Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013904.1 Kokia drynarioides strain JFW-HI SEQ_128933, 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: 71940
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:506 original size:17 final size:16
Alignment explanation
Indices: 458--518 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
448 TGTTTTTTTT
*
458 TTTTAA-TTAATTAAA
1 TTTTAACTTAATTTAA
* *
473 TTTTAAATTCAAATTAA
1 TTTTAACTT-AATTTAA
490 TTTTGAACTTAATTTAAA
1 TTTT-AACTTAATTT-AA
*
508 TTTAAACTTAA
1 TTTTAACTTAA
519 AAGAAAAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 6 0.16
16 2 0.05
17 20 0.54
18 9 0.24
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTAACTTAATTTAA
Found at i:2136 original size:23 final size:23
Alignment explanation
Indices: 2105--2307 Score: 334
Period size: 23 Copynumber: 8.8 Consensus size: 23
2095 CTATTTACAC
*
2105 AAATCACATTAATATTTAAGTAT
1 AAATCACATTAATATTTAAGCAT
* *
2128 AAATTACATTAACATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
2151 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
* *
2174 AAATCACATTAACATTCAAGCAT
1 AAATCACATTAATATTTAAGCAT
2197 AAATCACATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAT
*
2220 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAT
*
2243 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAT
*
2266 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAT
2289 AAATCACATTAATATTTAA
1 AAATCACATTAATATTTAA
2308 TTATCTTTCA
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 170 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAT
Found at i:8112 original size:3 final size:3
Alignment explanation
Indices: 8104--8128 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8094 CCCACAAGTT
8104 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
8129 ATTTTTTCCA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13810 original size:23 final size:23
Alignment explanation
Indices: 13783--14160 Score: 432
Period size: 23 Copynumber: 16.7 Consensus size: 23
13773 TTCATGGGTC
13783 CATTTACA-CATAAATCACATTAA
1 CATTTA-AGCATAAATCACATTAA
* *
13806 TATTTAAGCATAAATTACATT-A
1 CATTTAAGCATAAATCACATTAA
13828 -A--T-A--ATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
13845 CACTTAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
13868 TATTTAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
13891 CATTCAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
* *
13914 CGTTCAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
13937 TATTTAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
* * *
13960 TATTTAAGGATAACTCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
13983 CATTTAAGCATAAATCATATTAA
1 CATTTAAGCATAAATCACATTAA
*
14006 CATTTAAGCATAAATCATATTAA
1 CATTTAAGCATAAATCACATTAA
* * *
14029 TATTTAAGAACAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
14052 CATTTAAGCATAAATCACATTAA
1 CATTTAAGCATAAATCACATTAA
*
14075 CATTTAAGCATAGATCACATTAA
1 CATTTAAGCATAAATCACATTAA
** * * *
14098 TGTTTAATCACAAATAACATTAA
1 CATTTAAGCATAAATCACATTAA
* * * *
14121 TATTTAAGCACT-ATTCAAATTGA
1 CATTTAAGCA-TAAATCACATTAA
*
14144 TATTTAAGCATAAATCA
1 CATTTAAGCATAAATCA
14161 TATAAATATT
Statistics
Matches: 306, Mismatches: 39, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
16 11 0.04
17 1 0.00
18 2 0.01
19 1 0.00
20 1 0.00
21 2 0.01
22 3 0.01
23 285 0.93
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (23 bp):
CATTTAAGCATAAATCACATTAA
Found at i:14276 original size:10 final size:10
Alignment explanation
Indices: 14231--14283 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
14221 CATTTTACTC
14231 ATCACATATTA
1 ATCACATA-TA
14242 ATCACATAT-
1 ATCACATATA
* *
14251 ATCCACTTAAA
1 AT-CACATATA
14262 ATCACATATA
1 ATCACATATA
*
14272 ATCACATTTA
1 ATCACATATA
14282 AT
1 AT
14284 GATAGCCCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 2 0.06
10 23 0.66
11 10 0.29
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (10 bp):
ATCACATATA
Found at i:15580 original size:9 final size:9
Alignment explanation
Indices: 15556--15610 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
15546 ATATATTACC
*
15556 AATTCGGTT
1 AATTTGGTT
15565 AATTTTGGTT
1 AA-TTTGGTT
15575 AATTTGAG-T
1 AATTTG-GTT
15584 AATTT--TT
1 AATTTGGTT
15591 AATTTGGTT
1 AATTTGGTT
*
15600 AATTCGGTT
1 AATTTGGTT
15609 AA
1 AA
15611 ATGAATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 6 0.15
9 24 0.62
10 9 0.23
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (9 bp):
AATTTGGTT
Found at i:16119 original size:18 final size:19
Alignment explanation
Indices: 16098--16133 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16088 TTTTCAAATA
16098 TCTTTC-TATTTTTTTTTC
1 TCTTTCTTATTTTTTTTTC
16116 TCTTTCTTATTTTTTTTT
1 TCTTTCTTATTTTTTTTT
16134 ATTTAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TCTTTCTTATTTTTTTTTC
Found at i:18464 original size:66 final size:66
Alignment explanation
Indices: 18379--18510 Score: 176
Period size: 66 Copynumber: 2.0 Consensus size: 66
18369 ATGTTTGAAT
* *
18379 ATTAATTTTATTTTATGTAATGTAATATGTGCTTAAATGAGAAAATGATTACTGTG-TCAAATTA
1 ATTAATGTGATTTTATGTAATGTAATATGTGCTTAAATGAGAAAATGATTACTGTGCT-AAATTA
18443 TC
65 TC
* * * * * *
18445 ATTAATGTGATTTTGTGTAATGTGATATGTGCTTTAATGAGAATATTATTATTGTGCTAAATTAT
1 ATTAATGTGATTTTATGTAATGTAATATGTGCTTAAATGAGAAAATGATTACTGTGCTAAATTAT
18510 C
66 C
18511 GTTTAAATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 56 0.98
67 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.45
Consensus pattern (66 bp):
ATTAATGTGATTTTATGTAATGTAATATGTGCTTAAATGAGAAAATGATTACTGTGCTAAATTAT
C
Found at i:19534 original size:30 final size:28
Alignment explanation
Indices: 19500--19888 Score: 226
Period size: 30 Copynumber: 13.2 Consensus size: 28
19490 TGACTTTGAG
*
19500 AGTTTCGAGGTCAGAAATGAGATTTTTTGA
1 AGTTTCGAGGTCA-AAATG-GATTTTTGGA
19530 AGTTT-GAGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGA-GGTCAAAATGG--ATTTTTGGA
* * *
19559 GGTTTCGAGGACAAAAATGAGATTTTTGAA
1 AGTTTCGAGGTC-AAAATG-GATTTTTGGA
19589 AG-TTCGAGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGA-GGTCAAAATGG--ATTTTTGGA
* *
19618 AGTTTTGGGGTCAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTC-AAAAT-GGATTTTTGGA
* * **
19648 AGTTTTGGGGTCAAAAATGGGATTTTTAAA
1 AGTTTCGAGGTC-AAAAT-GGATTTTTGGA
*
19678 AGTTT-GAGGGT-AAAATGGTAATTTTTGGG
1 AGTTTCGA-GGTCAAAATGG--ATTTTTGGA
*
19707 AGTTTCGAGGTCAAAATTGGGATTTTTAGA
1 AGTTTCGAGGTCAAAA-T-GGATTTTTGGA
* *
19737 AG-TTCAAAGG-GAAAATGGTAATTTTTGGA
1 AGTTTC-GAGGTCAAAATGG--ATTTTTGGA
*
19766 AGTTTCAAGGTCAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTC-AAAAT-GGATTTTTGGA
* *
19796 AG-TTCGGGAGT-AAAATGGTAATTTTTAGA
1 AGTTTCGAG-GTCAAAATGG--ATTTTTGGA
* *
19825 AGTTTAGGGGTCAAAAATGAGATTTTTGGA
1 AGTTTCGAGGTC-AAAATG-GATTTTTGGA
*
19855 AG-TTCGAGGGT-AAAATGGTAATTTCTGGA
1 AGTTTCGA-GGTCAAAATGG--ATTTTTGGA
19884 AGTTT
1 AGTTT
19889 AGGGACTTTC
Statistics
Matches: 291, Mismatches: 29, Indels: 78
0.73 0.07 0.20
Matches are distributed among these distances:
27 9 0.03
28 28 0.10
29 100 0.34
30 123 0.42
31 23 0.08
32 8 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (28 bp):
AGTTTCGAGGTCAAAATGGATTTTTGGA
Found at i:19568 original size:59 final size:59
Alignment explanation
Indices: 19500--19652 Score: 218
Period size: 59 Copynumber: 2.6 Consensus size: 59
19490 TGACTTTGAG
*
19500 AGTTTCGAGGTCAGAAATGAGATTTTTTGAAGTTTGAGGGTAAAATGGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGAGATTTTTTGAAGTTTGAGGGTAAAATGGTAATTTTTGGA
* * *
19559 GGTTTCGAGGACAAAAATGAGA-TTTTTGAAAGTTCGAGGGTAAAATGGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGAGATTTTTTG-AAGTTTGAGGGTAAAATGGTAATTTTTGGA
* * * *
19618 AGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTT
1 AGTTTCGAGGTCAAAAATGAGATTTTTTGAAGTTT
19653 TGGGGTCAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
58 6 0.07
59 70 0.86
60 5 0.06
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATGAGATTTTTTGAAGTTTGAGGGTAAAATGGTAATTTTTGGA
Found at i:19672 original size:148 final size:148
Alignment explanation
Indices: 19508--19799 Score: 437
Period size: 148 Copynumber: 2.0 Consensus size: 148
19498 AGAGTTTCGA
* **
19508 GGTCAGAAATGAGATTTTTTGAAGTTTGAGGGTAAAATGGTAATTTTT-GGAGGTTTCGAGGACA
1 GGTCAAAAATGAGATTTTTAAAAGTTTGAGGGTAAAATGGTAATTTTTGGGA-GTTTCGAGGACA
* ***
19572 AAAATGAGATTTTT-GAAAGTTC-GAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAA
65 AAAATGAGATTTTTAG-AAGTTCAAAGGG-AAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAA
19635 TGGGATTTTTGGAAGTTTTGG
128 TGGGATTTTTGGAAGTTTTGG
* *
19656 GGTCAAAAATGGGATTTTTAAAAGTTTGAGGGTAAAATGGTAATTTTTGGGAGTTTCGAGGTCAA
1 GGTCAAAAATGAGATTTTTAAAAGTTTGAGGGTAAAATGGTAATTTTTGGGAGTTTCGAGGACAA
* *
19721 AATTGGGATTTTTAGAAGTTCAAAGGGAAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAATGG
66 AAATGAGATTTTTAGAAGTTCAAAGGGAAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAATGG
19786 GATTTTTGGAAGTT
131 GATTTTTGGAAGTT
19800 CGGGAGTAAA
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
148 122 0.94
149 8 0.06
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (148 bp):
GGTCAAAAATGAGATTTTTAAAAGTTTGAGGGTAAAATGGTAATTTTTGGGAGTTTCGAGGACAA
AAATGAGATTTTTAGAAGTTCAAAGGGAAAATGGTAATTTTTGGAAGTTTCAAGGTCAAAAATGG
GATTTTTGGAAGTTTTGG
Found at i:19889 original size:59 final size:59
Alignment explanation
Indices: 19600--19892 Score: 335
Period size: 59 Copynumber: 4.9 Consensus size: 59
19590 GTTCGAGGGT
* * * *
19600 AAAATGGTAATTTTTGGAAGTTTTG-GGGTCAAAAATGG-GATTTTTGGAAGTTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAG-TTCGAGGGT--AAAATGGTAATTTTTGGAAGTTTAGGGGTCA
** * * * *
19661 AAAATGGGATTTTTAAAAGTTTGAGGGTAAAATGGTAATTTTTGGGAGTTTCGAGGTCA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTCA
* * * *
19720 AAATTGGGATTTTTAGAAGTTCAAAGGG-AAAATGGTAATTTTTGGAAGTTTCA-AGGTCA
1 AAAATGGGATTTTTGGAAGTTC-GAGGGTAAAATGGTAATTTTTGGAAGTTT-AGGGGTCA
*
19779 AAAATGGGATTTTTGGAAGTTCG-GGAGTAAAATGGTAATTTTTAGAAGTTTAGGGGTCA
1 AAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATGGTAATTTTTGGAAGTTTAGGGGTCA
* *
19838 AAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTCTGGAAGTTTAGGG
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGG
19893 ACTTTCGAGG
Statistics
Matches: 203, Mismatches: 21, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
57 2 0.01
58 9 0.04
59 166 0.82
60 19 0.09
61 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTCA
Found at i:20996 original size:12 final size:13
Alignment explanation
Indices: 20979--21011 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
20969 TATTAATAAG
20979 TAATAATA-TTTT
1 TAATAATATTTTT
20991 TAATAATATTTTT
1 TAATAATATTTTT
21004 TAATAATA
1 TAATAATA
21012 ATAAATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATAATATTTTT
Found at i:21703 original size:17 final size:16
Alignment explanation
Indices: 21683--21759 Score: 91
Period size: 17 Copynumber: 4.6 Consensus size: 16
21673 AAATAAATTT
21683 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
21700 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
21717 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
21734 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
21751 TAAATTTAA
1 TAAATTTAA
21760 GCTAATTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
16 1 0.02
17 49 0.94
18 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:21724 original size:34 final size:34
Alignment explanation
Indices: 21684--21759 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
21674 AATAAATTTT
* * *
21684 AAATTTAAATTTATAATAAATTTAAATTTCAAAC
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
* *
21718 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
21752 AAATTTAA
1 AAATTTAA
21760 GCTAATTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
Found at i:22345 original size:46 final size:46
Alignment explanation
Indices: 22277--22429 Score: 110
Period size: 46 Copynumber: 3.5 Consensus size: 46
22267 ATTTGGTCTT
** *
22277 CTTCTCAGTATCTTGTCCGGAAGATGACCGCATCATTTTTAATTCG
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTTTAATTCG
* * *
22323 CTTCTCTGTATCTCATCAGG-A-A-GA-CG-A--ATTTGGT-A--CA
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTT-TTAATTCG
* ** * *
22360 CTTCTCAGTATTTTGTCCGGAAGATGACCGCATCGTTTTTAATTCG
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTTTAATTCG
* *
22406 CTTCTCTGCATCTCATCAGGAAGA
1 CTTCTCAGTATCTCATCAGGAAGA
22430 CGAATTTGGT
Statistics
Matches: 76, Mismatches: 20, Indels: 22
0.64 0.17 0.19
Matches are distributed among these distances:
37 16 0.21
38 1 0.01
39 6 0.08
40 3 0.04
41 3 0.04
42 3 0.04
43 3 0.04
44 5 0.07
45 1 0.01
46 35 0.46
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (46 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCATTTTTAATTCG
Found at i:22465 original size:83 final size:83
Alignment explanation
Indices: 22277--22455 Score: 331
Period size: 83 Copynumber: 2.2 Consensus size: 83
22267 ATTTGGTCTT
*
22277 CTTCTCAGTATCTTGTCCGGAAGATGACCGCATCATTTTTAATTCGCTTCTCTGTATCTCATCAG
1 CTTCTCAGTATCTTGTCCGGAAGATGACCGCATCATTTTTAATTCGCTTCTCTGCATCTCATCAG
22342 GAAGACGAATTTGGTACA
66 GAAGACGAATTTGGTACA
* *
22360 CTTCTCAGTATTTTGTCCGGAAGATGACCGCATCGTTTTTAATTCGCTTCTCTGCATCTCATCAG
1 CTTCTCAGTATCTTGTCCGGAAGATGACCGCATCATTTTTAATTCGCTTCTCTGCATCTCATCAG
22425 GAAGACGAATTTGGTACA
66 GAAGACGAATTTGGTACA
22443 CTTCTCAGTATCT
1 CTTCTCAGTATCT
22456 CATCAGGAAG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (83 bp):
CTTCTCAGTATCTTGTCCGGAAGATGACCGCATCATTTTTAATTCGCTTCTCTGCATCTCATCAG
GAAGACGAATTTGGTACA
Found at i:23322 original size:58 final size:58
Alignment explanation
Indices: 23252--23367 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
23242 AAATGCTTGG
23252 TCAAAATTGTAGAAACAAAGTCGTATTTCCAAAATTCTATTAAGAAGAGGATTAAGGA
1 TCAAAATTGTAGAAACAAAGTCGTATTTCCAAAATTCTATTAAGAAGAGGATTAAGGA
23310 TCAAAATTGTAGAAACAAAGTCGTATTTCCAAAATTCTATTAAGAAGAGGATTAAGGA
1 TCAAAATTGTAGAAACAAAGTCGTATTTCCAAAATTCTATTAAGAAGAGGATTAAGGA
23368 AAACAATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (58 bp):
TCAAAATTGTAGAAACAAAGTCGTATTTCCAAAATTCTATTAAGAAGAGGATTAAGGA
Found at i:23345 original size:28 final size:28
Alignment explanation
Indices: 23253--23345 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
23243 AATGCTTGGT
23253 CAAAATTGTAGAAACAAAGTCGTATTTC
1 CAAAATTGTAGAAACAAAGTCGTATTTC
* ** * *** **
23281 CAAAATTCTATTAAGAAGAGGATTAAGGAT-
1 CAAAATTGTAGAAACAA-AGTCGT-A-TTTC
23311 CAAAATTGTAGAAACAAAGTCGTATTTC
1 CAAAATTGTAGAAACAAAGTCGTATTTC
23339 CAAAATT
1 CAAAATT
23346 CTATTAAGAA
Statistics
Matches: 43, Mismatches: 18, Indels: 8
0.62 0.26 0.12
Matches are distributed among these distances:
27 1 0.02
28 21 0.49
29 6 0.14
30 14 0.33
31 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (28 bp):
CAAAATTGTAGAAACAAAGTCGTATTTC
Found at i:45161 original size:28 final size:30
Alignment explanation
Indices: 45106--45168 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
45096 GCACGGGGGG
45106 TAAAATGGAAATTTTGAGAAATTTTAGGGA
1 TAAAATGGAAATTTTGAGAAATTTTAGGGA
* *
45136 TAAAGATGG-AATTTT-AGACA-TTTAGGGG
1 TAAA-ATGGAAATTTTGAGAAATTTTAGGGA
45164 TAAAA
1 TAAAA
45169 AGGGTTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
28 11 0.37
29 4 0.13
30 10 0.33
31 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.32
Consensus pattern (30 bp):
TAAAATGGAAATTTTGAGAAATTTTAGGGA
Found at i:45224 original size:59 final size:58
Alignment explanation
Indices: 45177--45392 Score: 290
Period size: 59 Copynumber: 3.7 Consensus size: 58
45167 AAAGGGTTAC
**
45177 TTTGAGAGTTTCGAGGTTGAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATT
1 TTTG-GAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATT
* *
45236 TTTGGAGGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGA-GTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATT
* * *
45295 TTTGGAAGTTTCGAGATCAAAAATGAGATTTTTGGAAGTT-TGGGGTAAAATGGTAATT
1 TTTGG-AGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATT
* * * *
45353 TTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGAAAGTT
1 TTT-GGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
45393 TTGAGGTTAA
Statistics
Matches: 140, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 51 0.36
59 88 0.63
60 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.37
Consensus pattern (58 bp):
TTTGGAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATT
Found at i:45269 original size:30 final size:30
Alignment explanation
Indices: 45196--45745 Score: 451
Period size: 29 Copynumber: 18.7 Consensus size: 30
45186 TTCGAGGTTG
**
45196 AAAATGGGATTTTTGGAAGTTCAGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* * *
45224 AAAATGGTAATTTTTGGAGGTTTTGAGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
**
45255 AAAATGGGATTTTTGGAAGTTCGGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* * * *
45283 AAAATGGTAATTTTTGGAAGTTTCGAGATCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
*
45314 AAAATGAGATTTTTGGAAG-TTTGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* *
45341 AAAATGGTAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
* * *
45372 AAAATGGGATTTTTGAAAGTTTTGAGGTTA
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* * *
45402 AAAATGGGATTTTTAGAAGTTTAGGGAT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* * *
45430 AAAATGGTAATTTTTGGGAGTTTTGAGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
* *
45461 AAATTGGGATTTTTAGAAG-TTTGAGGGT--
1 AAAATGGGATTTTTGGAAGTTTTG-GGGTCA
*
45489 AAAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
* *
45520 AAAATGGGATTTTTAGAAGTTTGGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* * * *
45548 AAAATGGTAATTTTTGGGAGTTTCGAGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
* *
45579 AAAATGGGATTTTTAGAAGTTTGGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* *
45607 AAAATGGTAATTTTTGGAAATTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
* *
45638 AAAATGAGATTTTTAGAAG-TTTGGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
* *
45665 AAAATGGTAATTTTTAGAAGTTTTGGGGTC-
1 AAAATGG-GATTTTTGGAAGTTTTGGGGTCA
** **
45695 AAAATGGGATTTTAAGAAGTTTAAGGGT--
1 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
*
45723 AAAATGGTAATTTTTGGAAGTTT
1 AAAATGG-GATTTTTGGAAGTTT
45746 AGGGACTTTC
Statistics
Matches: 417, Mismatches: 77, Indels: 55
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.03
28 69 0.17
29 156 0.37
30 134 0.32
31 46 0.11
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (30 bp):
AAAATGGGATTTTTGGAAGTTTTGGGGTCA
Found at i:45469 original size:59 final size:59
Alignment explanation
Indices: 45322--45745 Score: 574
Period size: 59 Copynumber: 7.2 Consensus size: 59
45312 CAAAAATGAG
* * * *
45322 ATTTTTGGAAG-TTTGGGGT--AAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGG-G
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGG-GATTTTTAGAAGTTTAGGGGT--AAAATGGTA
* * *
45380 ATTTTTGAAAGTTTTGAGGTTAAAAATGGGATTTTTAGAAGTTTAGGGATAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
* *
45439 ATTTTTGGGAGTTTTGAGGTCAAAATTGGGATTTTTAGAAGTTT-GAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAG-GGGTAAAATGGTA
* *
45498 ATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
* * *
45557 ATTTTTGGGAGTTTCGAGGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
* * *
45616 ATTTTTGGAAATTTTGGGGTCAAAAATGAGATTTTTAGAAGTTT-GGGGTAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
* * * *
45674 ATTTTTAGAAGTTTTGGGGTC-AAAATGGGATTTTAAGAAGTTTAAGGGTAAAATGGTA
1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
45732 ATTTTTGGAAGTTT
1 ATTTTTGGAAGTTT
45746 AGGGACTTTC
Statistics
Matches: 331, Mismatches: 28, Indels: 14
0.89 0.08 0.04
Matches are distributed among these distances:
57 20 0.06
58 77 0.23
59 208 0.63
60 19 0.06
61 7 0.02
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (59 bp):
ATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAGTTTAGGGGTAAAATGGTA
Found at i:46505 original size:66 final size:66
Alignment explanation
Indices: 46428--46567 Score: 235
Period size: 66 Copynumber: 2.1 Consensus size: 66
46418 GGTACACGCG
* *
46428 CCGTCGCCTTCCACGCGTCACACGCCACGCGCCCCCATCGAAGGTGAGTCGTCTCCTCATCTCCG
1 CCGTCGCCTTCCACGCGTCACACGCCACGCGCCCCCATCGAAGATGAGCCGTCTCCTCATCTCCG
46493 T
66 T
* *
46494 CCGTCGCCTTCCACGCGTCACGCGCCACGCGCCCCCGTCGAAGATGAGCCGTCTCCTCATCTCCG
1 CCGTCGCCTTCCACGCGTCACACGCCACGCGCCCCCATCGAAGATGAGCCGTCTCCTCATCTCCG
46559 T
66 T
*
46560 CCGCCGCC
1 CCGTCGCC
46568 GTTTTCGACC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.12, C:0.48, G:0.22, T:0.18
Consensus pattern (66 bp):
CCGTCGCCTTCCACGCGTCACACGCCACGCGCCCCCATCGAAGATGAGCCGTCTCCTCATCTCCG
T
Found at i:46925 original size:12 final size:13
Alignment explanation
Indices: 46908--46940 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
46898 TATTAATAAG
46908 TAATAATA-TTTT
1 TAATAATATTTTT
46920 TAATAATATTTTT
1 TAATAATATTTTT
46933 TAATAATA
1 TAATAATA
46941 ATAAATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATAATATTTTT
Found at i:47436 original size:23 final size:20
Alignment explanation
Indices: 47387--47436 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
47377 GTTGAAGTTG
*
47387 GAGGTGGCAACTTGGTTGCT
1 GAGGTGGCAACCTGGTTGCT
*
47407 GACGTGGCACATCCTGGTTGGCT
1 GAGGTGGCA-A-CCTGGTT-GCT
47430 GAGGTGG
1 GAGGTGG
47437 AGGCAGCAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 6 0.25
23 9 0.38
ACGTcount: A:0.14, C:0.18, G:0.42, T:0.26
Consensus pattern (20 bp):
GAGGTGGCAACCTGGTTGCT
Found at i:47620 original size:6 final size:6
Alignment explanation
Indices: 47609--47690 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
47599 TTTTAAAATA
*
47609 AAATTT AAATTT AAATTT ATAA--T AAATTT AAATTT CAAA--C AAATTT
1 AAATTT AAATTT AAATTT A-AATTT AAATTT AAATTT -AAATTT AAATTT
* * *
47655 AAATTT AGAA--T AAACTT AATTTT AAA-AT AAATTT AA
1 AAATTT A-AATTT AAATTT AAATTT AAATTT AAATTT AA
47691 GCTGATTGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
4 7 0.12
5 8 0.14
6 37 0.63
7 7 0.12
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:47634 original size:17 final size:16
Alignment explanation
Indices: 47614--47690 Score: 91
Period size: 17 Copynumber: 4.6 Consensus size: 16
47604 AAATAAAATT
47614 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
47631 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
*
47648 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
47665 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
47682 TAAATTTAA
1 TAAATTTAA
47691 GCTGATTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
16 1 0.02
17 49 0.94
18 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:47654 original size:34 final size:34
Alignment explanation
Indices: 47615--47690 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
47605 AATAAAATTT
* * *
47615 AAATTTAAATTTATAATAAATTTAAATTTCAAAC
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
* *
47649 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
47683 AAATTTAA
1 AAATTTAA
47691 GCTGATTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTAGAATAAACTTAAATTTAAAAC
Found at i:50193 original size:2 final size:2
Alignment explanation
Indices: 50186--50212 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50176 TCCCTCAATT
50186 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
50213 GAAAAGTACT
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:57257 original size:24 final size:24
Alignment explanation
Indices: 57224--57274 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
57214 AGAAATAATC
* * *
57224 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
57248 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
57272 TTT
1 TTT
57275 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:57283 original size:24 final size:24
Alignment explanation
Indices: 57232--57294 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
57222 TCTTTCAGTT
* * *
57232 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTAGTTGTTTCAATC
* *
57256 AAACTCTGTTTAGTTGTTTGAGTC
1 AAACTCTGTTTAGTTGTTTCAATC
57280 AAACTCT-TATTAGTT
1 AAACTCTGT-TTAGTT
57295 TAGATTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTAGTTGTTTCAATC
Found at i:58891 original size:29 final size:29
Alignment explanation
Indices: 58858--59225 Score: 273
Period size: 29 Copynumber: 12.5 Consensus size: 29
58848 CTAAACTATT
* * *
58858 CAAAAATTACATTTTTACCCCCTAGCTTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * * *
58887 CAAAAATCCCATTTTTGACCTCGAGACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
58917 CAAAAATTCCATTTTAACCCCCAAACTAC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
*
58946 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
** *
58976 CAAAAATTCCA-TTTTACCCCTGAACCTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* *
59004 CAAAATTTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
59034 CAAAAATTCCATTTTTACCCCCGAACCTC
1 CAAAAATTCCATTTTTACCCCCAAACTTC
* * * *
59063 CAAAATTTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
* *
59093 CAAAAATTGCCA-TTTTGCCCCCGAA-TGTC
1 CAAAAATT-CCATTTTTACCCCCAAACT-TC
* * * *
59122 CAAAAACTCCATTTTCGACCTCAAAAC-TC
1 CAAAAATTCCATTTT-TACCCCCAAACTTC
* *
59151 TC-AAAATTACC-CTTTTA-CCCCAAAATATC
1 -CAAAAATT-CCATTTTTACCCCCAAACT-TC
* * ** *
59180 TAAAAATTTCATTTTTAACCCTAAAATTTC
1 CAAAAATTCCATTTTT-ACCCCCAAACTTC
59210 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
59226 GCCCCCGAGA
Statistics
Matches: 261, Mismatches: 59, Indels: 36
0.73 0.17 0.10
Matches are distributed among these distances:
27 5 0.02
28 26 0.10
29 109 0.42
30 106 0.41
31 15 0.06
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCCAAACTTC
Found at i:58919 original size:30 final size:30
Alignment explanation
Indices: 58858--59253 Score: 281
Period size: 30 Copynumber: 13.5 Consensus size: 30
58848 CTAAACTATT
* ** *
58858 CAAAAATTACATTTTT-ACCCCCTAGCTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* * *
58887 CAAAAATCCCATTTTTGACCTCGAGACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* * *
58917 CAAAAATTCCA-TTTTAACCCCCAAACTAC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
58946 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
58976 CAAAAATTCCA-TTTT-ACCCCTG-AACCTC
1 CAAAAATTCCATTTTTGACCCC-GAAACTTC
* *
59004 CAAAATTTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
59034 CAAAAATTCCATTTTT-ACCCCCG-AACCTC
1 CAAAAATTCCATTTTTGA-CCCCGAAACTTC
* * *
59063 CAAAATTTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
59093 CAAAAATTGCCA-TTTTGCCCCCG-AA-TGTC
1 CAAAAATT-CCATTTTTGACCCCGAAACT-TC
* * * *
59122 CAAAAACTCCATTTTCGACCTCAAAAC-TC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* *
59151 TC-AAAATTACC-CTTTT-ACCCC-AAAATATC
1 -CAAAAATT-CCATTTTTGACCCCGAAACT-TC
* * * ** *
59180 TAAAAATTTCATTTTTAACCCTAAAATTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
59210 CAAAAATTACCA-TTTTGCCCCCGAGAA--TC
1 CAAAAATT-CCATTTTTGACCCCGA-AACTTC
59239 C-AAAATTACCATTTT
1 CAAAAATT-CCATTTT
59254 GCCCCCGGTA
Statistics
Matches: 289, Mismatches: 53, Indels: 50
0.74 0.14 0.13
Matches are distributed among these distances:
27 3 0.01
28 39 0.13
29 116 0.40
30 120 0.42
31 11 0.04
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (30 bp):
CAAAAATTCCATTTTTGACCCCGAAACTTC
Found at i:59066 original size:117 final size:117
Alignment explanation
Indices: 58858--59253 Score: 392
Period size: 117 Copynumber: 3.4 Consensus size: 117
58848 CTAAACTATT
* * * * * *
58858 CAAAAATTA-CATTTTTACCCCCTAGCTTCCAAAAATCCCATTTTTGACCTCGAGACTTCCAAAA
1 CAAAAATTACCA-TTTTACCCCCGAACATCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAA
*
58922 ATTCCATTTTAACCCCCAAACTACCAAAAATTCCATTTTTGACCCCAAAACTTC
65 ATTCCATTTTTACCCCCAAACT-CCAAAAATTCCATTTTTGACCCCAAAACTTC
* * * *
58976 CAAAAATT-CCATTTTACCCCTGAACCTCCAAAATTTCCATTTTTGACCCCAAAACTTCCAAAAA
1 CAAAAATTACCATTTTACCCCCGAACATCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAA
* * * * *
59040 TTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCTCGAAACTTT
66 TTCCATTTTTACCCCC-AAACTCCAAAAATTCCATTTTTGACCCCAAAACTTC
* * ** * *
59093 CAAAAATTGCCATTTTGCCCCCGAATGTCCAAAAACTCCATTTTCGACCTCAAAAC-TCTC-AAA
1 CAAAAATTACCATTTTACCCCCGAACATCCAAAAATTCCATTTTTGACCTCAAAACTTC-CAAAA
* * * * * * * *
59156 ATTACC-CTTTTACCCCAAAATATCTAAAAATTTCATTTTTAACCCTAAAATTTC
65 ATT-CCATTTTTACCCCCAAA-CTCCAAAAATTCCATTTTTGACCCCAAAACTTC
*
59210 CAAAAATTACCATTTTGCCCCCGAGA-ATCC-AAAATTACCATTTT
1 CAAAAATTACCATTTTACCCCCGA-ACATCCAAAAATT-CCATTTT
59254 GCCCCCGGTA
Statistics
Matches: 231, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
116 7 0.03
117 167 0.72
118 57 0.25
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (117 bp):
CAAAAATTACCATTTTACCCCCGAACATCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAA
TTCCATTTTTACCCCCAAACTCCAAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:59169 original size:176 final size:176
Alignment explanation
Indices: 58858--59253 Score: 446
Period size: 176 Copynumber: 2.2 Consensus size: 176
58848 CTAAACTATT
* * * * * * *
58858 CAAAAATTACATTTTTACCCCCTAGCTTCCAAAAATCCCATTTTTGACCTCGAGACTTCCAAAAA
1 CAAAAATTCCATTTTTACCCCCGAACATCCAAAATTACCATTTTTGACCTCGAAACTTCCAAAAA
* *
58923 TTCCATTTTAACCCCCAAACTACCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCAT
66 TTCCATTTTAACCCCCAAACTACCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATTCCAT
** * * *
58988 TTTACCCCTGAACCTC-CAAAATTTCCATTTTTGACCCCAAAACTTC
131 TTTACCCCAAAACATCTAAAAATTT-CATTTTTAACCCCAAAACTTC
* * *
59034 CAAAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCTCGAAACTTTCAAAAA
1 CAAAAATTCCATTTTTACCCCCGAACATCCAAAATTACCATTTTTGACCTCGAAACTTCCAAAAA
* * * *
59099 TTGCCATTTT-GCCCCCGAA-TGTCCAAAAACTCCATTTTCGACCTCAAAAC-TCTC-AAAATTA
66 TT-CCATTTTAACCCCCAAACT-ACCAAAAACTCCATTTTCGACCCCAAAACTTC-CAAAAATT-
* * * *
59160 CCCTTTTACCCCAAAATATCTAAAAATTTCATTTTTAACCCTAAAATTTC
127 CCATTTTACCCCAAAACATCTAAAAATTTCATTTTTAACCCCAAAACTTC
*
59210 CAAAAATTACCA-TTTTGCCCCCGAGA-ATCCAAAATTACCATTTT
1 CAAAAATT-CCATTTTTACCCCCGA-ACATCCAAAATTACCATTTT
59254 GCCCCCGGTA
Statistics
Matches: 187, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
175 9 0.05
176 160 0.86
177 18 0.10
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (176 bp):
CAAAAATTCCATTTTTACCCCCGAACATCCAAAATTACCATTTTTGACCTCGAAACTTCCAAAAA
TTCCATTTTAACCCCCAAACTACCAAAAACTCCATTTTCGACCCCAAAACTTCCAAAAATTCCAT
TTTACCCCAAAACATCTAAAAATTTCATTTTTAACCCCAAAACTTC
Found at i:59252 original size:59 final size:57
Alignment explanation
Indices: 58858--59253 Score: 341
Period size: 59 Copynumber: 6.7 Consensus size: 57
58848 CTAAACTATT
* * * * * * * *
58858 CAAAAATTACATTTTTACCCCCTAGCTTCCAAAAATCCCATTTTTGACCTCGAGACTTC
1 CAAAAATTCCA-TTTTACCCCCGAACATCC-AAAATTCCATTTTTGACCCCAAAACTTC
*
58917 CAAAAATTCCATTTTAACCCCCAAAC-TACCAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTT-ACCCCCGAACAT-CC-AAAATTCCATTTTTGACCCCAAAACTTC
* *
58976 CAAAAATTCCATTTTACCCCTGAACCTCCAAAATTTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTACCCCCGAACATCCAAAA-TTCCATTTTTGACCCCAAAACTTC
* * * *
59034 CAAAAATTCCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTCCA-TTTTACCCCCGAACATCCAAAA-TTCCATTTTTGACCCCAAAACTTC
* ** * * *
59093 CAAAAATTGCCATTTTGCCCCCGAATGTCCAAAAACTCCATTTTCGACCTCAAAAC-TC
1 CAAAAATT-CCATTTTACCCCCGAACATCC-AAAATTCCATTTTTGACCCCAAAACTTC
* ** * * * * * *
59151 TC-AAAATTACCCTTTTACCCCAAAATATCTAAAAATTTCATTTTTAACCCTAAAATTTC
1 -CAAAAATT-CCATTTTACCCCCGAACATC-CAAAATTCCATTTTTGACCCCAAAACTTC
*
59210 CAAAAATTACCATTTTGCCCCCGAGA-ATCCAAAATTACCATTTT
1 CAAAAATT-CCATTTTACCCCCGA-ACATCCAAAATT-CCATTTT
59254 GCCCCCGGTA
Statistics
Matches: 284, Mismatches: 40, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
57 4 0.01
58 97 0.34
59 175 0.62
60 8 0.03
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (57 bp):
CAAAAATTCCATTTTACCCCCGAACATCCAAAATTCCATTTTTGACCCCAAAACTTC
Found at i:59266 original size:27 final size:28
Alignment explanation
Indices: 59212--59270 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
59202 AAAATTTCCA
59212 AAAATTACCATTTTGCCCCCGAGAATCC
1 AAAATTACCATTTTGCCCCCGAGAATCC
*
59240 AAAATTACCATTTTGCCCCCG-GTATCC
1 AAAATTACCATTTTGCCCCCGAGAATCC
59267 AAAA
1 AAAA
59271 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAGAATCC
Found at i:59278 original size:27 final size:28
Alignment explanation
Indices: 59212--59280 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
59202 AAAATTTCCA
*
59212 AAAATTACCATTTTGCCCCCGAGAATCC
1 AAAAGTACCATTTTGCCCCCGAGAATCC
* *
59240 AAAATTACCATTTTGCCCCCG-GTATCC
1 AAAAGTACCATTTTGCCCCCGAGAATCC
59267 AAAAGT-CTCATTTT
1 AAAAGTAC-CATTTT
59281 CAACTCCGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 1 0.03
27 16 0.42
28 21 0.55
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.30
Consensus pattern (28 bp):
AAAAGTACCATTTTGCCCCCGAGAATCC
Found at i:60888 original size:22 final size:20
Alignment explanation
Indices: 60858--60899 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
60848 TTTATACATT
60858 TTATATTTAAATTTAATTAAAA
1 TTATATTTAAA-TT-ATTAAAA
*
60880 TTATTTTTAAATTATTAAAA
1 TTATATTTAAATTATTAAAA
60900 ATTAAAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATATTTAAATTATTAAAA
Found at i:63178 original size:19 final size:20
Alignment explanation
Indices: 63151--63196 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
63141 TATTAATGTA
*
63151 TTTACAAAAATATTTATT-T
1 TTTAAAAAAATATTTATTAT
*
63170 TTT-AAAAAATATTTTTTAT
1 TTTAAAAAAATATTTATTAT
63189 TTTAAAAA
1 TTTAAAAA
63197 CCTTGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 12 0.52
19 7 0.30
20 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAAAAAAATATTTATTAT
Found at i:63179 original size:18 final size:19
Alignment explanation
Indices: 63151--63196 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
63141 TATTAATGTA
63151 TTTACAAAAATATTTATT-T
1 TTTA-AAAAATATTTATTAT
*
63170 TTTAAAAAATATTTTTTAT
1 TTTAAAAAATATTTATTAT
63189 TTTAAAAA
1 TTTAAAAA
63197 CCTTGTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAAAAATATTTATTAT
Found at i:64378 original size:29 final size:30
Alignment explanation
Indices: 64336--64399 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
64326 CAACTTAACA
* *
64336 AACAAATGTCTCTAAAATAGTAA-AAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
64365 AACAAATGCCTCTAAGATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
64395 AACAA
1 AACAA
64400 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:65109 original size:21 final size:20
Alignment explanation
Indices: 65085--65141 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
65075 AACTTAAAAA
65085 TCAAAACTTTAAACCCTAAAT
1 TCAAAAC-TTAAACCCTAAAT
*
65106 TCAAATCATT-AACCCTAAAT
1 TCAAAAC-TTAAACCCTAAAT
*
65126 TCATACACTTAAACCC
1 TCA-AAACTTAAACCC
65142 AATTTATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (20 bp):
TCAAAACTTAAACCCTAAAT
Found at i:70405 original size:72 final size:72
Alignment explanation
Indices: 70248--70394 Score: 294
Period size: 72 Copynumber: 2.0 Consensus size: 72
70238 TATGATTAAA
70248 TGTGAAGTATGTTGCTTGTGAATTTATGATATTGTGGACATATATGAGATGTTATGGCATGTGTT
1 TGTGAAGTATGTTGCTTGTGAATTTATGATATTGTGGACATATATGAGATGTTATGGCATGTGTT
70313 ACCAGCT
66 ACCAGCT
70320 TGTGAAGTATGTTGCTTGTGAATTTATGATATTGTGGACATATATGAGATGTTATGGCATGTGTT
1 TGTGAAGTATGTTGCTTGTGAATTTATGATATTGTGGACATATATGAGATGTTATGGCATGTGTT
70385 ACCAGCT
66 ACCAGCT
70392 TGT
1 TGT
70395 TATGACTGTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (72 bp):
TGTGAAGTATGTTGCTTGTGAATTTATGATATTGTGGACATATATGAGATGTTATGGCATGTGTT
ACCAGCT
Found at i:70444 original size:36 final size:36
Alignment explanation
Indices: 70404--70477 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
70394 TTATGACTGT
** * * *
70404 TGTGAAAGTGGATATGTGAGTATGTTTTTCATGCCA
1 TGTGAAAGTAAATATGTGAGTATGATATTAATGCCA
* *
70440 TGTGACAGTAAATATGTGGGTATGATATTAATGCCA
1 TGTGAAAGTAAATATGTGAGTATGATATTAATGCCA
70476 TG
1 TG
70478 AGACTGTGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.36
Consensus pattern (36 bp):
TGTGAAAGTAAATATGTGAGTATGATATTAATGCCA
Found at i:70490 original size:36 final size:35
Alignment explanation
Indices: 70415--70516 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 35
70405 GTGAAAGTGG
* * *
70415 ATATGTGAGTATGTTTTTCATGCCATGTGACAGTAA
1 ATATGTGGGTATGTTATT-ATGCCATGAGACAGTAA
* * *
70451 ATATGTGGGTATGATATTAATGCCATGAGACTGTGA
1 ATATGTGGGTATGTTATT-ATGCCATGAGACAGTAA
* *
70487 ATATGTGGGAATGTTA-TATGCCATGTGACA
1 ATATGTGGGTATGTTATTATGCCATGAGACA
70517 ATGAATATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 11 0.20
35 1 0.02
36 43 0.78
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (35 bp):
ATATGTGGGTATGTTATTATGCCATGAGACAGTAA
Found at i:70522 original size:34 final size:36
Alignment explanation
Indices: 70434--70524 Score: 114
Period size: 36 Copynumber: 2.6 Consensus size: 36
70424 TATGTTTTTC
* *
70434 ATGCCATGTGACAGTAAATATGTGGGTATGATATTA
1 ATGCCATGTGACAGTGAATATGTGGGAATGATATTA
* * *
70470 ATGCCATGAGACTGTGAATATGTGGGAATGTTA-T-
1 ATGCCATGTGACAGTGAATATGTGGGAATGATATTA
*
70504 ATGCCATGTGACAATGAATAT
1 ATGCCATGTGACAGTGAATAT
70525 ATTGTGCTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 18 0.38
35 1 0.02
36 28 0.60
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (36 bp):
ATGCCATGTGACAGTGAATATGTGGGAATGATATTA
Done.