Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 96 of 310
Found at i:30870198 original size:79 final size:79
Alignment explanation
Indices: 30869964--30870203 Score: 272
Period size: 79 Copynumber: 3.0 Consensus size: 79
30869954 TCAATTTCCA
* * * * *
30869964 TTTTTCAATTTCTACCTTTCAAAAAAAAATCGACTCATATTACGAGAGGTGAGTTGAGCCT-TGG
1 TTTTTCAATTTATATCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
30870028 CTCACGTGCTGAGCTA-
64 -TCACATGCTGAGGTAT
* * * *
30870044 -TTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
1 TTTTTCAATTTATATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
**
30870108 ACACACTGAGGTAT
66 ACATGCTGAGGTAT
* * *
30870122 TTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCAGGTC
1 TTTTTCAATTTATATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
30870187 ACATG-TCGAGGTAT
66 ACATGCT-GAGGTAT
30870201 TTT
1 TTT
30870204 CAAAATCTGT
Statistics
Matches: 135, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
77 47 0.35
78 2 0.01
79 86 0.64
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (79 bp):
TTTTTCAATTTATATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
ACATGCTGAGGTAT
Found at i:30870216 original size:13 final size:14
Alignment explanation
Indices: 30870200--30870235 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30870190 TGTCGAGGTA
30870200 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
*
30870214 TTTTCAAATTCTG-
1 TTTTCAAAATCTGT
30870227 TTTTCAAAA
1 TTTTCAAAA
30870236 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (14 bp):
TTTTCAAAATCTGT
Found at i:30870238 original size:244 final size:239
Alignment explanation
Indices: 30869743--30870342 Score: 708
Period size: 244 Copynumber: 2.5 Consensus size: 239
30869733 GTCTTTCAAA
* * *
30869743 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GCTGAGGTAATTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCT-ATTTCAA
* * * *
30869805 TTTCTATTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
64 TTTCT-GTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGCACACACTG
* **
30869870 AGGTAATTTCAATTTCTATTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTAAGCCTCAG
126 AGGTAATTTCAATTTATATTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAGTTAAGCCTCAG
** *
30869935 GTCACACGTCGAGGTATTTTCAATTTCCATTTTTCAATTTCTACCTTTC
191 GTCACACGTCGAGGTATTTTCAAAATCCATTTTTCAAATTCTACCTTTC
* *
30869984 AAAAAAAAATCGACTCATATTACGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTC
1 ---AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTA-TTTC
*
30870049 AATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACAC
62 AATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG--CACACAC
* * * * *
30870114 TGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGC
124 TGAGGTA--ATTTCAATTTATA-TTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAGTTAAGC
* ** **
30870179 CTCAGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCT-GTTTTC
186 CTCAGGTCACACGTCGAGGTATTTTCAAAATCCATTTTTCAAATTCTACCTTTC
* *
30870232 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTA-TTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTCAATT
***** * *
30870295 TCTGTTTTTTTTTAATTCAACTCATATTGCAAGAGGTGAGTTGAGCTT
66 TCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT
30870343 TTTAATTTCT
Statistics
Matches: 308, Mismatches: 38, Indels: 23
0.83 0.10 0.06
Matches are distributed among these distances:
241 36 0.12
242 11 0.04
243 2 0.01
244 132 0.43
245 2 0.01
246 33 0.11
248 15 0.05
249 77 0.25
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (239 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTCAATT
TCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGCACACACTGAGGTA
ATTTCAATTTATATTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAGTTAAGCCTCAGGTCAC
ACGTCGAGGTATTTTCAAAATCCATTTTTCAAATTCTACCTTTC
Found at i:30871029 original size:15 final size:15
Alignment explanation
Indices: 30871009--30871065 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
30870999 GAGAAAAAAG
30871009 AGCAAAAAAAATTCC
1 AGCAAAAAAAATTCC
30871024 AGCAAAAAAAATTCC
1 AGCAAAAAAAATTCC
** *
30871039 AAAAAAAAAAATTTTC
1 AGCAAAAAAAA-TTCC
30871055 AGCAAAAAAAA
1 AGCAAAAAAAA
30871066 CAAAAAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 24 0.67
16 12 0.33
ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14
Consensus pattern (15 bp):
AGCAAAAAAAATTCC
Found at i:30871074 original size:31 final size:30
Alignment explanation
Indices: 30871012--30871074 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
30871002 AAAAAAGAGC
*
30871012 AAAAAAAATTCCAGCAAAAAAAATTC-CAAAA
1 AAAAAAAATTCCAGCAAAAAAAA--CAAAAAA
* *
30871043 AAAAAAATTTTCAGCAAAAAAAACAAAAAA
1 AAAAAAAATTCCAGCAAAAAAAACAAAAAA
30871073 AA
1 AA
30871075 GGAACATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.04
30 6 0.21
31 21 0.75
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (30 bp):
AAAAAAAATTCCAGCAAAAAAAACAAAAAA
Found at i:30871885 original size:16 final size:17
Alignment explanation
Indices: 30871857--30871888 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30871847 TTTTTATAAC
30871857 TATATTATGTACATATA
1 TATATTATGTACATATA
30871874 TATATT-TGTACATAT
1 TATATTATGTACATAT
30871889 CATTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATTATGTACATATA
Found at i:30872828 original size:3 final size:3
Alignment explanation
Indices: 30872820--30872848 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30872810 TGGTTTCGAC
30872820 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30872849 AGAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30872916 original size:22 final size:22
Alignment explanation
Indices: 30872888--30872937 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
30872878 CAAATTAAAC
30872888 AAAGAAAAGAAAAGAAAAAAAG
1 AAAGAAAAGAAAAGAAAAAAAG
* *
30872910 AAAG-AAAGAAAAGGAAAAAGG
1 AAAGAAAAGAAAAGAAAAAAAG
30872931 AGAAGAA
1 A-AAGAA
30872938 GTGCACGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.67
22 7 0.29
23 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAAAGAAAAAAAG
Found at i:30873217 original size:30 final size:30
Alignment explanation
Indices: 30873182--30873241 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30873172 TTAATTGTTG
*
30873182 ATTTTG-AATAAAAGGGACTAAATTGTAAAA
1 ATTTTGAAATAAAAGGGAC-AAATTGGAAAA
* *
30873212 ATTTTGAAATTAAAGGGTCAAATTGGAAAA
1 ATTTTGAAATAAAAGGGACAAATTGGAAAA
30873242 GAAGTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (30 bp):
ATTTTGAAATAAAAGGGACAAATTGGAAAA
Found at i:30873664 original size:15 final size:16
Alignment explanation
Indices: 30873637--30873666 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30873627 GATTTTGTAT
30873637 ATTATGAAATATATTG
1 ATTATGAAATATATTG
30873653 ATTATG-AATATATT
1 ATTATGAAATATATT
30873667 TGTATTGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
ATTATGAAATATATTG
Found at i:30874288 original size:30 final size:30
Alignment explanation
Indices: 30874240--30874308 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
30874230 TGGCCCAAGA
* *
30874240 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TCAAAATTTGAAGGACTAATAGT
*
30874270 GTAAATATGAAAATTTTGAAGGACTAATAGT
1 GTAAATATCAAAA-TTTGAAGGACTAATAGT
*
30874301 GAAAATAT
1 GTAAATAT
30874309 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.30
Consensus pattern (30 bp):
GTAAATATCAAAATTTGAAGGACTAATAGT
Found at i:30877942 original size:2 final size:2
Alignment explanation
Indices: 30877935--30877987 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
30877925 AAAGTAATCT
30877935 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30877977 TC TC TC TC TC T
1 TC TC TC TC TC T
30877988 TTTTGTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30880642 original size:22 final size:22
Alignment explanation
Indices: 30880574--30880651 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
30880564 ATTGTTTTAT
30880574 TTTTTTATTTTGAAGCAAATAA
1 TTTTTTATTTTGAAGCAAATAA
** * * ** ** *
30880596 AATTATATTTTTAATTATTTTA
1 TTTTTTATTTTGAAGCAAATAA
30880618 TTTTTTATTTTGAAGCAAATAA
1 TTTTTTATTTTGAAGCAAATAA
30880640 TTTTTT-TTTTGA
1 TTTTTTATTTTGA
30880652 GTTTAGACTT
Statistics
Matches: 38, Mismatches: 18, Indels: 1
0.67 0.32 0.02
Matches are distributed among these distances:
21 6 0.16
22 32 0.84
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (22 bp):
TTTTTTATTTTGAAGCAAATAA
Found at i:30912762 original size:41 final size:43
Alignment explanation
Indices: 30912688--30912771 Score: 145
Period size: 41 Copynumber: 2.0 Consensus size: 43
30912678 ACGACATAAA
*
30912688 GCTAATAGTTTGTTCATGTTAAAATTTTGAATTATTTCAGGAC
1 GCTAATAGTTTGTTCATGTTAAAATTTTGAATTATTGCAGGAC
30912731 GCTAATAGTTTG-TCATGTT-AAATTTTGAATTATTGCAGGAC
1 GCTAATAGTTTGTTCATGTTAAAATTTTGAATTATTGCAGGAC
30912772 AAGTGCCCCC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 21 0.52
42 7 0.17
43 12 0.30
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (43 bp):
GCTAATAGTTTGTTCATGTTAAAATTTTGAATTATTGCAGGAC
Found at i:30914451 original size:31 final size:30
Alignment explanation
Indices: 30914409--30914478 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
30914399 ACTTATAATT
* * *
30914409 AGAATTGAATTTTTTTAAATTCAAAAATAGA
1 AGAATTAAATTTTTTAAAAAT-AAAAATAGA
30914440 AGAATTAAA-TTTTTAAAAATAAAAATAGA
1 AGAATTAAATTTTTTAAAAATAAAAATAGA
*
30914469 GGAA-TAAATT
1 AGAATTAAATT
30914479 CTAAATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.12
29 13 0.38
30 9 0.26
31 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (30 bp):
AGAATTAAATTTTTTAAAAATAAAAATAGA
Found at i:30917433 original size:9 final size:8
Alignment explanation
Indices: 30917398--30917467 Score: 50
Period size: 9 Copynumber: 8.0 Consensus size: 8
30917388 TTTTACGTAA
30917398 TATTTATT
1 TATTTATT
*
30917406 CATTCTATT
1 TATT-TATT
*
30917415 TGTTTAATAT
1 TATTT-AT-T
30917425 TATTTATAT
1 TATTTAT-T
* *
30917434 CATGTTATC
1 TAT-TTATT
30917443 TATTTATT
1 TATTTATT
30917451 TAGTTTATT
1 TA-TTTATT
30917460 TATTTATT
1 TATTTATT
30917468 ACTCTAGCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 16 0.33
9 24 0.49
10 9 0.18
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (8 bp):
TATTTATT
Found at i:30917450 original size:4 final size:4
Alignment explanation
Indices: 30917398--30917467 Score: 50
Period size: 4 Copynumber: 16.0 Consensus size: 4
30917388 TTTTACGTAA
* * * *
30917398 TATT TATT CATT CTATT TGTT TAATAT TATT TATAT CATGT TATC TATT
1 TATT TATT TATT -TATT TATT T-AT-T TATT TAT-T TAT-T TATT TATT
30917447 TATT TAGTT TATT TATT TATT
1 TATT TA-TT TATT TATT TATT
30917468 ACTCTAGCAC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
4 34 0.65
5 16 0.31
6 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (4 bp):
TATT
Found at i:30922690 original size:1 final size:1
Alignment explanation
Indices: 30922684--30922753 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
30922674 ATTTCACCTT
* * * * * * * ** *
30922684 AAAAAAATAAAAAGAAAATAAAAAAAATAAAAAAAGAGAAAACAAAAACGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30922749 AAAAA
1 AAAAA
30922754 GAAGAGGTCA
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.03, G:0.07, T:0.04
Consensus pattern (1 bp):
A
Found at i:30922703 original size:11 final size:11
Alignment explanation
Indices: 30922686--30922756 Score: 74
Period size: 11 Copynumber: 6.2 Consensus size: 11
30922676 TTCACCTTAA
30922686 AAAAATAAAAAG
1 AAAAA-AAAAAG
30922698 AAAATAAAAAA-
1 AAAA-AAAAAAG
30922709 AATAAAAAAAGAG
1 AA-AAAAAAA-AG
*
30922722 AAAACAAAAACG
1 AAAA-AAAAAAG
30922734 -AAAAAAAAAG
1 AAAAAAAAAAG
30922744 AAAAAAAAAAG
1 AAAAAAAAAAG
30922755 AA
1 AA
30922757 GAGGTCAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
10 6 0.12
11 22 0.43
12 15 0.29
13 8 0.16
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:30922730 original size:20 final size:20
Alignment explanation
Indices: 30922684--30922751 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
30922674 ATTTCACCTT
*
30922684 AAAAAAATAAAAAGAAAATA
1 AAAAAAATAAAAAGAAAAGA
*
30922704 AAAAAAATAAAAA-AAGAGA
1 AAAAAAATAAAAAGAAAAGA
*
30922723 AAACAAAA-ACGAAAAAAAAAGA
1 AAA-AAAATA--AAAAGAAAAGA
30922745 AAAAAAA
1 AAAAAAA
30922752 AAGAAGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.20
20 17 0.41
21 8 0.20
22 8 0.20
ACGTcount: A:0.85, C:0.03, G:0.07, T:0.04
Consensus pattern (20 bp):
AAAAAAATAAAAAGAAAAGA
Found at i:30922730 original size:24 final size:21
Alignment explanation
Indices: 30922684--30922753 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 21
30922674 ATTTCACCTT
*
30922684 AAAAAAATAAAAAGAAAATAAA
1 AAAAAAAAAAAAAGAAAA-AAA
30922706 AAAAATAAAAAAAGAGAAAACAAA
1 AAAAA-AAAAAAA-AGAAAA-AAA
**
30922730 AACGAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAGAAAAAAA
30922751 AAA
1 AAA
30922754 GAAGAGGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.12
22 11 0.27
23 13 0.32
24 12 0.29
ACGTcount: A:0.86, C:0.03, G:0.07, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAAAGAAAAAAA
Found at i:30922731 original size:35 final size:35
Alignment explanation
Indices: 30922687--30922755 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
30922677 TCACCTTAAA
*
30922687 AAAATAAAAA-GAAAATAAAAA-AAATAAAAAAAGAG
1 AAAACAAAAACGAAAA-AAAAAGAAA-AAAAAAAGAG
30922722 AAAACAAAAACGAAAAAAAAAGAAAAAAAAAAGA
1 AAAACAAAAACGAAAAAAAAAGAAAAAAAAAAGA
30922756 AGAGGTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 23 0.74
36 8 0.26
ACGTcount: A:0.84, C:0.03, G:0.09, T:0.04
Consensus pattern (35 bp):
AAAACAAAAACGAAAAAAAAAGAAAAAAAAAAGAG
Found at i:30923729 original size:44 final size:45
Alignment explanation
Indices: 30923680--30923782 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 45
30923670 CCTGAAGTAG
* * * *
30923680 CAGTGGAGCAGATTGAAG-TTGTAGATCTTATTTTCTTAAAGTTA
1 CAGTGGAGCAGATTGAAGATGGCAGATCTTATCTTCTTAAACTTA
* * * * *
30923724 CAGTGGAGTAGATCGAAGATGGCGGATCTTATCTTCTTGAACTTG
1 CAGTGGAGCAGATTGAAGATGGCAGATCTTATCTTCTTAAACTTA
*
30923769 CAGTGAAGCAGATT
1 CAGTGGAGCAGATT
30923783 AAAGCCACTA
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
44 16 0.35
45 30 0.65
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (45 bp):
CAGTGGAGCAGATTGAAGATGGCAGATCTTATCTTCTTAAACTTA
Found at i:30924007 original size:143 final size:142
Alignment explanation
Indices: 30923743--30924115 Score: 389
Period size: 143 Copynumber: 2.6 Consensus size: 142
30923733 AGATCGAAGA
* * * * *
30923743 TGGCGGATCTTATCTTCTTGAACTTGCAGTGAAGCAGATTAAAGCCACTAGCTTGATCTCCCTGA
1 TGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCTT-ATCTCCCTGA
* * * * *
30923808 AGTTGTAGCGGAGTAGACTGAAGACAGTGAATCTTATTTCCCTGACGTTGTAATGGAACAGATTA
65 AGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTCATTTCCCTGACATTGTAATGGAACAGATTA
* *
30923873 AAGCTTCAAATTG
130 AAGCTACAAACTG
30923886 TGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGA
1 TGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAG-CTTATCTCCCTGA
* * * **
30923951 AGTTACAGCGGAGCATACTGAAGATAGCGAATCTCATTTCCCTGA-ATT-TACTATGGAGTAGAT
65 AGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTCATTTCCCTGACATTGTA--ATGGAACAGAT
* *
30924014 TGAAGCTACAAGCTG
128 TAAAGCTACAAACTG
* * ** * *
30924029 T-G-AG-TCTTATC-TCCTTGAAGTTGCAGTAGGAGCAGACTGAAGATAGCAGATCTTATTTCCC
1 TGGCGGATCTTATCTTCC-TGAAGTTGCAGT-GGAGCAGATTGAAGCCACCAG--CTTATCTCCC
* *
30924090 TGAAGTTGCAGTGGAGCAGATTGAAG
62 TGAAGTTGCAGCGGAGCAGACTGAAG
30924116 CTAAAAGTTG
Statistics
Matches: 194, Mismatches: 30, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
139 3 0.02
140 19 0.10
141 20 0.10
142 34 0.18
143 115 0.59
144 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (142 bp):
TGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCTTATCTCCCTGAA
GTTGCAGCGGAGCAGACTGAAGACAGCGAATCTCATTTCCCTGACATTGTAATGGAACAGATTAA
AGCTACAAACTG
Found at i:30924105 original size:97 final size:96
Alignment explanation
Indices: 30923891--30924255 Score: 389
Period size: 96 Copynumber: 3.9 Consensus size: 96
30923881 AATTGTGGCG
* * *
30923891 GATCTTATCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-A-C--CAGCCTTATCTCCCT
1 GATCTTAT-TTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGCTGGAGTCTTATCTCCTT
* *
30923949 GAAGTTACAG-CGGAGCATACTGAAGATAGC-
65 GAAGTTACAGTAGGAGCAGACTGAAGATAGCA
* * * *
30923979 GAATCTCATTTCCCTGAATTTACTA-TGGAGTAGATTGAAGCTACAAGCTGTGAGTCTTATCTCC
1 G-ATCTTATTTCCCTGAAGTTGC-AGTGGAGCAGATTGAAGCTACAAGCTG-GAGTCTTATCTCC
*
30924043 TTGAAGTTGCAGTAGGAGCAGACTGAAGATAGCA
63 TTGAAGTTACAGTAGGAGCAGACTGAAGATAGCA
* *
30924077 GATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAAAGTTGCGAGTCTTATCTCAC-
1 GATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGCTG-GAGTCTTATCTC-CT
* * *
30924141 TAAAGTTGCAGTAGGAGC-GACTAAAGATAGCA
64 TGAAGTTACAGTAGGAGCAGACTGAAGATAGCA
* * * *
30924173 AATCTTATTTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGTTACGGA-TCTTATTTCCT
1 GATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGCT--GGAGTCTTATCTCCT
30924237 TGAAGTTACAGT-GGAGCAG
64 TGAAGTTACAGTAGGAGCAG
30924256 CTTAAGGCCG
Statistics
Matches: 234, Mismatches: 25, Indels: 28
0.82 0.09 0.10
Matches are distributed among these distances:
88 3 0.01
89 30 0.13
90 1 0.00
91 1 0.00
92 1 0.00
93 1 0.00
95 6 0.03
96 99 0.42
97 89 0.38
98 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (96 bp):
GATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGCTGGAGTCTTATCTCCTTG
AAGTTACAGTAGGAGCAGACTGAAGATAGCA
Found at i:30924291 original size:96 final size:96
Alignment explanation
Indices: 30923986--30924307 Score: 269
Period size: 96 Copynumber: 3.3 Consensus size: 96
30923976 AGCGAATCTC
* * * * * ** *
30923986 ATTTCCCTGAATTTACTA-TGGAGTAGATTGAAGCTACAAGCTGTGAGTCTTATCTC-CTTGAAG
1 ATTTCCCTGAAGTTGC-AGTGGAGCAGATTGAAGCTAAAAGTTACGAGTCTTATCTCAC-TAAAG
* * * * *
30924049 TTGCAGTAGGAGCAGACTGAAGATAGCAGATCTT
64 TTACAGTAGGAGC-GACTAAAGACAGCAAACCTT
*
30924083 ATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAAAGTTGCGAGTCTTATCTCACTAAAGTT
1 ATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAAAGTTACGAGTCTTATCTCACTAAAGTT
* * *
30924148 GCAGTAGGAGCGACTAAAGATAGCAAATCTT
66 ACAGTAGGAGCGACTAAAGACAGCAAACCTT
* * * *
30924179 ATTTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAGTTACG-GATCTTATTTC-CTTGAAG
1 ATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAAAGTTACGAG-TCTTATCTCAC-TAAAG
* * * ** *
30924242 TTACAGT-GGAGC-AGCTTAAGGCCGTTAGCCTT
64 TTACAGTAGGAGCGA-CTAAAGACAGCAAACCTT
* * *
30924274 ATCTCCCTGAAGATTGCAGTAGAACAGATTGAAG
1 ATTTCCCTGAAG-TTGCAGTGGAGCAGATTGAAG
30924308 ATAGTGGATC
Statistics
Matches: 192, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
94 1 0.01
95 27 0.14
96 98 0.51
97 65 0.34
98 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (96 bp):
ATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAAAAGTTACGAGTCTTATCTCACTAAAGTT
ACAGTAGGAGCGACTAAAGACAGCAAACCTT
Found at i:30924668 original size:24 final size:25
Alignment explanation
Indices: 30924616--30924671 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
30924606 AAAACAACAG
*
30924616 GCCCAAAATACAATAAAACCTATGA
1 GCCCAAAATACAATAAAACCTATCA
*
30924641 -CCCAAAATACAA-ACAAA-TTATCA
1 GCCCAAAATACAATA-AAACCTATCA
30924664 GCCCAAAA
1 GCCCAAAA
30924672 ATTAAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.54, C:0.27, G:0.05, T:0.14
Consensus pattern (25 bp):
GCCCAAAATACAATAAAACCTATCA
Found at i:30925024 original size:16 final size:18
Alignment explanation
Indices: 30924988--30925025 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30924978 AAGGTGGTTC
30924988 TTTTTTCTTTGCTCTATT
1 TTTTTTCTTTGCTCTATT
*
30925006 TTTTTTCTTT-CTTTATT
1 TTTTTTCTTTGCTCTATT
30925023 TTT
1 TTT
30925026 ATCTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTTGCTCTATT
Found at i:30926073 original size:9 final size:8
Alignment explanation
Indices: 30926038--30926107 Score: 50
Period size: 9 Copynumber: 8.0 Consensus size: 8
30926028 TTTTACGTAA
30926038 TATTTATT
1 TATTTATT
*
30926046 CATTCTATT
1 TATT-TATT
*
30926055 TGTTTAATAT
1 TATTT-AT-T
30926065 TATTTATAT
1 TATTTAT-T
* *
30926074 CATGTTATC
1 TAT-TTATT
30926083 TATTTATT
1 TATTTATT
30926091 TAGTTTATT
1 TA-TTTATT
30926100 TATTTATT
1 TATTTATT
30926108 ACTCTAGCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 16 0.33
9 24 0.49
10 9 0.18
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (8 bp):
TATTTATT
Found at i:30926090 original size:4 final size:4
Alignment explanation
Indices: 30926038--30926107 Score: 50
Period size: 4 Copynumber: 16.0 Consensus size: 4
30926028 TTTTACGTAA
* * * *
30926038 TATT TATT CATT CTATT TGTT TAATAT TATT TATAT CATGT TATC TATT
1 TATT TATT TATT -TATT TATT T-AT-T TATT TAT-T TAT-T TATT TATT
30926087 TATT TAGTT TATT TATT TATT
1 TATT TA-TT TATT TATT TATT
30926108 ACTCTAGCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
4 34 0.65
5 16 0.31
6 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (4 bp):
TATT
Found at i:30926262 original size:20 final size:20
Alignment explanation
Indices: 30926230--30926280 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
30926220 ATATTACATA
30926230 TATATGATTTATTTATTCATT
1 TATATG-TTTATTTATTCATT
*
30926251 TATATGTTTATTTATTCCTT
1 TATATGTTTATTTATTCATT
*
30926271 TATTTGTTTA
1 TATATGTTTA
30926281 CTATTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (20 bp):
TATATGTTTATTTATTCATT
Found at i:30928529 original size:13 final size:13
Alignment explanation
Indices: 30928511--30928535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30928501 TTCAACAAAA
30928511 ACTATATTAATTG
1 ACTATATTAATTG
30928524 ACTATATTAATT
1 ACTATATTAATT
30928536 AAGTTTTAAT
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
ACTATATTAATTG
Found at i:30929947 original size:17 final size:17
Alignment explanation
Indices: 30929927--30930004 Score: 73
Period size: 17 Copynumber: 5.1 Consensus size: 17
30929917 AGCAGTTGAA
*
30929927 AGATGCAAAATCCAAAT
1 AGATGCAAAATCCAAAC
*
30929944 AGAT--TAAA--CAAAC
1 AGATGCAAAATCCAAAC
30929957 AGATGCAAAATCCAAAC
1 AGATGCAAAATCCAAAC
*
30929974 AGAT--TAAA--CAAAC
1 AGATGCAAAATCCAAAC
30929987 AGATGCAAAATCCAAAC
1 AGATGCAAAATCCAAAC
30930004 A
1 A
30930005 TGAAATATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 17 0.35
15 12 0.25
17 19 0.40
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.14
Consensus pattern (17 bp):
AGATGCAAAATCCAAAC
Found at i:30929960 original size:13 final size:13
Alignment explanation
Indices: 30929939--30929990 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
30929929 ATGCAAAATC
*
30929939 CAAATAGATTAAA
1 CAAACAGATTAAA
*
30929952 CAAACAGATGCAAAA
1 CAAACAGAT--TAAA
30929967 TCCAAACAGATTAAA
1 --CAAACAGATTAAA
30929982 CAAACAGAT
1 CAAACAGAT
30929991 GCAAAATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.53
15 6 0.19
17 9 0.28
ACGTcount: A:0.58, C:0.17, G:0.10, T:0.15
Consensus pattern (13 bp):
CAAACAGATTAAA
Found at i:30929961 original size:30 final size:30
Alignment explanation
Indices: 30929927--30930004 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
30929917 AGCAGTTGAA
*
30929927 AGATGCAAAATCCAAATAGATTAAACAAAC
1 AGATGCAAAATCCAAACAGATTAAACAAAC
30929957 AGATGCAAAATCCAAACAGATTAAACAAAC
1 AGATGCAAAATCCAAACAGATTAAACAAAC
30929987 AGATGCAAAATCCAAACA
1 AGATGCAAAATCCAAACA
30930005 TGAAATATAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.14
Consensus pattern (30 bp):
AGATGCAAAATCCAAACAGATTAAACAAAC
Found at i:30930501 original size:38 final size:38
Alignment explanation
Indices: 30930459--30930534 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
30930449 TCTTTTTGCA
**
30930459 CTGCTTGACCAATTGAAAACTCTCTTTCCCTTTTTCTT
1 CTGCTTGACCAATTGAAAACTCTCTAGCCCTTTTTCTT
30930497 CTGCTTGACCAATTGAAAACTCTCTAGCCCTTTTTCTT
1 CTGCTTGACCAATTGAAAACTCTCTAGCCCTTTTTCTT
30930535 TTACAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.42
Consensus pattern (38 bp):
CTGCTTGACCAATTGAAAACTCTCTAGCCCTTTTTCTT
Found at i:30931560 original size:32 final size:32
Alignment explanation
Indices: 30931507--30931573 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
30931497 AACTCGGTTT
* * *
30931507 AATCGTCAGTTCAATCGGTTTTTAG-TTGATTC
1 AATCATCAATTCAATCAGTTTTTAGCTTG-TTC
30931539 AATCATCAATTCAATCAGTTTTTAGCTTGTTC
1 AATCATCAATTCAATCAGTTTTTAGCTTGTTC
30931571 AAT
1 AAT
30931574 TGTCGGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (32 bp):
AATCATCAATTCAATCAGTTTTTAGCTTGTTC
Found at i:30937839 original size:31 final size:32
Alignment explanation
Indices: 30937774--30937840 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
30937764 AAATTTATCA
*
30937774 TTTTAGATTTTTTAATATATATATATATTTAAT
1 TTTTAGATTTTTTAATATATATATATA-TAAAT
*
30937807 TTTTA-ATTTTTTGAATATATATGTATA-AAAT
1 TTTTAGATTTTTT-AATATATATATATATAAAT
30937838 TTT
1 TTT
30937841 AGAAGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.19
32 7 0.23
33 18 0.58
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (32 bp):
TTTTAGATTTTTTAATATATATATATATAAAT
Found at i:30938663 original size:23 final size:25
Alignment explanation
Indices: 30938637--30938683 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
30938627 TATCATTCAT
*
30938637 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
30938660 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
30938684 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:30939006 original size:46 final size:46
Alignment explanation
Indices: 30938954--30939116 Score: 173
Period size: 46 Copynumber: 3.7 Consensus size: 46
30938944 TGCTATAGTG
* *
30938954 TCTTTCAACTATGGTCTTACTCATTTTC-TATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTC-TTTTCATATCACGTTGCCATGGTA
* *
30939000 TCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCTTTTCATATCACGTTGCCATGGTA
* *
30939046 TCTTTCAACCATGGTCTTA-------CACA-CAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCTTTTCATATCACGTTGCCATGGTA
* * *
30939084 TTTTTCAACCATGGTCTTACACATTTCATATCA
1 TCTTTCAACCATGGTCTTACTCTTTTCATATCA
30939117 GAGAGCACAC
Statistics
Matches: 99, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
38 32 0.32
39 2 0.02
45 8 0.08
46 57 0.58
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACTCTTTTCATATCACGTTGCCATGGTA
Found at i:30939090 original size:38 final size:38
Alignment explanation
Indices: 30939034--30939106 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
30939024 TTCATGTCAC
30939034 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
*
30939072 GTTGCCATGGTATTTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
30939107 TTTCATATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:30940191 original size:11 final size:11
Alignment explanation
Indices: 30940162--30940258 Score: 113
Period size: 11 Copynumber: 8.8 Consensus size: 11
30940152 CCTAGCTCAC
*
30940162 TGCTGTTTTGC
1 TGCTGTTTTGG
* *
30940173 TGCAGTTTGGG
1 TGCTGTTTTGG
30940184 TGCTGTTTTGG
1 TGCTGTTTTGG
*
30940195 TGCTGTTTGGG
1 TGCTGTTTTGG
30940206 TGCTGTTTTGG
1 TGCTGTTTTGG
* *
30940217 TGTTGTTTGGG
1 TGCTGTTTTGG
30940228 TGCTGTTTTGG
1 TGCTGTTTTGG
* *
30940239 TGCTATTTTGC
1 TGCTGTTTTGG
*
30940250 TGCTATTTT
1 TGCTGTTTT
30940259 TTGTCGTGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 73 1.00
ACGTcount: A:0.03, C:0.10, G:0.34, T:0.53
Consensus pattern (11 bp):
TGCTGTTTTGG
Found at i:30940258 original size:22 final size:22
Alignment explanation
Indices: 30940162--30940242 Score: 135
Period size: 22 Copynumber: 3.7 Consensus size: 22
30940152 CCTAGCTCAC
* *
30940162 TGCTGTTTTGCTGCAGTTTGGG
1 TGCTGTTTTGGTGCTGTTTGGG
30940184 TGCTGTTTTGGTGCTGTTTGGG
1 TGCTGTTTTGGTGCTGTTTGGG
*
30940206 TGCTGTTTTGGTGTTGTTTGGG
1 TGCTGTTTTGGTGCTGTTTGGG
30940228 TGCTGTTTTGGTGCT
1 TGCTGTTTTGGTGCT
30940243 ATTTTGCTGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.01, C:0.10, G:0.38, T:0.51
Consensus pattern (22 bp):
TGCTGTTTTGGTGCTGTTTGGG
Found at i:30943862 original size:15 final size:15
Alignment explanation
Indices: 30943843--30943872 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
30943833 TTTTAAAATA
30943843 AAAAAATATATTTTTC
1 AAAAAAT-TATTTTTC
30943859 AAAAAATTATTTTT
1 AAAAAATTATTTTT
30943873 TGTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAAAATTATTTTTC
Found at i:30943873 original size:17 final size:17
Alignment explanation
Indices: 30943841--30943883 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
30943831 ATTTTTAAAA
*
30943841 TAAAAAAATATATTTT-
1 TAAAAAATTATATTTTG
*
30943857 TCAAAAAATTATTTTTTG
1 T-AAAAAATTATATTTTG
30943875 TAAAAAATT
1 TAAAAAATT
30943884 TTGCACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAAAATTATATTTTG
Found at i:30947099 original size:22 final size:22
Alignment explanation
Indices: 30947071--30947118 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
30947061 GAGGATATGT
30947071 GTTTAGGCAATTGGCCAAATTG
1 GTTTAGGCAATTGGCCAAATTG
30947093 GTTTAGGCAATTGGCCAAATTG
1 GTTTAGGCAATTGGCCAAATTG
30947115 GTTT
1 GTTT
30947119 GAGCATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
GTTTAGGCAATTGGCCAAATTG
Found at i:30954018 original size:6 final size:6
Alignment explanation
Indices: 30954007--30954034 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30953997 GTAAAACATA
30954007 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
30954035 AAAGTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:30955181 original size:54 final size:54
Alignment explanation
Indices: 30955123--30955241 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
30955113 TCTTAAACCG
* *
30955123 TGTAACTCACTGAGTTAGGTCACATAGCT-GTGTCGCAGGCCATGTGCCAGACCA
1 TGTAACTCACTGACTTAGGACACAT-GCTCGTGTCGCAGGCCATGTGCCAGACCA
* * * ** * *
30955177 TGTAACTCTCTGACTTATGACACATGGTCGTGTCGCAGGCTGTGTGCTAGACCG
1 TGTAACTCACTGACTTAGGACACATGCTCGTGTCGCAGGCCATGTGCCAGACCA
30955231 TGTAACTCACT
1 TGTAACTCACT
30955242 AAATTGAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.04
54 52 0.96
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (54 bp):
TGTAACTCACTGACTTAGGACACATGCTCGTGTCGCAGGCCATGTGCCAGACCA
Found at i:30956380 original size:31 final size:32
Alignment explanation
Indices: 30956328--30956389 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
30956318 TATTAAGAAG
30956328 TAAATTCCACTCATATTTCA-TTCATCATATGA
1 TAAATTCCACTCATATTTCATTTCAT-ATATGA
30956360 TAAATTCTCA-TCAT-TTTCATTTCATATATG
1 TAAATTC-CACTCATATTTCATTTCATATATG
30956390 CATATCCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 10 0.36
32 16 0.57
33 2 0.07
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.45
Consensus pattern (32 bp):
TAAATTCCACTCATATTTCATTTCATATATGA
Found at i:30961292 original size:26 final size:26
Alignment explanation
Indices: 30961253--30961360 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
30961243 TGGTACAAAT
30961253 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
30961279 TAATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30961305 TGATAATGGGTTAGGTAAATGCTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30961331 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
30961357 TGAT
1 TGAT
30961361 GGACATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:30963810 original size:24 final size:24
Alignment explanation
Indices: 30963783--30963832 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30963773 TAGCTTCCAT
30963783 TCACTTTAACCTATAATGAAATTA
1 TCACTTTAACCTATAATGAAATTA
30963807 TCACTTTAACCTATAATGAAATTA
1 TCACTTTAACCTATAATGAAATTA
30963831 TC
1 TC
30963833 TTTTAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (24 bp):
TCACTTTAACCTATAATGAAATTA
Found at i:30964620 original size:6 final size:7
Alignment explanation
Indices: 30964603--30964627 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30964593 GCCAAAACCC
30964603 AAAAATT
1 AAAAATT
30964610 AAAAATT
1 AAAAATT
30964617 AAAAATT
1 AAAAATT
30964624 AAAA
1 AAAA
30964628 CAAAAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:30973490 original size:33 final size:33
Alignment explanation
Indices: 30973443--30973506 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
30973433 TACTCTCTAA
*
30973443 CTTAATTAAGTAGTAGTATAGAGTAGTAGGGTC
1 CTTAATTAAATAGTAGTATAGAGTAGTAGGGTC
30973476 CTTAATTAAATAGTAGTATAGAGTAGTAGGG
1 CTTAATTAAATAGTAGTATAGAGTAGTAGGG
30973507 CCAATCCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.33
Consensus pattern (33 bp):
CTTAATTAAATAGTAGTATAGAGTAGTAGGGTC
Found at i:30984304 original size:6 final size:6
Alignment explanation
Indices: 30984293--30984317 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30984283 AGGAGTTTTT
30984293 TTTTAG TTTTAG TTTTAG TTTTAG T
1 TTTTAG TTTTAG TTTTAG TTTTAG T
30984318 GTTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTAG
Found at i:30987304 original size:24 final size:26
Alignment explanation
Indices: 30987266--30987313 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
30987256 ATGATTATGT
*
30987266 TAATGCGATATTTTTCA-AAAAATCA
1 TAATGCGAAATTTTTCAGAAAAATCA
30987291 TAATGC-AAATTTTTCAGAAAAAT
1 TAATGCGAAATTTTTCAGAAAAAT
30987314 TTCTATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (26 bp):
TAATGCGAAATTTTTCAGAAAAATCA
Found at i:31002876 original size:18 final size:19
Alignment explanation
Indices: 31002839--31002876 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31002829 TTTGAATGAG
31002839 AGAAGAAAATCTTCTAAAT
1 AGAAGAAAATCTTCTAAAT
* *
31002858 AGAAGCAAAT-TTCTTAAT
1 AGAAGAAAATCTTCTAAAT
31002876 A
1 A
31002877 TTTGTAGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AGAAGAAAATCTTCTAAAT
Found at i:31005213 original size:4 final size:4
Alignment explanation
Indices: 31005204--31005228 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31005194 TTCGTCATTA
31005204 TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT T
31005229 ATATCGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:31006531 original size:42 final size:42
Alignment explanation
Indices: 31006472--31006557 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
31006462 TTATGCTGGA
31006472 AAATTTGAGACTTATTAACTAAGTTCATTACGTATATAATAT
1 AAATTTGAGACTTATTAACTAAGTTCATTACGTATATAATAT
31006514 AAATTTGAGACTTATTAACTAAGTTCATTACGTATATAATAT
1 AAATTTGAGACTTATTAACTAAGTTCATTACGTATATAATAT
31006556 AA
1 AA
31006558 CTTGATTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (42 bp):
AAATTTGAGACTTATTAACTAAGTTCATTACGTATATAATAT
Found at i:31008420 original size:40 final size:40
Alignment explanation
Indices: 31008337--31009279 Score: 1654
Period size: 40 Copynumber: 23.5 Consensus size: 40
31008327 ACCCAAGTAT
* * * * * **
31008337 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAATTTT
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* * * * * **
31008376 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* * * * *
31008416 CTTCGGGACTTAGCCTGGACATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* * *
31008456 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACT--T-GCACAAATGC
31008499 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008539 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008579 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008619 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008659 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008699 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008739 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008779 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008819 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008859 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008899 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008939 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31008979 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009019 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009059 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009099 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009139 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009179 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009219 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31009259 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
31009280 TCATCCGAAT
Statistics
Matches: 874, Mismatches: 26, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
39 11 0.01
40 826 0.95
41 1 0.00
43 36 0.04
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
Found at i:31017338 original size:40 final size:40
Alignment explanation
Indices: 31017210--31018152 Score: 1645
Period size: 40 Copynumber: 23.5 Consensus size: 40
31017200 ACCCAAGTAT
* * * * * *
31017210 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAATTTC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* * * * * ** *
31017249 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATGAATGA
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* * * * * * *
31017289 CTTCAGGACTTATCCCGTACATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
* *
31017329 CTTCGGGACTTAGCCCGGGTATAGTAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACT--T-GCACAAATGC
31017372 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017412 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017452 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017492 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017532 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017572 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017612 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017652 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017692 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017732 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017772 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017812 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017852 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017892 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017932 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31017972 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31018012 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31018052 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31018092 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
31018132 CTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATA
31018153 TCATCCGAAT
Statistics
Matches: 871, Mismatches: 29, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
39 11 0.01
40 822 0.94
41 1 0.00
43 37 0.04
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATACAGTAACTTGCACAAATGC
Found at i:31023434 original size:5 final size:5
Alignment explanation
Indices: 31023424--31023456 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
31023414 TTATTATTGT
31023424 TATTA TATTA TATTA TATTA TA-TA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TAT
31023457 AAAAAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:31025648 original size:46 final size:46
Alignment explanation
Indices: 31025596--31025733 Score: 213
Period size: 46 Copynumber: 3.0 Consensus size: 46
31025586 AGTGTGCTCT
* *
31025596 CTGATATGAAATGTGTAAGGCCGTGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
31025642 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
31025688 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
31025734 GTGACAGAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:31025734 original size:46 final size:46
Alignment explanation
Indices: 31025619--31025749 Score: 201
Period size: 46 Copynumber: 2.8 Consensus size: 46
31025609 TGTAAGGCCG
* * * **
31025619 TGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCA
1 TGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCA
31025665 TGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCA
1 TGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCA
31025711 TGGTTGAAAGATACCATGGCAACGTGACA-GAAAATGAAT
1 TGGTTGAAAGATACCATGGCAACGTGACATGAAAA-GAAT
31025750 GAGTAAGACC
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.06
46 74 0.94
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
TGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCA
Found at i:31027622 original size:18 final size:17
Alignment explanation
Indices: 31027587--31027627 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
31027577 TGATCTGGAG
31027587 TGAAA-TAAAATAAAAT
1 TGAAATTAAAATAAAAT
*
31027603 TGAAATTAAAAGTTAAAT
1 TGAAATTAAAA-TAAAAT
31027621 TGAAATT
1 TGAAATT
31027628 TCAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 5 0.23
18 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (17 bp):
TGAAATTAAAATAAAAT
Found at i:31028372 original size:10 final size:10
Alignment explanation
Indices: 31028345--31028387 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
31028335 TTGAATTCTA
31028345 AAAGATAAAT
1 AAAGATAAAT
31028355 ACAA-ATAAAT
1 A-AAGATAAAT
*
31028365 AAAGATAATT
1 AAAGATAAAT
31028375 AAAGATAAAT
1 AAAGATAAAT
31028385 AAA
1 AAA
31028388 AACAAATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31028468 original size:34 final size:34
Alignment explanation
Indices: 31028428--31028495 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
31028418 ATCCTTAATA
31028428 ATTATCCTAATATAATTAAACATTAAATAGAGTC
1 ATTATCCTAATATAATTAAACATTAAATAGAGTC
31028462 ATTATCCTAATATAATTAAACATTAAATAGAGTC
1 ATTATCCTAATATAATTAAACATTAAATAGAGTC
31028496 TTGTGCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (34 bp):
ATTATCCTAATATAATTAAACATTAAATAGAGTC
Found at i:31034052 original size:20 final size:20
Alignment explanation
Indices: 31034029--31034078 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
31034019 TTAAATTCTA
*
31034029 AAAGATAAATACAA-ATAATT
1 AAAGATAAATA-AATATAAAT
*
31034049 AAAGATAATTAAATATAAAT
1 AAAGATAAATAAATATAAAT
*
31034069 AAAAATAAAT
1 AAAGATAAAT
31034079 CCTAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
AAAGATAAATAAATATAAAT
Found at i:31036218 original size:21 final size:21
Alignment explanation
Indices: 31036193--31036261 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
31036183 TATAATGATT
31036193 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
31036214 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
31036234 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
31036254 ATTATTAT
1 ATTATTAT
31036262 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:31036274 original size:15 final size:14
Alignment explanation
Indices: 31036248--31036278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
31036238 TATGGTTTTA
31036248 TATTAGATTATTAT
1 TATTAGATTATTAT
31036262 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
31036277 TA
1 TA
31036279 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:31036671 original size:12 final size:12
Alignment explanation
Indices: 31036654--31036684 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31036644 GAAGCAGGGG
31036654 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
31036666 AGAAAAAGGGAA
1 AGAAAAAGAGAA
31036678 AGAAAAA
1 AGAAAAA
31036685 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:31048964 original size:22 final size:22
Alignment explanation
Indices: 31048930--31048971 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31048920 TGTGCTTTAG
*
31048930 TCACTTGGCCGTGTGCCTCTCT
1 TCACATGGCCGTGTGCCTCTCT
*
31048952 TCACATGGGCGTGTGCCTCT
1 TCACATGGCCGTGTGCCTCT
31048972 GCCACACGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.33, G:0.26, T:0.33
Consensus pattern (22 bp):
TCACATGGCCGTGTGCCTCTCT
Found at i:31061861 original size:135 final size:135
Alignment explanation
Indices: 31061619--31061888 Score: 513
Period size: 135 Copynumber: 2.0 Consensus size: 135
31061609 TAATTAAGAA
31061619 AGTAAAATTCTTGTATAAACCATGGGAAATAAATTAGATATTCATGCCATGATGTATGGAGTAAT
1 AGTAAAATTCTTGTATAAACCATGGGAAATAAATTAGATATTCATGCCATGATGTATGGAGTAAT
31061684 GTGAGCTAGTGTAAGACATGTCTAGGACAAGTATCGGCCACATTATGAGAGCCAGTGTAAGACCA
66 GTGAGCTAGTGTAAGACATGTCTAGGACAAGTATCGGCCACATTATGAGAGCCAGTGTAAGACCA
31061749 TGTTC
131 TGTTC
*
31061754 AGTAAAATTCTTGTATGAACCATGGGAAATAAATTAGATATTCATGCCATGATGTATGGAGTAAT
1 AGTAAAATTCTTGTATAAACCATGGGAAATAAATTAGATATTCATGCCATGATGTATGGAGTAAT
* *
31061819 GTGAGCTAGTTTAAGACATGTCTAGGACATGTATCGGCCACATTATGAGAGCCAGTGTAAGACCA
66 GTGAGCTAGTGTAAGACATGTCTAGGACAAGTATCGGCCACATTATGAGAGCCAGTGTAAGACCA
31061884 TGTTC
131 TGTTC
31061889 GGGACATAAC
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (135 bp):
AGTAAAATTCTTGTATAAACCATGGGAAATAAATTAGATATTCATGCCATGATGTATGGAGTAAT
GTGAGCTAGTGTAAGACATGTCTAGGACAAGTATCGGCCACATTATGAGAGCCAGTGTAAGACCA
TGTTC
Found at i:31061924 original size:48 final size:46
Alignment explanation
Indices: 31061821--31061988 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 46
31061811 GGAGTAATGT
* * ** * * *
31061821 GAGCTAGTTTAAGACATGTCTAGGACATGTATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGA-GATGA
* *
31061867 GAGCCAGTGTAAGACCATGT-TCGGGACATAACATCAGCAGT-GAGATGA
1 GAGCTAGTGTAAGA-CATGTCT-GGGACAT-ACATCAGC-CTCGAGATGA
* *
31061915 GAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGAGATG-A
31061962 -AGCTAGTGTAAGACATGTCTGGGACAT
1 GAGCTAGTGTAAGACATGTCTGGGACAT
31061989 GCATTGGCTA
Statistics
Matches: 101, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
45 1 0.01
46 52 0.51
47 24 0.24
48 23 0.23
49 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATACATCAGCCTCGAGATGA
Found at i:31061967 original size:46 final size:46
Alignment explanation
Indices: 31061908--31062019 Score: 169
Period size: 46 Copynumber: 2.5 Consensus size: 46
31061898 CATCAGCAGT
31061908 GAGATG-AGAGCTAGTGTAAGACATGTCTGGGACATGCATTAGCCT-C
1 GAGATGTA-AGCTAGTGTAAGACATGTCTGGGACATGCATT-GCCTAC
*
31061954 GAGATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATTGGCTAC
1 GAGATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATTGCCTAC
31062000 GAG-T-TAAGCTAGTGTAAGAC
1 GAGATGTAAGCTAGTGTAAGAC
31062020 CAAGTCCAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
44 16 0.25
45 4 0.06
46 42 0.67
47 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.25
Consensus pattern (46 bp):
GAGATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATTGCCTAC
Found at i:31067218 original size:19 final size:21
Alignment explanation
Indices: 31067172--31067219 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
31067162 TTCTTTATGC
* *
31067172 AATAAAATAAAACATACTTAA
1 AATAACATAAAACATACTCAA
*
31067193 AACAACATAAAA-ATA-TCAA
1 AATAACATAAAACATACTCAA
31067212 AATAACAT
1 AATAACAT
31067220 CAATTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (21 bp):
AATAACATAAAACATACTCAA
Found at i:31069095 original size:30 final size:30
Alignment explanation
Indices: 31069054--31069111 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
31069044 AATTTTTAAA
31069054 ATTTTTAAAAATTCAAAAATATATAAAATT
1 ATTTTTAAAAATTCAAAAATATATAAAATT
* * *
31069084 ATTTTTTAAAATTTAAAAATATTTAAAA
1 ATTTTTAAAAATTCAAAAATATATAAAA
31069112 GTATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
ATTTTTAAAAATTCAAAAATATATAAAATT
Found at i:31069127 original size:40 final size:40
Alignment explanation
Indices: 31069046--31069127 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
31069036 ATTTAATTAA
* * *
31069046 TTTTTAAAATTTTTAAAAATTCAAAAATATATAAAATTAT
1 TTTTTAAAATTTTAAAAAATTCAAAAATATAAAAAAATAT
* *
31069086 TTTTTAAAA-TTTAAAAATATTTAAAAGTATAAAAAAATAT
1 TTTTTAAAATTTTAAAAA-ATTCAAAAATATAAAAAAATAT
31069126 TT
1 TT
31069128 ATAACTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
39 7 0.19
40 29 0.81
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
TTTTTAAAATTTTAAAAAATTCAAAAATATAAAAAAATAT
Found at i:31069128 original size:30 final size:29
Alignment explanation
Indices: 31069094--31069150 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
31069084 ATTTTTTAAA
31069094 ATTTAAAAATATTTAAAAGTATAAAAAAAT
1 ATTTAAAAATATTTAAAA-TATAAAAAAAT
* * * *
31069124 ATTTATAACTTTTTAAAATTTAAAAAA
1 ATTTAAAAATATTTAAAATATAAAAAA
31069151 TTAATGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
ATTTAAAAATATTTAAAATATAAAAAAAT
Found at i:31069141 original size:20 final size:20
Alignment explanation
Indices: 31069094--31069141 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
31069084 ATTTTTTAAA
*
31069094 ATTTAAAAATATTTAAAAGT
1 ATTTAAAAATATTTAAAACT
** *
31069114 ATAAAAAAATATTTATAACT
1 ATTTAAAAATATTTAAAACT
*
31069134 TTTTAAAA
1 ATTTAAAA
31069142 TTTAAAAAAT
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:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAAAATATTTAAAACT
Found at i:31070549 original size:20 final size:19
Alignment explanation
Indices: 31070525--31070583 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
31070515 CATTTTATTT
*
31070525 TTTATTTTTAAATATTTTA
1 TTTATTTTTAAAAATTTTA
*
31070544 TCTTA-TTCTAAAAATTTTCA
1 T-TTATTTTTAAAAATTTT-A
31070564 TTTATTTTTATAAAATTTTA
1 TTTATTTTTA-AAAATTTTA
31070584 AATTAGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 15 0.45
20 10 0.30
21 8 0.24
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTTTTAAAAATTTTA
Found at i:31073685 original size:4 final size:4
Alignment explanation
Indices: 31073639--31073666 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31073629 TTCGAACTTC
31073639 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
31073667 GAAAAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:31077163 original size:3 final size:3
Alignment explanation
Indices: 31077157--31077196 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
31077147 TTCTAAGATT
*
31077157 TTA TTA TTA TTA TTAA TTA TTA -AA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA T
31077197 GGTTCATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 29 0.88
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:31077570 original size:18 final size:18
Alignment explanation
Indices: 31077523--31077573 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
31077513 ATATGTTAAT
* *
31077523 TAAATAAACAAAG-TAAA
1 TAAAGAAACAAAGAAAAA
*
31077540 TAAAGCATA-AAAGAAAAA
1 TAAAG-AAACAAAGAAAAA
31077558 TAAAGAAACAAAGAAA
1 TAAAGAAACAAAGAAA
31077574 CAGAGAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.12
Consensus pattern (18 bp):
TAAAGAAACAAAGAAAAA
Found at i:31079110 original size:23 final size:23
Alignment explanation
Indices: 31079084--31079159 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 23
31079074 AGGCACTTTA
31079084 TGTGTCGTATTTCAAGCACCTCT
1 TGTGTCGTATTTCAAGCACCTCT
*
31079107 TGTGTCGTA--TCAAGCACCTCG
1 TGTGTCGTATTTCAAGCACCTCT
* *
31079128 TGTGTCGT-TTT-AGGCA-CTTT
1 TGTGTCGTATTTCAAGCACCTCT
31079148 ATGTGTCGTATT
1 -TGTGTCGTATT
31079160 CTAATCAGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 31 0.69
22 3 0.07
23 9 0.20
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (23 bp):
TGTGTCGTATTTCAAGCACCTCT
Found at i:31081488 original size:21 final size:23
Alignment explanation
Indices: 31081462--31081506 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
31081452 TAGTTTTAGG
31081462 TTTAA-TTTTCTCTA-AGTTTTC
1 TTTAATTTTTCTCTACAGTTTTC
*
31081483 TTTAATTTTTCTCTACATTTTTC
1 TTTAATTTTTCTCTACAGTTTTC
31081506 T
1 T
31081507 AAGGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.18, C:0.16, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTAATTTTTCTCTACAGTTTTC
Found at i:31081504 original size:12 final size:11
Alignment explanation
Indices: 31081467--31081506 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31081457 TTAGGTTTAA
*
31081467 TTTTCTCTAAG
1 TTTTCTCTAAT
*
31081478 TTTTCTTTAAT
1 TTTTCTCTAAT
31081489 TTTTCTCTACAT
1 TTTTCTCTA-AT
31081501 TTTTCT
1 TTTTCT
31081507 AAGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.15, C:0.17, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTCTCTAAT
Found at i:31089249 original size:28 final size:29
Alignment explanation
Indices: 31089218--31089280 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
31089208 TTTTTTTTAT
* *
31089218 ATTTAGTCTCTATATTTTT-ATTTTCAGA
1 ATTTAGTCTATATATTTTTAATTTTCAAA
* *
31089246 ATTTAGTTTATCTATTTTTCAATTTTCAAA
1 ATTTAGTCTATATATTTTT-AATTTTCAAA
31089276 ATTTA
1 ATTTA
31089281 AATCGAACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 16 0.55
30 13 0.45
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTTAGTCTATATATTTTTAATTTTCAAA
Found at i:31089402 original size:104 final size:102
Alignment explanation
Indices: 31089294--31089511 Score: 235
Period size: 104 Copynumber: 2.1 Consensus size: 102
31089284 CGAACTGTTA
* * *
31089294 ATATATATATATATTAAAGCT-AATGATTTTTATAT-TTTTCAATAAATTTAATCTTCAGATTTT
1 ATATATATATATATTAAAGCTAAAT--TTTTTATATATTTTCAACAAATTTAATCTTCAAAGTTT
* *
31089357 ACACATTCAGTCTCTCTATATATATTTAAAGGTAATGAGTT
64 ACACATTCAGTCTCTC--TATATATTTAAAGCTAATGACTT
* *** * * *
31089398 ATATATA-AGTATATTTATTTTAAATTTTTTATATATTTTTAACAAATTTAGTTTTCAAAGTTTA
1 ATATATATA-TATATTAAAGCTAAATTTTTTATATATTTTCAACAAATTTAATCTTCAAAGTTTA
* **
31089462 CATATTTGGTCTCTCTATATATTTAAAGCTAATGACTT
65 CACATTCAGTCTCTCTATATATTTAAAGCTAATGACTT
31089500 ATATATATATAT
1 ATATATATATAT
31089512 TTCAACGTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
102 31 0.33
103 11 0.12
104 50 0.53
105 3 0.03
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (102 bp):
ATATATATATATATTAAAGCTAAATTTTTTATATATTTTCAACAAATTTAATCTTCAAAGTTTAC
ACATTCAGTCTCTCTATATATTTAAAGCTAATGACTT
Found at i:31089502 original size:102 final size:100
Alignment explanation
Indices: 31089320--31089513 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 100
31089310 AAGCTAATGA
* * *
31089320 TTTTTATATTTTTCAATAAATTTAATCTTCAGATTTTACACATTCAGTCTCTCTATATATATTTA
1 TTTTTATATTTTTCAACAAATTTAATCTTCAAAGTTTACACATTCAGTCTCTC-ATATATATTTA
* *
31089385 AAGGTAATGAGTTATATATAAGTATATTTATTTTAAAT
65 AAGCTAATGACTTATATAT-A-TATATTTATTTTAAAT
* * * * **
31089423 TTTTTATATATTTTTAACAAATTTAGTTTTCAAAGTTTACATATTTGGTCTCTC-TATATATTTA
1 TTTTTATAT-TTTTCAACAAATTTAATCTTCAAAGTTTACACATTCAGTCTCTCATATATATTTA
31089487 AAGCTAATGACTTATATATATATATTT
65 AAGCTAATGACTTATATATATATATTT
31089514 CAACGTTGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
100 7 0.09
101 1 0.01
102 27 0.34
103 9 0.11
104 35 0.44
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.51
Consensus pattern (100 bp):
TTTTTATATTTTTCAACAAATTTAATCTTCAAAGTTTACACATTCAGTCTCTCATATATATTTAA
AGCTAATGACTTATATATATATATTTATTTTAAAT
Found at i:31092031 original size:16 final size:15
Alignment explanation
Indices: 31091991--31092031 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
31091981 TACAGTTATG
31091991 CCCTCATTA-TTTTC
1 CCCTCATTACTTTTC
*
31092005 CCATC-TTACTTTTC
1 CCCTCATTACTTTTC
31092019 CCCTCCATTACTT
1 CCCT-CATTACTT
31092032 CCTTTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.14
14 12 0.55
15 1 0.05
16 6 0.27
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.46
Consensus pattern (15 bp):
CCCTCATTACTTTTC
Found at i:31099536 original size:17 final size:17
Alignment explanation
Indices: 31099516--31099549 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31099506 GATTTCGGAC
31099516 GAGAAAATAATTTAATT
1 GAGAAAATAATTTAATT
* *
31099533 GAGAAATTGATTTAATT
1 GAGAAAATAATTTAATT
31099550 TAATTAATTA
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:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (17 bp):
GAGAAAATAATTTAATT
Found at i:31105887 original size:22 final size:22
Alignment explanation
Indices: 31105862--31105903 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31105852 CATAAAATTA
31105862 AAAAAGAA-AAACGAATCAATAC
1 AAAAAGAATAAA-GAATCAATAC
*
31105884 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
31105904 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATAC
Found at i:31106656 original size:21 final size:23
Alignment explanation
Indices: 31106631--31106687 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
31106621 TCGTGATTAC
*
31106631 TTATAATTTAAA-TT-TGTGAT-A
1 TTATAATTCAAACTTCT-TGATAA
31106652 TTATAATTCAAACTTCTTGATAA
1 TTATAATTCAAACTTCTTGATAA
31106675 TTATAATTCAAAC
1 TTATAATTCAAAC
31106688 ATGAGAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 11 0.34
22 6 0.19
23 15 0.47
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (23 bp):
TTATAATTCAAACTTCTTGATAA
Found at i:31107147 original size:26 final size:29
Alignment explanation
Indices: 31107091--31107151 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
31107081 TCATTATTTT
* *
31107091 ATATTATTTTTTTTTGTTTTTTTAAATAAA
1 ATATTATTTTTTTATGTTTTATT-AATAAA
31107121 ATATTATTTTTTTAT-TTTTATT-A-AAA
1 ATATTATTTTTTTATGTTTTATTAATAAA
31107147 ATATT
1 ATATT
31107152 TAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.28
27 1 0.03
29 6 0.21
30 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
ATATTATTTTTTTATGTTTTATTAATAAA
Found at i:31107474 original size:17 final size:17
Alignment explanation
Indices: 31107452--31107502 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
31107442 TCCTCACACG
*
31107452 GAAGAGAGAAAGGAGAA
1 GAAGAGAGAAAGAAGAA
31107469 GAAGAGA-AGAAGAAGAA
1 GAAGAGAGA-AAGAAGAA
* *
31107486 GAAGAAAGAAAAAAGAA
1 GAAGAGAGAAAGAAGAA
31107503 AAAAAAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAGAGAAAGAAGAA
Found at i:31107482 original size:14 final size:15
Alignment explanation
Indices: 31107452--31107495 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
31107442 TCCTCACACG
*
31107452 GAAG-AGAGAAAGGA
1 GAAGAAGAGAAAGAA
31107466 GAAGAAGAG-AAGAA
1 GAAGAAGAGAAAGAA
31107480 GAAGAAGAAGAAAGAA
1 GAAGAAG-AGAAAGAA
31107496 AAAAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 15 0.58
15 6 0.23
16 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGAAAGAA
Found at i:31107830 original size:23 final size:24
Alignment explanation
Indices: 31107802--31107846 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
31107792 TTTAATTTTC
31107802 AAAA-TTTAAAAAAATAAAAATAA
1 AAAATTTTAAAAAAATAAAAATAA
*
31107825 AAAATTTTCAAAAAATAAAAAT
1 AAAATTTTAAAAAAATAAAAAT
31107847 TGCATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTTTAAAAAAATAAAAATAA
Found at i:31107899 original size:29 final size:29
Alignment explanation
Indices: 31107843--31107962 Score: 109
Period size: 30 Copynumber: 4.1 Consensus size: 29
31107833 CAAAAAATAA
*
31107843 AAATTGCATTTTTACCCCTAAACTTTTCCT
1 AAATTGCATTTTGACCCCTAAAC-TTTCCT
* * *
31107873 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTGCATTTTGACCCCTAAACTTTC-CT
* * *
31107903 AAATTTCACTTAGACCCCTAAACTTTCCTT
1 AAATTGCATTTTGACCCCTAAACTTTCC-T
* * *
31107933 AAATTGCATCTT-AACCCTAAA-TTTTCT
1 AAATTGCATTTTGACCCCTAAACTTTCCT
31107960 AAA
1 AAA
31107963 AATTACATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.05
28 4 0.05
29 12 0.16
30 54 0.73
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATTGCATTTTGACCCCTAAACTTTCCT
Found at i:31109552 original size:45 final size:45
Alignment explanation
Indices: 31109488--31109580 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
31109478 TCGGCTCGTG
31109488 TTAAAAAAGGGACACCCTTTCTAAAAAAACGAAAAATAAAAATTC
1 TTAAAAAAGGGACACCCTTTCTAAAAAAACGAAAAATAAAAATTC
* * *
31109533 TTAAAAACGGGACACCCTTTCTAAAAAATCGAAAACTAAAAATTC
1 TTAAAAAAGGGACACCCTTTCTAAAAAAACGAAAAATAAAAATTC
31109578 TTA
1 TTA
31109581 TTTTTCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.23
Consensus pattern (45 bp):
TTAAAAAAGGGACACCCTTTCTAAAAAAACGAAAAATAAAAATTC
Found at i:31112973 original size:4 final size:4
Alignment explanation
Indices: 31112966--31112993 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31112956 GACATTTATG
31112966 CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT
31112994 GCATATCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:31121422 original size:14 final size:14
Alignment explanation
Indices: 31121403--31121432 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31121393 GCTGAGGTAA
*
31121403 TTTCAATTTATGTT
1 TTTCAATTTATATT
31121417 TTTCAATTTATATT
1 TTTCAATTTATATT
31121431 TT
1 TT
31121433 GCAAAAATCA
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:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:31121660 original size:172 final size:173
Alignment explanation
Indices: 31121356--31121909 Score: 599
Period size: 172 Copynumber: 3.3 Consensus size: 173
31121346 AAAAAAGTCG
31121356 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-TT-TATGTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTAT-TTTT
* * *
31121419 TCAATTTATATTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTG
65 TCAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGTTG
* *
31121484 AGGTATTTTTAATTTCTGTTCTT-AA-TGACTGTTTTT-AAATCA
130 AGGTATTTTCAATTTCCGTTCTTCAATTGA-TGTTTTTAAAATCA
*
31121526 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTTTT
* *
31121591 CCAATCTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGTCTCAGGACACGTTG
66 -CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGTTG
* * *
31121656 AGGTATTTTCGATTTCCGTTTTTCAATTTATGTTTTTCAAAAATCA
130 AGGTATTTTCAATTTCCGTTCTTCAATTGATGTTTTT--AAAATCA
* * * *
31121702 ATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAA-TTC----CTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTTTT
* ** * * * *
31121762 ---T-T-T-TTTT--AAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAA
66 CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGTTGA
**
31121819 GGTATTTTCAATTT-CAATCTTTCAA---A-------AAAATCA
131 GGTATTTTCAATTTCCGTTC-TTCAATTGATGTTTTTAAAATCA
* *
31121852 ACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTATTTTCAATTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTCAATTT
31121910 TTTGCTTTTT
Statistics
Matches: 339, Mismatches: 33, Indels: 41
0.82 0.08 0.10
Matches are distributed among these distances:
150 36 0.11
152 19 0.06
153 2 0.01
159 1 0.00
161 2 0.01
162 60 0.18
164 4 0.01
165 1 0.00
166 1 0.00
167 1 0.00
170 52 0.15
171 10 0.03
172 81 0.24
173 9 0.03
174 2 0.01
175 3 0.01
176 55 0.16
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (173 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTTTT
CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGTTGA
GGTATTTTCAATTTCCGTTCTTCAATTGATGTTTTTAAAATCA
Found at i:31121723 original size:259 final size:252
Alignment explanation
Indices: 31121347--31121833 Score: 672
Period size: 259 Copynumber: 1.9 Consensus size: 252
31121337 TTGTCAAAAA
* *
31121347 AAAAAGTCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAGTCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* *
31121412 ATGTTTTTCAATTTATATTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
66 ACGTTTTTCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
* * * * *
31121477 CACGTTGAGGTATTTTTAATTTCTGTTCTTAATGACTGTTTTTAAA-TCAACTCATATTGCGAGA
131 CACGCTGAGGTAATTTCAA-TTC-CTT-TT--T---T-TTTTAAAAGTCAACTCATATTGCGAGA
** * * *
31121541 GGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTTTCCAATCTATATTTTT
187 AATGAGTTGAGCCTCAAGACACACTAAGGTATTTTCAATTTCTATTTTTTCCAATCTATATTTTT
31121606 C
252 C
* * * *
31121607 AAAAA-TCAACTCATATTGCGAGAGGTGAATTGAGTCTCAGGACACGTTGAGGTATTTTCGATTT
1 AAAAAGTCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
* * * *
31121671 CCGTTTTTCAATTTATGTTTTTCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGA
66 ACGTTTTTCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
31121736 CACGCTGAGGTAATTTCAATTCCTTTTTTTTTTAAAAGTCAACTCATATTGCGAGAAATGAGTTG
131 CACGCTGAGGTAATTTCAATTCCTTTTTTTTTTAAAAGTCAACTCATATTGCGAGAAATGAGTTG
*
31121801 AGCCTCAAGACACATTAAGGTATTTTCAATTTC
196 AGCCTCAAGACACACTAAGGTATTTTCAATTTC
31121834 AATCTTTCAA
Statistics
Matches: 203, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
250 7 0.03
251 55 0.27
254 1 0.00
256 2 0.01
257 2 0.01
258 3 0.01
259 128 0.63
260 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (252 bp):
AAAAAGTCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
ACGTTTTTCAATTTATATTTTGCAAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCAGGA
CACGCTGAGGTAATTTCAATTCCTTTTTTTTTTAAAAGTCAACTCATATTGCGAGAAATGAGTTG
AGCCTCAAGACACACTAAGGTATTTTCAATTTCTATTTTTTCCAATCTATATTTTTC
Found at i:31121765 original size:87 final size:87
Alignment explanation
Indices: 31121347--31121909 Score: 563
Period size: 87 Copynumber: 6.7 Consensus size: 87
31121337 TTGTCAAAAA
* *
31121347 AAAAAGTCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* *
31121412 ATGTTTTTCAATTTATATTTTGC
65 CTGTTTTTCAATTTATATTTTTC
* * *
31121435 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * *
31121500 TGTTCTT-AA-TGACTGTTTTT-
66 TGTTTTTCAATTTA-TATTTTTC
31121520 --AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
31121583 TATTTTTTCCAATCTATATTTTTC
66 T-GTTTTT-CAATTTATATTTTTC
* * * *
31121607 AAAAATCAACTCATATTGCGAGAGGTGAATTGAGTCTCAGGACACGTTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
31121672 CGTTTTTCAATTTATGTTTTTC
66 TGTTTTTCAATTTATATTTTTC
* * * *
31121694 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAA-TTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
31121758 -------C--TTT-T-TTTTTT
66 TGTTTTTCAATTTATATTTTTC
* ** * ** *
31121769 AAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
** *
31121834 AATCTTTC-----A-A------
66 TGTTTTTCAATTTATATTTTTC
*
31121844 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATT
31121909 T
64 T
31121910 TTTGCTTTTT
Statistics
Matches: 401, Mismatches: 54, Indels: 51
0.79 0.11 0.10
Matches are distributed among these distances:
75 91 0.23
76 4 0.01
77 23 0.06
79 1 0.00
83 62 0.15
84 4 0.01
85 2 0.00
86 18 0.04
87 127 0.32
88 10 0.02
89 59 0.15
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAATTTATATTTTTC
Found at i:31121944 original size:78 final size:74
Alignment explanation
Indices: 31121675--31121954 Score: 289
Period size: 75 Copynumber: 3.7 Consensus size: 74
31121665 CGATTTCCGT
* * *
31121675 TTTTCAA-TTTATGTTTTTCAAAA-ATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACA
1 TTTTCAATTTTAT-TTTTTCAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
31121738 CGCTGAGGTA
65 CGCTGAGGTA
* * * ** *
31121748 ATTTCAATTCCTTTTTTTTTTAAAAG-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
1 TTTTCAATT--TTATTTTTTCAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
** *
31121812 ACATTAAGGTA
64 ACGCTGAGGTA
* * * * *
31121823 TTTTCAATTTCAATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCA
1 TTTTCAATTTTATTTTTTC-AAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--A
31121888 CACGCTGAGGTA
63 CACGCTGAGGTA
*
31121900 TTTTCAATTTTTTGCTTTTTCAAAAGATCAACTCATAATT-CGAGAGGTGAGTTGA
1 TTTTCAATTTTAT--TTTTTCAAAAGATCAACTCAT-ATTGCGAGAGGTGAGTTGA
31121955 ACTTCGGGTC
Statistics
Matches: 164, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
73 11 0.07
74 5 0.03
75 89 0.54
76 3 0.02
77 20 0.12
78 28 0.17
79 8 0.05
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (74 bp):
TTTTCAATTTTATTTTTTCAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTA
Found at i:31121980 original size:78 final size:79
Alignment explanation
Indices: 31121675--31121990 Score: 202
Period size: 75 Copynumber: 4.2 Consensus size: 79
31121665 CGATTTCCGT
* * * *
31121675 TTTTCAA-TTTATG-TTTTTC--AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTC-GG-
1 TTTTCAATTTTTTGCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGT
* * *
31121734 GACACGCTGAGGTA
66 CACACGCCGAGCTA
* * * ** * *
31121748 ATTTCAATTCCTTTT--TTTTT--TAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
1 TTTTCAATT--TTTTGCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAG
**** *
31121809 G--ACACATTAAGGTA
64 GTCACACGCCGAGCTA
**
31121823 TTTTCAATTTCAAT-C--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG
1 TTTTCAATTT-TTTGCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGG
* *
31121885 TCACACGCTGAGGTA
65 TCACACGCCGAGCTA
* * *
31121900 TTTTCAATTTTTTGCTTTTTC-AAAAGATCAACTCATAATT-CGAGAGGTGAGTTGAA-CTTCGG
1 TTTTCAATTTTTTGCTTTTTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTT-AAGCCTCAG
*
31121962 GTCGCATC-CCGAGCTA
64 GTCACA-CGCCGAGCTA
31121978 TTTTCAATTTTTT
1 TTTTCAATTTTTT
31121991 TTTTGTTTTT
Statistics
Matches: 195, Mismatches: 31, Indels: 29
0.76 0.12 0.11
Matches are distributed among these distances:
73 10 0.05
74 2 0.01
75 92 0.47
76 5 0.03
77 21 0.11
78 55 0.28
79 10 0.05
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (79 bp):
TTTTCAATTTTTTGCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGT
CACACGCCGAGCTA
Found at i:31122225 original size:30 final size:30
Alignment explanation
Indices: 31122185--31122304 Score: 104
Period size: 30 Copynumber: 4.1 Consensus size: 30
31122175 CAAAAAATAA
31122185 AAATTGCATTTTTACCCCTAAACTTTTCCT
1 AAATTGCATTTTTACCCCTAAACTTTTCCT
* * * **
31122215 AAATTTCATTTTAACCCTTAAACTTTTTTT
1 AAATTGCATTTTTACCCCTAAACTTTTCCT
* * ** *
31122245 AAATTTCACTTAGACCCCAAAAC-TTTCCTT
1 AAATTGCATTTTTACCCCTAAACTTTTCC-T
*
31122275 AAATTGCA-TTTTAACCCTAAA-TTTT-CT
1 AAATTGCATTTTTACCCCTAAACTTTTCCT
31122302 AAA
1 AAA
31122305 AAATACAATT
Statistics
Matches: 71, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
27 4 0.06
28 1 0.01
29 15 0.21
30 51 0.72
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (30 bp):
AAATTGCATTTTTACCCCTAAACTTTTCCT
Found at i:31122551 original size:16 final size:16
Alignment explanation
Indices: 31122527--31122569 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
31122517 GAGAAAAAAG
31122527 AGCAAAAAAAAATT-C
1 AGCAAAAAAAAATTCC
**
31122542 AGCAAAAAAATTTTCC
1 AGCAAAAAAAAATTCC
31122558 AGCAAAAAAAAA
1 AGCAAAAAAAAA
31122570 ACAACAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.65, C:0.14, G:0.07, T:0.14
Consensus pattern (16 bp):
AGCAAAAAAAAATTCC
Found at i:31123381 original size:17 final size:17
Alignment explanation
Indices: 31123323--31123383 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
31123313 TCCGAATTTA
31123323 ATATATATATTTT-T-C
1 ATATATATATTTTGTAC
*
31123338 -TA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
31123354 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
31123371 ATATCAT-TATTTT
1 ATAT-ATATATTTT
31123384 ATATTATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 1 0.03
16 1 0.03
17 23 0.61
18 3 0.08
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:31125388 original size:15 final size:15
Alignment explanation
Indices: 31125368--31125397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31125358 AATAATAATT
31125368 ATAATAGTAAAAATA
1 ATAATAGTAAAAATA
*
31125383 ATAATAGTAATAATA
1 ATAATAGTAAAAATA
31125398 GCTAAGTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATAGTAAAAATA
Found at i:31125509 original size:15 final size:15
Alignment explanation
Indices: 31125489--31125519 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31125479 ATATATATTA
31125489 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
31125504 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
31125519 A
1 A
31125520 GAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:31125803 original size:15 final size:15
Alignment explanation
Indices: 31125783--31125813 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31125773 ATATATATTA
31125783 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
31125798 ATAATAGTAATAAAT
1 ATAATAGTAATAAAT
31125813 A
1 A
31125814 GAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
ATAATAGTAATAAAT
Found at i:31125844 original size:294 final size:294
Alignment explanation
Indices: 31125315--31125901 Score: 1129
Period size: 294 Copynumber: 2.0 Consensus size: 294
31125305 TCAGAAATAA
31125315 AGGAGTAAAACAAACAAGTAATGTAAGAGAATAATAAAAGATTAATAATAATTATAATAGTAAAA
1 AGGAGTAAAACAAACAAGTAATGTAAGAGAATAATAAAAGATTAATAATAATTATAATAGTAAAA
* *
31125380 ATAATAATAGTAATAATAGCTAAGTGAGAAATAGTAACAGTACATTAATAACACAAATAATATAA
66 ATAAAAATAATAATAATAGCTAAGTGAGAAATAGTAACAGTACATTAATAACACAAATAATATAA
31125445 TAATAGTGATAGCACTAAAGAAAAGAAAAGAAAAATATATATTAATAATAGTAATAAATATAATA
131 TAATAGTGATAGCACTAAAGAAAAGAAAAGAAAAATATATATTAATAATAGTAATAAATATAATA
31125510 GTAATAAATAGAAAATAATAGTACATTAATAATAATAGTATATGTTGATATCAATAATGATATAT
196 GTAATAAATAGAAAATAATAGTACATTAATAATAATAGTATATGTTGATATCAATAATGATATAT
*
31125575 ATAAAAAAAGGGAAATAATAATATGGTAAAAAAG
261 ATAAAAAAAAGGAAATAATAATATGGTAAAAAAG
*
31125609 AGGAGTAAAGCAAACAAGTAATGTAAGAGAATAATAAAAGATTAATAATAATTATAATAGTAAAA
1 AGGAGTAAAACAAACAAGTAATGTAAGAGAATAATAAAAGATTAATAATAATTATAATAGTAAAA
*
31125674 ATAAAAATAATAATAATAGCTAAGTGGGAAATAGTAACAGTACATTAATAACACAAATAATATAA
66 ATAAAAATAATAATAATAGCTAAGTGAGAAATAGTAACAGTACATTAATAACACAAATAATATAA
31125739 TAATAGTGATAGCACTAAAGAAAAGAAAAGAAAAATATATATTAATAATAGTAATAAATATAATA
131 TAATAGTGATAGCACTAAAGAAAAGAAAAGAAAAATATATATTAATAATAGTAATAAATATAATA
31125804 GTAATAAATAGAAAATAATAGTACATTAATAATAATAGTATATGTTGATATCAATAATGATATAT
196 GTAATAAATAGAAAATAATAGTACATTAATAATAATAGTATATGTTGATATCAATAATGATATAT
31125869 ATAAAAAAAAGGAAATAATAATATGGTAAAAAA
261 ATAAAAAAAAGGAAATAATAATATGGTAAAAAA
31125902 TATGTTAATA
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
294 288 1.00
ACGTcount: A:0.58, C:0.04, G:0.12, T:0.26
Consensus pattern (294 bp):
AGGAGTAAAACAAACAAGTAATGTAAGAGAATAATAAAAGATTAATAATAATTATAATAGTAAAA
ATAAAAATAATAATAATAGCTAAGTGAGAAATAGTAACAGTACATTAATAACACAAATAATATAA
TAATAGTGATAGCACTAAAGAAAAGAAAAGAAAAATATATATTAATAATAGTAATAAATATAATA
GTAATAAATAGAAAATAATAGTACATTAATAATAATAGTATATGTTGATATCAATAATGATATAT
ATAAAAAAAAGGAAATAATAATATGGTAAAAAAG
Found at i:31125947 original size:5 final size:6
Alignment explanation
Indices: 31125929--31125957 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31125919 CAGTAGTAGT
31125929 AATAAA AATAAA AATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAA
31125958 TAGTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:31125978 original size:33 final size:33
Alignment explanation
Indices: 31125881--31125978 Score: 83
Period size: 33 Copynumber: 3.0 Consensus size: 33
31125871 AAAAAAAAGG
* * *
31125881 AAATAATAAT-ATGGTAA-AAAATATGTTAATAA
1 AAATAAAAATAATAGTAATAAAA-ATATTAATAA
* * * **
31125913 AAATAACAGTAGTAGTAATAAAAATAAAAATAA
1 AAATAAAAATAATAGTAATAAAAATATTAATAA
**
31125946 AAATAAAAATAATAGTAATAATGATATTAATAA
1 AAATAAAAATAATAGTAATAAAAATATTAATAA
31125979 TAGTAATAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
32 8 0.16
33 38 0.76
34 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (33 bp):
AAATAAAAATAATAGTAATAAAAATATTAATAA
Found at i:31126135 original size:3 final size:3
Alignment explanation
Indices: 31126129--31126250 Score: 88
Period size: 3 Copynumber: 40.7 Consensus size: 3
31126119 ATAGTTGTAG
* * * * * * *
31126129 TAA TAA TAA TAG TAA GAA AAA TAG TGA TAA T-A TAA CAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31126176 T-A TAA -AA AAA TAA TAA TAG TAA CTGAGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -T-A-A TAA TAA TAA TAA TAA TAA
* * *
31126222 TAA TGA TAA TAA TGA TAC TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31126251 TAAATAAAAA
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
2 6 0.07
3 80 0.88
4 2 0.02
5 2 0.02
6 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:31126173 original size:20 final size:21
Alignment explanation
Indices: 31126134--31126173 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31126124 TGTAGTAATA
*
31126134 ATAATAGTAAGAAAAATAGTG
1 ATAATAGTAACAAAAATAGTG
*
31126155 ATAATA-TAACAATAATAGT
1 ATAATAGTAACAAAAATAGT
31126174 AATATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (21 bp):
ATAATAGTAACAAAAATAGTG
Found at i:31126256 original size:12 final size:12
Alignment explanation
Indices: 31126205--31126266 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
31126195 TAACTGAGAT
31126205 AATAATAATA-A
1 AATAATAATATA
31126216 TAATAATAATGAT-
1 -AATAATAAT-ATA
*
31126229 AATAATGATACT-
1 AATAATAATA-TA
31126241 AATAATAATATA
1 AATAATAATATA
*
31126253 AATAAAAATATA
1 AATAATAATATA
31126265 AA
1 AA
31126267 CAACAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
11 2 0.05
12 40 0.93
13 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (12 bp):
AATAATAATATA
Found at i:31126740 original size:10 final size:10
Alignment explanation
Indices: 31126725--31126773 Score: 64
Period size: 10 Copynumber: 4.7 Consensus size: 10
31126715 AAGCAAAATC
31126725 AAAAATGAAA
1 AAAAATGAAA
31126735 AAAAATGAAA
1 AAAAATGAAA
31126745 AAAAA-GAAATCA
1 AAAAATG-AA--A
31126757 AAAAATGAAA
1 AAAAATGAAA
31126767 AAAAATG
1 AAAAATG
31126774 TAACCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.03
10 25 0.71
12 8 0.23
13 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:31128158 original size:40 final size:40
Alignment explanation
Indices: 31128075--31128212 Score: 143
Period size: 40 Copynumber: 3.5 Consensus size: 40
31128065 CGTTTAAATG
* * * **
31128075 AAAACGCCGTTAAAAAATGAGCATTAGCGGCGCTTTTCGA
1 AAAACGCCGCTAAAGAATAAGCATTAGCGGCGCTTTTTAA
*
31128115 AAAACACCGCTAAAGAATAAGCATTAGCGGCGCTTTTTAA
1 AAAACGCCGCTAAAGAATAAGCATTAGCGGCGCTTTTTAA
* * * * *
31128155 AAAATGCCGCTATAG-GTACACCTTTAGCGGCGCTTTTTAA
1 AAAACGCCGCTAAAGAATA-AGCATTAGCGGCGCTTTTTAA
* *
31128195 AAAACGCTGCAAAAGAAT
1 AAAACGCCGCTAAAGAAT
31128213 TTTGCAAAAC
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 2 0.03
40 76 0.96
41 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAGAATAAGCATTAGCGGCGCTTTTTAA
Done.