Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 168 of 325
Found at i:53133312 original size:21 final size:21
Alignment explanation
Indices: 53133288--53133331 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
53133278 ACGACCTAAT
*
53133288 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
53133309 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
53133330 TA
1 TA
53133332 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:53141092 original size:5 final size:5
Alignment explanation
Indices: 53141082--53141148 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
53141072 CTCTTGCCTC
*
53141082 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
*
53141129 TCTTT TC-TT TGTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT T
53141149 TACAAGAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 7 0.14
5 33 0.65
6 6 0.12
7 5 0.10
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:53141124 original size:31 final size:30
Alignment explanation
Indices: 53141082--53141148 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
53141072 CTCTTGCCTC
53141082 TCTTTTCTTTTT-ATTTCGTTTTCTTT-TTCT
1 TCTTTTCTTTTTCATTTC-TTTTCTTTGTT-T
*
53141112 TCTTTTGCTTTTTCTTTTCTTTTCTTTGTTT
1 TCTTTT-CTTTTTCATTTCTTTTCTTTGTTT
53141143 TCTTTT
1 TCTTTT
53141149 TACAAGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 6 0.18
31 21 0.64
32 6 0.18
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (30 bp):
TCTTTTCTTTTTCATTTCTTTTCTTTGTTT
Found at i:53142077 original size:13 final size:12
Alignment explanation
Indices: 53142049--53142103 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
53142039 CATAAATCAC
53142049 TTTTTTTTTGAA
1 TTTTTTTTTGAA
53142061 ---TTTTTTGAA
1 TTTTTTTTTGAA
*
53142070 TTTTTTTTTCAAA
1 TTTTTTTTT-GAA
*
53142083 TTTTTTTTAGAA
1 TTTTTTTTTGAA
53142095 TTTTTTTTT
1 TTTTTTTTT
53142104 CGGTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 9 0.26
12 16 0.46
13 10 0.29
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:53144580 original size:20 final size:20
Alignment explanation
Indices: 53144555--53144621 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
53144545 TTGCTGGTCA
53144555 TTAATACAACTCATCTTAGT
1 TTAATACAACTCATCTTAGT
* * *
53144575 TTAATA-AA-TAAGTTTCTGGT
1 TTAATACAACTCA-TCT-TAGT
53144595 CATTAATACAACTCATCTTAGT
1 --TTAATACAACTCATCTTAGT
53144617 TTAAT
1 TTAAT
53144622 TAAATGAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 14 0.40
22 9 0.26
23 4 0.11
24 2 0.06
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (20 bp):
TTAATACAACTCATCTTAGT
Found at i:53144633 original size:14 final size:14
Alignment explanation
Indices: 53144614--53144658 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53144604 AACTCATCTT
*
53144614 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
53144628 AGTTT-ATTTAATT
1 AGTTTAATTTAATG
*
53144641 AATTTAATTTAATG
1 AGTTTAATTTAATG
53144655 AGTT
1 AGTT
53144659 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53144643 original size:42 final size:42
Alignment explanation
Indices: 53144526--53144632 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
53144516 CATTTAAGCC
*
53144526 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTTCTGGTCATTAATACAACTCA
*
53144568 TCTTAGTTTAATAAATAAGTTTCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTTCTGGTCATTAATACAACTCA
53144610 TCTTAGTTTAATTAAATGAGTTT
1 TCTTAGTTTAA-TAAATGAGTTT
53144633 ATTTAATTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
42 51 0.84
43 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTTCTGGTCATTAATACAACTCA
Found at i:53145838 original size:11 final size:11
Alignment explanation
Indices: 53145824--53145874 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
53145814 CAAGTAAGTT
53145824 TCAAAAAAAAA
1 TCAAAAAAAAA
*
53145835 TCAAAAAAAAT
1 TCAAAAAAAAA
53145846 TCAAAAAAAAA
1 TCAAAAAAAAA
*
53145857 TTGAAAAAAAAA
1 -TCAAAAAAAAA
*
53145869 ACAAAA
1 TCAAAA
53145875 TCTGAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 24 0.71
12 10 0.29
ACGTcount: A:0.78, C:0.08, G:0.02, T:0.12
Consensus pattern (11 bp):
TCAAAAAAAAA
Found at i:53145843 original size:12 final size:12
Alignment explanation
Indices: 53145826--53145874 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
53145816 AGTAAGTTTC
53145826 AAAAAAAAATC-
1 AAAAAAAAATCA
*
53145837 AAAAAAAATTCA
1 AAAAAAAAATCA
* *
53145849 AAAAAAAATTGA
1 AAAAAAAAATCA
53145861 AAAAAAAAA-CA
1 AAAAAAAAATCA
53145872 AAA
1 AAA
53145875 TCTGAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 14 0.42
12 19 0.58
ACGTcount: A:0.82, C:0.06, G:0.02, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATCA
Found at i:53145848 original size:22 final size:23
Alignment explanation
Indices: 53145823--53145867 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
53145813 TCAAGTAAGT
53145823 TTCAAAAAAAAA-TCAAAAAAAA
1 TTCAAAAAAAAATTCAAAAAAAA
*
53145845 TTCAAAAAAAAATTGAAAAAAAA
1 TTCAAAAAAAAATTCAAAAAAAA
53145868 AACAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (23 bp):
TTCAAAAAAAAATTCAAAAAAAA
Found at i:53145863 original size:19 final size:21
Alignment explanation
Indices: 53145841--53145884 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
53145831 AAAATCAAAA
*
53145841 AAAATTCAAAAA-AAAAT-TG
1 AAAATTAAAAAACAAAATCTG
53145860 AAAA--AAAAAACAAAATCTG
1 AAAATTAAAAAACAAAATCTG
53145879 AAAATT
1 AAAATT
53145885 TGAACATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAATTAAAAAACAAAATCTG
Found at i:53149268 original size:19 final size:19
Alignment explanation
Indices: 53149244--53149283 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53149234 AGCTCCCATG
53149244 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
53149263 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
53149282 TA
1 TA
53149284 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:53150546 original size:14 final size:14
Alignment explanation
Indices: 53150524--53150571 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53150514 ACCTAAACCG
* *
53150524 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
53150538 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
53150552 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
53150566 ACCATT
1 ACCATT
53150572 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:53150968 original size:23 final size:23
Alignment explanation
Indices: 53150942--53150992 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
53150932 TATACAAGTT
53150942 AAAAAAAT-AAAAAAAAATTCGAA
1 AAAAAAATCAAAAAAAAA-TCGAA
*
53150965 AAAAAAATCAAAAGAAAATCGAA
1 AAAAAAATCAAAAAAAAATCGAA
53150988 AAAAA
1 AAAAA
53150993 GTGATTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAAAAATCAAAAAAAAATCGAA
Found at i:53150984 original size:11 final size:12
Alignment explanation
Indices: 53150942--53150992 Score: 63
Period size: 11 Copynumber: 4.4 Consensus size: 12
53150932 TATACAAGTT
53150942 AAAAAAAT--AA
1 AAAAAAATCGAA
53150952 AAAAAAATTCGAA
1 AAAAAAA-TCGAA
53150965 AAAAAAATC-AA
1 AAAAAAATCGAA
*
53150976 AAGAAAATCGAA
1 AAAAAAATCGAA
53150988 AAAAA
1 AAAAA
53150993 GTGATTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 7 0.20
11 11 0.31
12 8 0.23
13 9 0.26
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAAATCGAA
Found at i:53161631 original size:23 final size:22
Alignment explanation
Indices: 53161579--53161631 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53161569 TCCATGTCTT
*
53161579 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53161601 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53161624 TTTCTTTT
1 TTTCTTTT
53161632 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53164855 original size:17 final size:18
Alignment explanation
Indices: 53164816--53164857 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53164806 AAGAAGAAAA
53164816 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
53164833 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
53164850 TCAAAAGA
1 ACAAAAGA
53164858 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:53170206 original size:30 final size:30
Alignment explanation
Indices: 53170172--53170268 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
53170162 TAAACTAAAA
53170172 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53170202 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
53170232 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
53170261 ATGAGCTA
1 -TGAGCTA
53170269 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53173720 original size:42 final size:42
Alignment explanation
Indices: 53173661--53173766 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
53173651 CATTTAAGCC
53173661 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
53173703 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
53173745 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
53173767 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:53173768 original size:14 final size:14
Alignment explanation
Indices: 53173749--53173793 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
53173739 AACTCATCTT
*
53173749 AGTTTAATTAAATG
1 AGTTTAATTTAATG
53173763 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
53173776 AATTTAATTTAATG
1 AGTTTAATTTAATG
53173790 AGTT
1 AGTT
53173794 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53175834 original size:15 final size:15
Alignment explanation
Indices: 53175814--53175861 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53175804 TCAAAGATGG
53175814 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53175829 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
53175843 GTTTATGGATATAAA
1 GTTTATGGATATGAA
53175858 GTTT
1 GTTT
53175862 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53175848 original size:14 final size:14
Alignment explanation
Indices: 53175808--53175851 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53175798 AAGGATTCAA
53175808 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53175822 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53175837 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53175851 A
1 A
53175852 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53175877 original size:29 final size:29
Alignment explanation
Indices: 53175808--53175867 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53175798 AAGGATTCAA
*
53175808 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
53175837 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
53175866 AG
1 AG
53175868 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:53176878 original size:14 final size:14
Alignment explanation
Indices: 53176836--53176880 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53176826 TTAAAGAAGC
53176836 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
53176850 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
53176863 AACTCATTTAATTA
1 AACTCATTAAATTA
53176877 AACT
1 AACT
53176881 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:53179364 original size:18 final size:18
Alignment explanation
Indices: 53179343--53179394 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
53179333 TCTTTCTCTC
*
53179343 TCTCAAACTCTTTTTCAA
1 TCTCAATCTCTTTTTCAA
* * *
53179361 TCTCATTTTCTTTTTCAC
1 TCTCAATCTCTTTTTCAA
53179379 TCTCAATCTCTTTTTC
1 TCTCAATCTCTTTTTC
53179395 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTCAATCTCTTTTTCAA
Found at i:53180120 original size:15 final size:15
Alignment explanation
Indices: 53180100--53180147 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53180090 TCAAAGATGG
53180100 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53180115 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
53180129 GTTTATGGATATAAA
1 GTTTATGGATATGAA
53180144 GTTT
1 GTTT
53180148 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53180134 original size:14 final size:14
Alignment explanation
Indices: 53180094--53180137 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53180084 AAGGATTCAA
53180094 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53180108 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53180123 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53180137 A
1 A
53180138 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53180163 original size:29 final size:29
Alignment explanation
Indices: 53180094--53180153 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53180084 AAGGATTCAA
*
53180094 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
53180123 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
53180152 AG
1 AG
53180154 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:53181620 original size:20 final size:20
Alignment explanation
Indices: 53181597--53181644 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53181587 AGCTCCGTCC
53181597 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
53181617 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
53181637 AGCTCAAC
1 AGCTCAAC
53181645 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:53187956 original size:20 final size:21
Alignment explanation
Indices: 53187929--53187982 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
53187919 TTTTTCAATT
*
53187929 TCATTTTTCTTT-TTCTCATTC
1 TCATTTTTCTTTCTT-TCATAC
53187950 TCATTTTTCTTTCTTTCATAC
1 TCATTTTTCTTTCTTTCATAC
53187971 TC-TTTTTCTTTC
1 TCATTTTTCTTTC
53187983 ATTTTTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 10 0.32
21 19 0.61
22 2 0.06
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (21 bp):
TCATTTTTCTTTCTTTCATAC
Found at i:53188597 original size:22 final size:22
Alignment explanation
Indices: 53188567--53188610 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53188557 TTTGGTATTT
53188567 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
53188589 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
53188611 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:53192999 original size:11 final size:11
Alignment explanation
Indices: 53192983--53193008 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53192973 TAGAGAATTA
53192983 AGTTAAAACAT
1 AGTTAAAACAT
53192994 AGTTAAAACAT
1 AGTTAAAACAT
53193005 AGTT
1 AGTT
53193009 TATTGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.31
Consensus pattern (11 bp):
AGTTAAAACAT
Found at i:53196094 original size:23 final size:22
Alignment explanation
Indices: 53196043--53196094 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53196033 CCTCGTCTTT
*
53196043 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53196065 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53196088 TTCTTTT
1 TTCTTTT
53196095 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53199446 original size:23 final size:22
Alignment explanation
Indices: 53199394--53199446 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53199384 TCCACGTCTT
*
53199394 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53199416 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53199439 TTTCTTTT
1 TTTCTTTT
53199447 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53201799 original size:12 final size:13
Alignment explanation
Indices: 53201784--53201812 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53201774 TTTAAACTAG
53201784 TAAATAAAT-AAA
1 TAAATAAATAAAA
53201796 TAAATAAATAAAA
1 TAAATAAATAAAA
53201809 TAAA
1 TAAA
53201813 AATAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:53205578 original size:13 final size:12
Alignment explanation
Indices: 53205560--53205590 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
53205550 ATACAAGTTT
53205560 AAAAAAAATTCGA
1 AAAAAAAATT-GA
53205573 AAAAAAAATTGA
1 AAAAAAAATTGA
53205585 AAAAAA
1 AAAAAA
53205591 GAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:53206173 original size:14 final size:14
Alignment explanation
Indices: 53206154--53206198 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53206144 AACTCATCTT
*
53206154 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
53206168 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
53206181 AATTTAATTTAATG
1 AGTTTAATTTAATG
53206195 AGTT
1 AGTT
53206199 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53212155 original size:29 final size:29
Alignment explanation
Indices: 53212122--53212178 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
53212112 ATAACCAAAC
*
53212122 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
53212151 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
53212179 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:53213133 original size:22 final size:23
Alignment explanation
Indices: 53213102--53213144 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
53213092 TATTTGGGAA
*
53213102 TTGGTTCGAAATGGT-ATGGTAT
1 TTGGTACGAAATGGTAATGGTAT
*
53213124 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGTAATGGT
53213145 TCAAAGAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.33, T:0.40
Consensus pattern (23 bp):
TTGGTACGAAATGGTAATGGTAT
Found at i:53230744 original size:93 final size:93
Alignment explanation
Indices: 53230631--53230802 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
53230621 CGCCCATAAG
* *
53230631 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
53230696 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
53230724 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
53230789 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53230803 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53230799 original size:46 final size:46
Alignment explanation
Indices: 53230624--53230799 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
53230614 TGTAACCCGC
* * *
53230624 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
53230670 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
* *
53230720 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
53230763 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
53230800 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:53235807 original size:20 final size:20
Alignment explanation
Indices: 53235782--53235836 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53235772 TGTGGTTCAA
*
53235782 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53235802 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53235822 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53235837 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53245160 original size:40 final size:40
Alignment explanation
Indices: 53245123--53245346 Score: 242
Period size: 40 Copynumber: 5.6 Consensus size: 40
53245113 GCTACTCGTT
* *
53245123 CAAATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
53245163 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
53245203 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
53245243 CCAATGCCTTCGGG-CTTAGCCTGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * * * *
53245282 TAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
53245323 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
53245347 ACATCATTCA
Statistics
Matches: 155, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 28 0.18
40 112 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:53245301 original size:119 final size:120
Alignment explanation
Indices: 53245090--53245347 Score: 294
Period size: 119 Copynumber: 2.2 Consensus size: 120
53245080 AAATCACGTA
* * * *
53245090 CCTTCGGAATTTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG
1 CCTTCGGGACTTAACCCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCGGATATAG
* *
53245154 TGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTT-GCACAAATG
66 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCACAAA-G
* * * *
53245209 CCTTCGGGACTTAACCCGGATTTAG-TAACTCGTACCAATGCCTTCGGG-CTTAGCCTGGA-ATT
1 CCTTCGGGACTTAACCCGGATATAGCT-ACTCGTACAAATGCCTTCGGGACATAGCCCGGATA-T
* * * * *
53245271 AGTAACTCGCATAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCACAAAG
64 AGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTTAGCACAAAG
*
53245328 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
53245348 CATCATTCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.03
119 79 0.67
120 35 0.30
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (120 bp):
CCTTCGGGACTTAACCCGGATATAGCTACTCGTACAAATGCCTTCGGGACATAGCCCGGATATAG
TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTAGCACAAAG
Found at i:53261081 original size:118 final size:119
Alignment explanation
Indices: 53260838--53261087 Score: 303
Period size: 118 Copynumber: 2.1 Consensus size: 119
53260828 AAATCACGTA
* * ** *
53260838 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGT
1 CCTTCGGGACTTAACCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGT
* * *
53260903 GACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
66 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
* * *
53260957 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGA-ATTA
1 CCTTCGGGACTTAACCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAGCCCGGATA-TA
* * *
53261019 GTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
64 GTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCACAAATG
53261075 CCTTCGGGACTTA
1 CCTTCGGGACTTA
53261088 GCCCGGACAT
Statistics
Matches: 113, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
117 4 0.04
118 62 0.55
119 47 0.42
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
CCTTCGGGACTTAACCGGATATAGCTACTCGCACAAATGCCTTCGGGACATAGCCCGGATATAGT
AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:53261094 original size:40 final size:40
Alignment explanation
Indices: 53260852--53261094 Score: 291
Period size: 40 Copynumber: 6.1 Consensus size: 40
53260842 CGGAATTTAA
** *
53260852 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53260892 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53260932 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTA-A
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
53260971 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
53261010 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
53261050 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
53261090 CCGGA
1 CCGGA
53261095 CATCATTCAA
Statistics
Matches: 178, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
38 6 0.03
39 58 0.33
40 102 0.57
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:53268205 original size:46 final size:46
Alignment explanation
Indices: 53268138--53268312 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
53268128 TGTAACCCGC
*
53268138 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * *
53268184 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
53268234 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
53268277 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
53268313 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:53268253 original size:93 final size:93
Alignment explanation
Indices: 53268145--53268316 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
53268135 CGCCCATAAG
* * *
53268145 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
53268210 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
53268238 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
53268303 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
53268317 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:53269899 original size:30 final size:30
Alignment explanation
Indices: 53269865--53269961 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
53269855 TAAACTAAAA
*
53269865 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
53269895 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
53269925 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
53269955 TGAGCTA
1 TGAGCTA
53269962 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:53271481 original size:30 final size:30
Alignment explanation
Indices: 53271447--53271543 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
53271437 TAAACTAAAA
53271447 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
53271477 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
53271507 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
53271537 TGAGCTA
1 TGAGCTA
53271544 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:53273236 original size:12 final size:12
Alignment explanation
Indices: 53273221--53273251 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53273211 TTATTTTTGC
53273221 TTTTCAAAGGCT
1 TTTTCAAAGGCT
53273233 TTTTCAAAGGCT
1 TTTTCAAAGGCT
53273245 TTTTCAA
1 TTTTCAA
53273252 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:53273309 original size:5 final size:5
Alignment explanation
Indices: 53273299--53273355 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53273289 CTCTTGCCTC
*
53273299 TCTTT TCTTT T-TATT TCTTTT TCTTTT TCTTCT T-TTT CCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTT-T TCTTT TCTTT TCTTT
53273346 TCTTT TCTTT
1 TCTTT TCTTT
53273356 ATTTTCTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 2 0.04
5 30 0.67
6 12 0.27
7 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:53273319 original size:15 final size:15
Alignment explanation
Indices: 53273301--53273362 Score: 72
Period size: 16 Copynumber: 4.0 Consensus size: 15
53273291 CTTGCCTCTC
53273301 TTTTCTTTTTATTTCT
1 TTTTCTTTTT-TTTCT
*
53273317 TTTTCTTTTTCTTCT
1 TTTTCTTTTTTTTCT
53273332 TTTTCCTTTTCTTTTC-
1 TTTT-CTTTT-TTTTCT
*
53273348 TTTTCTTTATTTTCT
1 TTTTCTTTTTTTTCT
53273363 CTTTACAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.12
15 12 0.30
16 19 0.47
17 4 0.10
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:53273365 original size:16 final size:16
Alignment explanation
Indices: 53273297--53273366 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
53273287 GCCTCTTGCC
53273297 TCTCTTTTCTTTTTATT
1 TCTCTTTTC-TTTTATT
53273314 TCT-TTTTCTTTT-TCT
1 TCTCTTTTCTTTTAT-T
*
53273329 TCT-TTTTCCTTTTCTT
1 TCTCTTTT-CTTTTATT
53273345 T-TCTTTTC-TTTATTT
1 TCTCTTTTCTTTTA-TT
53273360 TCTCTTT
1 TCTCTTT
53273367 ACAAGAATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
14 4 0.09
15 17 0.37
16 21 0.46
17 4 0.09
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTCTTTTCTTTTATT
Found at i:53273489 original size:24 final size:24
Alignment explanation
Indices: 53273458--53273508 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
53273448 ACTTCGTGAA
53273458 GAATACTCCGAGTAAGTTTTCTTT
1 GAATACTCCGAGTAAGTTTTCTTT
53273482 GAATACTCCGAGTAAGTTTTCTTT
1 GAATACTCCGAGTAAGTTTTCTTT
53273506 GAA
1 GAA
53273509 GATCTAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (24 bp):
GAATACTCCGAGTAAGTTTTCTTT
Found at i:53275935 original size:30 final size:30
Alignment explanation
Indices: 53275901--53275997 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
53275891 TAAACTAAAA
*
53275901 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
53275931 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* *
53275961 TGAGCTAAGGTTTAGCTCGTAAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
53275991 TGAGCTA
1 TGAGCTA
53275998 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:53276917 original size:5 final size:5
Alignment explanation
Indices: 53276907--53276946 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
53276897 AAATAATTAT
53276907 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
53276947 CCAACATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:53281300 original size:18 final size:17
Alignment explanation
Indices: 53281247--53281301 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
53281237 TGAATAAATT
53281247 ACTCATCTTAGTTAATTGA
1 ACTCATCTTAGTTAA-T-A
**
53281266 GTTCATCTTAGTTAATA
1 ACTCATCTTAGTTAATA
53281283 ACTCATCTTAGATTAATA
1 ACTCATCTTAG-TTAATA
53281301 A
1 A
53281302 ATGAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 8 0.26
19 13 0.42
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCATCTTAGTTAATA
Found at i:53283136 original size:30 final size:30
Alignment explanation
Indices: 53283102--53283189 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
53283092 CTAGCTTATA
53283102 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
53283132 TTCAGCTTAGGAGTTTAATCTCAGCTTAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * *
53283162 TTTAGCTCATGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
53283190 CGAGCTAAAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:53283176 original size:19 final size:19
Alignment explanation
Indices: 53283163--53283209 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
53283153 CAGCTTAACT
53283163 TTAGCTCATGAGCTAAAGC
1 TTAGCTCATGAGCTAAAGC
*
53283182 TTAGCTCACGAGCTAAAGC
1 TTAGCTCATGAGCTAAAGC
53283201 TTAGCTCAT
1 TTAGCTCAT
53283210 TTTAGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (19 bp):
TTAGCTCATGAGCTAAAGC
Found at i:53284848 original size:12 final size:11
Alignment explanation
Indices: 53284831--53284897 Score: 89
Period size: 11 Copynumber: 5.8 Consensus size: 11
53284821 ATACAAGTAT
53284831 AAAAAAAATTC
1 AAAAAAAATTC
53284842 AAAAAAAATTC
1 AAAAAAAATTC
*
53284853 GGAAAAAAATTC
1 -AAAAAAAATTC
*
53284865 GAAAAAAATTC
1 AAAAAAAATTC
53284876 AAAAAAAAGTTTC
1 AAAAAAAA--TTC
53284889 AAAAAAAAT
1 AAAAAAAAT
53284898 GATTTGTGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
11 30 0.59
12 10 0.20
13 11 0.22
ACGTcount: A:0.69, C:0.07, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:53284858 original size:23 final size:22
Alignment explanation
Indices: 53284831--53284897 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 22
53284821 ATACAAGTAT
53284831 AAAAAAAATTCAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAATTC
* *
53284853 GGAAAAAAATTCGAAAAAAATTC
1 -AAAAAAAATTCAAAAAAAATTC
53284876 AAAAAAAAGTTTCAAAAAAAAT
1 AAAAAAAA--TTCAAAAAAAAT
53284898 GATTTGTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 7 0.18
23 20 0.53
24 11 0.29
ACGTcount: A:0.69, C:0.07, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAATTC
Found at i:53285988 original size:14 final size:14
Alignment explanation
Indices: 53285941--53285988 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53285931 GTACGAATGG
*
53285941 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
53285955 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
53285969 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
53285983 ATTGGT
1 AATGGT
53285989 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:53295749 original size:9 final size:10
Alignment explanation
Indices: 53295742--53295798 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
53295732 AAGAGAAAAT
53295742 AAAGAAAAGA
1 AAAGAAAAGA
53295752 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
53295764 AAAGAAGA-A
1 AAAGAAAAGA
53295773 AAAGAAAATGA
1 AAAGAAAA-GA
53295784 AATA-AAAAGA
1 AA-AGAAAAGA
53295794 AAAGA
1 AAAGA
53295799 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:53295766 original size:6 final size:5
Alignment explanation
Indices: 53295742--53295798 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
53295732 AAGAGAAAAT
*
53295742 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
53295789 AAAGA AAAGA
1 AAAGA AAAGA
53295799 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:53295773 original size:15 final size:14
Alignment explanation
Indices: 53295742--53295798 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
53295732 AAGAGAAAAT
53295742 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
53295758 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
53295773 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
53295789 AAAGAAAAGA
1 AAAGAAAAGA
53295799 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:53295875 original size:12 final size:12
Alignment explanation
Indices: 53295867--53295891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53295857 TTTGAAAAGC
53295867 AAAAAGAAAATG
1 AAAAAGAAAATG
53295879 AAAAAGAAAATG
1 AAAAAGAAAATG
53295891 A
1 A
53295892 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:53295888 original size:18 final size:18
Alignment explanation
Indices: 53295861--53295916 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53295851 AAAGCCTTTG
53295861 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
53295880 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
53295898 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
53295915 AA
1 AA
53295917 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:53295901 original size:30 final size:31
Alignment explanation
Indices: 53295867--53295948 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
53295857 TTTGAAAAGC
*
53295867 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
53295897 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
53295927 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
53295949 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:53298222 original size:30 final size:30
Alignment explanation
Indices: 53298188--53298275 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
53298178 CTAACTCATA
53298188 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
53298218 TTCAGCTTAGGAGTTTAATCTCAGCTTAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
53298248 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
53298276 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:53302645 original size:19 final size:19
Alignment explanation
Indices: 53302618--53302669 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
53302608 AATAAATTAC
53302618 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTGAGT
* *
53302637 TCATTTTAGTTTATTGAGT
1 TCATCTTAGTTAATTGAGT
53302656 TCATCTTAGTTAAT
1 TCATCTTAGTTAAT
53302670 AACTCACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (19 bp):
TCATCTTAGTTAATTGAGT
Found at i:53304447 original size:12 final size:12
Alignment explanation
Indices: 53304432--53304494 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
53304422 TCAAGCTCTC
53304432 TTTCAATTTCTT
1 TTTCAATTTCTT
*
53304444 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
53304459 TTTC---TTCTT
1 TTTCAATTTCTT
53304468 TTTCAATTTCTT
1 TTTCAATTTCTT
*
53304480 TTTCAATCTCTT
1 TTTCAATTTCTT
53304492 TTT
1 TTT
53304495 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:53304553 original size:15 final size:14
Alignment explanation
Indices: 53304533--53304580 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
53304523 CTCATTTTCA
53304533 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
53304548 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
53304562 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
53304577 TCTT
1 TCTT
53304581 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:53304585 original size:22 final size:21
Alignment explanation
Indices: 53304533--53304591 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
53304523 CTCATTTTCA
* *
53304533 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
53304554 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
53304575 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
53304592 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:53305519 original size:24 final size:26
Alignment explanation
Indices: 53305482--53305530 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
53305472 CAATCACTCT
53305482 TTTTTTTTTCAATTTAG-ATTTTTTC
1 TTTTTTTTTCAATTTAGAATTTTTTC
*
53305507 TTTTTTTTT-AATTTCGAATTTTTT
1 TTTTTTTTTCAATTTAGAATTTTTT
53305531 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTTTTTTCAATTTAGAATTTTTTC
Found at i:53305541 original size:13 final size:13
Alignment explanation
Indices: 53305525--53305549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53305515 TAATTTCGAA
53305525 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
53305538 TTTTTTTTCTTC
1 TTTTTTTTCTTC
53305550 AATACTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:53305616 original size:12 final size:13
Alignment explanation
Indices: 53305598--53305634 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
53305588 GCTCTTTTTG
53305598 AATTTTTTTTTCA
1 AATTTTTTTTTCA
53305611 AATTTTTTTTTCA
1 AATTTTTTTTTCA
*
53305624 AGTTTTTTTTT
1 AATTTTTTTTT
53305635 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (13 bp):
AATTTTTTTTTCA
Found at i:53307204 original size:82 final size:82
Alignment explanation
Indices: 53307101--53307263 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
53307091 TTTTACTTCC
** * * **
53307101 CTTTAAATACCGTTCCATGCATGGGAACTTCTCCTT-AATGCATGTTTCCTTTTCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
53307165 CCGAATTTCAATGACCTT
66 CCGAA-TTCAATGACCTT
* * **
53307183 CTTTAAATGCCGTTCCTTGCATGTTAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
53307248 CCGAATTCAATGACCT
66 CCGAATTCAATGACCT
53307264 GCAGACACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
82 40 0.57
83 30 0.43
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (82 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
CCGAATTCAATGACCTT
Found at i:53307999 original size:12 final size:11
Alignment explanation
Indices: 53307970--53308026 Score: 64
Period size: 12 Copynumber: 5.1 Consensus size: 11
53307960 GTATTACGGT
53307970 ATTGTAAAAAAA
1 ATTG-AAAAAAA
53307982 A-T-AAAAAAA
1 ATTGAAAAAAA
53307991 ACTTGAAAAAAA
1 A-TTGAAAAAAA
53308003 ATTCGAAAAAAA
1 ATT-GAAAAAAA
*
53308015 ATTCAAAAAAA
1 ATTGAAAAAAA
53308026 A
1 A
53308027 GTTTGTATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 8 0.20
11 12 0.30
12 20 0.50
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:53308085 original size:13 final size:13
Alignment explanation
Indices: 53308067--53308091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53308057 ATTTAGTATT
53308067 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
53308080 GAAGAAAAAAAA
1 GAAGAAAAAAAA
53308092 TTCGGAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:53308113 original size:25 final size:26
Alignment explanation
Indices: 53308074--53308133 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
53308064 ATTGAAGAAA
*
53308074 AAAAAAGAAGAAAAAAAATTCGGAATT-
1 AAAAAA-AAGAAAAAAAATT-GAAATTG
53308101 AAAAAAAAG-AAAAAAATTGAAATTG
1 AAAAAAAAGAAAAAAAATTGAAATTG
53308126 AAAAAAAA
1 AAAAAAAA
53308134 AGAGTGATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 5 0.16
25 17 0.55
26 3 0.10
27 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (26 bp):
AAAAAAAAGAAAAAAAATTGAAATTG
Found at i:53308134 original size:26 final size:26
Alignment explanation
Indices: 53308073--53308136 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
53308063 TATTGAAGAA
*
53308073 AAAAAAAGAAGAAAAAAAATTCGGAATT
1 AAAAAAA-AAG-AAAAAAATTCGAAATT
53308101 -AAAAAAAAGAAAAAAATT-GAAATT
1 AAAAAAAAAGAAAAAAATTCGAAATT
53308125 GAAAAAAAAAGA
1 -AAAAAAAAAGA
53308137 GTGATTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.15
25 9 0.27
26 13 0.39
27 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAATTCGAAATT
Found at i:53309063 original size:21 final size:21
Alignment explanation
Indices: 53309023--53309081 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
53309013 AATCTTGAAT
*
53309023 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
*
53309044 TAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
53309065 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
53309082 TGAAAATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 10 0.31
21 22 0.69
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.08
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:53309137 original size:12 final size:12
Alignment explanation
Indices: 53309120--53309193 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
53309110 AGTGAAAAGC
53309120 AAAAAGAGATTG
1 AAAAAGAGATTG
*
53309132 AAAAAGAAATTG
1 AAAAAGAGATTG
53309144 AAAAAGA-A--G
1 AAAAAGAGATTG
*
53309153 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
53309168 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
53309180 AAAGAGAGCTTG
1 AAAAAGAGATTG
53309192 AA
1 AA
53309194 CAGAAATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:53310881 original size:82 final size:82
Alignment explanation
Indices: 53310722--53310884 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
53310712 TTGTGTCTGC
* * * **
53310722 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGAAGTTAACATGCAA
53310787 GGAACGACATTTAAAGA
66 GGAACGACATTTAAAGA
**
53310804 AGGTCATTGAAATTCGGCTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGAAGTTCCCATGCA
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGAAGTTAACATGCA
* **
53310868 TGGAACGGTATTTAAAG
65 AGGAACGACATTTAAAG
53310885 GGAAGTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
82 39 0.56
83 31 0.44
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGAAGTTAACATGCAA
GGAACGACATTTAAAGA
Found at i:53312148 original size:23 final size:22
Alignment explanation
Indices: 53312097--53312148 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53312087 CCTCGTCTTT
*
53312097 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53312119 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53312142 TTCTTTT
1 TTCTTTT
53312149 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53316347 original size:19 final size:19
Alignment explanation
Indices: 53316302--53316347 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
53316292 ATTAACACAC
*
53316302 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
53316321 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
53316339 AATTAATAA
1 AATTAATAA
53316348 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:53316574 original size:10 final size:10
Alignment explanation
Indices: 53316561--53316597 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
53316551 AAGCTCGGTT
53316561 GAGCTGAAAC
1 GAGCTGAAAC
53316571 GAGCTGAAAC
1 GAGCTGAAAC
* *
53316581 GAGCTCAAAT
1 GAGCTGAAAC
53316591 GAGCTGA
1 GAGCTGA
53316598 GTTGAGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.14
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:53316604 original size:20 final size:20
Alignment explanation
Indices: 53316558--53316605 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
53316548 AGTAAGCTCG
*
53316558 GTTGAGCTGAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
53316578 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
53316598 GTTGAGCT
1 GTTGAGCT
53316606 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:53317101 original size:30 final size:30
Alignment explanation
Indices: 53317006--53317102 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
53316996 AGCTCACTCC
* * *
53317006 TAGCTC-ACTTTCAACTTACGAGCGAAACCT
1 TAGCTCAACTTT-AGCTTACGAGCTAAAGCT
* * **
53317036 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTTACGAGCTAAAG-CT
* *
53317066 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTTACGAGCTAAAGCT
53317096 TAGCTCA
1 TAGCTCA
53317103 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 1 0.02
30 42 0.84
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTTACGAGCTAAAGCT
Found at i:53320619 original size:20 final size:19
Alignment explanation
Indices: 53320596--53320660 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53320586 AAGCTCAAAC
53320596 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53320616 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53320636 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53320656 GAGCT
1 GAGCT
53320661 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53322473 original size:33 final size:33
Alignment explanation
Indices: 53322435--53322497 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
53322425 GATTACTCAC
53322435 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
53322468 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
53322498 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:53322558 original size:21 final size:22
Alignment explanation
Indices: 53322519--53322560 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
53322509 TCGCTTTTTC
53322519 TTTTTCAATTTTTCATTTCTTT
1 TTTTTCAATTTTTCATTTCTTT
*
53322541 TTTTTCAA-TTTTCTTTTCTT
1 TTTTTCAATTTTTCATTTCTT
53322561 CATTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTCAATTTTTCATTTCTTT
Found at i:53322566 original size:21 final size:22
Alignment explanation
Indices: 53322520--53322567 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
53322510 CGCTTTTTCT
**
53322520 TTTTCAATTTTTCATTTCTTTT
1 TTTTCAATTTTTCATTTCTTCA
*
53322542 TTTTCAA-TTTTCTTTTCTTCA
1 TTTTCAATTTTTCATTTCTTCA
53322563 TTTTC
1 TTTTC
53322568 TTTTTCTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTCAATTTTTCATTTCTTCA
Found at i:53322566 original size:22 final size:22
Alignment explanation
Indices: 53322519--53322566 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53322509 TCGCTTTTTC
*
53322519 TTTTTCAATTTTTCATTTCTTT
1 TTTTTCAATTTTTCATTTCTTA
*
53322541 TTTTTCAA-TTTTCTTTTCTTCA
1 TTTTTCAATTTTTCATTTCTT-A
53322563 TTTT
1 TTTT
53322567 CTTTTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTCAATTTTTCATTTCTTA
Found at i:53322573 original size:15 final size:15
Alignment explanation
Indices: 53322530--53322574 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
53322520 TTTTCAATTT
*
53322530 TTCA-TTTCTTTTTT
1 TTCATTTTCTTTTTC
53322544 TTCAATTTTC-TTTTC
1 TTC-ATTTTCTTTTTC
53322559 TTCATTTTCTTTTTC
1 TTCATTTTCTTTTTC
53322574 T
1 T
53322575 CTCACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 9 0.33
15 14 0.52
16 4 0.15
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCATTTTCTTTTTC
Found at i:53322600 original size:18 final size:18
Alignment explanation
Indices: 53322579--53322637 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
53322569 TTTTCTCTCA
53322579 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
53322597 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
53322615 CTTTTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
53322633 GTTTT
1 CTTTT
53322638 CTTTCAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:53322654 original size:6 final size:6
Alignment explanation
Indices: 53322512--53322641 Score: 73
Period size: 6 Copynumber: 20.7 Consensus size: 6
53322502 TCTTTTTTCG
* *
53322512 CTTTTT CTTTTT CAATTTTT CATTTCTT TTTTTT CAATTTT CTTTTCTT
1 CTTTTT CTTTTT C--TTTTT C-TTT-TT CTTTTT C-TTTTT C-TTT-TT
* * ** ** * **
53322561 CATTTT CTTTTT CTCTCA CTTTTT CGATTT CTTTTT CTTTTG CAATTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* *
53322609 CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
53322642 CAATTTCTTT
Statistics
Matches: 91, Mismatches: 27, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
5 4 0.04
6 60 0.66
7 16 0.18
8 11 0.12
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:53323687 original size:20 final size:20
Alignment explanation
Indices: 53323641--53323687 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53323631 AGCTCGTTTC
*
53323641 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
53323661 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
53323681 CAGCTCA
1 CAGCTCA
53323688 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:53326390 original size:48 final size:47
Alignment explanation
Indices: 53326311--53326416 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
53326301 GAGTGTCATG
*
53326311 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
53326359 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
53326407 GAAAAAGAAA
1 GAAAAAGAAA
53326417 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:53328132 original size:20 final size:20
Alignment explanation
Indices: 53328086--53328132 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
53328076 AGCTCGTTTC
*
53328086 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
53328106 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
53328126 CAGCTCA
1 CAGCTCA
53328133 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:53329689 original size:12 final size:12
Alignment explanation
Indices: 53329674--53329698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53329664 TTTTTTTCGA
53329674 TTTTTTTGAATT
1 TTTTTTTGAATT
53329686 TTTTTTTGAATT
1 TTTTTTTGAATT
53329698 T
1 T
53329699 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:53331342 original size:20 final size:19
Alignment explanation
Indices: 53331319--53331383 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53331309 AAGCTCAAAC
53331319 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53331339 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53331359 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53331379 GAGCT
1 GAGCT
53331384 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53331870 original size:22 final size:20
Alignment explanation
Indices: 53331838--53331886 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
53331828 GCCGAATTTA
53331838 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
53331861 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
53331881 TGAACA
1 TGAACA
53331887 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:53334805 original size:30 final size:30
Alignment explanation
Indices: 53334734--53334816 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53334724 CTTTTGTTTC
* *
53334734 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
53334765 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
53334794 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
53334817 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:53334816 original size:18 final size:18
Alignment explanation
Indices: 53334767--53334822 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53334757 CACTCTCAAA
* *
53334767 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
53334784 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
53334802 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
53334821 TT
1 TT
53334823 CAAAGGTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:53334823 original size:12 final size:12
Alignment explanation
Indices: 53334792--53334816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53334782 TTTTTCAATC
53334792 TCATTTTCTTTT
1 TCATTTTCTTTT
53334804 TCATTTTCTTTT
1 TCATTTTCTTTT
53334816 T
1 T
53334817 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:53334895 original size:5 final size:5
Alignment explanation
Indices: 53334885--53334947 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
53334875 CTCTTGCCTC
*
53334885 TCTTT TCTTT T-TATT TCTTTT TCTTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
53334933 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
53334948 ATTTTCTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.58
6 12 0.24
7 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:53334905 original size:15 final size:15
Alignment explanation
Indices: 53334885--53334943 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
53334875 CTCTTGCCTC
53334885 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTATT
*
53334900 TCTTTTTCTTTTTCTT
1 TC-TTTTCTTTTTATT
*
53334916 T-TTCTTCTTTTGCTTTT
1 TCTT-TTCTTTT--TATT
53334933 TCTTTTCTTTT
1 TCTTTTCTTTT
53334944 CTTTATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 13 0.35
17 11 0.30
18 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TCTTTTCTTTTTATT
Found at i:53334907 original size:6 final size:6
Alignment explanation
Indices: 53334898--53334947 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
53334888 TTTCTTTTTA
53334898 TTTCTT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
53334947 T
1 T
53334948 ATTTTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.25
6 19 0.47
7 5 0.12
8 5 0.12
9 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:53334909 original size:21 final size:21
Alignment explanation
Indices: 53334887--53334947 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
53334877 CTTGCCTCTC
53334887 TTTTCTTTTTATTTCTTTTTCT
1 TTTTCTTTTT-TTTCTTTTTCT
* *
53334909 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCTTTTTCT
53334930 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTT-TTTTCTTT
53334948 ATTTTCTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTTTTCTTTTTCT
Found at i:53334926 original size:31 final size:30
Alignment explanation
Indices: 53334889--53334947 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
53334879 TGCCTCTCTT
53334889 TTCTTTT-TATTTCTTTTTCTTTTTCTTTTTC
1 TTCTTTTCTATTTC-TTTTC-TTTTCTTTTTC
*
53334920 TTCTTTTGCTTTTTCTTTTCTTTTCTTT
1 TTCTTTT-CTATTTCTTTTCTTTTCTTT
53334948 ATTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 15 0.60
32 5 0.20
33 5 0.20
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (30 bp):
TTCTTTTCTATTTCTTTTCTTTTCTTTTTC
Found at i:53338364 original size:19 final size:19
Alignment explanation
Indices: 53338340--53338378 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53338330 AATAAATTAC
*
53338340 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
53338359 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
53338378 T
1 T
53338379 GATGGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:53338706 original size:11 final size:11
Alignment explanation
Indices: 53338690--53338714 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53338680 TGTTTGCTTG
53338690 TTTTGAATTTA
1 TTTTGAATTTA
53338701 TTTTGAATTTA
1 TTTTGAATTTA
53338712 TTT
1 TTT
53338715 CGTTTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGAATTTA
Found at i:53341896 original size:10 final size:10
Alignment explanation
Indices: 53341881--53341910 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
53341871 TAAGTATTTG
53341881 AAAAAAATTC
1 AAAAAAATTC
*
53341891 AAAAAAATTA
1 AAAAAAATTC
53341901 AAAAAAATTC
1 AAAAAAATTC
53341911 GTGAATGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:53344820 original size:23 final size:22
Alignment explanation
Indices: 53344768--53344820 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53344758 TCCACGTCTT
*
53344768 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53344790 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53344813 TTTCTTTT
1 TTTCTTTT
53344821 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53355934 original size:18 final size:17
Alignment explanation
Indices: 53355911--53355964 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
53355901 AGCAACTCAT
53355911 TTATTAATCTAAGATGAG
1 TTATTAA-CTAAGATGAG
* *
53355929 TTATTAACTAATATGAAC
1 TTATTAACTAAGATG-AG
*
53355947 TCAATTAACTAAGATGAG
1 T-TATTAACTAAGATGAG
53355965 CAATTTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 7 0.24
18 10 0.34
19 12 0.41
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (17 bp):
TTATTAACTAAGATGAG
Found at i:53355944 original size:17 final size:18
Alignment explanation
Indices: 53355911--53355944 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53355901 AGCAACTCAT
53355911 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
*
53355929 TTATTAA-CTAATATGA
1 TTATTAATCTAAGATGA
53355945 ACTCAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:53359099 original size:26 final size:26
Alignment explanation
Indices: 53359063--53359172 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
53359053 TGATACAAAT
*
53359063 TGATAAAAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53359089 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
53359115 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
53359141 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
53359167 TGATAA
1 TGATAA
53359173 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:53360832 original size:27 final size:27
Alignment explanation
Indices: 53360791--53360903 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
53360781 GAGGAAGCGT
*
53360791 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
53360818 TCTGGTGGCTCTGCCACATATAACTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
53360845 TCTGGTGGCTCTGCCGCGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
53360873 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
53360899 TCTGG
1 TCTGG
53360904 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.07
27 52 0.73
28 14 0.20
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Done.