACTAGGAACCATGACTGGT
*
4336011 GGTTCATATGGAGGACTAGGAACCTTGACTGGT
1 GGTTCATATGGAGGACTAGGAACCATGACTGGT
4336044 GGT
1 GGT
4336047 GGAGCTGGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (33 bp):
GGTTCATATGGAGGACTAGGAACCATGACTGGT
Found at i:4340223 original size:20 final size:21
Alignment explanation
Indices: 4340193--4340232 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4340183 CATGACTCGT
4340193 AAATGAATATTAGATATTATG
1 AAATGAATATTAGATATTATG
*
4340214 AAAT-AATATTAGCTATTAT
1 AAATGAATATTAGATATTAT
4340233 TTATGGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
AAATGAATATTAGATATTATG
Found at i:4347533 original size:6 final size:6
Alignment explanation
Indices: 4347528--4347592 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
4347518 AATGGCTATA
* *
4347528 TATATA TATATA TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
4347576 TATATG TATATG TATAT
1 TATATG TATATG TATAT
4347593 TCTCCTGCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:4353615 original size:59 final size:58
Alignment explanation
Indices: 4353540--4353689 Score: 178
Period size: 59 Copynumber: 2.6 Consensus size: 58
4353530 ATTTGATACT
* * * *
4353540 TGAACTTGATATTTTTTACTAATTTGGTACTTAAA-TTTTTTTTGACTCAATTTAGTACC
1 TGAACTTGATAATTTTT-CTAATTTGGTACCTAAACCTTTGTTT-ACTCAATTTAGTACC
* * *
4353599 TGAACTTGATAATTTTTCTTAATTTGGTACCTAAACCTTTGTTTACTCGATTTGGTACT
1 TGAACTTGATAATTTTTC-TAATTTGGTACCTAAACCTTTGTTTACTCAATTTAGTACC
**
4353658 TGAACTTG-GCATTTTTCTAATTTGGTACCTAA
1 TGAACTTGATAATTTTTCTAATTTGGTACCTAA
4353690 GCTTTTTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
57 15 0.19
58 8 0.10
59 51 0.64
60 6 0.08
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (58 bp):
TGAACTTGATAATTTTTCTAATTTGGTACCTAAACCTTTGTTTACTCAATTTAGTACC
Found at i:4353987 original size:31 final size:30
Alignment explanation
Indices: 4353924--4354001 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
4353914 AGACTCCAAA
* * *
4353924 AAGTTTAGGTGCCAACTTAAAAAAATTATC
1 AAGTTTAGGTACCAAATTAAAAAAAATATC
*
4353954 AAGTTTAGGTACCAAATTAAAAAAAAATGTC
1 AAGTTTAGGTACCAAATT-AAAAAAAATATC
* *
4353985 AAGTTCAGATACCAAAT
1 AAGTTTAGGTACCAAAT
4354002 ATTATATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 16 0.39
31 25 0.61
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (30 bp):
AAGTTTAGGTACCAAATTAAAAAAAATATC
Found at i:4355755 original size:23 final size:24
Alignment explanation
Indices: 4355728--4355780 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
4355718 TTATAAATTC
4355728 AAATATTATAA-TAAAA-ATTTCTT
1 AAATATTATAATTAAAACATTT-TT
4355751 AAATA--ATAATTAAAACATTTTT
1 AAATATTATAATTAAAACATTTTT
4355773 AACATATT
1 AA-ATATT
4355781 CAACCTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.16
22 9 0.36
23 12 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTATAATTAAAACATTTTT
Found at i:4355951 original size:20 final size:20
Alignment explanation
Indices: 4355914--4355952 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4355904 TTACATCAAT
* *
4355914 AAAATTAGCACAACTTTTAA
1 AAAAATAGCACAAATTTTAA
*
4355934 AAAAATAGCATAAATTTTA
1 AAAAATAGCACAAATTTTA
4355953 TTTAGGTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAATAGCACAAATTTTAA
Found at i:4363341 original size:2 final size:2
Alignment explanation
Indices: 4363325--4363359 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4363315 CCCCAGCATT
* *
4363325 TA TA TA TG TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4363360 CTGTGTCCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4368476 original size:27 final size:30
Alignment explanation
Indices: 4368423--4368485 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
4368413 TATAGCTAAA
*
4368423 TTATCACTTTGGTACCTATACTATTTT-T-
1 TTATCAATTTGGTACCTATACTATTTTCTG
*
4368451 TTATCAATTTGG-ACCTTGTACT-TTTTCTG
1 TTATCAATTTGGTACC-TATACTATTTTCTG
4368480 TTATCA
1 TTATCA
4368486 GTCTGGCCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.23
28 17 0.57
29 6 0.20
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (30 bp):
TTATCAATTTGGTACCTATACTATTTTCTG
Found at i:4369557 original size:24 final size:25
Alignment explanation
Indices: 4369505--4369557 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
4369495 AACCAAGCTA
4369505 AAAAATCATTGAACTAGTAATTGAATT
1 AAAAATCATTGAACTAG--ATTGAATT
4369532 AAAAATCATTGAACTAG-TTGAATT
1 AAAAATCATTGAACTAGATTGAATT
4369556 AA
1 AA
4369558 TGTTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 9 0.35
27 17 0.65
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (25 bp):
AAAAATCATTGAACTAGATTGAATT
Found at i:4371740 original size:2 final size:2
Alignment explanation
Indices: 4371733--4371757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4371723 TTTAGTGTAT
4371733 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4371758 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4374618 original size:6 final size:6
Alignment explanation
Indices: 4374600--4374651 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
4374590 TTAAATTGAT
* *
4374600 TTTAAA TTT--A TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
4374645 TTATAAA
1 TT-TAAA
4374652 ACAAATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 4 0.11
5 3 0.08
6 27 0.71
7 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:4374639 original size:23 final size:21
Alignment explanation
Indices: 4374601--4374642 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
4374591 TAAATTGATT
4374601 TTAAATTTATTTAAATTTACC
1 TTAAATTTATTTAAATTTACC
4374622 TTAAATTTAAATTTAAATTTA
1 TTAAATTT--ATTTAAATTTA
4374643 AATTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAATTTATTTAAATTTACC
Found at i:4374646 original size:12 final size:11
Alignment explanation
Indices: 4374590--4374643 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
4374580 AATTTAAAGG
* *
4374590 TTAAATTGATT
1 TTAAATTTAAT
4374601 TTAAATTT-AT
1 TTAAATTTAAT
**
4374611 TTAAATTTACC
1 TTAAATTTAAT
4374622 TTAAATTTAAAT
1 TTAAATTT-AAT
4374634 TTAAATTTAA
1 TTAAATTTAA
4374644 ATTATAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 9 0.26
11 17 0.49
12 9 0.26
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:4374738 original size:34 final size:34
Alignment explanation
Indices: 4374699--4374776 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
4374689 CCATTTACAA
4374699 GCCCGATTGGGCTAAATCTGACCCAATTACAAAG
1 GCCCGATTGGGCTAAATCTGACCCAATTACAAAG
4374733 GCCCGATTGGGCTAAATCTGACCCAATTACAAAG
1 GCCCGATTGGGCTAAATCTGACCCAATTACAAAG
4374767 GCCCGATTGG
1 GCCCGATTGG
4374777 ACCCAATCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (34 bp):
GCCCGATTGGGCTAAATCTGACCCAATTACAAAG
Found at i:4376630 original size:58 final size:58
Alignment explanation
Indices: 4376535--4377195 Score: 914
Period size: 58 Copynumber: 11.4 Consensus size: 58
4376525 CAAAACTTCC
** * *
4376535 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGAATTCACCA
1 AAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCA
*
4376594 AAAATTACCATTTTACCCCCGAACTTCCAAATTTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * *
4376652 AAAATTACTATTTTACCCCCGAACTTCCAAAATTCTATTTTCAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * *
4376710 AAAATTACCATTTTACCCCCGAACTTCTAAAATTTCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* *
4376768 AAAATTACTATTTTACCCCCGAACTTCCAAATTTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
** * * *
4376826 AAAATTACCATTTTACCCCCGAACTTTTAAAATTCTATTCTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
** * *
4376884 AAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC-
1 AAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCA
*
4376942 -AAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAATCTCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
** * *
4376999 AAAATTACCATTTTACCGTCGAACTTTCCAAAATTCTATTTTTAACCTCGATTTTACCA
1 AAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCA
** * * * *
4377058 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTTATCA
1 AAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCACCA
* * * *
4377117 AAAATTACCATTTTACCCTCAAAGCCTCAAAAATTCCATTTTTAACCTCGATTTCACC-
1 AAAATTACCATTTTACCCCCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
*
4377175 AAAATTACCATTTTTCCCCCG
1 AAAATTACCATTTTACCCCCG
4377196 GGTATCCAAA
Statistics
Matches: 536, Mismatches: 61, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
56 30 0.06
57 21 0.04
58 302 0.56
59 182 0.34
60 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCA
Found at i:4376826 original size:174 final size:174
Alignment explanation
Indices: 4376535--4377195 Score: 1006
Period size: 174 Copynumber: 3.8 Consensus size: 174
4376525 CAAAACTTCC
*
4376535 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGAATTCACCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* *
4376600 ACCATTTTACCCCCGAACTTCCAAATTTCCATTTTTAACCTCGATTTCACCAAAAATTACTATTT
66 ACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
4376665 TACCCCCGAACTTCCAAAATTCTATTTTCAACCTCGATTTCACCA
131 TACCCCCGAACTTCCAAAATTCTATTTT-AACCTCGATTTCACCA
** * *
4376710 AAAATTACCATTTTACCCCCGAAC-TTCTAAAATTTCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* *
4376774 ACTATTTTACCCCCGAACTTCCAAATTTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
66 ACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
** *
4376839 TACCCCCGAACTTTTAAAATTCTATTCTTAACCCCGATTTCACCA
131 TACCCCCGAACTTCCAAAATTCTATT-TTAACCTCGATTTCACCA
* * *
4376884 AAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC--AAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
*
4376947 ACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAATCTCGATTTCACCAAAAATTACCATTT
66 ACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
** *
4377012 TACCGTCGAACTTTCCAAAATTCTATTTTTAACCTCGATTTTACCA
131 TACCCCCGAAC-TTCCAAAATTCTA-TTTTAACCTCGATTTCACCA
* * *
4377058 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTTATCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* * * *
4377123 ACCATTTTACCCTCAAAGCCTCAAAAATTCCATTTTTAACCTCGATTTCACC-AAAATTACCATT
66 ACCATTTTACCCCCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATT
*
4377187 TTTCCCCCG
130 TTACCCCCG
4377196 GGTATCCAAA
Statistics
Matches: 441, Mismatches: 38, Indels: 13
0.90 0.08 0.03
Matches are distributed among these distances:
173 76 0.17
174 240 0.54
175 56 0.13
176 38 0.09
177 31 0.07
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (174 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTT
TACCCCCGAACTTCCAAAATTCTATTTTAACCTCGATTTCACCA
Found at i:4377118 original size:29 final size:29
Alignment explanation
Indices: 4376562--4377119 Score: 203
Period size: 30 Copynumber: 19.2 Consensus size: 29
4376552 CCTAAACTTT
* * *
4376562 CCAAAATTCCATTTTTAACCCCGAATTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * **
4376591 CCAAAAATTACCA-TTTTACCCCCGAACTT-
1 CC-AAAATT-CTATTTTTAACCCCGATTTTA
* * * *
4376620 CCAAATTTCCATTTTTAACCTCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* **
4376649 CCAAAAATTACTA-TTTTACCCCCGAACTT-
1 CC-AAAATT-CTATTTTTAACCCCGATTTTA
* * *
4376678 CCAAAATTCTATTTTCAACCTCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * **
4376707 CCAAAAATTACCA-TTTTACCCCCGAACTT-
1 CC-AAAATT-CTATTTTTAACCCCGATTTTA
* *
4376736 CTAAAATT-TCATTTTTAACCCCGATTTCA
1 CCAAAATTCT-ATTTTTAACCCCGATTTTA
* **
4376765 CCAAAAATTACTA-TTTTACCCCCGAACTT-
1 CC-AAAATT-CTATTTTTAACCCCGATTTTA
* * * *
4376794 CCAAATTTCCATTTTTAACCTCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* *
4376823 CCAAAAATTACCA-TTTTACCCCCGAACTTTT-
1 CC-AAAATT-CTATTTTTAACCCCG-A-TTTTA
* *
4376854 --AAAATTCTATTCTTAACCCCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * *
4376881 CCAAAAATTACCA-TTTT-ACCCTTGAACTTT-
1 CC-AAAATT-CTATTTTTAACCC-CG-ATTTTA
* * *
4376911 CCAAAATTCCATTTTCAACCCCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * **
4376940 CC-AAATTACCA-TTTTACCCCCGAACTT-
1 CCAAAATT-CTATTTTTAACCCCGATTTTA
* * * *
4376967 CCAAAATTCCATTTTTAATCTCGATTTCA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * *
4376996 CCAAAAATTACCA-TTTT-ACCGTCGAACTTT-
1 CC-AAAATT-CTATTTTTAACC-CCG-ATTTTA
*
4377026 CCAAAATTCTATTTTTAACCTCGATTTTA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
* * *
4377055 CCAAAAATTACCA-TTTT-ACCCCTAAACTTT-
1 CC-AAAATT-CTATTTTTAACCCC--GATTTTA
4377085 CCAAAATTCTATTTTTAACCCCGATTTTA
1 CCAAAATTCTATTTTTAACCCCGATTTTA
*
4377114 TCAAAA
1 CCAAAA
4377120 ATTACCATTT
Statistics
Matches: 390, Mismatches: 88, Indels: 102
0.67 0.15 0.18
Matches are distributed among these distances:
26 3 0.01
27 17 0.04
28 130 0.33
29 73 0.19
30 134 0.34
31 29 0.07
32 4 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
CCAAAATTCTATTTTTAACCCCGATTTTA
Found at i:4389231 original size:31 final size:31
Alignment explanation
Indices: 4389196--4389443 Score: 169
Period size: 31 Copynumber: 7.4 Consensus size: 31
4389186 TCTTCATCTC
4389196 TGAAATTGAAGTAAGAGCAACGTCATTCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATTCCCT
** *
4389227 TGAAATTGAAGTAGAGTGGATAACACGTC-TTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATTC-CCT
*
4389263 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATTCCCT
** *
4389295 TGAAATTGAAGTAGAGTGGATAACACGTC-TTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATTC-CCT
*
4389331 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATTCCCT
** *
4389363 TGAAATTGAAGTAGAGTGGATAACACGTC-TTCATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATTC-CCT
*
4389399 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATTCCCT
*
4389431 CGAAATTGAAGTA
1 TGAAATTGAAGTA
4389444 GAGTGGATAA
Statistics
Matches: 169, Mismatches: 24, Indels: 48
0.70 0.10 0.20
Matches are distributed among these distances:
31 51 0.30
32 24 0.14
33 15 0.09
35 16 0.09
36 24 0.14
37 39 0.23
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATTCCCT
Found at i:4389760 original size:76 final size:74
Alignment explanation
Indices: 4389151--4389846 Score: 784
Period size: 68 Copynumber: 9.6 Consensus size: 74
4389141 GTCTCAACGT
* * * *
4389151 CATCCCCTTGAAATCGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
4389216 CG-TCA--T-
66 -GATCATTTC
* *
4389222 --TCC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
4389284 CG-TCA--T-
66 -GATCATTTC
* *
4389290 C--CC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
4389352 CG-TCA--T-
66 -GATCATTTC
* *
4389358 C--CC-CTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
1 CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
4389420 CG-TCA--TC
66 -GATCATTTC
* *
4389427 C--CCTC--GAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTAAAGTAAGAGCAA
1 CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
4389488 GATCATTTC
66 GATCATTTC
* *
4389497 CTATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 C-ATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
4389562 AGATCGTTTCC
65 AGATCATTT-C
* ** *
4389573 CATCCTCTTGAAATTGAAGTAAAGCTGGATGTCAAGTCTTTATCTCTGAAATT-AAATAAGAGCA
1 CATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
4389637 AGATCGTTTCC
65 AGATCATTT-C
* * **
4389648 CATCCTCTTGAAATTGAAGTAAAGCTAGATGTCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 CATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
4389713 AGATCATTTC
65 AGATCATTTC
* *
4389723 ACATCCTCTTGAAATTGAAGTAGAGTTGGATGACAAGTCTTTATCTCTGAAATTGAAGTAAGAAC
1 -CATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGC
* *
4389788 AAGATCGTCTCC
64 AAGATCAT-TTC
* * * *
4389800 CATCCTCTTGAAATTGAAGAAAAGTTGGATAGCAAGTCCTTATCTCT
1 CATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTATCTCT
4389847 CTGAAGAGCA
Statistics
Matches: 582, Mismatches: 27, Indels: 27
0.92 0.04 0.04
Matches are distributed among these distances:
67 1 0.00
68 256 0.44
69 6 0.01
70 4 0.01
73 3 0.01
75 157 0.27
76 153 0.26
77 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (74 bp):
CATCCTCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
GATCATTTC
Found at i:4390163 original size:6 final size:6
Alignment explanation
Indices: 4390145--4390233 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
4390135 TTAAATTGAT
4390145 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* *
4390192 TTTAAA TTT-AC CTTAAA TTTAAA TTTAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
4390234 ACAAATTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
4 6 0.09
5 5 0.07
6 47 0.67
7 6 0.09
8 6 0.09
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4390163 original size:17 final size:16
Alignment explanation
Indices: 4390145--4390233 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 16
4390135 TTAAATTGAT
4390145 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
4390161 TTTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
4390178 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
*
4390192 TTTAAATTTACCTTAAA
1 TTTAAATTTA-TTTAAA
4390209 TTTAAATTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
4390227 TTATAAA
1 TT-TAAA
4390234 ACAAATTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.17
15 2 0.03
16 13 0.21
17 25 0.40
18 7 0.11
19 5 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:4390176 original size:11 final size:11
Alignment explanation
Indices: 4390162--4390212 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
4390152 TTATTTAAAT
4390162 TTAAATTTATC
1 TTAAATTTATC
**
4390173 TTAAATTTAAA
1 TTAAATTTATC
*
4390184 TTTAA-TTAT-
1 TTAAATTTATC
*
4390193 TTAAATTTACC
1 TTAAATTTATC
4390204 TTAAATTTA
1 TTAAATTTA
4390213 AATTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 22 0.69
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTATC
Found at i:4390198 original size:37 final size:38
Alignment explanation
Indices: 4390145--4390230 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 38
4390135 TTAAATTGAT
*
4390145 TTTAAATTTATTTAAATTTAAATT-TATCTTAAATTTAAA
1 TTTAAA-TTATTTAAATTTAAATTAAAT-TTAAATTTAAA
**
4390184 TTT-AATTATTTAAATTTACCTTAAATTTAAATTTAAA
1 TTTAAATTATTTAAATTTAAATTAAATTTAAATTTAAA
4390221 TTTAAATTAT
1 TTTAAATTAT
4390231 AAAACAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 29 0.69
38 10 0.24
39 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAAATTATTTAAATTTAAATTAAATTTAAATTTAAA
Found at i:4392114 original size:29 final size:29
Alignment explanation
Indices: 4392070--4392184 Score: 119
Period size: 29 Copynumber: 4.0 Consensus size: 29
4392060 GTTTATGGGT
*
4392070 CCCCAAAACTTCTAAAATTACTATTTTAC
1 CCCCAAAACTTCTAAAATTACCATTTTAC
* * *
4392099 CCCCAAACCTTTTAAAATT-CCATTTTTAA
1 CCCCAAAACTTCTAAAATTACCA-TTTTAC
* *
4392128 CCCTAAAACTTCCAAAAATTACCATTTTAC
1 CCCCAAAACTT-CTAAAATTACCATTTTAC
*
4392158 CCCC-AAACTTTCCAAAATT-CCATTTTA
1 CCCCAAAAC-TTCTAAAATTACCATTTTA
4392185 ACCTCGATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.14
29 42 0.59
30 16 0.23
31 3 0.04
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.34
Consensus pattern (29 bp):
CCCCAAAACTTCTAAAATTACCATTTTAC
Found at i:4392156 original size:30 final size:28
Alignment explanation
Indices: 4392075--4392711 Score: 167
Period size: 30 Copynumber: 21.9 Consensus size: 28
4392065 TGGGTCCCCA
* * *
4392075 AAACTTCTAAAATTACTATTTT-ACCCCC
1 AAACTTCCAAAATT-CCATTTTAACCCTC
** *
4392103 AAACCTTTTAAAATTCCATTTTTAACCCTA
1 AAA-CTTCCAAAATTCCA-TTTTAACCCTC
*
4392133 AAACTTCCAAAAATTACCATTTT-ACCCCC
1 AAACTTCC-AAAATT-CCATTTTAACCCTC
4392162 AAACTTTCCAAAATTCCATTTTAA-CCTC
1 AAAC-TTCCAAAATTCCATTTTAACCCTC
* *
4392190 -GATTTCACCAAAAATTACCATTTT-ACCCTC
1 AAACTT--CC-AAAATT-CCATTTTAACCCTC
* *
4392220 GAACTTCCAAATTTCCATTTTTAACCC-C
1 AAACTTCCAAAATTCCA-TTTTAACCCTC
* * *
4392248 -GATTTCACTAAAAATTACTATTTT-ACCCTC
1 AAACTTC-C--AAAATT-CCATTTTAACCCTC
* *
4392278 GAACTTCCAAAATTCTATTTTCAACCC-C
1 AAACTTCCAAAATTCCATTTT-AACCCTC
* *
4392306 -GATTTCACCAAAAATTACCATTTT-ACCCTC
1 AAACTT--CC-AAAATT-CCATTTTAACCCTC
* * *
4392336 GAACTTCTAAAATTCTATTTTTAACCC-C
1 AAACTTCCAAAATTCCA-TTTTAACCCTC
* * * *
4392364 -GATTTCACCAAAAATTACTATTTTACCCCT-
1 AAACTT--CC-AAAATT-CCATTTTAACCCTC
* *
4392394 GAACTTCCAAATTTCCATTTTTAA-CCTC
1 AAACTTCCAAAATTCCA-TTTTAACCCTC
* *
4392422 -GATTTCACTAAAAATTACCATTTT-ACCCTC
1 AAACTTC-C--AAAATT-CCATTTTAACCCTC
* * *
4392452 GAACTTTCAAAATTCTATTCTTAACCC-C
1 AAACTTCCAAAATTCCATT-TTAACCCTC
* *
4392480 -GATTTCACCAAAAATTACCATTTT-ACCCTC
1 AAACTT--CC-AAAATT-CCATTTTAACCCTC
*
4392510 GAACTTTCCAAAATTCCATTTTCAACCC-C
1 AAAC-TTCCAAAATTCCATTTT-AACCCTC
* * *
4392539 -GATTTCACCAAAATTACCATTTT-ACCCCC
1 AAACTT--CCAAAATT-CCATTTTAACCCTC
* *
4392568 GAACTTCCAAAATTCTATTTTTAA-CCTC
1 AAACTTCCAAAATTCCA-TTTTAACCCTC
* **
4392596 GATTTTACCAAAAGTTACCATTTT-ACCCTC
1 AAACTT-CCAAAA-TT-CCATTTTAACCCTC
* **
4392626 GAACTTTCCAAAATTTTATTTTTAACCC-C
1 AAAC-TTCCAAAATTCCA-TTTTAACCCTC
*** *
4392655 GATTTTATCAAAAATTACCATTTT-ACCCTC
1 -AAACT-TCCAAAATT-CCATTTTAACCCTC
* *
4392685 AAAGCCTCAAAAATTCCATTTTAACCC
1 AAA-CTTCCAAAATTCCATTTTAACCC
4392712 CGATTTCACC
Statistics
Matches: 460, Mismatches: 73, Indels: 151
0.67 0.11 0.22
Matches are distributed among these distances:
26 2 0.00
27 43 0.09
28 105 0.23
29 127 0.28
30 138 0.30
31 43 0.09
32 2 0.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
AAACTTCCAAAATTCCATTTTAACCCTC
Found at i:4392212 original size:58 final size:58
Alignment explanation
Indices: 4392139--4392735 Score: 844
Period size: 58 Copynumber: 10.3 Consensus size: 58
4392129 CCTAAAACTT
* * *
4392139 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCA
*
4392197 CCAAAAATTACCATTTTACCCTCGAACTTCCAAATTTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
4392255 CTAAAAATTACTATTTTACCCTCGAACTTCCAAAATTCTATTTTCAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
4392313 CCAAAAATTACCATTTTACCCTCGAACTTCTAAAATTCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
4392371 CCAAAAATTACTATTTTACCC-CTGAACTTCCAAATTTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTC-GAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
4392429 CTAAAAATTACCATTTTACCCTCGAACTTTCAAAATTCTATTCTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
4392487 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
4392546 CC-AAAATTACCATTTTACCCCCGAACTTCCAAAATTCTATTTTTAACCTCGATTTTA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ** *
4392603 CCAAAAGTTACCATTTTACCCTCGAACTTTCCAAAATTTTATTTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
4392662 TCAAAAATTACCATTTTACCCTCAAAGCCTCAAAAATTCCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAA-CTTCCAAAATTCCATTTTTAACCCCGATTTCA
4392720 CC-AAAATTACCATTTT
1 CCAAAAATTACCATTTT
4392736 TCCCCCGGGT
Statistics
Matches: 484, Mismatches: 48, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
57 56 0.12
58 336 0.69
59 91 0.19
60 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:4392770 original size:58 final size:58
Alignment explanation
Indices: 4392083--4392777 Score: 723
Period size: 58 Copynumber: 12.0 Consensus size: 58
4392073 CAAAACTTCT
* * * * ** * *
4392083 AAAATTACTATTTTACCCCCAAACCTTT-TAAAATTCCATTTTTAACCCTAAAACTTC-CA
1 AAAATTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTTTCAACCC--CGATTTCACC
* *
4392142 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTT-AACCTCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* * * *
4392199 AAAAATTACCATTTTACCCTCGAAC-TTCCAAATTTCCATTTTTAACCCCGATTTCACTA
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCAC-C
* * *
4392258 AAAATTACTATTTTACCCTCGAAC-TTCCAAAATTCTATTTTCAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* * * *
4392315 AAAAATTACCATTTTACCCTCGAAC-TTCTAAAATTCTATTTTTAACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* * * * * *
4392373 AAAAATTACTATTTTACCCCTGAAC-TTCCAAATTTCCATTTTTAACCTCGATTTCACTA
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCAC-C
* *
4392432 AAAATTACCATTTTACCCTCGAACTTT-CAAAATTCTATTCTT-AACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATT-TTCAACCCCGATTTCACC
*
4392489 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* * * *
4392548 AAAATTACCATTTTACCCCCGAAC-TTCCAAAATTCTATTTTTAACCTCGATTTTACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* ** * * *
4392605 AAAAGTTACCATTTTACCCTCGAACTTTCCAAAATTTTATTTTTAACCCCGATTTTATCA
1 AAAA-TTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCA-CC
* * * *
4392665 AAAATTACCATTTTACCCTCAAAGC-CTCAAAAATTCCATTTT-AACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
* ** * * *
4392722 AAAATTACCATTTTTCCCCCG-GGTATCCAAAAGTCCCATTTTCCACCCCGATTTCA
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAA-TTCCATTTTCAACCCCGATTTCA
4392778 TCGTTTCTTA
Statistics
Matches: 556, Mismatches: 61, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
56 10 0.02
57 77 0.14
58 338 0.61
59 125 0.22
60 6 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACC
Found at i:4396719 original size:19 final size:19
Alignment explanation
Indices: 4396695--4396733 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4396685 TACAATGTAA
4396695 TTAAA-TAATATAAATTAAT
1 TTAAATTAA-ATAAATTAAT
*
4396714 TTAAATTAAATAATTTAAT
1 TTAAATTAAATAAATTAAT
4396733 T
1 T
4396734 AACTATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATTAAATAAATTAAT
Found at i:4400687 original size:17 final size:17
Alignment explanation
Indices: 4400665--4400701 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4400655 ACCCGACCGT
4400665 TATTTGAATCCCTGAGA
1 TATTTGAATCCCTGAGA
4400682 TATTTGAATCCCTGAGA
1 TATTTGAATCCCTGAGA
4400699 TAT
1 TAT
4400702 ATAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (17 bp):
TATTTGAATCCCTGAGA
Found at i:4401821 original size:22 final size:23
Alignment explanation
Indices: 4401797--4401841 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4401787 CTTTAAAATT
4401797 AAAATATAAAAAAATT-ATTTTTA
1 AAAAT-TAAAAAAATTCATTTTTA
*
4401820 AAAATTCAAAAAATTCATTTTT
1 AAAATTAAAAAAATTCATTTTT
4401842 TTAATTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTAAAAAAATTCATTTTTA
Found at i:4404915 original size:21 final size:20
Alignment explanation
Indices: 4404866--4404916 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
4404856 TTTTTTTCAA
4404866 TATTTAATAATTTAAATTTT
1 TATTTAATAATTTAAATTTT
*
4404886 T-TTGATAATCATTTAAATTTT
1 TATT--TAATAATTTAAATTTT
4404907 CTATTTAATA
1 -TATTTAATA
4404917 CAAAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
19 2 0.08
20 1 0.04
21 19 0.76
22 1 0.04
23 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTAATAATTTAAATTTT
Found at i:4408422 original size:14 final size:14
Alignment explanation
Indices: 4408403--4408450 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4408393 TATAGGCTTA
4408403 GGGTTTGGAGTTAT
1 GGGTTTGGAGTTAT
* *
4408417 GTGTTTGGGGTTAT
1 GGGTTTGGAGTTAT
* *
4408431 GGGTTTTGAGTTTT
1 GGGTTTGGAGTTAT
4408445 GGGTTT
1 GGGTTT
4408451 AGGGTTTAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (14 bp):
GGGTTTGGAGTTAT
Found at i:4408450 original size:28 final size:28
Alignment explanation
Indices: 4408390--4408456 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
4408380 AATGGTTTGC
*
4408390 GGTTATAGGCTTA-GGGTTTGGAGTTATG
1 GGTT-TAGGGTTATGGGTTTGGAGTTATG
* * * *
4408418 TGTTTGGGGTTATGGGTTTTGAGTTTTG
1 GGTTTAGGGTTATGGGTTTGGAGTTATG
4408446 GGTTTAGGGTT
1 GGTTTAGGGTT
4408457 TAGGGTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.12, C:0.01, G:0.40, T:0.46
Consensus pattern (28 bp):
GGTTTAGGGTTATGGGTTTGGAGTTATG
Found at i:4409073 original size:2 final size:2
Alignment explanation
Indices: 4409068--4409108 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4409058 TAAAAAAAGA
4409068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4409109 CTGGTGCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4409275 original size:151 final size:152
Alignment explanation
Indices: 4409085--4409409 Score: 521
Period size: 151 Copynumber: 2.1 Consensus size: 152
4409075 TATATATATA
* *
4409085 TATATATATATATATATATATATACTGGTGCGATTACATGGTAGTATATGTCTATACTTTTTTAA
1 TATATATATATATATATATATATACTGGTGCGATTACATGATAGTATATGTCCATACTTTTTTAA
* * * *
4409150 TCCTTTGACAACGCACACACAAGTGCTCAAACCCGAA-TCTTTTAAAATGAACAACATCCTCTTT
66 CCCTTTGACAACGCACACACAAGTGCT-AAAACCGAAGTCTCTTAAAATGAACAACATCATCTTT
4409214 TCTACTAGAGCCACTCGTTGAGT
130 TCTACTAGAGCCACTCGTTGAGT
* *
4409237 TATATATATATATAT-TGA-ATATACTGGTGTGATTACATGATAGTATCTGTCCATACTTTTTTA
1 TATATATATATATATAT-ATATATACTGGTGCGATTACATGATAGTATATGTCCATACTTTTTTA
* *
4409300 ACCCTTTGACAACGCACACACAAGTGCTAAAACCTAAGTCTCTTAAAATGAACAACATTATCTTT
65 ACCCTTTGACAACGCACACACAAGTGCTAAAACCGAAGTCTCTTAAAATGAACAACATCATCTTT
4409365 TCTACTAGAGCCACTCGTTGAGT
130 TCTACTAGAGCCACTCGTTGAGT
4409388 TATATATATATATATATATATA
1 TATATATATATATATATATATA
4409410 AGTTTCACTT
Statistics
Matches: 159, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
150 7 0.04
151 132 0.83
152 20 0.13
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (152 bp):
TATATATATATATATATATATATACTGGTGCGATTACATGATAGTATATGTCCATACTTTTTTAA
CCCTTTGACAACGCACACACAAGTGCTAAAACCGAAGTCTCTTAAAATGAACAACATCATCTTTT
CTACTAGAGCCACTCGTTGAGT
Found at i:4414339 original size:16 final size:16
Alignment explanation
Indices: 4414318--4414348 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4414308 CTAAGTAAAA
4414318 TATGTGAACTATGATT
1 TATGTGAACTATGATT
*
4414334 TATGTGAGCTATGAT
1 TATGTGAACTATGAT
4414349 ATGAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (16 bp):
TATGTGAACTATGATT
Found at i:4414549 original size:76 final size:75
Alignment explanation
Indices: 4414432--4414631 Score: 187
Period size: 76 Copynumber: 2.6 Consensus size: 75
4414422 ATTGTCAGGA
* * *
4414432 AATCCGAGGGGTAGGCTATCGTTGTCTAGCAATCCGAGATGACATATTTGATCCAGTAAACCATC
1 AATCCGAGGGGTAGGCTATCATTGTCTAGCAATCCGAGATGACAAATTTGATCCAATAAACCATC
4414497 GTTGCCGGGC
66 GTTGCCGGGC
* *
4414507 AATCCGAGGTGGTAGG-TCATCATTGT-TGGACAATCCCG-GATGACAAATTTGATTCAATAAAC
1 AATCCGAGG-GGTAGGCT-ATCATTGTCTAG-CAAT-CCGAGATGACAAATTTGATCCAATAAAC
**
4414569 CATCGTT-CCAGACC
62 CATCGTTGCC-GGGC
* * * *
4414583 AAT-CTAGGGTGGTAGG-TCATCGTTGGCGAGCAATCCGAGATGACAAATT
1 AATCCGA-GG-GGTAGGCT-ATCATTGTCTAGCAATCCGAGATGACAAATT
4414632 GAAATATATG
Statistics
Matches: 105, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
75 19 0.18
76 82 0.78
77 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (75 bp):
AATCCGAGGGGTAGGCTATCATTGTCTAGCAATCCGAGATGACAAATTTGATCCAATAAACCATC
GTTGCCGGGC
Found at i:4414675 original size:17 final size:17
Alignment explanation
Indices: 4414654--4414697 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4414644 TTATGGAGTG
4414654 GTATGAATTGTTATGT-
1 GTATGAATTGTTATGTA
* *
4414670 GATATGAACTATTATGTA
1 G-TATGAATTGTTATGTA
4414688 GTATGAATTG
1 GTATGAATTG
4414698 CTATTTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (17 bp):
GTATGAATTGTTATGTA
Found at i:4414692 original size:34 final size:34
Alignment explanation
Indices: 4414654--4414747 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 34
4414644 TTATGGAGTG
* *
4414654 GTATGAATTGTTATGTGATATGAACTATTATGTA
1 GTATGAATTGTTATCTGATATGAACTACTATGTA
* * * *
4414688 GTATGAATTGCTATTTGGA-ATGAACTACTATTTG
1 GTATGAATTGTTATCT-GATATGAACTACTATGTA
* *
4414722 GTATGAACTGTTATCTCATATGAACT
1 GTATGAATTGTTATCTGATATGAACT
4414748 GGTGTTTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 1 0.02
34 46 0.94
35 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (34 bp):
GTATGAATTGTTATCTGATATGAACTACTATGTA
Found at i:4414710 original size:17 final size:17
Alignment explanation
Indices: 4414698--4414730 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4414688 GTATGAATTG
4414698 CTATTTGGAATGAACTA
1 CTATTTGGAATGAACTA
*
4414715 CTATTTGGTATGAACT
1 CTATTTGGAATGAACT
4414731 GTTATCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (17 bp):
CTATTTGGAATGAACTA
Found at i:4415237 original size:7 final size:7
Alignment explanation
Indices: 4415225--4415251 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4415215 TGATTAAATG
4415225 GTGAATT
1 GTGAATT
4415232 GTGAATT
1 GTGAATT
4415239 GTGAATT
1 GTGAATT
4415246 GTGAAT
1 GTGAAT
4415252 GCTTGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (7 bp):
GTGAATT
Found at i:4416589 original size:17 final size:17
Alignment explanation
Indices: 4416567--4416605 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
4416557 AATTAACGAT
4416567 ATTAATTATTTGAACTA
1 ATTAATTATTTGAACTA
*
4416584 ATTAATTGTTTGAACTA
1 ATTAATTATTTGAACTA
4416601 ATTAA
1 ATTAA
4416606 ATATAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (17 bp):
ATTAATTATTTGAACTA
Found at i:4426952 original size:3 final size:3
Alignment explanation
Indices: 4426939--4427030 Score: 57
Period size: 3 Copynumber: 29.7 Consensus size: 3
4426929 TCTCTTTTTG
*
4426939 TTA TT- TTA TTA TTA -TA TTA TTA TTA TT- TCA TTTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA
* * *
4426983 TCTA TT- TAA TTT TTA TTT TTA TTTA TTTA TTTA TTTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA -TTA TTA TTA TTA
4427029 TT
1 TT
4427031 TTCCAAACTT
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
2 6 0.08
3 44 0.60
4 23 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:4426965 original size:22 final size:22
Alignment explanation
Indices: 4426939--4427032 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 22
4426929 TCTCTTTTTG
4426939 TTATTTTA-TTATTATATTATTA
1 TTATTTTATTTATT-TATTATTA
*
4426961 TTATTTCATTTA-TTATTTATTA
1 TTATTTTATTTATTTA-TTATTA
* *
4426983 TCTA-TTTAATT-TTTATTTTTA
1 T-TATTTTATTTATTTATTATTA
4427004 TT-TATTTATTTATTTATTATTA
1 TTAT-TTTATTTATTTATTATTA
4427026 TTATTTT
1 TTATTTT
4427033 CCAAACTTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
20 1 0.02
21 14 0.24
22 37 0.64
23 6 0.10
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTTATTTATTTATTATTA
Found at i:4426975 original size:12 final size:11
Alignment explanation
Indices: 4426943--4427031 Score: 75
Period size: 11 Copynumber: 8.3 Consensus size: 11
4426933 TTTTTGTTAT
4426943 TTTATTA-TTA
1 TTTATTATTTA
4426953 TATTATTA-TTA
1 T-TTATTATTTA
4426964 TTTCATT-TATTA
1 TTT-ATTAT-TTA
*
4426976 TTTATTATCTA
1 TTTATTATTTA
4426987 TTTAATT-TTTA
1 TTT-ATTATTTA
4426998 TTT-TTATTTA
1 TTTATTATTTA
4427008 TTTATTTATTTA
1 TTTA-TTATTTA
4427020 -TTATTA-TTA
1 TTTATTATTTA
4427029 TTT
1 TTT
4427032 TCCAAACTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 20
0.75 0.02 0.22
Matches are distributed among these distances:
9 5 0.07
10 15 0.22
11 30 0.45
12 17 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:4427009 original size:4 final size:4
Alignment explanation
Indices: 4426961--4427021 Score: 60
Period size: 4 Copynumber: 16.2 Consensus size: 4
4426951 TATATTATTA
* *
4426961 TTAT TTCAT TTA- TTAT TTA- TTAT CTAT TTAA TT-T TTA- TT-T TTAT
1 TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
4427005 TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT T
4427022 ATTATTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 12 0.26
4 31 0.66
5 4 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:4427031 original size:25 final size:24
Alignment explanation
Indices: 4426943--4427030 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 24
4426933 TTTTTGTTAT
4426943 TTTATTATTATATTATTATTATTTCA
1 TTTATTATT-TATTATTATTATTT-A
*
4426969 TTTATTATTTATTATCTA-T-TTAA
1 TTTATTATTTATTAT-TATTATTTA
4426992 TTT-TTATTT-TTATTTATTTATTTA
1 TTTATTATTTATTA-TTA-TTATTTA
4427016 TTTATTA-TTATTATT
1 TTTATTATTTATTATT
4427031 TTCCAAACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
21 5 0.09
22 7 0.13
23 5 0.09
24 12 0.23
25 13 0.25
26 11 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTATTATTTATTATTATTATTTA
Found at i:4429759 original size:21 final size:20
Alignment explanation
Indices: 4429730--4429781 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4429720 TTCGACTTCC
4429730 TTATTTTCTATTT-CTTTTAA
1 TTATTTTCT-TTTACTTTTAA
*
4429750 TTATATTTCTTTTATTTTTAA
1 TTAT-TTTCTTTTACTTTTAA
4429771 TTATGTTTCTT
1 TTAT-TTTCTT
4429782 CTATTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATTTTCTTTTACTTTTAA
Found at i:4429786 original size:21 final size:21
Alignment explanation
Indices: 4429744--4429789 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4429734 TTTCTATTTC
*
4429744 TTTTAATTATATTTCTTTTAT
1 TTTTAATTATATTTCTTCTAT
*
4429765 TTTTAATTATGTTTCTTCTAT
1 TTTTAATTATATTTCTTCTAT
4429786 TTTT
1 TTTT
4429790 CCTCATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTAATTATATTTCTTCTAT
Found at i:4431761 original size:10 final size:10
Alignment explanation
Indices: 4431746--4431771 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4431736 AGGTACATCG
4431746 ATATATATAC
1 ATATATATAC
4431756 ATATATATAC
1 ATATATATAC
4431766 ATATAT
1 ATATAT
4431772 GCGAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAC
Found at i:4432188 original size:22 final size:21
Alignment explanation
Indices: 4432160--4432200 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4432150 ATAGGGAGGG
*
4432160 GAGAGAGAAGAGAG-AATTTT
1 GAGAGAGAGGAGAGCAATTTT
4432180 GAGAGAGAGGAGAGCAATTTT
1 GAGAGAGAGGAGAGCAATTTT
4432201 TTTAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.41, C:0.02, G:0.37, T:0.20
Consensus pattern (21 bp):
GAGAGAGAGGAGAGCAATTTT
Found at i:4432568 original size:30 final size:30
Alignment explanation
Indices: 4432537--4432769 Score: 188
Period size: 30 Copynumber: 7.8 Consensus size: 30
4432527 TATTTTATTT
* * *
4432537 AAAAATTATATTTTAA-CTCTCAAAATTTTT
1 AAAAATTATATTTTAACCCCT-AAACTTTTC
*
4432567 AAAAATTATATTTTGACCCCTAAACTTTTC
1 AAAAATTATATTTTAACCCCTAAACTTTTC
* *
4432597 AAAAATTACATTTTAACCCTTAAACTTTTC
1 AAAAATTATATTTTAACCCCTAAACTTTTC
* *
4432627 AAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAAATTATATTTTAACCCCTAAACTTTTC
* **
4432657 AAAAATTATATTTTGA-TTCTAAAACTTTTC
1 AAAAATTATATTTTAACCCCT-AAACTTTTC
* * * * *
4432687 AAGAATTACATTTTTACCCCCAAATTTTTTC
1 AAAAATTATATTTTAACCCCTAAA-CTTTTC
* * * *
4432718 -AAAATCACT-TTTTGACCCCTAAAGTTTCC
1 AAAAATTA-TATTTTAACCCCTAAACTTTTC
* * *
4432747 CAAAATCACATTTTAA-CCCTAAA
1 AAAAATTATATTTTAACCCCTAAA
4432770 TTCTCTGAAA
Statistics
Matches: 168, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
29 13 0.08
30 146 0.87
31 9 0.05
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAAATTATATTTTAACCCCTAAACTTTTC
Found at i:4432694 original size:90 final size:90
Alignment explanation
Indices: 4432562--4432740 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 90
4432552 ACTCTCAAAA
* **
4432562 TTTTTAAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAA-CTTTT
1 TTTTCAAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCCCAAATCTTTT
*
4432626 CAAAAATTACATTTTGACCCCTAAAC
66 C-AAAATCACATTTTGACCCCTAAAC
** * * *
4432652 TTTTCAAAAATTATATTTTGA-TTCTAAAACTTTTCAAGAATTACATTTTTACCCCCAAATTTTT
1 TTTTCAAAAATTATATTTTGACCCCT-AAACTTTTCAAAAATTACATTTTAACCCCCAAATCTTT
*
4432716 TCAAAATCACTTTTTGACCCCTAAA
65 TCAAAATCACATTTTGACCCCTAAA
4432741 GTTTCCCAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 2 0.03
90 70 0.91
91 5 0.06
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (90 bp):
TTTTCAAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCCCAAATCTTTT
CAAAATCACATTTTGACCCCTAAAC
Found at i:4432722 original size:60 final size:60
Alignment explanation
Indices: 4432537--4432721 Score: 246
Period size: 60 Copynumber: 3.1 Consensus size: 60
4432527 TATTTTATTT
* *
4432537 AAAAATTATATTTTAACTCTCAAAA-TTTTTAAAAATTATATTTTGACCCCTAAACTTTTC
1 AAAAATTATATTTTAACTCT-AAAACTTTTCAAAAATTACATTTTGACCCCTAAACTTTTC
* * *
4432597 AAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTGACCCCTAAACTTTTC
1 AAAAATTATATTTTAACTCTAAAACTTTTCAAAAATTACATTTTGACCCCTAAACTTTTC
* * * * * *
4432657 AAAAATTATATTTTGATTCTAAAACTTTTCAAGAATTACATTTTTACCCCCAAATTTTTTC
1 AAAAATTATATTTTAACTCTAAAACTTTTCAAAAATTACATTTTGACCCCTAAA-CTTTTC
4432718 AAAA
1 AAAA
4432722 TCACTTTTTG
Statistics
Matches: 109, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
59 3 0.03
60 97 0.89
61 9 0.08
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (60 bp):
AAAAATTATATTTTAACTCTAAAACTTTTCAAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:4432752 original size:90 final size:90
Alignment explanation
Indices: 4432567--4432769 Score: 232
Period size: 90 Copynumber: 2.3 Consensus size: 90
4432557 CAAAATTTTT
**
4432567 AAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCTTAAACTTTTCAAAAA
1 AAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCCCAAACTTTTCAAAAA
* *
4432632 TTACATTTTGACCCCTAAACTTTTC
66 TCACATTTTGACCCCTAAACTTTCC
** * * *
4432657 AAAAATTATATTTTGA-TTCTAAAACTTTTCAAGAATTACATTTTTACCCCCAAATTTTTTC-AA
1 AAAAATTATATTTTGACCCCT-AAACTTTTCAAAAATTACATTTTAACCCCCAAA-CTTTTCAAA
* *
4432720 AATCACTTTTTGACCCCTAAAGTTTCC
64 AATCACATTTTGACCCCTAAACTTTCC
* * * *
4432747 CAAAATCACATTTT-AACCCTAAA
1 AAAAATTATATTTTGACCCCTAAA
4432770 TTCTCTGAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
89 6 0.06
90 83 0.88
91 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.38
Consensus pattern (90 bp):
AAAAATTATATTTTGACCCCTAAACTTTTCAAAAATTACATTTTAACCCCCAAACTTTTCAAAAA
TCACATTTTGACCCCTAAACTTTCC
Found at i:4432993 original size:7 final size:7
Alignment explanation
Indices: 4432981--4433038 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
4432971 AAAGAGAAAG
4432981 AAAGGAA
1 AAAGGAA
4432988 AAAGGAA
1 AAAGGAA
4432995 AAAGGAA
1 AAAGGAA
4433002 AAAGGAAA
1 AAAGG-AA
**
4433010 AAAAAAA
1 AAAGGAA
**
4433017 AAAATAA
1 AAAGGAA
4433024 AAAGGAA
1 AAAGGAA
4433031 AAA-GAA
1 AAAGGAA
4433037 AA
1 AA
4433039 TAGGGAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.11
7 35 0.78
8 5 0.11
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAGGAA
Found at i:4433032 original size:6 final size:6
Alignment explanation
Indices: 4432955--4433038 Score: 61
Period size: 6 Copynumber: 14.2 Consensus size: 6
4432945 GGATTCAATG
* *
4432955 AAGAAA AA-ATAA AA-AAA AAGAGA AAG-AA AGGAAA AAGGAAA AAGGAAA
1 AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AA-GAAA
* *
4433003 AAGGAA AA-AAA AA-AAA AATAAA AAGGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AAGAAA A
4433039 TAGGGAAGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
5 17 0.26
6 30 0.46
7 18 0.28
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:4434102 original size:50 final size:50
Alignment explanation
Indices: 4433972--4434439 Score: 348
Period size: 50 Copynumber: 9.5 Consensus size: 50
4433962 GCGATACCAT
* * * **
4433972 GAAGATTTGAAGGGAAAGGTTGAGGTCGTAATAGCGAACCCGGTACCATT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC-TTA
* * * ** ***
4434022 -AAGAT-TTAGAGGGAATGGTTAAGGTTGCAACGATTAACCCGGTACCTTA
1 GAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* *
4434071 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * *
4434120 GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * * *
4434170 GAAAATGTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCAGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * *** *
4434220 GAAAATGTGAAGGGAAAGATTGAGATAGTAACGGCGAACCCGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * * * * *
4434270 AAAGATATGATAGGG--AGGATTGAGGCTGTAATGGCGAACCCGATACCTTA
1 GAAGATGTGA-AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * * * * * *
4434320 GAAGATGTG-A-TGAAGATGATTGAGGCCGCAATGGCGAATCCGATTCCAT-
1 GAAGATGTGAAGGGAA-A-GGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
* * * * * * *
4434369 GAA-ATATGATGGGAAAGGTTGAGGCCACAACGACAAACCCAGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
*
4434417 GAAGA-GTTGAAGGAAAAGGTTGA
1 GAAGATG-TGAAGGGAAAGGTTGA
4434440 CGTCGCAAAG
Statistics
Matches: 334, Mismatches: 69, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
47 1 0.00
48 35 0.10
49 98 0.29
50 193 0.58
51 7 0.02
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (50 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTA
Found at i:4434109 original size:99 final size:99
Alignment explanation
Indices: 4433972--4434437 Score: 309
Period size: 99 Copynumber: 4.7 Consensus size: 99
4433962 GCGATACCAT
* * * ** * *
4433972 GAAGATTTGAAGGGAAAGGTTGAGGTCGTAATAGCGAACCCGGTACCATTAAGAT-TTAGAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGA-AGGGA
* ** *
4434036 ATGGTTAAGGTTGCAACGATTAACCCGGTACCTTA
65 AAGGTTAAGGCCGCAACGATGAACCCGGTACCTTA
*
4434071 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAGGGAA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAGGGAA
* * *
4434136 AGGTTGAGGCCGCAACGGTGAACCTGGTACCTTA
66 AGGTTAAGGCCGCAACGATGAACCCGGTACCTTA
* * * * * * *
4434170 GAAAATGTGAAGGGAAAGATTGAGGCCGCAACGGTGAACCCAGTACCTTAGAAAATGTGAAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAAGGGA
* * *** * **
4434235 AAGATTGAGATAGTAACGGCGAACCCGGTACCTTA
65 AAGGTTAAGGCCGCAACGATGAACCCGGTACCTTA
* * * * * * * * *
4434270 AAAGATATGATAGGG--AGGATTGAGGCTGTAATGGCGAACCCGATACCTTAGAAGATGTG-A-T
1 GAAGATGTGA-AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACCAT-GAAGATATGAAGG
* * * ** * * * *
4434331 GAAGATGATTGAGGCCGCAATGGCGAATCCGATTCCAT-
63 GAA-A-GGTTAAGGCCGCAACGATGAACCCGGTACCTTA
* * * * * * *
4434369 GAA-ATATGATGGGAAAGGTTGAGGCCACAACGACAAACCCAGTACCATGAAGAGT-TGAAGGAA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGA-TATGAAGGGA
4434432 AAGGTT
65 AAGGTT
4434438 GACGTCGCAA
Statistics
Matches: 291, Mismatches: 65, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
97 13 0.04
98 33 0.11
99 135 0.46
100 106 0.36
101 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (99 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATATGAAGGGAA
AGGTTAAGGCCGCAACGATGAACCCGGTACCTTA
Found at i:4434813 original size:82 final size:82
Alignment explanation
Indices: 4434632--4434909 Score: 348
Period size: 82 Copynumber: 3.4 Consensus size: 82
4434622 ATCATTCCAA
* * *
4434632 TCTTTTACCCCTAAATCAAGAAGCGCAGATTGAAGATTTCAATCTTTTTACCCTTAATCAAGAAG
1 TCTTTTACCTCT-AATCAAGAAGGGCAGATTGAAGATTTCAATC-TTTTACCCTTAATCAAGAGG
* * *
4434697 GGCAGATTGAATATTCCAA
64 GGCAGATTGAAGATTCTAG
*
4434716 TATTTTACC-CTTAATCAAGAAGGGCAGATTGAAGATTTCAATCTTTTACCCTTAATCAAGAGGG
1 TCTTTTACCTC-TAATCAAGAAGGGCAGATTGAAGATTTCAATCTTTTACCCTTAATCAAGAGGG
* *
4434780 GTACATTGAAGATTCTAG
65 GCAGATTGAAGATTCTAG
* **
4434798 TCTTTTACCTCTAATCAAGAAGGGCAGATTGGAGATTTTGATCTTTTA-CCTCTAATCAAGAGGG
1 TCTTTTACCTCTAATCAAGAAGGGCAGATTGAAGATTTCAATCTTTTACCCT-TAATCAAGAGGG
*
4434862 GCAGATT-AGAGATT-TTG
65 GCAGATTGA-AGATTCTAG
*
4434879 ATCTTTTACCTCTAATCAAGAGGGGCAGATT
1 -TCTTTTACCTCTAATCAAGAAGGGCAGATT
4434910 AAAGCCACTC
Statistics
Matches: 173, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
81 6 0.03
82 126 0.73
83 32 0.18
84 9 0.05
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (82 bp):
TCTTTTACCTCTAATCAAGAAGGGCAGATTGAAGATTTCAATCTTTTACCCTTAATCAAGAGGGG
CAGATTGAAGATTCTAG
Found at i:4434910 original size:41 final size:40
Alignment explanation
Indices: 4434629--4434909 Score: 314
Period size: 41 Copynumber: 6.8 Consensus size: 40
4434619 TGCATCATTC
*
4434629 CAATCTTTTACCCCTAAATCAAGAAGCGCAGATTGAAGATTT
1 CAATCTTTTA-CCCT-AATCAAGAAGGGCAGATTGAAGATTT
* *
4434671 CAATCTTTTTACCCTTAATCAAGAAGGGCAGATTGAATATTC
1 CAATC-TTTTACCC-TAATCAAGAAGGGCAGATTGAAGATTT
*
4434713 CAATATTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTT
1 CAATCTTTTACCC-TAATCAAGAAGGGCAGATTGAAGATTT
* * *
4434754 CAATCTTTTACCCTTAATCAAGAGGGGTACATTGAAGA-TT
1 CAATCTTTTACCC-TAATCAAGAAGGGCAGATTGAAGATTT
* *
4434794 CTAGTCTTTTACCTCTAATCAAGAAGGGCAGATTGGAGATTT
1 C-AATCTTTTACC-CTAATCAAGAAGGGCAGATTGAAGATTT
** *
4434836 TGATCTTTTACCTCTAATCAAGAGGGGCAGATT-AGAGATTT
1 CAATCTTTTACC-CTAATCAAGAAGGGCAGATTGA-AGATTT
** *
4434877 TGATCTTTTACCTCTAATCAAGAGGGGCAGATT
1 CAATCTTTTACC-CTAATCAAGAAGGGCAGATT
4434910 AAAGCCACTC
Statistics
Matches: 213, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
40 3 0.01
41 166 0.78
42 38 0.18
43 6 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (40 bp):
CAATCTTTTACCCTAATCAAGAAGGGCAGATTGAAGATTT
Found at i:4435085 original size:48 final size:48
Alignment explanation
Indices: 4435014--4435149 Score: 209
Period size: 48 Copynumber: 2.8 Consensus size: 48
4435004 ACCAAATCTG
* *
4435014 TCTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAGGTGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGGTCA
*
4435062 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGGTCA
* * **
4435110 TCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGA
4435150 AGTGAAGCTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGGTCA
Found at i:4435420 original size:208 final size:207
Alignment explanation
Indices: 4435059--4435501 Score: 658
Period size: 208 Copynumber: 2.1 Consensus size: 207
4435049 AATGAGGTGG
4435059 TCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCTTGATGAGA
1 TCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCTTGATGAGA
* *
4435124 TACAGAGAAGTAGACCAAATCAATGAAGTGAAGCTCAATACAAATGAAACTTCAAGCCCTATCTT
66 TACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCAAGCCCCATCTT
* * * *
4435189 CCTCATGAGATACAGAAAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATTCGGAG
131 CCTCATGAGATACAGAAAAGTGGGTCAAACCAAT-AAGCGGTCATCTTCCTGATGAGATACAGAG
* *
4435254 AAGTGGACCAAA-
195 AAGTGAAACAAAT
* * *
4435266 TCTATCTTCCTGATGAGATATAAAGAAGTGGATTGAAACAACT-AGGCGGTCATCTTCTTGATGA
1 TC-ATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAA-TGAGGCGGTCATCTTCTTGATGA
* * *
4435330 GATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATTAGACTTCGAA-CCCCAT
64 GATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTC-AAGCCCCAT
* * * *
4435394 CTTCCTGATGAGATACAGAGAAGTGGGTCGAACCAATAAGTGGTCATCTTCCTGATGAGATACAG
128 CTTCCTCATGAGATACAGAAAAGTGGGTCAAACCAATAAGCGGTCATCTTCCTGATGAGATACAG
4435459 AGAAGTGAAACAAAT
193 AGAAGTGAAACAAAT
*
4435474 TCGTCTTCCTGATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGT
4435502 AGACCAAATC
Statistics
Matches: 211, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
207 61 0.29
208 147 0.70
209 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (207 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCTTGATGAGA
TACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCAAGCCCCATCTT
CCTCATGAGATACAGAAAAGTGGGTCAAACCAATAAGCGGTCATCTTCCTGATGAGATACAGAGA
AGTGAAACAAAT
Found at i:4435528 original size:159 final size:160
Alignment explanation
Indices: 4435318--4435661 Score: 501
Period size: 159 Copynumber: 2.2 Consensus size: 160
4435308 TAGGCGGTCA
* * *
4435318 TCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATTAGACT
1 TCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATACGAATGAGACT
* * **
4435383 TCGAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCGAACCAAT-AAGTGGTCATCTTCCT
66 TCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAACCAATAAAAAGGTCATCTTCCT
* * *
4435447 GATGAGATACAGAGAAGTGAAACAAATTCG
131 GACGAGATACAGAGAAATGAAACAAATCCG
*
4435477 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATACGAATGAGACT
1 TCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATACGAATGAGACT
* * * * *
4435542 TCAAACCTCATCTTTCTGATGAGATACAGAAAAGTGGGTCGAAGCAATAAAAAGTTCATCTTTCT
66 TCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAACCAATAAAAAGGTCATCTTCCT
** *
4435607 GACGAGATGTAGAGAAATGAACCAAATCCG
131 GACGAGATACAGAGAAATGAAACAAATCCG
*
4435637 TCTTCTTGATGAGATCCAGAGAAGT
1 TCTTCTTGATGAGATACAGAGAAGT
4435662 GAATTAAAAT
Statistics
Matches: 163, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
159 104 0.64
160 59 0.36
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (160 bp):
TCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATACGAATGAGACT
TCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAACCAATAAAAAGGTCATCTTCCT
GACGAGATACAGAGAAATGAAACAAATCCG
Found at i:4435839 original size:209 final size:208
Alignment explanation
Indices: 4435477--4435925 Score: 659
Period size: 209 Copynumber: 2.2 Consensus size: 208
4435467 AACAAATTCG
* *
4435477 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAACTCAATACGAATGAGACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAACGAAGCAAAACTCAATACGAATGAAACT
* *
4435542 TCAAACCTCATCTTTCTGATGAGATACAGAAAAGTGGGTCGAAGCAATAAAAAGTTCATCTTTCT
66 TCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAAGCAATAAAAAGTTCATCTTTCT
* *
4435607 GACGAGATGTAGAGAAATGAACCAAATCCGTC-TTCTTGATGAGATCCAGAGAAGTGAATTAAAA
131 GACGAGATGCAGAGAAATGAACCAAATCCGTCTTTC-TGATGAGATACAGAGAAGTGAATTAAAA
4435671 TAATGAAGCGGTCA
195 TAATGAAGCGGTCA
* * * * * *
4435685 TCTTCCTGATGAGATACAGAGAAGTAGACCGATTCAACGAAGTAAAGCTCAATATGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAACGAAGCAAAACTCAATACGAATGAAAC-
* ** * **
4435750 TTCAAACCCCATCTTCCTGATGAGATATAGAGGAGTGGGTTGAAGCAATAAAGTGTTCAT-TTTC
65 TTCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAAGCAATAAAAAGTTCATCTTT-
* *
4435814 CTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTTCTGATGAGATACAGAGAAGTGGATTAAA
129 CTGACGAGATGCAGAGAAATGAACCAAATCCGTCTTTCTGATGAGATACAGAGAAGTGAATTAAA
*
4435879 ATAATGAAGTGGTCA
194 ATAATGAAGCGGTCA
*
4435894 TCTTCCTGATGAGATGCAGAGAAGTAGACCAA
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAA
4435926 GAGATGAAGC
Statistics
Matches: 215, Mismatches: 23, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
208 59 0.27
209 153 0.71
210 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (208 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAACGAAGCAAAACTCAATACGAATGAAACT
TCAAACCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCGAAGCAATAAAAAGTTCATCTTTCT
GACGAGATGCAGAGAAATGAACCAAATCCGTCTTTCTGATGAGATACAGAGAAGTGAATTAAAAT
AATGAAGCGGTCA
Found at i:4435925 original size:85 final size:85
Alignment explanation
Indices: 4435761--4435918 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
4435751 TCAAACCCCA
* * * * * * *
4435761 TCTTCCTGATGAGATATAGAGGAGTGGGTTGAAGCAATAAAGTGTTCATTTTCCTGACGAGATGC
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATAAAGTGGTCATCTTCCTGACGAGATGC
4435826 AGAGAAGTGAACCAAATCCG
66 AGAGAAGTGAACCAAATCCG
* * * *
4435846 TCTTTCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGTGGTCATCTTCCTGATGAGATGC
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATAAAGTGGTCATCTTCCTGACGAGATGC
4435911 AGAGAAGT
66 AGAGAAGT
4435919 AGACCAAGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATAAAGTGGTCATCTTCCTGACGAGATGC
AGAGAAGTGAACCAAATCCG
Found at i:4436817 original size:2 final size:2
Alignment explanation
Indices: 4436812--4436917 Score: 81
Period size: 2 Copynumber: 53.0 Consensus size: 2
4436802 ATATACAAAC
*
4436812 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * ** * * *
4436854 AT ACG AT AT AT AT AC AT AC AT AT AT GT GC AT AC AT AT GT TT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4436897 -T AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4436918 TATTTTATTT
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
1 2 0.02
2 77 0.95
3 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:4437679 original size:30 final size:30
Alignment explanation
Indices: 4437645--4437766 Score: 133
Period size: 30 Copynumber: 4.1 Consensus size: 30
4437635 ATTTTATTTG
*
4437645 AAAATTATATTTTGACCCCAAAAATTTTCA
1 AAAATTATATTTTAACCCCAAAAATTTTCA
*
4437675 AAAATTATATTTTGA--CCATAAAATTTTCA
1 AAAATTATATTTTAACCCCA-AAAATTTTCA
* * * *
4437704 AAAATTACATTTTAACTCCTAAACTTTTCA
1 AAAATTATATTTTAACCCCAAAAATTTTCA
* *
4437734 AAAATTATGTTTTAACCCTC-AAACTTTTCA
1 AAAATTATATTTTAACCC-CAAAAATTTTCA
4437764 AAA
1 AAA
4437767 TCACTTTTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
28 3 0.04
29 23 0.28
30 52 0.64
31 3 0.04
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCAAAAATTTTCA
Found at i:4437767 original size:59 final size:59
Alignment explanation
Indices: 4437645--4437785 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 59
4437635 ATTTTATTTG
* * *
4437645 AAAATTATATTTTGACCCCAAAAATTTTCAAAAATTATATTTTGACCATAAAATTTTCA
1 AAAATTACATTTTGACCCCTAAAATTTTCAAAAATTATATTTTAACCATAAAATTTTCA
* * * * * *
4437704 AAAATTACATTTTAACTCCTAAACTTTTCAAAAATTATGTTTTAACCCTCAAACTTTTC-
1 AAAATTACATTTTGACCCCTAAAATTTTCAAAAATTATATTTTAACCAT-AAAATTTTCA
* *
4437763 AAAATCACTTTTTGACCCCTAAA
1 AAAATTACATTTTGACCCCTAAA
4437786 GTTTCCTAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 60 0.88
60 8 0.12
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTGACCCCTAAAATTTTCAAAAATTATATTTTAACCATAAAATTTTCA
Found at i:4437780 original size:29 final size:30
Alignment explanation
Indices: 4437645--4437780 Score: 115
Period size: 30 Copynumber: 4.6 Consensus size: 30
4437635 ATTTTATTTG
4437645 AAAATTA-TATTTTGACCC-CAAAAATTTTCA
1 AAAATTACT-TTTTGACCCTC-AAAATTTTCA
*
4437675 AAAATTA-TATTTTGACCAT-AAAATTTTCA
1 AAAATTACT-TTTTGACCCTCAAAATTTTCA
* * *
4437704 AAAATTACATTTTAACTCCT-AAACTTTTCA
1 AAAATTACTTTTTGAC-CCTCAAAATTTTCA
* *
4437734 AAAATTA-TGTTTTAACCCTCAAACTTTTC-
1 AAAATTACT-TTTTGACCCTCAAAATTTTCA
*
4437763 AAAATCACTTTTTGACCC
1 AAAATTACTTTTTGACCC
4437781 CTAAAGTTTC
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
29 40 0.43
30 52 0.57
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACTTTTTGACCCTCAAAATTTTCA
Found at i:4438961 original size:7 final size:7
Alignment explanation
Indices: 4438951--4439038 Score: 153
Period size: 7 Copynumber: 12.9 Consensus size: 7
4438941 CCCTTCCTCT
4438951 TTTCTCC
1 TTTCTCC
4438958 TTTCTCC
1 TTTCTCC
4438965 TTTCTCC
1 TTTCTCC
4438972 TTTC-CC
1 TTTCTCC
4438978 TTTCTCC
1 TTTCTCC
4438985 TTTCTCC
1 TTTCTCC
4438992 TTTCTCC
1 TTTCTCC
4438999 TTTCTCC
1 TTTCTCC
4439006 TTTCTCC
1 TTTCTCC
4439013 TTTCTCC
1 TTTCTCC
*
4439020 TTTCCCC
1 TTTCTCC
4439027 TTTC-CC
1 TTTCTCC
4439033 TTTCTC
1 TTTCTC
4439039 GTTTTCAATT
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
6 12 0.15
7 66 0.85
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTCTCC
Found at i:4439003 original size:48 final size:48
Alignment explanation
Indices: 4438925--4439038 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
4438915 CCGAAGCCTC
* * *
4438925 TCCCCATTTCCCTTCCCCCTTCCTCTTTTCTCCTTTCTCCTTTCTCCTT
1 TCCCC-TTTCCCTTTCTCCTTCCTCCTTTCTCCTTTCTCCTTTCTCCTT
*
4438974 T-CCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTT
1 TCCCCTTTC-CCTTTCTCCTTCCTCCTTTCTCCTTTCTCCTTTCTCCTT
4439022 TCCCCTTTCCCTTTCTC
1 TCCCCTTTCCCTTTCTC
4439039 GTTTTCAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
47 4 0.07
48 47 0.80
49 8 0.14
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.52
Consensus pattern (48 bp):
TCCCCTTTCCCTTTCTCCTTCCTCCTTTCTCCTTTCTCCTTTCTCCTT
Found at i:4441341 original size:22 final size:22
Alignment explanation
Indices: 4441316--4441359 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4441306 AAGTACTATG
4441316 CATCAGCTAACTAGGTATGATT
1 CATCAGCTAACTAGGTATGATT
* *
4441338 CATCATCTAACTATGTATGATT
1 CATCAGCTAACTAGGTATGATT
4441360 ATTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (22 bp):
CATCAGCTAACTAGGTATGATT
Found at i:4441753 original size:31 final size:31
Alignment explanation
Indices: 4441725--4441786 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4441715 GTCATATGAT
4441725 AAATGCTCATTCTTTTCATTTCGTATATGCA
1 AAATGCTCATTCTTTTCATTTCGTATATGCA
* *
4441756 AAATGCTCTTTTTTTTCATTTCGTATATGCA
1 AAATGCTCATTCTTTTCATTTCGTATATGCA
4441787 TACTCATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (31 bp):
AAATGCTCATTCTTTTCATTTCGTATATGCA
Found at i:4442189 original size:40 final size:40
Alignment explanation
Indices: 4442085--4442315 Score: 309
Period size: 40 Copynumber: 5.8 Consensus size: 40
4442075 ATAGCATCGA
* * * *
4442085 CACGAAACCTGCTAGGCTCAAAGCCTGATAATATACACCGG
1 CACGAAGCCTGCTAGGCACTAAGCCCGATAA-ATACACCGG
* * * *
4442126 CACGAAGCCTACTTGGCATTAAGCCCGATAAATACATCGG
1 CACGAAGCCTGCTAGGCACTAAGCCCGATAAATACACCGG
* * *
4442166 CATGAAACCTGCTAGGCACTAAGCCCGATAAATACACTGG
1 CACGAAGCCTGCTAGGCACTAAGCCCGATAAATACACCGG
* *
4442206 CACGAAGCCTACTAGACACTAAGCCCGATAAATACACCGG
1 CACGAAGCCTGCTAGGCACTAAGCCCGATAAATACACCGG
*
4442246 CACGAAGCCTGCTAGGCACTAAGCTCGATAAATACACCGG
1 CACGAAGCCTGCTAGGCACTAAGCCCGATAAATACACCGG
* *
4442286 CACGAAGCCTGCTAGGTATTAAGCCCGATA
1 CACGAAGCCTGCTAGGCACTAAGCCCGATA
4442316 TAACGAGGAA
Statistics
Matches: 164, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
40 140 0.85
41 24 0.15
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (40 bp):
CACGAAGCCTGCTAGGCACTAAGCCCGATAAATACACCGG
Found at i:4442232 original size:80 final size:80
Alignment explanation
Indices: 4442073--4442315 Score: 342
Period size: 80 Copynumber: 3.0 Consensus size: 80
4442063 GAACTTAAGA
* * * *
4442073 AAATAGCATCGACACGAAACCTGCTAGGCTCAAAGCCTGATAATATACACCGGCACGAAGCCTAC
1 AAATA-CATCGGCACGAAACCTGCTAGGCACTAAGCCCGATAA-ATACACCGGCACGAAGCCTAC
*
4442138 TTGGCATTAAGCCCGAT
64 TAGGCATTAAGCCCGAT
* *
4442155 AAATACATCGGCATGAAACCTGCTAGGCACTAAGCCCGATAAATACACTGGCACGAAGCCTACTA
1 AAATACATCGGCACGAAACCTGCTAGGCACTAAGCCCGATAAATACACCGGCACGAAGCCTACTA
* *
4442220 GACACTAAGCCCGAT
66 GGCATTAAGCCCGAT
* * * *
4442235 AAATACACCGGCACGAAGCCTGCTAGGCACTAAGCTCGATAAATACACCGGCACGAAGCCTGCTA
1 AAATACATCGGCACGAAACCTGCTAGGCACTAAGCCCGATAAATACACCGGCACGAAGCCTACTA
*
4442300 GGTATTAAGCCCGAT
66 GGCATTAAGCCCGAT
4442315 A
1 A
4442316 TAACGAGGAA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 106 0.74
81 32 0.22
82 5 0.03
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (80 bp):
AAATACATCGGCACGAAACCTGCTAGGCACTAAGCCCGATAAATACACCGGCACGAAGCCTACTA
GGCATTAAGCCCGAT
Found at i:4443523 original size:14 final size:15
Alignment explanation
Indices: 4443499--4443529 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4443489 AGAAAATAAA
4443499 AAAATTTAAAAAAAG
1 AAAATTTAAAAAAAG
4443514 AAAA-TTAAAAAAAG
1 AAAATTTAAAAAAAG
4443528 AA
1 AA
4443530 GAAGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAATTTAAAAAAAG
Found at i:4459350 original size:11 final size:11
Alignment explanation
Indices: 4459336--4459414 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
4459326 TTTTATGTAG
4459336 TATTTAATT-TT
1 TATTT-ATTATT
4459347 TATTTATTATT
1 TATTTATTATT
*
4459358 TACTTATTATT
1 TATTTATTATT
4459369 TATTTATT-TGT
1 TATTTATTAT-T
* *
4459380 GATTCATT-TT
1 TATTTATTATT
4459390 TACTTTA-TATT
1 TA-TTTATTATT
*
4459401 TAATT-TTATT
1 TATTTATTATT
4459411 TATT
1 TATT
4459415 ATTGTTATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 16 0.29
11 39 0.71
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTTATTATT
Found at i:4459367 original size:18 final size:19
Alignment explanation
Indices: 4459336--4459377 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
4459326 TTTTATGTAG
*
4459336 TATTTAATTTTTATTTA-T
1 TATTTAATTATTATTTATT
*
4459354 TATTTACTTATTATTTATT
1 TATTTAATTATTATTTATT
4459373 TATTT
1 TATTT
4459378 GTGATTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTAATTATTATTTATT
Found at i:4459730 original size:29 final size:30
Alignment explanation
Indices: 4459696--4459787 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 30
4459686 TTTGTTGTCA
4459696 TTATTATTATGATTATATTA-TTATTTTAT
1 TTATTATTATGATTATATTATTTATTTTAT
* *
4459725 TTATTACTATGATTATGTTATTTTATTTTAT
1 TTATTATTATGATTATATTA-TTTATTTTAT
* * *
4459756 TGTGTTATTA--ATTGTATTCATTTAATTTAT
1 T-TATTATTATGATTATATT-ATTTATTTTAT
4459786 TT
1 TT
4459788 TATTCATGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 19 0.37
30 16 0.31
31 11 0.21
32 6 0.12
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (30 bp):
TTATTATTATGATTATATTATTTATTTTAT
Found at i:4459740 original size:21 final size:20
Alignment explanation
Indices: 4459707--4459747 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4459697 TATTATTATG
* *
4459707 ATTATATTATTATTTTATTT
1 ATTATATGATTATGTTATTT
4459727 ATTACTATGATTATGTTATTT
1 ATTA-TATGATTATGTTATTT
4459748 TATTTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTATATGATTATGTTATTT
Found at i:4460889 original size:46 final size:45
Alignment explanation
Indices: 4460790--4460903 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 45
4460780 AAGTGCTGGG
* * *
4460790 GAAACAGTAGGCACACACAGTGCAATCAGTAGGCGCACATAGCGC
1 GAAACAGTAGGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
*
4460835 -AAATCAGTAGGCACACGA-AGTGCGAAACAGTAGGCACACAAAGTGC
1 GAAA-CAGTAGGCACAC-ACAGTGC-AAACAGTAGGCACACAAAGCGC
*
4460881 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACACAGTGC
4460904 TGAACGGTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
44 3 0.05
45 18 0.31
46 35 0.59
47 3 0.05
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (45 bp):
GAAACAGTAGGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
Found at i:4460902 original size:23 final size:22
Alignment explanation
Indices: 4460766--4460903 Score: 127
Period size: 23 Copynumber: 5.9 Consensus size: 22
4460756 CGAAGTACTT
*
4460766 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAGGCACACAAGTGC----GA
4460792 AACAGTAGGCACACACAGTGC-A
1 AACAGTAGGCACACA-AGTGCGA
* * *
4460814 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAGGCACACA-AGTGCGA
4460836 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAGGCACAC-AAGTGCGA
4460860 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAGGCACAC-AAGTGCGA
*
4460883 AACAGTAAGCACACACAGTGC
1 AACAGTAGGCACACA-AGTGC
4460904 TGAACGGTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
22 21 0.22
23 53 0.55
24 4 0.04
26 14 0.14
27 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (22 bp):
AACAGTAGGCACACAAGTGCGA
Found at i:4464038 original size:22 final size:22
Alignment explanation
Indices: 4463990--4464038 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4463980 AAAATTTATT
*
4463990 AAAATTATTAGAAATAGAAATA
1 AAAATTATTAAAAATAGAAATA
*
4464012 TAAATTATTAAAAAATAGAAA-A
1 AAAATTATT-AAAAATAGAAATA
4464034 AAAAT
1 AAAAT
4464039 ATAATTACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAATTATTAAAAATAGAAATA
Found at i:4464039 original size:28 final size:28
Alignment explanation
Indices: 4463998--4464090 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 28
4463988 TTAAAATTAT
*
4463998 TAGAAATAGAAATATAAATTATTAAAAAA
1 TAGAAA-AAAAATATAAATTATTAAAAAA
*
4464027 TAGAAAAAAAATAT-AATTA-CAAAAAA
1 TAGAAAAAAAATATAAATTATTAAAAAA
* *
4464053 TTA-CACAAAAATATTAAAATTATTTAAAAAA
1 -TAGAAAAAAAATA-T-AAATTA-TTAAAAAA
4464084 TACGAAA
1 TA-GAAA
4464091 CTTATTAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
26 14 0.29
27 8 0.16
28 7 0.14
29 11 0.22
30 2 0.04
31 6 0.12
32 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (28 bp):
TAGAAAAAAAATATAAATTATTAAAAAA
Found at i:4464622 original size:20 final size:19
Alignment explanation
Indices: 4464593--4464642 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
4464583 TTAACTTTCT
* *
4464593 TTATATATTTTTTAGAAAA
1 TTATAAATTTTTTAAAAAA
* *
4464612 TTTTAGAATTTCTTAAAAAA
1 TTATA-AATTTTTTAAAAAA
4464632 TTATAAATTTT
1 TTATAAATTTT
4464643 AAAATTCTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TTATAAATTTTTTAAAAAA
Found at i:4464648 original size:27 final size:27
Alignment explanation
Indices: 4464609--4464673 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
4464599 ATTTTTTAGA
*
4464609 AAATTTTAGAATTTCTTA-AAAAATTAT
1 AAATTTTA-AAATTCTTATAAAAATTAT
* *
4464636 AAATTTTAAAATTCTTATAAATATTTT
1 AAATTTTAAAATTCTTATAAAAATTAT
*
4464663 GAATTTTAAAA
1 AAATTTTAAAA
4464674 ATAATTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
AAATTTTAAAATTCTTATAAAAATTAT
Found at i:4465052 original size:14 final size:14
Alignment explanation
Indices: 4465033--4465062 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4465023 TTTTTTTCAA
4465033 ATTATTGAAATAAT
1 ATTATTGAAATAAT
*
4465047 ATTATTTAAATAAT
1 ATTATTGAAATAAT
4465061 AT
1 AT
4465063 AATTTGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATTATTGAAATAAT
Found at i:4465449 original size:31 final size:31
Alignment explanation
Indices: 4465414--4465504 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 31
4465404 GTTTTTTTAA
* * * *
4465414 ATGTATATAATTAAATCAGAATGAAAGTTTC
1 ATGTATATAATTAAATAACAATCAAAATTTC
** *
4465445 ATGTATATTTTTAAATAACAATCAAAATTTT
1 ATGTATATAATTAAATAACAATCAAAATTTC
* *
4465476 ATATATATAATT--ACAACAAATCAAAATTT
1 ATGTATATAATTAAATAAC-AATCAAAATTT
4465505 ATTATAATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
29 4 0.08
30 11 0.23
31 33 0.69
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
ATGTATATAATTAAATAACAATCAAAATTTC
Found at i:4465987 original size:28 final size:29
Alignment explanation
Indices: 4465923--4466011 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 29
4465913 TATTTTTAAA
4465923 ATTT-TTTAATATATTTATATTATATTATTTT
1 ATTTATTTAATA-ATTT-TA-TATATTATTTT
*
4465954 A-ATATTTAATAATTTTATATATT-TTTT
1 ATTTATTTAATAATTTTATATATTATTTT
* *
4465981 ATTTATTGAA-AATTTTTATATAATCATTTT
1 ATTTATTTAATAA-TTTTATAT-ATTATTTT
4466011 A
1 A
4466012 ACATTATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 7 0.14
28 20 0.41
29 4 0.08
30 10 0.20
31 8 0.16
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTATTTAATAATTTTATATATTATTTT
Found at i:4466000 original size:26 final size:27
Alignment explanation
Indices: 4465942--4466001 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
4465932 TATATTTATA
*
4465942 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
4465969 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
4465996 TTATAT
1 TTATAT
4466002 AATCATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:4469186 original size:3 final size:3
Alignment explanation
Indices: 4469178--4469203 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4469168 TCAAACCCTT
4469178 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
4469204 TCATCTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:4471140 original size:74 final size:74
Alignment explanation
Indices: 4471018--4471234 Score: 317
Period size: 74 Copynumber: 2.9 Consensus size: 74
4471008 CGAGTTATGT
** * *
4471018 TACTCGAATTCGGGTATATTCGAAACGTATCTTTACACATGTTCGAATATTAGTAAGACATGGGT
1 TACTCGAATTCGGGTATATTCGAAACGTATCTACACACATGTTCGAATATAAATAAGACATGGGT
4471083 ATTTCGAAA
66 ATTTCGAAA
* * * * *
4471092 TACTCGAATTCAGGTATATTCAAAACATATCTACACACATGTTTGAATATAATTAAGACATGGGT
1 TACTCGAATTCGGGTATATTCGAAACGTATCTACACACATGTTCGAATATAAATAAGACATGGGT
4471157 ATTTCGAAA
66 ATTTCGAAA
* *
4471166 TGCTCGAATTCGGGTATATTTGAAACGTATCTTTACACACATGTTCGAATATAAATAAGACATGG
1 TACTCGAATTCGGGTATATTCGAAACGTATC--TACACACATGTTCGAATATAAATAAGACATGG
4471231 GTAT
64 GTAT
4471235 CTCGGAAAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
74 92 0.73
76 34 0.27
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (74 bp):
TACTCGAATTCGGGTATATTCGAAACGTATCTACACACATGTTCGAATATAAATAAGACATGGGT
ATTTCGAAA
Found at i:4474597 original size:22 final size:23
Alignment explanation
Indices: 4474555--4474602 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
4474545 AATTTTAAAA
* *
4474555 TATAAAAAATCTAATATATAT-T
1 TATAAAAAATCTAAAAAATATAT
4474577 TATAAAAATAT-TAAAAAATATAT
1 TATAAAAA-ATCTAAAAAATATAT
4474600 TAT
1 TAT
4474603 TTGATATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TATAAAAAATCTAAAAAATATAT
Found at i:4474742 original size:3 final size:3
Alignment explanation
Indices: 4474724--4474800 Score: 129
Period size: 3 Copynumber: 26.0 Consensus size: 3
4474714 ATTTAGAAAA
*
4474724 TAT TA- TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4474771 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4474801 GAAATTAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4475121 original size:10 final size:9
Alignment explanation
Indices: 4475098--4475130 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
4475088 TTGAATGTTA
4475098 TAAAAA-AT
1 TAAAAATAT
4475106 TAAAAATAT
1 TAAAAATAT
4475115 ATAAAAATAT
1 -TAAAAATAT
4475125 TAAAAA
1 TAAAAA
4475131 GGTGTCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 8 0.35
10 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAATAT
Found at i:4475937 original size:20 final size:19
Alignment explanation
Indices: 4475912--4475975 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
4475902 AAAATTATTA
*
4475912 TTTTAGGGATTTTTTTTAAT
1 TTTTA-GGATTTTTTATAAT
*
4475932 TTTTAGCA-TTTTTATATAT
1 TTTTAGGATTTTTTATA-AT
4475951 TCTTTAGGATTTTTTATAAT
1 T-TTTAGGATTTTTTATAAT
*
4475971 ATTTA
1 TTTTA
4475976 TATTTGGTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.19
19 9 0.24
20 13 0.35
21 8 0.22
ACGTcount: A:0.25, C:0.03, G:0.09, T:0.62
Consensus pattern (19 bp):
TTTTAGGATTTTTTATAAT
Found at i:4475942 original size:19 final size:19
Alignment explanation
Indices: 4475920--4475975 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4475910 TATTTTAGGG
*
4475920 ATTTTTTTTAATTTTTAGC
1 ATTTTTTATAATTTTTAGC
*
4475939 A-TTTTTATATATTCTTTAGG
1 ATTTTTTATA-ATT-TTTAGC
*
4475959 ATTTTTTATAATATTTA
1 ATTTTTTATAATTTTTA
4475976 TATTTGGTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 7 0.23
19 8 0.26
20 8 0.26
21 8 0.26
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTTTTATAATTTTTAGC
Found at i:4476011 original size:18 final size:17
Alignment explanation
Indices: 4475990--4476032 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4475980 TGGTGGAAGA
4475990 TATAAATTTTAGAATTGT
1 TATAAATTTTAGAATT-T
*
4476008 TATAAATATTTTGAATTT
1 TATAAAT-TTTAGAATTT
4476026 TA-AAATT
1 TATAAATT
4476033 AAAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 4 0.17
18 10 0.43
19 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:4482052 original size:40 final size:40
Alignment explanation
Indices: 4481997--4482076 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
4481987 AAAAATGGAG
4481997 AAAGGATTGTATGAAACAGAGATATCATCCCTTTCCAATA
1 AAAGGATTGTATGAAACAGAGATATCATCCCTTTCCAATA
* * *
4482037 AAAGGATTGTATGAAACAGGGATATTATCCCTTTTCAATA
1 AAAGGATTGTATGAAACAGAGATATCATCCCTTTCCAATA
4482077 GTTTTACGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (40 bp):
AAAGGATTGTATGAAACAGAGATATCATCCCTTTCCAATA
Found at i:4488054 original size:97 final size:97
Alignment explanation
Indices: 4487879--4488072 Score: 259
Period size: 97 Copynumber: 2.0 Consensus size: 97
4487869 AATTTTGGAA
*
4487879 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACGAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACGAATTTTCA
* *
4487944 GAATCGGAGAT-AAAGAAACATTGCCTCAATTT
66 GAATCCGAAATAAAAG-AACATTGCCTCAATTT
* * * *
4487976 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCAC-AAGTTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACGAA-TTTTC
* *
4488040 A-AATCTCGAAATAAAAGAATATTGCCTCGATTT
65 AGAATC-CGAAATAAAAGAACATTGCCTCAATTT
4488073 TAAAGTTTTC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
96 6 0.07
97 75 0.88
98 4 0.05
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACGAATTTTCA
GAATCCGAAATAAAAGAACATTGCCTCAATTT
Found at i:4488354 original size:29 final size:28
Alignment explanation
Indices: 4488291--4488350 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
4488281 AAAATGAGAC
* *
4488291 TTTTGGATACCCGGGGGTAAAACGGTAA
1 TTTTGGACACCCGGGGGCAAAACGGTAA
* *
4488319 TTTTGGACACTCGGGGGCAAAATGGTAA
1 TTTTGGACACCCGGGGGCAAAACGGTAA
4488347 TTTT
1 TTTT
4488351 TGGAAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (28 bp):
TTTTGGACACCCGGGGGCAAAACGGTAA
Found at i:4488381 original size:30 final size:30
Alignment explanation
Indices: 4488337--4488418 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 30
4488327 ACTCGGGGGC
*
4488337 AAAATGGTAATTTTTGGAAGGTTCAAGGTT
1 AAAATGGTAATTTTTGGAAGGTTCAAGGGT
*
4488367 AAAAATGG-AATTTTTGGACA--TTCGAGGGT
1 -AAAATGGTAATTTTTGGA-AGGTTCAAGGGT
4488396 AAAATGGTAA-TTTTGGAAGGTTC
1 AAAATGGTAATTTTTGGAAGGTTC
4488419 GAGATCAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 1 0.02
28 14 0.31
29 12 0.27
30 10 0.22
31 8 0.18
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGGTTCAAGGGT
Found at i:4488400 original size:59 final size:58
Alignment explanation
Indices: 4488319--4488710 Score: 396
Period size: 59 Copynumber: 6.7 Consensus size: 58
4488309 AAAACGGTAA
* * * *
4488319 TTTTGGACACTCGGGGGCAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAATGGAAT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTC-AGGTTAAAAATGGAAT
* * * * * *
4488378 TTTTGGACATTCGAGGGTAAAATGGTAA-TTTTGGAAGGTTCGAGATCAAAAATTGG-GT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTC-AGGTTAAAAA-TGGAAT
* * * *
4488436 TTTTAGACATTTGAGGGTAAAATGGTAATTTTTGAAAAGTT-AGGTGTCAAAAATGGAGT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGT-T-AAAAATGGAAT
* * *
4488495 TTTTAGACATTTGGGGGTAAAATGGTAATTTTTAGAAAGTTCAGGATTAAAAATAGAAT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGG-TTAAAAATGGAAT
* ** * *
4488554 TTTTAGATATTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTTGGAGTAAAAAATGGAGTT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAG-TTCAG-GTTAAAAATGGA-AT
* ** * * * * *
4488614 TTTTGGACATTTAGGGGTGAAATTGTAATTTTTGAAAAGTTTAGGGTTAAAAATAGAAT
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCA-GGTTAAAAATGGAAT
4488673 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAA
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAA
4488711 AATTGGGGTC
Statistics
Matches: 278, Mismatches: 43, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
57 3 0.01
58 54 0.19
59 169 0.61
60 47 0.17
61 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGTTAAAAATGGAAT
Found at i:4488419 original size:29 final size:29
Alignment explanation
Indices: 4488305--4488708 Score: 144
Period size: 29 Copynumber: 13.8 Consensus size: 29
4488295 GGATACCCGG
* * *
4488305 GGGTAAAACGGTAA-TTTTGGACACTCGG
1 GGGTAAAATGGTAATTTTTGGACATTCGA
* *
4488333 GGGCAAAATGGTAATTTTTGGA-AGGTTCAA
1 GGGTAAAATGGTAATTTTTGGACA--TTCGA
*
4488363 GGTTAAAAATGG-AATTTTTGGACATTCGA
1 GGGT-AAAATGGTAATTTTTGGACATTCGA
4488392 GGGTAAAATGGTAA-TTTTGGA-AGGTTCGA
1 GGGTAAAATGGTAATTTTTGGACA--TTCGA
* * * *
4488421 -GATCAAAAATTGG--GTTTTTAGACATTTGA
1 GGGT--AAAA-TGGTAATTTTTGGACATTCGA
* *
4488450 GGGTAAAATGGTAATTTTTGAAAAGTT--A
1 GGGTAAAATGGTAATTTTTGGACA-TTCGA
* * * *
4488478 GGTGTCAAAAATGG-AGTTTTTAGACATTTGG
1 GG-GT--AAAATGGTAATTTTTGGACATTCGA
* *
4488509 GGGTAAAATGGTAATTTTTAGAAAGTTC-A
1 GGGTAAAATGGTAATTTTTGGACA-TTCGA
* * * * *
4488538 GGATTAAAAATAG-AATTTTTAGATATTCGG
1 GG-GT-AAAATGGTAATTTTTGGACATTCGA
*
4488568 GGGTAAAATGGTAATTTTTGGA-AGTTTTG-
1 GGGTAAAATGGTAATTTTTGGACA--TTCGA
* * *
4488597 GAGTAAAAAATGG-AGTTTTTTGGACATT-TA
1 GGGT--AAAATGGTA-ATTTTTGGACATTCGA
* * * * *
4488627 GGGGTGAAATTGTAATTTTTGAAAAGTT-TA
1 -GGGTAAAATGGTAATTTTTGGACA-TTCGA
* * *
4488657 GGGTTAAAAATAG-AATTTTTAGACATTCGG
1 GGG-T-AAAATGGTAATTTTTGGACATTCGA
4488687 GGGTAAAATGGTAATTTTTGGA
1 GGGTAAAATGGTAATTTTTGGA
4488709 AAAATTGGGG
Statistics
Matches: 281, Mismatches: 53, Indels: 83
0.67 0.13 0.20
Matches are distributed among these distances:
27 4 0.01
28 56 0.20
29 92 0.33
30 78 0.28
31 50 0.18
32 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGACATTCGA
Found at i:4488670 original size:119 final size:117
Alignment explanation
Indices: 4488319--4488776 Score: 442
Period size: 119 Copynumber: 3.9 Consensus size: 117
4488309 AAAACGGTAA
* * * * ** * *
4488319 TTTTGGACACTCGGGGGCAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAATGGAATTTTTGG
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTGGA-GTCAAAAATGGAGTTTTTGG
* * * * * * * * **
4488384 ACA-TTCGAGGGTAAAATGGTAA-TTTTG-GAAGGTTCGAGATCAAAAATTGGGT
65 ACATTTAG-GGGTAAAATTGTAATTTTTGAAAAGTTTAG-GGTTAAAAATAGAAT
* * * * * *
4488436 TTTTAGACATTTGAGGGTAAAATGGTAATTTTTGAAAAGTTAGGTGTCAAAAATGGAGTTTTTAG
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTG-GAAGTTTGGAGTCAAAAATGGAGTTTTTGG
* * * *
4488501 ACATTTGGGGGTAAAATGGTAATTTTT-AGAAAGTTCAGGATTAAAAATAGAAT
65 ACATTTAGGGGTAAAATTGTAATTTTTGA-AAAGTTTAGGGTTAAAAATAGAAT
* *
4488554 TTTTAGATATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTTGGAGTAAAAAATGGAGTTTTTTG
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAG-TTTGGAGTCAAAAATGGAG-TTTTTG
*
4488619 GACATTTAGGGGTGAAATTGTAATTTTTGAAAAGTTTAGGGTTAAAAATAGAAT
64 GACATTTAGGGGTAAAATTGTAATTTTTGAAAAGTTTAGGGTTAAAAATAGAAT
** * *
4488673 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGG-GATTTTGG
1 TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTGGAGTCAAAAATGGAGTTTTTGG
* * * *
4488737 AAAGTTTA-GGGTAAAAATATAATTTTTGAATAGTTTAGGG
65 ACA-TTTAGGGGTAAAATTGTAATTTTTGAAAAGTTTAGGG
4488777 ACCTTTAGAG
Statistics
Matches: 284, Mismatches: 47, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
117 102 0.36
118 74 0.26
119 105 0.37
120 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (117 bp):
TTTTAGACATTCGGGGGTAAAATGGTAATTTTTGGAAGTTTGGAGTCAAAAATGGAGTTTTTGGA
CATTTAGGGGTAAAATTGTAATTTTTGAAAAGTTTAGGGTTAAAAATAGAAT
Found at i:4488763 original size:29 final size:29
Alignment explanation
Indices: 4488579--4488776 Score: 86
Period size: 29 Copynumber: 6.7 Consensus size: 29
4488569 GGTAAAATGG
*
4488579 TAATTTTTGG-AAGTTTTGGAGTAAAAA-A
1 TAATTTTTGGAAAGTTTAGG-GTAAAAATA
* * * * *
4488607 TGGAGTTTTTTGGACA-TTTAGGGGTGAAATTG
1 T--A-ATTTTTGGAAAGTTTA-GGGTAAAAATA
*
4488639 TAATTTTTGAAAAGTTTAGGGTTAAAAATA
1 TAATTTTTGGAAAGTTTAGGG-TAAAAATA
* * * ** *
4488669 GAATTTTTAGACA-TTCGGGGGT-AAAATGG
1 TAATTTTTGGAAAGTT-TAGGGTAAAAAT-A
** * *
4488698 TAATTTTTGGAAAAATTGGGGTCAAAAATG
1 TAATTTTTGGAAAGTTTAGGGT-AAAAATA
**
4488728 GGA-TTTTGGAAAGTTTAGGGTAAAAATA
1 TAATTTTTGGAAAGTTTAGGGTAAAAATA
4488756 TAATTTTT-GAATAGTTTAGGG
1 TAATTTTTGGAA-AGTTTAGGG
4488777 ACCTTTAGAG
Statistics
Matches: 123, Mismatches: 32, Indels: 29
0.67 0.17 0.16
Matches are distributed among these distances:
28 16 0.13
29 57 0.46
30 26 0.21
31 20 0.16
32 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
TAATTTTTGGAAAGTTTAGGGTAAAAATA
Found at i:4489862 original size:13 final size:13
Alignment explanation
Indices: 4489846--4489875 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4489836 TTTATTAAAA
*
4489846 ATTAATATTAATT
1 ATTAATAATAATT
4489859 ATTAATAATAATT
1 ATTAATAATAATT
4489872 ATTA
1 ATTA
4489876 GTACGGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAATAATAATT
Done.