Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 94 of 147
Found at i:17279716 original size:14 final size:15
Alignment explanation
Indices: 17279692--17279725 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
17279682 ATTATTTAAT
17279692 TATACATAAATATTA
1 TATACATAAATATTA
17279707 TATA-ATAAATATTA
1 TATACATAAATATTA
17279721 TATAC
1 TATAC
17279726 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATACATAAATATTA
Found at i:17283886 original size:23 final size:22
Alignment explanation
Indices: 17283860--17283908 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
17283850 AAAAGAAATG
**
17283860 CAAACTCAAGATTCAAAACAGAA
1 CAAACTCAA-ATAAAAAACAGAA
* *
17283883 CAAATTCAAATAAAAAAGAGAA
1 CAAACTCAAATAAAAAACAGAA
17283905 CAAA
1 CAAA
17283909 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.63, C:0.16, G:0.08, T:0.12
Consensus pattern (22 bp):
CAAACTCAAATAAAAAACAGAA
Found at i:17286838 original size:13 final size:14
Alignment explanation
Indices: 17286810--17286838 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17286800 GATTTAAAAT
17286810 TAATTTAATGATTA
1 TAATTTAATGATTA
17286824 TAATTTAAT-ATTA
1 TAATTTAATGATTA
17286837 TA
1 TA
17286839 TTAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TAATTTAATGATTA
Found at i:17286916 original size:16 final size:18
Alignment explanation
Indices: 17286878--17286915 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
17286868 TATACCTTAG
17286878 TTTTATATAAAATAATAT
1 TTTTATATAAAATAATAT
*
17286896 TTTTAT-TAAATTAATAT
1 TTTTATATAAAATAATAT
17286913 TTT
1 TTT
17286916 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATAAAATAATAT
Found at i:17286922 original size:17 final size:17
Alignment explanation
Indices: 17286878--17286923 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
17286868 TATACCTTAG
*
17286878 TTTTATATAAAATAATA
1 TTTTAAATAAAATAATA
* * *
17286895 TTTTTATTAAATTAATA
1 TTTTAAATAAAATAATA
17286912 TTTTAAATAAAA
1 TTTTAAATAAAA
17286924 ATATTAAATA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAATAAAATAATA
Found at i:17288679 original size:20 final size:22
Alignment explanation
Indices: 17288654--17288693 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17288644 ATATGATAAC
*
17288654 TTTTTA-A-TCCATTAATAGAA
1 TTTTTACATTCCACTAATAGAA
17288674 TTTTTACATTCCACTAATAG
1 TTTTTACATTCCACTAATAG
17288694 TAAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTTACATTCCACTAATAGAA
Found at i:17288903 original size:59 final size:58
Alignment explanation
Indices: 17288832--17289003 Score: 245
Period size: 59 Copynumber: 2.9 Consensus size: 58
17288822 TAACTAATTT
* *
17288832 CTTATATTATTATTGCATCTAAATAAGTCATTCAACTCTTATTTTTCATTATCTATGCC
1 CTTATACTATTATTGCATCTAAATAAGTCA-TAAACTCTTATTTTTCATTATCTATGCC
* * * * *
17288891 CTTATACTATTATTGCATCTAAATAACTCCTAAACTTTTATTTTTAATTATCTATGCT
1 CTTATACTATTATTGCATCTAAATAAGTCATAAACTCTTATTTTTCATTATCTATGCC
* *
17288949 TTTATACTATTATTACATCTAAATAAGTTCATAAACTCTTATTTTTCATTATCTA
1 CTTATACTATTATTGCATCTAAATAAG-TCATAAACTCTTATTTTTCATTATCTA
17289004 AGCTCTACTA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 48 0.48
59 51 0.52
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.48
Consensus pattern (58 bp):
CTTATACTATTATTGCATCTAAATAAGTCATAAACTCTTATTTTTCATTATCTATGCC
Found at i:17289199 original size:21 final size:19
Alignment explanation
Indices: 17289162--17289210 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
17289152 GATATCATGA
*
17289162 AAATAATAATTATTAAAACT
1 AAATAAAAATTATTAAAA-T
17289182 GAAATAAAAA-TATATAAAAT
1 -AAATAAAAATTAT-TAAAAT
17289202 AAATAAAAA
1 AAATAAAAA
17289211 AGGAAATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 13 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATAAAAATTATTAAAAT
Found at i:17290669 original size:19 final size:19
Alignment explanation
Indices: 17290629--17290671 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17290619 CTAATAATTA
*
17290629 AATTAAATTAAATTTAAAT
1 AATTAAATTAAATTAAAAT
*
17290648 AATTAAA-TACATTAAAAGT
1 AATTAAATTAAATTAAAA-T
17290667 AATTA
1 AATTA
17290672 TCTATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTAAATTAAATTAAAAT
Found at i:17292348 original size:51 final size:51
Alignment explanation
Indices: 17292247--17292378 Score: 139
Period size: 52 Copynumber: 2.6 Consensus size: 51
17292237 CTAAGAAGAC
**
17292247 ATTTTTAAAAGTTTCAAAGCTTTCGTTCAAGAGGATCCCTTTTCAAATGAG
1 ATTTTTAAAAGTTTCAAAGCTTTCGTTCAAGAGGAAACCTTTTCAAATGAG
* * *
17292298 ATTTTTTAAAAGTTTCAATGGCTTT-GTTTAGGA-GAAACCTTTT-AAGATGAG
1 A-TTTTTAAAAGTTTCAA-AGCTTTCGTTCAAGAGGAAACCTTTTCAA-ATGAG
*
17292349 ATTTTT-AAAGTTTCAAAACTTTTC-TTCAAG
1 ATTTTTAAAAGTTTCAAAGC-TTTCGTTCAAG
17292379 TGTAATTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
48 1 0.01
49 17 0.25
50 7 0.10
51 15 0.22
52 22 0.33
53 5 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (51 bp):
ATTTTTAAAAGTTTCAAAGCTTTCGTTCAAGAGGAAACCTTTTCAAATGAG
Found at i:17297125 original size:31 final size:32
Alignment explanation
Indices: 17297067--17297129 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
17297057 ACACTTTTCC
17297067 TGAAGACTTTGATGATTTTGCTTTGAATTTTT
1 TGAAGACTTTGATGATTTTGCTTTGAATTTTT
*
17297099 TGAAGACTTT-AT-ATTTTTTCTTTGAATTTTT
1 TGAAGACTTTGATGA-TTTTGCTTTGAATTTTT
17297130 GTGTTTAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.03
31 18 0.62
32 10 0.34
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.57
Consensus pattern (32 bp):
TGAAGACTTTGATGATTTTGCTTTGAATTTTT
Found at i:17297493 original size:2 final size:2
Alignment explanation
Indices: 17297486--17297516 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17297476 GTAATTAGTT
17297486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17297517 CAGTTTACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17300201 original size:2 final size:2
Alignment explanation
Indices: 17300182--17300223 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
17300172 CCATCTGTCT
* *
17300182 TA TA TT TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17300224 GCCATCTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17318011 original size:18 final size:18
Alignment explanation
Indices: 17317978--17318012 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17317968 ACCGTAAGTC
*
17317978 TCCTCTACCGCTTCCACA
1 TCCTCTACCGCGTCCACA
*
17317996 TCCTCTACCTCGTCCAC
1 TCCTCTACCGCGTCCAC
17318013 CATGTCCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.51, G:0.06, T:0.29
Consensus pattern (18 bp):
TCCTCTACCGCGTCCACA
Found at i:17321399 original size:73 final size:72
Alignment explanation
Indices: 17321317--17321459 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 72
17321307 ACAACATGTA
* * * * * * *
17321317 ATATTTTCAACAAAGATTGTATTTTTATCTTAAAAATATCCTTTTTATTAAATTTTGAGAAATAA
1 ATATTTTCAACAAAGACTGCAATTTTATCTT-AAAACATCATCTTTATTAAATTTTGACAAATAA
*
17321382 TTTTTTTT
65 ATTTTTTT
*
17321390 ATATTTTCAACAAAGACTGCAATTTTATCTTAAAACATCATCTTTATTGAATTTTGACAAATAAA
1 ATATTTTCAACAAAGACTGCAATTTTATCTTAAAACATCATCTTTATTAAATTTTGACAAATAAA
17321455 TTTTT
66 TTTTT
17321460 CATAATATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 33 0.54
73 28 0.46
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (72 bp):
ATATTTTCAACAAAGACTGCAATTTTATCTTAAAACATCATCTTTATTAAATTTTGACAAATAAA
TTTTTTT
Found at i:17330640 original size:16 final size:17
Alignment explanation
Indices: 17330613--17330644 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17330603 TATAAAATAT
17330613 TTTTATTATTTATTTAA
1 TTTTATTATTTATTTAA
17330630 TTTTA-TATTTATTTA
1 TTTTATTATTTATTTA
17330645 TATTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTATTTATTTAA
Found at i:17330712 original size:22 final size:20
Alignment explanation
Indices: 17330687--17330729 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
17330677 ATTTTTAATT
17330687 TAATAAAAAGATTATATTTATA
1 TAATAAAAAGA-TA-ATTTATA
* *
17330709 TAATTAAAATATAATTTATA
1 TAATAAAAAGATAATTTATA
17330729 T
1 T
17330730 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATAAAAAGATAATTTATA
Found at i:17332456 original size:47 final size:47
Alignment explanation
Indices: 17332381--17332471 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
17332371 AATCTTCAGG
* *
17332381 TAATCCTTTTTCTAAACTTTTGTATATCATTTTAAAACCATATTTCT
1 TAATCCTTTTTCTAAACCTTCGTATATCATTTTAAAACCATATTTCT
* * *
17332428 TAATCTTTTTTCTAGACCTTCGTGTATCATTTTAAAACCATATT
1 TAATCCTTTTTCTAAACCTTCGTATATCATTTTAAAACCATATT
17332472 CTTTTCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (47 bp):
TAATCCTTTTTCTAAACCTTCGTATATCATTTTAAAACCATATTTCT
Found at i:17336597 original size:57 final size:55
Alignment explanation
Indices: 17336503--17336887 Score: 418
Period size: 57 Copynumber: 6.7 Consensus size: 55
17336493 TTTGTGCAAG
* * **
17336503 GAAAATTGATACTTTCAACTTTTTCCT-AAAATATTTTTTGGAAACTTTAATTTCGAA
1 GAAAATTGATACTTTCAAC-TTTTCCTCAAAA-ATTTTTTTGAAAATTT-ATTTTTAA
*
17336560 GAAAATTGATACTTTTAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAA-TTTTTTTGAAAATTTATTTTTAA
** * *
17336616 GGAAAATTGATACTTTCAACTTTTTCC-C-AAAATATTTTTAAAAAATTTATATTTGAG
1 -GAAAATTGATACTTTCAAC-TTTTCCTCAAAAAT-TTTTTTGAAAATTTAT-TTTTAA
* * * * *
17336673 GAAAATTGATACTTTCAATTTTTTCTCAAAATTTTTTTTAAAAATTTATCTTTAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAAATTTATTTTTAA
*
17336728 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTAGAAAATTTATTTTTAA
1 -GAAAATTGATACTTTCAAC-TTTTCCTCAAAAAT-TTTTTTGAAAATTTATTTTTAA
17336785 GAAAAATTGATACTTTCAACTTTTCCTCAAAGAAAAACCTTTTTTTGAAAATTTATTTTTAAA
1 G-AAAATTGATACTTTCAACTTTTCCTC----AAAAA--TTTTTTTGAAAATTTATTTTT-AA
*
17336848 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAAT-TTTTTT
17336888 TTGGATTTTG
Statistics
Matches: 282, Mismatches: 25, Indels: 42
0.81 0.07 0.12
Matches are distributed among these distances:
55 9 0.03
56 98 0.35
57 111 0.39
58 11 0.04
61 5 0.02
62 44 0.16
63 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (55 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGAAAATTTATTTTTAA
Found at i:17336680 original size:56 final size:56
Alignment explanation
Indices: 17336500--17336887 Score: 451
Period size: 56 Copynumber: 6.8 Consensus size: 56
17336490 TTTTTTGTGC
* * **
17336500 AAGGAAAATTGATACTTTCAACTTTTTCCTAAAATATTTTTTGGAAACTTTAATTTCG
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTT-GAAAATTT-ATTTTT
*
17336558 AA-GAAAATTGATACTTTTAAC-TTTTCCTCAAAA-ACTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCC-CAAAATA--TTTTTTGAAAATTTATTTTT
** *
17336614 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTAAAAAATTTATATTT
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTGAAAATTTATTTTT
* * * * * *
17336670 GAGGAAAATTGATACTTTCAATTTTTTCTCAAAATTTTTTTTAAAAATTTATCTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTGAAAATTTATTTTT
*
17336726 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTTTGAAAATTTATTTTT
* *
17336783 AAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAGAAAAACCTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCC-C--A-AAATA---TTTTTTGAAAATTTATTTTT
* *
17336845 AAAGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTTT
17336888 TTGGATTTTG
Statistics
Matches: 287, Mismatches: 29, Indels: 29
0.83 0.08 0.08
Matches are distributed among these distances:
56 113 0.39
57 102 0.36
58 17 0.06
59 4 0.01
60 4 0.01
61 2 0.01
62 40 0.14
63 5 0.02
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (56 bp):
AAGGAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTGAAAATTTATTTTT
Found at i:17336774 original size:113 final size:114
Alignment explanation
Indices: 17336500--17336886 Score: 539
Period size: 113 Copynumber: 3.4 Consensus size: 114
17336490 TTTTTTGTGC
* * * *
17336500 AAGGAAAATTGATACTTTCAACTTTTT-CCTAAAATATTTTTTGGAAACTTTA-ATTTCGAAGAA
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTAGAAAATTTATATTT-GAGGAA
*
17336563 AATTGATACTTTTAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
64 AATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
*
17336614 AAGGAAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTTAAAAAATTTATATTTGAGGAAAA
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATATTTGAGGAAAA
* * * * *
17336678 TTGATACTTTCAATTTTTTCTC-AAAATTTTTTTTAAAAATTTATCTTT
66 TTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
* * *
17336726 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATTTTTAAGAAAAA
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATATTTGAGGAAAA
17336791 TTGATACTTTCAACTTTTCCTCAAAGAAAAACCTTTTTTTGAAAATTTATTTTT
66 TTGATACTTTCAACTTTTCCTC----AAAAA-CTTTTTTTGAAAATTTATTTTT
* *
17336845 AAAGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTT
17336887 TTTGGATTTT
Statistics
Matches: 243, Mismatches: 21, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
112 53 0.22
113 88 0.36
114 37 0.15
115 2 0.01
118 4 0.02
119 59 0.24
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (114 bp):
AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATATTTGAGGAAAA
TTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
Found at i:17336915 original size:5 final size:5
Alignment explanation
Indices: 17336905--17337008 Score: 77
Period size: 5 Copynumber: 19.8 Consensus size: 5
17336895 TTGTTTAAAG
*
17336905 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* * * * *
17336955 AAAAAG AAAAGT AAAACA AAAAT AAAAAT AAAAAT AAAAG AATAT TAAAT
1 -AAAAT AAAA-T AAAA-T AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT
17337005 AAAA
1 AAAA
17337009 CTAATCTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
3 3 0.04
5 47 0.59
6 25 0.32
7 4 0.05
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:17336938 original size:17 final size:16
Alignment explanation
Indices: 17336917--17336987 Score: 72
Period size: 17 Copynumber: 4.3 Consensus size: 16
17336907 AATAAAATAA
17336917 TAAAACAAAATAAAAG
1 TAAAACAAAATAAAAG
*
17336933 TGAAAATAAAATAAAA-
1 T-AAAACAAAATAAAAG
* *
17336949 TAAAATAAAAAGAAAAG
1 TAAAA-CAAAATAAAAG
*
17336966 TAAAACAAAAATAAAAA
1 TAAAAC-AAAATAAAAG
17336983 TAAAA
1 TAAAA
17336988 ATAAAAGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.09
16 10 0.22
17 31 0.69
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
TAAAACAAAATAAAAG
Found at i:17336945 original size:27 final size:27
Alignment explanation
Indices: 17336915--17336994 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
17336905 AAAATAAAAT
*
17336915 AATAAAACAAAATAAAAGTGAAAA-TAA
1 AATAAAACAAAATAAAA-AGAAAAGTAA
*
17336942 AATAAAATAAAATAAAAAGAAAAGTAA
1 AATAAAACAAAATAAAAAGAAAAGTAA
* * *
17336969 AACAAAAATAAAAATAAAAATAAAAG
1 AA-TAAAA-CAAAATAAAAAGAAAAG
17336995 AATATTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 5 0.11
27 21 0.47
28 4 0.09
29 15 0.33
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (27 bp):
AATAAAACAAAATAAAAAGAAAAGTAA
Found at i:17336964 original size:6 final size:6
Alignment explanation
Indices: 17336905--17336993 Score: 73
Period size: 6 Copynumber: 15.5 Consensus size: 6
17336895 TTGTTTAAAG
* *
17336905 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTG AAAAT- AAAAT- AAAAT-
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
17336950 AAAATA AAAAGA AAAGT- AAAACA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
17336994 GAATATTAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
5 23 0.33
6 41 0.59
7 5 0.07
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:17336980 original size:23 final size:23
Alignment explanation
Indices: 17336940--17336993 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
17336930 AAGTGAAAAT
*
17336940 AAAATAAAA-TAAAATAAAAAGA
1 AAAATAAAACAAAAATAAAAAGA
* *
17336962 AAAGTAAAACAAAAATAAAAATA
1 AAAATAAAACAAAAATAAAAAGA
17336985 AAAATAAAA
1 AAAATAAAA
17336994 GAATATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAATAAAACAAAAATAAAAAGA
Found at i:17336993 original size:17 final size:16
Alignment explanation
Indices: 17336905--17336993 Score: 81
Period size: 18 Copynumber: 5.2 Consensus size: 16
17336895 TTGTTTAAAG
*
17336905 AAAATAAAATAATAAAA
1 AAAATAAAATAA-AATA
17336922 CAAAATAAAAGTGAAAAT-
1 -AAAATAAAA-T-AAAATA
17336940 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
17336956 AAAAGAAAAGTAAAACA
1 AAAATAAAA-TAAAATA
17336973 AAAATAAAAATAAAAATA
1 AAAAT-AAAAT-AAAATA
17336991 AAA
1 AAA
17336994 GAATATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.08
16 9 0.15
17 20 0.33
18 21 0.35
19 3 0.05
20 2 0.03
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:17337593 original size:16 final size:17
Alignment explanation
Indices: 17337572--17337605 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
17337562 AAAATTTTCT
17337572 AAAAATTTT-CAGAAAA
1 AAAAATTTTACAGAAAA
17337588 AAAAATTTTACAGAAAA
1 AAAAATTTTACAGAAAA
17337605 A
1 A
17337606 TCTCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAAATTTTACAGAAAA
Found at i:17338088 original size:6 final size:6
Alignment explanation
Indices: 17338055--17338170 Score: 66
Period size: 6 Copynumber: 19.5 Consensus size: 6
17338045 TAGTAGTAAT
* * * *
17338055 AAATAA ATAATAA ATACAT-A AGATAA AAAT-A AAAGAA AAATAC ATAT-A
1 AAATAA A-AATAA A-A-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * *
17338103 AAA-AA TAATAA TAATAA AAATAA AAAT-A AAAT-A AAATAA AAATGTA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA
17338149 AAATACA AAA-ATA AAATAA AAA
1 AAATA-A AAATA-A AAATAA AAA
17338171 AGAAAATAGA
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
5 21 0.24
6 44 0.51
7 20 0.23
8 2 0.02
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:17338090 original size:13 final size:12
Alignment explanation
Indices: 17338055--17338170 Score: 66
Period size: 11 Copynumber: 9.8 Consensus size: 12
17338045 TAGTAGTAAT
17338055 AAATAAATAATAA
1 AAATAAA-AATAA
*
17338068 ATACAT-AAGATAA
1 A-A-ATAAAAATAA
*
17338081 AAAT-AAAAGAA
1 AAATAAAAATAA
* *
17338092 AAATACATAT-A
1 AAATAAAAATAA
*
17338103 AAA-AATAATAA
1 AAATAAAAATAA
*
17338114 TAATAAAAATAA
1 AAATAAAAATAA
17338126 AAAT-AAAAT-A
1 AAATAAAAATAA
*
17338136 AAATAAAAATGTA
1 AAATAAAAAT-AA
17338149 AAATACAAAA-ATA
1 AAATA-AAAATA-A
17338162 AAATAAAAA
1 AAATAAAAA
17338171 AGAAAATAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 21
0.70 0.11 0.18
Matches are distributed among these distances:
10 8 0.10
11 28 0.35
12 17 0.21
13 18 0.22
14 7 0.09
15 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:17338109 original size:39 final size:38
Alignment explanation
Indices: 17338055--17338169 Score: 107
Period size: 39 Copynumber: 3.1 Consensus size: 38
17338045 TAGTAGTAAT
* *
17338055 AAAT-AAATAATAAATACATAA-GATAAAAATAAAAGA-A
1 AAATAAAATAAAAAATA-ATAATAATAAAAATAAAA-ATA
*
17338092 AAATACATATAAAAAATAATAATAATAAAAATAAAAATA
1 AAATA-AAATAAAAAATAATAATAATAAAAATAAAAATA
* *
17338131 AAATAAAATAAAAATGTAA-AAT-ACAAAAAT-AAAATA
1 AAATAAAATAAAAA-ATAATAATAATAAAAATAAAAATA
17338167 AAA
1 AAA
17338170 AAGAAAATAG
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
36 9 0.13
37 11 0.16
38 16 0.24
39 31 0.46
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (38 bp):
AAATAAAATAAAAAATAATAATAATAAAAATAAAAATA
Found at i:17338123 original size:15 final size:15
Alignment explanation
Indices: 17338077--17338169 Score: 71
Period size: 15 Copynumber: 6.1 Consensus size: 15
17338067 AATACATAAG
17338077 ATAAAAATAAAAGAAA
1 ATAAAAATAAAA-AAA
* * *
17338093 A-ATACATATAAAAA
1 ATAAAAATAAAAAAA
* *
17338107 ATAATAATAATAAAA
1 ATAAAAATAAAAAAA
17338122 ATAAAAATAAAATAAA
1 ATAAAAATAAAA-AAA
** *
17338138 ATAAAAATGTAAAAT
1 ATAAAAATAAAAAAA
*
17338153 ACAAAAATAAAATAAA
1 ATAAAAATAAAA-AAA
17338169 A
1 A
17338170 AAGAAAATAG
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
14 4 0.07
15 36 0.63
16 17 0.30
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (15 bp):
ATAAAAATAAAAAAA
Found at i:17338159 original size:26 final size:25
Alignment explanation
Indices: 17338130--17338178 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
17338120 AAATAAAAAT
*
17338130 AAAATAAAATAAAAATGTAAAATACA
1 AAAATAAAATAAAAAAG-AAAATACA
17338156 AAAATAAAATAAAAAAGAAAATA
1 AAAATAAAATAAAAAAGAAAATA
17338179 GACTTACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAAATAAAAAAGAAAATACA
Found at i:17338171 original size:13 final size:13
Alignment explanation
Indices: 17338080--17338171 Score: 73
Period size: 13 Copynumber: 6.8 Consensus size: 13
17338070 ACATAAGATA
17338080 AAAATAAAAGAAA-
1 AAAATAAAA-AAAT
17338093 AATACATATAAAAAAT
1 AA-A-ATA-AAAAAAT
17338109 AATAATAATAAAAAT
1 AA-AATAA-AAAAAT
*
17338124 -AAA-AATAAAAT
1 AAAATAAAAAAAT
**
17338135 AAAATAAAAATGT
1 AAAATAAAAAAAT
*
17338148 AAAATACAAAAAT
1 AAAATAAAAAAAT
17338161 AAAATAAAAAA
1 AAAATAAAAAA
17338172 GAAAATAGAC
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
11 5 0.08
12 5 0.08
13 29 0.45
14 3 0.05
15 15 0.23
16 7 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:17338500 original size:85 final size:87
Alignment explanation
Indices: 17338345--17338513 Score: 243
Period size: 85 Copynumber: 2.0 Consensus size: 87
17338335 AGATTTGGTC
* * * * *
17338345 AAAACTCCTCTAAGCAGAGGCTCAACTACTTCAAAAAATGTAAATAAAGCTCTTTTAATCAGAGG
1 AAAACTCCCCTAAGCAGAGGCTCAACGACTTCAAAAAA-GTAAATAAAGCTCCTCTAATCAAAGG
17338410 CTCAACAACTTT-AAAAATGAAT
65 CTCAACAACTTTGAAAAATGAAT
** *
17338432 AAAACTCCCCTATTCAGAGGCTCAACGACTTTAAAAAA-TAAATAAAGCTCCTCTAATCAAAGGC
1 AAAACTCCCCTAAGCAGAGGCTCAACGACTTCAAAAAAGTAAATAAAGCTCCTCTAATCAAAGGC
17338496 TCAACAACTTTGAAAAAT
66 TCAACAACTTTGAAAAAT
17338514 AAACAAAGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
85 34 0.47
86 6 0.08
87 33 0.45
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (87 bp):
AAAACTCCCCTAAGCAGAGGCTCAACGACTTCAAAAAAGTAAATAAAGCTCCTCTAATCAAAGGC
TCAACAACTTTGAAAAATGAAT
Found at i:17338538 original size:43 final size:43
Alignment explanation
Indices: 17338349--17338530 Score: 222
Period size: 43 Copynumber: 4.2 Consensus size: 43
17338339 TTGGTCAAAA
* * *
17338349 CTCCTCTAAGCAGAGGCTCAACTACTTCAAAAAATGTAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTAAAAAA--TAAATAAAG
* * * *
17338394 CTCTTTTAATCAGAGGCTCAACAACTTT-AAAAATGAATAAAA
1 CTCCTCTAATCAGAGGCTCAACAACTTTAAAAAATAAATAAAG
* * *
17338436 CTCCCCTATTCAGAGGCTCAACGACTTTAAAAAATAAATAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTAAAAAATAAATAAAG
* * *
17338479 CTCCTCTAATCAAAGGCTCAACAACTTTGAAAAATAAACAAAG
1 CTCCTCTAATCAGAGGCTCAACAACTTTAAAAAATAAATAAAG
17338522 CTCCTCTAA
1 CTCCTCTAA
17338531 ACAAAGGCAA
Statistics
Matches: 116, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 30 0.26
43 58 0.50
44 5 0.04
45 23 0.20
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (43 bp):
CTCCTCTAATCAGAGGCTCAACAACTTTAAAAAATAAATAAAG
Found at i:17338652 original size:41 final size:41
Alignment explanation
Indices: 17338583--17338856 Score: 309
Period size: 41 Copynumber: 6.7 Consensus size: 41
17338573 TTTGATCAAT
* * *
17338583 GCTCTTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAATG
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
* *
17338624 GCTCCTCTAACCAGAGGCTCGACGACTTTGGAAAAATAAATG
1 GCTCCTCTAAACAGAGGCTCAACGACTTT-GAAAAATAAATG
* *
17338666 GCTCCTCTAATCAGAGG-TCAACGACTTTGGAAAATAAATG
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
* * * *
17338706 GCTCATCTAATCAGAGGCTCAACGAC-TCGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
* * * * * * *
17338746 GCTCCTCTAAATAGAGGCACCATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
* * * *
17338787 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
* *
17338828 GCTCCTCTAAACAGAGGCACCACGACTTT
1 GCTCCTCTAAACAGAGGCTCAACGACTTT
17338857 TGGAAAGTAA
Statistics
Matches: 207, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
40 58 0.28
41 121 0.58
42 28 0.14
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATG
Found at i:17338812 original size:122 final size:122
Alignment explanation
Indices: 17338583--17338854 Score: 325
Period size: 122 Copynumber: 2.2 Consensus size: 122
17338573 TTTGATCAAT
* * * * * * *
17338583 GCTCTTCTAAGCAGAGGCTCAACAACTTTGAAAAATAAATGGCTCCTCTAACCAGAGGCTCGACG
1 GCTCATCTAAACAGAGGCTCAACGAC-TCGAAAAATAAATGGCTCCTCTAAACAGAGGCACCACG
*
17338648 ACTTTGGAAAAATAAATGGCTCCTCTAATCAGAGGTCAACGACTTTGGAAAA-TAAATG
65 ACTTTGGAAAAATAAATGGCTCCTCTAAACAGAGGTCAACGACTTT-GAAAAGTAAATG
* * * *
17338706 GCTCATCTAATCAGAGGCTCAACGACTCGAAAAATAAATTGCTCCTCTAAATAGAGGCACCATGA
1 GCTCATCTAAACAGAGGCTCAACGACTCGAAAAATAAATGGCTCCTCTAAACAGAGGCACCACGA
* * *
17338771 CTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGG-CACCACGACTTTGAAAAGTAAATT
66 CTTTGGAAAAATAAATGGCTCCTCTAAACAGAGGTCA--ACGACTTTGAAAAGTAAATG
* * *
17338828 GCTCCTCTAAACAGAGGCACCACGACT
1 GCTCATCTAAACAGAGGCTCAACGACT
17338855 TTTGGAAAGT
Statistics
Matches: 128, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
120 2 0.02
121 29 0.23
122 74 0.58
123 23 0.18
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (122 bp):
GCTCATCTAAACAGAGGCTCAACGACTCGAAAAATAAATGGCTCCTCTAAACAGAGGCACCACGA
CTTTGGAAAAATAAATGGCTCCTCTAAACAGAGGTCAACGACTTTGAAAAGTAAATG
Found at i:17339895 original size:13 final size:14
Alignment explanation
Indices: 17339879--17339907 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17339869 TCATTTTTCA
17339879 TTCACTTTTT-TTT
1 TTCACTTTTTATTT
17339892 TTCACTTTTTATTT
1 TTCACTTTTTATTT
17339906 TT
1 TT
17339908 TTTTGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCACTTTTTATTT
Found at i:17339906 original size:17 final size:18
Alignment explanation
Indices: 17339886--17339925 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17339876 TCATTCACTT
17339886 TTTTTTTTCAC-TTTTTA
1 TTTTTTTTCACTTTTTTA
**
17339903 TTTTTTTTTGCTTTTTTA
1 TTTTTTTTCACTTTTTTA
17339921 TTTTT
1 TTTTT
17339926 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCACTTTTTTA
Found at i:17339906 original size:18 final size:18
Alignment explanation
Indices: 17339884--17339930 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
17339874 TTTCATTCAC
*
17339884 TTTTTTTTTTCACTTTTTA
1 TTTTTTTTTGC-CTTTTTA
*
17339903 TTTTTTTTTGCTTTTTTA
1 TTTTTTTTTGCCTTTTTA
17339921 TTTTTATTTT
1 TTTTT-TTTT
17339931 TTTAAGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTGCCTTTTTA
Found at i:17339911 original size:24 final size:23
Alignment explanation
Indices: 17339884--17339933 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
17339874 TTTCATTCAC
*
17339884 TTTTT-TTTTTCACTTTTTATTTT
1 TTTTTCTTTTTTA-TTTTTATTTT
17339907 TTTTTGCTTTTTTATTTTTATTTT
1 TTTTT-CTTTTTTATTTTTATTTT
17339931 TTT
1 TTT
17339934 AAGCATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.08, C:0.06, G:0.02, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTTTATTTTTATTTT
Found at i:17350410 original size:57 final size:57
Alignment explanation
Indices: 17350341--17350901 Score: 704
Period size: 57 Copynumber: 9.8 Consensus size: 57
17350331 TTTTTTGTGC
17350341 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
* * * * * * *
17350398 AAGAAAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTTGAAGACTTAATTTC
1 AAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAA-CTTTTTTTGAAAATTTATTTTT
* *
17350456 GAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAA-TTATCTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
* * * *
17350512 AAGGAAAATTGATATTTTCAATTTTTTCC-CAAAAA-TATTTTTAGAAAATTTATTTTC
1 AAGGAAAATTGATACTTTCAA-CTTTTCCTCAAAAACT-TTTTTTGAAAATTTATTTTT
* * * *
17350569 GAGGAAAATTGATACTTTTAACTTTTCCTCAAAAACGTTTTTTGAAAATTTATCTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
*
17350626 AAGGAAAATTGATACTTTCAACTTTT-CTCCAAAAA-TATTTTTAGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAACT-TTTTTTGAAAATTTATTTTT
* *
17350683 AAGGAAAATTGATACTTTTAACTTTTCCTCAAAAA-TATTTTTAGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTGAAAATTTATTTTT
* *
17350740 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTC---AAAAA-CTTTTTTTGAAAATTTATTTTT
* * * *
17350801 AAGAAAAATTGATACTTTCAACTTTTCTTCAAAAACCTTTTTTCAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
* * *
17350858 GAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTT
17350902 TGGATTTTGT
Statistics
Matches: 438, Mismatches: 49, Indels: 33
0.84 0.09 0.06
Matches are distributed among these distances:
55 1 0.00
56 49 0.11
57 274 0.63
58 60 0.14
59 1 0.00
60 5 0.01
61 47 0.11
62 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (57 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTT
Found at i:17350610 original size:114 final size:114
Alignment explanation
Indices: 17350340--17350899 Score: 784
Period size: 114 Copynumber: 4.9 Consensus size: 114
17350330 TTTTTTTGTG
*
17350340 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAA
* * * * *
17350405 ATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTTGAAGACTTAATTT
66 ATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTAGAAAATTTATTTT
* *
17350455 CGAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAA-TTATCTTTAAGGAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAA
* *
17350519 ATTGATATTTTCAATTTTTTCCCAAAAATATTTTTAGAAAATTTATTTT
66 ATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATTTT
* * * *
17350568 CGAGGAAAATTGATACTTTTAACTTTTCCTCAAAAACGTTTTTTGAAAATTTATCTTTAAGGAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAA
17350633 ATTGATACTTTCAAC-TTTTCTCCAAAAATATTTTTAGAAAATTTATTTT
66 ATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTAGAAAATTTATTTT
* * * *
17350682 TAAGGAAAATTGATACTTTTAACTTTTCCTCAAAAA-TATTTTTAGAAAATTTATTTTTAAGAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTGAAAATTTATTTTTAAGGAA
* * *
17350746 AATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTTTGAAAATTTATTTT
65 AATTGATACTTTCAACTTTTTC-CCAAAAATA---TTTTTAGAAAATTTATTTT
* * * * * *
17350800 TAAGAAAAATTGATACTTTCAACTTTTCTTCAAAAACCTTTTTTCAAAATTTATTTTTGAGGAAA
1 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAA
*
17350865 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTT
66 ATTGATACTTTCAACTTTTTCCCAAAAATATTTTT
17350900 TTTGGATTTT
Statistics
Matches: 403, Mismatches: 34, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
113 67 0.17
114 174 0.43
115 61 0.15
117 7 0.02
118 94 0.23
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (114 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAA
ATTGATACTTTCAACTTTTTCCCAAAAATATTTTTAGAAAATTTATTTT
Found at i:17350928 original size:5 final size:5
Alignment explanation
Indices: 17350918--17351032 Score: 71
Period size: 5 Copynumber: 22.8 Consensus size: 5
17350908 TTGTTTAAAG
*
17350918 AAAAT AAAAT --AAT AAAAT AAAAT AAAAGT GAAAAT AAAAT TAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* *
17350967 -AAA- AAAAT AAAGA- AAAGT AAAACG AAAAT AAAAAT AAAAAT AAAGAT
1 AAAAT AAAAT AAA-AT AAAAT AAAA-T AAAAT -AAAAT -AAAAT AAA-AT
* * *
17351014 AAAAG AAGAT TAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
17351033 CTAATCTAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
3 3 0.03
4 9 0.10
5 47 0.55
6 23 0.27
7 4 0.05
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:17350967 original size:44 final size:43
Alignment explanation
Indices: 17350912--17351006 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 43
17350902 TGGATTTTGT
* *
17350912 TTAAAGAAAATAAAATAATAAA-ATAAAATAAAAGTGAAAATAAAA
1 TTAAA-AAAATAAAAAAATAAAGA-AAAATAAAA-CGAAAATAAAA
*
17350957 TTAAAAAAATAAAAAAATAAAGAAAAGTAAAACGAAAATAAAA
1 TTAAAAAAATAAAAAAATAAAGAAAAATAAAACGAAAATAAAA
*
17351000 ATAAAAA
1 TTAAAAA
17351007 TAAAGATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 16 0.36
44 23 0.51
45 6 0.13
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (43 bp):
TTAAAAAAATAAAAAAATAAAGAAAAATAAAACGAAAATAAAA
Found at i:17350995 original size:38 final size:38
Alignment explanation
Indices: 17350923--17351020 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 38
17350913 TAAAGAAAAT
* * *
17350923 AAAATAATAAAATAAAATAAAAGTGAAAATAAAATTAAA
1 AAAATAAAAAAATAAAAGAAAAGTGAAAAGAAAA-TAAA
17350962 AAAATAAAAAAAT-AAAGAAAAGT-AAAACGAAAATAAA
1 AAAATAAAAAAATAAAAGAAAAGTGAAAA-GAAAATAAA
17350999 AATAA-AAATAAAGATAAAAGAA
1 AA-AATAAA-AAA-ATAAAAGAA
17351021 GATTAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
37 13 0.25
38 18 0.35
39 14 0.27
40 6 0.12
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (38 bp):
AAAATAAAAAAATAAAAGAAAAGTGAAAAGAAAATAAA
Found at i:17351017 original size:17 final size:16
Alignment explanation
Indices: 17350918--17351017 Score: 69
Period size: 17 Copynumber: 5.9 Consensus size: 16
17350908 TTGTTTAAAG
17350918 AAAATAAAATAATAAAAT
1 AAAATAAAAT-A-AAAAT
*
17350936 AAAATAAAAGTGAAAAT
1 AAAATAAAA-TAAAAAT
*
17350953 AAAATTAAAA-AAATAAA
1 AAAA-TAAAATAAA-AAT
* *
17350970 AAAAT-AAAGAAAAGT
1 AAAATAAAATAAAAAT
*
17350985 AAAACGAAAATAAAAAT
1 AAAA-TAAAATAAAAAT
17351002 AAAAATAAAGATAAAA
1 -AAAATAAA-ATAAAA
17351018 GAAGATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
15 8 0.12
16 6 0.09
17 26 0.40
18 24 0.37
19 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:17351921 original size:11 final size:11
Alignment explanation
Indices: 17351905--17351932 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17351895 AATAAATCAA
17351905 AAAAATCAAAT
1 AAAAATCAAAT
17351916 AAAAATCAAAT
1 AAAAATCAAAT
17351927 AAAAAT
1 AAAAAT
17351933 ATTAATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATCAAAT
Found at i:17351972 original size:20 final size:21
Alignment explanation
Indices: 17351940--17351999 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 21
17351930 AATATTAATG
17351940 AAAATAAAT--CAGATAAATC
1 AAAATAAATAACAGATAAATC
* *
17351959 AAAA-AATTAACAGATAAATT
1 AAAATAAATAACAGATAAATC
17351979 AAAATTAAATAACAGATAAAT
1 AAAA-TAAATAACAGATAAAT
17352000 ATAACATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 13 0.38
22 14 0.41
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATAAATAACAGATAAATC
Found at i:17352131 original size:12 final size:12
Alignment explanation
Indices: 17352083--17352195 Score: 61
Period size: 12 Copynumber: 8.9 Consensus size: 12
17352073 GTAGTAATAA
17352083 ATAAATAATAAAT
1 ATAAATAA-AAAT
17352096 ACATAAGATAAAAAT
1 --ATAA-ATAAAAAT
* *
17352111 A-GAAGAAAAAT
1 ATAAATAAAAAT
* *
17352122 ATATATAAAAAA
1 ATAAATAAAAAT
17352134 ATAATAATAAAAAT
1 AT-A-AATAAAAAT
* *
17352148 ACAAATACAAAT
1 ATAAATAAAAAT
17352160 A-AAATAAAAAT
1 ATAAATAAAAAT
*
17352171 GTAAAATACAAAA-
1 AT-AAATA-AAAAT
17352184 ATAAAATAAAAA
1 AT-AAATAAAAA
17352196 AATAGACTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
11 17 0.22
12 22 0.28
13 15 0.19
14 12 0.15
15 8 0.10
16 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (12 bp):
ATAAATAAAAAT
Found at i:17352145 original size:26 final size:24
Alignment explanation
Indices: 17352105--17352195 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 24
17352095 TACATAAGAT
* *
17352105 AAAAATAGAAGAAAAATATATATAA
1 AAAAATAAAATAAAAATATA-ATAA
* *
17352130 AAAAATAATAATAAAAATACAA-AT
1 AAAAATAA-AATAAAAATATAATAA
* * *
17352154 ACAAATAAAATAAAAATGTAAAATAC
1 AAAAATAAAATAAAAA--TATAATAA
17352180 AAAAATAAAATAAAAA
1 AAAAATAAAATAAAAA
17352196 AATAGACTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 8 0.15
24 8 0.15
25 12 0.22
26 26 0.48
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (24 bp):
AAAAATAAAATAAAAATATAATAA
Found at i:17352148 original size:6 final size:6
Alignment explanation
Indices: 17352130--17352195 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
17352120 ATATATATAA
* * * *
17352130 AAAAAT AATAAT AAAAAT ACAAAT ACAAAT -AAAAT AAAAAT GTAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT
17352178 ACAAAA- ATAAAAT AAAAA
1 A-AAAAT A-AAAAT AAAAA
17352196 AATAGACTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 4 0.08
6 35 0.71
7 10 0.20
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:17352177 original size:13 final size:12
Alignment explanation
Indices: 17352129--17352196 Score: 68
Period size: 12 Copynumber: 5.5 Consensus size: 12
17352119 AATATATATA
17352129 AAAAAATAATAAT
1 AAAAAATAA-AAT
17352142 -AAAAATACAAAT
1 AAAAAATA-AAAT
*
17352154 -ACAAATAAAAT
1 AAAAAATAAAAT
*
17352165 AAAAATGTAAAAT
1 AAAAA-ATAAAAT
17352178 ACAAAAATAAAAT
1 A-AAAAATAAAAT
17352191 AAAAAA
1 AAAAAA
17352197 ATAGACTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.09
12 24 0.51
13 15 0.32
14 4 0.09
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:17352197 original size:13 final size:13
Alignment explanation
Indices: 17352116--17352199 Score: 68
Period size: 13 Copynumber: 6.5 Consensus size: 13
17352106 AAAATAGAAG
*
17352116 AAAAATATATATAA
1 AAAAATA-AAATAA
17352130 AAAAAT--AATAA
1 AAAAATAAAATAA
17352141 TAAAAATACAAAT--
1 -AAAAATA-AAATAA
*
17352154 ACAAATAAAATAA
1 AAAAATAAAATAA
** *
17352167 AAATGTAAAATAC
1 AAAAATAAAATAA
17352180 AAAAATAAAATAA
1 AAAAATAAAATAA
17352193 AAAAATA
1 AAAAATA
17352200 GACTTACCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.15
12 12 0.22
13 26 0.47
14 6 0.11
15 3 0.05
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:17357035 original size:11 final size:11
Alignment explanation
Indices: 17357016--17357105 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
17357006 AAAAACTAGT
17357016 AAAAT-AAAAA
1 AAAATGAAAAA
17357026 AAAATGAAAATA
1 AAAATGAAAA-A
*
17357038 AAAATGAAAAT
1 AAAATGAAAAA
* *
17357049 ATAA-GATAAA
1 AAAATGAAAAA
* * *
17357059 TATATGAAAAG
1 AAAATGAAAAA
17357070 AAAATGAAATCAA
1 AAAATGAAA--AA
*
17357083 AAAATAAAAATA
1 AAAATGAAAA-A
17357095 AAAATAGAAAA
1 AAAAT-GAAAA
17357106 GGAAAACATG
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
10 10 0.17
11 19 0.32
12 17 0.29
13 13 0.22
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (11 bp):
AAAATGAAAAA
Found at i:17357035 original size:16 final size:19
Alignment explanation
Indices: 17356997--17357041 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 19
17356987 TAAGAAAAAT
17356997 AAATAAATAAAAAACTAGTA
1 AAATAAA-AAAAAACTAGTA
17357017 AAATAAAAAAAAA-T-G-A
1 AAATAAAAAAAAACTAGTA
17357033 AAATAAAAA
1 AAATAAAAA
17357042 TGAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
17 1 0.04
18 1 0.04
19 6 0.24
20 7 0.28
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (19 bp):
AAATAAAAAAAAACTAGTA
Found at i:17357042 original size:12 final size:12
Alignment explanation
Indices: 17357016--17357049 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17357006 AAAAACTAGT
17357016 AAAAT-AAAA-A
1 AAAATGAAAATA
17357026 AAAATGAAAATA
1 AAAATGAAAATA
17357038 AAAATGAAAATA
1 AAAATGAAAATA
17357050 TAAGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 4 0.18
12 13 0.59
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:17357104 original size:32 final size:31
Alignment explanation
Indices: 17357021--17357110 Score: 78
Period size: 32 Copynumber: 2.9 Consensus size: 31
17357011 CTAGTAAAAT
* *
17357021 AAAA-AAAAATGAAAATA-AAAATGAAAATAT
1 AAAATAAAAATAAAAATAGAAAATG-AAATAA
* * *
17357051 AAGATAAATATATGAAA-AGAAAATGAAATCAA
1 AAAATAAAAATA-AAAATAGAAAATGAAAT-AA
*
17357083 AAAATAAAAATAAAAATAGAAAAGGAAA
1 AAAATAAAAATAAAAATAGAAAATGAAA
17357111 ACATGCGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
30 3 0.07
31 13 0.28
32 30 0.65
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (31 bp):
AAAATAAAAATAAAAATAGAAAATGAAATAA
Found at i:17357922 original size:3 final size:3
Alignment explanation
Indices: 17357900--17358009 Score: 105
Period size: 3 Copynumber: 36.3 Consensus size: 3
17357890 TGAAAACAAA
*
17357900 AAT AA- AAT AAAT AAT AAAT AAT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * *
17357946 GAT AAC AAT AAC AAC AAC AAC AAC AAC CAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17357994 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
17358010 GTATAATAGC
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
2 2 0.02
3 86 0.91
4 6 0.06
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:17358699 original size:123 final size:123
Alignment explanation
Indices: 17358428--17358785 Score: 416
Period size: 123 Copynumber: 2.9 Consensus size: 123
17358418 AAGTGAGCAA
* * ** * *
17358428 GACCAAGTCAAGGTCAAAGATGAATGACCAAAATGAAATCGTGAGTTAGGAAAATGATCTGGATT
1 GACCAAGTCAAGGTCGAAGATGAATGACCAAAATGAAATCGTGAGTCAAAAAAATGATCTGAACT
* * * ** * * * *
17358493 AAGCCAATATCGAATGGCCGAGATGAAACCATGAACCTAAAAAATAACAAAGGGAACAG
66 GAGCCAAGATCAAATGATCGAGAT-AAATCATGAATCTAAAAAATGACAAAGGCAACAG
* * * ** * *
17358552 GACCGAGTCAAGGTCGAAGATGAATGACCGAGATGAAATTATGAGACAAAAAAATGATCTAAACT
1 GACCAAGTCAAGGTCGAAGATGAATGACCAAAATGAAATCGTGAGTCAAAAAAATGATCTGAACT
*
17358617 GAGCCAAGATCAAATGATCGAGATAAATCATGAATCTAGAAAATGACAAA-GCAACTAG
66 GAGCCAAGATCAAATGATCGAGATAAATCATGAATCTAAAAAATGACAAAGGCAAC-AG
* *
17358675 GACCAAGTCAAGGTTGAAGATGAATGA-CAAACATGAAATCGTGAGTCAAAAAAATTATCTGAAC
1 GACCAAGTCAAGGTCGAAGATGAATGACCAAA-ATGAAATCGTGAGTCAAAAAAATGATCTGAAC
* *
17358739 TGAGCCAAGATCAAATGATCTG-GATGAATTATGAATCTAAAAAATGA
65 TGAGCCAAGATCAAATGATC-GAGATAAATCATGAATCTAAAAAATGA
17358786 TTTGGATTGA
Statistics
Matches: 196, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
122 6 0.03
123 118 0.60
124 72 0.37
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (123 bp):
GACCAAGTCAAGGTCGAAGATGAATGACCAAAATGAAATCGTGAGTCAAAAAAATGATCTGAACT
GAGCCAAGATCAAATGATCGAGATAAATCATGAATCTAAAAAATGACAAAGGCAACAG
Found at i:17358979 original size:69 final size:69
Alignment explanation
Indices: 17358799--17358948 Score: 210
Period size: 69 Copynumber: 2.2 Consensus size: 69
17358789 GGATTGAACC
* *** * *
17358799 AAGATCGAATGACTGAGATGAAACCATTTGTCTAAAAAATGACAAAGCGACCAGGATCGAGTCAA
1 AAGAT-GAATGACTGAGACGAAACCACAAGTCTGAAAAATGATAAAGCGACCAGGATCGAGTCAA
17358864 GGTCA
65 GGTCA
* * *
17358869 AATATGAATGACTGGGACGAAACCACAAGTCTGAAAAATGATAAAGCGACTAGGATCGAGTCAAG
1 AAGATGAATGACTGAGACGAAACCACAAGTCTGAAAAATGATAAAGCGACCAGGATCGAGTCAAG
17358934 GTCA
66 GTCA
17358938 AAGATGAATGA
1 AAGATGAATGA
17358949 TCGAGATTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
69 66 0.94
70 4 0.06
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (69 bp):
AAGATGAATGACTGAGACGAAACCACAAGTCTGAAAAATGATAAAGCGACCAGGATCGAGTCAAG
GTCA
Found at i:17364460 original size:12 final size:12
Alignment explanation
Indices: 17364431--17364474 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
17364421 GAAAACTAGT
*
17364431 AAAATAAAAAATTA
1 AAAAT-AAAAA-TC
17364445 AAAATAAAAATC
1 AAAATAAAAATC
*
17364457 AAAATCAAAATC
1 AAAATAAAAATC
17364469 AAAATA
1 AAAATA
17364475 TAAGATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 5 0.19
14 5 0.19
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:17364517 original size:13 final size:12
Alignment explanation
Indices: 17364438--17364527 Score: 53
Period size: 13 Copynumber: 7.3 Consensus size: 12
17364428 AGTAAAATAA
*
17364438 AAAATTAAAAAT
1 AAAATCAAAAAT
17364450 AAAAATC-AAAAT
1 -AAAATCAAAAAT
17364462 CAAAATCAAAATAT
1 -AAAATCAAAA-AT
* *
17364476 AAGAT-AAATAT
1 AAAATCAAAAAT
*
17364487 ATAA-CAAGAAAAT
1 AAAATC-A-AAAAT
*
17364500 GAAATCAAAAAAT
1 AAAATC-AAAAAT
17364513 AAAAT-AAAAAT
1 AAAATCAAAAAT
17364524 AAAA
1 AAAA
17364528 AAGAGAAACA
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
11 14 0.23
12 15 0.25
13 27 0.44
14 5 0.08
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAATCAAAAAT
Found at i:17365348 original size:20 final size:21
Alignment explanation
Indices: 17365325--17365364 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17365315 TGAAAAAAGA
17365325 AATAAATAAAAATAA-AATAG
1 AATAAATAAAAATAATAATAG
*
17365345 AATAAATAATAATAATAATA
1 AATAAATAAAAATAATAATA
17365365 TAACATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAATAATAATAG
Found at i:17365361 original size:23 final size:23
Alignment explanation
Indices: 17365324--17365395 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
17365314 TTGAAAAAAG
*
17365324 AAATAAATAAAAATAAAATAGAAT
1 AAAT-AATAATAATAAAATAGAAT
*
17365348 AAATAATAATAATAATATA-ACAT
1 AAATAATAATAATAAAATAGA-AT
* *
17365371 AATATCAT-ATAATAAAATAGTAT
1 AA-ATAATAATAATAAAATAGAAT
17365394 AA
1 AA
17365396 TAGCATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.03
23 31 0.77
24 8 0.20
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
AAATAATAATAATAAAATAGAAT
Found at i:17365367 original size:5 final size:5
Alignment explanation
Indices: 17365335--17365476 Score: 76
Period size: 5 Copynumber: 27.2 Consensus size: 5
17365325 AATAAATAAA
* * * *
17365335 AATAA AATAG AATA- AATAAT AATAAT AATAT AACAT AATAT CATAT AATA-
1 AATAT AATAT AATAT AAT-AT AAT-AT AATAT AATAT AATAT AATAT AATAT
* * * *
17365385 AA-AT AGTAT AATAGCAT AATAT AACAT GATAAT AATAC AATATCT AATA-
1 AATAT AATAT AAT---AT AATAT AATAT AAT-AT AATAT AATA--T AATAT
* *
17365434 ATATAT AATAT AATCAC AATGT AATAT AATAT AATAT AATAT A
1 A-ATAT AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT A
17365477 TTAAATTCTA
Statistics
Matches: 107, Mismatches: 17, Indels: 26
0.71 0.11 0.17
Matches are distributed among these distances:
3 1 0.01
4 7 0.07
5 72 0.67
6 18 0.17
7 4 0.04
8 5 0.05
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:17365396 original size:23 final size:23
Alignment explanation
Indices: 17365335--17365402 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
17365325 AATAAATAAA
*
17365335 AATAAAATAGAATAA-ATAATAAT
1 AATAAAATAGAATAATATCAT-AT
*
17365358 AATAATATA-ACATAATATCATAT
1 AATAAAATAGA-ATAATATCATAT
* *
17365381 AATAAAATAGTATAATAGCATA
1 AATAAAATAGAATAATATCATA
17365403 ATATAACATG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 32 0.86
24 4 0.11
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
AATAAAATAGAATAATATCATAT
Found at i:17367167 original size:16 final size:16
Alignment explanation
Indices: 17367143--17367176 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17367133 CTACAAACTG
17367143 TTGTAGAATATAAAAT
1 TTGTAGAATATAAAAT
*
17367159 TTGTTGAATATAAAAT
1 TTGTAGAATATAAAAT
17367175 TT
1 TT
17367177 TTAGTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TTGTAGAATATAAAAT
Found at i:17369463 original size:24 final size:23
Alignment explanation
Indices: 17369398--17369464 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
17369388 GGGAAGGACT
* *
17369398 AGAAAAAAAGTGAAACAAAGGAG
1 AGAAAAAAAGAGAAAAAAAGGAG
* *
17369421 AGAAAAACCAA-AGATAAAAAGGTG
1 AGAAAAA--AAGAGAAAAAAAGGAG
17369445 AGAAGAAAAAGAGAAAAAAA
1 AGAA-AAAAAGAGAAAAAAA
17369465 TTTTTATTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 9 0.26
24 21 0.60
25 5 0.14
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.04
Consensus pattern (23 bp):
AGAAAAAAAGAGAAAAAAAGGAG
Found at i:17373258 original size:22 final size:23
Alignment explanation
Indices: 17373221--17373265 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
17373211 TTATCACAAC
17373221 ATTTTCTTAAAAATAAAAATAAT
1 ATTTTCTTAAAAATAAAAATAAT
* *
17373244 ATTTT-TTGAAAATAATAATAAT
1 ATTTTCTTAAAAATAAAAATAAT
17373266 TGGTGACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTTCTTAAAAATAAAAATAAT
Found at i:17373700 original size:13 final size:12
Alignment explanation
Indices: 17373682--17373765 Score: 55
Period size: 13 Copynumber: 6.7 Consensus size: 12
17373672 CATATAGAAA
17373682 TTAAGGTTTCATT
1 TTAAGGTTTCA-T
*
17373695 TTAAGGTTTAAT
1 TTAAGGTTTCAT
*
17373707 ATTAGGGTTTCACT
1 -TTAAGGTTTCA-T
*
17373721 TTAGAGTTTTGC-T
1 TTA-AGGTTT-CAT
*
17373734 TT-AGGTTTCAAG
1 TTAAGGTTTC-AT
*
17373746 TTAAGGTTTCAC
1 TTAAGGTTTCAT
17373758 TTAAGGTT
1 TTAAGGTT
17373766 CCAAGTTAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
10 1 0.02
11 5 0.09
12 12 0.21
13 32 0.57
14 5 0.09
15 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (12 bp):
TTAAGGTTTCAT
Found at i:17373754 original size:25 final size:23
Alignment explanation
Indices: 17373712--17373790 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 23
17373702 TTAATATTAG
**
17373712 GGTTTCACTTTAGAGTTTTGCTTTA
1 GGTTTCAAGTTAG-GTTTT-CTTTA
* *
17373737 GGTTTCAAGTTAAGGTTTCACTTAA
1 GGTTTCAAGTT-AGGTTT-TCTTTA
* *
17373762 GGTTCCAAGTTAGGATTTCATTTA
1 GGTTTCAAGTTAGGTTTTC-TTTA
17373786 GGTTT
1 GGTTT
17373791 TCATATATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.02
24 12 0.29
25 27 0.64
26 2 0.05
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (23 bp):
GGTTTCAAGTTAGGTTTTCTTTA
Found at i:17373910 original size:14 final size:15
Alignment explanation
Indices: 17373893--17373922 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17373883 TTTTTATATT
17373893 TATATTTAT-TTTTC
1 TATATTTATATTTTC
17373907 TATATTTATATTTTC
1 TATATTTATATTTTC
17373922 T
1 T
17373923 TTTTCATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TATATTTATATTTTC
Found at i:17375876 original size:7 final size:7
Alignment explanation
Indices: 17375864--17375889 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17375854 TTTGTTAATT
17375864 TTTTTAG
1 TTTTTAG
17375871 TTTTTAG
1 TTTTTAG
17375878 TTTTTAG
1 TTTTTAG
17375885 TTTTT
1 TTTTT
17375890 TGAATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (7 bp):
TTTTTAG
Found at i:17375904 original size:23 final size:22
Alignment explanation
Indices: 17375841--17375914 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
17375831 ATTATTATTA
*
17375841 TTTTAATTTTGATTTTGTTAATTT
1 TTTTAATTTTGAATTT-TTAA-TT
* * * *
17375865 TTTTAGTTTTTAGTTTTTAGTT
1 TTTTAATTTTGAATTTTTAATT
*
17375887 TTTTGAATTTTGAATTTTTTATT
1 TTTT-AATTTTGAATTTTTAATT
*
17375910 ATTTA
1 TTTTA
17375915 TAATAATAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
22 7 0.18
23 19 0.49
24 13 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTAATTTTGAATTTTTAATT
Found at i:17376549 original size:15 final size:15
Alignment explanation
Indices: 17376529--17376557 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17376519 TATGTCTTTC
17376529 TTCTTCTCTAGAAGT
1 TTCTTCTCTAGAAGT
17376544 TTCTTCTCTAGAAG
1 TTCTTCTCTAGAAG
17376558 CTTCAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (15 bp):
TTCTTCTCTAGAAGT
Found at i:17376627 original size:15 final size:15
Alignment explanation
Indices: 17376607--17376639 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17376597 TTATGTCTTT
*
17376607 CTTTTTCTCCATAAG
1 CTTTTTCTCCAAAAG
17376622 CTTTTTCTCCAAAAG
1 CTTTTTCTCCAAAAG
17376637 CTT
1 CTT
17376640 CAAAGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.27, G:0.06, T:0.45
Consensus pattern (15 bp):
CTTTTTCTCCAAAAG
Found at i:17379620 original size:2 final size:2
Alignment explanation
Indices: 17379613--17379643 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17379603 ATACATTTAC
17379613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17379644 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17383331 original size:153 final size:153
Alignment explanation
Indices: 17383043--17383364 Score: 506
Period size: 153 Copynumber: 2.1 Consensus size: 153
17383033 TCTAACTAAG
* *
17383043 TGAATAT-CATAATGAAGTTTAGCAAGTTAATTTGGTTTGAAAAGCAAAGATAAGTTAAAAGTAA
1 TGAATATCCACAATGAAGTTTAGCAAGTCAATTTGGTTTGAAAAGCAAAGATAAGTTAAAAGTAA
*
17383107 AAAGTTTTCTTTTCGTCCCACACTTAAATGGAATCATATATCAAAAACTCAAAGGAAAAAAAAAA
66 AAAGTTTTCTTTTCGTCCCACACTTAAATGGAATCACATATCAAAAACTCAAAGGAAAAAAAAAA
*
17383172 TACTCCCTAAAATTCTTTAAGGT
131 AACTCCCTAAAATTCTTTAAGGT
*
17383195 TGAATATCCACAATGAAGTTTAGCAAGTCAATTTGGTTTGAAAAGCAAAGATGAA-TTAAAATTA
1 TGAATATCCACAATGAAGTTTAGCAAGTCAATTTGGTTTGAAAAGCAAAGAT-AAGTTAAAAGTA
* * *
17383259 AAATGTTTTCTTTTC-TCCTTACACTTAAATGGAATCACATATCAAAACCTCAAAGGAAAAAAAA
65 AAAAGTTTTCTTTTCGTCC-CACACTTAAATGGAATCACATATCAAAAACTCAAAGGAAAAAAAA
*
17383323 AAAACTCCCTAAAATTCTTTAATGT
129 AAAACTCCCTAAAATTCTTTAAGGT
* *
17383348 TGAATAGCCACGATGAA
1 TGAATATCCACAATGAA
17383365 TCCTCTTGCT
Statistics
Matches: 156, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
152 10 0.06
153 144 0.92
154 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (153 bp):
TGAATATCCACAATGAAGTTTAGCAAGTCAATTTGGTTTGAAAAGCAAAGATAAGTTAAAAGTAA
AAAGTTTTCTTTTCGTCCCACACTTAAATGGAATCACATATCAAAAACTCAAAGGAAAAAAAAAA
AACTCCCTAAAATTCTTTAAGGT
Found at i:17387976 original size:22 final size:22
Alignment explanation
Indices: 17387950--17387993 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17387940 CCAAACCCTT
17387950 AAACCCCAACCTTAAACCATAA
1 AAACCCCAACCTTAAACCATAA
*
17387972 AAACCCTAACCTTAAACCATAA
1 AAACCCCAACCTTAAACCATAA
17387994 CCTTACCTAG
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:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (22 bp):
AAACCCCAACCTTAAACCATAA
Found at i:17387994 original size:13 final size:13
Alignment explanation
Indices: 17387946--17387998 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
17387936 AATCCCAAAC
**
17387946 CCTTAAACCCCAA
1 CCTTAAACCATAA
17387959 CCTTAAACCATAA
1 CCTTAAACCATAA
*
17387972 ----AAACCCTAA
1 CCTTAAACCATAA
17387981 CCTTAAACCATAA
1 CCTTAAACCATAA
17387994 CCTTA
1 CCTTA
17387999 CCTAGACCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 8 0.25
13 24 0.75
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (13 bp):
CCTTAAACCATAA
Found at i:17388460 original size:16 final size:16
Alignment explanation
Indices: 17388439--17388471 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17388429 GTTTTGTTTC
*
17388439 AAAAAAGAGAAAAGGA
1 AAAAAAAAGAAAAGGA
17388455 AAAAAAAAGAAAAGGA
1 AAAAAAAAGAAAAGGA
17388471 A
1 A
17388472 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAGGA
Found at i:17389126 original size:25 final size:25
Alignment explanation
Indices: 17389088--17389166 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
17389078 ATATGTTTTG
*
17389088 CATTTCATGCATATTTTATTTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
17389113 CATTTCATGTATATTTTAAATATGT
1 CATTTCATGCATATTTTAATTATGT
*
17389138 CA-TTCATGCATATTTTAATAATGT
1 CATTTCATGCATATTTTAATTATGT
17389162 CATTT
1 CATTT
17389167 ATTATATATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 21 0.45
25 26 0.55
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (25 bp):
CATTTCATGCATATTTTAATTATGT
Found at i:17389150 original size:24 final size:24
Alignment explanation
Indices: 17389091--17389165 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
17389081 TGTTTTGCAT
**
17389091 TTCATGCATATTTTATTTATGTCA
1 TTCATGCATATTTTAAATATGTCA
*
17389115 TTTCATGTATATTTTAAATATGTCA
1 -TTCATGCATATTTTAAATATGTCA
17389140 TTCATGCATATTTT-AATAATGTCA
1 TTCATGCATATTTTAAAT-ATGTCA
17389164 TT
1 TT
17389166 TATTATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
23 3 0.07
24 21 0.47
25 21 0.47
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (24 bp):
TTCATGCATATTTTAAATATGTCA
Found at i:17390299 original size:37 final size:37
Alignment explanation
Indices: 17390242--17390382 Score: 124
Period size: 37 Copynumber: 3.9 Consensus size: 37
17390232 TTCATACAAG
* * * *
17390242 TTTTGATAGATAGTACATGCATTTCATTTTATGCACA
1 TTTTGATAGATAATACATGCATTCCATTTCATGAACA
*
17390279 TTTTGATAGATAATATATGCATTCCATTTCATGAACA
1 TTTTGATAGATAATACATGCATTCCATTTCATGAACA
* * ** * *
17390316 TGTTAATAGATGGTACATACATTCCA--TCATGCACA
1 TTTTGATAGATAATACATGCATTCCATTTCATGAACA
* * ** *
17390351 TTTTAATAGGTAGCACATGCATTCCACTTCAT
1 TTTTGATAGATAATACATGCATTCCATTTCAT
17390383 TGTATATCTT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
35 29 0.34
37 56 0.66
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (37 bp):
TTTTGATAGATAATACATGCATTCCATTTCATGAACA
Found at i:17390772 original size:15 final size:15
Alignment explanation
Indices: 17390733--17390776 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
17390723 CTTTTGTTCT
* *
17390733 AAAAAGAAATAAAGA
1 AAAAAGAAAGAAAAA
*
17390748 GAAAAG-AAGAAAAA
1 AAAAAGAAAGAAAAA
17390762 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
17390777 CTGTTGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAAA
Found at i:17392015 original size:15 final size:15
Alignment explanation
Indices: 17391991--17392030 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
17391981 AAAGAAGAAG
17391991 AAAAAA-GAAAACAA
1 AAAAAATGAAAACAA
**
17392005 AAAAAATGAAAAGTA
1 AAAAAATGAAAACAA
17392020 AAAAAATGAAA
1 AAAAAATGAAA
17392031 TAAATGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAATGAAAACAA
Found at i:17392110 original size:19 final size:19
Alignment explanation
Indices: 17392067--17392110 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
17392057 AAAACATAAC
**
17392067 AAAAAAGGGGAAAAAGGAA
1 AAAAAAGGGGAAAAAACAA
17392086 AAAAAA-GGGAAAAAACAA
1 AAAAAAGGGGAAAAAACAA
17392104 AAGAAAA
1 AA-AAAA
17392111 AAGAAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAAGGGGAAAAAACAA
Found at i:17394313 original size:33 final size:34
Alignment explanation
Indices: 17394275--17394351 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
17394265 AACTTTTTCG
*
17394275 GTGGTGATATATGAGTTTTTACAAA-ATCTCTTA
1 GTGGTGATATATGAGCTTTTACAAACATCTCTTA
* * * *
17394308 GTGGTGACATCTGAGCTTTTACAAACATTTCTTG
1 GTGGTGATATATGAGCTTTTACAAACATCTCTTA
*
17394342 GTGGAGATAT
1 GTGGTGATAT
17394352 CTTTGCTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 22 0.61
34 14 0.39
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (34 bp):
GTGGTGATATATGAGCTTTTACAAACATCTCTTA
Found at i:17394853 original size:12 final size:12
Alignment explanation
Indices: 17394836--17394878 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
17394826 AGATTTCTTT
17394836 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
17394848 AAAAAAGAAAAC
1 AAAAAAAAAAAC
* *
17394860 AAAAATAAAAAG
1 AAAAAAAAAAAC
17394872 AAAAAAA
1 AAAAAAA
17394879 TTTTCAAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:17394863 original size:17 final size:17
Alignment explanation
Indices: 17394837--17394878 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17394827 GATTTCTTTA
*
17394837 AAAAAAAAAACAAAAAAG
1 AAAAAAAAAA-TAAAAAG
*
17394855 AAAACAAAAATAAAAAG
1 AAAAAAAAAATAAAAAG
17394872 AAAAAAA
1 AAAAAAA
17394879 TTTTCAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAATAAAAAG
Found at i:17395119 original size:63 final size:61
Alignment explanation
Indices: 17395023--17395200 Score: 171
Period size: 63 Copynumber: 2.8 Consensus size: 61
17395013 TTGTATTATT
* * *
17395023 TATTATTATTATGTATTAATATATGTATATATTTATTTAT-TTATTTATTGTTAGT-ATTTATGT
1 TATT-TTATTATTTATT-ATATATATATATATTTTTTTATATTATTTATT-TTAGTCATTT-T-T
17395086 G
61 G
* * *
17395087 TATTTTATTATTTATGTATATATATATATATTTTTTTATCTTTTTTATTTTATTCATTTTTG
1 TATTTTATTATTTAT-TATATATATATATATTTTTTTATATTATTTATTTTAGTCATTTTTG
* *
17395149 TATTTTTACTTATCTAATTATATATCTGATATATTTTTTTATTATTATTTAT
1 TA-TTTTA-TTAT-TTATTATATATAT-ATATATTTTTTTA-TATTATTTAT
17395201 CCTATAATAT
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
62 4 0.04
63 40 0.41
64 29 0.30
65 16 0.16
66 8 0.08
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (61 bp):
TATTTTATTATTTATTATATATATATATATTTTTTTATATTATTTATTTTAGTCATTTTTG
Found at i:17395605 original size:31 final size:31
Alignment explanation
Indices: 17395570--17395632 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
17395560 AATTTTTGGG
*
17395570 AATTTCCAGATTCCGGCGAA-AATTCCGGCGA
1 AATTTCAAGATTCCGGC-AACAATTCCGGCGA
* **
17395601 AATTTGAATTTTCCGGCAACAATTCCGGCGA
1 AATTTCAAGATTCCGGCAACAATTCCGGCGA
17395632 A
1 A
17395633 CATTGAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (31 bp):
AATTTCAAGATTCCGGCAACAATTCCGGCGA
Found at i:17395639 original size:31 final size:32
Alignment explanation
Indices: 17395580--17395653 Score: 109
Period size: 31 Copynumber: 2.4 Consensus size: 32
17395570 AATTTCCAGA
*
17395580 TTCCGGCGAA-AATTCCGGCGAAATTTGAATT
1 TTCCGGCGAACAATTCCGGCGAAATTTGAAGT
17395611 TTCCGGC-AACAATTCCGGCGAACA-TTGAAGT
1 TTCCGGCGAACAATTCCGGCGAA-ATTTGAAGT
17395642 TTCCGGCGAACA
1 TTCCGGCGAACA
17395654 GCCCAGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 2 0.05
31 32 0.82
32 5 0.13
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (32 bp):
TTCCGGCGAACAATTCCGGCGAAATTTGAAGT
Found at i:17395967 original size:5 final size:5
Alignment explanation
Indices: 17395957--17395983 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17395947 CAGCCACCCT
17395957 CCGAG CCGAG CCGAG CCGAG CCGAG CC
1 CCGAG CCGAG CCGAG CCGAG CCGAG CC
17395984 ACTTAGCCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.44, G:0.37, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:17396253 original size:57 final size:57
Alignment explanation
Indices: 17396172--17396559 Score: 549
Period size: 57 Copynumber: 6.7 Consensus size: 57
17396162 AAAAATTCTA
17396172 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
17396230 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-----
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
17396282 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
*
17396339 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCC
*
17396396 AAAAAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
* *
17396458 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 --AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
17396517 AAAAAA-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCC
17396560 CTACAAAAAA
Statistics
Matches: 302, Mismatches: 10, Indels: 35
0.87 0.03 0.10
Matches are distributed among these distances:
52 50 0.17
56 2 0.01
57 146 0.48
58 6 0.02
59 42 0.14
60 1 0.00
61 2 0.01
62 11 0.04
63 1 0.00
64 41 0.14
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:17396295 original size:109 final size:110
Alignment explanation
Indices: 17396172--17396559 Score: 523
Period size: 109 Copynumber: 3.4 Consensus size: 110
17396162 AAAAATTCTA
17396172 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAT
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAT
*
17396237 ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-
65 ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
17396282 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATA
**
17396347 TTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTT
66 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAA--T
*
17396394 CCAAAAAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCA
1 --AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC-
17396459 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
58 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA---T
17396516 CAAAAAA-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAAAAATA---TTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCC
17396560 CTACAAAAAA
Statistics
Matches: 252, Mismatches: 7, Indels: 25
0.89 0.02 0.09
Matches are distributed among these distances:
108 1 0.00
109 99 0.39
110 5 0.02
114 42 0.17
117 2 0.01
119 12 0.05
120 1 0.00
121 55 0.22
122 5 0.02
123 30 0.12
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (110 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATA
TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
Found at i:17396407 original size:30 final size:30
Alignment explanation
Indices: 17396316--17396407 Score: 70
Period size: 30 Copynumber: 3.2 Consensus size: 30
17396306 GAAAGTATCA
17396316 ATTTTCCTT-AGAAATAAATTTCCAAAAAAT
1 ATTTTCCTTAAG-AATAAATTTCCAAAAAAT
* * * **
17396346 A-TTT--TTAAGGA-AAAGTT-GAAAGTAT
1 ATTTTCCTTAAGAATAAATTTCCAAAAAAT
17396371 CAATTTTCCTTAAGAATAAATTTCCAAAAAAT
1 --ATTTTCCTTAAGAATAAATTTCCAAAAAAT
17396403 ATTTT
1 ATTTT
17396408 TAGGGAAAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
25 5 0.11
26 5 0.11
27 4 0.09
28 5 0.11
29 3 0.07
30 12 0.27
31 5 0.11
32 5 0.11
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.38
Consensus pattern (30 bp):
ATTTTCCTTAAGAATAAATTTCCAAAAAAT
Found at i:17397128 original size:47 final size:47
Alignment explanation
Indices: 17397065--17397223 Score: 185
Period size: 47 Copynumber: 3.4 Consensus size: 47
17397055 TTTTTTTTTT
**
17397065 AAGTTTGATGCCTATTTTATTGGAGCCTTTTTCCAAAAAAATTT-TTA
1 AAGTTTGATGCCTATTTTATAAGAGCCTTTTT-CAAAAAAATTTCTTA
* * * * *
17397112 AAGTTTGATGTCTATTTTGTAAGAGCCTTTTTCTAGATAATTTCTTA
1 AAGTTTGATGCCTATTTTATAAGAGCCTTTTTCAAAAAAATTTCTTA
* * * * *
17397159 AAATTTGATGCCTATTTTATAAGAGCCCTTTTTGATACAAATTTGTTA
1 AAGTTTGATGCCTATTTTATAAGAG-CCTTTTTCAAAAAAATTTCTTA
17397207 AAGTTTGATGCCTATTT
1 AAGTTTGATGCCTATTT
17397224 CGTAAGAGTA
Statistics
Matches: 92, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
46 8 0.09
47 53 0.58
48 31 0.34
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (47 bp):
AAGTTTGATGCCTATTTTATAAGAGCCTTTTTCAAAAAAATTTCTTA
Found at i:17397230 original size:95 final size:95
Alignment explanation
Indices: 17397068--17397284 Score: 246
Period size: 95 Copynumber: 2.3 Consensus size: 95
17397058 TTTTTTTAAG
** * *
17397068 TTTGATGCCTATTTTATTGGAG-CCTTTTTCCAAAAAAATTTTTAAAGTTTGATGTCTATTTTGT
1 TTTGATGCCTATTTTATAAGAGCCCTTTTTCCAAAAAAATTTTTAAAGTTTGATGCCTATTTCGT
* * *
17397132 AAGAGCCT-TTTTCTAGATA-A-TTTCTTAAAA
66 AAGAG--TACTTTCCAAATAGATTTTC-TAAAA
* * *
17397162 TTTGATGCCTATTTTATAAGAGCCCTTTTT-GATACAAATTTGTTAAAGTTTGATGCCTATTTCG
1 TTTGATGCCTATTTTATAAGAGCCCTTTTTCCAAAAAAATTT-TTAAAGTTTGATGCCTATTTCG
17397226 TAAGAGTACTTTCCAAATAGATTTTCTAAAA
65 TAAGAGTACTTTCCAAATAGATTTTCTAAAA
* * *
17397257 TTTGATACCGATTTTATAAAAGCCCTTT
1 TTTGATGCCTATTTTATAAGAGCCCTTT
17397285 CCAAACAAGT
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
93 1 0.01
94 36 0.34
95 64 0.61
96 4 0.04
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (95 bp):
TTTGATGCCTATTTTATAAGAGCCCTTTTTCCAAAAAAATTTTTAAAGTTTGATGCCTATTTCGT
AAGAGTACTTTCCAAATAGATTTTCTAAAA
Found at i:17399596 original size:27 final size:27
Alignment explanation
Indices: 17399531--17399624 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
17399521 CCAAAAAATT
* * * *
17399531 TTGAAACCCCAAGTTAAAACCTCAAAC
1 TTGAAACCCTAAATCAAAACCACAAAC
17399558 TTGAAACCCTAAATCAAAACCACAAAC
1 TTGAAACCCTAAATCAAAACCACAAAC
* * *
17399585 TTGAAACTCTAAATCCCAAACC-CTAAC
1 TTGAAACCCTAAAT-CAAAACCACAAAC
*
17399612 TTTAAACCCTAAA
1 TTGAAACCCTAAA
17399625 CCTAAACGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 51 0.89
28 6 0.11
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (27 bp):
TTGAAACCCTAAATCAAAACCACAAAC
Found at i:17399617 original size:20 final size:20
Alignment explanation
Indices: 17399589--17399679 Score: 53
Period size: 20 Copynumber: 4.4 Consensus size: 20
17399579 ACAAACTTGA
17399589 AACTCTAAATCCC-AAACCCT
1 AACTCTAAA-CCCTAAACCCT
*
17399609 AACTTTAAACCCTAAACCTAAACGT
1 AACTCTAAACCCTAAACC----C-T
*
17399634 AACCCTAAA-CCTAAA-CCT
1 AACTCTAAACCCTAAACCCT
* * * *
17399652 AAATCTTAACCCCAAAACCT
1 AACTCTAAACCCTAAACCCT
17399672 AACTCTAA
1 AACTCTAA
17399680 CTATAAGCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
18 7 0.13
19 9 0.17
20 22 0.41
23 1 0.02
24 7 0.13
25 8 0.15
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.21
Consensus pattern (20 bp):
AACTCTAAACCCTAAACCCT
Found at i:17399630 original size:6 final size:6
Alignment explanation
Indices: 17399614--17399654 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
17399604 ACCCTAACTT
* *
17399614 TAAACCC TAAACC TAAACG TAACCC TAAACC TAAACC TAAA
1 TAAA-CC TAAACC TAAACC TAAACC TAAACC TAAACC TAAA
17399655 TCTTAACCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.49, C:0.32, G:0.02, T:0.17
Consensus pattern (6 bp):
TAAACC
Found at i:17399630 original size:13 final size:13
Alignment explanation
Indices: 17399561--17399654 Score: 52
Period size: 13 Copynumber: 7.2 Consensus size: 13
17399551 CTCAAACTTG
* *
17399561 AAACCCTAAATCA
1 AAACCCTAAACCT
*
17399574 AAACCAC-AAACTT
1 AAACC-CTAAACCT
* *
17399587 GAAACTCTAAATCCC
1 -AAACCCTAAA-CCT
*
17399602 AAACCCT-AACTTT
1 AAACCCTAAAC-CT
17399615 AAACCCTAAACCT
1 AAACCCTAAACCT
* *
17399628 AAA-CGTAACCCT
1 AAACCCTAAACCT
17399640 AAA-CCTAAACCT
1 AAACCCTAAACCT
17399652 AAA
1 AAA
17399655 TCTTAACCCC
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
12 21 0.34
13 22 0.36
14 17 0.28
15 1 0.02
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:17400931 original size:13 final size:13
Alignment explanation
Indices: 17400913--17400943 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17400903 GTAACATAAA
*
17400913 TAAAAATTAAAAT
1 TAAAAACTAAAAT
17400926 TAAAAACTAAAAT
1 TAAAAACTAAAAT
17400939 TAAAA
1 TAAAA
17400944 CTCACTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAACTAAAAT
Found at i:17413560 original size:16 final size:17
Alignment explanation
Indices: 17413539--17413570 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17413529 CTACTATAGA
17413539 ATTTTTTT-ACCTCGAT
1 ATTTTTTTCACCTCGAT
17413555 ATTTTTTTCACCTCGA
1 ATTTTTTTCACCTCGA
17413571 CTTTCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTTTTTTCACCTCGAT
Found at i:17420811 original size:18 final size:18
Alignment explanation
Indices: 17420788--17420828 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17420778 AAAGCACGCC
17420788 CTTAAGCCACTTTGAGCT
1 CTTAAGCCACTTTGAGCT
* *
17420806 CTTAAGTCATTTTGAGCT
1 CTTAAGCCACTTTGAGCT
*
17420824 TTTAA
1 CTTAA
17420829 ACTCCACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (18 bp):
CTTAAGCCACTTTGAGCT
Found at i:17422744 original size:13 final size:12
Alignment explanation
Indices: 17422696--17422745 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
17422686 GTTGGCCATT
17422696 AAAT-ATATAAA
1 AAATAATATAAA
17422707 AAATAA-ATAAA
1 AAATAATATAAA
17422718 AAGTATATATATAAA
1 AA--ATA-ATATAAA
17422733 AAATAGATATAAA
1 AAATA-ATATAAA
17422746 GAAAAGCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 11 0.33
12 1 0.03
13 13 0.39
14 1 0.03
15 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (12 bp):
AAATAATATAAA
Found at i:17422988 original size:37 final size:37
Alignment explanation
Indices: 17422938--17423013 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
17422928 TGGCCATTTT
* *
17422938 GGCTTAAGCTTGCTACATGAATAAGTGAAAGGAAAGG
1 GGCTTAAGCTTGCTACATGAACAAGTGAAAGAAAAGG
*
17422975 GGCTTAAGCTTGCTACATGAACACGTGAAAGAAAAGG
1 GGCTTAAGCTTGCTACATGAACAAGTGAAAGAAAAGG
17423012 GG
1 GG
17423014 AAAAGCTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (37 bp):
GGCTTAAGCTTGCTACATGAACAAGTGAAAGAAAAGG
Found at i:17423326 original size:36 final size:35
Alignment explanation
Indices: 17423281--17423348 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
17423271 CGAAAGCAAG
17423281 AAAAAAAACTGAG-AGGGAAGCATGAAACAAAAACAA
1 AAAAAAAACTGAGCAGGGAAGCAT-AAA-AAAAACAA
* *
17423317 AAAAAAAACTGGGCAGTGAAGCATAAAAAAAA
1 AAAAAAAACTGAGCAGGGAAGCATAAAAAAAA
17423349 TTAAGGTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 15 0.52
37 9 0.31
ACGTcount: A:0.63, C:0.10, G:0.19, T:0.07
Consensus pattern (35 bp):
AAAAAAAACTGAGCAGGGAAGCATAAAAAAAACAA
Found at i:17423706 original size:17 final size:18
Alignment explanation
Indices: 17423673--17423706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17423663 AAAAATGGAG
17423673 CAGCAGTAGCGAGAAAAC
1 CAGCAGTAGCGAGAAAAC
*
17423691 CAGCGGTAGC-AGAAAA
1 CAGCAGTAGCGAGAAAA
17423707 GAATGCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.21, G:0.29, T:0.06
Consensus pattern (18 bp):
CAGCAGTAGCGAGAAAAC
Found at i:17425007 original size:19 final size:19
Alignment explanation
Indices: 17424949--17425010 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
17424939 CTAAAACGAT
* *
17424949 ACCCTAAATGAAACCCTAA
1 ACCCTAAGTGAAAACCTAA
* *
17424968 A-CCTTAG-GTAAACCTTAAA
1 ACCCTAAGTGAAAACC-T-AA
17424987 ACCCTAAGTGAAAACCTAA
1 ACCCTAAGTGAAAACCTAA
17425006 ACCCT
1 ACCCT
17425011 TAAACCCGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.15
18 5 0.15
19 11 0.33
20 6 0.18
21 6 0.18
ACGTcount: A:0.44, C:0.29, G:0.08, T:0.19
Consensus pattern (19 bp):
ACCCTAAGTGAAAACCTAA
Found at i:17430394 original size:6 final size:6
Alignment explanation
Indices: 17430383--17430410 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17430373 CAAATTGAGA
17430383 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
17430411 AGAGGAGATT
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:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:17430631 original size:17 final size:17
Alignment explanation
Indices: 17430596--17430635 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
17430586 GTTAAATGGG
17430596 TATTTTTAAAATTCATTA
1 TATTTTTAAAATT-ATTA
17430614 TATTTTATAAAATT-TTA
1 TATTTT-TAAAATTATTA
17430631 TATTT
1 TATTT
17430636 CAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 6 0.29
19 7 0.33
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTAAAATTATTA
Found at i:17430716 original size:23 final size:24
Alignment explanation
Indices: 17430687--17430733 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
17430677 TAATTTTTTA
17430687 AAATACA-ATTCAAA-TAAACATAT
1 AAATACACA-TCAAATTAAACATAT
*
17430710 AAATACACATCAAATTACACATAT
1 AAATACACATCAAATTAAACATAT
17430734 TTCACACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (24 bp):
AAATACACATCAAATTAAACATAT
Found at i:17433811 original size:6 final size:6
Alignment explanation
Indices: 17433800--17433825 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17433790 CAATCCTTCA
17433800 TTCCTT TTCCTT TTCCTT TTCCTT TT
1 TTCCTT TTCCTT TTCCTT TTCCTT TT
17433826 TATTAATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCCTT
Found at i:17434869 original size:12 final size:13
Alignment explanation
Indices: 17434828--17434869 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
17434818 TTAGTGAGGG
* *
17434828 TTTTTAATTTATG
1 TTTTTAATTGATA
17434841 TTTTTAATTGATA
1 TTTTTAATTGATA
17434854 -TTTTAA-TGATA
1 TTTTTAATTGATA
17434865 TTTTT
1 TTTTT
17434870 TTGTTGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTTAATTGATA
Found at i:17435098 original size:21 final size:23
Alignment explanation
Indices: 17435074--17435116 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
17435064 AGATTAAATA
17435074 TTATTAAAAT-ATTTT-ATATTG
1 TTATTAAAATAATTTTAATATTG
*
17435095 TTATTAATATAATTTTAATATT
1 TTATTAAAATAATTTTAATATT
17435117 CTTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTAAAATAATTTTAATATTG
Found at i:17439357 original size:26 final size:26
Alignment explanation
Indices: 17439327--17439392 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
17439317 TTTTATTTGA
* *
17439327 GTATTGCTCGTTGATTTAGAGCTTGT
1 GTATTGCTCATTGATTTAGAGCTTAT
*
17439353 GTATTACTCATTGATTTAGAGCTTAT
1 GTATTGCTCATTGATTTAGAGCTTAT
*
17439379 GTGTTGCTCATTGA
1 GTATTGCTCATTGA
17439393 CTTAAACTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (26 bp):
GTATTGCTCATTGATTTAGAGCTTAT
Done.