Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015243.1 Kokia drynarioides strain JFW-HI SEQ_130288, 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: 178175
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:471 original size:18 final size:17
Alignment explanation
Indices: 441--529 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 17
431 ACTGGTCCTT
441 TTTTAAATT-AATTAAA
1 TTTTAAATTAAATTAAA
457 TTTTAAATTCAAATT-AA
1 TTTTAAATT-AAATTAAA
*
474 TTTTAAACTTAATTTAAA
1 TTTTAAA-TTAAATTAAA
* **
492 TTTT-AACTAAAAAAAA
1 TTTTAAATTAAATTAAA
*
508 GTTTAAACTTTAAATTAAA
1 TTTTAAA--TTAAATTAAA
527 TTT
1 TTT
530 AAACCCAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 18 0.32
17 17 0.30
18 12 0.21
19 9 0.16
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTTAAATTAAATTAAA
Found at i:499 original size:17 final size:16
Alignment explanation
Indices: 441--497 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 16
431 ACTGGTCCTT
441 TTTTAAATTAATTAAA
1 TTTTAAATTAATTAAA
457 TTTTAAATTCAAATT-AA
1 TTTTAAATT--AATTAAA
474 TTTTAAACTTAATTTAAA
1 TTTTAAA-TTAA-TTAAA
492 TTTTAA
1 TTTTAA
498 CTAAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.31
17 11 0.31
18 14 0.39
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAATTAATTAAA
Found at i:532 original size:18 final size:17
Alignment explanation
Indices: 442--533 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
432 CTGGTCCTTT
442 TTTAAA-TT-AATTAAA
1 TTTAAACTTAAATTAAA
*
457 TTTTAAA-TTCAAATTAAT
1 -TTTAAACTT-AAATTAAA
*
475 TTTAAACTTAATTTAAA
1 TTTAAACTTAAATTAAA
* **
492 TTTTAAC-TAAAAAAAA
1 TTTAAACTTAAATTAAA
508 GTTTAAACTTTAAATTAAA
1 -TTTAAAC-TTAAATTAAA
527 TTTAAAC
1 TTTAAAC
534 CCAAAATGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
16 14 0.23
17 24 0.40
18 15 0.25
19 7 0.12
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAACTTAAATTAAA
Found at i:4911 original size:30 final size:29
Alignment explanation
Indices: 4861--5123 Score: 158
Period size: 30 Copynumber: 8.8 Consensus size: 29
4851 GTTTTTGGAT
**
4861 GTTTAGGGGCAAAAGTGTAATTTTGGAAAA
1 GTTTAGGGTTAAAA-TGTAATTTTGGAAAA
* *
4891 ATTTAGGGTTAAAATGGTAATCTTTTTGG-ATA
1 GTTTAGGGTTAAAAT-GTAA---TTTTGGAAAA
* * *
4923 --TTCGAGG-CAAAATGGTAATTTTGGTGAAA
1 GTTTAG-GGTTAAAAT-GTAATTTTGG-AAAA
* *
4952 -TTTAGGGTGAAAATGTGATTTTGGAAAA
1 GTTTAGGGTTAAAATGTAATTTTGGAAAA
* *
4980 GTTTGAAGGTTAAAATGTAATTTTGGAGAA
1 GTTT-AGGGTTAAAATGTAATTTTGGAAAA
* ** * *
5010 GTTCGATTGTCAAAATGTGATTTTTGGAAAA
1 GTT-TAGGGTTAAAATGT-AATTTTGGAAAA
* *
5041 GTTTAGGGGTTAAAATGTAATTTTAGAGAA
1 GTTTA-GGGTTAAAATGTAATTTTGGAAAA
* * *
5071 GTTTGGGGTTAAAATATAATTTTGGAGAA
1 GTTTAGGGTTAAAATGTAATTTTGGAAAA
* * *
5100 GTTCGAGGGTCAAAATTTAATTTT
1 GTT-TAGGGTTAAAATGTAATTTT
5124 TAAATGAAAT
Statistics
Matches: 183, Mismatches: 35, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.03
28 3 0.02
29 42 0.23
30 100 0.55
31 24 0.13
32 2 0.01
33 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GTTTAGGGTTAAAATGTAATTTTGGAAAA
Found at i:5090 original size:29 final size:29
Alignment explanation
Indices: 5039--5123 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
5029 ATTTTTGGAA
*
5039 AAGTTTAGGGGTTAAAATGTAATTTTAGAG
1 AAGTTT-GGGGTTAAAATATAATTTTAGAG
*
5069 AAGTTTGGGGTTAAAATATAATTTTGGAG
1 AAGTTTGGGGTTAAAATATAATTTTAGAG
* * *
5098 AAGTTCGAGGGTCAAAATTTAATTTT
1 AAGTTTG-GGGTTAAAATATAATTTT
5124 TAAATGAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 27 0.55
30 22 0.45
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (29 bp):
AAGTTTGGGGTTAAAATATAATTTTAGAG
Found at i:5124 original size:90 final size:90
Alignment explanation
Indices: 4923--5124 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 90
4913 TTTTTGGATA
* * *
4923 TTCGA-GG-CAAAATGGTAA-TTTTGGTGAAA-TTTAGGGTGAAAATGTGATTTTGGAAAAGTTT
1 TTCGAGGGTCAAAAT-GTAATTTTTGG-AAAAGTTTAGGGTGAAAATGTAATTTTAGAAAAGTTT
*
4984 GAAGGTTAAAATGTAATTTTGGAGAAG
64 GAAGGTTAAAATATAATTTTGGAGAAG
** * * *
5011 TTCGATTGTCAAAATGTGATTTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTTG
1 TTCGAGGGTCAAAATGTAATTTTTGGAAAAGTTTA-GGGTGAAAATGTAATTTTAGAAAAGTTTG
*
5076 -GGGTTAAAATATAATTTTGGAGAAG
65 AAGGTTAAAATATAATTTTGGAGAAG
*
5101 TTCGAGGGTCAAAATTTAATTTTT
1 TTCGAGGGTCAAAATGTAATTTTT
5125 AAATGAAATA
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
88 5 0.05
89 7 0.07
90 59 0.61
91 25 0.26
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (90 bp):
TTCGAGGGTCAAAATGTAATTTTTGGAAAAGTTTAGGGTGAAAATGTAATTTTAGAAAAGTTTGA
AGGTTAAAATATAATTTTGGAGAAG
Found at i:5585 original size:36 final size:36
Alignment explanation
Indices: 5538--5623 Score: 154
Period size: 36 Copynumber: 2.4 Consensus size: 36
5528 AGATAGGGTT
* *
5538 AAACGACGTCGTTTTGAAGGCTATAGGTAAGACCTA
1 AAACGGCGTCGTTTTGAAGGCTATAGGCAAGACCTA
5574 AAACGGCGTCGTTTTGAAGGCTATAGGCAAGACCTA
1 AAACGGCGTCGTTTTGAAGGCTATAGGCAAGACCTA
5610 AAACGGCGTCGTTT
1 AAACGGCGTCGTTT
5624 AGTGAGCCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (36 bp):
AAACGGCGTCGTTTTGAAGGCTATAGGCAAGACCTA
Found at i:6997 original size:17 final size:16
Alignment explanation
Indices: 6977--7028 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
6967 AATTAAATTT
6977 TAAATTTAAATTCAAAA
1 TAAATTTAAATT-AAAA
6994 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTAAAA
*
7011 TAAATTAAAATTTAAAA
1 TAAATTTAAA-TTAAAA
7028 T
1 T
7029 TGGGTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:7008 original size:23 final size:22
Alignment explanation
Indices: 6970--7026 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
6960 GACTTTTAAT
* *
6970 TAAATTTTAAATTTAAATTCAAAA
1 TAAA-TTTAAACTTAAAAT-AAAA
*
6994 TAAATTTAAACTTAAAATAAAT
1 TAAATTTAAACTTAAAATAAAA
7016 TAAAATTTAAA
1 T-AAATTTAAA
7027 ATTGGGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 21 0.72
24 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAAACTTAAAATAAAA
Found at i:7650 original size:39 final size:39
Alignment explanation
Indices: 7541--8061 Score: 303
Period size: 39 Copynumber: 13.4 Consensus size: 39
7531 CTACCCTTAA
* * *
7541 CTCGGTGTAAGAGATTGGCTGATAGTGATCTGCCCTAGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* * **** **
7580 CTCGGGGTAAAAAATCAAATGACT-GCAATCTGCCCCAGG
1 CTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAGG
*
7619 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCGGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* * ** * * * *
7658 CTCGGGGAAAGAGATCGAATGGTTGTAATCTGTCCCAGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* * *
7697 CTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
*** *** *
7736 CTCGGGGTAAGAGATTAAATGACT-ACAATCTGCCCTAGG
1 CTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAGG
* * *
7775 CTCGGGGTAAGAGATTGGCTGATGGTGATCTACTCCAAG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* ** * **
7814 CTCGGGGTAAGAGATCGAATTACT-GCAATCT-CCCTCAGG
1 CTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCC-CAGG
* * ** * ****
7853 CTCGGGGTAAAAGATCGAATGGTTACAATCTG-CCCAGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* * *
7891 CTCGGGGTAAGAGATTGGCTGATGGTGATCTACCTCATG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* *
7930 CTTGGGGTAAGAGA-T--C-GAATGGCTGCAATCTGCTCCAGG
1 CTCGGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCAGG
*
7969 CTCGGGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCCAGG
1 CTCGGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCAGG
* * * *
8008 CTCAGGGTAAGAGATTGGTTGATGGTGATCTACCCTAGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
* *
8047 CTTGGGGTAAAAGAT
1 CTCGGGGTAAGAGAT
8062 CGGATCTTCA
Statistics
Matches: 368, Mismatches: 97, Indels: 34
0.74 0.19 0.07
Matches are distributed among these distances:
35 1 0.00
36 5 0.01
37 2 0.01
38 32 0.09
39 317 0.86
40 4 0.01
41 2 0.01
42 4 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG
Found at i:7660 original size:78 final size:78
Alignment explanation
Indices: 7541--8063 Score: 486
Period size: 78 Copynumber: 6.7 Consensus size: 78
7531 CTACCCTTAA
* * * * *
7541 CTCGGTGTAAGAGATTGGCTGATAGTGATCTGCCCTAGGCTCGGGGTAAAAAATCAAATGACTGC
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGC
7606 AATCTGCCCCAGG
66 AATCTGCCCCAGG
* **
7619 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCGGGCTCGGGG-AAAGAGATCGAATGGTTG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAA-AGATCGAATGACTG
* *
7683 TAATCTGTCCCAGG
65 CAATCTGCCCCAGG
* * * * ** *
7697 CTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATTAAATGACTAC
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGC
*
7762 AATCTGCCCTAGG
66 AATCTGCCCCAGG
* * * * *
7775 CTCGGGGTAAGAGATTGGCTGATGGTGATCTACTCCAAGCTCGGGGTAAGAGATCGAATTACTGC
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGC
7840 AATCT-CCCTCAGG
66 AATCTGCCC-CAGG
* * ** * **** * * **
7853 CTCGGGGTAAAAGATCGAATGGTTACAATCTG-CCCAGGCTCGGGGTAAGAGATTGGCTGA-TGG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACT-G
** * * *
7916 TGATCTACCTCATG
65 CAATCTGCCCCAGG
* * *
7930 CTTGGGGTAAGAGA-T--C-GAATGGCTGCAATCTGCTCCAGGCTCGGGGTAAAAGATCGAATGG
1 CTCGGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGA
7991 CTGCAATCTGCCCCAGG
62 CTGCAATCTGCCCCAGG
* * * * *
8008 CTCAGGGTAAGAGATTGGTTGATGGTGATCTACCCTAGGCTTGGGGTAAAAGATCG
1 CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCG
8064 GATCTTCAAT
Statistics
Matches: 351, Mismatches: 79, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
73 1 0.00
74 1 0.00
76 1 0.00
77 53 0.15
78 284 0.81
79 4 0.01
80 2 0.01
81 4 0.01
82 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (78 bp):
CTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGACTGC
AATCTGCCCCAGG
Found at i:7937 original size:116 final size:116
Alignment explanation
Indices: 7735--8063 Score: 457
Period size: 116 Copynumber: 2.8 Consensus size: 116
7725 TCTGCCCCAA
* ** *
7735 GCTCGGGGTAAGAGATTAAATGACTACAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGG
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCC-AGGCTCGGGGTAAGAGATTGGCTGATGG
* *
7800 TGATCTA-CTCCAAGCTCGGGGTAAGAGATCGAATTACTGCAATCTCC-CTCAG
65 TGATCTACCT-CAAGCTTGGGGTAAGAGATCGAATGACTGCAATCTCCTC-CAG
*
7852 GCTCGGGGTAAAAGATCGAATGGTTACAATCTGCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
* * *
7917 GATCTACCTCATGCTTGGGGTAAGAGATCGAATGGCTGCAATCTGCTCCAG
66 GATCTACCTCAAGCTTGGGGTAAGAGATCGAATGACTGCAATCTCCTCCAG
* * *
7968 GCTCGGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAGGCTCAGGGTAAGAGATTGGTTGATGG
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTG-CCCAGGCTCGGGGTAAGAGATTGGCTGATGG
* *
8033 TGATCTACC-CTAGGCTTGGGGTAAAAGATCG
65 TGATCTACCTC-AAGCTTGGGGTAAGAGATCG
8064 GATCTTCAAT
Statistics
Matches: 192, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
116 102 0.53
117 90 0.47
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (116 bp):
GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCAGGCTCGGGGTAAGAGATTGGCTGATGGT
GATCTACCTCAAGCTTGGGGTAAGAGATCGAATGACTGCAATCTCCTCCAG
Found at i:14111 original size:16 final size:16
Alignment explanation
Indices: 14090--14124 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
14080 CGTTGTAATT
14090 TCAAGGAACCTTTTTG
1 TCAAGGAACCTTTTTG
14106 TCAAGGAACCTTTTTG
1 TCAAGGAACCTTTTTG
14122 TCA
1 TCA
14125 TCCTTGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (16 bp):
TCAAGGAACCTTTTTG
Found at i:20269 original size:60 final size:60
Alignment explanation
Indices: 20171--20285 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
20161 GAAAATGTGG
*
20171 TTTTTGGATGTTCGAGGGAAAAAAGGTAATTTTGGAAAAATTTAGGGTT-AAAATGGTAATC
1 TTTTTGGATATTCGA-GGAAAAAAGGTAATTTTGGAAAAATTTA-GGTTGAAAATGGTAATC
* *
20232 TTTTTGGATATTCGA-GATAAAATGGTAATTTTGGAAAAGTTTAGGTTGAAAATG
1 TTTTTGGATATTCGAGGA-AAAAAGGTAATTTTGGAAAAATTTAGGTTGAAAATG
20286 TGATTTTGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 6 0.12
60 29 0.59
61 14 0.29
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (60 bp):
TTTTTGGATATTCGAGGAAAAAAGGTAATTTTGGAAAAATTTAGGTTGAAAATGGTAATC
Found at i:20284 original size:30 final size:29
Alignment explanation
Indices: 20250--20441 Score: 172
Period size: 30 Copynumber: 6.4 Consensus size: 29
20240 TATTCGAGAT
* *
20250 AAAATGGTAATTTTGGAAAAGTTTAGGTTG
1 AAAAT-GTAATTTTAGAAAAGTTTAGGTTC
* * * *
20280 AAAATGTGATTTTGGAAAAATTTAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGTTC
* *
20309 AAAATATAATTTTAGAGAAGTTCTAAGG-TC
1 AAAATGTAATTTTAGAAAAGTT-T-AGGTTC
* * *
20339 AAAATGTGATTTTGGAAAAGTTTGAGTTTC
1 AAAATGTAATTTTAGAAAAGTTT-AGGTTC
*
20369 AAAATGTAATTTTAGAGAAGTTTTAGGGTT-
1 AAAATGTAATTTTAGAAAAG-TTTA-GGTTC
* *
20399 AAAATGTAATTTTAGAGAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTA-GGTTC
*
20429 AAAATGTGATTTT
1 AAAATGTAATTTT
20442 TAAATAAAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
29 48 0.36
30 78 0.58
31 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTAGGTTC
Found at i:20386 original size:60 final size:58
Alignment explanation
Indices: 20250--20441 Score: 206
Period size: 60 Copynumber: 3.2 Consensus size: 58
20240 TATTCGAGAT
* * * *
20250 AAAATGGTAATTTTGGAAAAGTTT-AGGTTGAAAATGTGATTTTGGAAAAATTTAGGGTC
1 AAAAT-GTAATTTTAGAGAAGTTTAAGG-TCAAAATGTGATTTTGGAAAAGTTTAGGGTC
* **
20309 AAAATATAATTTTAGAGAAGTTCTAAGGTCAAAATGTGATTTTGGAAAAGTTTGAGTTTC
1 AAAATGTAATTTTAGAGAAGTT-TAAGGTCAAAATGTGATTTTGGAAAAGTTT-AGGGTC
* * * * *
20369 AAAATGTAATTTTAGAGAAGTTTTAGGGTTAAAATGTAATTTTAGAGAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAGAAG-TTTAAGGTCAAAATGTGATTTTGGAAAAGTTTA-GGGTC
*
20429 AAAATGTGATTTT
1 AAAATGTAATTTT
20442 TAAATAAAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
58 14 0.12
59 30 0.27
60 66 0.59
61 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTAGAGAAGTTTAAGGTCAAAATGTGATTTTGGAAAAGTTTAGGGTC
Found at i:20409 original size:90 final size:88
Alignment explanation
Indices: 20250--20441 Score: 251
Period size: 90 Copynumber: 2.1 Consensus size: 88
20240 TATTCGAGAT
* * * *
20250 AAAATGGTAATTTTGGAAAAGTTTAGGTTGAAAATGTGATTTTGGAAAAATTTAGGGTCAAAATA
1 AAAAT-GTGATTTTGGAAAAGTTTAGGTTCAAAATGTAATTTTAGAAAAATTTAGGGTCAAAATA
20315 TAATTTTAGAGAAGTTCTA-AGGTC
65 TAATTTTAGAGAAGTT-TAGAGGTC
* ** *
20339 AAAATGTGATTTTGGAAAAGTTTGAGTTTCAAAATGTAATTTTAGAGAAGTTTTAGGGTTAAAAT
1 AAAATGTGATTTTGGAAAAGTTT-AGGTTCAAAATGTAATTTTAGA-AAAATTTAGGGTCAAAAT
* *
20404 GTAATTTTAGAGAAGTTTAGGGGTC
64 ATAATTTTAGAGAAGTTTAGAGGTC
20429 AAAATGTGATTTT
1 AAAATGTGATTTT
20442 TAAATAAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
88 17 0.19
89 25 0.28
90 48 0.53
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (88 bp):
AAAATGTGATTTTGGAAAAGTTTAGGTTCAAAATGTAATTTTAGAAAAATTTAGGGTCAAAATAT
AATTTTAGAGAAGTTTAGAGGTC
Found at i:22274 original size:17 final size:16
Alignment explanation
Indices: 22254--22305 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
22244 AATTAAATTT
22254 TAAATTTAAATTCAAAA
1 TAAATTTAAATT-AAAA
22271 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTAAAA
*
22288 TAAATTAAAATTTAAAA
1 TAAATTTAAA-TTAAAA
22305 T
1 T
22306 TGGGTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 30 0.94
18 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:22285 original size:23 final size:22
Alignment explanation
Indices: 22247--22303 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
22237 GACTTTTAAT
* *
22247 TAAATTTTAAATTTAAATTCAAAA
1 TAAA-TTTAAACTTAAAAT-AAAA
*
22271 TAAATTTAAACTTAAAATAAAT
1 TAAATTTAAACTTAAAATAAAA
22293 TAAAATTTAAA
1 T-AAATTTAAA
22304 ATTGGGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 21 0.72
24 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAAACTTAAAATAAAA
Found at i:22481 original size:23 final size:23
Alignment explanation
Indices: 22455--22530 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
22445 TGAATTTTAA
*
22455 GAATCTTTGTTGTTTCTTGCAGG
1 GAATCTTTATTGTTTCTTGCAGG
* * *
22478 GAAT-TTTCACTGTTTATTGTAGG
1 GAATCTTT-ATTGTTTCTTGCAGG
* *
22501 GAATTTTTATTG-TTCATTGCAGA
1 GAATCTTTATTGTTTC-TTGCAGG
22524 GAATCTT
1 GAATCTT
22531 CACTGTTCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 5 0.12
23 33 0.80
24 3 0.07
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (23 bp):
GAATCTTTATTGTTTCTTGCAGG
Found at i:22537 original size:23 final size:23
Alignment explanation
Indices: 22471--22695 Score: 195
Period size: 23 Copynumber: 9.9 Consensus size: 23
22461 TTGTTGTTTC
* * *
22471 TTGCAGGGAATTTTCACTGTTTA
1 TTGCAGAGAATCTTCACTGTTCA
* * * * *
22494 TTGTAGGGAATTTTTATTGTTCA
1 TTGCAGAGAATCTTCACTGTTCA
22517 TTGCAGAGAATCTTCACTGTTCA
1 TTGCAGAGAATCTTCACTGTTCA
* *
22540 TTGCAAATAATCTTCACTG---A
1 TTGCAGAGAATCTTCACTGTTCA
*
22560 TTGCAGAAAATCTTCACTGTTCA
1 TTGCAGAGAATCTTCACTGTTCA
* *
22583 TTGCAGAGAATATTTACTGTTCA
1 TTGCAGAGAATCTTCACTGTTCA
* * * * *
22606 TTGTAGAAAATATTTACTATTCA
1 TTGCAGAGAATCTTCACTGTTCA
* * *
22629 TTGCAAAGAATCTTCATTGTTTA
1 TTGCAGAGAATCTTCACTGTTCA
* * *
22652 TTGTAGAGAATCTTTATTGTTCA
1 TTGCAGAGAATCTTCACTGTTCA
* *
22675 TTGTAGAGATTCTTCACTGTT
1 TTGCAGAGAATCTTCACTGTT
22696 TATTTTTTTC
Statistics
Matches: 165, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
20 18 0.11
23 147 0.89
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (23 bp):
TTGCAGAGAATCTTCACTGTTCA
Found at i:29936 original size:21 final size:21
Alignment explanation
Indices: 29911--29952 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29901 TGTGGAGTCA
29911 CACAAGTCAATCTTTCAAGCC
1 CACAAGTCAATCTTTCAAGCC
29932 CACAAGTCAATCTTTCAAGCC
1 CACAAGTCAATCTTTCAAGCC
29953 TTGTGAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (21 bp):
CACAAGTCAATCTTTCAAGCC
Found at i:31811 original size:15 final size:15
Alignment explanation
Indices: 31793--31822 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31783 ATTGGGTTTT
31793 AGTGAGTGCATGATC
1 AGTGAGTGCATGATC
31808 AGTGAGTGCATGATC
1 AGTGAGTGCATGATC
31823 CCACTATCTT
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:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (15 bp):
AGTGAGTGCATGATC
Found at i:32708 original size:22 final size:23
Alignment explanation
Indices: 32663--32708 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
32653 TTACTAAAAC
*
32663 GATAAAGTTTTTCTTGAAACAGAT
1 GATAAAG-TTTTCTTGAAAAAGAT
*
32687 GATAAAG-TTTCTTTAAAAAGAT
1 GATAAAGTTTTCTTGAAAAAGAT
32709 CTAAACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (23 bp):
GATAAAGTTTTCTTGAAAAAGAT
Found at i:56651 original size:43 final size:43
Alignment explanation
Indices: 56584--56774 Score: 220
Period size: 43 Copynumber: 4.4 Consensus size: 43
56574 TTATGTGGCA
*
56584 AAACGCCGCTATAGAACATGATCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * *
56627 AAATGTCGCTATAGAACATGATCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * * * * ** *
56670 AAACACCGCTATAGTACATGGTCTTTAACGACATTTTTGCCAC
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
* * * *
56713 AAACGCCGTTATAGAACATGATCTTTAGTGCCGCTTTTCCCAT
1 AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
**
56756 AAACGTTGCTATAGAACAT
1 AAACGCCGCTATAGAACAT
56775 TGCAACACAC
Statistics
Matches: 121, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTCCCAC
Found at i:58900 original size:13 final size:11
Alignment explanation
Indices: 58868--58910 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
58858 TCATTTTCTA
*
58868 AATAAAATAAT
1 AATAAAATATT
58879 AAT-AAATATTT
1 AATAAAATA-TT
58890 AAGTAAAATATT
1 AA-TAAAATATT
58902 AATAAAATA
1 AATAAAATA
58911 ATATTTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:59293 original size:3 final size:3
Alignment explanation
Indices: 59285--59309 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59275 CTACTTCTTA
59285 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
59310 CACTCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:59528 original size:43 final size:43
Alignment explanation
Indices: 59422--59539 Score: 157
Period size: 43 Copynumber: 2.7 Consensus size: 43
59412 GTTACAAGCG
* * *
59422 TGATCTTTAGCGACGTTTTTACCACAAGCGCCGCTATAAAACA
1 TGATCTTTAGCGGCGTTTTTCCCACAAACGCCGCTATAAAACA
* * *
59465 TGGTATTTAGCAGC-TCTTTTCCCACAAACGCCGCTATAAAACA
1 TGATCTTTAGCGGCGT-TTTTCCCACAAACGCCGCTATAAAACA
*
59508 TGATCTTTAGCGGCGTTTTTCCTACAAACGCC
1 TGATCTTTAGCGGCGTTTTTCCCACAAACGCC
59540 ACTAACATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 61 0.97
44 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (43 bp):
TGATCTTTAGCGGCGTTTTTCCCACAAACGCCGCTATAAAACA
Found at i:62179 original size:18 final size:19
Alignment explanation
Indices: 62145--62180 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62135 ACCCAAAAAA
*
62145 AAATAAAAAGTATAATAAC
1 AAATAAAAAGTAAAATAAC
62164 AAATAAAAA-TAAAATAA
1 AAATAAAAAGTAAAATAA
62181 AATTCTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATAAAAAGTAAAATAAC
Found at i:80354 original size:29 final size:28
Alignment explanation
Indices: 80308--80381 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
80298 CAAAAGTTTT
* *
80308 CCACAAATG-CTTTCTTTTTCATAGGTCG
1 CCACAAA-GACTTCCTTTTTCATAGGTCA
* *
80336 TCACAAAGATTTCCTTTTTCATAGGTCA
1 CCACAAAGACTTCCTTTTTCATAGGTCA
80364 CCACAAAGACTTCCTTTT
1 CCACAAAGACTTCCTTTT
80382 CAAAGATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (28 bp):
CCACAAAGACTTCCTTTTTCATAGGTCA
Found at i:81257 original size:19 final size:19
Alignment explanation
Indices: 81199--81257 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
81189 CAGAATCTAA
*
81199 TAAAATTGAAAAATATATT
1 TAAAATTGAAAAATGTATT
*
81218 T-AAATTGAAAAATGT-TA
1 TAAAATTGAAAAATGTATT
*
81235 TAAAATTGAAAAAGGTATT
1 TAAAATTGAAAAATGTATT
81254 TAAA
1 TAAA
81258 TTTCAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.06
18 26 0.76
19 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (19 bp):
TAAAATTGAAAAATGTATT
Found at i:89659 original size:20 final size:23
Alignment explanation
Indices: 89621--89661 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
89611 CAATTCACAA
89621 TGTTTTAATATTTATATATTTTT
1 TGTTTTAATATTTATATATTTTT
89644 TGTTTT-AT-TTTA-ATATTT
1 TGTTTTAATATTTATATATTT
89662 AATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 2 0.11
23 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (23 bp):
TGTTTTAATATTTATATATTTTT
Found at i:98575 original size:2 final size:2
Alignment explanation
Indices: 98568--98593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98558 TATCATCTTC
98568 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
98594 TTCCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115381 original size:35 final size:35
Alignment explanation
Indices: 115335--115409 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
115325 AAAATATATT
*
115335 TTTTGTTTAACTTGACTTACAAGCAATCTCTTAGA
1 TTTTGTCTAACTTGACTTACAAGCAATCTCTTAGA
* *
115370 TTTTGTCTAACTTGACTTGCAAGTAATCTCTTAGA
1 TTTTGTCTAACTTGACTTACAAGCAATCTCTTAGA
*
115405 ATTTG
1 TTTTG
115410 AGTCAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (35 bp):
TTTTGTCTAACTTGACTTACAAGCAATCTCTTAGA
Found at i:115748 original size:35 final size:36
Alignment explanation
Indices: 115709--115798 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
115699 ATCGAGGGTC
* * **
115709 GTGATCTTAAATCAACGA-ATTTGGTGATATCAGTT
1 GTGATATTAAATCAACGAGACTTAATGATATCAGTT
* *
115744 GTGATTTTAAATCAACGAGCCTTAATGATATCAGTT
1 GTGATATTAAATCAACGAGACTTAATGATATCAGTT
115780 GTGATATTAAATCAACGAG
1 GTGATATTAAATCAACGAG
115799 CTATTTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 17 0.35
36 31 0.65
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (36 bp):
GTGATATTAAATCAACGAGACTTAATGATATCAGTT
Found at i:121254 original size:17 final size:17
Alignment explanation
Indices: 121232--121291 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
121222 TTTTATTTCA
121232 AAATAAATTTAAATTTT
1 AAATAAATTTAAATTTT
*
121249 AAATAAGTTTAAA-TTT
1 AAATAAATTTAAATTTT
*
121265 ACAATAAATTTAAATTTA
1 A-AATAAATTTAAATTTT
*
121283 AAATGAATT
1 AAATAAATT
121292 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.11
17 30 0.81
18 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATAAATTTAAATTTT
Found at i:123170 original size:37 final size:36
Alignment explanation
Indices: 123125--123204 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 36
123115 ACCACCGGTA
123125 TTTC-TTTCTCTTAATTTTTTATATTCAGTTTTTAT
1 TTTCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
123160 TTTCCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
1 TTT-CTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
123197 TTTCTTTT
1 TTTCTTTT
123205 ATATTTTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 3 0.07
36 6 0.14
37 34 0.79
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (36 bp):
TTTCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
Found at i:125418 original size:3 final size:3
Alignment explanation
Indices: 125410--125466 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
125400 TGTTTAACAC
*
125410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
125458 ATT ATT ATT
1 ATT ATT ATT
125467 TAACACAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:127165 original size:17 final size:17
Alignment explanation
Indices: 127143--127240 Score: 53
Period size: 17 Copynumber: 5.7 Consensus size: 17
127133 AAACTCCCTT
127143 TAAATTTATTTTAAGAA
1 TAAATTTATTTTAAGAA
*
127160 TAAATTT-GTTT-AGAAA
1 TAAATTTATTTTAAG-AA
* *
127176 TTTAAATTTATATTAA-ATT
1 --TAAATTTATTTTAAGA-A
*
127195 TAAATTTA-TTT-CGAA
1 TAAATTTATTTTAAGAA
**
127210 TTTAAATTTATTTTAAGTT
1 --TAAATTTATTTTAAGAA
127229 TAAATTTATTTT
1 TAAATTTATTTT
127241 CCAAATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
15 2 0.03
16 8 0.13
17 35 0.58
18 11 0.18
19 3 0.05
20 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (17 bp):
TAAATTTATTTTAAGAA
Found at i:127180 original size:35 final size:34
Alignment explanation
Indices: 127141--127239 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
127131 CCAAACTCCC
* *
127141 TTTAAATTTATTTTAAGAATAAATTTGTTTAGAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTAG-AA
* *
127176 TTTAAATTTATATTAA-ATTTAAATTTATTTCGAA
1 TTTAAATTTATTTTAAGA-TTAAATTTATTTAGAA
*
127210 TTTAAATTTATTTTAAGTTTAAATTTATTT
1 TTTAAATTTATTTTAAGATTAAATTTATTT
127240 TCCAAATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 30 0.54
35 26 0.46
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTAGAA
Found at i:127184 original size:6 final size:6
Alignment explanation
Indices: 127173--127236 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
127163 ATTTGTTTAG
* *
127173 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* *
127219 -ATTTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
127237 TTTTCCAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 31 0.66
7 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:127217 original size:34 final size:35
Alignment explanation
Indices: 127141--127268 Score: 136
Period size: 35 Copynumber: 3.7 Consensus size: 35
127131 CCAAACTCCC
* *
127141 TTTAAATTTATTTTAAGA-ATAAATTTGTTTAGAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTAGAAA
* *
127176 TTTAAATTTATATTAAATTTAAATTTATTTCG-AA
1 TTTAAATTTATTTTAAATTTAAATTTATTTAGAAA
* **
127210 TTTAAATTTATTTTAAGTTTAAATTTATTTTCCAAA
1 TTTAAATTTATTTTAAATTTAAATTTA-TTTAGAAA
*
127246 TTTAAGA-TTATTATAAATTTAAA
1 TTTAA-ATTTATTTTAAATTTAAA
127269 ATAAATAAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
34 28 0.35
35 30 0.38
36 21 0.26
37 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAGAAA
Found at i:128300 original size:11 final size:11
Alignment explanation
Indices: 128284--128344 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 11
128274 CAAAACCTTT
128284 TAGATCTAGGC
1 TAGATCTAGGC
*
128295 TAGATC-AGGT
1 TAGATCTAGGC
*
128305 TCGATCTAGGC
1 TAGATCTAGGC
*
128316 TAGATC-AGGT
1 TAGATCTAGGC
* *
128326 TCGATCTAGACC
1 TAGATCTAG-GC
128338 TAGATCT
1 TAGATCT
128345 GTTTCCTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
10 16 0.42
11 16 0.42
12 6 0.16
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (11 bp):
TAGATCTAGGC
Found at i:128312 original size:21 final size:21
Alignment explanation
Indices: 128286--128343 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
128276 AAACCTTTTA
128286 GATCTAGGCTAGATCAGGTTC
1 GATCTAGGCTAGATCAGGTTC
128307 GATCTAGGCTAGATCAGGTTC
1 GATCTAGGCTAGATCAGGTTC
*
128328 GATCTAGACCTAGATC
1 GATCTAG-GCTAGATC
128344 TGTTTCCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
GATCTAGGCTAGATCAGGTTC
Found at i:129232 original size:30 final size:29
Alignment explanation
Indices: 129177--129274 Score: 133
Period size: 29 Copynumber: 3.3 Consensus size: 29
129167 TAAATTGTTT
*
129177 AAAAATTCCATTTTTACCCCCAAACTTCC
1 AAAAATCCCATTTTTACCCCCAAACTTCC
* *
129206 AAAAATCCCATTTTTAACCCCAAAACTTTC
1 AAAAATCCCATTTTT-ACCCCCAAACTTCC
* * *
129236 AAAAATTCTATTTTTACCCCCGAACTTCC
1 AAAAATCCCATTTTTACCCCCAAACTTCC
129265 AAAAATCCCA
1 AAAAATCCCA
129275 AAAATCCCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 33 0.57
30 25 0.43
ACGTcount: A:0.38, C:0.32, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAAATCCCATTTTTACCCCCAAACTTCC
Found at i:129339 original size:28 final size:29
Alignment explanation
Indices: 129303--129366 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
129293 CCGAATTTTC
*
129303 CCAAAATTA-CCGTTTCACCCCCGAGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
* * *
129331 CCAAAATTATCATTTTTACCCCCGGGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
129360 CCGAAAA
1 CC-AAAA
129367 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.30
29 17 0.57
30 4 0.13
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (29 bp):
CCAAAATTATCAGTTTCACCCCCGAGAAT
Found at i:129351 original size:29 final size:30
Alignment explanation
Indices: 129319--129376 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
129309 TTACCGTTTC
*
129319 ACCCCCGAGAATCC-AAAATTATCATTTTT
1 ACCCCCGAGAATCCGAAAAGTATCATTTTT
* *
129348 ACCCCCGGGAATCCGAAAAGTCTCATTTT
1 ACCCCCGAGAATCCGAAAAGTATCATTTT
129377 GAACTCCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
ACCCCCGAGAATCCGAAAAGTATCATTTTT
Found at i:136493 original size:17 final size:17
Alignment explanation
Indices: 136471--136530 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
136461 TTTTATTTCA
136471 AAATAAATTTAAATTTT
1 AAATAAATTTAAATTTT
*
136488 AAATAAGTTTAAA-TTT
1 AAATAAATTTAAATTTT
*
136504 ACAATAAATTTAAATTTA
1 A-AATAAATTTAAATTTT
*
136522 AAATGAATT
1 AAATAAATT
136531 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.11
17 30 0.81
18 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (17 bp):
AAATAAATTTAAATTTT
Found at i:138409 original size:37 final size:36
Alignment explanation
Indices: 138364--138443 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 36
138354 ACCACCGGTA
138364 TTTC-TTTCTCTTAATTTTTTATATTCAGTTTTTAT
1 TTTCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
138399 TTTCCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
1 TTT-CTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
138436 TTTCTTTT
1 TTTCTTTT
138444 ATATTTTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 3 0.07
36 6 0.14
37 34 0.79
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (36 bp):
TTTCTTTTCTCTTAATTTTTTATATTCAGTTTTTAT
Found at i:140657 original size:3 final size:3
Alignment explanation
Indices: 140649--140705 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
140639 TGTTTAACAC
*
140649 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
140697 ATT ATT ATT
1 ATT ATT ATT
140706 TAACACAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:142404 original size:17 final size:17
Alignment explanation
Indices: 142382--142479 Score: 53
Period size: 17 Copynumber: 5.7 Consensus size: 17
142372 AAACTCCCTT
142382 TAAATTTATTTTAAGAA
1 TAAATTTATTTTAAGAA
*
142399 TAAATTT-GTTT-AGAAA
1 TAAATTTATTTTAAG-AA
* *
142415 TTTAAATTTATATTAA-ATT
1 --TAAATTTATTTTAAGA-A
*
142434 TAAATTTA-TTT-CGAA
1 TAAATTTATTTTAAGAA
**
142449 TTTAAATTTATTTTAAGTT
1 --TAAATTTATTTTAAGAA
142468 TAAATTTATTTT
1 TAAATTTATTTT
142480 CCAAATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
15 2 0.03
16 8 0.13
17 35 0.58
18 11 0.18
19 3 0.05
20 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (17 bp):
TAAATTTATTTTAAGAA
Found at i:142419 original size:35 final size:34
Alignment explanation
Indices: 142380--142478 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
142370 CCAAACTCCC
* *
142380 TTTAAATTTATTTTAAGAATAAATTTGTTTAGAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTAG-AA
* *
142415 TTTAAATTTATATTAA-ATTTAAATTTATTTCGAA
1 TTTAAATTTATTTTAAGA-TTAAATTTATTTAGAA
*
142449 TTTAAATTTATTTTAAGTTTAAATTTATTT
1 TTTAAATTTATTTTAAGATTAAATTTATTT
142479 TCCAAATTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
34 30 0.54
35 26 0.46
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTAGAA
Found at i:142423 original size:6 final size:6
Alignment explanation
Indices: 142412--142475 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
142402 ATTTGTTTAG
* *
142412 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* *
142458 -ATTTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
142476 TTTTCCAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 31 0.66
7 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:142456 original size:34 final size:35
Alignment explanation
Indices: 142380--142507 Score: 136
Period size: 35 Copynumber: 3.7 Consensus size: 35
142370 CCAAACTCCC
* *
142380 TTTAAATTTATTTTAAGA-ATAAATTTGTTTAGAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTAGAAA
* *
142415 TTTAAATTTATATTAAATTTAAATTTATTTCG-AA
1 TTTAAATTTATTTTAAATTTAAATTTATTTAGAAA
* **
142449 TTTAAATTTATTTTAAGTTTAAATTTATTTTCCAAA
1 TTTAAATTTATTTTAAATTTAAATTTA-TTTAGAAA
*
142485 TTTAAGA-TTATTATAAATTTAAA
1 TTTAA-ATTTATTTTAAATTTAAA
142508 ATAAATAAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
34 28 0.35
35 30 0.38
36 21 0.26
37 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAGAAA
Found at i:143539 original size:11 final size:11
Alignment explanation
Indices: 143523--143583 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 11
143513 CAAAACCTTT
143523 TAGATCTAGGC
1 TAGATCTAGGC
*
143534 TAGATC-AGGT
1 TAGATCTAGGC
*
143544 TCGATCTAGGC
1 TAGATCTAGGC
*
143555 TAGATC-AGGT
1 TAGATCTAGGC
* *
143565 TCGATCTAGACC
1 TAGATCTAG-GC
143577 TAGATCT
1 TAGATCT
143584 GTTTCCTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
10 16 0.42
11 16 0.42
12 6 0.16
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (11 bp):
TAGATCTAGGC
Found at i:143551 original size:21 final size:21
Alignment explanation
Indices: 143525--143582 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
143515 AAACCTTTTA
143525 GATCTAGGCTAGATCAGGTTC
1 GATCTAGGCTAGATCAGGTTC
143546 GATCTAGGCTAGATCAGGTTC
1 GATCTAGGCTAGATCAGGTTC
*
143567 GATCTAGACCTAGATC
1 GATCTAG-GCTAGATC
143583 TGTTTCCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
GATCTAGGCTAGATCAGGTTC
Found at i:144471 original size:30 final size:29
Alignment explanation
Indices: 144416--144513 Score: 133
Period size: 29 Copynumber: 3.3 Consensus size: 29
144406 TAAATTGTTT
*
144416 AAAAATTCCATTTTTACCCCCAAACTTCC
1 AAAAATCCCATTTTTACCCCCAAACTTCC
* *
144445 AAAAATCCCATTTTTAACCCCAAAACTTTC
1 AAAAATCCCATTTTT-ACCCCCAAACTTCC
* * *
144475 AAAAATTCTATTTTTACCCCCGAACTTCC
1 AAAAATCCCATTTTTACCCCCAAACTTCC
144504 AAAAATCCCA
1 AAAAATCCCA
144514 AAAATCCCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 33 0.57
30 25 0.43
ACGTcount: A:0.38, C:0.32, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAAATCCCATTTTTACCCCCAAACTTCC
Found at i:144578 original size:28 final size:29
Alignment explanation
Indices: 144542--144605 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
144532 CCGAATTTTC
*
144542 CCAAAATTA-CCGTTTCACCCCCGAGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
* * *
144570 CCAAAATTATCATTTTTACCCCCGGGAAT
1 CCAAAATTATCAGTTTCACCCCCGAGAAT
144599 CCGAAAA
1 CC-AAAA
144606 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.30
29 17 0.57
30 4 0.13
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (29 bp):
CCAAAATTATCAGTTTCACCCCCGAGAAT
Found at i:144590 original size:29 final size:30
Alignment explanation
Indices: 144558--144615 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
144548 TTACCGTTTC
*
144558 ACCCCCGAGAATCC-AAAATTATCATTTTT
1 ACCCCCGAGAATCCGAAAAGTATCATTTTT
* *
144587 ACCCCCGGGAATCCGAAAAGTCTCATTTT
1 ACCCCCGAGAATCCGAAAAGTATCATTTT
144616 GAACTCCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
ACCCCCGAGAATCCGAAAAGTATCATTTTT
Found at i:151523 original size:105 final size:105
Alignment explanation
Indices: 151336--151548 Score: 417
Period size: 105 Copynumber: 2.0 Consensus size: 105
151326 TGTTGCGCTC
151336 TTATGGTTATTTTTGGGGCTAAAATAGGTGGTTTGAATGATTATTGAATAAAATCATTCATTGGG
1 TTATGGTTATTTTTGGGGCTAAAATAGGTGGTTTGAATGATTATTGAATAAAATCATTCATTGGG
151401 CGAGATTCTGTAAATGTAAAATCATTGTGTCTAAATTATG
66 CGAGATTCTGTAAATGTAAAATCATTGTGTCTAAATTATG
151441 TTATGGTTATTTTTGGGGCTAAAATAGGTGGTTTGAATGATTATTGAATAAAATCATTCATTGGG
1 TTATGGTTATTTTTGGGGCTAAAATAGGTGGTTTGAATGATTATTGAATAAAATCATTCATTGGG
*
151506 CGAGATTCTGTATATGTAAAATCATTGTGTCTAAATTATG
66 CGAGATTCTGTAAATGTAAAATCATTGTGTCTAAATTATG
151546 TTA
1 TTA
151549 ATAAAGATTG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (105 bp):
TTATGGTTATTTTTGGGGCTAAAATAGGTGGTTTGAATGATTATTGAATAAAATCATTCATTGGG
CGAGATTCTGTAAATGTAAAATCATTGTGTCTAAATTATG
Found at i:152796 original size:3 final size:3
Alignment explanation
Indices: 152788--152822 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
152778 TTGGCATACT
152788 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
152823 TTAGATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:153616 original size:3 final size:3
Alignment explanation
Indices: 153608--153636 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
153598 TAGAATTTAT
153608 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
153637 GAGAATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:159234 original size:4 final size:4
Alignment explanation
Indices: 159227--159253 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
159217 ACCTAATATA
159227 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
159254 TTTTTTAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:159845 original size:2 final size:2
Alignment explanation
Indices: 159838--159863 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
159828 ATGAAAAACA
159838 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
159864 TCAAGGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169737 original size:17 final size:17
Alignment explanation
Indices: 169702--169737 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
169692 ATTAAAAATG
*
169702 AAAATTTAAAATTTAAA
1 AAAATTTAAAAATTAAA
169719 AAAATTTAAAAAATTAAA
1 AAAATTT-AAAAATTAAA
169737 A
1 A
169738 TTAACCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTTAAAAATTAAA
Found at i:169833 original size:17 final size:17
Alignment explanation
Indices: 169803--169837 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
169793 ACCCATATTA
169803 TATATGTTTATTACATT
1 TATATGTTTATTACATT
169820 TATAT-TTTATTTACATT
1 TATATGTTTA-TTACATT
169837 T
1 T
169838 TAGAAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (17 bp):
TATATGTTTATTACATT
Found at i:172771 original size:153 final size:155
Alignment explanation
Indices: 172493--172804 Score: 461
Period size: 153 Copynumber: 2.0 Consensus size: 155
172483 GGTCATATGC
* *
172493 ACAATAAAATATAGTATAGTCAGCTTCAAGGCCTATTTTGATTTTTCCATATATTGTTAGCTAAT
1 ACAATAAAATATACTATAGTCAGCTTAAAGGCCTATTTTGATTTTTCCATATATTGTTAGCTAAT
* **
172558 AAAGCTAAGTATCAGATAAAGTTCCATTTAGGGGGGGAAAACAGATTGCAATTAGAACCAATA-C
66 AAAGCCAAGTATCAGATAAAGTTCCATTTAGGGGAAGAAAACAGATTGCAATTAGAACCAATATC
*
172622 -CTATGTCTAT-AAAAAATTTGCAAA
131 TCTATGTCCATCAAAAAA-TTGCAAA
* * *
172646 ACAATAAAATATTCTATTGTCAGCTTAAAGGCCTATTTTGATTTTTCCATATATTGTTCGCTAAT
1 ACAATAAAATATACTATAGTCAGCTTAAAGGCCTATTTTGATTTTTCCATATATTGTTAGCTAAT
* * *
172711 AAAGCCAAGTATCGGATCAAA-TTCCATTTAGGGGAATAAAACCGATTGCAATTAGAACCAATAT
66 AAAGCCAAGTATCAGAT-AAAGTTCCATTTAGGGGAAGAAAACAGATTGCAATTAGAACCAATAT
*
172775 CTCTATGTCCATCAAAAAATTGCAAT
130 CTCTATGTCCATCAAAAAATTGCAAA
172801 ACAA
1 ACAA
172805 CTTGTATCAT
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
153 113 0.80
154 4 0.03
155 19 0.13
156 6 0.04
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (155 bp):
ACAATAAAATATACTATAGTCAGCTTAAAGGCCTATTTTGATTTTTCCATATATTGTTAGCTAAT
AAAGCCAAGTATCAGATAAAGTTCCATTTAGGGGAAGAAAACAGATTGCAATTAGAACCAATATC
TCTATGTCCATCAAAAAATTGCAAA
Found at i:175308 original size:7 final size:7
Alignment explanation
Indices: 175291--175325 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
175281 ATTTACCAAT
175291 TTTTTATA
1 TTTTTA-A
175299 TTTTTAA
1 TTTTTAA
175306 TTTTTAA
1 TTTTTAA
*
175313 TTTATAA
1 TTTTTAA
175320 TTTTTA
1 TTTTTA
175326 CTTTACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:175309 original size:14 final size:14
Alignment explanation
Indices: 175291--175330 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
175281 ATTTACCAAT
*
175291 TTTTTATATTTTTAA
1 TTTTTA-ATTTATAA
175306 TTTTTAATTTATAA
1 TTTTTAATTTATAA
*
175320 TTTTTACTTTA
1 TTTTTAATTTA
175331 CATATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTATAA
Found at i:175488 original size:20 final size:19
Alignment explanation
Indices: 175450--175488 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
175440 AATATCAACT
*
175450 AAATAAAAAAATAAATACA
1 AAATAAAAAAACAAATACA
*
175469 AAATTAAAAAACAAACTACA
1 AAATAAAAAAACAAA-TACA
175489 TATTAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAAAAACAAATACA
Found at i:175868 original size:15 final size:15
Alignment explanation
Indices: 175848--175877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
175838 TATTTAACTG
175848 AATTAACCAAATTAA
1 AATTAACCAAATTAA
*
175863 AATTAACCGAATTAA
1 AATTAACCAAATTAA
175878 CTAGAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (15 bp):
AATTAACCAAATTAA
Found at i:175886 original size:10 final size:10
Alignment explanation
Indices: 175871--175947 Score: 88
Period size: 10 Copynumber: 7.8 Consensus size: 10
175861 AAAATTAACC
175871 GAATTAACTA
1 GAATTAACTA
175881 GAATTAACTA
1 GAATTAACTA
*
175891 AAATTAACT-
1 GAATTAACTA
*
175900 GAAATTAAC-C
1 G-AATTAACTA
175910 GAATTAACTA
1 GAATTAACTA
175920 GAATTAACTA
1 GAATTAACTA
*
175930 AAATTAACT-
1 GAATTAACTA
175939 GAAATTAAC
1 G-AATTAAC
175948 CGAATTAGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
9 7 0.12
10 51 0.88
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.29
Consensus pattern (10 bp):
GAATTAACTA
Found at i:175907 original size:39 final size:39
Alignment explanation
Indices: 175862--175954 Score: 186
Period size: 39 Copynumber: 2.4 Consensus size: 39
175852 AACCAAATTA
175862 AAATTAACCGAATTAACTAGAATTAACTAAAATTAACTG
1 AAATTAACCGAATTAACTAGAATTAACTAAAATTAACTG
175901 AAATTAACCGAATTAACTAGAATTAACTAAAATTAACTG
1 AAATTAACCGAATTAACTAGAATTAACTAAAATTAACTG
175940 AAATTAACCGAATTA
1 AAATTAACCGAATTA
175955 GTAATACATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.28
Consensus pattern (39 bp):
AAATTAACCGAATTAACTAGAATTAACTAAAATTAACTG
Found at i:175913 original size:29 final size:29
Alignment explanation
Indices: 175860--175947 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
175850 TTAACCAAAT
*
175860 TAAAATTAACCG-AATTAACTAGAATTAAC
1 TAAAATTAACTGAAATTAAC-AGAATTAAC
*
175889 TAAAATTAACTGAAATTAACCGAATTAAC
1 TAAAATTAACTGAAATTAACAGAATTAAC
* * *
175918 TAGAATTAACTAAAATTAACTGAAATTAAC
1 TAAAATTAACTGAAATTAACAG-AATTAAC
175948 CGAATTAGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 38 0.73
30 14 0.27
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.28
Consensus pattern (29 bp):
TAAAATTAACTGAAATTAACAGAATTAAC
Done.