Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 92 of 143
Found at i:28618450 original size:70 final size:67
Alignment explanation
Indices: 28618366--28618498 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 67
28618356 TTTGAATAAG
* *
28618366 AAAAGGCAAAATTATGTCGTTTTGATAAATGTTTACCCTTACTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGCAAAATTATGTCATTTTGATAAATGTTTA--CTCA-TAAAGTTAAAAGTCAAAACCATT
28618431 AAGTT
63 AAGTT
* *
28618436 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTACTCATTAAGTTAAAAGTCAAAACCATTA
1 AAAAGGCAAAATTATGTCATTTTGATAAATGTTTACTCATAAAGTTAAAAGTCAAAACCATTA
28618499 TATTATTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 23 0.39
68 3 0.05
70 33 0.56
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (67 bp):
AAAAGGCAAAATTATGTCATTTTGATAAATGTTTACTCATAAAGTTAAAAGTCAAAACCATTAAG
TT
Found at i:28623167 original size:13 final size:11
Alignment explanation
Indices: 28623139--28623181 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
28623129 AGTTAAATAT
28623139 TATTTTATTAA
1 TATTTTATTAA
28623150 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
28623163 TA-TTTATTAT
1 TATTTTATTAA
28623173 TATTTTATT
1 TATTTTATT
28623182 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28623168 original size:23 final size:23
Alignment explanation
Indices: 28623142--28623185 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28623132 TAAATATTAT
28623142 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
28623165 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
28623186 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:28624906 original size:19 final size:19
Alignment explanation
Indices: 28624882--28624924 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
28624872 AATGAAGTGG
28624882 CGGTTATAACATCTGAATA
1 CGGTTATAACATCTGAATA
*
28624901 CGGTTATGACATCTGAATA
1 CGGTTATAACATCTGAATA
28624920 CGGTT
1 CGGTT
28624925 TAGGTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (19 bp):
CGGTTATAACATCTGAATA
Found at i:28628022 original size:18 final size:17
Alignment explanation
Indices: 28627989--28628022 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28627979 AGATGACTAT
*
28627989 ATAAAAATTTTCAATAA
1 ATAAAAATTTTAAATAA
28628006 ATAAAAATTATTAAATA
1 ATAAAAATT-TTAAATA
28628023 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAAAATTTTAAATAA
Found at i:28628029 original size:22 final size:22
Alignment explanation
Indices: 28628004--28628046 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28627994 AATTTTCAAT
*
28628004 AAATAAAA-ATTATTAAATATTA
1 AAATAAAACAATA-TAAATATTA
28628026 AAATAAAACAATATAAATATT
1 AAATAAAACAATATAAATATT
28628047 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAAACAATATAAATATTA
Found at i:28630086 original size:13 final size:14
Alignment explanation
Indices: 28630048--28630087 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
28630038 GAAAAGTAAT
28630048 TAAAATATA-T-AA
1 TAAAATATATTAAA
*
28630060 TATAATATATTAAA
1 TAAAATATATTAAA
28630074 TAAAATA-ATTAAA
1 TAAAATATATTAAA
28630087 T
1 T
28630088 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATATATTAAA
Found at i:28630857 original size:14 final size:16
Alignment explanation
Indices: 28630822--28630862 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
28630812 TATTGTTTTA
28630822 TTCAATATGATCATTT
1 TTCAATATGATCATTT
*
28630838 TACAATA-GAT-ATTT
1 TTCAATATGATCATTT
*
28630852 TTCAATGTGAT
1 TTCAATATGAT
28630863 AGCCTGATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (16 bp):
TTCAATATGATCATTT
Found at i:28638720 original size:21 final size:21
Alignment explanation
Indices: 28638673--28638729 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
28638663 ATAGTAGCAG
**
28638673 ACTTCTACTGATACTTGTGAT
1 ACTTCTACTGATACAAGTGAT
*
28638694 AGTTCTACTGATACAAGTG-T
1 ACTTCTACTGATACAAGTGAT
*
28638714 ACCTTCTACCGATACA
1 A-CTTCTACTGATACA
28638730 CGACATGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (21 bp):
ACTTCTACTGATACAAGTGAT
Found at i:28639487 original size:18 final size:18
Alignment explanation
Indices: 28639437--28639478 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28639427 TAATGCTCTT
*
28639437 ACGAGCCATTATGCTCAA
1 ACGAGCCAATATGCTCAA
*
28639455 ATGAGCCAATATGCTCAA
1 ACGAGCCAATATGCTCAA
28639473 ACGAGC
1 ACGAGC
28639479 TAGTATGCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (18 bp):
ACGAGCCAATATGCTCAA
Found at i:28648575 original size:29 final size:29
Alignment explanation
Indices: 28648543--28648733 Score: 204
Period size: 30 Copynumber: 6.4 Consensus size: 29
28648533 ACCGGTGTCA
* * *
28648543 AAAATGAAATTTTGGAAGGTTTTAGGGTT
1 AAAATGTAATTTTGAAAAGTTTTAGGGTT
* * *
28648572 AAAATGTAATTTTAGAAAAATTTTGGGGTC
1 AAAATGTAATTTT-GAAAAGTTTTAGGGTT
* *
28648602 AAAATGTAATTTTGGAAAAG-TTTGGGGAT
1 AAAATGTAATTTT-GAAAAGTTTTAGGGTT
**
28648631 AAAATGTAATTTTGGAAAAGTTTTAGGGAG
1 AAAATGTAATTTT-GAAAAGTTTTAGGGTT
* *
28648661 AAAATGTGATTTTAGAAAAGTTTTGGGGTT
1 AAAATGTAATTTT-GAAAAGTTTTAGGGTT
*
28648691 AAAATGTAATTTTCAAAGAGTTTTAGGGTT
1 AAAATGTAATTTTGAAA-AGTTTTAGGGTT
*
28648721 AAAATATAATTTT
1 AAAATGTAATTTT
28648734 TGGACAGTTT
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
29 42 0.30
30 96 0.70
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTGAAAAGTTTTAGGGTT
Found at i:28648615 original size:59 final size:59
Alignment explanation
Indices: 28648543--28648743 Score: 199
Period size: 59 Copynumber: 3.4 Consensus size: 59
28648533 ACCGGTGTCA
* * * * *
28648543 AAAATGAAATTTTGGAAGGTTTTAGGGTTAAAATGTAATTTTAGAAAAATTTTGGGGTC
1 AAAATGTAATTTTGGAAAGTTTTGGGGTTAAAATGTAATTTTAGAAAAATTTTAGGGAC
* * * *
28648602 AAAATGTAATTTTGGAAAAG-TTTGGGGATAAAATGTAATTTTGGAAAAGTTTTAGGGAG
1 AAAATGTAATTTTGG-AAAGTTTTGGGGTTAAAATGTAATTTTAGAAAAATTTTAGGGAC
* * * * **
28648661 AAAATGTGATTTTAGAAAAGTTTTGGGGTTAAAATGTAATTTTCA-AAGAGTTTTAGGGTT
1 AAAATGTAATTTT-GGAAAGTTTTGGGGTTAAAATGTAATTTT-AGAAAAATTTTAGGGAC
* *
28648721 AAAATATAATTTTTGGACAGTTT
1 AAAATGTAA-TTTTGGAAAGTTT
28648744 AGGGACCTAC
Statistics
Matches: 117, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
59 62 0.53
60 51 0.44
61 4 0.03
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.38
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAGTTTTGGGGTTAAAATGTAATTTTAGAAAAATTTTAGGGAC
Found at i:28649451 original size:11 final size:12
Alignment explanation
Indices: 28649435--28649465 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28649425 TTTCTTTTCC
28649435 TTTTATTTC-TT
1 TTTTATTTCATT
28649446 TTTTATTTCATT
1 TTTTATTTCATT
28649458 TTTTATTT
1 TTTTATTT
28649466 TGTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTATTTCATT
Found at i:28649848 original size:3 final size:3
Alignment explanation
Indices: 28649840--28649972 Score: 88
Period size: 3 Copynumber: 42.3 Consensus size: 3
28649830 TATTTAAACC
* *
28649840 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT AGCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
** * * *
28649886 ATT GATT GCT GTT ATT AAT ACT A-T ATTT ATT ATT ATT ATT ATT GATGCT
1 ATT -ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT -AT--T
* * ** *
28649935 GTT ATT TTT ATT AGA ATT ATT ATT AAT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
28649973 AGGAGATGTT
Statistics
Matches: 103, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
2 2 0.02
3 87 0.84
4 12 0.12
5 1 0.01
6 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28650621 original size:6 final size:6
Alignment explanation
Indices: 28650610--28650673 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
28650600 TTATAATAAT
** *
28650610 TTTAAA TTTAAA -TTAAA TCCAAAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
28650657 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
28650674 ACAAATTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
5 14 0.32
6 26 0.59
7 4 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:28650625 original size:11 final size:11
Alignment explanation
Indices: 28650611--28650666 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
28650601 TATAATAATT
28650611 TTAAATTTAAA
1 TTAAATTTAAA
**
28650622 TTAAATCCAAAA
1 TTAAAT-TTAAA
28650634 TTTAAA-TTAAA
1 -TTAAATTTAAA
28650645 TTCAAATTTAAA
1 TT-AAATTTAAA
*
28650657 ATAAATTTAA
1 TTAAATTTAA
28650667 TTTTAAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 2 0.06
11 20 0.56
12 9 0.25
13 5 0.14
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:28650636 original size:18 final size:17
Alignment explanation
Indices: 28650613--28650662 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
28650603 TAATAATTTT
28650613 AAATTTAAATTAAATCC
1 AAATTTAAATTAAATCC
*
28650630 AAAATTTAAATTAAATTC
1 -AAATTTAAATTAAATCC
*
28650648 AAATTTAAAATAAAT
1 AAATTTAAATTAAAT
28650663 TTAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTAAATTAAATCC
Found at i:28650653 original size:17 final size:17
Alignment explanation
Indices: 28650597--28650684 Score: 86
Period size: 17 Copynumber: 5.1 Consensus size: 17
28650587 TTGGACATTG
* * *
28650597 AATTTATAATAATTTTA
1 AATTTAAAATAAATTCA
* *
28650614 AATTTAAATTAAATCCAA
1 AATTTAAAATAAATTC-A
*
28650632 AATTTAAATTAAATTCA
1 AATTTAAAATAAATTCA
*
28650649 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* *
28650666 ATTTTAAAACAAATTCA
1 AATTTAAAATAAATTCA
28650683 AA
1 AA
28650685 ATAGTTTGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
17 42 0.72
18 16 0.28
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:28651105 original size:92 final size:92
Alignment explanation
Indices: 28650947--28651766 Score: 1428
Period size: 92 Copynumber: 8.9 Consensus size: 92
28650937 CGAGGTTTCG
* * ** * * *
28650947 TCTTGCTCTTACTTCAATTTCAGAGAGGA--ATGATTTGATATCCAACTCTACTTCAATTTCAAG
1 TCTTACTCTTACTTCAATTTCAGAG-GGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAG
* *
28651010 AGGATAGGAAAATGATGTTTGTGCTTCA
65 AGGATAGGAAAATGATGTTGGTCCTTCA
*
28651038 TCTTACTCTTACTTCGATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651103 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCA
*
28651130 TCTTACTCTTACTTCGATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651195 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCA
28651222 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651287 GGATAGGAAAATGATGTTGGTGCTTCA
66 GGATAGGAAAATGATGTTGGTCCTTCA
*
28651314 TCTTACTCTTACTTCAATTTTAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651379 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCA
28651406 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651471 GGATAGGAAAATGATGTTGGTGCTTCA
66 GGATAGGAAAATGATGTTGGTCCTTCA
*
28651498 ACTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651563 GGATAGGAAAATGATGTTGGTCCTTCT
66 GGATAGGAAAATGATGTTGGTCCTTCA
28651590 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
*
28651655 GGATAGGAAAATGATGTTGGTGCTTCA
66 GGATAGGAAAATGATGTTGGTCCTTCA
*
28651682 TCTTACTCTTACTTCAATTTCATAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
1 TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
28651747 GGATAGGAAAATGATGTTGG
66 GGATAGGAAAATGATGTTGG
28651767 ATTGATGTGA
Statistics
Matches: 700, Mismatches: 27, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
90 3 0.00
91 23 0.03
92 674 0.96
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (92 bp):
TCTTACTCTTACTTCAATTTCAGAGGGACGAAGGCTTGTTATCCAGCTTTACTTCAATTTCAAGA
GGATAGGAAAATGATGTTGGTCCTTCA
Found at i:28663769 original size:28 final size:28
Alignment explanation
Indices: 28663737--28663801 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
28663727 AAAACGGGAC
28663737 TTTTGGA-TACCCGAGGGCAAAATGGTAA
1 TTTTGGACT-CCCGAGGGCAAAATGGTAA
** *
28663765 TTTTGGACTTTCGAGGGCAAAATTGTAA
1 TTTTGGACTCCCGAGGGCAAAATGGTAA
28663793 TTTTGGACT
1 TTTTGGACT
28663802 TTTGGGGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
TTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:28663802 original size:28 final size:28
Alignment explanation
Indices: 28663748--28663827 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
28663738 TTTGGATACC
*
28663748 CGAGGGCAAAATGGTAATTTTGGACTTT
1 CGAGGGCAAAATTGTAATTTTGGACTTT
28663776 CGAGGGCAAAATTGTAATTTTGGACTTT
1 CGAGGGCAAAATTGTAATTTTGGACTTT
* * *
28663804 TGGGGGGAAAATTGTAATTTTGGA
1 CGAGGGCAAAATTGTAATTTTGGA
28663828 AAAATCGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.34
Consensus pattern (28 bp):
CGAGGGCAAAATTGTAATTTTGGACTTT
Found at i:28663964 original size:90 final size:91
Alignment explanation
Indices: 28663870--28664122 Score: 232
Period size: 90 Copynumber: 2.8 Consensus size: 91
28663860 TTCGGGGGTA
* *
28663870 AAAATGGTAAATTTTGGTAAAA-CCGA-GGTCAAAAATGAAATTTTAG-AAGGTTTTGAGGTTAA
1 AAAATGGT-AATTTTGGAAAAATCCGAGGGT-AAAAATGAAATTTTAGAAAAGTTTTGAGGTTAA
* *
28663932 AATGTAATTTTGGAAAAGTTTTGAGGTT
64 AATGTAATTTTGGAAAAGTTTTAAGGTC
*** * * * *
28663960 AAAAT-GTAATTTTGGAAAAATTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAA
1 AAAATGGTAATTTTGGAAAAATCCGAGGGTAAAAATGAAATTTTAGAAAAGTTTTGAGGTTAAAA
28664024 TGTAATTTTGGAAAAGTTTTAAGGTC
66 TGTAATTTTGGAAAAGTTTTAAGGTC
* * * *** * * *
28664050 AAAAT-GTGATTTTAGAAAAGTTTTAGGGTCAAAATGTAATTTTCA-AAGAGTTTT-AGGGTTAA
1 AAAATGGTAATTTTGGAAAAATCCGAGGGTAAAAATGAAATTTT-AGAAAAGTTTTGA-GGTTAA
*
28664112 AATATAATTTT
64 AATGTAATTTT
28664123 TGGACAGTTT
Statistics
Matches: 139, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
88 12 0.09
89 16 0.12
90 111 0.80
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (91 bp):
AAAATGGTAATTTTGGAAAAATCCGAGGGTAAAAATGAAATTTTAGAAAAGTTTTGAGGTTAAAA
TGTAATTTTGGAAAAGTTTTAAGGTC
Found at i:28664132 original size:30 final size:30
Alignment explanation
Indices: 28663901--28664122 Score: 281
Period size: 30 Copynumber: 7.4 Consensus size: 30
28663891 ACCGAGGTCA
* * *
28663901 AAAATGAAATTTTAG-AAGGTTTT-GAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAG-GGTT
28663930 AAAATGTAATTTTGGAAAAGTTTT-GAGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAG-GGTT
*
28663960 AAAATGTAATTTTGGAAAAATTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
*
28663990 AAAATGTAATTTTGGAAAAGTTTTGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
* *
28664020 AAAATGTAATTTTGGAAAAGTTTTAAGGTC
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
* * *
28664050 AAAATGTGATTTTAGAAAAGTTTTAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
*
28664080 AAAATGTAATTTT-CAAAGAGTTTTAGGGTT
1 AAAATGTAATTTTGGAAA-AGTTTTAGGGTT
*
28664110 AAAATATAATTTT
1 AAAATGTAATTTT
28664123 TGGACAGTTT
Statistics
Matches: 174, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.09
30 157 0.90
31 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTTAGGGTT
Found at i:28665328 original size:36 final size:37
Alignment explanation
Indices: 28665261--28665332 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
28665251 TATTAATGGC
* *
28665261 TATTGATTGCTGTTATTAATACTATATTTATTATTAT
1 TATTGATTGCTGTTATTAATACTAGAATTATTATTAT
** *
28665298 TATTGA-TGCTGTTATTGTTATTAGAATTATTATTA
1 TATTGATTGCTGTTATTAATACTAGAATTATTATTA
28665333 ATACTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (37 bp):
TATTGATTGCTGTTATTAATACTAGAATTATTATTAT
Found at i:28665986 original size:11 final size:11
Alignment explanation
Indices: 28665970--28666021 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
28665960 TTGGACATTG
28665970 AATTTATAA-TA
1 AATTTA-AATTA
28665981 AATTTAAATTTA
1 AATTTAAA-TTA
28665993 AA-TTAAATTCA
1 AATTTAAATT-A
*
28666004 AATTTAAAATA
1 AATTTAAATTA
28666015 AATTTAA
1 AATTTAA
28666022 TTTTAAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 4 0.11
11 22 0.61
12 10 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:28665990 original size:6 final size:6
Alignment explanation
Indices: 28665979--28666028 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
28665969 GAATTTATAA
* * *
28665979 TAAATT TAAATT TAAA-T TAAATT CAAATT TAAA-A TAAATT TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
28666025 TAAA
1 TAAA
28666029 ACAAATTCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:28666008 original size:34 final size:34
Alignment explanation
Indices: 28665970--28666039 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
28665960 TTGGACATTG
* **
28665970 AATTTATAATAAATTTAAATTTAAATTAAATTCA
1 AATTTAAAATAAATTTAAATTTAAAACAAATTCA
*
28666004 AATTTAAAATAAATTTAATTTTAAAACAAATTCA
1 AATTTAAAATAAATTTAAATTTAAAACAAATTCA
28666038 AA
1 AA
28666040 ATGGTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
AATTTAAAATAAATTTAAATTTAAAACAAATTCA
Found at i:28666029 original size:17 final size:17
Alignment explanation
Indices: 28665970--28666035 Score: 87
Period size: 17 Copynumber: 3.9 Consensus size: 17
28665960 TTGGACATTG
*
28665970 AATTTATAATAAATTTA
1 AATTTAAAATAAATTTA
* *
28665987 AATTTAAATTAAATTCA
1 AATTTAAAATAAATTTA
28666004 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
28666021 ATTTTAAAACAAATT
1 AATTTAAAATAAATT
28666036 CAAAATGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:28666033 original size:28 final size:28
Alignment explanation
Indices: 28665985--28666041 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28665975 ATAATAAATT
* *
28665985 TAAATTTAAATTAAATTCAAATTTAAAA
1 TAAATTTAAATTAAATACAAATTCAAAA
*
28666013 TAAATTTAATTTTAAA-ACAAATTCAAAA
1 TAAATTTAA-ATTAAATACAAATTCAAAA
28666041 T
1 T
28666042 GGTTTGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATTTAAATTAAATACAAATTCAAAA
Found at i:28673871 original size:39 final size:39
Alignment explanation
Indices: 28673828--28673917 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
28673818 GGAAAATCTT
* * *
28673828 ATTCAGTATATTTATTAGATAATGCTCATTCGAGCAAGC
1 ATTCAATATAATTAGTAGATAATGCTCATTCGAGCAAGC
* * *
28673867 ATTCAATATAATTAGTAGTTATTGCTCATTTGAGCAAGC
1 ATTCAATATAATTAGTAGATAATGCTCATTCGAGCAAGC
28673906 ATTCAATATAAT
1 ATTCAATATAAT
28673918 CAGCGGATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (39 bp):
ATTCAATATAATTAGTAGATAATGCTCATTCGAGCAAGC
Found at i:28673947 original size:38 final size:38
Alignment explanation
Indices: 28673859--28674079 Score: 282
Period size: 38 Copynumber: 5.8 Consensus size: 38
28673849 ATGCTCATTC
* * **
28673859 GAGCAAGCATTCAATATAATTAGTAGTTATT-GCTCATTT
1 GAGCAAGCATTCAGTATAATCAGTAG--ATTCGCTCGCTT
* ** *
28673898 GAGCAAGCATTCAATATAATCAGCGGATTCGCTTGCTT
1 GAGCAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
* * *
28673936 GAGCAAACATTCAATATAATCAGTAGATTCACTCGCTT
1 GAGCAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
*
28673974 GAGCAAGCATTCAGTATATTCAGTAGATTCGCTCGCTT
1 GAGCAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
* *
28674012 GAGCAAGCATTCAGTATAATCAATGGATTCGCTCGCTT
1 GAGCAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
*
28674050 GAGCAAGCATTCAGTATATTCAGTAGATTC
1 GAGCAAGCATTCAGTATAATCAGTAGATTC
28674080 ATTTCGTTTC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
37 3 0.02
38 134 0.84
39 23 0.14
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (38 bp):
GAGCAAGCATTCAGTATAATCAGTAGATTCGCTCGCTT
Found at i:28674030 original size:114 final size:114
Alignment explanation
Indices: 28673859--28674080 Score: 313
Period size: 114 Copynumber: 1.9 Consensus size: 114
28673849 ATGCTCATTC
* *
28673859 GAGCAAGCATTCAATATAATTAGTAGTTATTGCTCATTTGAGCAAGCATTCAATATAATCAGCGG
1 GAGCAAGCATTCAATATAATTAGTAG-TATTGCTCACTTGAGCAAGCATTCAATATAATCAACGG
*
28673924 ATTCGCTTGCTTGAGCAAACATTCAATATAATCAGTAGATTCACTCGCTT
65 ATTCGCTCGCTTGAGCAAACATTCAATATAATCAGTAGATTCACTCGCTT
* * * *
28673974 GAGCAAGCATTCAGTAT-ATTCAGTAG-ATTCGCTCGCTTGAGCAAGCATTCAGTATAATCAATG
1 GAGCAAGCATTCAATATAATT-AGTAGTATT-GCTCACTTGAGCAAGCATTCAATATAATCAACG
* * *
28674037 GATTCGCTCGCTTGAGCAAGCATTCAGTATATTCAGTAGATTCA
64 GATTCGCTCGCTTGAGCAAACATTCAATATAATCAGTAGATTCA
28674081 TTTCGTTTCA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
113 3 0.03
114 71 0.75
115 21 0.22
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (114 bp):
GAGCAAGCATTCAATATAATTAGTAGTATTGCTCACTTGAGCAAGCATTCAATATAATCAACGGA
TTCGCTCGCTTGAGCAAACATTCAATATAATCAGTAGATTCACTCGCTT
Found at i:28675134 original size:18 final size:18
Alignment explanation
Indices: 28675111--28675151 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
28675101 AATACCGCAA
* *
28675111 TAATAACCTCGTAAATAT
1 TAATAAACTAGTAAATAT
*
28675129 TAATAAATTAGTAAATAT
1 TAATAAACTAGTAAATAT
28675147 TAATA
1 TAATA
28675152 TTTACGGACC
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:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (18 bp):
TAATAAACTAGTAAATAT
Found at i:28686389 original size:25 final size:25
Alignment explanation
Indices: 28686360--28686478 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
28686350 AACCAAACAG
*
28686360 AGCCTATGTGGCATATTATCTGGAA
1 AGCCTATGTGGCATATTATCTGAAA
* *
28686385 AGCCTTTGTGG--TGAGTTATCCGAAA
1 AGCCTATGTGGCAT-A-TTATCTGAAA
* *
28686410 ACCCTATGTGGCATATTATCTTAAA
1 AGCCTATGTGGCATATTATCTGAAA
* * *
28686435 AGCCTTTGTGACGA-GTTATCTGAAA
1 AGCCTATGTGGC-ATATTATCTGAAA
*
28686460 GGCCTATGTGGCATATTAT
1 AGCCTATGTGGCATATTAT
28686479 TTAGGAAGCC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 66 0.92
26 2 0.03
27 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (25 bp):
AGCCTATGTGGCATATTATCTGAAA
Found at i:28686421 original size:50 final size:50
Alignment explanation
Indices: 28686362--28686478 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 50
28686352 CCAAACAGAG
* **
28686362 CCTATGTGGCATATTATCTGGAAAGCCTTTGTGGTGAGTTATCCGAAAAC
1 CCTATGTGGCATATTATCTGAAAAGCCTTTGTGACGAGTTATCCGAAAAC
* * **
28686412 CCTATGTGGCATATTATCTTAAAAGCCTTTGTGACGAGTTATCTGAAAGG
1 CCTATGTGGCATATTATCTGAAAAGCCTTTGTGACGAGTTATCCGAAAAC
28686462 CCTATGTGGCATATTAT
1 CCTATGTGGCATATTAT
28686479 TTAGGAAGCC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (50 bp):
CCTATGTGGCATATTATCTGAAAAGCCTTTGTGACGAGTTATCCGAAAAC
Found at i:28686488 original size:50 final size:50
Alignment explanation
Indices: 28686360--28686490 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 50
28686350 AACCAAACAG
* **
28686360 AGCCTATGTGGCATATTATCT-GGAAAGCCTTTGTGGTGAGTTATCCGAAA
1 AGCCTATGTGGCATATTATTTAGG-AAGCCTTTGTGACGAGTTATCCGAAA
* * *
28686410 ACCCTATGTGGCATATTATCTTA-AAAGCCTTTGTGACGAGTTATCTGAAA
1 AGCCTATGTGGCATATTAT-TTAGGAAGCCTTTGTGACGAGTTATCCGAAA
*
28686460 GGCCTATGTGGCATATTATTTAGGAAGCCTT
1 AGCCTATGTGGCATATTATTTAGGAAGCCTT
28686491 AGTCATGAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.04
50 65 0.94
51 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (50 bp):
AGCCTATGTGGCATATTATTTAGGAAGCCTTTGTGACGAGTTATCCGAAA
Found at i:28688812 original size:14 final size:14
Alignment explanation
Indices: 28688780--28688813 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28688770 CGCCATGGCA
*
28688780 GTAAGGTAAATGGT
1 GTAAGGTAAATAGT
*
28688794 ATAAGGTAAATAGT
1 GTAAGGTAAATAGT
28688808 GTAAGG
1 GTAAGG
28688814 CCATAGATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.26
Consensus pattern (14 bp):
GTAAGGTAAATAGT
Found at i:28692603 original size:26 final size:26
Alignment explanation
Indices: 28692574--28692626 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28692564 AGGCCCTTCG
28692574 ATGGCTGGGACTTATGCTTTATGCAT
1 ATGGCTGGGACTTATGCTTTATGCAT
28692600 ATGGCTGGGACTTATGCTTTATGCAT
1 ATGGCTGGGACTTATGCTTTATGCAT
28692626 A
1 A
28692627 CTCCCGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (26 bp):
ATGGCTGGGACTTATGCTTTATGCAT
Found at i:28693754 original size:25 final size:23
Alignment explanation
Indices: 28693726--28693790 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
28693716 CTTCCAGAAT
28693726 TTAGCTCATACGAGCCTAGAGA-ACA
1 TTAGCTC-TACGAGCCTAG-GATA-A
* *
28693751 TTAGATCTCACGAGCCTAGGATAG
1 TTAGCTCT-ACGAGCCTAGGATAA
28693775 TTAGCTCTTACGAGCC
1 TTAGCTC-TACGAGCC
28693791 CAAAATGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (23 bp):
TTAGCTCTACGAGCCTAGGATAA
Found at i:28693787 original size:24 final size:24
Alignment explanation
Indices: 28693751--28693825 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
28693741 CTAGAGAACA
* * * *
28693751 TTAGATCTCACGAGCCTAGGATAG
1 TTAGCTCTTACGAGCCCAGAATAG
* *
28693775 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATAG
28693799 TTAGCTCTTACGAGCCCAGAATAG
1 TTAGCTCTTACGAGCCCAGAATAG
28693823 TTA
1 TTA
28693826 ACCAGTATAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATAG
Found at i:28694489 original size:33 final size:33
Alignment explanation
Indices: 28694452--28694520 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
28694442 AACATGCAAA
28694452 ATACTCATTTTCTCCTCAACCCACACTAGCCAG
1 ATACTCATTTTCTCCTCAACCCACACTAGCCAG
*
28694485 ATACTCATTTTCTCCTCAACCCATACTAGCCAG
1 ATACTCATTTTCTCCTCAACCCACACTAGCCAG
28694518 ATA
1 ATA
28694521 TACCTTGATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.36, G:0.06, T:0.29
Consensus pattern (33 bp):
ATACTCATTTTCTCCTCAACCCACACTAGCCAG
Found at i:28696210 original size:21 final size:21
Alignment explanation
Indices: 28696183--28696238 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28696173 AGAGTTTTTG
28696183 GTATCGGTAGAAGTAAG-ACTT
1 GTATCGGTAGAAGT-AGCACTT
*
28696204 GTTTCGGTAGAAG-AGTCACTT
1 GTATCGGTAGAAGTAG-CACTT
28696225 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
28696239 CTGCACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.07
21 28 0.93
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTAGCACTT
Found at i:28696686 original size:184 final size:184
Alignment explanation
Indices: 28696326--28696686 Score: 544
Period size: 184 Copynumber: 2.0 Consensus size: 184
28696316 AATGTCGAAA
28696326 ATGACCTTTTTACCCTTGTTAAATTGTGTTTATAATCAAATGACGATATATGACGTGTGGAGTGC
1 ATGACCTTTTTACCCTTGTTAAATTGTGTTTATAATCAAATGACGATATATGACGTGTGGAGTGC
* * *
28696391 AATTCTTTAATAAAATAAGACTAAATAACATGATGTTAAAGATGAATAGTGTTAAATGTATAATA
66 AATTCTTTAATAAAATAAGACTAAACAACATGATGTTAAAGATGAACAATGTTAAATGTATAATA
* * *
28696456 AGACACCGAAACCCTATCCATCGATGATTTATGAGTTTTAGGTGTTACATTTAG
131 AGACACCGAAACCCTAGCCATCGATGATATAAGAGTTTTAGGTGTTACATTTAG
* * *
28696510 ATGACCTTTTTGCCCTTGTTGAATTGTGTTTATAATCAAATGACGATATATGACGTGTGGAGTGT
1 ATGACCTTTTTACCCTTGTTAAATTGTGTTTATAATCAAATGACGATATATGACGTGTGGAGTGC
* * *
28696575 AATTCTTTATTAAAATAAGACTGAACAACATGATGTTAAAGATGAACAATGTTAAATGTATAGTA
66 AATTCTTTAATAAAATAAGACTAAACAACATGATGTTAAAGATGAACAATGTTAAATGTATAATA
* * * * * *
28696640 AGACATCGGAACTCTAGCCGTCGATGGTATACAG-GTTTTGGGTGTTA
131 AGACACCGAAACCCTAGCCATCGATGATATA-AGAGTTTTAGGTGTTA
28696687 TAGTGATGTC
Statistics
Matches: 158, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
184 157 0.99
185 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (184 bp):
ATGACCTTTTTACCCTTGTTAAATTGTGTTTATAATCAAATGACGATATATGACGTGTGGAGTGC
AATTCTTTAATAAAATAAGACTAAACAACATGATGTTAAAGATGAACAATGTTAAATGTATAATA
AGACACCGAAACCCTAGCCATCGATGATATAAGAGTTTTAGGTGTTACATTTAG
Found at i:28701270 original size:27 final size:27
Alignment explanation
Indices: 28701230--28701281 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
28701220 GGTGTTTACT
** * *
28701230 TGACAAGCGGCACTAGTGGTGCCTACC
1 TGACAAGCACCACTAATGATGCCTACC
28701257 TGACAAGCACCACTAATGATGCCTA
1 TGACAAGCACCACTAATGATGCCTA
28701282 TTGGGTAGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (27 bp):
TGACAAGCACCACTAATGATGCCTACC
Found at i:28701462 original size:14 final size:15
Alignment explanation
Indices: 28701437--28701465 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28701427 TAAAATTTTA
28701437 ACAATAATTTTATTT
1 ACAATAATTTTATTT
28701452 ACAATAA-TTTATTT
1 ACAATAATTTTATTT
28701466 GTTGTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ACAATAATTTTATTT
Found at i:28705567 original size:26 final size:26
Alignment explanation
Indices: 28705527--28705585 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
28705517 ATGAATTTGG
* *
28705527 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTATATTT
* **
28705553 AATTAATAATTTTTATGTTTATATTT
1 AATTAATAATGTTTAAATTTATATTT
28705579 AATTAAT
1 AATTAAT
28705586 TAATCTCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTATATTT
Found at i:28705776 original size:14 final size:14
Alignment explanation
Indices: 28705754--28705801 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
28705744 GGGATTAAAG
28705754 TTTAGGGTTTAAGAT
1 TTTA-GGTTTAAGAT
*
28705769 TTTAGGTTTAAGGTT
1 TTTAGGTTTAA-GAT
*
28705784 TTATAGGTTTAAGGT
1 TT-TAGGTTTAAGAT
28705799 TTT
1 TTT
28705802 GGGTATAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 8 0.28
15 12 0.41
16 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (14 bp):
TTTAGGTTTAAGAT
Found at i:28705777 original size:21 final size:21
Alignment explanation
Indices: 28705753--28705849 Score: 88
Period size: 21 Copynumber: 4.5 Consensus size: 21
28705743 GGGGATTAAA
*
28705753 GTTTAGGGTTTAAGATTTTAG
1 GTTTAGGGTTTAAGGTTTTAG
* *
28705774 GTTTAAGGTTTTATAGGTTTAAG
1 GTTT-AGGGTTTA-AGGTTTTAG
* *
28705797 GTTTTGGGTATAAGG-TTTAG
1 GTTTAGGGTTTAAGGTTTTAG
* *
28705817 TGTTTAGTGTTTAAGGTTTTGG
1 -GTTTAGGGTTTAAGGTTTTAG
*
28705839 GTCTAGGGTTT
1 GTTTAGGGTTT
28705850 TGGGTATAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 4 0.07
21 28 0.47
22 16 0.27
23 11 0.19
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (21 bp):
GTTTAGGGTTTAAGGTTTTAG
Found at i:28705782 original size:7 final size:7
Alignment explanation
Indices: 28705748--28705835 Score: 63
Period size: 7 Copynumber: 12.3 Consensus size: 7
28705738 ATTTTGGGGA
*
28705748 TTAAAGT
1 TTAAGGT
*
28705755 TTAGGGT
1 TTAAGGT
*
28705762 TTAAGAT
1 TTAAGGT
*
28705769 TTTAGGT
1 TTAAGGT
28705776 TTAAGGTT
1 TTAAGG-T
28705784 TTATAGGT
1 TTA-AGGT
28705792 TTAAGGT
1 TTAAGGT
**
28705799 TTTGGGT
1 TTAAGGT
*
28705806 ATAAGGT
1 TTAAGGT
28705813 TT-AGTGT
1 TTAAG-GT
28705820 TT-AGTGT
1 TTAAG-GT
28705827 TTAAGGT
1 TTAAGGT
28705834 TT
1 TT
28705836 TGGGTCTAGG
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
6 2 0.03
7 49 0.77
8 10 0.16
9 3 0.05
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (7 bp):
TTAAGGT
Found at i:28705835 original size:14 final size:14
Alignment explanation
Indices: 28705748--28705849 Score: 64
Period size: 14 Copynumber: 7.1 Consensus size: 14
28705738 ATTTTGGGGA
*
28705748 TTAAAGTTTAGGGT
1 TTAAGGTTTAGGGT
*
28705762 TTAAGATTTTA-GGT
1 TTAAG-GTTTAGGGT
*
28705776 TTAAGGTTTTATAGGT
1 TTAAGG-TTTA-GGGT
*
28705792 TTAAGGTTTTGGGT
1 TTAAGGTTTAGGGT
* *
28705806 ATAAGGTTTAGTGT
1 TTAAGGTTTAGGGT
*
28705820 TT-AGTGTTTAAGGT
1 TTAAG-GTTTAGGGT
** *
28705834 TTTGGGTCTAGGGT
1 TTAAGGTTTAGGGT
28705848 TT
1 TT
28705850 TGGGTATAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
13 2 0.03
14 49 0.72
15 8 0.12
16 9 0.13
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (14 bp):
TTAAGGTTTAGGGT
Found at i:28705959 original size:27 final size:27
Alignment explanation
Indices: 28705921--28705982 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
28705911 ACCTAAAACC
* * * *
28705921 GTACTACAACGGGTTAAAAGGCGTAGA
1 GTACTGCAACGGGCTAAAAGACATAGA
28705948 GTACTGCAACGGGCTAAAAGACATAGA
1 GTACTGCAACGGGCTAAAAGACATAGA
28705975 GTACTGCA
1 GTACTGCA
28705983 GTGGTATCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (27 bp):
GTACTGCAACGGGCTAAAAGACATAGA
Found at i:28706198 original size:18 final size:18
Alignment explanation
Indices: 28706177--28706220 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28706167 GAGCTTGGGG
*
28706177 TTTGGCTCATGCTCGAGC
1 TTTGGATCATGCTCGAGC
*
28706195 TTTGGATCGTGCTCGAGC
1 TTTGGATCATGCTCGAGC
*
28706213 TTAGGATC
1 TTTGGATC
28706221 GAGCTCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (18 bp):
TTTGGATCATGCTCGAGC
Found at i:28706221 original size:18 final size:18
Alignment explanation
Indices: 28706186--28706226 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28706176 GTTTGGCTCA
*
28706186 TGCTCGAGCTTTGGATCG
1 TGCTCGAGCTTAGGATCG
28706204 TGCTCGAGCTTAGGATCG
1 TGCTCGAGCTTAGGATCG
*
28706222 AGCTC
1 TGCTC
28706227 ATGCTCAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (18 bp):
TGCTCGAGCTTAGGATCG
Found at i:28724573 original size:27 final size:26
Alignment explanation
Indices: 28724543--28724595 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28724533 ATTTAAATCC
28724543 AAATAATTAATGAAAT-ATTTTATATTT
1 AAATAATTAA--AAATAATTTTATATTT
* *
28724570 AAATTATTAAATATAATTTTATATTT
1 AAATAATTAAAAATAATTTTATATTT
28724596 TATTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 11 0.48
27 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
AAATAATTAAAAATAATTTTATATTT
Found at i:28726128 original size:12 final size:12
Alignment explanation
Indices: 28726113--28726162 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
28726103 GAAAAGGATC
28726113 AAGAAGAAAAAG
1 AAGAAGAAAAAG
28726125 AAGAAGAAGGAAAG
1 AAGAAGAA--AAAG
28726139 --GAAG-AAAAG
1 AAGAAGAAAAAG
28726148 AAAGAAGAAAAAG
1 -AAGAAGAAAAAG
28726161 AA
1 AA
28726163 CCTGCCGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
9 4 0.12
11 1 0.03
12 18 0.56
13 5 0.16
14 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:28726139 original size:30 final size:30
Alignment explanation
Indices: 28726105--28726162 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
28726095 AGTTGAAAGA
* *
28726105 AAAGGATCAAGAAGAAA-AAGAAGAAGAAGG
1 AAAGGAACAA-AAGAAAGAAGAAAAAGAAGG
*
28726135 AAAGGAAGAAAAGAAAGAAGAAAAAGAA
1 AAAGGAACAAAAGAAAGAAGAAAAAGAA
28726163 CCTGCCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.69, C:0.02, G:0.28, T:0.02
Consensus pattern (30 bp):
AAAGGAACAAAAGAAAGAAGAAAAAGAAGG
Found at i:28732433 original size:20 final size:20
Alignment explanation
Indices: 28732398--28732447 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
28732388 TAATATTAAT
28732398 TAAATTATACAATGTATCTATA
1 TAAATTA-A-AATGTATCTATA
*
28732420 TTAATTAAAATGTATCTATA
1 TAAATTAAAATGTATCTATA
28732440 TAAATTAA
1 TAAATTAA
28732448 TGTTTAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 19 0.73
21 1 0.04
22 6 0.23
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
TAAATTAAAATGTATCTATA
Found at i:28733164 original size:3 final size:3
Alignment explanation
Indices: 28733156--28733191 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
28733146 CGATGTTTTA
*
28733156 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28733192 GTTGTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28734706 original size:34 final size:34
Alignment explanation
Indices: 28734638--28734708 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
28734628 AATCCTATTA
*
28734638 TTTAAACACAACTAAACAAATAATAAAAATTACC
1 TTTAAACACAACTAAACAAACAATAAAAATTACC
* *
28734672 TTTAAACAC-ACTTAACTAAACATATAAACA-TACC
1 TTTAAACACAACTAAAC-AAACA-ATAAAAATTACC
28734706 TTT
1 TTT
28734709 CAAAAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 6 0.19
34 20 0.62
35 6 0.19
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (34 bp):
TTTAAACACAACTAAACAAACAATAAAAATTACC
Found at i:28734891 original size:27 final size:26
Alignment explanation
Indices: 28734844--28734902 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
28734834 CATTTAATCA
* * *
28734844 AAAATTAAATTATAATGAACAACATTTT
1 AAAA-TAAATTAAAATCAACAA-AATTT
28734872 AAAATAAATTAAAATCAACAAAATTT
1 AAAATAAATTAAAATCAACAAAATTT
28734898 AAAAT
1 AAAAT
28734903 TTAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 9 0.32
27 15 0.54
28 4 0.14
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATAAATTAAAATCAACAAAATTT
Found at i:28734914 original size:28 final size:27
Alignment explanation
Indices: 28734844--28734923 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
28734834 CATTTAATCA
* *
28734844 AAAATTAAA-TTATAATGAACAACATTTT
1 AAAATTAAATTTA-AATAAACAA-AATTT
* *
28734872 AAAA-TAAATTAAAATCAACAAAATTT
1 AAAATTAAATTTAAATAAACAAAATTT
28734898 AAAATTTAAATTTAAATAAAACAAAA
1 AAAA-TTAAATTTAAAT-AAACAAAA
28734924 CCCTAAACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 8 0.19
27 12 0.28
28 16 0.37
29 7 0.16
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAATTAAATTTAAATAAACAAAATTT
Found at i:28735684 original size:18 final size:18
Alignment explanation
Indices: 28735644--28735686 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28735634 TTTTCAATTG
28735644 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
28735662 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
28735680 TAATTAA
1 TAATTAA
28735687 AATTTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:28736860 original size:15 final size:15
Alignment explanation
Indices: 28736838--28736892 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
28736828 AATTCACAAG
28736838 TAAATAGTTCGCATA
1 TAAATAGTTCGCATA
*
28736853 TGAATAGTTCGCATA
1 TAAATAGTTCGCATA
* *
28736868 TAAAACAGTTCACATA
1 T-AAATAGTTCGCATA
28736884 TAAATAGTT
1 TAAATAGTT
28736893 TGCAAATAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
TAAATAGTTCGCATA
Found at i:28736878 original size:31 final size:31
Alignment explanation
Indices: 28736843--28736901 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
28736833 ACAAGTAAAT
* * *
28736843 AGTTCGCATATGAATAGTTCGCATATAAAAC
1 AGTTCACATATAAATAGTTCGCAAATAAAAC
*
28736874 AGTTCACATATAAATAGTTTGCAAATAA
1 AGTTCACATATAAATAGTTCGCAAATAA
28736902 GCAATTTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (31 bp):
AGTTCACATATAAATAGTTCGCAAATAAAAC
Found at i:28737460 original size:16 final size:17
Alignment explanation
Indices: 28737441--28737472 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28737431 CAAACATACA
28737441 ATAACA-ATGTTCGCAC
1 ATAACATATGTTCGCAC
28737457 ATAACATATGTTCGCA
1 ATAACATATGTTCGCA
28737473 TGCAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (17 bp):
ATAACATATGTTCGCAC
Found at i:28737679 original size:20 final size:20
Alignment explanation
Indices: 28737641--28737759 Score: 72
Period size: 20 Copynumber: 6.0 Consensus size: 20
28737631 GTACTTCCTA
28737641 ATTTTTGGTA-TC-CCTTCAT
1 ATTTTTGGTATTCTCC-TCAT
*
28737660 GTTATTTGGTATTCT-CTCAT
1 ATT-TTTGGTATTCTCCTCAT
28737680 AATTTTTGGTATT-TCCTCATT
1 -ATTTTTGGTATTCTCCTCA-T
* *
28737701 TTTTTTGGTATTC-CCTAAT
1 ATTTTTGGTATTCTCCTCAT
** *
28737720 AATTTTTTATATTCT-ATCAT
1 -ATTTTTGGTATTCTCCTCAT
28737740 ATCTATTTGGTATTC-CCTCA
1 AT-T-TTTGGTATTCTCCTCA
28737760 GAGTTCTTGG
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
19 6 0.08
20 53 0.70
21 17 0.22
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
ATTTTTGGTATTCTCCTCAT
Found at i:28737683 original size:40 final size:40
Alignment explanation
Indices: 28737639--28737757 Score: 123
Period size: 40 Copynumber: 3.0 Consensus size: 40
28737629 TAGTACTTCC
* *
28737639 TAATTTTTGGTA-TCCCTTCATGTTATTTGGTATTCTCTCA
1 TAATTTTTGGTATTCCC-TCATGTTATTTGGTATTCCCTAA
* * *
28737679 TAATTTTTGGTATTTCCTCATTTTTTTTGGTATTCCCTAA
1 TAATTTTTGGTATTCCCTCATGTTATTTGGTATTCCCTAA
** ** *
28737719 TAATTTTTTATATTCTATCATATCTATTTGGTATTCCCT
1 TAATTTTTGGTATTCCCTCATGT-TATTTGGTATTCCCT
28737758 CAGAGTTCTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 48 0.74
41 17 0.26
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.55
Consensus pattern (40 bp):
TAATTTTTGGTATTCCCTCATGTTATTTGGTATTCCCTAA
Found at i:28741618 original size:27 final size:26
Alignment explanation
Indices: 28741566--28741620 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
28741556 CACTCATTCA
*
28741566 TATTTAATATATTCTCTAATCTAATT
1 TATTTAATATATTCTATAATCTAATT
*
28741592 TATTTAATTTATTTCTATAAT-TCAATT
1 TATTTAATATA-TTCTATAATCT-AATT
28741619 TA
1 TA
28741621 ACTTTAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTAATATATTCTATAATCTAATT
Found at i:28746994 original size:16 final size:16
Alignment explanation
Indices: 28746973--28747028 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
28746963 TATTTGGTTC
*
28746973 GTTGTAATGAAATAAG
1 GTTGTAATGGAATAAG
*
28746989 GTTGTAATGGAATAAA
1 GTTGTAATGGAATAAG
28747005 GTTGTAATGGAAT-AG
1 GTTGTAATGGAATAAG
28747020 AGTTGTAAT
1 -GTTGTAAT
28747029 CAGTAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 1 0.03
16 35 0.97
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (16 bp):
GTTGTAATGGAATAAG
Found at i:28747103 original size:44 final size:46
Alignment explanation
Indices: 28747010--28747103 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
28747000 ATAAAGTTGT
*
28747010 AATGGAATAGAGTTGTAATCAGTAATTTAGTTGTTTGATTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTTAGTTGTTTGATTGAATGG
* *
28747056 AATGGAATAGAGCTGTAAT-AGT-ATTCTTG-TGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATT-TAGTTGTTTGATTGAATGG
28747100 AATG
1 AATG
28747104 ATGCTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 21 0.48
45 5 0.11
46 18 0.41
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTTAGTTGTTTGATTGAATGG
Found at i:28747264 original size:58 final size:59
Alignment explanation
Indices: 28747202--28747358 Score: 221
Period size: 58 Copynumber: 2.7 Consensus size: 59
28747192 TTTTAATAAG
* * *
28747202 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTTAACATA
*
28747260 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTTAACATA
*
28747318 ATTATTATTAAAATATGAA-TTAATAAATCATAATATATAAT
1 ATTATTATT-AAATAT-AATTTAATAAA-AATAATATATAAT
28747359 ATTGGAAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
57 21 0.24
58 41 0.46
59 11 0.12
60 4 0.04
61 12 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAACATTTTTAACATA
Found at i:28750846 original size:19 final size:19
Alignment explanation
Indices: 28750805--28750846 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28750795 AAATGTTATG
* *
28750805 TATAAATATGATAATTATT
1 TATAAATATGATAAATATA
28750824 TATAAATAAT-ATAAATATA
1 TATAAAT-ATGATAAATATA
28750843 TATA
1 TATA
28750847 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATAAATATGATAAATATA
Found at i:28750897 original size:19 final size:20
Alignment explanation
Indices: 28750873--28750915 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28750863 ATAAATTTTA
* *
28750873 AAAATAATTTTAATATA-TT
1 AAAATAAATTTAAAATATTT
28750892 AAAATAAATTTAAAATATTT
1 AAAATAAATTTAAAATATTT
28750912 AAAA
1 AAAA
28750916 GAGTTGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAAATTTAAAATATTT
Found at i:28756959 original size:18 final size:18
Alignment explanation
Indices: 28756936--28756999 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 18
28756926 TGTATTCATG
28756936 TTGTGTTCATGTTATATTT
1 TTGTGTTCATGTTATA-TT
*
28756955 TGTGTGATTCATG-TATTCATG
1 T-TGTG-TTCATGTTA-T-ATT
28756976 TTGTGTTCATGTTATATT
1 TTGTGTTCATGTTATATT
28756994 TTGTGT
1 TTGTGT
28757000 GCTGTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 12 0.32
21 9 0.24
22 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.20, T:0.58
Consensus pattern (18 bp):
TTGTGTTCATGTTATATT
Found at i:28756972 original size:40 final size:40
Alignment explanation
Indices: 28756925--28757000 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
28756915 TGAGATATTT
28756925 ATGTATTCATGTTGTGTTCATGTTATATTTTGTGTGATTC
1 ATGTATTCATGTTGTGTTCATGTTATATTTTGTGTGATTC
28756965 ATGTATTCATGTTGTGTTCATGTTATATTTTGTGTG
1 ATGTATTCATGTTGTGTTCATGTTATATTTTGTGTG
28757001 CTGTGTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (40 bp):
ATGTATTCATGTTGTGTTCATGTTATATTTTGTGTGATTC
Found at i:28756993 original size:22 final size:22
Alignment explanation
Indices: 28756928--28756993 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 22
28756918 GATATTTATG
28756928 TATTCATGTTGTGTTCATGTTA
1 TATTCATGTTGTGTTCATGTTA
*
28756950 TATT-TTG-TGTGATTCATG---
1 TATTCATGTTGTG-TTCATGTTA
28756968 TATTCATGTTGTGTTCATGTTA
1 TATTCATGTTGTGTTCATGTTA
28756990 TATT
1 TATT
28756994 TTGTGTGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
18 4 0.11
19 8 0.22
20 8 0.22
21 8 0.22
22 8 0.22
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (22 bp):
TATTCATGTTGTGTTCATGTTA
Found at i:28764272 original size:22 final size:22
Alignment explanation
Indices: 28764240--28764288 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28764230 AAAATTAGGC
*
28764240 AAAAAAGCATTAATTCCAAAAA
1 AAAAAAACATTAATTCCAAAAA
* *
28764262 AAAAAAACATTAATTTCAAGAA
1 AAAAAAACATTAATTCCAAAAA
28764284 AAAAA
1 AAAAA
28764289 TTAGACAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.18
Consensus pattern (22 bp):
AAAAAAACATTAATTCCAAAAA
Found at i:28768644 original size:12 final size:12
Alignment explanation
Indices: 28768627--28768652 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28768617 TTCACGTCTA
28768627 TTTAAAAGAGGC
1 TTTAAAAGAGGC
28768639 TTTAAAAGAGGC
1 TTTAAAAGAGGC
28768651 TT
1 TT
28768653 GTTCAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (12 bp):
TTTAAAAGAGGC
Found at i:28772456 original size:17 final size:17
Alignment explanation
Indices: 28772428--28772495 Score: 84
Period size: 17 Copynumber: 3.9 Consensus size: 17
28772418 TTAAACCCAT
28772428 TTTAAGATTTATTTTAAG
1 TTTAA-ATTTATTTTAAG
*
28772446 ATTAAATTTATTTTGAA-
1 TTTAAATTTATTTT-AAG
*
28772463 TTTAAATTTATCTTAAG
1 TTTAAATTTATTTTAAG
*
28772480 TTTAAATTTGTTTTAA
1 TTTAAATTTATTTTAA
28772496 AATTTAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
16 2 0.05
17 35 0.81
18 6 0.14
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:28772472 original size:6 final size:6
Alignment explanation
Indices: 28772447--28772548 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
28772437 TATTTTAAGA
* * * **
28772447 TTAAAT TT-ATT TTGAAT TTAAAT TT--AT CTTAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT
* * * *
28772492 TTAAAAT TTAAAT ATAAAT ATAAAT TTAAAT TTAAGAC TT-AAT ATAAAT
1 TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
28772541 ATTAAAT T
1 -TTAAAT T
28772549 CCAAATTACA
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 11 0.15
6 47 0.65
7 12 0.17
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:28773411 original size:23 final size:23
Alignment explanation
Indices: 28773367--28773411 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28773357 CCCTTGCGCC
** *
28773367 GTTGCCGAAGGTTTGCCTAATCT
1 GTTGCCGAAGGTCCGCCAAATCT
28773390 GTTGCCGAAGGTCCGCCAAATC
1 GTTGCCGAAGGTCCGCCAAATC
28773412 CATCTCTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GTTGCCGAAGGTCCGCCAAATCT
Found at i:28773946 original size:10 final size:10
Alignment explanation
Indices: 28773933--28773959 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28773923 CCGTCCGAAT
28773933 CGACCCGATC
1 CGACCCGATC
28773943 CGACCCGATC
1 CGACCCGATC
28773953 CGACCCG
1 CGACCCG
28773960 TAGGATCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (10 bp):
CGACCCGATC
Found at i:28774380 original size:30 final size:29
Alignment explanation
Indices: 28774344--28774598 Score: 174
Period size: 30 Copynumber: 8.6 Consensus size: 29
28774334 AAGCTATCCA
* *
28774344 AAAATTATATTTTTACCCCCGAACTTCTCC
1 AAAATTACATTTTTACCCCCAAACTTC-CC
** ** *
28774374 AAAATTACATTTTTGATTCAAAAACTTCCA
1 AAAATTACATTTTT-ACCCCCAAACTTCCC
* * *
28774404 AAAATTCCATTTTTACTCCTAAACTT-CC
1 AAAATTACATTTTTACCCCCAAACTTCCC
*
28774432 AAAACTTACATTTTTGACCCCGAAACTTCCC
1 AAAA-TTACATTTTT-ACCCCCAAACTTCCC
* * *
28774463 AAAATCATATTTTTACCCCTAAACTT-CC
1 AAAATTACATTTTTACCCCCAAACTTCCC
* *** *
28774491 AAAATTCCATTTTTAGCCTTAAAACTTCCA
1 AAAATTACATTTTTA-CCCCCAAACTTCCC
* ** *
28774521 AAAACTACATTTTTACCCTTGAAACTTCCA
1 AAAATTACATTTTTACCC-CCAAACTTCCC
* * * *
28774551 AAAATTTCATTTTTGACCCCGAAACTTTCA
1 AAAATTACATTTTT-ACCCCCAAACTTCCC
28774581 AAAATTACCA-TTTTACCC
1 AAAATTA-CATTTTTACCC
28774599 TTAGATATCC
Statistics
Matches: 182, Mismatches: 34, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
28 19 0.10
29 43 0.24
30 100 0.55
31 20 0.11
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTCCC
Found at i:28774475 original size:59 final size:58
Alignment explanation
Indices: 28774352--28774577 Score: 215
Period size: 59 Copynumber: 3.8 Consensus size: 58
28774342 CAAAAATTAT
** ** * *
28774352 ATTTTTACCCCCGAACTTCTCCAAAATTACATTTTTGATTCAAAAACTTCCAAAAATTC-C
1 ATTTTTACCCCTAAAC-T-TCCAAAATTACATTTTTGACCCCAAAACTTCCCAAAA-TCAC
* * *
28774412 ATTTTTACTCCTAAACTTCCAAAACTTACATTTTTGACCCCGAAACTTCCCAAAATCAT
1 ATTTTTACCCCTAAACTTCCAAAA-TTACATTTTTGACCCCAAAACTTCCCAAAATCAC
* ** *
28774471 ATTTTTACCCCTAAACTTCCAAAATTCCATTTTT-AGCCTTAAAACTT-CCAAAAACTAC
1 ATTTTTACCCCTAAACTTCCAAAATTACATTTTTGA-CCCCAAAACTTCCCAAAATC-AC
* * *
28774529 ATTTTTACCCTTGAAACTTCCAAAAATTTCATTTTTGACCCCGAAACTT
1 ATTTTTACCCCT-AAACTTCC-AAAATTACATTTTTGACCCCAAAACTT
28774578 TCAAAAATTA
Statistics
Matches: 138, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
57 8 0.06
58 38 0.28
59 57 0.41
60 34 0.25
61 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
ATTTTTACCCCTAAACTTCCAAAATTACATTTTTGACCCCAAAACTTCCCAAAATCAC
Found at i:28782137 original size:340 final size:341
Alignment explanation
Indices: 28781516--28782200 Score: 1318
Period size: 340 Copynumber: 2.0 Consensus size: 341
28781506 TGAACTCCTT
*
28781516 GTAAAGGGGACGAACCCTGTTCTTGAAAAATCAATAGACGAGTTTTCAAAAAAAAAGAAATCAAT
1 GTAAAGGGGACGAACCATGTTCTTGAAAAATCAATAGACGAGTTTTCAAAAAAAAAGAAATCAAT
*
28781581 ACAAAGACTAATTCCAAATTCAATATCTAAAGCAAACAAACTGCATTCAGAATTACGAGCAAAGA
66 ACAAAGACTAATTCCAAATTCAATATCTAAAGCAAACAAACTACATTCAGAATTACGAGCAAAGA
28781646 ACATTGGAAGCAACAAAGATCTTTTCTTTTCAGCTTGGTCGAACCGTTATAAGGTACCCCGTTTC
131 ACATTGGAAGCAACAAAGATCTTTTCTTTTCAGCTTGGTCGAACCGTTATAAGGTACCCCGTTTC
*
28781711 CATTTGTTATTATTAACCATCCATGTTCAGAAACGTTTTGTATTTTTTGAAGTCTGTTAATGGAT
196 CATTTGTTATTATTAACCATCCATGTTCAGAAACGTTTTGTATTTTTCGAAGTCTGTTAATGGAT
28781776 TATTTATTATAATATTAAAGTCATTTATTTTTTTTAAAAATATACATTTATTATATGTTAAGAGC
261 TATTTATTATAATATTAAAGTCATTTATTTTTTTTAAAAATATACATTTATTATATGTTAAGAGC
28781841 ATTAAATAAATACTAA
326 ATTAAATAAATACTAA
28781857 GTAAAGGGGACGAACCATGTTCTTGAAAAATCAATAGACGAGTTTTCAAAAAAAAAGAAATCAA-
1 GTAAAGGGGACGAACCATGTTCTTGAAAAATCAATAGACGAGTTTTCAAAAAAAAAGAAATCAAT
28781921 ACAAAGACTAATTCCAAATTCAATATCTAAAGCAAACAAACTACATTCAGAATTACGAGCAAAGA
66 ACAAAGACTAATTCCAAATTCAATATCTAAAGCAAACAAACTACATTCAGAATTACGAGCAAAGA
28781986 ACATTGGAAGCAACAAAGATCTTTTCTTTTCAGCTTGGTCGAACCGTTATAAGGTACCCCGTTTC
131 ACATTGGAAGCAACAAAGATCTTTTCTTTTCAGCTTGGTCGAACCGTTATAAGGTACCCCGTTTC
*
28782051 CATTTGTTATTATTAACCATCCATGTTCTGAAACGTTTTGTATTTTTCGAAGTCTGTTAATGGAT
196 CATTTGTTATTATTAACCATCCATGTTCAGAAACGTTTTGTATTTTTCGAAGTCTGTTAATGGAT
28782116 TATTTATTATAATATTAAAGTCATTTATTTTTTTTAAAAATATACATTTATTATATGTTAAGAGC
261 TATTTATTATAATATTAAAGTCATTTATTTTTTTTAAAAATATACATTTATTATATGTTAAGAGC
*
28782181 ATTAAATAAATATTAA
326 ATTAAATAAATACTAA
28782197 GTAA
1 GTAA
28782201 CATTTATAAA
Statistics
Matches: 339, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
340 276 0.81
341 63 0.19
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (341 bp):
GTAAAGGGGACGAACCATGTTCTTGAAAAATCAATAGACGAGTTTTCAAAAAAAAAGAAATCAAT
ACAAAGACTAATTCCAAATTCAATATCTAAAGCAAACAAACTACATTCAGAATTACGAGCAAAGA
ACATTGGAAGCAACAAAGATCTTTTCTTTTCAGCTTGGTCGAACCGTTATAAGGTACCCCGTTTC
CATTTGTTATTATTAACCATCCATGTTCAGAAACGTTTTGTATTTTTCGAAGTCTGTTAATGGAT
TATTTATTATAATATTAAAGTCATTTATTTTTTTTAAAAATATACATTTATTATATGTTAAGAGC
ATTAAATAAATACTAA
Found at i:28783441 original size:30 final size:29
Alignment explanation
Indices: 28783392--28783614 Score: 186
Period size: 29 Copynumber: 7.7 Consensus size: 29
28783382 TAAGCTGTCA
* *
28783392 AAAAATTATATTTTTACCCTTAAACTTCT
1 AAAAATTACATTTTTACCCTTAAACTTCC
* *
28783421 AAAAATTACATTTTTGACCCTAAAACTTTC
1 AAAAATTACATTTTT-ACCCTTAAACTTCC
* * * *
28783451 AAAAATCACATTTGTACCC-CAAAGTTCC
1 AAAAATTACATTTTTACCCTTAAACTTCC
* * *
28783479 AAATATTACATTTTTAACCTCGAAA-TTCC
1 AAAAATTACATTTTTACCCT-TAAACTTCC
* *
28783508 TAAAAATTACATTTTTGCCCCTAAACTTCC
1 -AAAAATTACATTTTTACCCTTAAACTTCC
* *
28783538 AAAAATTCCATTTTTGACCC-TAAAATTCC
1 AAAAATTACATTTTT-ACCCTTAAACTTCC
* ** *
28783567 AAAAATTCCATTTTTAACCCCGACACTTCC
1 AAAAATTACATTTTT-ACCCTTAAACTTCC
28783597 -AAAATTACCA-TTTTACCC
1 AAAAATTA-CATTTTTACCC
28783615 CTGAATGTTT
Statistics
Matches: 159, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
28 25 0.16
29 76 0.48
30 58 0.36
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTTAAACTTCC
Found at i:28783551 original size:59 final size:58
Alignment explanation
Indices: 28783392--28783610 Score: 237
Period size: 58 Copynumber: 3.7 Consensus size: 58
28783382 TAAGCTGTCA
* * * *
28783392 AAAAATTATATTTTTACCCTTAAACTTCTAAAAATTACATTTTTGACCCTAAAACTTTC
1 AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCTAAAA-TTCC
* * * * * *
28783451 AAAAATCACATTTGTACCCC-AAAGTTCCAAATATTACATTTTT-AACCTCGAAATTCC
1 AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCT-AAAATTCC
* *
28783508 TAAAAATTACATTTTTGCCCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAAATTCC
1 -AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCTAAAATTCC
* * *
28783567 AAAAATTCCATTTTTAACCCCGACACTTCC-AAAATTACCATTTT
1 AAAAATTACATTTTT-ACCCCTAAACTTCCAAAAATTA-CATTTT
28783611 ACCCCTGAAT
Statistics
Matches: 131, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 7 0.05
58 60 0.46
59 60 0.46
60 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCTAAAATTCC
Found at i:28783567 original size:88 final size:90
Alignment explanation
Indices: 28783419--28783641 Score: 255
Period size: 88 Copynumber: 2.5 Consensus size: 90
28783409 CCTTAAACTT
* * *
28783419 CTAAAAATTACATTTTTGACCCTAAAACTTTCAAAAA-TCACATTTGT-ACCCCAAAGTTCCAAA
1 CTAAAAATTACATTTTTGCCCCTAAAACTTTCAAAAATTC-CATTTTTGACCCCAAAATTCCAAA
* *
28783482 TATTACATTTTTAACCTCGA-AATTC
65 AATTACATTTTTAACCCCGACAATTC
* *
28783507 CTAAAAATTACATTTTTGCCCCT-AAACTTCCAAAAATTCCATTTTTGACCCTAAAATTCCAAAA
1 CTAAAAATTACATTTTTGCCCCTAAAACTTTCAAAAATTCCATTTTTGACCCCAAAATTCCAAAA
* *
28783571 ATTCCATTTTTAACCCCGACACTTC
66 ATTACATTTTTAACCCCGACAATTC
* * **
28783596 C--AAAATTACCA-TTTTACCCCTGAATGTTTC-AAAATTCCATTTTTGA
1 CTAAAAATTA-CATTTTTGCCCCTAAAACTTTCAAAAATTCCATTTTTGA
28783642 TCCTGATTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
87 50 0.43
88 62 0.53
89 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (90 bp):
CTAAAAATTACATTTTTGCCCCTAAAACTTTCAAAAATTCCATTTTTGACCCCAAAATTCCAAAA
ATTACATTTTTAACCCCGACAATTC
Found at i:28783639 original size:29 final size:29
Alignment explanation
Indices: 28783475--28783639 Score: 99
Period size: 29 Copynumber: 5.6 Consensus size: 29
28783465 TACCCCAAAG
* * *
28783475 TTCCAAATATTACATTTTTAACCTCGA-AA
1 TTCCAAA-ATTCCATTTTTAACCCCGACAC
* * * *
28783504 TTCCTAAAAATTACATTTTT-GCCCCTAAAC
1 TTCC--AAAATTCCATTTTTAACCCCGACAC
* * * *
28783534 TTCCAAAAATTCCATTTTTGA-CCCTAAAA
1 TTCC-AAAATTCCATTTTTAACCCCGACAC
28783563 TTCCAAAAATTCCATTTTTAACCCCGACAC
1 TTCC-AAAATTCCATTTTTAACCCCGACAC
*
28783593 TTCCAAAATTACCA-TTTT-ACCCCTGA-ATG
1 TTCCAAAATT-CCATTTTTAACCCC-GACA-C
*
28783622 TTTCAAAATTCCATTTTT
1 TTCCAAAATTCCATTTTT
28783640 GATCCTGATT
Statistics
Matches: 114, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
28 9 0.08
29 74 0.65
30 28 0.25
31 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
TTCCAAAATTCCATTTTTAACCCCGACAC
Found at i:28793310 original size:29 final size:31
Alignment explanation
Indices: 28793266--28793372 Score: 102
Period size: 30 Copynumber: 3.6 Consensus size: 31
28793256 TACCCGGGGC
*
28793266 AAAATGGTAATTTTTGGAAAAATCGGGATCA
1 AAAATGGTAATTTTTGGAAAAATCGGGGTCA
*
28793297 AAAATGG-AA-TTTT-GAAACATTCGGGGGT--
1 AAAATGGTAATTTTTGGAAA-AATC-GGGGTCA
***
28793325 AAAATGGTAA-TTTTGGAAGTGTCGGGGTCA
1 AAAATGGTAATTTTTGGAAAAATCGGGGTCA
28793355 AAAAT-GTAATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
28793373 GTTCGAGGGT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
28 16 0.25
29 19 0.30
30 22 0.34
31 7 0.11
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAAATCGGGGTCA
Found at i:28793383 original size:58 final size:59
Alignment explanation
Indices: 28793266--28793386 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 59
28793256 TACCCGGGGC
*
28793266 AAAATGGTAATTTTTGGAAAAATCGGGATCAAAAATGGAATTTTGAAACATTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGGGATCAAAAATGGAATTTTGAAACATTCGAGGGT
*** * * * *
28793325 AAAATGGTAA-TTTTGGAAGTGTCGGGGTCAAAAATGTAATTTTTGGAA-GTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGGGATCAAAAATGGAA-TTTTGAAACATTCGAGGGT
28793383 AAAA
1 AAAA
28793387 ATACAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 36 0.68
59 17 0.32
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCGGGATCAAAAATGGAATTTTGAAACATTCGAGGGT
Found at i:28793386 original size:29 final size:28
Alignment explanation
Indices: 28793266--28793400 Score: 96
Period size: 29 Copynumber: 4.6 Consensus size: 28
28793256 TACCCGGGGC
** *
28793266 AAAATGGTAATTTTTGGAAAAATCGGGATCA
1 AAAAT-GTAATTTTTGG-AAGTTCGGGGT-A
* * *
28793297 AAAATGGAA-TTTTGAAACATTCGGGGGT-
1 AAAATGTAATTTTTGGAA-GTTC-GGGGTA
28793325 AAAATGGTAA-TTTTGGAAGTGTCGGGGTCA
1 AAAAT-GTAATTTTTGGAAGT-TCGGGGT-A
28793355 AAAATGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTCG-GGGTA
**
28793384 AAAATACAATTTTTGGA
1 AAAATGTAATTTTTGGA
28793401 CAGCTTAGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
28 13 0.15
29 43 0.49
30 26 0.30
31 5 0.06
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGGGGTA
Found at i:28795591 original size:17 final size:17
Alignment explanation
Indices: 28795552--28795599 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
28795542 TGATATGTGG
**
28795552 AAATGCAATGACAATCT
1 AAATGCAATGACAATAA
* *
28795569 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
28795586 AAATGCAATGACAA
1 AAATGCAATGACAA
28795600 AGGAAATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:28796068 original size:22 final size:23
Alignment explanation
Indices: 28796039--28796088 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
28796029 ACATTAGGTC
28796039 CTTCTCTTC-TTTCCTCTTTT-T
1 CTTCTCTTCTTTTCCTCTTTTGT
28796060 CTTCGTCTTCTTTTTCCTCTTTTGT
1 CTTC-TCTTC-TTTTCCTCTTTTGT
28796085 CTTC
1 CTTC
28796089 ACAGGTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
24 11 0.44
25 5 0.20
ACGTcount: A:0.00, C:0.32, G:0.04, T:0.64
Consensus pattern (23 bp):
CTTCTCTTCTTTTCCTCTTTTGT
Found at i:28799964 original size:18 final size:18
Alignment explanation
Indices: 28799943--28799981 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28799933 AATCTTTATC
*
28799943 ACCTAAACAATATTTCTT
1 ACCTAAACAATATTCCTT
* *
28799961 ACCTGAACAATCTTCCTT
1 ACCTAAACAATATTCCTT
28799979 ACC
1 ACC
28799982 ATCTTTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (18 bp):
ACCTAAACAATATTCCTT
Found at i:28802491 original size:22 final size:22
Alignment explanation
Indices: 28802463--28802509 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
28802453 TGTTCATTGG
28802463 TTTGTATATGTGGGATTAATGC
1 TTTGTATATGTGGGATTAATGC
28802485 TTTGTATATGTGGGATTAATGC
1 TTTGTATATGTGGGATTAATGC
28802507 TTT
1 TTT
28802510 CTTTTCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (22 bp):
TTTGTATATGTGGGATTAATGC
Found at i:28826482 original size:37 final size:38
Alignment explanation
Indices: 28826396--28826488 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
28826386 TAACATCCAA
* **
28826396 ATTTGCACCCAAAACTATCGCTGCATGAGCACCTCTAG
1 ATTTGCACCAAAAACTATCGCCACATGAGCACCTCTAG
* *
28826434 ATTGTGC-CCAAAAACTGTCGCCACATGAGCACTTCTAG
1 ATT-TGCACCAAAAACTATCGCCACATGAGCACCTCTAG
28826472 ATTT-CACC-AAAACTATC
1 ATTTGCACCAAAAACTATC
28826489 ACCGCAGGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 9 0.19
37 3 0.06
38 32 0.68
39 3 0.06
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (38 bp):
ATTTGCACCAAAAACTATCGCCACATGAGCACCTCTAG
Found at i:28836949 original size:18 final size:18
Alignment explanation
Indices: 28836934--28836968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28836924 CCAGATGCGA
28836934 TCATAAAATCAAATGCAT
1 TCATAAAATCAAATGCAT
* *
28836952 TCATATAATCAGATGCA
1 TCATAAAATCAAATGCA
28836969 GTCACAAGCT
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:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (18 bp):
TCATAAAATCAAATGCAT
Found at i:28843100 original size:18 final size:18
Alignment explanation
Indices: 28843065--28843124 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
28843055 AAACATAGCT
* **
28843065 GAGAAGGAGGAACTTGAG
1 GAGAAGAAGGAAAATGAG
28843083 GAGAAGAAGGAAAATGAG
1 GAGAAGAAGGAAAATGAG
*
28843101 GAAGAA-AA-GAAAGAAGAG
1 G-AGAAGAAGGAAA-ATGAG
28843119 GAGAAG
1 GAGAAG
28843125 GATGAAGAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.23
18 23 0.66
19 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.40, T:0.05
Consensus pattern (18 bp):
GAGAAGAAGGAAAATGAG
Found at i:28843580 original size:17 final size:18
Alignment explanation
Indices: 28843538--28843581 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
28843528 ATGCATAGCA
* *
28843538 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
*
28843556 TTTTTTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
28843573 TTTATTTGT
1 TTTATTTGT
28843582 TAGTACATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:28847983 original size:23 final size:23
Alignment explanation
Indices: 28847953--28848210 Score: 302
Period size: 23 Copynumber: 11.3 Consensus size: 23
28847943 TATATCTATA
28847953 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATATGATTTGTG
*** * * *
28847976 CACGAATATTAATGTAATTTTTG
1 CTTAAATATTAATATGATTTGTG
*
28847999 CTTAAATATTAATATGATTTGTT
1 CTTAAATATTAATATGATTTGTG
28848022 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATATGATTTGTG
* * * *
28848045 CTCAAATATTAATATTACTTCTG
1 CTTAAATATTAATATGATTTGTG
* *
28848068 CTTAAATA-TAATGTGATTTATG
1 CTTAAATATTAATATGATTTGTG
* * *
28848090 GTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATATGATTTGTG
* * *
28848113 CATAAATATTAATGTGATCTGTG
1 CTTAAATATTAATATGATTTGTG
*
28848136 CTTAAATATTAATCTGATTTGTG
1 CTTAAATATTAATATGATTTGTG
*
28848159 CTCAAATATTAATATGATTTGTG
1 CTTAAATATTAATATGATTTGTG
* *
28848182 CTCAAATATTAATGTGATTTGTG
1 CTTAAATATTAATATGATTTGTG
28848205 CTTAAA
1 CTTAAA
28848211 GAATTAAGAT
Statistics
Matches: 199, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
22 17 0.09
23 182 0.91
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (23 bp):
CTTAAATATTAATATGATTTGTG
Found at i:28848167 original size:114 final size:115
Alignment explanation
Indices: 28847956--28848210 Score: 341
Period size: 114 Copynumber: 2.2 Consensus size: 115
28847946 ATCTATACTT
* * *** * * *
28847956 AAATATTAATATGATTTGTGCACGAATATTAATGTAATTTTTGCTTAAATATTAATATGATTTGT
1 AAATATTAATGTGATTTATGCTTAAATATTAATGTAATTTATGCATAAATATTAATATGATCTGT
* * *
28848021 TCTTAAATATTAATATGATTTGTGCTCAAATATTAATATTACTTCTGCTT
66 GCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTC
* * *
28848071 AAATA-TAATGTGATTTATGGTTAAATATTAATGTGATTTATGCATAAATATTAATGTGATCTGT
1 AAATATTAATGTGATTTATGCTTAAATATTAATGTAATTTATGCATAAATATTAATATGATCTGT
* * *
28848135 GCTTAAATATTAATCTGATTTGTGCTCAAATATTAATATGATTTGTGCTC
66 GCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTC
*
28848185 AAATATTAATGTGATTTGTGCTTAAA
1 AAATATTAATGTGATTTATGCTTAAA
28848211 GAATTAAGAT
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
114 97 0.81
115 23 0.19
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (115 bp):
AAATATTAATGTGATTTATGCTTAAATATTAATGTAATTTATGCATAAATATTAATATGATCTGT
GCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTC
Found at i:28848207 original size:137 final size:137
Alignment explanation
Indices: 28847954--28848210 Score: 388
Period size: 137 Copynumber: 1.9 Consensus size: 137
28847944 ATATCTATAC
* * * *
28847954 TTAAATATTAATATGATTTGTGCACGAATATTAATGTAATTTTTGCTTAAATATTAATATGATTT
1 TTAAATATTAATATGATTTATGCACAAATATTAATGTAATCTGTGCTTAAATATTAATATGATTT
* * *
28848019 GTTCTTAAATATTAATATGATTTGTGCTCAAATATTAATATTACTTCTGCTTAAATATAATGTGA
66 GTGCTCAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTTAAATATAATGTGA
28848084 TTTATGG
131 TTTATGG
* * * *
28848091 TTAAATATTAATGTGATTTATGCATAAATATTAATGTGATCTGTGCTTAAATATTAATCTGATTT
1 TTAAATATTAATATGATTTATGCACAAATATTAATGTAATCTGTGCTTAAATATTAATATGATTT
* * *
28848156 GTGCTCAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCTTAAA
66 GTGCTCAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTTAAA
28848211 GAATTAAGAT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
137 106 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (137 bp):
TTAAATATTAATATGATTTATGCACAAATATTAATGTAATCTGTGCTTAAATATTAATATGATTT
GTGCTCAAATATTAATATGATTTGTGCTCAAATATTAATATGACTTCTGCTTAAATATAATGTGA
TTTATGG
Found at i:28861360 original size:20 final size:21
Alignment explanation
Indices: 28861338--28861376 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
28861328 TTTTTTTCTC
28861338 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTATTTGTTTCACT
28861359 TTTACTTTT-TTTGTTTCA
1 TTTACTTTTATTTGTTTCA
28861377 AATTCCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTACTTTTATTTGTTTCACT
Found at i:28864903 original size:30 final size:30
Alignment explanation
Indices: 28864867--28864928 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
28864857 GATGTCGACG
28864867 CACTGAACATGAACTCCGAATTGAAAAACT
1 CACTGAACATGAACTCCGAATTGAAAAACT
* **
28864897 CACTGAACATGAACTCTGAATTGGTAAACT
1 CACTGAACATGAACTCCGAATTGAAAAACT
28864927 CA
1 CA
28864929 AGCTAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (30 bp):
CACTGAACATGAACTCCGAATTGAAAAACT
Found at i:28865904 original size:13 final size:14
Alignment explanation
Indices: 28865875--28865904 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28865865 TTCAGTACAT
28865875 TGACATTTAATCTC
1 TGACATTTAATCTC
28865889 TGACATTTAA-CTC
1 TGACATTTAATCTC
28865902 TGA
1 TGA
28865905 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (14 bp):
TGACATTTAATCTC
Found at i:28872211 original size:17 final size:17
Alignment explanation
Indices: 28872189--28872221 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28872179 GTTAGTGCAC
*
28872189 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
28872206 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
28872222 AATATTAGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:28883522 original size:11 final size:11
Alignment explanation
Indices: 28883506--28883557 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
28883496 TCACTTAAAA
28883506 AGAAAAAAATG
1 AGAAAAAAATG
28883517 AGAAAAAGAA--
1 AGAAAAA-AATG
28883527 AGAAAAAAATG
1 AGAAAAAAATG
*
28883538 AGAAAAAAA-A
1 AGAAAAAAATG
28883548 AGAAAAAAAT
1 AGAAAAAAAT
28883558 TGTTCTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 2 0.06
10 16 0.44
11 16 0.44
12 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AGAAAAAAATG
Found at i:28883528 original size:21 final size:21
Alignment explanation
Indices: 28883502--28883557 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
28883492 TTAGTCACTT
28883502 AAAAAGAAAAAAATGAGAAAA
1 AAAAAGAAAAAAATGAGAAAA
*
28883523 AGAAAGAAAAAAATGAGAAAA
1 AAAAAGAAAAAAATGAGAAAA
28883544 AAAAAGAAAAAAAT
1 AAAAAGAAAAAAAT
28883558 TGTTCTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAAAGAAAAAAATGAGAAAA
Found at i:28892902 original size:24 final size:24
Alignment explanation
Indices: 28892855--28892900 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
28892845 AGAATTAATC
*
28892855 TGTCAATGCAAATATAAAATAAAT
1 TGTCAAAGCAAATATAAAATAAAT
*
28892879 TGTCAAAGCAAAT-TAAGATAAA
1 TGTCAAAGCAAATATAAAATAAA
28892901 ATGAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (24 bp):
TGTCAAAGCAAATATAAAATAAAT
Found at i:28897979 original size:13 final size:14
Alignment explanation
Indices: 28897953--28897981 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28897943 GGTTTTTTAT
28897953 AAAATTAATATAAA
1 AAAATTAATATAAA
28897967 AAAATTAAT-TAAA
1 AAAATTAATATAAA
28897980 AA
1 AA
28897982 TCAAAATAAT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTAATATAAA
Found at i:28903357 original size:24 final size:24
Alignment explanation
Indices: 28903311--28903369 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
28903301 TTCATCCGCC
* * **
28903311 TGAGCTCGAGCTCGAGCTTGAGCA
1 TGAGCTCGATCTCAAGCCCGAGCA
*
28903335 TGAGCTCGATCTCAAGCCCGAGCC
1 TGAGCTCGATCTCAAGCCCGAGCA
*
28903359 TGAGCACGATC
1 TGAGCTCGATC
28903370 CGGAGTCTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.19
Consensus pattern (24 bp):
TGAGCTCGATCTCAAGCCCGAGCA
Found at i:28903444 original size:27 final size:27
Alignment explanation
Indices: 28903414--28903515 Score: 96
Period size: 27 Copynumber: 3.8 Consensus size: 27
28903404 GGCCAAGTTG
* *
28903414 TATCATCCGGGGTGGTCAGGCGATTGA
1 TATCATACGGGGTGGTCAGGCGATAGA
* *
28903441 TATCATTCGGGGTAGTCAGGCGATAGA
1 TATCATACGGGGTGGTCAGGCGATAGA
* * * * *
28903468 AATCATAAGGGTTGGTCAGGCCATGGA
1 TATCATACGGGGTGGTCAGGCGATAGA
* * *
28903495 TATAATACGAGTTGGTCAGGC
1 TATCATACGGGGTGGTCAGGC
28903516 CACGAGTATC
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.25
Consensus pattern (27 bp):
TATCATACGGGGTGGTCAGGCGATAGA
Found at i:28903931 original size:28 final size:28
Alignment explanation
Indices: 28903872--28903957 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
28903862 GACATTTTTC
* * *
28903872 ATTTGGAATTAATTATGCTTATGA-ATGA
1 ATTTGGAATTAATTATGTTTAT-ATTTGT
28903900 ATTTGGAATTAATTATGTTTATATTTGT
1 ATTTGGAATTAATTATGTTTATATTTGT
*
28903928 ATTT--AATTAATTATGTTTATGTTTGT
1 ATTTGGAATTAATTATGTTTATATTTGT
28903954 ATTT
1 ATTT
28903958 AAGGTTTAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.47
27 1 0.02
28 27 0.51
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (28 bp):
ATTTGGAATTAATTATGTTTATATTTGT
Found at i:28903942 original size:26 final size:26
Alignment explanation
Indices: 28903906--28903959 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28903896 ATGAATTTGG
28903906 AATTAATTATGTTTATATTTGTATTT
1 AATTAATTATGTTTATATTTGTATTT
*
28903932 AATTAATTATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATATTTGTATTT
28903958 AA
1 AA
28903960 GGTTTAGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (26 bp):
AATTAATTATGTTTATATTTGTATTT
Found at i:28904688 original size:14 final size:14
Alignment explanation
Indices: 28904665--28904716 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
28904655 TAAAACTCTA
*
28904665 AAACCCTAAACCTT
1 AAACCATAAACCTT
* *
28904679 AAACCATAAATCTA
1 AAACCATAAACCTT
* *
28904693 AAACCATATACCCT
1 AAACCATAAACCTT
*
28904707 AAACCCTAAA
1 AAACCATAAA
28904717 TACAAATATC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCATAAACCTT
Found at i:28904709 original size:28 final size:28
Alignment explanation
Indices: 28904661--28904717 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
28904651 GAGTTAAAAC
* *
28904661 TCTAAAACCCTAAACCTTAAACCATAAA
1 TCTAAAACCATAAACCCTAAACCATAAA
* *
28904689 TCTAAAACCATATACCCTAAACCCTAAA
1 TCTAAAACCATAAACCCTAAACCATAAA
28904717 T
1 T
28904718 ACAAATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (28 bp):
TCTAAAACCATAAACCCTAAACCATAAA
Found at i:28904743 original size:26 final size:26
Alignment explanation
Indices: 28904713--28904845 Score: 158
Period size: 26 Copynumber: 5.0 Consensus size: 26
28904703 CCCTAAACCC
* *
28904713 TAAATACAAATATCAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
28904739 TAAATACAAACATAAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
* *
28904765 TAAATACAAACATAAAAATTATTAAT
1 TAAATACAAACATAAACATAATTAAT
* * *
28904791 TAAATACAAATATAAACATAGTTTAT
1 TAAATACAAACATAAACATAATTAAT
* **
28904817 TCCAAATTCATTCATAAACATAATTAAT
1 T--AAATACAAACATAAACATAATTAAT
28904845 T
1 T
28904846 CCAAATGAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 70 0.78
28 20 0.22
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
TAAATACAAACATAAACATAATTAAT
Found at i:28907643 original size:20 final size:20
Alignment explanation
Indices: 28907618--28907664 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
28907608 TTGTTTGAAC
28907618 AAAATTTACCTCATTCTTCA
1 AAAATTTACCTCATTCTTCA
** *
28907638 AAAATTTGTCTCTTTCTTCA
1 AAAATTTACCTCATTCTTCA
28907658 AAAATTT
1 AAAATTT
28907665 GTGTTTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTACCTCATTCTTCA
Found at i:28907753 original size:27 final size:27
Alignment explanation
Indices: 28907723--28907784 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28907713 CTACCTGTAT
* * *
28907723 GGCACTACTGGTGCC-CCTTACCCCGTA
1 GGCACCACTAGTGCCGCC-TACCCCATA
*
28907750 GGCACCATTAGTGCCGCCTACCCCATA
1 GGCACCACTAGTGCCGCCTACCCCATA
28907777 GGCACCAC
1 GGCACCAC
28907785 CCCAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.18
Consensus pattern (27 bp):
GGCACCACTAGTGCCGCCTACCCCATA
Done.