Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 8 of 297
Found at i:2649570 original size:27 final size:26
Alignment explanation
Indices: 2649537--2649652 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 26
2649527 CTGCCAGAAT
* *
2649537 AGATATTGTGATAGAGTCACCAAATAC
1 AGATATTGTGACAGAGCCACCAAA-AC
* *
2649564 AGATATTGTGGCAGAGCCACCATAAC
1 AGATATTGTGACAGAGCCACCAAAAC
* * *
2649590 AGATATTTGTGGCATAGCCACCAGAAAT
1 AGATA-TTGTGACAGAGCCACCA-AAAC
*
2649618 AGATATTTGTGGCATG-GCCACCAGAAAC
1 AGATA-TTGTGACA-GAGCCACCA-AAAC
2649646 AGATATT
1 AGATATT
2649653 TGTAGCATGG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
26 7 0.09
27 38 0.49
28 32 0.42
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (26 bp):
AGATATTGTGACAGAGCCACCAAAAC
Found at i:2649630 original size:28 final size:27
Alignment explanation
Indices: 2649554--2649671 Score: 148
Period size: 28 Copynumber: 4.3 Consensus size: 27
2649544 GTGATAGAGT
*
2649554 CACCAAATACAGATA-TTGTGGCAGAGC
1 CACCAAA-ACAGATATTTGTGGCATAGC
*
2649581 CACCATAACAGATATTTGTGGCATAGC
1 CACCAAAACAGATATTTGTGGCATAGC
* *
2649608 CACCAGAAATAGATATTTGTGGCATGGC
1 CACCA-AAACAGATATTTGTGGCATAGC
* *
2649636 CACCAGAAACAGATATTTGTAGCATGGC
1 CACCA-AAACAGATATTTGTGGCATAGC
2649664 CACCAAAA
1 CACCAAAA
2649672 TGCTTCCTCC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.09
27 25 0.30
28 50 0.61
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (27 bp):
CACCAAAACAGATATTTGTGGCATAGC
Found at i:2649830 original size:26 final size:26
Alignment explanation
Indices: 2649773--2649835 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
2649763 CAAAATCAAC
*
2649773 CCTAGGGGTATAACGGTCACTTTACA
1 CCTAGGGGTATAACGGTCAATTTACA
* *
2649799 CCTAGGGGTATAATGGT-AATTTCATA
1 CCTAGGGGTATAACGGTCAATTT-ACA
*
2649825 CTTAGGGGTAT
1 CCTAGGGGTAT
2649836 TTTAGTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (26 bp):
CCTAGGGGTATAACGGTCAATTTACA
Found at i:2657580 original size:18 final size:18
Alignment explanation
Indices: 2657557--2657591 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2657547 ATAAGTTTTA
2657557 AAAGTAAAAACGAAAAAT
1 AAAGTAAAAACGAAAAAT
*
2657575 AAAGTAAAACCGAAAAA
1 AAAGTAAAAACGAAAAA
2657592 AGAGAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAGTAAAAACGAAAAAT
Found at i:2661519 original size:140 final size:138
Alignment explanation
Indices: 2661254--2661540 Score: 303
Period size: 140 Copynumber: 2.0 Consensus size: 138
2661244 GATAAAATGA
* * *
2661254 TTTTCCTTGTAAAAGTCCAAGTAATTCCCTACAAAACCAAAAGTTTTTCCCTTTTACTAGAAAAA
1 TTTTTCTTGTAAAAATCCAAATAATTCCCTACAAAACCAAAAGTTTTTCCCTTTTACTAGAAAAA
* *
2661319 AACTAAAATTAATTTTGAAAAGAGAAAAAATAAAGGAAATTAACGAGTTAAATAA-TTTTTCCTA
66 AACTAAAATTAATTTTGAAAAGAGAAAAAATAAA-GAAATT-A-GAGTAAAATAAGTTTTCCCTA
*
2661383 TAAAACCCAAT
128 TAAAACCCAAG
** ** * * * **
2661394 TTTTTCTTGTAAAAATCCAAATAATTCCCTGTAAAACCCTAAGTTTTTCTCTTTTATTGGAGGAA
1 TTTTTCTTGTAAAAATCCAAATAATTCCCTACAAAACCAAAAGTTTTTCCCTTTTACTAGAAAAA
* *
2661459 AACTAAAATTAATTTTGCAAAAGGGGAAAAAATTAA-AAA-T-GATGTAAAAACCTAAGTTTTCC
66 AACTAAAATTAATTTTG-AAAA-GAGAAAAAATAAAGAAATTAGA-GT-AAAA--TAAGTTTTCC
*
2661521 CTATAAAACTCAAG
125 CTATAAAACCCAAG
2661535 TTTTTC
1 TTTTTC
2661541 CTTTTTATTG
Statistics
Matches: 122, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
136 2 0.02
137 2 0.02
138 3 0.02
139 1 0.01
140 76 0.62
141 27 0.22
142 11 0.09
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (138 bp):
TTTTTCTTGTAAAAATCCAAATAATTCCCTACAAAACCAAAAGTTTTTCCCTTTTACTAGAAAAA
AACTAAAATTAATTTTGAAAAGAGAAAAAATAAAGAAATTAGAGTAAAATAAGTTTTCCCTATAA
AACCCAAG
Found at i:2700506 original size:14 final size:14
Alignment explanation
Indices: 2700489--2700518 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2700479 ACTATGATAG
2700489 TATGTATATGGAAT
1 TATGTATATGGAAT
2700503 TATGTATATGGAAT
1 TATGTATATGGAAT
2700517 TA
1 TA
2700519 AGTAATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (14 bp):
TATGTATATGGAAT
Found at i:2709129 original size:6 final size:6
Alignment explanation
Indices: 2709112--2709158 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2709102 TTTGAACTAA
** *
2709112 GTTTTAG GTTTTG GTTTT- GTTTTG GACTTG GTTTTG GTTTTT GTTTT
1 GTTTT-G GTTTTG GTTTTG GTTTTG GTTTTG GTTTTG GTTTTG GTTTT
2709159 TCATCGGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.04, C:0.02, G:0.28, T:0.66
Consensus pattern (6 bp):
GTTTTG
Found at i:2709135 original size:30 final size:29
Alignment explanation
Indices: 2709101--2709158 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2709091 GACTTTTGAT
2709101 TTTTGAACTAAGTTTTAGGTTTTGGTTTTG
1 TTTTGAACTAAGTTTT-GGTTTTGGTTTTG
* ** *
2709131 TTTTGGACTTGGTTTTGGTTTTTGTTTT
1 TTTTGAACTAAGTTTTGGTTTTGGTTTT
2709159 TCATCGGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.10, C:0.03, G:0.24, T:0.62
Consensus pattern (29 bp):
TTTTGAACTAAGTTTTGGTTTTGGTTTTG
Found at i:2709838 original size:66 final size:70
Alignment explanation
Indices: 2709767--2709896 Score: 173
Period size: 71 Copynumber: 1.9 Consensus size: 70
2709757 GATTTAATAT
2709767 TTAATTTAATTTAAT-ACTTATCTTAATAG-T-AT-TT-TA-TAAATTTAATATTAAAGTGATTA
1 TTAATTTAATTTAATGACTTATCTT-ATAGATAATATTCTACT-AATTTAATATTAAAGTGATTA
2709826 TCTTATC
64 TCTTATC
**
2709833 TTAATTTAATTTAATGTTTTATCTTATAGATAAATATTCTACTAATTTAATATTAAAGTGATTA
1 TTAATTTAATTTAATGACTTATCTTATAGAT-AATATTCTACTAATTTAATATTAAAGTGATTA
2709897 AGTTTAATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
66 19 0.35
67 8 0.15
69 2 0.04
70 2 0.04
71 23 0.42
72 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (70 bp):
TTAATTTAATTTAATGACTTATCTTATAGATAATATTCTACTAATTTAATATTAAAGTGATTATC
TTATC
Found at i:2720518 original size:45 final size:45
Alignment explanation
Indices: 2720415--2720633 Score: 288
Period size: 45 Copynumber: 4.9 Consensus size: 45
2720405 TCGAATTCAT
* *
2720415 TCACCGGCATT-TCA-CCTGCTAGGCTC-GAGGCCCG-AT-ATCATT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCAAAGGCCCGAATAAT-ATC
* *
2720457 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCAAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAATATC
* *
2720502 TCACCGGCATTGTAGCCTGCTAGGCTCAAAGGCCCGAATAATAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
2720547 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
2720592 TCACCGGCATTATAGTCTGCTAGGCTCAAAGGCCCGAATAAT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAAT
2720634 CAAATCCACA
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
42 12 0.08
43 13 0.08
44 7 0.05
45 122 0.79
46 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:2725608 original size:12 final size:12
Alignment explanation
Indices: 2725569--2725610 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2725559 GTGTTGTCGC
2725569 CCGTGTGGTAGG
1 CCGTGTGGTAGG
* * *
2725581 CCGCGTGGTCGC
1 CCGTGTGGTAGG
2725593 CCGTGTGGTAGG
1 CCGTGTGGTAGG
2725605 CCGTGT
1 CCGTGT
2725611 AGCAGTACAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.26, G:0.45, T:0.24
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:2729532 original size:3 final size:3
Alignment explanation
Indices: 2729524--2729555 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2729514 GGTGTTAAAT
2729524 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2729556 TCCTTCGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2731846 original size:22 final size:22
Alignment explanation
Indices: 2731821--2731863 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2731811 ATGACATCAT
2731821 CACTCATTTGGGGGCACACGGG
1 CACTCATTTGGGGGCACACGGG
2731843 CACTCATTTGGGGGCACACGG
1 CACTCATTTGGGGGCACACGG
2731864 CCAAGGCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.28, G:0.35, T:0.19
Consensus pattern (22 bp):
CACTCATTTGGGGGCACACGGG
Found at i:2733798 original size:79 final size:78
Alignment explanation
Indices: 2733696--2733918 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
2733686 GCTCCTCGTT
* *
2733696 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
2733761 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
2733776 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
2733840 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
2733854 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
2733917 GA
63 GA
2733919 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:2733813 original size:39 final size:40
Alignment explanation
Indices: 2733696--2733918 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
2733686 GCTCCTCGTT
* *
2733696 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
2733736 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
2733776 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
2733815 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
2733854 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
2733895 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2733919 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:2741775 original size:79 final size:78
Alignment explanation
Indices: 2741673--2741895 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
2741663 GCTCCTCGTT
* *
2741673 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
2741738 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
2741753 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
2741816 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
2741831 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGGAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
2741894 GA
63 GA
2741896 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 19 0.15
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:2741790 original size:39 final size:40
Alignment explanation
Indices: 2741673--2741895 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
2741663 GCTCCTCGTT
* *
2741673 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
2741713 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
2741753 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
2741792 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
2741831 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGGA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
2741872 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2741896 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:2752372 original size:20 final size:22
Alignment explanation
Indices: 2752330--2752372 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2752320 GCTTTTGACT
* *
2752330 CTTACAATTTTTTTTTGTGTTG
1 CTTACAATTTTTTATTCTGTTG
2752352 CTTAC-ATTTTTTATTCT-TTG
1 CTTACAATTTTTTATTCTGTTG
2752372 C
1 C
2752373 ACATTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (22 bp):
CTTACAATTTTTTATTCTGTTG
Found at i:2756516 original size:13 final size:13
Alignment explanation
Indices: 2756498--2756522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2756488 TTCAACAAAA
2756498 ACTATATTAATTG
1 ACTATATTAATTG
2756511 ACTATATTAATT
1 ACTATATTAATT
2756523 ATAAATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
ACTATATTAATTG
Found at i:2761195 original size:14 final size:13
Alignment explanation
Indices: 2761159--2761196 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2761149 AAAATTAAAT
2761159 CTAAATAATTATC
1 CTAAATAATTATC
*
2761172 CTTAATAATTATC
1 CTAAATAATTATC
2761185 CTAATATAATTA
1 CTAA-ATAATTA
2761197 AACATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (13 bp):
CTAAATAATTATC
Found at i:2766819 original size:16 final size:17
Alignment explanation
Indices: 2766793--2766829 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2766783 GTTTAATCGG
*
2766793 TTTAGTTGTTTGTTTAT
1 TTTAGTTGTTTATTTAT
2766810 TTTA-TTGTTTATTTAT
1 TTTAGTTGTTTATTTAT
2766826 TTTA
1 TTTA
2766830 ATTATTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (17 bp):
TTTAGTTGTTTATTTAT
Found at i:2773871 original size:13 final size:13
Alignment explanation
Indices: 2773855--2773881 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2773845 ATATTCTCAG
2773855 AGTATAATGACAA
1 AGTATAATGACAA
2773868 AGTATAATGACAA
1 AGTATAATGACAA
2773881 A
1 A
2773882 TGTAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (13 bp):
AGTATAATGACAA
Found at i:2774145 original size:38 final size:38
Alignment explanation
Indices: 2774094--2774169 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2774084 CTAAAAAGAC
2774094 CATTATATTTAGTTGTAATTTCTATTTTGTGTTTTATA
1 CATTATATTTAGTTGTAATTTCTATTTTGTGTTTTATA
2774132 CATTATATTTAGTTGTAATTTCTATTTTGTGTTTTATA
1 CATTATATTTAGTTGTAATTTCTATTTTGTGTTTTATA
2774170 AAGATTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (38 bp):
CATTATATTTAGTTGTAATTTCTATTTTGTGTTTTATA
Found at i:2778012 original size:39 final size:39
Alignment explanation
Indices: 2777954--2778108 Score: 247
Period size: 39 Copynumber: 4.0 Consensus size: 39
2777944 AAGACACTGA
* *
2777954 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTGG
*
2777993 AAATGTATCCGGCCCAAAGTCCCACAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTGG
2778032 AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTGG
1 AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTGG
** * *
2778071 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTG
2778109 ATAATATAAT
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCCAAAGTCCCACAGGCTTCGTGCTGG
Found at i:2783777 original size:39 final size:39
Alignment explanation
Indices: 2783732--2784008 Score: 331
Period size: 39 Copynumber: 6.8 Consensus size: 39
2783722 GTATCACGGA
*
2783732 TAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGC
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
* * *
2783771 TTAAGTCCCGCAGGCTTCGTGCTAGAAATATATTCGGGC
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
2783810 TAAAGTCCCGCAGGCTTCGTGCTGGCTTCGTGCTGGAAATATATCCGGGC
1 TAAAGTCCCGCA-----------GGCTTCGTGCTGGAAATATATCCGGGC
* *
2783860 TAAAGTCCGGCAGGCTTCGTGCTGGAAATATATCCAGGC
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
* *
2783899 CAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGC
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
* * *
2783938 CAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGT
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
*
2783977 TAAAGTCCCGCAGGCTTTGTGCT-GATAATATA
1 TAAAGTCCCGCAGGCTTCGTGCTGGA-AATATA
2784009 ATTTCGGGTT
Statistics
Matches: 209, Mismatches: 17, Indels: 24
0.84 0.07 0.10
Matches are distributed among these distances:
38 2 0.01
39 171 0.82
50 36 0.17
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.25
Consensus pattern (39 bp):
TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGGC
Found at i:2783849 original size:50 final size:50
Alignment explanation
Indices: 2783783--2783884 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
2783773 AAGTCCCGCA
*
2783783 GGCTTCGTGCTAGAAATATATTCGGGCTAAAGTCCCGCAGGCTTCGTGCT
1 GGCTTCGTGCTAGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
* *
2783833 GGCTTCGTGCTGGAAATATATCCGGGCTAAAGTCCGGCAGGCTTCGTGCT
1 GGCTTCGTGCTAGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
2783883 GG
1 GG
2783885 AAATATATCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (50 bp):
GGCTTCGTGCTAGAAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCT
Found at i:2783904 original size:89 final size:88
Alignment explanation
Indices: 2783744--2784000 Score: 336
Period size: 89 Copynumber: 3.0 Consensus size: 88
2783734 AAGTCCCGCA
* * *
2783744 GGCTTCGTGCTGGAAATGTATCCGGGCTTAAGTCCCGCAGGCTTCGTGCTAGAAATATATTCGGG
1 GGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGG
2783809 CTAAAGTCCCGCAGGCTTCGTGCT
66 CTAAAGTCCCGCAGGCTT-GTGCT
* * *
2783833 GGCTTCGTGCTGGAAATATATCCGGGCTAAAGTCCGGCAGGCTTCGTGCTGGAAATATATCCAGG
1 GGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGG
*
2783898 CCAAAGTCCCGCA----------
66 CTAAAGTCCCGCAGGCTTGTGCT
* *
2783911 GGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGG
1 GGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGG
*
2783976 TTAAAGTCCCGCAGGCTTTGTGCT
66 CTAAAGTCCCGCAGGC-TTGTGCT
2784000 G
1 G
2784001 ATAATATAAT
Statistics
Matches: 143, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
78 71 0.50
89 72 0.50
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (88 bp):
GGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCGGG
CTAAAGTCCCGCAGGCTTGTGCT
Found at i:2783910 original size:128 final size:128
Alignment explanation
Indices: 2783732--2783962 Score: 381
Period size: 128 Copynumber: 1.8 Consensus size: 128
2783722 GTATCACGGA
* * **
2783732 TAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTTAAGTCCCGCAGGCTTCGTGCTAGA
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCAGGCCAAAGTCCCGCAGGCTTCGTGCTAGA
* *
2783797 AATATATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGCTTCGTGCTGGAAATATATCCGGGC
66 AATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGCTTCGTGCTGGAAATATATCCGGGC
* *
2783860 TAAAGTCCGGCAGGCTTCGTGCTGGAAATATATCCAGGCCAAAGTCCCGCAGGCTTCGTGCTGGA
1 TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCAGGCCAAAGTCCCGCAGGCTTCGTGCTAGA
*
2783925 AATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
66 AATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
2783963 AAATGTATCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 94 1.00
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (128 bp):
TAAAGTCCCGCAGGCTTCGTGCTGGAAATATATCCAGGCCAAAGTCCCGCAGGCTTCGTGCTAGA
AATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGCTTCGTGCTGGAAATATATCCGGGC
Found at i:2787138 original size:17 final size:17
Alignment explanation
Indices: 2787118--2787150 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2787108 ATTAAGAATG
2787118 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
2787135 TTATTAAATTATATTT
1 TTATTAAATTATATTT
2787151 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:2787156 original size:55 final size:57
Alignment explanation
Indices: 2787095--2787228 Score: 152
Period size: 58 Copynumber: 2.4 Consensus size: 57
2787085 TTAATTCATA
* *
2787095 TAATAATAATTATATTAAGAATGTTATTAAA-T-TATA-T-TTTTTATTAAATTATATT
1 TAATAATAATTATATTAA-AATATGATTAAACTATATATTATTTTTATTAAATTAT-TT
* * *
2787150 TAATAATAATTATGTTAAAATATGGTTAAACTATTTATTATTTTTATTAAATTATTT
1 TAATAATAATTATATTAAAATATGATTAAACTATATATTATTTTTATTAAATTATTT
2787207 TCAATAATAATCT-TATTAAAAT
1 T-AATAATAAT-TATATTAAAAT
2787229 TTAATAGCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
54 9 0.13
55 18 0.27
56 3 0.04
57 4 0.06
58 32 0.48
59 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (57 bp):
TAATAATAATTATATTAAAATATGATTAAACTATATATTATTTTTATTAAATTATTT
Found at i:2787419 original size:16 final size:16
Alignment explanation
Indices: 2787398--2787452 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
2787388 TGAATAACTT
2787398 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTTC
2787414 ATTACAGCTCTA-TTC
1 ATTACAGCTCTATTTC
* * *
2787429 AATTACAACACTATTCC
1 -ATTACAGCTCTATTTC
2787446 ATTACAG
1 ATTACAG
2787453 TAAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 28 0.85
17 2 0.06
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:2791162 original size:96 final size:97
Alignment explanation
Indices: 2791062--2791250 Score: 258
Period size: 96 Copynumber: 2.0 Consensus size: 97
2791052 AGCCATTCTA
* *
2791062 AATGGCGCCACCACTTTATTACCAAG-ATTTTTTTAATGTG-GTTTTTTTAATTTAAAAATTTTT
1 AATGGCGCCACCACTGTACT-CCAAGTATTTTTTTAATGTGTGTTTTTTTAATTTAAAAA-TTTT
2791125 AAAAATAATATTTTA-TTTGGTGGAGTCATATAG
64 AAAAATAATATTTTATTTTGGTGGAGTCATATAG
* ** * * *
2791158 AATGGCGCCACCAGTGTACTGTATGTTTTTTTTTAATGTGTTTTTTTTTAATTTAAAAATTTTAA
1 AATGGCGCCACCACTGTACTCCAAGTATTTTTTTAATGTGTGTTTTTTTAATTTAAAAATTTTAA
*
2791223 AAATGATATTTTATTTTGGTGGAGTCAT
66 AAATAATATTTTATTTTGGTGGAGTCAT
2791251 TCTTTATGGC
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
95 2 0.02
96 48 0.59
97 31 0.38
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (97 bp):
AATGGCGCCACCACTGTACTCCAAGTATTTTTTTAATGTGTGTTTTTTTAATTTAAAAATTTTAA
AAATAATATTTTATTTTGGTGGAGTCATATAG
Found at i:2791201 original size:15 final size:15
Alignment explanation
Indices: 2791181--2791209 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2791171 GTGTACTGTA
2791181 TGTTTTTTTTTAATG
1 TGTTTTTTTTTAATG
2791196 TGTTTTTTTTTAAT
1 TGTTTTTTTTTAAT
2791210 TTAAAAATTT
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:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
TGTTTTTTTTTAATG
Found at i:2792179 original size:3 final size:3
Alignment explanation
Indices: 2792166--2792204 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2792156 TAAAAACACA
2792166 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2792205 CAACGCTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2793332 original size:22 final size:22
Alignment explanation
Indices: 2793307--2793351 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2793297 TGACCTAATT
** *
2793307 AATATAATTTTAATAGTTTAAA
1 AATATAATTAGAATAATTTAAA
2793329 AATATAATTAGAATAATTTAAA
1 AATATAATTAGAATAATTTAAA
2793351 A
1 A
2793352 CTACCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATATAATTAGAATAATTTAAA
Found at i:2793793 original size:19 final size:19
Alignment explanation
Indices: 2793767--2793807 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
2793757 CAATAAAAGC
2793767 AATAAAAATTATT-AAATATT
1 AATAAAAA--ATTCAAATATT
2793787 AATAAAAAATTCAAATATT
1 AATAAAAAATTCAAATATT
2793806 AA
1 AA
2793808 AAATTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 9 0.45
20 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAAAAAATTCAAATATT
Found at i:2793849 original size:10 final size:10
Alignment explanation
Indices: 2793806--2793843 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2793796 TTCAAATATT
2793806 AAAAATTAGA
1 AAAAATTAGA
2793816 AAAAATTAGA
1 AAAAATTAGA
*
2793826 AAAAATATAAA
1 AAAAAT-TAGA
2793837 AAAAATT
1 AAAAATT
2793844 GTAAAATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (10 bp):
AAAAATTAGA
Found at i:2793901 original size:28 final size:29
Alignment explanation
Indices: 2793827--2793905 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
2793817 AAAATTAGAA
*
2793827 AAAATATAAAAAAAATTGTAAAATTCTAT
1 AAAATATAAAAAAAATTATAAAATTCTAT
** *
2793856 AAAGAT-TGTAAAAGATTATAAAATT-TAT
1 AAA-ATATAAAAAAAATTATAAAATTCTAT
2793884 AGAAATAT-AAAAAAATTATAAA
1 A-AAATATAAAAAAAATTATAAA
2793906 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 18 0.44
29 21 0.51
30 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAATATAAAAAAAATTATAAAATTCTAT
Found at i:2794144 original size:11 final size:12
Alignment explanation
Indices: 2794110--2794159 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
2794100 ACGGTCGTTA
*
2794110 TTTTTTA-TGAT
1 TTTTTTACTAAT
* *
2794121 TTTTATAATAAT
1 TTTTTTACTAAT
2794133 TTTTTTAC-AAT
1 TTTTTTACTAAT
*
2794144 TTTTTTTCTAAT
1 TTTTTTACTAAT
2794156 TTTT
1 TTTT
2794160 AATAAGAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (12 bp):
TTTTTTACTAAT
Found at i:2794264 original size:85 final size:87
Alignment explanation
Indices: 2794171--2794338 Score: 232
Period size: 86 Copynumber: 2.0 Consensus size: 87
2794161 ATAAGAGCAG
* * ** * *
2794171 GGGCTTAATTG-CTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTAC
1 GGGCTTAATTGACTTTTTTGAAAAAGTTCGAGGACCTTTTTGATGCATTTTAAAAGTTCAAGTAC
2794235 CCAATTGAGTG-AAAAAATCAA
66 CCAATTGAGTGCAAAAAATCAA
* * *
2794256 GGGCTTAATTGATTTTTTTGAAAAAGTTCGAGGACCTTTTTGATGCATTTTAAAAGTTGAAGTGC
1 GGGCTTAATTGACTTTTTTGAAAAAGTTCGAGGACCTTTTTGATGCATTTTAAAAGTTCAAGTAC
*
2794321 TCAATTGAGTGCAAAAAA
66 CCAATTGAGTGCAAAAAA
2794339 ATATGAGGTG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 11 0.15
86 54 0.76
87 6 0.08
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (87 bp):
GGGCTTAATTGACTTTTTTGAAAAAGTTCGAGGACCTTTTTGATGCATTTTAAAAGTTCAAGTAC
CCAATTGAGTGCAAAAAATCAA
Found at i:2795030 original size:9 final size:10
Alignment explanation
Indices: 2795018--2795093 Score: 59
Period size: 10 Copynumber: 7.7 Consensus size: 10
2795008 TTTTTATGGT
*
2795018 TTTTAATAAT
1 TTTTAATAAA
*
2795028 TTTTAATATA
1 TTTTAATAAA
* *
2795038 TTTT-ATGAT
1 TTTTAATAAA
2795047 TTTTAA-ATAA
1 TTTTAATA-AA
2795057 TTTCTAATAAA
1 TTT-TAATAAA
2795068 TTTT-ATAAA
1 TTTTAATAAA
*
2795077 TTTTAGTAAA
1 TTTTAATAAA
*
2795087 CTTTAAT
1 TTTTAAT
2795094 GATTTTTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
9 15 0.29
10 27 0.53
11 8 0.16
12 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:2795031 original size:30 final size:30
Alignment explanation
Indices: 2795004--2795073 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
2794994 TCTTTTTTTC
*
2795004 TAAATTTTTATGGTTTTT-AATAATTTTTAA
1 TAAA-TTTTATGATTTTTAAATAATTTTTAA
* *
2795034 TATATTTTATGATTTTTAAATAATTTCTAA
1 TAAATTTTATGATTTTTAAATAATTTTTAA
2795064 TAAATTTTAT
1 TAAATTTTAT
2795074 AAATTTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (30 bp):
TAAATTTTATGATTTTTAAATAATTTTTAA
Found at i:2795081 original size:30 final size:30
Alignment explanation
Indices: 2795017--2795081 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
2795007 ATTTTTATGG
* * * * *
2795017 TTTTTAATAATTTTTAATATATTTTATGAT
1 TTTTAAATAATTTCTAATAAATTTTATAAA
2795047 TTTTAAATAATTTCTAATAAATTTTATAAA
1 TTTTAAATAATTTCTAATAAATTTTATAAA
2795077 TTTTA
1 TTTTA
2795082 GTAAACTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTAAATAATTTCTAATAAATTTTATAAA
Found at i:2814950 original size:21 final size:21
Alignment explanation
Indices: 2814925--2814968 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2814915 CGTTCTCTCA
2814925 CACCACCAGAGTCAAGACACT
1 CACCACCAGAGTCAAGACACT
* *
2814946 CACCACCAGATTCAGGACACT
1 CACCACCAGAGTCAAGACACT
2814967 CA
1 CA
2814969 TCACACTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.39, G:0.14, T:0.11
Consensus pattern (21 bp):
CACCACCAGAGTCAAGACACT
Found at i:2821623 original size:14 final size:15
Alignment explanation
Indices: 2821595--2821623 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2821585 TCACCTAATT
2821595 CATCCCAATTCCAAA
1 CATCCCAATTCCAAA
2821610 CATCCCAA-TCCAAA
1 CATCCCAATTCCAAA
2821624 TTACAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (15 bp):
CATCCCAATTCCAAA
Found at i:2824148 original size:20 final size:20
Alignment explanation
Indices: 2824115--2824164 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2824105 TATCGATCTA
* * *
2824115 GTATCGATACATTTCTTAAG
1 GTATCAATATATTTCCTAAG
*
2824135 GTATTAATATATTTCCTAAG
1 GTATCAATATATTTCCTAAG
2824155 GTATCAATAT
1 GTATCAATAT
2824165 TCCTACTCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
GTATCAATATATTTCCTAAG
Found at i:2831171 original size:40 final size:40
Alignment explanation
Indices: 2831088--2831350 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
2831078 TTGAATGCTG
* * * * * *
2831088 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
2831128 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
2831168 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
2831208 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
2831248 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
2831288 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
2831327 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2831351 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:2831370 original size:79 final size:80
Alignment explanation
Indices: 2831127--2831385 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
2831117 AAGTGAATAT
* * * * * *
2831127 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
2831191 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
2831207 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
2831272 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
2831287 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
2831351 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
2831366 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
2831386 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:2839158 original size:40 final size:40
Alignment explanation
Indices: 2839075--2839337 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
2839065 TTGAATGCTG
* * * * * *
2839075 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
2839115 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
2839155 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
2839195 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
2839235 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
2839275 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
2839314 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2839338 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:2839357 original size:79 final size:80
Alignment explanation
Indices: 2839114--2839372 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
2839104 AAGTGAATAT
* * * * * *
2839114 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
2839178 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
2839194 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
2839259 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
2839274 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
2839338 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
2839353 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
2839373 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:2842080 original size:48 final size:48
Alignment explanation
Indices: 2842007--2842125 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 48
2841997 CATGTTCCAG
* ** *
2842007 ACATGGTCTTACACGAAATCACATATCGATGCCAACGCCATATCCTAG
1 ACATGGTCTTACATGGGATCACATATCGATGCCAACGCCATATCCTAA
* * * * * *
2842055 ATATGGTCTTACATGGGATCGCATATTGATGCCAATGCTATGTCCTAA
1 ACATGGTCTTACATGGGATCACATATCGATGCCAACGCCATATCCTAA
*
2842103 ACATGTTCTTACATGGGATCACA
1 ACATGGTCTTACATGGGATCACA
2842126 CATAACCCTA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (48 bp):
ACATGGTCTTACATGGGATCACATATCGATGCCAACGCCATATCCTAA
Found at i:2844737 original size:15 final size:15
Alignment explanation
Indices: 2844717--2844746 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2844707 GCCATGAAAA
2844717 GAAATCCAAGATAAG
1 GAAATCCAAGATAAG
2844732 GAAATCCAAGATAAG
1 GAAATCCAAGATAAG
2844747 ATACCATACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAATCCAAGATAAG
Found at i:2848611 original size:50 final size:49
Alignment explanation
Indices: 2848537--2848632 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 49
2848527 AATTCTCATA
*
2848537 TACATAGTAAGGTGCCAATGCCATATCCTAGATATGGTCTTACATGTCT
1 TACATAGTAAGATGCCAATGCCATATCCTAGATATGGTCTTACATGTCT
2848586 TACATGAGTAAGATGCCAATGCCATATCCTAGATATGGTCTTACATG
1 TACAT-AGTAAGATGCCAATGCCATATCCTAGATATGGTCTTACATG
2848633 GGATCACATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 5 0.11
50 40 0.89
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (49 bp):
TACATAGTAAGATGCCAATGCCATATCCTAGATATGGTCTTACATGTCT
Found at i:2850772 original size:33 final size:32
Alignment explanation
Indices: 2850735--2850798 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
2850725 ACCTTTATGC
*
2850735 CTTAAATTGAAAATGATTTTTATATAAGGGGAG
1 CTTAAATTGAAAATGACTTTTAT-TAAGGGGAG
2850768 CTTAAATTGAAAATGACTTTTATTAAGGGGA
1 CTTAAATTGAAAATGACTTTTATTAAGGGGA
2850799 AGCAATCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (32 bp):
CTTAAATTGAAAATGACTTTTATTAAGGGGAG
Found at i:2851200 original size:20 final size:20
Alignment explanation
Indices: 2851152--2851200 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2851142 ATTGATCCAA
* *
2851152 TATCGATATTTTTCTTAAGG
1 TATCGATATATTTCCTAAGG
*
2851172 TATCAATATATTTCCTAAGG
1 TATCGATATATTTCCTAAGG
*
2851192 TATTGATAT
1 TATCGATAT
2851201 TCCTGCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TATCGATATATTTCCTAAGG
Found at i:2852326 original size:23 final size:23
Alignment explanation
Indices: 2852271--2852327 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2852261 GGTTATGCCT
2852271 CACACGCCCGTGTGGAGACAAAG
1 CACACGCCCGTGTGGAGACAAAG
* *
2852294 CACACACCCGTGTGGAGGCAAAG
1 CACACGCCCGTGTGGAGACAAAG
*
2852317 CACATGCCCGT
1 CACACGCCCGT
2852328 ATGCTTAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.28, T:0.11
Consensus pattern (23 bp):
CACACGCCCGTGTGGAGACAAAG
Found at i:2859167 original size:15 final size:15
Alignment explanation
Indices: 2859144--2859178 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2859134 TTCAAATTAC
*
2859144 TCTCTGTTTTGTTCT
1 TCTCGGTTTTGTTCT
2859159 TCTCGGTTTTGTTCT
1 TCTCGGTTTTGTTCT
2859174 TCTCG
1 TCTCG
2859179 CAGTGTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.17, T:0.60
Consensus pattern (15 bp):
TCTCGGTTTTGTTCT
Found at i:2859325 original size:19 final size:20
Alignment explanation
Indices: 2859281--2859325 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2859271 ATAATGTTCA
*
2859281 TATTTTTAACATAATTTAAT
1 TATTTTTAACATAATTTAAC
2859301 TA-TTTTATA-AT-ATTTAAC
1 TATTTTTA-ACATAATTTAAC
2859319 TATTTTT
1 TATTTTT
2859326 TTGACAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 8 0.36
19 11 0.50
20 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTAACATAATTTAAC
Found at i:2859375 original size:21 final size:20
Alignment explanation
Indices: 2859333--2859376 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2859323 TTTTTGACAA
* *
2859333 GAATTTAATCGAATTTGCAT
1 GAATTTAATAGAATTAGCAT
*
2859353 GAATTTAAGTAGAATTAGTAT
1 GAATTTAA-TAGAATTAGCAT
2859374 GAA
1 GAA
2859377 AAAGTATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (20 bp):
GAATTTAATAGAATTAGCAT
Found at i:2871717 original size:43 final size:43
Alignment explanation
Indices: 2871656--2871743 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
2871646 ACACTTTTAC
*
2871656 AATTTAGTCCTAAGACTCGTATAATGAAATGCATGAAATTTCT
1 AATTTAGTCCTAAGACTCGTATAAGGAAATGCATGAAATTTCT
2871699 AATTTAGTCCTAAGACTCGTATAAGGAAATGCATGAAATTTCT
1 AATTTAGTCCTAAGACTCGTATAAGGAAATGCATGAAATTTCT
2871742 AA
1 AA
2871744 GTTACCAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (43 bp):
AATTTAGTCCTAAGACTCGTATAAGGAAATGCATGAAATTTCT
Found at i:2874086 original size:44 final size:44
Alignment explanation
Indices: 2874017--2874103 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
2874007 TTCGATTATG
* *
2874017 TATTGGCACTTGGTGTGTGAAATTGAAATAGCT-TCGGCTATATT
1 TATTGGCACTTAGTGTGCGAAATTGAAATAGCTCT-GGCTATATT
** *
2874061 TATTGGCACTTAGTGTGCGTGATTGAGATAGCTCTGGCTATAT
1 TATTGGCACTTAGTGTGCGAAATTGAAATAGCTCTGGCTATAT
2874104 ATATAGATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (44 bp):
TATTGGCACTTAGTGTGCGAAATTGAAATAGCTCTGGCTATATT
Found at i:2876592 original size:5 final size:5
Alignment explanation
Indices: 2876563--2876627 Score: 87
Period size: 5 Copynumber: 13.0 Consensus size: 5
2876553 TATAAATTTA
* * *
2876563 ATTAT GTTAA ATTAT AATA- ATTAT ATTAT AATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT
2876613 ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT
2876628 GATATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 3 0.06
5 44 0.85
6 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:2876739 original size:21 final size:21
Alignment explanation
Indices: 2876713--2876752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2876703 ATACATATAT
2876713 TTATTATTAAATAGATATTTA
1 TTATTATTAAATAGATATTTA
* *
2876734 TTATTATTTAATTGATATT
1 TTATTATTAAATAGATATT
2876753 AAATTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTATTAAATAGATATTTA
Found at i:2877053 original size:3 final size:3
Alignment explanation
Indices: 2877036--2877068 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2877026 AAATAGATAT
2877036 TTA TTA -TA TTA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2877069 GTTGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2877073 original size:3 final size:3
Alignment explanation
Indices: 2877067--2877092 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2877057 ATTATTATTA
2877067 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2877093 AACTAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2877892 original size:11 final size:11
Alignment explanation
Indices: 2877876--2877900 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2877866 ATTGAAAGTG
2877876 ATTCAAATTGA
1 ATTCAAATTGA
2877887 ATTCAAATTGA
1 ATTCAAATTGA
2877898 ATT
1 ATT
2877901 GAGCAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTCAAATTGA
Found at i:2878008 original size:77 final size:78
Alignment explanation
Indices: 2877935--2878079 Score: 172
Period size: 78 Copynumber: 1.9 Consensus size: 78
2877925 TGAAAGTGAA
* * * *
2877935 AAGTCATTTGAATTAAA-T-AATTGAATTATG-AATTATGTGAATATTTGAAGA-TATATTGATT
1 AAGTCAATTGAATCAAATTGAATTGAATGATGAAAATATGTGAATATTTGAA-ATTATATTGATT
2877996 GGAAATTAAAAGTG
65 GGAAATTAAAAGTG
** * *
2878010 ATTTGAATTGAATCAAATTGAATTGAATGATGAAAATATGTGATTATTTGAAATTTATATTGATT
1 AAGTCAATTGAATCAAATTGAATTGAATGATGAAAATATGTGAATATTTGAAA-TTATATTGATT
2878075 GGAAA
65 GGAAA
2878080 GTGAATAGTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
75 12 0.21
76 1 0.02
77 12 0.21
78 17 0.30
79 15 0.26
ACGTcount: A:0.42, C:0.01, G:0.17, T:0.39
Consensus pattern (78 bp):
AAGTCAATTGAATCAAATTGAATTGAATGATGAAAATATGTGAATATTTGAAATTATATTGATTG
GAAATTAAAAGTG
Found at i:2878048 original size:70 final size:71
Alignment explanation
Indices: 2877916--2878048 Score: 164
Period size: 70 Copynumber: 1.9 Consensus size: 71
2877906 ATTGAGATGC
* * **
2877916 ATATTGATTTGAAAGTGAAAAGTCATTTGAATTAAATAATTGAATTATGAATTATGTGAATATTT
1 ATATTGATTGGAAAGTGAAAAGTCATTTGAATTAAATAATTGAATTATGAATGATGAAAATATTT
2877981 GAAGAT
66 GAAGAT
* * *
2877987 ATATTGATTGGAAA-TTAAAAGTGATTTGAATTGAATCAAATTGAA-T-TGAATGATGAAAATAT
1 ATATTGATTGGAAAGTGAAAAGTCATTTGAATTAAAT--AATTGAATTATGAATGATGAAAATAT
2878049 GTGATTATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
70 32 0.60
71 14 0.26
72 7 0.13
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.38
Consensus pattern (71 bp):
ATATTGATTGGAAAGTGAAAAGTCATTTGAATTAAATAATTGAATTATGAATGATGAAAATATTT
GAAGAT
Found at i:2878096 original size:75 final size:71
Alignment explanation
Indices: 2877916--2878097 Score: 177
Period size: 75 Copynumber: 2.5 Consensus size: 71
2877906 ATTGAGATGC
* * * * * * *
2877916 ATATTGATTTGAAAGTGAAAAGTCATTTGAATTAAATAATTGAATTATGAATTATGTGAATATTT
1 ATATTGATTGGAAAGTGAATAGTGAATTGAATCAAATAATTGAATGATGAAATATGTGAATATTT
2877981 GAAGAT
66 GAAGAT
* * *
2877987 ATATTGATTGGAAATTAAAAGTGATTTGAATTGAATCAAATTGAATTGAATGATGAAAATATGTG
1 ATATTGATTGGAAAGT-GAA-T-A-GTGAATTGAATCAAA-T-AATTGAATGATG-AAATATGTG
*
2878052 ATTATTTGAA-ATTT
59 AATATTTGAAGA--T
2878066 ATATTGATTGGAAAGTGAATAGTGAATTGAAT
1 ATATTGATTGGAAAGTGAATAGTGAATTGAAT
2878098 TTGATTGAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
71 14 0.16
72 2 0.02
74 1 0.01
75 21 0.24
76 2 0.02
77 13 0.15
78 19 0.22
79 16 0.18
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (71 bp):
ATATTGATTGGAAAGTGAATAGTGAATTGAATCAAATAATTGAATGATGAAATATGTGAATATTT
GAAGAT
Found at i:2878125 original size:29 final size:29
Alignment explanation
Indices: 2878069--2878126 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2878059 GAAATTTATA
* *
2878069 TTGATTGGAAAGTGAATAGTGAATTGAAT
1 TTGATTGGAAAGTGAATAGAGAAGTGAAT
*
2878098 TTGATT-GAAAGTGAATTGAGAAAGTGAAT
1 TTGATTGGAAAGTGAATAGAG-AAGTGAAT
2878127 CGAATACCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (29 bp):
TTGATTGGAAAGTGAATAGAGAAGTGAAT
Found at i:2878492 original size:18 final size:19
Alignment explanation
Indices: 2878471--2878511 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2878461 AATGAAATGA
2878471 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
2878489 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
2878508 GAAA
1 GAAA
2878512 GCATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:2880235 original size:21 final size:21
Alignment explanation
Indices: 2880211--2880261 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
2880201 TCTAAACAAG
*
2880211 AACCCAAAATCCTAAACTTTT
1 AACCCAAAATCCTAAACTTTA
* *
2880232 AACCCATAACTCTTAAACTTTA
1 AACCCA-AAATCCTAAACTTTA
2880254 AACCCAAA
1 AACCCAAA
2880262 CCTCAAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCAAAATCCTAAACTTTA
Found at i:2881311 original size:22 final size:21
Alignment explanation
Indices: 2881283--2881337 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
2881273 TTTTAAATTA
* * *
2881283 TTTAAATCGAATTAACTTGAAT
1 TTTAAATCAAATAAAATT-AAT
2881305 TTTAAATTCAAATAAAATTAAT
1 TTTAAA-TCAAATAAAATTAAT
2881327 TTTAAAT-AAAT
1 TTTAAATCAAAT
2881338 CAATTACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.14
21 1 0.03
22 15 0.52
23 9 0.31
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (21 bp):
TTTAAATCAAATAAAATTAAT
Found at i:2881882 original size:19 final size:19
Alignment explanation
Indices: 2881855--2881900 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2881845 CAAAATTATT
*
2881855 TACGGTGGACAAATTTGAC
1 TACGATGGACAAATTTGAC
*
2881874 TAGGATGGACAAATTTGAC
1 TACGATGGACAAATTTGAC
2881893 TACGATGG
1 TACGATGG
2881901 GTGATTGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (19 bp):
TACGATGGACAAATTTGAC
Found at i:2881977 original size:11 final size:11
Alignment explanation
Indices: 2881961--2881987 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2881951 AAATATATTC
2881961 AATTCGATTTG
1 AATTCGATTTG
2881972 AATTCGATTTG
1 AATTCGATTTG
2881983 AATTC
1 AATTC
2881988 CATCTCACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (11 bp):
AATTCGATTTG
Found at i:2883152 original size:15 final size:13
Alignment explanation
Indices: 2883104--2883181 Score: 68
Period size: 14 Copynumber: 5.7 Consensus size: 13
2883094 TTCCTTCCTA
*
2883104 AATTCTCAATCCTT
1 AATTTTCAAT-CTT
2883118 AATTTTCAATCATT
1 AATTTTCAATC-TT
*
2883132 -ATTTTCCAATTTT
1 AATTTT-CAATCTT
2883145 ACATTTTCAATCTT
1 A-ATTTTCAATCTT
* *
2883159 AATTTTTAATTTTT
1 AATTTTCAA-TCTT
2883173 AATTTTCAA
1 AATTTTCAA
2883182 GCCTCCATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 15 0.28
14 33 0.62
15 5 0.09
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTCAATCTT
Found at i:2883177 original size:27 final size:27
Alignment explanation
Indices: 2883116--2883181 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
2883106 TTCTCAATCC
2883116 TTAATTTTCAATCATTATTTTCCAATT
1 TTAATTTTCAATCATTATTTTCCAATT
*
2883143 TTACATTTTCAATC-TTAATTTT-TAATTT
1 TTA-ATTTTCAATCATT-ATTTTCCAA-TT
2883171 TTAATTTTCAA
1 TTAATTTTCAA
2883182 GCCTCCATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAATTTTCAATCATTATTTTCCAATT
Found at i:2885881 original size:20 final size:20
Alignment explanation
Indices: 2885856--2885895 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2885846 TCATCTTAAG
2885856 TTGACTTTGATAAAGTCTAA
1 TTGACTTTGATAAAGTCTAA
*
2885876 TTGACTTTGATGAAGTCTAA
1 TTGACTTTGATAAAGTCTAA
2885896 CTTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGACTTTGATAAAGTCTAA
Found at i:2888513 original size:72 final size:72
Alignment explanation
Indices: 2888396--2888539 Score: 207
Period size: 72 Copynumber: 2.0 Consensus size: 72
2888386 TCCATATCCG
* * * ** *
2888396 GCAAAGTTGAAGAAATATCGCATGGACGAACAATTTGGTAAATTTCTTGAACTTTTTAAACAATT
1 GCAAAGTTGAAGAAAGACCACATGGACGAACAATTTGACAAATTTCTTAAACTTTTTAAACAATT
2888461 AAATATT
66 AAATATT
* *
2888468 GCAAAGTTTAAGAAAGACCACATGGATGAACAATTTGACAAATTTCTTAAACTTTTTAAACAATT
1 GCAAAGTTGAAGAAAGACCACATGGACGAACAATTTGACAAATTTCTTAAACTTTTTAAACAATT
*
2888533 ACATATT
66 AAATATT
2888540 AACTTTCCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (72 bp):
GCAAAGTTGAAGAAAGACCACATGGACGAACAATTTGACAAATTTCTTAAACTTTTTAAACAATT
AAATATT
Found at i:2889645 original size:30 final size:30
Alignment explanation
Indices: 2889609--2889669 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2889599 CATGGCTTGG
** *
2889609 CACATGGGCGTGTGGTCTGCCCGTATGGAT
1 CACATGGGCGTGTGCCCAGCCCGTATGGAT
2889639 CACATGGGCGTGTGCCCAGCCCGTATGGAT
1 CACATGGGCGTGTGCCCAGCCCGTATGGAT
2889669 C
1 C
2889670 TTGAAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.28, G:0.34, T:0.23
Consensus pattern (30 bp):
CACATGGGCGTGTGCCCAGCCCGTATGGAT
Found at i:2901851 original size:27 final size:26
Alignment explanation
Indices: 2901795--2901945 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 26
2901785 AAATTGTACA
* * *
2901795 GCACTAAGTGTGCG-ATTCTACTTTGTT
1 GCACTAAGTGTGCGAAAT-GACTATG-T
*
2901822 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGACTATG-T
* * *
2901849 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAAATGACTATG-T
*
2901876 GCACTAAGTGTGCGAGATGGACTATGT
1 GCACTAAGTGTGCGAAAT-GACTATGT
** * *
2901903 GGCACTAAGTGTGCGATTTGATTACGT
1 -GCACTAAGTGTGCGAAATGACTATGT
*
2901930 GGCACTAAATGTGCGA
1 -GCACTAAGTGTGCGA
2901946 GTTGATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 78 0.76
28 24 0.24
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAATGACTATGT
Found at i:2901855 original size:54 final size:54
Alignment explanation
Indices: 2901795--2901920 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
2901785 AAATTGTACA
* ** **
2901795 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCGAAATGGAATATG-TG
* *
2901849 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
2901904 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
2901921 TGATTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
54 39 0.63
55 23 0.37
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:2901918 original size:55 final size:54
Alignment explanation
Indices: 2901822--2901971 Score: 160
Period size: 55 Copynumber: 2.8 Consensus size: 54
2901812 CTACTTTGTT
* *
2901822 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
* * ** *
2901876 GCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGAT-GAATATGAT-GCACTAAGTGTGCGAATTGACCACGCG
* * * *
2901931 GCACTAAATGTGCGAGTTGATTAT-ATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGATGAATATGAT-GCACTAAGTGTGCG
2901972 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 37 0.46
55 44 0.54
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
Found at i:2901935 original size:82 final size:81
Alignment explanation
Indices: 2901795--2901950 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
2901785 AAATTGTACA
* * * * * *
2901795 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
2901860 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
2901876 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAAT
1 GCACTAAGTGTGCGA-ATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
2901940 GTGCGAGTTGA
64 GTGCGAATTGA
2901951 TTATATAGCA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:2901950 original size:27 final size:27
Alignment explanation
Indices: 2901822--2901971 Score: 113
Period size: 27 Copynumber: 5.5 Consensus size: 27
2901812 CTACTTTGTT
** * *
2901822 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAGTTGATTACG-TG
* ** * *
2901849 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* * *
2901876 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGAG-TTGATTACGTG
*
2901904 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* ** *
2901931 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTACGTG
*
2901958 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
2901972 GGCTCAATAT
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTACGTG
Found at i:2904487 original size:3 final size:3
Alignment explanation
Indices: 2904479--2904514 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2904469 AAAAAGGAAG
2904479 ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2904515 ACTCAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2904577 original size:19 final size:17
Alignment explanation
Indices: 2904555--2904606 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
2904545 TTGTAATGAC
2904555 AAAAGTAAAAAAAATACGA
1 AAAAG-AAAAAAAATA-GA
2904574 AAAAGAAAAAAAATAGA
1 AAAAGAAAAAAAATAGA
*
2904591 AATAGCAAAATAAAAT
1 AAAAG-AAAA-AAAAT
2904607 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 10 0.33
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAGAAAAAAAATAGA
Found at i:2909865 original size:26 final size:26
Alignment explanation
Indices: 2909834--2909941 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
2909824 TGAAATGCCC
*
2909834 ATCATGAAACATTTACCTAAACCATT
1 ATCATGAAACATTTACCTAACCCATT
*
2909860 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
*
2909886 ATCATGAAACATTTACCTAGCCCATT
1 ATCATGAAACATTTACCTAACCCATT
*
2909912 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
2909938 ATCA
1 ATCA
2909942 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:2916457 original size:204 final size:204
Alignment explanation
Indices: 2916099--2916502 Score: 673
Period size: 204 Copynumber: 2.0 Consensus size: 204
2916089 AACCCGAATG
2916099 TTTTTTATATTACTTTATTTTATTTTCATTTAAGTATGTTGCACGCTTATTACATTTATTTTTAT
1 TTTTTTATATTACTTTATTTTATTTTCATTTAAGTATGTTGCACGCTTATTACATTTATTTTTAT
**
2916164 CACTTAAAAAAATAGAGACCACATGGTTAAGGGTAGACCACACGACCATGTCATCTACACGGCTT
66 CACTTAAAAAAATAGAGACCACAAAGTTAAGGGTAGACCACACGACCATGTCATCTACACGGCTT
* * *
2916229 GGGCACATGCCCGTGTATACTTGGGCATAAAAAATTTTTTGAAGCCAAAAGGCCGTGTAACCCAC
131 GGGCACACGCCCGTGCAAACTTGGGCATAAAAAATTTTTTGAAGCCAAAAGGCCGTGTAACCCAC
2916294 ACACCTCAT
196 ACACCTCAT
* *
2916303 TTTTTTATATTATTTTATTTTATTTTCATTTAATTATGTTGCACGCTTATTACATTTATTTTTAT
1 TTTTTTATATTACTTTATTTTATTTTCATTTAAGTATGTTGCACGCTTATTACATTTATTTTTAT
* * * * *
2916368 CACTTAAAAAAATAGAGACCACAAAGTTAGGGGTGGACCATACGGCCATGTCATCTACATGGCTT
66 CACTTAAAAAAATAGAGACCACAAAGTTAAGGGTAGACCACACGACCATGTCATCTACACGGCTT
* * *
2916433 GGGCACACGCCTGTGCAAACTTGGGCATAAAAAATTTTTTGGAGCCAAACGGCCGTGTAACCCAC
131 GGGCACACGCCCGTGCAAACTTGGGCATAAAAAATTTTTTGAAGCCAAAAGGCCGTGTAACCCAC
2916498 ACACC
196 ACACC
2916503 CCATGGCACG
Statistics
Matches: 185, Mismatches: 15, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
204 185 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (204 bp):
TTTTTTATATTACTTTATTTTATTTTCATTTAAGTATGTTGCACGCTTATTACATTTATTTTTAT
CACTTAAAAAAATAGAGACCACAAAGTTAAGGGTAGACCACACGACCATGTCATCTACACGGCTT
GGGCACACGCCCGTGCAAACTTGGGCATAAAAAATTTTTTGAAGCCAAAAGGCCGTGTAACCCAC
ACACCTCAT
Found at i:2920440 original size:6 final size:6
Alignment explanation
Indices: 2920404--2920492 Score: 80
Period size: 6 Copynumber: 15.5 Consensus size: 6
2920394 ACTGAGCTCA
* * * * *
2920404 TTTAGT TTTATAT TTTA-- TTTATT TTTCTT TTTATT TTTAGT TGTACT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
2920451 TTTATT TTTATT TTTATT TTTA-- TTTGTT TTTA-T TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
2920493 CAAAATTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
4 7 0.10
5 5 0.07
6 50 0.75
7 5 0.07
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:2920457 original size:30 final size:28
Alignment explanation
Indices: 2920421--2920492 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 28
2920411 TTATATTTTA
*
2920421 TTTATTTTTCTTTTTATTTTTAGTTGTACT
1 TTTATTTTTATTTTTATTTTTAGTTGT--T
*
2920451 TTTATTTTTATTTTTATTTTTATTTGTT
1 TTTATTTTTATTTTTATTTTTAGTTGTT
2920479 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
2920493 CAAAATTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.25
28 5 0.12
30 25 0.62
ACGTcount: A:0.14, C:0.03, G:0.04, T:0.79
Consensus pattern (28 bp):
TTTATTTTTATTTTTATTTTTAGTTGTT
Found at i:2920514 original size:28 final size:27
Alignment explanation
Indices: 2920450--2920514 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
2920440 TTAGTTGTAC
*** *
2920450 TTTTATTTTTATTTTTATTTTTATTTG
1 TTTTATTTTTATTTTTAAAATTATATG
2920477 TTTT-TATTTTATTTTTCAAAATTATATG
1 TTTTAT-TTTTATTTTT-AAAATTATATG
2920505 TTTTATTTTT
1 TTTTATTTTT
2920515 TTATCATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 14 0.45
28 15 0.48
29 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTATTTTTATTTTTAAAATTATATG
Found at i:2924314 original size:40 final size:39
Alignment explanation
Indices: 2924277--2924368 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
2924267 GCTACTCGTT
*
2924277 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
2924317 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
2924356 CAAATGCCTTCGG
1 CAAATGCCTTCGG
2924369 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:2924348 original size:39 final size:40
Alignment explanation
Indices: 2924258--2924421 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
2924248 CGGAATTTAA
** *
2924258 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
2924298 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
2924337 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
2924377 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
2924417 CCGGA
1 CCGGA
2924422 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:2932011 original size:29 final size:29
Alignment explanation
Indices: 2931979--2932048 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
2931969 TAAATCCAAT
** * *
2931979 TAGTTGAGTGACCATTTTAATAAAATTCA
1 TAGTTGAGTGACCAAATAAAAAAAATTCA
*
2932008 TAGTTGAGTGGCCAAATAAAAAAAATTCA
1 TAGTTGAGTGACCAAATAAAAAAAATTCA
*
2932037 TAGTTGACTGAC
1 TAGTTGAGTGAC
2932049 GAGTGGTGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (29 bp):
TAGTTGAGTGACCAAATAAAAAAAATTCA
Found at i:2940738 original size:9 final size:9
Alignment explanation
Indices: 2940732--2940782 Score: 56
Period size: 8 Copynumber: 6.0 Consensus size: 9
2940722 TTATTTTTTG
2940732 AATTTTTAT
1 AATTTTTAT
2940741 AATTTTTAT
1 AATTTTTAT
*
2940750 --TTTGTAT
1 AATTTTTAT
2940757 -ATTTTTAT
1 AATTTTTAT
2940765 AA-TTTTAT
1 AATTTTTAT
2940773 AATTATTTAT
1 AATT-TTTAT
2940783 TGACATAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
7 6 0.17
8 14 0.39
9 11 0.31
10 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
AATTTTTAT
Found at i:2951946 original size:14 final size:13
Alignment explanation
Indices: 2951910--2951959 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 13
2951900 GTAAAAAAGG
2951910 ATAAAA-AAATAA
1 ATAAAATAAATAA
*
2951922 AT-GAATAAATAA
1 ATAAAATAAATAA
2951934 ATAAAAGTAAATAA
1 ATAAAA-TAAATAA
*
2951948 GTAAAATAAATA
1 ATAAAATAAATA
2951960 TATATAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 2 0.06
12 10 0.31
13 8 0.25
14 12 0.38
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:2952982 original size:18 final size:18
Alignment explanation
Indices: 2952936--2952984 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
2952926 TTCGTATATG
2952936 GAAATAAAAAAAAAACTA
1 GAAATAAAAAAAAAACTA
* *
2952954 -AAATAGTAAAAATAACTA
1 GAAATA-AAAAAAAAACTA
2952972 GAAATAAAAAAAA
1 GAAATAAAAAAAA
2952985 TGAAAATCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (18 bp):
GAAATAAAAAAAAAACTA
Found at i:2952983 original size:19 final size:19
Alignment explanation
Indices: 2952936--2952985 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2952926 TTCGTATATG
2952936 GAAATAAAAAAAA-AACTA
1 GAAATAAAAAAAATAACTA
**
2952954 -AAATAGTAAAAATAACTA
1 GAAATAAAAAAAATAACTA
2952972 GAAATAAAAAAAAT
1 GAAATAAAAAAAAT
2952986 GAAAATCACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.38
18 5 0.19
19 11 0.42
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (19 bp):
GAAATAAAAAAAATAACTA
Found at i:2953184 original size:16 final size:17
Alignment explanation
Indices: 2953160--2953193 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2953150 TTACTGCTAC
*
2953160 TGTTCTTTTTC-TCTTT
1 TGTTATTTTTCTTCTTT
2953176 TGTTATTTTTCTTCTTT
1 TGTTATTTTTCTTCTTT
2953193 T
1 T
2953194 CTCCTCTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (17 bp):
TGTTATTTTTCTTCTTT
Found at i:2954289 original size:45 final size:45
Alignment explanation
Indices: 2954131--2954350 Score: 158
Period size: 44 Copynumber: 4.9 Consensus size: 45
2954121 TGACTTATAG
* * * ***
2954131 CTTCAATCTGTTCCATTATAACTTCAGGGAAATAAGATTCATTGT
1 CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGCTGT
* ** ** * * * * **
2954176 TTTTTATCTGCTCCACTGCAAATTCAAGGAGATAAGATCTAC-AA
1 CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGCTGT
*
2954220 CTTCAATCTGCTCCACTGCT-ACTTCAGGGAGATAAGATTTGCTGT
1 CTTCAATCTGCTCCACT-ATAACTTCAGGGAGATAAGATTTGCTGT
* ** * *
2954265 CTTCAATCTGCTCCACTATAACTTCAGGGGGATAAGGCTCG-TGG
1 CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGCTGT
* ** * *
2954309 CTTCAATCTTCTCCACTGCAACTTTAGGGAGATACGATTTGC
1 CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGC
2954351 CATAATTTGT
Statistics
Matches: 130, Mismatches: 41, Indels: 8
0.73 0.23 0.04
Matches are distributed among these distances:
44 67 0.52
45 63 0.48
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGCTGT
Found at i:2954299 original size:89 final size:88
Alignment explanation
Indices: 2954131--2954350 Score: 199
Period size: 89 Copynumber: 2.5 Consensus size: 88
2954121 TGACTTATAG
* * ** * *** * ** *
2954131 CTTCAATCTGTTCCATTATAACTTCAGGGAAATAAGATTCATTGTTTTTTATCTGCTCCACTGCA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTGTCTTCAATCTGCTCCACTACA
*
2954196 AATTCAAGGAGATAAGATCTAC-AA
66 AATTCAAGGAGATAAG-GCT-CGAA
* *
2954220 CTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCAATCTGCTCCACTATA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTGTCTTCAATCTGCTCCACTACA
* * * **
2954285 ACTTCAGGGGGATAAGGCTCGTGG
66 AATTCAAGGAGATAAGGCTCG-AA
* * *
2954309 CTTCAATCTTCTCCACTGCAACTTTAGGGAGATACGATTTGC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGC
2954351 CATAATTTGT
Statistics
Matches: 105, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
87 1 0.01
88 2 0.02
89 102 0.97
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (88 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTGTCTTCAATCTGCTCCACTACA
AATTCAAGGAGATAAGGCTCGAA
Found at i:2954332 original size:44 final size:45
Alignment explanation
Indices: 2954181--2954342 Score: 159
Period size: 44 Copynumber: 3.6 Consensus size: 45
2954171 ATTGTTTTTT
* * * **
2954181 ATCTGCTCCACTGCAAATTCAAGGAGATAAGA-TCTAC-AACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTC-GCTGGCTTCA
* * * *
2954225 ATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTGGCTTCA
** * *
2954270 ATCTGCTCCACTATAACTTCAGGGGGATAAGGCTCG-TGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTGGCTTCA
* *
2954314 ATCTTCTCCACTGCAACTTTAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGGGAGATA
2954343 CGATTTGCCA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
44 61 0.64
45 35 0.36
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTGGCTTCA
Found at i:2954452 original size:23 final size:23
Alignment explanation
Indices: 2954426--2954480 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
2954416 TGTTCCACTG
2954426 CAACTTCAAGGAGATAAGATCTA
1 CAACTTCAAGGAGATAAGATCTA
*
2954449 CAACTTTAAGGAGATAAGATCTA
1 CAACTTCAAGGAGATAAGATCTA
2954472 CAACTTCAA
1 CAACTTCAA
2954481 TCTGCTCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (23 bp):
CAACTTCAAGGAGATAAGATCTA
Found at i:2954684 original size:255 final size:255
Alignment explanation
Indices: 2954201--2954698 Score: 617
Period size: 255 Copynumber: 2.0 Consensus size: 255
2954191 CTGCAAATTC
* *
2954201 AAGGAGATAAGATCTACAACTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTGTC
1 AAGGAGATAAGATCTACAACTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTATA
* * * * *
2954266 TTCAATCTGCTCCACTATAACTTCAGGGGGATAAGGCTCGTGGCTTCAATCTTCTCCACTGCAAC
66 TTCAATCTACTCCACTACAACTTCAGGGAGATAAAGCTCGTGGCTTCAATCTACTCCACTGCAAC
* ** * * * * * * * *
2954331 TTTAGGGAGATACGATTTGCCATAATTTGTAACTTTAATTTGATCCGCTGCAACGTTAGGGAAAT
131 TTCAGAAAGATAAGATTCGCCATAATTTGTAACTTTAATCTGATCCACAGCAACATCAAGGAAAT
* *
2954396 AAGATTCGCTATCTTCGATCTGTTCCACTGCAACTTCAAGGAGATAAGATCTACAACTTT
196 AAGATTCGCTATCTTCGATCTGCTCCACTGCAACTACAAGGAGATAAGATCTACAACTTT
*
2954456 AAGGAGATAAGATCTACAACTTCAATCTGCTCCACTGCTACTTCAGGGAGATGAGA-TTGACTAT
1 AAGGAGATAAGATCTACAACTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTG-CTAT
* ** * * * *
2954520 ATTCAGTCTACTCTGCTGCAACTTTAGGGAGATAAAGC-CGCTGGCTTCAGTCTACTTCACTGCA
65 ATTCAATCTACTCCACTACAACTTCAGGGAGATAAAGCTCG-TGGCTTCAATCTACTCCACTGCA
*
2954584 ACTTCAGAAAGATAAGATTCGCCATAATTTGTAGCTTTAATCT-ATTCCACAGCAACATCAAGGA
129 ACTTCAGAAAGATAAGATTCGCCATAATTTGTAACTTTAATCTGA-TCCACAGCAACATCAAGGA
* * * * * *
2954648 AGTATGATTTGCTGTCTTC-AGTCTGCTCCGCTGCAACTACAGGGAGATAAG
193 AATAAGATTCGCTATCTTCGA-TCTGCTCCACTGCAACTACAAGGAGATAAG
2954699 GCTGGTGGCT
Statistics
Matches: 204, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
254 7 0.03
255 197 0.97
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (255 bp):
AAGGAGATAAGATCTACAACTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGCTATA
TTCAATCTACTCCACTACAACTTCAGGGAGATAAAGCTCGTGGCTTCAATCTACTCCACTGCAAC
TTCAGAAAGATAAGATTCGCCATAATTTGTAACTTTAATCTGATCCACAGCAACATCAAGGAAAT
AAGATTCGCTATCTTCGATCTGCTCCACTGCAACTACAAGGAGATAAGATCTACAACTTT
Found at i:2959524 original size:30 final size:30
Alignment explanation
Indices: 2959490--2959550 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2959480 TTCCCGAGCC
*
2959490 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGAAAAAGTT
* * * *
2959520 TAGGGGCAAAATTGTAATTTTGAAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGAAAAAGTT
2959550 T
1 T
2959551 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGAAAAAGTT
Found at i:2959972 original size:68 final size:63
Alignment explanation
Indices: 2959900--2960047 Score: 156
Period size: 63 Copynumber: 2.3 Consensus size: 63
2959890 GAGTGCGCAT
* *
2959900 CATGTGTACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACT-ATGTGT
1 CATGTGTACAAGAGAGCTAC--GACA-TA-AAT-TAGCTAGGTCACATGGGTGATACTGA-GTGT
2959964 ACAC
60 ACAC
* * * * *
2959968 CATGTAG-ACAAGAGAGCTACGAGATAAATTGGCTAGGTTACATGGGTGGTACTGAGTGTTCAC
1 CATGT-GTACAAGAGAGCTACGACATAAATTAGCTAGGTCACATGGGTGATACTGAGTGTACAC
2960031 CATGTGTACAAGAGAGC
1 CATGTGTACAAGAGAGC
2960048 CGAACTCTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 42 0.60
64 3 0.04
65 2 0.03
66 3 0.04
68 18 0.26
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (63 bp):
CATGTGTACAAGAGAGCTACGACATAAATTAGCTAGGTCACATGGGTGATACTGAGTGTACAC
Found at i:2960964 original size:37 final size:37
Alignment explanation
Indices: 2960914--2960988 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2960904 AGTGACTATG
2960914 ACTCGTGTGGACAGTTTGATGTGAGCATTTATTAGTA
1 ACTCGTGTGGACAGTTTGATGTGAGCATTTATTAGTA
2960951 ACTCGTGTGGACAGTTTGATGTGAGCATTTATTAGTA
1 ACTCGTGTGGACAGTTTGATGTGAGCATTTATTAGTA
2960988 A
1 A
2960989 ATTGTGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (37 bp):
ACTCGTGTGGACAGTTTGATGTGAGCATTTATTAGTA
Found at i:2964387 original size:14 final size:13
Alignment explanation
Indices: 2964357--2964400 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
2964347 AAGGGTAAAC
*
2964357 AAATAAAT-GAAT
1 AAATAAATAAAAT
2964369 AAATAAATAAAAGT
1 AAATAAATAAAA-T
*
2964383 AAATAAGTAAAAT
1 AAATAAATAAAAT
2964396 AAATA
1 AAATA
2964401 TATATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:2966227 original size:49 final size:44
Alignment explanation
Indices: 2966155--2966276 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
2966145 TCACTATTTT
* * * *
2966155 AATCTGCTCCTCTACAACTTCAGGGAGATAAAATTTGTAGCCTGTCTTC
1 AATCTGCCCCACTGCAACTTCAGGGAGATAAAA--T-TAG--TGGCTTC
* * * *
2966204 AATCTTCCCCACTGCAACTTCAGGGATATAAGATTAGTGGCTTT
1 AATCTGCCCCACTGCAACTTCAGGGAGATAAAATTAGTGGCTTC
*
2966248 AATCTGCCCCACTGTAACTTCAGGGAGAT
1 AATCTGCCCCACTGCAACTTCAGGGAGAT
2966277 GAGATTCACC
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 31 0.50
46 3 0.05
47 1 0.02
49 27 0.44
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCCCCACTGCAACTTCAGGGAGATAAAATTAGTGGCTTC
Found at i:2966713 original size:89 final size:88
Alignment explanation
Indices: 2966556--2966759 Score: 207
Period size: 89 Copynumber: 2.3 Consensus size: 88
2966546 TGACTTATAG
* * * * * ** * *
2966556 CTTCAATCTGTTCCATTGCAAATTCA-GGAAAATAAGATTCACTGTCTTCGATCTGCTCGACTGC
1 CTTCAATCTGCTCCACTGCAACTTCATGG-AGATGAGATTTGCTGTCTTCGATCTGCTCCACTAC
*
2966620 AACTTCAAGGAGATAAGATCTACA-A
65 AACTTCAAGGAGATAAG-GCT-CAGA
* *
2966645 CTTCAATTTGCTCCACTGCTACTTCATGGAGATGAGATTTGCTGTCTTC-AGTCTGCTCCACTAC
1 CTTCAATCTGCTCCACTGCAACTTCATGGAGATGAGATTTGCTGTCTTCGA-TCTGCTCCACTAC
* * *
2966709 AACTTTAGGGAGATAAGGCTCATGG
65 AACTTCAAGGAGATAAGGCTCA-GA
2966734 CTTCAATCTGCTCCACTGCAACTTCA
1 CTTCAATCTGCTCCACTGCAACTTCA
2966760 GGGCGATACG
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
87 2 0.02
88 3 0.03
89 87 0.93
90 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (88 bp):
CTTCAATCTGCTCCACTGCAACTTCATGGAGATGAGATTTGCTGTCTTCGATCTGCTCCACTACA
ACTTCAAGGAGATAAGGCTCAGA
Found at i:2966892 original size:23 final size:23
Alignment explanation
Indices: 2966861--2966905 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2966851 TAACCCTAAT
*
2966861 GAGATAAGATATACAACTTCAAA
1 GAGAAAAGATATACAACTTCAAA
* *
2966884 GAGAAAAGATCTTCAACTTCAA
1 GAGAAAAGATATACAACTTCAA
2966906 CCTGCTCCAC
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:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (23 bp):
GAGAAAAGATATACAACTTCAAA
Found at i:2967070 original size:255 final size:255
Alignment explanation
Indices: 2966619--2967082 Score: 644
Period size: 255 Copynumber: 1.8 Consensus size: 255
2966609 TGCTCGACTG
* * ** ** *
2966619 CAACTTCAAGGAGATAAGATCTACAACTTCAATTTGCTCCACTGCTACTTCATGGAGATGAGATT
1 CAACTTCAAAGAGAAAAGATCTACAACTTCAACCTGCTCCACAACTACTTCATGAAGATGAGATT
* *
2966684 TGCTGTCTTCAGTCTGCTCCACTACAACTTTAGGGAGATAAGGCTCATGGCTTCAATCTGCTCCA
66 TGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTCATGGCTTCAATCTGCTCCA
**** * * * *
2966749 CTGCAACTTCAGGGCGATACGATTCGCCATAATTTGTTGCTTTAATCTGTTTCACTATAACGTCA
131 CTGCAACTTCAGAAAAATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACGTCA
2966814 GGGAAATAAGATTTGCTATCTTCGATCTGTTCCACTGTAACCCTAATGAGATAAGATATA
196 GGGAAATAAGATTTGCTATCTTCGATCTGTTCCACTGTAACCCTAATGAGATAAGATATA
*
2966874 CAACTTCAAAGAGAAAAGATCTTCAACTTCAACCTGCTCCACAACTACTTCA-GTAAGATGAGAT
1 CAACTTCAAAGAGAAAAGATCTACAACTTCAACCTGCTCCACAACTACTTCATG-AAGATGAGAT
* * * * *
2966938 TTGCTATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAGGC-CGGTGGCTTCAATTTGCTT
65 TTGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTC-ATGGCTTCAATCTGCTC
* * * *
2967002 CACTGTAACTTCAGAAAAATAAGATTCGTCATAATTTGTAGCTTTAATTTGTTCCACTGCAACGT
129 CACTGCAACTTCAGAAAAATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACGT
*
2967067 CAGGGAAGTAAGATTT
194 CAGGGAAATAAGATTT
2967083 TCTGTCTACA
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
254 2 0.01
255 177 0.99
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (255 bp):
CAACTTCAAAGAGAAAAGATCTACAACTTCAACCTGCTCCACAACTACTTCATGAAGATGAGATT
TGCTATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCTCATGGCTTCAATCTGCTCCA
CTGCAACTTCAGAAAAATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACGTCA
GGGAAATAAGATTTGCTATCTTCGATCTGTTCCACTGTAACCCTAATGAGATAAGATATA
Found at i:2967247 original size:44 final size:45
Alignment explanation
Indices: 2967132--2967258 Score: 150
Period size: 45 Copynumber: 2.8 Consensus size: 45
2967122 AGGCTGGTGG
*
2967132 CTTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAGATCCGCCAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATCCACCAT
* * * * *
2967177 CTTCTATCTACTCCACTGCAACTTCAAGGAGATAATATCTACGA-
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCCACCAT
* * *
2967221 CTTCAATCTGCTCCACTGCTACTTCAAAGAGATGAGAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGAT
2967259 TTATGGATTC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 32 0.46
45 34 0.49
46 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATCCACCAT
Found at i:2969730 original size:13 final size:13
Alignment explanation
Indices: 2969712--2969736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2969702 TTCGTGCAAT
2969712 CAAAATCCAAATC
1 CAAAATCCAAATC
2969725 CAAAATCCAAAT
1 CAAAATCCAAAT
2969737 TACTAGTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAATCCAAATC
Found at i:2974413 original size:46 final size:45
Alignment explanation
Indices: 2974309--2974483 Score: 156
Period size: 47 Copynumber: 3.8 Consensus size: 45
2974299 CAAGACAAGT
* *
2974309 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTTGAGATGTAA
* * *
2974355 GCCAATGCAAGACATGAT-TGGGACATGCATCGGCTATGAGATG-ATA
1 GCTAGTGTAAGACATG-TCTGGGACATGCATCGGCT-TGAGATGTA-A
* * * *
2974401 GTTAGTGTAAGACCATGTCTGAGACATGGCATCGGCTTGAGATATGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTGAGATGTAA
* * *
2974448 GCTAATGTGAGACCATGTCTGGGACCTAGCATCGGC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
2974484 ACCTTACCCC
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.03
46 43 0.41
47 49 0.47
48 9 0.09
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTGAGATGTAA
Found at i:2981954 original size:46 final size:47
Alignment explanation
Indices: 2981896--2982117 Score: 206
Period size: 46 Copynumber: 4.7 Consensus size: 47
2981886 GGGTGATTGT
* * **
2981896 GAGCTAGTGTAAGACGTGTTTGGGACATGCATCGGCCA-CATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATGA
* *
2981942 GAGCCAGTGTAAGATCATGTCTGGGACATGGCATTGG-CATCAAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATCAAGATGA
* * *
2981990 -ATGCTAGTATAAGACATGTCTGGGACATGCATCGGCC-TCGAGACGTA
1 GA-GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATG-A
* * * *
2982037 -AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCTA-CGAGATAA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATGA
*
2982082 TAGTCT-GTGTAAGACCATGTCTGGGACATGGCATCG
1 GAG-CTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
2982118 ACACCTTACC
Statistics
Matches: 148, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
45 1 0.01
46 72 0.49
47 47 0.32
48 28 0.19
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATGA
Found at i:2987930 original size:22 final size:23
Alignment explanation
Indices: 2987905--2987964 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2987895 TGGACTGAAT
2987905 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
2987927 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
2987949 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
2987965 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:2987932 original size:4 final size:4
Alignment explanation
Indices: 2987914--2987947 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
2987904 TATAAAAATT
2987914 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
2987948 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:2990271 original size:14 final size:13
Alignment explanation
Indices: 2990241--2990284 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
2990231 AAGGATAAAC
*
2990241 AAATAAAT-GAAT
1 AAATAAATAAAAT
2990253 AAATAAATAAAAGT
1 AAATAAATAAAA-T
*
2990267 AAATAAGTAAAAT
1 AAATAAATAAAAT
2990280 AAATA
1 AAATA
2990285 TATATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.29
13 8 0.29
14 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Done.