Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019283.1 Corchorus olitorius cultivar O-4 contig19316, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 217260
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2762 original size:12 final size:12
Alignment explanation
Indices: 2745--2788 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
2735 ACCTGGCAAT
2745 TCGTGTTTCGTG
1 TCGTGTTTCGTG
2757 TCGTGTTTCGTG
1 TCGTGTTTCGTG
2769 TCGTGTTTCGTG
1 TCGTGTTTCGTG
2781 TCGTGTTT
1 TCGTGTTT
2789 ACATAGGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:9152 original size:22 final size:22
Alignment explanation
Indices: 9124--9173 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
9114 ATAAGCTGTG
9124 CAACAATTTTAAATTTAATGTC
1 CAACAATTTTAAATTTAATGTC
*
9146 CAACAATTTTAAATTTGATGTC
1 CAACAATTTTAAATTTAATGTC
9168 CAACAA
1 CAACAA
9174 AAGCTTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (22 bp):
CAACAATTTTAAATTTAATGTC
Found at i:9922 original size:17 final size:16
Alignment explanation
Indices: 9876--9918 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
9866 GATCACCACT
9876 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
9893 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
9910 GGTGATCAA
1 AGTGATCAA
9919 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:17491 original size:10 final size:10
Alignment explanation
Indices: 17473--17546 Score: 54
Period size: 10 Copynumber: 8.0 Consensus size: 10
17463 TTTGTTTTTT
*
17473 TAATTATTAA
1 TAATAATTAA
*
17483 TTATAATTAA
1 TAATAATTAA
*
17493 TAATAA-CAA
1 TAATAATTAA
*
17502 T-TTAAATTAA
1 TAAT-AATTAA
17512 TAATAA-T--
1 TAATAATTAA
17519 TAATAATT-A
1 TAATAATTAA
17528 -AATAATTAA
1 TAATAATTAA
17537 TAATAATTAA
1 TAATAATTAA
17547 AAAATAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 6 0.12
8 9 0.18
9 7 0.14
10 27 0.54
11 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATAATTAA
Found at i:17518 original size:22 final size:21
Alignment explanation
Indices: 17485--17542 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
17475 ATTATTAATT
17485 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
17507 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
17529 ATAATTAATAATAA
1 ATAATTAATAATAA
17543 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:17524 original size:7 final size:7
Alignment explanation
Indices: 17473--17540 Score: 61
Period size: 7 Copynumber: 9.6 Consensus size: 7
17463 TTTGTTTTTT
*
17473 TAATTAT
1 TAATTAA
17480 TAATT-A
1 TAATTAA
17486 TAATTAA
1 TAATTAA
17493 TAA-TAA
1 TAATTAA
*
17499 CAATTTAAA
1 TAA-TT-AA
17508 TTAA-TAA
1 -TAATTAA
17515 TAATTAA
1 TAATTAA
17522 TAATTAAA
1 TAATT-AA
17530 TAATTAA
1 TAATTAA
17537 TAAT
1 TAAT
17541 AATTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.25
7 25 0.49
8 9 0.18
9 2 0.04
10 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:17554 original size:25 final size:25
Alignment explanation
Indices: 17506--17554 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
17496 TAACAATTTA
* *
17506 AATTAATAATAATTAATAATTAAAT
1 AATTAATAATAATTAAAAAATAAAT
17531 AATTAATAATAATTAAAAAATAAA
1 AATTAATAATAATTAAAAAATAAA
17555 AAAAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATAATAATTAAAAAATAAAT
Found at i:24496 original size:22 final size:21
Alignment explanation
Indices: 24466--24506 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
24456 CCTTTTATCT
24466 TAAATCTAAAATATAAAAATATA
1 TAAATCT-AAAT-TAAAAATATA
24489 TAAA-CTAAATTAAAAATA
1 TAAATCTAAATTAAAAATA
24507 AAACTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 2 0.11
23 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATCTAAATTAAAAATATA
Found at i:28076 original size:21 final size:22
Alignment explanation
Indices: 28050--28092 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28040 GTAGTATTAT
* *
28050 TATTTCA-AGAAAATAAATATA
1 TATTTCACAAAAAAAAAATATA
28071 TATTTCACAAAAAAAAAATATA
1 TATTTCACAAAAAAAAAATATA
28093 GCCAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
TATTTCACAAAAAAAAAATATA
Found at i:31044 original size:17 final size:17
Alignment explanation
Indices: 31022--31054 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31012 GTCACTAAAT
*
31022 GGAAACACTTAAAAGAA
1 GGAAACACCTAAAAGAA
31039 GGAAACACCTAAAAGA
1 GGAAACACCTAAAAGA
31055 TAAGCCAAAC
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:0.58, C:0.15, G:0.18, T:0.09
Consensus pattern (17 bp):
GGAAACACCTAAAAGAA
Found at i:37084 original size:2 final size:2
Alignment explanation
Indices: 37077--37105 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37067 GAAAATTAGA
37077 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
37106 CACACTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:45700 original size:41 final size:39
Alignment explanation
Indices: 45652--45765 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 39
45642 CAGAAATGGG
*
45652 AACAACACCTCCCGATGAGGGAGGGCAAACTGAGAAATATA
1 AACAACACCT-CCGATGAGGAAGGGCAAACTGAGAAAT-TA
* * *
45693 GACAACACCTTCCGATGAGGAAGGGCAAACTAGTGAACTTA
1 AACAACACC-TCCGATGAGGAAGGGCAAACT-GAGAAATTA
45734 AACAACACCATCCGATGAGGAAGGGCAAACTG
1 AACAACACC-TCCGATGAGGAAGGGCAAACTG
45766 GGAATGCTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
40 1 0.02
41 58 0.89
42 6 0.09
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (39 bp):
AACAACACCTCCGATGAGGAAGGGCAAACTGAGAAATTA
Found at i:47598 original size:40 final size:40
Alignment explanation
Indices: 47543--47662 Score: 197
Period size: 40 Copynumber: 3.0 Consensus size: 40
47533 CGACCGATCA
*
47543 GCTGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT
1 GCTGACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
47583 GCTGACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
1 GCTGACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
* *
47623 -TTAAACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
1 GCT-GACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
47663 TATCGAAGAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (40 bp):
GCTGACAACACCTTCCGATGAGGAATGGCAAACTGGGAAT
Found at i:47757 original size:42 final size:43
Alignment explanation
Indices: 47672--48189 Score: 610
Period size: 43 Copynumber: 11.9 Consensus size: 43
47662 TTATCGAAGA
* * * *
47672 AAAACTAGGACTTTCCGACCGGGAAGGGGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * *
47715 AAAACAAGGACTTTCCGACCGGGAA-GGGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* *
47757 AAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTT-GAAAAG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * * * *
47799 AGAATAAAGACCTTCCAACTAGGAAGGGGCATTTTT-GAAAAG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * * *
47841 AGAATAAGGACCTTCCAACCAGGAAGGGGCATTTTAAAAAAGAGATATCG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTT-----TG-GAAAT-G
** * **
47891 AAAACTGGGACCTTCCAACCGGGAAATAGGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGG-AAGGGGCATTTTTGGAAATG
* *
47935 AAAATAAGGACCTTCCAACCAGGAAGGAGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
47978 AAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
*
48021 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTAGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* * * *
48064 AAAAACAGGGACCTTCCAAATCAGAAATGGGCATTTTTGGAAATG
1 -AAAACAAGGACCTTCC-AACCAGGAAGGGGCATTTTTGGAAATG
* *
48109 AAAATAAGTACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
* *
48152 AAAATAAGGACCTTCCAACCAAGAAGGGGCATTTTTGG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGG
48190 TATAAAAGAA
Statistics
Matches: 415, Mismatches: 48, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
42 113 0.27
43 194 0.47
44 48 0.12
45 27 0.07
46 1 0.00
49 3 0.01
50 19 0.05
51 10 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (43 bp):
AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
Found at i:48116 original size:174 final size:172
Alignment explanation
Indices: 47672--48189 Score: 691
Period size: 174 Copynumber: 3.0 Consensus size: 172
47662 TTATCGAAGA
* * * * * * * *
47672 AAAACTAGGACTTTCCGACCGGGAAGGGGCATTTTTGGAAATGAAAACAAGGACTTTCCGACCGG
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTAGAAATGAAAACAGGGACCTTCCAACCGG
* * * *
47737 GAA-GGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTT-GAAAAGA
66 AAATGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGA
* * *
47800 GAATAAAGACCTTCCAACTAGGAAGGGGCATTTTT-GAAAAG
131 AAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAG
* * * *
47841 AGAATAAGGACCTTCCAACCAGGAAGGGGCATTTTAAAAAAGAGATATCGAAAACTGGGACCTTC
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTT----TAGA-A-AT-GAAAACAGGGACCTTC
* *
47906 CAACCGGGAAATAGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGAGCATTTTT
59 CAACC-GGAAATGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTT
*
47971 GGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG
123 GGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAG
*
48021 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTAGAAATGAAAAACAGGGACCTTCCAAATC
1 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTAGAAATG-AAAACAGGGACCTTCC-AACC
* *
48086 AGAAATGGGCATTTTTGGAAATGAAAATAAGTACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT
64 GGAAATGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT
*
48151 GAAAATAAGGACCTTCCAACCAAGAAGGGGCATTTTTGG
129 GAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGG
48190 TATAAAAGAA
Statistics
Matches: 304, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
169 29 0.10
173 3 0.01
174 117 0.38
175 6 0.02
176 20 0.07
177 4 0.01
178 49 0.16
179 38 0.12
180 38 0.12
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (172 bp):
AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTAGAAATGAAAACAGGGACCTTCCAACCGG
AAATGGGCATTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGA
AAATAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAAG
Found at i:50648 original size:34 final size:34
Alignment explanation
Indices: 50617--50686 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
50607 GATCAATGCT
*
50617 TGTTTCATTTCTGTTCTTTTTTTGCTGCAATGTG
1 TGTTTCATTTCTGTTCTTTTCTTGCTGCAATGTG
* *
50651 TGTTTCTTTTCTGTTCTTTTCTTGCTGCAGTGTG
1 TGTTTCATTTCTGTTCTTTTCTTGCTGCAATGTG
50685 TG
1 TG
50687 ACATTAGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.06, C:0.16, G:0.20, T:0.59
Consensus pattern (34 bp):
TGTTTCATTTCTGTTCTTTTCTTGCTGCAATGTG
Found at i:56554 original size:2 final size:2
Alignment explanation
Indices: 56547--56595 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
56537 ATCATGGAGA
56547 AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
56588 AT AT AT AT
1 AT AT AT AT
56596 TTATTTGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57353 original size:69 final size:69
Alignment explanation
Indices: 57253--57407 Score: 213
Period size: 69 Copynumber: 2.2 Consensus size: 69
57243 TGGAAGCAAA
* * * * * *
57253 CTTGTCTTATGGAAAAGGCCCTGTTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
1 CTTGACTTATGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTAAGAAAA
57318 CGAG
66 CGAG
* *
57322 CTTGGCTGT-TGGAAAAGCCCCTGCTGCTTGGATGGAACCGAGGCTTAAACTGACTCGTAAGAAA
1 CTTGACT-TATGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTAAGAAA
57386 ACGAG
65 ACGAG
*
57391 TTTGACTTATGGAAAAG
1 CTTGACTTATGGAAAAG
57408 TCAAAGCATT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
68 1 0.01
69 73 0.97
70 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (69 bp):
CTTGACTTATGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTAAGAAAA
CGAG
Found at i:58086 original size:20 final size:20
Alignment explanation
Indices: 58061--58100 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
58051 CATGGCATGC
58061 TTGCAATATAAATACAATGT
1 TTGCAATATAAATACAATGT
*
58081 TTGCAATATGAATACAATGT
1 TTGCAATATAAATACAATGT
58101 CCCCTTTTGC
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:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (20 bp):
TTGCAATATAAATACAATGT
Found at i:59351 original size:15 final size:15
Alignment explanation
Indices: 59331--59367 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
59321 AAACTCATTT
**
59331 TTGAAAACCTTTTTC
1 TTGAAAACAATTTTC
59346 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
59361 TTGAAAA
1 TTGAAAA
59368 ATATCTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Found at i:60905 original size:160 final size:155
Alignment explanation
Indices: 60570--60887 Score: 503
Period size: 154 Copynumber: 2.0 Consensus size: 155
60560 ACTAATGCAC
*
60570 AATGTATGCATGATCATATACACAAGTTGATGGCTTGACAACTCTATAACTCTTGTAACTGTGCA
1 AATGTATGCATGATCATATACACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGC-
** *
60635 TAGAAATGCAAAATGCAAGTGACGTGGTGTTCAAAGTCTCATGCCGGTGGATACATAGAAAAGAT
65 ----AATGCAAAATGCAAGTGACGTGGCATTCAAAGTCTCATGCCGATGGATACATAGAAAAGAT
*
60700 GCATGACATGGAAAACTATTTTGATGAGCA
126 GCATGACATGGAAAACTATGTTGATGAGCA
** *
60730 AATGTATGCATGATCATATGTACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAGCTGTGC-
1 AATGTATGCATGATCATATACACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGCA
60794 ATGCAAAATGCAAGTGACGTGGCATTCAAAGTCTCATGCCGATGGATACATAGAAAAGATGCATG
66 ATGCAAAATGCAAGTGACGTGGCATTCAAAGTCTCATGCCGATGGATACATAGAAAAGATGCATG
*
60859 ACATGGCAAACTATGTTGATGAGCA
131 ACATGGAAAACTATGTTGATGAGCA
60884 AATG
1 AATG
60888 CGTGAGCATG
Statistics
Matches: 149, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
154 89 0.60
160 60 0.40
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (155 bp):
AATGTATGCATGATCATATACACAAGTTGATGGCTTGACAACTCTACAACTCTTGTAACTGTGCA
ATGCAAAATGCAAGTGACGTGGCATTCAAAGTCTCATGCCGATGGATACATAGAAAAGATGCATG
ACATGGAAAACTATGTTGATGAGCA
Found at i:62385 original size:40 final size:40
Alignment explanation
Indices: 62066--62385 Score: 387
Period size: 40 Copynumber: 8.0 Consensus size: 40
62056 ATAGAAATAG
* * * *
62066 AAACAACACCTCCCGATGAGGTAGGGCAAACTGAGAAATGT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTG-GGAATTT
* *
62107 AGACAACACCTTCCGATGAGGAAGGGCAAACTGGTGAACTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAATTT
* * * * *
62148 AAACAACACCATCCG-GGAGGAATGGCAAACTCGGAATGCT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TT
* *
62188 -GACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATGCT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-TT
* * * *
62228 -GACAATACCTTCCGATGAGGAAAGACAAACTGGGAATTCT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT-T
*
62268 -AACAACACCTTCCGATGAGAAAGGGCAAACTGGGAATTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
*
62307 AAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATTT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
*
62347 AAACAACACCATCCGATGAGGAAGGGCAAACTGGGAATT
1 AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT
62386 ATCAAAGGAA
Statistics
Matches: 243, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
39 16 0.07
40 181 0.74
41 46 0.19
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (40 bp):
AAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT
Found at i:62549 original size:42 final size:43
Alignment explanation
Indices: 62401--62909 Score: 657
Period size: 43 Copynumber: 11.7 Consensus size: 43
62391 AGGAAAACTG
* * *
62401 GGACCTTTCGACCGGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
62444 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
62487 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAA-GAGAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* * * * *
62529 AGACCTTCCAACCAGAAAGGGGCATTTTT-GAAAAGAGAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* **
62571 GGACCTTCCAACTAGGAAGGGGCATTTTTGAAAAGAGATATCGAAAACTT
1 GGACCTTCCAACCAGGAAGGGGCATTTTTG----GA-A-AT-GAAAACAA
* * *
62621 GGACCTTCCGACCTGGAAGGGGCATTTTTGGAAATGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
*
62664 GGACCTTCCAACCGGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
62707 GGACCTTACAACCATGAAGGTGG-ATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGG-GGCATTTTTGGAAATGAAAACAA
*
62750 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAAACAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG-AAAACAA
* *
62794 GGACCTTCCAACCAGAAAGGGGCATTTTTGGAAATGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
62837 GGACCTTCCAACCAGGAGGGGGCATTTTTTGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
62880 AGACCTTCCAAACA-GAAGGGGCATTTTTGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGG
62910 TATAAAAGAA
Statistics
Matches: 413, Mismatches: 41, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.01
42 83 0.20
43 243 0.59
44 45 0.11
45 1 0.00
46 2 0.00
47 2 0.00
48 1 0.00
49 1 0.00
50 31 0.08
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (43 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
Found at i:66627 original size:2 final size:2
Alignment explanation
Indices: 66620--66649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66610 ATCATGGAGA
66620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66650 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69405 original size:15 final size:12
Alignment explanation
Indices: 69364--69400 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
69354 ACACCCTTAG
69364 GAAAAACTAGAA
1 GAAAAACTAGAA
69376 GAAAAACTAGAA
1 GAAAAACTAGAA
69388 GAAAAACTAGAA
1 GAAAAACTAGAA
69400 G
1 G
69401 TAGAAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.65, C:0.08, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAACTAGAA
Found at i:71036 original size:21 final size:21
Alignment explanation
Indices: 70992--71036 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
70982 GGCGTCCACA
* *
70992 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAACACCCAGG
* *
71013 TGGTTTGTCTGATCACCTAGG
1 TGGTTTGTCTGAACACCCAGG
71034 TGG
1 TGG
71037 GCAGTGTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.36
Consensus pattern (21 bp):
TGGTTTGTCTGAACACCCAGG
Found at i:72080 original size:3 final size:3
Alignment explanation
Indices: 72072--72102 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
72062 GTTACTAACC
72072 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
72103 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:72107 original size:2 final size:2
Alignment explanation
Indices: 72100--72126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72090 TTATTATTAT
72100 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
72127 TTAGAGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79663 original size:2 final size:2
Alignment explanation
Indices: 79656--79690 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79646 ATGAGAAGAA
79656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79691 AGAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80300 original size:28 final size:28
Alignment explanation
Indices: 80257--80402 Score: 148
Period size: 28 Copynumber: 5.0 Consensus size: 28
80247 ACACAGCAGG
* * *
80257 GCTCTCTAGCAAATCCTCGACAAATAAA
1 GCTCTCCAGCAGATCCTCGACAAACAAA
80285 GCTCTCCAGCAGATCCTCGACAAACAAA
1 GCTCTCCAGCAGATCCTCGACAAACAAA
* * * *
80313 GCTCGTTGCTAGCATATCCTCGACAGATAAA
1 GCTC--T-CCAGCAGATCCTCGACAAACAAA
*
80344 GCTCTCCAACAGATCCTCGACAAACAAA
1 GCTCTCCAGCAGATCCTCGACAAACAAA
* *
80372 GCTCATTGCCAGCAGATCCTCAACAAGCAAA
1 GCTC--T-CCAGCAGATCCTCGACAAACAAA
80403 CCTCATTGCC
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
28 51 0.53
29 1 0.01
30 2 0.02
31 43 0.44
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (28 bp):
GCTCTCCAGCAGATCCTCGACAAACAAA
Found at i:80335 original size:31 final size:30
Alignment explanation
Indices: 80264--80422 Score: 157
Period size: 31 Copynumber: 5.4 Consensus size: 30
80254 AGGGCTCTCT
* *
80264 AGCAAATCCTCGACAAATAAAGCTC-T-CC
1 AGCAGATCCTCGACAAACAAAGCTCTTGCC
*
80292 AGCAGATCCTCGACAAACAAAGCTCGTTGCT
1 AGCAGATCCTCGACAAACAAAGCTC-TTGCC
* * *
80323 AGCATATCCTCGACAGATAAAGCTC-T-CC
1 AGCAGATCCTCGACAAACAAAGCTCTTGCC
*
80351 AACAGATCCTCGACAAACAAAGCTCATTGCC
1 AGCAGATCCTCGACAAACAAAGCTC-TTGCC
* * *
80382 AGCAGATCCTCAACAAGCAAACCTCATTGCC
1 AGCAGATCCTCGACAAACAAAGCTC-TTGCC
*
80413 AACAGA-CCTC
1 AGCAGATCCTC
80423 TAATAGTGAG
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
28 45 0.41
29 1 0.01
30 6 0.06
31 57 0.52
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.18
Consensus pattern (30 bp):
AGCAGATCCTCGACAAACAAAGCTCTTGCC
Found at i:80357 original size:59 final size:59
Alignment explanation
Indices: 80262--80397 Score: 209
Period size: 59 Copynumber: 2.3 Consensus size: 59
80252 GCAGGGCTCT
* *
80262 CTAGCAAATCCTCGACAAATAAAGCTCTCCAGCAGATCCTCGACAAACAAAGCTCGTTG
1 CTAGCAAATCCTCGACAAATAAAGCTCTCCAACAGATCCTCGACAAACAAAGCTCATTG
* *
80321 CTAGCATATCCTCGACAGATAAAGCTCTCCAACAGATCCTCGACAAACAAAGCTCATTG
1 CTAGCAAATCCTCGACAAATAAAGCTCTCCAACAGATCCTCGACAAACAAAGCTCATTG
* * *
80380 CCAGCAGATCCTCAACAA
1 CTAGCAAATCCTCGACAA
80398 GCAAACCTCA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.36, C:0.32, G:0.14, T:0.18
Consensus pattern (59 bp):
CTAGCAAATCCTCGACAAATAAAGCTCTCCAACAGATCCTCGACAAACAAAGCTCATTG
Found at i:83270 original size:87 final size:90
Alignment explanation
Indices: 83163--83394 Score: 292
Period size: 87 Copynumber: 2.6 Consensus size: 90
83153 TTCCAAGATG
* *
83163 AGGCCAAGGCATTATTAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC-TCA-TCACATG
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCCGTCACACACATG
* *
83226 GTTTAGT-CTACCATGATTAAA-ACA
66 ATTTA-TCCCACCATGATTAAAGACA
* * *
83250 AGGTCAAGGCATCATCAAGCCAAGGCAGCTAAAGGTTTCTTACCTAGCCTTCCTCGTCACACACA
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTT-C-CGTCACACACA
* ***
83315 TGATTTATCCCATCATGATTAAAGGTG
64 TGATTTATCCCACCATGATTAAAGACA
* *
83342 TGGCCAAGGCATTATCAAGGCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC
83395 ACACCACGAG
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
87 47 0.38
88 1 0.01
89 1 0.01
90 5 0.04
91 23 0.19
92 46 0.37
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (90 bp):
AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCCGTCACACACATG
ATTTATCCCACCATGATTAAAGACA
Found at i:83391 original size:92 final size:88
Alignment explanation
Indices: 83163--83394 Score: 288
Period size: 92 Copynumber: 2.6 Consensus size: 88
83153 TTCCAAGATG
* * *
83163 AGGCCAAGGCATTATTAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTT-CCTCATCACATGG
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCCCTCAACACATGA
*
83227 TTTAGTCTACCATGATTAAAACA
66 TTTAGTCCACCATGATTAAAACA
* * *
83250 AGGTCAAGGCATCATCAAGCCAAGGCAGCTAAAGGTTTCTTACCTAGCCTTCCTCGTCACACACA
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC-C-TCA-ACACA
* ***
83315 TGATTTA-TCCCATCATGATTAAAGGTG
63 TGATTTAGT-CCACCATGATTAAA-ACA
* *
83342 TGGCCAAGGCATTATCAAGGCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC
1 AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCC
83395 ACACCACGAG
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
87 47 0.38
88 1 0.01
89 1 0.01
90 4 0.03
91 22 0.18
92 48 0.39
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (88 bp):
AGGCCAAGGCATTATCAAGCCAAGGCAACTAAAGGTTTCTTACCTAGCCTTCCCTCAACACATGA
TTTAGTCCACCATGATTAAAACA
Found at i:84697 original size:14 final size:13
Alignment explanation
Indices: 84678--84707 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
84668 GAGTTCTACA
84678 CTTCCATTCTCCTC
1 CTTCCATTCTCC-C
84692 CTTCCATTCTCCC
1 CTTCCATTCTCCC
84705 CTT
1 CTT
84708 AAAGACCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (13 bp):
CTTCCATTCTCCC
Found at i:84910 original size:25 final size:25
Alignment explanation
Indices: 84876--84923 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
84866 TCGCTGCCAG
*
84876 GAAGCTCACTGCTGGGAAGCTCGTT
1 GAAGCTCACTGCTAGGAAGCTCGTT
84901 GAAGCTCACTGCTAGGAAGCTCG
1 GAAGCTCACTGCTAGGAAGCTCG
84924 CTGCTAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (25 bp):
GAAGCTCACTGCTAGGAAGCTCGTT
Found at i:84941 original size:15 final size:15
Alignment explanation
Indices: 84823--84941 Score: 60
Period size: 15 Copynumber: 8.6 Consensus size: 15
84813 CACTGCTAGG
*
84823 AGCTCGCTGCCAAGA
1 AGCTCGCTGCTAAGA
84838 AGCTCGCTG---A-A
1 AGCTCGCTGCTAAGA
**
84849 A-CTCGCTGCTTTGA
1 AGCTCGCTGCTAAGA
* * *
84863 CGCTCGCTGCCAGGA
1 AGCTCGCTGCTAAGA
* **
84878 AGCTCACTGCTGGGA
1 AGCTCGCTGCTAAGA
84893 AGCTCG-T--T--GA
1 AGCTCGCTGCTAAGA
* *
84903 AGCTCACTGCTAGGA
1 AGCTCGCTGCTAAGA
84918 AGCTCGCTGCTAAGA
1 AGCTCGCTGCTAAGA
*
84933 AGCTTGCTG
1 AGCTCGCTG
84942 ACGCTCGTTG
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
10 14 0.17
11 3 0.04
12 2 0.03
13 1 0.01
14 2 0.03
15 58 0.73
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.22
Consensus pattern (15 bp):
AGCTCGCTGCTAAGA
Found at i:84959 original size:40 final size:40
Alignment explanation
Indices: 84860--84961 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
84850 CTCGCTGCTT
* ** *
84860 TGACGCTCGCTGCCAGGAAGCTCACTGCTGGGAAGCTCGT
1 TGACGCTCGCTGCTAGGAAGCTCACTGCTAAGAAGCTCGC
* * * *
84900 TGAAGCTCACTGCTAGGAAGCTCGCTGCTAAGAAGCTTGC
1 TGACGCTCGCTGCTAGGAAGCTCACTGCTAAGAAGCTCGC
* *
84940 TGACGCTCGTTGCTGGGAAGCT
1 TGACGCTCGCTGCTAGGAAGCT
84962 GGCAGAGATA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (40 bp):
TGACGCTCGCTGCTAGGAAGCTCACTGCTAAGAAGCTCGC
Found at i:86552 original size:21 final size:21
Alignment explanation
Indices: 86526--86581 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
86516 ACCCTAATCG
** *
86526 TAATTTTCTTTTTCTTTTCTT
1 TAATTTTCGATTTCTTTGCTT
86547 TAATTTTCGATTTCTTTGCTT
1 TAATTTTCGATTTCTTTGCTT
* *
86568 TCAGTTTCGATTTC
1 TAATTTTCGATTTC
86582 AATTGTGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.12, C:0.16, G:0.07, T:0.64
Consensus pattern (21 bp):
TAATTTTCGATTTCTTTGCTT
Found at i:94086 original size:30 final size:30
Alignment explanation
Indices: 94050--94177 Score: 186
Period size: 30 Copynumber: 4.3 Consensus size: 30
94040 GGCTGACATC
*
94050 TCAAAATCTTCCTCGGGATCCTCA-TCTGGG
1 TCAAAATCCTCCTCGGGATCCTCATTC-GGG
*
94080 TCAAAATCCTCTTCGGGATCCTCATTCGGG
1 TCAAAATCCTCCTCGGGATCCTCATTCGGG
* *
94110 TCGAAATCCTCCTCGGGATCCTCGTTCGGG
1 TCAAAATCCTCCTCGGGATCCTCATTCGGG
* *
94140 TCGAAATCCTCCTCGGGATCCTCATCCGGG
1 TCAAAATCCTCCTCGGGATCCTCATTCGGG
94170 TCAAAATC
1 TCAAAATC
94178 ATCTTCGGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
30 87 0.98
31 2 0.02
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (30 bp):
TCAAAATCCTCCTCGGGATCCTCATTCGGG
Found at i:95684 original size:21 final size:22
Alignment explanation
Indices: 95659--95700 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
95649 AATCTAAAGG
*
95659 TTACATT-AATCTACTCCTAAA
1 TTACATTAAAACTACTCCTAAA
95680 TTACATTAAAACTACTCCTAA
1 TTACATTAAAACTACTCCTAA
95701 GATAAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (22 bp):
TTACATTAAAACTACTCCTAAA
Found at i:95974 original size:20 final size:19
Alignment explanation
Indices: 95938--95986 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
95928 TTCCACCTGT
95938 ATAGAGAAAATAATGTAAA
1 ATAGAGAAAATAATGTAAA
*
95957 ATAGAGTAAATAAATGT-AA
1 ATAGAGAAAAT-AATGTAAA
*
95976 TTAGAGAAAAT
1 ATAGAGAAAAT
95987 CTCTCCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
ATAGAGAAAATAATGTAAA
Found at i:97239 original size:42 final size:42
Alignment explanation
Indices: 97180--97266 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
97170 TTTCTTTCAG
97180 AAGGAGTGGATCGAGAGACTGATTACATGGTGAAATTTGACT
1 AAGGAGTGGATCGAGAGACTGATTACATGGTGAAATTTGACT
97222 AAGGAGTGGATCGAGAGACTGATTACATGGTGAAATTTGACT
1 AAGGAGTGGATCGAGAGACTGATTACATGGTGAAATTTGACT
97264 AAG
1 AAG
97267 TTTTTGGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.25
Consensus pattern (42 bp):
AAGGAGTGGATCGAGAGACTGATTACATGGTGAAATTTGACT
Found at i:98501 original size:98 final size:98
Alignment explanation
Indices: 98387--98576 Score: 308
Period size: 98 Copynumber: 1.9 Consensus size: 98
98377 ATGCTTTAAA
*
98387 TATTTGGTTTGATTTTTTTCTTTTTTCCATATTATTAAATTCAATATTAATGATTATGTTTATGC
1 TATTTGGTTTGATTTTTTTATTTTTTCCATATTATTAAATTCAATATTAATGATTATGTTTATGC
98452 TTTTAAAATAAAAATATTAATCAATGCCTTTTT
66 TTTTAAAATAAAAATATTAATCAATGCCTTTTT
* * * *
98485 TATTTGTTTTTATTTTTTTATTTTTTCCATATTATTAAATTCCATATTAATGATTATGTTTATGT
1 TATTTGGTTTGATTTTTTTATTTTTTCCATATTATTAAATTCAATATTAATGATTATGTTTATGC
* * *
98550 TTTTTAAATTAACATATTAATCAATGC
66 TTTTAAAATAAAAATATTAATCAATGC
98577 TTAGTTGCTT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (98 bp):
TATTTGGTTTGATTTTTTTATTTTTTCCATATTATTAAATTCAATATTAATGATTATGTTTATGC
TTTTAAAATAAAAATATTAATCAATGCCTTTTT
Found at i:98566 original size:50 final size:50
Alignment explanation
Indices: 98414--98568 Score: 127
Period size: 50 Copynumber: 3.1 Consensus size: 50
98404 TTCTTTTTTC
* * * *
98414 CATATTATTAAATTCAATATTAATGATTATGTTTATGCTTTTAAAATAAA
1 CATATTATTAAATTCCATATTAATGATTATGTTTATGTTTTTTAAATTAA
* * * * * * * * * ** **
98464 AATATTAATCAATGCCTTTTTTAT--TTGTTTTTAT-TTTTTTATTTTTTC
1 CATATTATTAAATTCCATATTAATGATTATGTTTATGTTTTTTA-AATTAA
98512 CATATTATTAAATTCCATATTAATGATTATGTTTATGTTTTTTAAATTAA
1 CATATTATTAAATTCCATATTAATGATTATGTTTATGTTTTTTAAATTAA
98562 CATATTA
1 CATATTA
98569 ATCAATGCTT
Statistics
Matches: 71, Mismatches: 30, Indels: 8
0.65 0.28 0.07
Matches are distributed among these distances:
47 5 0.07
48 26 0.37
50 33 0.46
51 7 0.10
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (50 bp):
CATATTATTAAATTCCATATTAATGATTATGTTTATGTTTTTTAAATTAA
Found at i:102313 original size:30 final size:32
Alignment explanation
Indices: 102277--102337 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
102267 AGCCAATCAA
102277 TGAACTTCACT-G-GACATCACTTGAACCTTT
1 TGAACTTCACTGGCGACATCACTTGAACCTTT
102307 TGAACTTCACTGGCTCGACATCACTTGAACC
1 TGAACTTCACTGG--CGACATCACTTGAACC
102338 AATTGGCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 11 0.41
31 1 0.04
34 15 0.56
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (32 bp):
TGAACTTCACTGGCGACATCACTTGAACCTTT
Found at i:105144 original size:30 final size:30
Alignment explanation
Indices: 105108--105166 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
105098 GTTAATAAGC
105108 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
*
105138 CATTAAAATTTGAGGGTATAAGAGGAAAG
1 CATTAAAATTTGAGGGTATAAGAGAAAAG
105167 CCAAGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.25, T:0.25
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGAAAAGT
Found at i:107107 original size:110 final size:110
Alignment explanation
Indices: 106914--107135 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
106904 TCAGGCACTG
106914 TTCAAAAATGTGGAAGAATATTTTGCAGCCTTTGTATGAGGATAATAGGCTTTTCTCAATTGTTA
1 TTCAAAAATGTGGAAGAATATTTTGCAGCCTTTGTATGAGGATAATAGGCTTTTCTCAATTGTTA
106979 GGTCTGGTATAGGGATGTGTCTTGGAGATGGAGAAAACATTAATT
66 GGTCTGGTATAGGGATGTGTCTTGGAGATGGAGAAAACATTAATT
107024 TTCAAAAATGTGGAAGAATATTTTGCAGCCTTTGTATGAGGATAATAGGCTTTTCTCAATTGTTA
1 TTCAAAAATGTGGAAGAATATTTTGCAGCCTTTGTATGAGGATAATAGGCTTTTCTCAATTGTTA
107089 GGTCTGGTATAGGGATGTGTCTTGGAGATGGAGAAAACATTAATT
66 GGTCTGGTATAGGGATGTGTCTTGGAGATGGAGAAAACATTAATT
107134 TT
1 TT
107136 TGGAGTGACT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (110 bp):
TTCAAAAATGTGGAAGAATATTTTGCAGCCTTTGTATGAGGATAATAGGCTTTTCTCAATTGTTA
GGTCTGGTATAGGGATGTGTCTTGGAGATGGAGAAAACATTAATT
Found at i:114384 original size:393 final size:393
Alignment explanation
Indices: 113659--114445 Score: 1493
Period size: 393 Copynumber: 2.0 Consensus size: 393
113649 TTGTTCCTAC
*
113659 CATAACTAATGCACCTTTATTGATAACTGGCTCTGCTGCATTCAACTCATAAATCCCACTTCTAC
1 CATAACTAATGCACCTTTATTGATAACTGGCTCTGCTGCATTCAACTCATAAATCCCACCTCTAC
*
113724 TCTGGCCTTGTGCAAGAAGCTCCCTCGAAGACAGATCCTTCATAAGATAATTAAAAGGAAAAAAT
66 TCTGGCCTTGTGCAAGAAGCTCCCTCGAAGACAAATCCTTCATAAGATAATTAAAAGGAAAAAAT
*
113789 TAAACAGAGGCATGGTTAGTAAGGCAAAATTTAGAAACTAAACATAAATTAGTATCCGCCTTTGA
131 TAAACAGAGGCATGGTTAGTAAGGCAAAATTTAGAAACTAAACATAAATTAATATCCGCCTTTGA
113854 AACAAGTAAAACATCTAATTGAAATTTTTTATTTGGGGTTTGAATAGAGGCAGAACCAGTGTAAG
196 AACAAGTAAAACATCTAATTGAAATTTTTTATTTGGGGTTTGAATAGAGGCAGAACCAGTGTAAG
113919 ATATGGGTAGTCCAGAGCCATCGCCTTTGACCAAAGCATTTATTCCAGTGTAGTGTTCCAGCTTG
261 ATATGGGTAGTCCAGAGCCATCGCCTTTGACCAAAGCATTTATTCCAGTGTAGTGTTCCAGCTTG
*
113984 TCAAGACTTGCAGCATTTGAACTTACATGATGCGAGGCATTAGTATCAAGCAACCATCCATTCTG
326 TCAAGACTTGCAGCATTTGAACTTACATGATGCAAGGCATTAGTATCAAGCAACCATCCATTCTG
114049 AGG
391 AGG
114052 CATAACTAATGCACCTTTATTGATAACTGGCTCTGCTGCATTCAACTCATAAATCCCACCTCTAC
1 CATAACTAATGCACCTTTATTGATAACTGGCTCTGCTGCATTCAACTCATAAATCCCACCTCTAC
114117 TCTGGCCTTGTGCAAGAAGCTCCCTCGAAGACAAATCCTTCATAAGATAATTAAAAGGAAAAAAT
66 TCTGGCCTTGTGCAAGAAGCTCCCTCGAAGACAAATCCTTCATAAGATAATTAAAAGGAAAAAAT
*
114182 TAAACAGAGGCATGGTTAGTAAGGCAAAATTTAGAAACTAAACATAAATTAATATCTGCCTTTGA
131 TAAACAGAGGCATGGTTAGTAAGGCAAAATTTAGAAACTAAACATAAATTAATATCCGCCTTTGA
* * *
114247 AACAAGTAAAACATCTAATTGAAATTTTTTATTTGGGGTTTGAATAGAGGCAGAACTAGTGTGAT
196 AACAAGTAAAACATCTAATTGAAATTTTTTATTTGGGGTTTGAATAGAGGCAGAACCAGTGTAAG
*
114312 CTATGGGTAGTCCAGAGCCATCGCCTTTGACCAAAGCATTTATTCCAGTGTAGTGTTCCAGCTTG
261 ATATGGGTAGTCCAGAGCCATCGCCTTTGACCAAAGCATTTATTCCAGTGTAGTGTTCCAGCTTG
114377 TCAAGACTTGCAGCATTTGAACTTACATGATGCAAGGCATTAGTATCAAGCAACCATCCATTCTG
326 TCAAGACTTGCAGCATTTGAACTTACATGATGCAAGGCATTAGTATCAAGCAACCATCCATTCTG
114442 AGG
391 AGG
114445 C
1 C
114446 TTTGAAGCAC
Statistics
Matches: 385, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
393 385 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (393 bp):
CATAACTAATGCACCTTTATTGATAACTGGCTCTGCTGCATTCAACTCATAAATCCCACCTCTAC
TCTGGCCTTGTGCAAGAAGCTCCCTCGAAGACAAATCCTTCATAAGATAATTAAAAGGAAAAAAT
TAAACAGAGGCATGGTTAGTAAGGCAAAATTTAGAAACTAAACATAAATTAATATCCGCCTTTGA
AACAAGTAAAACATCTAATTGAAATTTTTTATTTGGGGTTTGAATAGAGGCAGAACCAGTGTAAG
ATATGGGTAGTCCAGAGCCATCGCCTTTGACCAAAGCATTTATTCCAGTGTAGTGTTCCAGCTTG
TCAAGACTTGCAGCATTTGAACTTACATGATGCAAGGCATTAGTATCAAGCAACCATCCATTCTG
AGG
Found at i:118221 original size:29 final size:31
Alignment explanation
Indices: 118172--118240 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
118162 TTTTCATAAA
*
118172 TCTCAAATAAGGGCCTGAACT-TTAAAAAAG
1 TCTCAAATAAGGGCCTCAACTCTTAAAAAAG
* *
118202 -GTCAAATAAGGG-CTCCAACTCTTAAGAAAG
1 TCTCAAATAAGGGCCT-CAACTCTTAAAAAAG
118232 TCTCAAATA
1 TCTCAAATA
118241 GGTCCAATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.06
29 15 0.47
30 8 0.25
31 7 0.22
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (31 bp):
TCTCAAATAAGGGCCTCAACTCTTAAAAAAG
Found at i:120238 original size:16 final size:16
Alignment explanation
Indices: 120219--120261 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
120209 GAAAATAAGA
120219 AAAATGAAAAAGAAAT
1 AAAATGAAAAAGAAAT
* **
120235 AAAATGATAATTAAAT
1 AAAATGAAAAAGAAAT
*
120251 AAATTGAAAAA
1 AAAATGAAAAA
120262 AAGGACTTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAATGAAAAAGAAAT
Found at i:123144 original size:2 final size:2
Alignment explanation
Indices: 123137--123192 Score: 94
Period size: 2 Copynumber: 27.0 Consensus size: 2
123127 TGTCCAAATC
123137 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT CAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT
123181 AT AT AT AT AT AT
1 AT AT AT AT AT AT
123193 TAAAACTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:125140 original size:168 final size:168
Alignment explanation
Indices: 124853--125169 Score: 476
Period size: 168 Copynumber: 1.9 Consensus size: 168
124843 AATATATTTG
** * *
124853 ATTGATTGAACATGCAAAATAAATAAATGAATCAAGTTAGTTGTTAGTTAACTTTGCCAATCAAA
1 ATTGATTGAACATGCAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATCAAA
* * *
124918 TTTATAATTGATGGATGATTATTTAATTTTTCCATAAATAAATAAATAAATTAGTAATTATGTT-
66 GTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAATAAATAAATTAGTAATTATGTTA
*
124982 GTCAAAAAAATAACTTGATTTTTTTTTCCACTAAAAAAA
131 G-CAAAAAAATAAATTGATTTTTTTTTCCACTAAAAAAA
* *
125021 ATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGTCAATCAAA
1 ATTGATTGAACATGCAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATCAAA
* * * *
125086 GTTATAATTGATTGATGATGATTTGATTTTGCTATAAATAAA-AGAATCAATTAGTAATTATGTT
66 GTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAATA-AATAAATTAGTAATTATGTT
125150 AGCAAAAAAATAAATTGATT
130 AGCAAAAAAATAAATTGATT
125170 GAACATACTA
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
167 1 0.01
168 131 0.98
169 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (168 bp):
ATTGATTGAACATGCAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATCAAA
GTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAATAAATAAATTAGTAATTATGTTA
GCAAAAAAATAAATTGATTTTTTTTTCCACTAAAAAAA
Found at i:125173 original size:142 final size:142
Alignment explanation
Indices: 125014--125536 Score: 612
Period size: 142 Copynumber: 3.8 Consensus size: 142
125004 TTTTTCCACT
*
125014 AAAAA-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGT
1 AAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGC
* * * *
125078 CAATCAAAGTTATAATTGATTGATGATGATTTGATTTTGCTATAAATAAAAGAATCAATTAGTAA
66 CAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAA
125143 TTATGTTAGCAA
131 TTATGTTAGCAA
* * * * * *
125155 AAAAATAAATTGATTGAACATACTAAATAAATAAATAAATCAAATTAGTCGTTAATTAACTTTGT
1 AAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGC
* * * * *
125220 CAATCAAAGTTATAACTAATTGATGATTATTAAATTTTGTCATAAATAAATGAATCAATTAATAA
66 CAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAA
125285 TTATGTTAGC--
131 TTATGTTAGCAA
* * * *
125295 AAAAATAAACTGATTCAACATGCTAAATAAACAAATGAACCAAGTTAGTCC-TAAGTCAACTTTG
1 AAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAA-TCAACTTTG
* ** * * *
125359 CCAATAAAAG-T-T-ACT-CCT-AT-A--A--T--TTTT-CCATGAATAAACGAATCAATTAGCA
65 CCAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTA
125411 ATTATGTTAGCAA
130 ATTATGTTAGCAA
* * * *
125424 AAAAATAAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTG
1 AAAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTG
* * *
125489 CCAATCAAAGTTGTAATTGATTGATGATTATTTAATTTTACCATAAAT
65 CCAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAAT
125537 CGCTACCAAA
Statistics
Matches: 317, Mismatches: 46, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
127 31 0.10
128 4 0.01
129 6 0.02
130 56 0.18
131 3 0.01
132 2 0.01
133 2 0.01
134 2 0.01
135 4 0.01
136 2 0.01
137 3 0.01
138 2 0.01
139 4 0.01
140 60 0.19
141 5 0.02
142 124 0.39
143 7 0.02
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (142 bp):
AAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGC
CAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAA
TTATGTTAGCAA
Found at i:125425 original size:127 final size:129
Alignment explanation
Indices: 125264--125500 Score: 343
Period size: 130 Copynumber: 1.8 Consensus size: 129
125254 TTTTGTCATA
* *
125264 AATAAATGAATCAATTAATAATTATGTTAGC-AAAAAT-AAACTGATTCAACATGCTAAATAAAC
1 AATAAACGAATCAATTAACAATTATGTTAGCAAAAAATAAAACTGATTCAACATGCTAAATAAAC
125327 AAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTATAATTTTTCCATG
66 AAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTATAATTTTTCCATG
* * *
125391 AATAAACGAATCAATTAGCAATTATGTTAGCAAAAAAATAAAATTGATTGAACATGCTAAATAAA
1 AATAAACGAATCAATTAACAATTATGTTAGC-AAAAAATAAAACTGATTCAACATGCTAAATAAA
* * * * * * *
125456 TAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTT
65 CAAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTT
125501 GTAATTGATT
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
127 28 0.29
129 6 0.06
130 61 0.64
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (129 bp):
AATAAACGAATCAATTAACAATTATGTTAGCAAAAAATAAAACTGATTCAACATGCTAAATAAAC
AAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTATAATTTTTCCATG
Found at i:125673 original size:165 final size:165
Alignment explanation
Indices: 125399--125866 Score: 708
Period size: 165 Copynumber: 2.8 Consensus size: 165
125389 TGAATAAACG
* *
125399 AATCAATTAGCAATTATGTTAGCAAAAAAATAAAATTGATTGAACATGCTAAATAAATAAATGAA
1 AATCAATTAGTAATTATGTTA-CCAAAAAAT-AAATT-ATTGAACATGCTAAATAAATAAATGAA
* *
125464 TCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATTTAATTTTA
63 TCAAGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTAATTTTA
125529 CCATAAATCGCT-ACCAAAAAAATTACCAT-AATAAATA
128 CCATAAATCGCTAACC-AAAAAATTACCATAAATAAATA
*
125566 AATCAATTAGTAATTATGTTACCAAAAAATAAATTATTGAACATGGTAAATAAATAAATGAATCC
1 AATCAATTAGTAATTATGTTACCAAAAAATAAATTATTGAACATGCTAAATAAATAAATGAAT-C
* * *
125631 AAGTTAGTCGTTAGTTAATTTTGTGAATCAAAGTTTTAATTGATTGATAATT-TTTAATTTTACC
65 AAGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTAATTTTACC
* *
125695 ATAAATTGCTAACCAAAAATTTACCATAAATAAATA
130 ATAAATCGCTAACCAAAAAATTACCATAAATAAATA
* * * *
125731 AATCAATTAGTGATTATGTTACCAAAAAAATTAATTATTGAACATGCTAAATAGACAAATGAATC
1 AATCAATTAGTAATTATGTTACC-AAAAAATAAATTATTGAACATGCTAAATAAATAAATGAATC
* * *
125796 AAGTTAGTCATTAGTTAACTTTGTCAATCAAAGTTATAACTGATTGATGATTATTTAATTTTACC
65 AAGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTAATTTTACC
125861 ATAAAT
130 ATAAAT
125867 AAATCAATCA
Statistics
Matches: 276, Mismatches: 20, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
164 60 0.22
165 134 0.49
166 62 0.22
167 20 0.07
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (165 bp):
AATCAATTAGTAATTATGTTACCAAAAAATAAATTATTGAACATGCTAAATAAATAAATGAATCA
AGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTATAATTGATTGATGATTATTTAATTTTACCA
TAAATCGCTAACCAAAAAATTACCATAAATAAATA
Found at i:125989 original size:174 final size:175
Alignment explanation
Indices: 125770--126084 Score: 481
Period size: 174 Copynumber: 1.8 Consensus size: 175
125760 ATTAATTATT
* * * * * *
125770 GAACATGCTAAATAGACAAATGAATCAAGTTAGTCATTAGTTAACTTTGTCAATCAAAGTTATAA
1 GAACATGCTAAATAAACAAATCAATCAACTTAGTCACTAGTTAACTTTGCCAATCAAAATTATAA
* * *
125835 CTGATTGATGATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTATGTTA-GCAAAA
66 CTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTATGCAAAA
*
125899 AAATCAATTGAGGATGGTGTTAAATAAATTGATCCAAAAAAAAAA
131 AAATAAATTGAGGATGGTGTTAAATAAATTGATCCAAAAAAAAAA
* *
125944 GAACATGCTAAATAAATC-AATCAATCAACTTAGTCGCTCGTTAACTTTGCCAATCAAAATTATA
1 GAACATGCTAAATAAA-CAAATCAATCAACTTAGTCACTAGTTAACTTTGCCAATCAAAATTATA
*
126008 ATTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTATGCAAA
65 ACTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTATGCAAA
*
126073 AAACTAAATTGA
130 AAAATAAATTGA
126085 TTGAACATGC
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
174 109 0.87
175 16 0.13
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (175 bp):
GAACATGCTAAATAAACAAATCAATCAACTTAGTCACTAGTTAACTTTGCCAATCAAAATTATAA
CTGATTCATAATTATTTAATTTTACCATAAATAAATCAATCAATTAGTAATTACGTTATGCAAAA
AAATAAATTGAGGATGGTGTTAAATAAATTGATCCAAAAAAAAAA
Found at i:127647 original size:14 final size:14
Alignment explanation
Indices: 127628--127657 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
127618 TTATATTCGT
*
127628 TTTTTGTTTCTTAA
1 TTTTTGTTTCTCAA
127642 TTTTTGTTTCTCAA
1 TTTTTGTTTCTCAA
127656 TT
1 TT
127658 AGATAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTGTTTCTCAA
Found at i:129112 original size:8 final size:8
Alignment explanation
Indices: 129099--129173 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
129089 CAATCAATTA
129099 AATTGATT
1 AATTGATT
129107 AATTGATT
1 AATTGATT
129115 AA-TGATCAAT
1 AATTGAT---T
129125 CAATTGATT
1 -AATTGATT
* *
129134 GATTAATT
1 AATTGATT
129142 AATTGATT
1 AATTGATT
*
129150 AATTGATC
1 AATTGATT
**
129158 AATCAATT
1 AATTGATT
129166 AATTGATT
1 AATTGATT
129174 GTTTAATCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
7 4 0.08
8 40 0.77
9 1 0.02
10 1 0.02
11 2 0.04
12 4 0.08
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (8 bp):
AATTGATT
Found at i:129141 original size:12 final size:12
Alignment explanation
Indices: 129108--129156 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
129098 AAATTGATTA
129108 ATTGATTAA-TG
1 ATTGATTAATTG
** *
129119 ATCAATCAATTG
1 ATTGATTAATTG
*
129131 ATTGATTAATTA
1 ATTGATTAATTG
129143 ATTGATTAATTG
1 ATTGATTAATTG
129155 AT
1 AT
129157 CAATCAATTA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
11 6 0.21
12 23 0.79
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (12 bp):
ATTGATTAATTG
Found at i:129180 original size:36 final size:36
Alignment explanation
Indices: 129084--129180 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
129074 AAATTAACAT
129084 TTGATCAATCAATTAA---ATTGATTAATTGATTAA
1 TTGATCAATCAATTAATTGATTGATTAATTGATTAA
* *
129117 -TGATCAATCAATTGATTGATTAATTAATTGATTAA
1 TTGATCAATCAATTAATTGATTGATTAATTGATTAA
*
129152 TTGATCAATCAATTAATTGATTGTTTAAT
1 TTGATCAATCAATTAATTGATTGATTAAT
129181 CTACCTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.25
35 16 0.29
36 25 0.45
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (36 bp):
TTGATCAATCAATTAATTGATTGATTAATTGATTAA
Found at i:136537 original size:21 final size:21
Alignment explanation
Indices: 136513--136557 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
136503 TTGGAGCTCA
*
136513 TTGAATTCAAACTTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
*
136534 TTGAGTTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
136555 TTG
1 TTG
136558 GTTGATTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGAATTCAAAATTAGGGTTC
Found at i:136751 original size:21 final size:21
Alignment explanation
Indices: 136727--136766 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
136717 AGAGCTAGAA
*
136727 AACCTTGCCTAGGCGTGGCCC
1 AACCTTGCCCAGGCGTGGCCC
136748 AACCTTGCCCAGGCGTGGC
1 AACCTTGCCCAGGCGTGGC
136767 TTATCCCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.30, T:0.17
Consensus pattern (21 bp):
AACCTTGCCCAGGCGTGGCCC
Found at i:138039 original size:15 final size:16
Alignment explanation
Indices: 138019--138058 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
138009 AGAGGTTGAA
138019 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
138034 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
138050 AGAAAACAA
1 AGAAAACAA
138059 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:140940 original size:30 final size:30
Alignment explanation
Indices: 140904--140970 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
140894 TAAACTCCAA
* *
140904 TCTTCAATTCTTGAAATAAATCTTC-AATAG
1 TCTTCAAGTCTTCAAAT-AATCTTCAAATAG
* *
140934 TCTTCAAGTCTTCAAATTATTTTCAAATAG
1 TCTTCAAGTCTTCAAATAATCTTCAAATAG
140964 TCTTCAA
1 TCTTCAA
140971 ACACGAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (30 bp):
TCTTCAAGTCTTCAAATAATCTTCAAATAG
Found at i:147999 original size:29 final size:29
Alignment explanation
Indices: 147930--148006 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
147920 TCTCGGTGTA
* *
147930 TCAAGTGCGGGTTGTGCACTTGTGTTTGT
1 TCAAGTGCGGGTTGTGCACTTGGGATTGT
*
147959 TCAAATGCGGGTTGTGCACTTGGGATTGT
1 TCAAGTGCGGGTTGTGCACTTGGGATTGT
** *
147988 TTGAGTGTGGGTT-TGCACT
1 TCAAGTGCGGGTTGTGCACT
148007 CGGTGTTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 6 0.15
29 35 0.85
ACGTcount: A:0.13, C:0.13, G:0.35, T:0.39
Consensus pattern (29 bp):
TCAAGTGCGGGTTGTGCACTTGGGATTGT
Found at i:149601 original size:21 final size:21
Alignment explanation
Indices: 149555--149602 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
149545 CTCTTATTTC
149555 TTTTGATAATTTACAATTTGA
1 TTTTGATAATTTACAATTTGA
* *
149576 ATTTGATAATTTA-TATTATGA
1 TTTTGATAATTTACAATT-TGA
149597 TTTTGA
1 TTTTGA
149603 GAAATTGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTTGATAATTTACAATTTGA
Found at i:150668 original size:68 final size:68
Alignment explanation
Indices: 150559--150696 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
150549 ATCTTGTCTC
150559 GGGCTTACCCAAACTGAATTTTAGTACTAACAAAGTTTGTGAAGCATGTCAGTTTGGCAAACAGG
1 GGGCTTACCCAAACTGAATTTTAGTACTAACAAAGTTTGTGAAGCATGTCAGTTTGGCAAACAGG
150624 TCA
66 TCA
150627 GGGCTTACCCAAACTGAATTTTAGTACTAACAAAGTTTGTGAAGCATGTCAGTTTGGCAAACAGG
1 GGGCTTACCCAAACTGAATTTTAGTACTAACAAAGTTTGTGAAGCATGTCAGTTTGGCAAACAGG
150692 TCA
66 TCA
150695 GG
1 GG
150697 ACCTCCTTCC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (68 bp):
GGGCTTACCCAAACTGAATTTTAGTACTAACAAAGTTTGTGAAGCATGTCAGTTTGGCAAACAGG
TCA
Found at i:152587 original size:19 final size:18
Alignment explanation
Indices: 152554--152589 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
152544 TGGAAATAAT
152554 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
152572 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
152590 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:154671 original size:19 final size:20
Alignment explanation
Indices: 154634--154672 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
154624 TTACTTACTC
154634 CTTCCTCTTCCCGAAAAACT
1 CTTCCTCTTCCCGAAAAACT
*
154654 CTTCCTCTTTCC-AAAAACT
1 CTTCCTCTTCCCGAAAAACT
154673 TTTCATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.33
Consensus pattern (20 bp):
CTTCCTCTTCCCGAAAAACT
Found at i:154729 original size:2 final size:2
Alignment explanation
Indices: 154722--154751 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
154712 AACCCTAATC
154722 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
154752 TCCTCTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:155936 original size:24 final size:25
Alignment explanation
Indices: 155893--155941 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
155883 AGGAAGTCTT
*
155893 AAAAGAAACTGAGCAGCAAAAGAAG
1 AAAAGAAACTGAGCAACAAAAGAAG
*
155918 AAAA-AAAGTGAGCAACAAAAGAAG
1 AAAAGAAACTGAGCAACAAAAGAAG
155942 GACAAGGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.63, C:0.10, G:0.22, T:0.04
Consensus pattern (25 bp):
AAAAGAAACTGAGCAACAAAAGAAG
Found at i:156121 original size:15 final size:15
Alignment explanation
Indices: 156101--156132 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
156091 AGATGATGAG
156101 AAAGTTGAAGAAGAA
1 AAAGTTGAAGAAGAA
*
156116 AAAGTTGAGGAAGAA
1 AAAGTTGAAGAAGAA
156131 AA
1 AA
156133 GCAAACAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (15 bp):
AAAGTTGAAGAAGAA
Found at i:160182 original size:19 final size:18
Alignment explanation
Indices: 160158--160193 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
160148 AGCTCCAGTT
*
160158 TCTCCCTTCTTTGTCTTTC
1 TCTCCCTCCTTT-TCTTTC
160177 TCTCCCTCCTTTTCTTT
1 TCTCCCTCCTTTTCTTT
160194 ACCGTCGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.00, C:0.39, G:0.03, T:0.58
Consensus pattern (18 bp):
TCTCCCTCCTTTTCTTTC
Found at i:168461 original size:22 final size:22
Alignment explanation
Indices: 168431--168473 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
168421 AAAATTCAGA
* * *
168431 ACAAGTCCTGTCCAGGGCTTGG
1 ACAACTCCTGCCCAGGACTTGG
168453 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
168474 TTGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:173787 original size:21 final size:21
Alignment explanation
Indices: 173757--173799 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
173747 CTAAAAACAG
*
173757 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
173778 GACAACTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
173799 G
1 G
173800 GTCTGTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:177219 original size:13 final size:12
Alignment explanation
Indices: 177198--177242 Score: 72
Period size: 13 Copynumber: 3.6 Consensus size: 12
177188 TGTATGATGT
177198 TTTTTTTTTTTA
1 TTTTTTTTTTTA
177210 TTTTTATTTTTTA
1 TTTTT-TTTTTTA
177223 TTTTTTTATTTTA
1 TTTTTTT-TTTTA
177236 TTTTTTT
1 TTTTTTT
177243 CTCTCTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.23
13 24 0.77
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:177226 original size:21 final size:19
Alignment explanation
Indices: 177197--177242 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
177187 ATGTATGATG
177197 TTTTTTTTTTTTATTTTTAT
1 TTTTTTTTTTTTA-TTTTAT
177217 TTTTTATTTTTTTATTTTAT
1 TTTTT-TTTTTTTATTTTAT
177237 TTTTTT
1 TTTTTT
177243 CTCTCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 8 0.32
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTATTTTAT
Found at i:191762 original size:27 final size:27
Alignment explanation
Indices: 191722--191776 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
191712 GCTTTGATAT
*
191722 TACTGAATTTAACTTTCCATTCACTTA
1 TACTGAATTGAACTTTCCATTCACTTA
191749 TACTGAATTGAACTTTCCATTCACTTA
1 TACTGAATTGAACTTTCCATTCACTTA
191776 T
1 T
191777 CAGGGTATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (27 bp):
TACTGAATTGAACTTTCCATTCACTTA
Found at i:197462 original size:38 final size:38
Alignment explanation
Indices: 197408--197485 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
197398 TTACTTGTGT
* * ** *
197408 CTGTTGATACTCTTAAAT-TCCTATCTTTTCTTACCTAG
1 CTGTTAATACTATTAAATAT-CTATCCCTTCTTACCAAG
197446 CTGTTAATACTATTAAATATCTATCCCTTCTTACCAAG
1 CTGTTAATACTATTAAATATCTATCCCTTCTTACCAAG
197484 CT
1 CT
197486 TATTGTAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (38 bp):
CTGTTAATACTATTAAATATCTATCCCTTCTTACCAAG
Found at i:199928 original size:65 final size:63
Alignment explanation
Indices: 199829--199957 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 63
199819 TTCTTATCAG
* *
199829 TATAAAATAATATAATTATGTCTGTTTGTATGTATGTACATTAAGGGCAATTATAAAGTGTAA
1 TATAAAATAATATAATTATGCCTGTTTGTATGTATGTAAATTAAGGGCAATTATAAAGTGTAA
199892 TATAAAATAATATAATTATATGCCTGTTTGTATGTATGTAAATTAAGGGCAATTATAAAGTGTAA
1 TATAAAATAATATAA-T-TATGCCTGTTTGTATGTATGTAAATTAAGGGCAATTATAAAGTGTAA
199957 T
1 T
199958 GGGTGGAAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 15 0.24
64 1 0.02
65 46 0.74
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (63 bp):
TATAAAATAATATAATTATGCCTGTTTGTATGTATGTAAATTAAGGGCAATTATAAAGTGTAA
Found at i:205146 original size:46 final size:46
Alignment explanation
Indices: 205079--205171 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
205069 CCTTTGGCCG
205079 CTCTTCCTCTCAAGCCCAGGTATGTTTCCTTTCACCATGGTTTCAT
1 CTCTTCCTCTCAAGCCCAGGTATGTTTCCTTTCACCATGGTTTCAT
205125 CTCTTCCTCTCAAGCCCAGGTATGTTTCCTTTCACCATGGTTTCAT
1 CTCTTCCTCTCAAGCCCAGGTATGTTTCCTTTCACCATGGTTTCAT
205171 C
1 C
205172 GTGCCTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.15, C:0.33, G:0.13, T:0.39
Consensus pattern (46 bp):
CTCTTCCTCTCAAGCCCAGGTATGTTTCCTTTCACCATGGTTTCAT
Found at i:205154 original size:22 final size:22
Alignment explanation
Indices: 205082--205154 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
205072 TTGGCCGCTC
205082 TTCCTCTCAAGCCCAGGTATGT
1 TTCCTCTCAAGCCCAGGTATGT
* *
205104 TTCCTTTC-A--CCATGGTTTCATCT
1 TTCCTCTCAAGCCCA-GG--T-ATGT
205127 CTTCCTCTCAAGCCCAGGTATGT
1 -TTCCTCTCAAGCCCAGGTATGT
205150 TTCCT
1 TTCCT
205155 TTCACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 1 0.03
22 13 0.33
23 6 0.15
24 8 0.21
25 1 0.03
26 2 0.05
27 3 0.08
ACGTcount: A:0.15, C:0.33, G:0.14, T:0.38
Consensus pattern (22 bp):
TTCCTCTCAAGCCCAGGTATGT
Found at i:209035 original size:25 final size:25
Alignment explanation
Indices: 209007--209055 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
208997 AAATATGGGA
209007 ATCTT-CCCGAAAAACAAAATTTGCC
1 ATCTTGCCC-AAAAACAAAATTTGCC
209032 ATCTTGCCCAAAAACAAAATTTGC
1 ATCTTGCCCAAAAACAAAATTTGC
209056 GAACATGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (25 bp):
ATCTTGCCCAAAAACAAAATTTGCC
Found at i:209064 original size:25 final size:25
Alignment explanation
Indices: 209016--209064 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
209006 AATCTTCCCG
* *
209016 AAAAACAAAATTTGCCATCTTGCCC
1 AAAAACAAAATTTGCCAACATGCCC
*
209041 AAAAACAAAATTTGCGAACATGCC
1 AAAAACAAAATTTGCCAACATGCC
209065 TATGACATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (25 bp):
AAAAACAAAATTTGCCAACATGCCC
Found at i:212888 original size:44 final size:45
Alignment explanation
Indices: 212823--212908 Score: 129
Period size: 44 Copynumber: 1.9 Consensus size: 45
212813 CGGATAAATG
* *
212823 AAATGGATTATAAGTTATAATATAACTTAAGAAAAGA-AAACCTC
1 AAATGGATAATAAATTATAATATAACTTAAGAAAAGATAAACCTC
* *
212867 AAATTGATAATAAATTATAATATAACTTAGGAAAAGATAAAC
1 AAATGGATAATAAATTATAATATAACTTAAGAAAAGATAAAC
212909 TAAAAAACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (45 bp):
AAATGGATAATAAATTATAATATAACTTAAGAAAAGATAAACCTC
Found at i:213088 original size:2 final size:2
Alignment explanation
Indices: 213076--213110 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
213066 ATATTCAACA
213076 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213111 TCGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:213535 original size:42 final size:42
Alignment explanation
Indices: 213466--213556 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
213456 AGTGCATTAC
213466 CTAA-ATTCTACTCCATCTATATGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTATATGTAATTCATCAAAATAAAG
*
213507 CTAATATTCTACTCCATCTCTA-GATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTATATG-TAATTCATCAAAATAAAG
*
213549 TTAATATT
1 CTAATATT
213557 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTATATGTAATTCATCAAAATAAAG
Found at i:214699 original size:107 final size:99
Alignment explanation
Indices: 214574--214855 Score: 306
Period size: 107 Copynumber: 2.8 Consensus size: 99
214564 TTTTTTTTTA
* *
214574 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCTCAAATTAAAGTTGT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCC-CAAATTAAA-TTAT
*
214639 ATTTTTATTTTAAGGGTAAATTTTAAAATTAATAATTTATTC
64 ATTTTTATTTTAAGGGTAAA--TT-AAA-TAATAA-TTA-AC
**
214681 TTATAGGGTTTTAGAAATAAAATACGAAACTAATTTCACTAAGTTTAGCCCCAAATT--ATTAT-
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAATTATA
* ** *
214743 TTTTTATTTTGAGGGTAAATTCCATAATTATTAAC
65 TTTTTATTTTAAGGGTAAATTAAATAATAATTAAC
* * * *
214778 --ATAGGGTTTTAGAAATAAAACATATAACTAA-TTCACTAAGTTTAGTCCAAATTAAAATTAAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATT-AAATTATA
*
214840 ATTTTATTTTAAGGGT
65 TTTTTATTTTAAGGGT
214856 TAGAAAAATT
Statistics
Matches: 153, Mismatches: 17, Indels: 20
0.81 0.09 0.11
Matches are distributed among these distances:
93 7 0.05
94 14 0.09
95 27 0.18
96 4 0.03
97 15 0.10
98 3 0.02
99 5 0.03
100 1 0.01
101 2 0.01
103 18 0.12
104 3 0.02
105 1 0.01
107 51 0.33
108 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (99 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAATTATAT
TTTTATTTTAAGGGTAAATTAAATAATAATTAAC
Done.