Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000001.1 Kokia drynarioides strain JFW-HI SEQ_130271, 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: 277740
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 747 characters in sequence are not A, C, G, or T
Found at i:7921 original size:96 final size:96
Alignment explanation
Indices: 7732--7923 Score: 226
Period size: 96 Copynumber: 2.0 Consensus size: 96
7722 TCTTTGCGAA
* ** *
7732 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCG
* * * * * *
7797 GAATCGAAGATAAGGAAACATTGTCTCGATT
66 AAACCCAAAATAAAGAAACATTGCCTCGATT
* * *
7828 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGTAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTC
*
7892 GAAACCCAAAATGAAAG-AATATTGCCTCGATT
65 GAAACCCAAAAT-AAAGAAACATTGCCTCGATT
7924 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
96 74 0.93
97 6 0.08
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCG
AAACCCAAAATAAAGAAACATTGCCTCGATT
Found at i:8265 original size:59 final size:59
Alignment explanation
Indices: 8215--8483 Score: 405
Period size: 59 Copynumber: 4.6 Consensus size: 59
8205 TTTGAGAAAA
* *
8215 TTCGGGGTTAAAAATCGGATTTTTGAAAGTTTGGGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGT
* * * * *
8274 TTCGAGGTTAAGAATGAGA-TTTTGGAAGTTCGGGGGTAAAAATAAAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGT
* * *
8332 TTCGGGGTTAAGAATGGGATTTTTGAAAGGTCGGGGGTAAAAATAGAATTTTTAAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGT
* *
8391 TTCGAGGTTAAAAATGGGATTTTTGAAAGGTCGGGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGT
* *
8450 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGG
1 TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGG
8484 NNNNNNNNNN
Statistics
Matches: 189, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 53 0.28
59 136 0.72
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
TTCGGGGTTAAAAATGGGATTTTTGAAAGTTCGGGGGTAAAAATAGAATTTTTGAAAGT
Found at i:8473 original size:30 final size:30
Alignment explanation
Indices: 8215--8480 Score: 274
Period size: 29 Copynumber: 9.0 Consensus size: 30
8205 TTTGAGAAAA
*
8215 TTCGGGGTTAAAAATCGGATTTTTGAAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* *
8245 TT-GGGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* * *
8274 TTCGAGGTTAAGAAT-GAGA-TTTTGGAAG-
1 TTCGGGGTTAAAAATAG-GATTTTTGAAAGT
* **
8302 TTCGGGGGTAAAAATAAAATTTTTGAAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* *
8332 TTCGGGGTTAAGAATGGGATTTTTGAAAG-
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* * * *
8361 GTCGGGGGTAAAAATAGAATTTTTAAAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* *
8391 TTCGAGGTTAAAAATGGGATTTTTGAAAG-
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* * *
8420 GTCGGGGGTAAAAATAGAATTTTTGAAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
* * *
8450 TTTGGGGTTAAAAATGGGATTTTTGGAAGT
1 TTCGGGGTTAAAAATAGGATTTTTGAAAGT
8480 T
1 T
8481 CGGNNNNNNN
Statistics
Matches: 187, Mismatches: 42, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
28 13 0.07
29 90 0.48
30 84 0.45
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
TTCGGGGTTAAAAATAGGATTTTTGAAAGT
Found at i:8621 original size:28 final size:28
Alignment explanation
Indices: 8550--8630 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
8540 NNNTCGGGGG
* **
8550 TAAAAATAGAATTTTTGAAAGTTTTGGGGT
1 TAAAAATAGAATTTTTGAAAG--TTCGGAA
* * *
8580 TAAAAATGGGATTTTTGGAAGTTCGGAA
1 TAAAAATAGAATTTTTGAAAGTTCGGAA
8608 TAAAAATAGAATTTTTGAAAGTT
1 TAAAAATAGAATTTTTGAAAGTT
8631 TCGAGGCCTA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 24 0.57
30 18 0.43
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (28 bp):
TAAAAATAGAATTTTTGAAAGTTCGGAA
Found at i:10168 original size:17 final size:16
Alignment explanation
Indices: 10148--10213 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
10138 AAATAAACTT
10148 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
* *
10165 TAAACTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
10182 CAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
**
10199 TAAAAATAAATTTAA
1 TAAATTTAAATTTAA
10214 GGTTATTGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
16 2 0.05
17 36 0.92
18 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:14687 original size:22 final size:22
Alignment explanation
Indices: 14641--14687 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
14631 ACTCGCTAGC
*
14641 TTTTTTGAAAATAGACTAAATT
1 TTTTTTGAAAATAGAATAAATT
* *
14663 TTTTTTTAAAATA-AATAAATG
1 TTTTTTGAAAATAGAATAAATT
14684 TTTT
1 TTTT
14688 AAATTGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (22 bp):
TTTTTTGAAAATAGAATAAATT
Found at i:15434 original size:13 final size:13
Alignment explanation
Indices: 15416--15441 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15406 TGGCTTCGAC
15416 TAAAAGAATATTT
1 TAAAAGAATATTT
15429 TAAAAGAATATTT
1 TAAAAGAATATTT
15442 ACATTACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TAAAAGAATATTT
Found at i:17696 original size:36 final size:32
Alignment explanation
Indices: 17653--17726 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
17643 ATTAATTAAA
*
17653 TTTTAAAATATAAAAAATTGAAAAATATATAAATTT
1 TTTTAAAA-ATAAAAAAGT-AAAAATATAT--ATTT
* *
17689 TTTTAAAAATTAAAAAGTATAAATATATATTT
1 TTTTAAAAATAAAAAAGTAAAAATATATATTT
17721 TTTTAA
1 TTTTAA
17727 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 10 0.29
34 9 0.26
35 8 0.23
36 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTTAAAAATAAAAAAGTAAAAATATATATTT
Found at i:18276 original size:17 final size:17
Alignment explanation
Indices: 18238--18276 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18228 ATGAAAATTT
*
18238 AAAAACTAAAAGAAACA
1 AAAAACTAAAAGAAAAA
* *
18255 AAAAATTAAATGAAAAA
1 AAAAACTAAAAGAAAAA
18272 AAAAA
1 AAAAA
18277 AATATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.10
Consensus pattern (17 bp):
AAAAACTAAAAGAAAAA
Found at i:28957 original size:22 final size:22
Alignment explanation
Indices: 28917--29006 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 22
28907 TAAACGGAAC
* ** *
28917 AAACAGAGAGTACCGAAGTACT
1 AAACAGAGAGCACAAAAGTGCT
*
28939 AAACAGAGAGCACATAAGTGCT
1 AAACAGAGAGCACAAAAGTGCT
*
28961 GGGTAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACA-AAAGTGCT
*
28987 AAACAGAGAGTACACAAAGT
1 AAACAGAGAGCACA-AAAGT
29007 ACCGAGCACA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 18 0.32
23 18 0.32
25 13 0.23
26 7 0.12
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (22 bp):
AAACAGAGAGCACAAAAGTGCT
Found at i:28991 original size:23 final size:23
Alignment explanation
Indices: 28917--29089 Score: 87
Period size: 23 Copynumber: 7.7 Consensus size: 23
28907 TAAACGGAAC
* * *
28917 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
28939 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
28961 GGGTAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
28987 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* * * *
29007 --AC--CGAGCACACGAGGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
29026 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
* *
29051 AAACAGATAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
29074 AATCAGAGAGCACACA
1 AAACAGAGAGCACACA
29090 TAATGCTGCA
Statistics
Matches: 114, Mismatches: 21, Indels: 31
0.69 0.13 0.19
Matches are distributed among these distances:
16 8 0.07
18 2 0.02
19 1 0.01
20 1 0.01
21 1 0.01
22 19 0.17
23 48 0.42
24 1 0.01
25 25 0.22
26 8 0.07
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:29096 original size:23 final size:23
Alignment explanation
Indices: 29029--29096 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
29019 AGGTACTAAT
* *
29029 AACAGAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCAC-ACACAATGCTA
* *
29052 AACAGATAGCACACACAGTGCTA
1 AACAGAGAGCACACACAATGCTA
* *
29075 ATCAGAGAGCACACATAATGCT
1 AACAGAGAGCACACACAATGCT
29097 GCATAGTAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 3 0.08
23 35 0.92
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:37777 original size:21 final size:21
Alignment explanation
Indices: 37753--37792 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37743 TTCTTCTTGT
*
37753 GTTTCTTCTTTTTGTCCTTAC
1 GTTTCCTCTTTTTGTCCTTAC
37774 GTTTCCTCTTTTTGTCCTT
1 GTTTCCTCTTTTTGTCCTT
37793 CGAACCAATT
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:0.03, C:0.25, G:0.10, T:0.62
Consensus pattern (21 bp):
GTTTCCTCTTTTTGTCCTTAC
Found at i:46557 original size:24 final size:24
Alignment explanation
Indices: 46520--46578 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
46510 GACAGCCCAC
* *
46520 ATGAGCCCAAAATGGTTAGCTCTT
1 ATGAGCCCAGAATGATTAGCTCTT
*
46544 ATGAGCACAGAATGATTAGCTCTT
1 ATGAGCCCAGAATGATTAGCTCTT
*
46568 ACGAGCCCAGA
1 ATGAGCCCAGA
46579 CAGAGTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
ATGAGCCCAGAATGATTAGCTCTT
Found at i:52796 original size:16 final size:17
Alignment explanation
Indices: 52775--52808 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
52765 TAATTACAAG
52775 CAATTACAT-CCAAATT
1 CAATTACATGCCAAATT
52791 CAATTACATGCCAAATT
1 CAATTACATGCCAAATT
52808 C
1 C
52809 TTAACGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (17 bp):
CAATTACATGCCAAATT
Found at i:53083 original size:58 final size:58
Alignment explanation
Indices: 52977--53166 Score: 159
Period size: 58 Copynumber: 3.2 Consensus size: 58
52967 AATATAACAT
* * * * ** * *
52977 TTGGTACCTGAATTTGATATTTTTTTATAATTTGGTACTTAAACTTTTTTTTACCCAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTAC-TAAACTTTTTTTTAACCAAA
* * * *
53036 TTGGTTCCTGAACTT-ACACTTTTTCCTGATTTGGTATCTAAA-TTTTTTTGGAACCAAA
1 TTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTA-CTAAACTTTTTTT-TAACCAAA
* ** * *
53094 TTGGTACCTAAACTTGGCTTTTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGATTCAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTA-CTAAACTTTTTTTTA-A-CCAAA
53155 TTGGTACCTAAA
1 TTGGTACCTAAA
53167 TTTATTAAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
57 7 0.07
58 38 0.36
59 37 0.35
60 8 0.08
61 15 0.14
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (58 bp):
TTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACTAAACTTTTTTTTAACCAAA
Found at i:53422 original size:55 final size:56
Alignment explanation
Indices: 53363--53469 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 56
53353 ATTGGACCCC
* * * * * *
53363 AAAAAGTTT-AAGTACCAACTT-AAAAGAAGTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAATTTAAAGTACCAAATTAAAAAAAAATGTCAAGTTCAGATACCAAATTAGG
53417 AAAAAATTTAAAGTACCAAATTAAAAAAAAAATGTCAAGTTCAGATACCAAAT
1 AAAAAATTTAAAGTACCAAATT-AAAAAAAAATGTCAAGTTCAGATACCAAAT
53470 ATTATATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 8 0.18
55 11 0.25
57 25 0.57
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (56 bp):
AAAAAATTTAAAGTACCAAATTAAAAAAAAATGTCAAGTTCAGATACCAAATTAGG
Found at i:53456 original size:26 final size:25
Alignment explanation
Indices: 53404--53456 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
53394 TCAAGTTTAG
** *
53404 GTACCAAATTAGGAAAAAATTTAAA
1 GTACCAAATTAAAAAAAAATGTAAA
*
53429 GTACCAAATTAAAAAAAAAATGTCAA
1 GTACCAAATT-AAAAAAAAATGTAAA
53455 GT
1 GT
53457 TCAGATACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (25 bp):
GTACCAAATTAAAAAAAAATGTAAA
Found at i:62201 original size:15 final size:15
Alignment explanation
Indices: 62181--62237 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
62171 ATTCAATATT
62181 AATATTTTAATAATA
1 AATATTTTAATAATA
*
62196 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
62215 AATATATTAATAATA
1 AATATTTTAATAATA
62230 AATATTTT
1 AATATTTT
62238 GTAGCATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 18 0.53
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:64311 original size:22 final size:22
Alignment explanation
Indices: 64286--64329 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
64276 ATTACGTGTC
64286 TAAAAAATAATATAA-AATAATA
1 TAAAAAATAA-ATAATAATAATA
**
64308 TAAATTATAAATAATAATAATA
1 TAAAAAATAAATAATAATAATA
64330 AAAGTTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAAAATAAATAATAATAATA
Found at i:64337 original size:22 final size:22
Alignment explanation
Indices: 64292--64337 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
64282 TGTCTAAAAA
64292 ATAATATAAAATAATATAAATT
1 ATAATATAAAATAATATAAATT
64314 ATAA-ATAATAATAATA-AAAGTT
1 ATAATATAA-AATAATATAAA-TT
64336 AT
1 AT
64338 GTTAGTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATATAAAATAATATAAATT
Found at i:65457 original size:27 final size:27
Alignment explanation
Indices: 65427--65479 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
65417 TTTTTTCTAG
*
65427 TTTTCTAAAATT-TTAACAATACTTTTA
1 TTTTCTAAAATTATCAA-AATACTTTTA
*
65454 TTTTTTAAAATTATCAAAATACTTTT
1 TTTTCTAAAATTATCAAAATACTTTT
65480 TTGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTCTAAAATTATCAAAATACTTTTA
Found at i:68736 original size:51 final size:50
Alignment explanation
Indices: 68641--68737 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
68631 TTATTTTCAA
* *
68641 ATATGATGTTTTAAATAAATATAAATATTTATTTAATTTGTTTTGTTTAG
1 ATATGATGTTTTAAATAAACATAAATATTTATTTAATTTATTTTGTTTAG
* * *
68691 ATATGATGTTTTTACATAAACATAAATGTTTGTTT-ATATTATTTTGT
1 ATATGATG-TTTTAAATAAACATAAATATTTATTTAAT-TTATTTTGT
68738 ACAGATCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 10 0.25
51 30 0.75
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (50 bp):
ATATGATGTTTTAAATAAACATAAATATTTATTTAATTTATTTTGTTTAG
Found at i:72952 original size:27 final size:25
Alignment explanation
Indices: 72889--72952 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
72879 TCACGTCAGT
* * *
72889 AAATTATTTTAAAATATAATTTTTT
1 AAATTATTTTAAAATATAAGTATTA
72914 AAATTATTTTTTAAAATATAAAAGTATTA
1 AAATTA--TTTTAAAATAT--AAGTATTA
72943 AAATTATTTT
1 AAATTATTTT
72953 TTTTGAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 6 0.19
27 15 0.47
29 11 0.34
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AAATTATTTTAAAATATAAGTATTA
Found at i:72983 original size:29 final size:28
Alignment explanation
Indices: 72890--72983 Score: 73
Period size: 31 Copynumber: 3.2 Consensus size: 28
72880 CACGTCAGTA
** *
72890 AATTATTTTAAAATAT-AATTTTTTAAAT
1 AATT-TTTTAAAATATAAAAGTATTAAAT
*
72918 TATTTTTTAAAATATAAAAGTATTAAAATT
1 AATTTTTTAAAATATAAAAGTATT-AAA-T
* * *
72948 ATTTTTTTTGAAATAATAAAATTATTAAAT
1 A-ATTTTTTAAAAT-ATAAAAGTATTAAAT
72978 AATTTT
1 AATTTT
72984 AATTTCCAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
27 11 0.21
28 8 0.15
29 7 0.13
30 3 0.06
31 13 0.25
32 10 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AATTTTTTAAAATATAAAAGTATTAAAT
Found at i:72983 original size:31 final size:31
Alignment explanation
Indices: 72915--72983 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
72905 TAATTTTTTA
72915 AATTATTTTTTAAAATATAAAAGTATTAAAAT
1 AATT-TTTTTTAAAATATAAAAGTATTAAAAT
* * *
72947 TATTTTTTTTGAAATAATAAAATTATT-AAAT
1 AATTTTTTTTAAAAT-ATAAAAGTATTAAAAT
72978 AATTTT
1 AATTTT
72984 AATTTCCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTTTTTTTAAAATATAAAAGTATTAAAAT
Found at i:74044 original size:10 final size:10
Alignment explanation
Indices: 74012--74044 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
74002 AATTTTATAT
74012 TTAAAA-AAA
1 TTAAAATAAA
74021 TTAAAATAAAA
1 TTAAAAT-AAA
74032 TTAAAATAAA
1 TTAAAATAAA
74042 TTA
1 TTA
74045 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:74401 original size:16 final size:17
Alignment explanation
Indices: 74372--74404 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
74362 TAATTATCAA
74372 AAAAAATTAACTCAGTAG
1 AAAAAATT-ACTCAGTAG
74390 AAAAAATT-CTCAGTA
1 AAAAAATTACTCAGTA
74405 AACAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAAATTACTCAGTAG
Found at i:85815 original size:55 final size:55
Alignment explanation
Indices: 85744--85855 Score: 143
Period size: 55 Copynumber: 2.0 Consensus size: 55
85734 GAAGGAACGT
* * * * * *
85744 ATTACTGGCTCTTAAGAGCACGCTGGCTCGTAAGAGCATATTGGCTCGTTAGAGC
1 ATTACTGACTCGTAAGAGCACACTAGCTCGTAAGAGCATACTGGCTCGTAAGAGC
* * *
85799 ATTACTGACTCGTAAGAGTATACTAGCTGGTAAGAGCATACTGGCTCGTAAGAGC
1 ATTACTGACTCGTAAGAGCACACTAGCTCGTAAGAGCATACTGGCTCGTAAGAGC
85854 AT
1 AT
85856 ATTGGCTTGT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (55 bp):
ATTACTGACTCGTAAGAGCACACTAGCTCGTAAGAGCATACTGGCTCGTAAGAGC
Found at i:85871 original size:18 final size:18
Alignment explanation
Indices: 85746--85862 Score: 135
Period size: 18 Copynumber: 6.4 Consensus size: 18
85736 AGGAACGTAT
*
85746 TACTGGCTCTTAAGAGCA
1 TACTGGCTCGTAAGAGCA
**
85764 CGCTGGCTCGTAAGAGCA
1 TACTGGCTCGTAAGAGCA
* *
85782 TATTGGCTCGTTAGAGCA
1 TACTGGCTCGTAAGAGCA
* *
85800 TTACTGACTCGTAAGAGTA
1 -TACTGGCTCGTAAGAGCA
* *
85819 TACTAGCTGGTAAGAGCA
1 TACTGGCTCGTAAGAGCA
85837 TACTGGCTCGTAAGAGCA
1 TACTGGCTCGTAAGAGCA
*
85855 TATTGGCT
1 TACTGGCT
85863 TGTTAGAGCG
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
18 66 0.82
19 14 0.17
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (18 bp):
TACTGGCTCGTAAGAGCA
Found at i:87366 original size:17 final size:18
Alignment explanation
Indices: 87346--87379 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
87336 ACTTCTTGTT
*
87346 TAGTTTAATTAA-AGTTC
1 TAGTATAATTAATAGTTC
87363 TAGTATAATTAATAGTT
1 TAGTATAATTAATAGTT
87380 TTATTTGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (18 bp):
TAGTATAATTAATAGTTC
Found at i:96575 original size:78 final size:78
Alignment explanation
Indices: 96482--96626 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 78
96472 AACTTTTTTT
* *
96482 TTTTTTTTAGATTTTAAGAGCTTAAATATTTGTACGAGATCTAAAAATATTTTTCTCCAACTTTT
1 TTTTTTTTAGATTTTAAGAGCTTAAATATTTGTACGAGACCTAAAAACATTTTTCTCCAACTTTT
96547 AAGAGGCCCCAAC
66 AAGAGGCCCCAAC
* * *
96560 TTTTTTTTA-ACTTTTAAGAGCTTAAATTTTTGTACGATACCTAAAAACATTTTTCTCTAACTTT
1 TTTTTTTTAGA-TTTTAAGAGCTTAAATATTTGTACGAGACCTAAAAACATTTTTCTCCAACTTT
96624 TAA
65 TAA
96627 AGAAATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 1 0.02
78 60 0.98
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (78 bp):
TTTTTTTTAGATTTTAAGAGCTTAAATATTTGTACGAGACCTAAAAACATTTTTCTCCAACTTTT
AAGAGGCCCCAAC
Found at i:97279 original size:24 final size:22
Alignment explanation
Indices: 97229--97292 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
97219 CAATATTAAA
*
97229 ATAAA-AAAATAAA-TTAAATT
1 ATAAATAAAATAAATTTAAATC
*
97249 ATGAATAAAATAAAATTTAAATAC
1 ATAAATAAAAT-AAATTTAAAT-C
*
97273 ATAAAT-ACATCAAATTTAAA
1 ATAAATAAAAT-AAATTTAAA
97293 ATATTAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 3 0.09
23 18 0.51
24 5 0.14
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAATAAAATAAATTTAAATC
Found at i:98138 original size:24 final size:24
Alignment explanation
Indices: 98111--98173 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
98101 ATAAATAATC
98111 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
98135 TTTCAATTAAACTATGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
98159 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
98174 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:106425 original size:17 final size:18
Alignment explanation
Indices: 106405--106438 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
106395 AAATGCTAGC
106405 ATTTT-AAAAATCTTCAA
1 ATTTTCAAAAATCTTCAA
*
106422 ATTTTCAAAATTCTTCA
1 ATTTTCAAAAATCTTCA
106439 TCCAAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTCAAAAATCTTCAA
Found at i:111208 original size:15 final size:15
Alignment explanation
Indices: 111190--111231 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
111180 TTTTCAAATC
111190 TATTTTTATATTTTA
1 TATTTTTATATTTTA
*
111205 TATTTTTAT-TTTCA
1 TATTTTTATATTTTA
*
111219 T-TTTTTTTATTTT
1 TATTTTTATATTTT
111232 TTTGTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 8 0.35
15 9 0.39
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTTTATATTTTA
Found at i:111214 original size:21 final size:21
Alignment explanation
Indices: 111190--111232 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
111180 TTTTCAAATC
*
111190 TATTTTTATATTTTATATTTT
1 TATTTTCATATTTTATATTTT
* *
111211 TATTTTCATTTTTTTTATTTT
1 TATTTTCATATTTTATATTTT
111232 T
1 T
111233 TTGTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (21 bp):
TATTTTCATATTTTATATTTT
Found at i:115372 original size:30 final size:31
Alignment explanation
Indices: 115299--115375 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
115289 TTAAAATCGA
115299 TGATCAAAATGAAAGTGACCTATATATTTAG
1 TGATCAAAATGAAAGTGACCTATATATTTAG
115330 TGATCAAAATGAAAGTGACCTATATATTTAG
1 TGATCAAAATGAAAGTGACCTATATATTTAG
115361 TGATC-AAATGAAAGT
1 TGATCAAAATGAAAGT
115376 ATAAACATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 10 0.22
31 36 0.78
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (31 bp):
TGATCAAAATGAAAGTGACCTATATATTTAG
Found at i:119043 original size:16 final size:17
Alignment explanation
Indices: 119022--119056 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
119012 ATTGGAACGA
*
119022 AAAT-AAATTTTTAATT
1 AAATAAAATTTTAAATT
119038 AAATAAAATTTTAAATT
1 AAATAAAATTTTAAATT
119055 AA
1 AA
119057 TTACATCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAAATTTTAAATT
Found at i:121187 original size:97 final size:96
Alignment explanation
Indices: 121007--121190 Score: 208
Period size: 97 Copynumber: 1.9 Consensus size: 96
120997 ATAGTTTGTG
* ** * *
121007 GGTCATTGAAGGATTTATCTCCATATCTAAGTTCAAATATAAGTTGGAAACATGAACTTGAAACA
1 GGTCATTGAAGGATTTATCTCCATACCTAAGTTCAAATATAAGTCAGAAACAAGAACTTCAAACA
**
121072 AAATGAAGGGCTGGAGCAACATGGATATACA
66 AAATGAAGGGCTAAAGCAACATGGATATACA
* * * ** * *
121103 GGTCATTGCAGGGTCTTATCTCCATACCTACGTTCGGATATAAGTCAGAAACAAGTACTTCAAGC
1 GGTCATTGAAGGAT-TTATCTCCATACCTAAGTTCAAATATAAGTCAGAAACAAGAACTTCAAAC
*
121168 AAAATGAAGAG-TCAAAGCAACAT
65 AAAATGAAGGGCT-AAAGCAACAT
121191 AAATTAGCAG
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
96 13 0.18
97 58 0.82
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (96 bp):
GGTCATTGAAGGATTTATCTCCATACCTAAGTTCAAATATAAGTCAGAAACAAGAACTTCAAACA
AAATGAAGGGCTAAAGCAACATGGATATACA
Found at i:121769 original size:17 final size:16
Alignment explanation
Indices: 121733--121771 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
121723 TTTTGTTTGA
121733 GTTTTA-TTTATAAAT
1 GTTTTATTTTATAAAT
*
121748 ATTTTATTTTATGAAAT
1 GTTTTATTTTAT-AAAT
121765 GTTTTAT
1 GTTTTAT
121772 AGAATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
GTTTTATTTTATAAAT
Found at i:125196 original size:24 final size:24
Alignment explanation
Indices: 125167--125239 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
125157 AATGACTCGT
*
125167 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
125191 CTGGAAGAAGCAGTCACGTAAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
125215 CTGGAAGAAGCAGCCATGGCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
125239 C
1 C
125240 AATTACACTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (24 bp):
CTGGAAGAAGCAGTCATGTCAGCA
Found at i:127472 original size:21 final size:21
Alignment explanation
Indices: 127448--127513 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
127438 AGCAATGGTG
127448 ATTGCCAACCTAATGAAATTC
1 ATTGCCAACCTAATGAAATTC
** *
127469 ATTGAAAACGCCAAGTAGAAA---
1 ATTGCCAAC-CTAA-T-GAAATTC
127490 -TTGCCAACCTAATGAAATTC
1 ATTGCCAACCTAATGAAATTC
127510 ATTG
1 ATTG
127514 AAAACGCCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 3 0.09
20 6 0.19
21 10 0.31
22 3 0.09
23 1 0.03
24 4 0.12
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (21 bp):
ATTGCCAACCTAATGAAATTC
Found at i:127493 original size:41 final size:41
Alignment explanation
Indices: 127448--127530 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
127438 AGCAATGGTG
127448 ATTGCCAACCTAATGAAATTCATTGAAAACGCCAAGTAGAA
1 ATTGCCAACCTAATGAAATTCATTGAAAACGCCAAGTAGAA
127489 ATTGCCAACCTAATGAAATTCATTGAAAACGCCAAGTAGAA
1 ATTGCCAACCTAATGAAATTCATTGAAAACGCCAAGTAGAA
127530 A
1 A
127531 CAGCCGAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (41 bp):
ATTGCCAACCTAATGAAATTCATTGAAAACGCCAAGTAGAA
Found at i:132063 original size:22 final size:21
Alignment explanation
Indices: 132022--132067 Score: 51
Period size: 21 Copynumber: 2.1 Consensus size: 21
132012 TTTATTCATC
132022 TTAATTTTTAATCATTTTAATA
1 TTAATTTTTAATCATTTTAA-A
132044 TTAA-TTTTAAGTC-TTCTTAAA
1 TTAATTTTTAA-TCATT-TTAAA
132065 TTA
1 TTA
132068 CATCAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATTTTTAATCATTTTAAA
Found at i:136676 original size:39 final size:40
Alignment explanation
Indices: 136621--136720 Score: 150
Period size: 39 Copynumber: 2.5 Consensus size: 40
136611 ATAAACACTC
136621 AATGGACACCTTTTGAAGAGTCACAACCC-TTTCATATT-
1 AATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTG
* *
136659 AGATGGACACCTTTTGAAAAGTCATAACCCTTTTCATATTG
1 A-ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTG
136700 AATGGACACCTTTTGGAAGAG
1 AATGGACACCTTTT-GAAGAG
136721 ACTTGTCTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.02
39 26 0.47
40 22 0.40
41 6 0.11
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (40 bp):
AATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTG
Found at i:141683 original size:40 final size:39
Alignment explanation
Indices: 141561--141698 Score: 240
Period size: 39 Copynumber: 3.5 Consensus size: 39
141551 TATGCACTTA
141561 ATGGACACCTTTTGAAGAGTCACAACCCTTTCATATTAG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTCATATTAG
*
141600 ATGGACACATTTTGAAGAGTCACAACCCTTTCATATTAG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTCATATTAG
*
141639 ATGGACACCTTTTGAAAAGTCACAACCCTTTTCATATTAG
1 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCATATTAG
141679 ATGGACACCTTTTGGAAGAG
1 ATGGACACCTTTT-GAAGAG
141699 ACTTGTCCCA
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 64 0.69
40 24 0.26
41 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (39 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTCATATTAG
Found at i:141691 original size:21 final size:21
Alignment explanation
Indices: 141628--141691 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
141618 GTCACAACCC
141628 TTTCATATTAGATGGACACCT
1 TTTCATATTAGATGGACACCT
* * *
141649 TTTGA-A-AAG-T-CACAACCCT
1 TTTCATATTAGATGGAC-A-CCT
141668 TTTCATATTAGATGGACACCT
1 TTTCATATTAGATGGACACCT
141689 TTT
1 TTT
141692 GGAAGAGACT
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 9 0.29
20 2 0.06
21 12 0.39
22 2 0.06
23 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCATATTAGATGGACACCT
Found at i:141856 original size:31 final size:31
Alignment explanation
Indices: 141843--141958 Score: 171
Period size: 31 Copynumber: 3.7 Consensus size: 31
141833 TAAACACTGG
*
141843 TACAAAGTACCTGATATAATATAGTCATCGA
1 TACATAGTACCTGATATAATATAGTCATCGA
* *
141874 TATATAGTACCTGATATAATATAGTCA-CTGG
1 TACATAGTACCTGATATAATATAGTCATC-GA
*
141905 TACATAGTACTTGATATAATATAGTCATCGA
1 TACATAGTACCTGATATAATATAGTCATCGA
*
141936 TACATAGTACCTGATACAATATA
1 TACATAGTACCTGATATAATATA
141959 ATCACAAGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.01
31 73 0.97
32 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (31 bp):
TACATAGTACCTGATATAATATAGTCATCGA
Found at i:141895 original size:17 final size:17
Alignment explanation
Indices: 141848--141898 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
141838 ACTGGTACAA
141848 AGTACCTGATATAATAT
1 AGTACCTGATATAATAT
*
141865 AGT-CATCG--AT-ATAT
1 AGTACCT-GATATAATAT
141879 AGTACCTGATATAATAT
1 AGTACCTGATATAATAT
141896 AGT
1 AGT
141899 CACTGGTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
16 4 0.15
17 11 0.41
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (17 bp):
AGTACCTGATATAATAT
Found at i:141970 original size:62 final size:62
Alignment explanation
Indices: 141821--141981 Score: 243
Period size: 62 Copynumber: 2.6 Consensus size: 62
141811 ACACATAATG
* * * *
141821 CCTGATACAATATAAACACTGGTACAAAGTACCTGATATAATATAGTCATCGATATATAGTA
1 CCTGATACAATATAATCACTGGTACATAGTACTTGATATAATATAGTCATCGATACATAGTA
* *
141883 CCTGATATAATATAGTCACTGGTACATAGTACTTGATATAATATAGTCATCGATACATAGTA
1 CCTGATACAATATAATCACTGGTACATAGTACTTGATATAATATAGTCATCGATACATAGTA
**
141945 CCTGATACAATATAATCACAAGTACATAGT-CTTGATA
1 CCTGATACAATATAATCACTGGTACATAGTACTTGATA
141982 CTTTAAAACC
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
61 7 0.08
62 82 0.92
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (62 bp):
CCTGATACAATATAATCACTGGTACATAGTACTTGATATAATATAGTCATCGATACATAGTA
Found at i:141971 original size:31 final size:31
Alignment explanation
Indices: 141821--141982 Score: 154
Period size: 31 Copynumber: 5.3 Consensus size: 31
141811 ACACATAATG
** *
141821 CCTGATACAATATAAACACTG-GTACAAAGTA
1 CCTGATACAATATAGTCAC-GAGTACATAGTA
* *
141852 CCTGATATAATATAGTCATCGA-TATATAGTA
1 CCTGATACAATATAGTCA-CGAGTACATAGTA
*
141883 CCTGATATAATATAGTCACTG-GTACATAGTA
1 CCTGATACAATATAGTCAC-GAGTACATAGTA
* *
141914 CTTGATATAATATAGTCATCGA-TACATAGTA
1 CCTGATACAATATAGTCA-CGAGTACATAGTA
* *
141945 CCTGATACAATATAATCACAAGTACATAGT-
1 CCTGATACAATATAGTCACGAGTACATAGTA
*
141975 CTTGATAC
1 CCTGATAC
141983 TTTAAAACCA
Statistics
Matches: 112, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
30 10 0.09
31 100 0.89
32 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (31 bp):
CCTGATACAATATAGTCACGAGTACATAGTA
Found at i:142345 original size:2 final size:2
Alignment explanation
Indices: 142338--142365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
142328 ACCAAAACTT
142338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142366 GAACAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:146897 original size:12 final size:12
Alignment explanation
Indices: 146861--146906 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
146851 TAAATTGTAA
146861 ATAATTAAAATT
1 ATAATTAAAATT
146873 -TCAATT-AAA-T
1 AT-AATTAAAATT
146883 ATAATTAAAATT
1 ATAATTAAAATT
146895 ATAATTATAAAT
1 ATAATTA-AAAT
146907 GCATAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 5 0.17
11 8 0.28
12 12 0.41
13 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATTAAAATT
Found at i:150665 original size:159 final size:156
Alignment explanation
Indices: 150363--150671 Score: 394
Period size: 159 Copynumber: 2.0 Consensus size: 156
150353 TCCTTCTCAG
* * * *
150363 TTTTGAAATTGAGCAATTTGGTCCCTCTAAAAATATTAGAGCAATTTAATCCTTGTCAATTTTGA
1 TTTTGAAATTGAGCAAATTGGTCCCTCTAAAAAAATCAGAGCAATTTAATCCTTATCAATTTTGA
* * * *
150428 AAGTGAACAACTAAGGATAGTTAATCACGATGTTAATATTTTCCATCAATTATATATTATTTTGA
66 AAGTGAACAACTAAGGACAATTAATCACGATGTTAATATTTTCCATCAATTATAAATGATTTTGA
* *
150493 TTGGTGTAATATCAAATTTAGATCAA
131 ATGGTGAAATATCAAATTTAGATCAA
*
150519 TTTTGAAATTGAGCAAATTGGTCCCTCTTAAAAAAATCGGAGCAATTTAATATCGC-TATCAATT
1 TTTTGAAATTGAGCAAATTGGTCCCTC-TAAAAAAATCAGAGCAATTT-A-ATC-CTTATCAATT
* *
150583 TTGAAAGTGAGCAACTGAA-GACAATTAATCACGATGTTAATA-TTTCTCATCAATTGTAAATGA
62 TTGAAAGTGAACAACT-AAGGACAATTAATCACGATGTTAATATTTTC-CATCAATTATAAATGA
150646 -TTTGTAATGGT-AAATTATCAAATTTA
125 TTTTG-AATGGTGAAA-TATCAAATTTA
150672 TCCCTTAAAG
Statistics
Matches: 132, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
156 26 0.20
157 17 0.13
158 11 0.08
159 75 0.57
160 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (156 bp):
TTTTGAAATTGAGCAAATTGGTCCCTCTAAAAAAATCAGAGCAATTTAATCCTTATCAATTTTGA
AAGTGAACAACTAAGGACAATTAATCACGATGTTAATATTTTCCATCAATTATAAATGATTTTGA
ATGGTGAAATATCAAATTTAGATCAA
Found at i:156023 original size:21 final size:22
Alignment explanation
Indices: 155999--156044 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
155989 TCTAGAATTA
155999 TAAAAAAACATA-AAAATTTAT
1 TAAAAAAACATATAAAATTTAT
* *
156020 T-AAAAAATATATATAATTTAT
1 TAAAAAAACATATAAAATTTAT
156041 TAAA
1 TAAA
156045 TTATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 9 0.43
21 10 0.48
22 2 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAAAACATATAAAATTTAT
Found at i:156024 original size:20 final size:21
Alignment explanation
Indices: 155996--156044 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
155986 CATTCTAGAA
*
155996 TTATAAAAAAACATA-AAAAT
1 TTATTAAAAAACATATAAAAT
* *
156016 TTATTAAAAAATATATATAAT
1 TTATTAAAAAACATATAAAAT
156037 TTATTAAA
1 TTATTAAA
156045 TTATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTATTAAAAAACATATAAAAT
Found at i:156412 original size:20 final size:19
Alignment explanation
Indices: 156374--156414 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
156364 TTTTTCATAA
**
156374 TTTTTATAATTTATTATGC
1 TTTTTATAATTTAAAATGC
156393 TTTTTATAATTTCAAAATGC
1 TTTTTATAATTT-AAAATGC
156413 TT
1 TT
156415 GATAAATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTATAATTTAAAATGC
Found at i:158634 original size:30 final size:30
Alignment explanation
Indices: 158600--158656 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
158590 ATTAATATTA
158600 ATTAATAA-CGAGTGATTAAAATAAAAAATT
1 ATTAA-AATCGAGTGATTAAAATAAAAAATT
** *
158630 ATTAAAATTTAGTGATTAAAATGAAAA
1 ATTAAAATCGAGTGATTAAAATAAAAA
158657 CAATACTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.32
Consensus pattern (30 bp):
ATTAAAATCGAGTGATTAAAATAAAAAATT
Found at i:169234 original size:12 final size:12
Alignment explanation
Indices: 169217--169341 Score: 93
Period size: 12 Copynumber: 10.8 Consensus size: 12
169207 ATAACATCCA
169217 AACAACAAAAAT
1 AACAACAAAAAT
* *
169229 AACAACCAAAAC
1 AACAACAAAAAT
* *
169241 AGCAGCAAAAAT
1 AACAACAAAAAT
169253 AACAAC----A-
1 AACAACAAAAAT
*
169260 AACAACATTAAA-
1 AACAACA-AAAAT
169272 AACAACAAAAAT
1 AACAACAAAAAT
* *
169284 AGCAACAAAAAC
1 AACAACAAAAAT
*
169296 AATAACAAAAAT
1 AACAACAAAAAT
* *
169308 AACAGCAAAAAC
1 AACAACAAAAAT
169320 AAC-ACAAAAAT
1 AACAACAAAAAT
169331 AACAACCAAAA
1 AACAA-CAAAA
169342 CAGTAAAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.07
8 1 0.01
11 12 0.14
12 62 0.72
13 5 0.06
ACGTcount: A:0.70, C:0.21, G:0.03, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:169250 original size:24 final size:20
Alignment explanation
Indices: 169199--169266 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 20
169189 GTAAAAACGC
*
169199 ACAA-AAAAATAACATCCAA
1 ACAACAAAAATAACAACCAA
169218 ACAACAAAAATAACAACCAAA
1 ACAACAAAAATAACAACC-AA
169239 ACAGCAGCAAAAATAACAA-CAA
1 ACA--A-CAAAAATAACAACCAA
169261 ACAACA
1 ACAACA
169267 TTAAAAACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
19 6 0.14
20 13 0.30
21 5 0.12
22 5 0.12
23 2 0.05
24 12 0.28
ACGTcount: A:0.68, C:0.24, G:0.03, T:0.06
Consensus pattern (20 bp):
ACAACAAAAATAACAACCAA
Found at i:169275 original size:55 final size:54
Alignment explanation
Indices: 169216--169320 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 54
169206 AATAACATCC
* * *
169216 AAACAACAAAAATAACAACCAAAACAGCAGCAAAAATAACAACAAACAACATTAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAA-AACATTAA
* * *
169271 AAACAACAAAAATAGCAACAAAAACAATAACAAAAATAACAGCAAAAACA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAAAACA
169321 ACACAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 4 0.09
55 40 0.91
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (54 bp):
AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAAAACATTAA
Found at i:169276 original size:43 final size:43
Alignment explanation
Indices: 169203--169304 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
169193 AAACGCACAA
* * *
169203 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAGCAGC
1 AAAAATAACA-ACAAACAACAAAAATAACAACAAAAACAGCAAC
* *
169247 AAAAATAACAACAAACAACATTAAA-AACAACAAAAATAGCAAC
1 AAAAATAACAACAAACAACA-AAAATAACAACAAAAACAGCAAC
* *
169290 AAAAACAATAACAAA
1 AAAAATAACAACAAA
169305 AATAACAGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 37 0.74
44 13 0.26
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.08
Consensus pattern (43 bp):
AAAAATAACAACAAACAACAAAAATAACAACAAAAACAGCAAC
Found at i:169302 original size:24 final size:24
Alignment explanation
Indices: 169275--169362 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 24
169265 CATTAAAAAC
*
169275 AACAAAAATAGCAACAAAAACAAT
1 AACAAAAATAACAACAAAAACAAT
*
169299 AACAAAAATAACAGCAAAAACAA-
1 AACAAAAATAACAACAAAAACAAT
* * *
169322 CACAAAAATAACAACCAAAACAGT
1 AACAAAAATAACAACAAAAACAAT
*
169346 AA-AAAAA-AACACCAAAA
1 AACAAAAATAACAACAAAA
169363 CAACAATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 8 0.15
23 24 0.44
24 22 0.41
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.06
Consensus pattern (24 bp):
AACAAAAATAACAACAAAAACAAT
Found at i:169368 original size:47 final size:47
Alignment explanation
Indices: 169250--169367 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 47
169240 CAGCAGCAAA
* ** *
169250 AATAACAACAAACAACATTAAAAAC-A-ACAAAAATAGCAACAAAAAC
1 AATAACAA-AAATAACACCAAAAACAACACAAAAATAACAACAAAAAC
* *
169296 AATAACAAAAATAACAGCAAAAACAACACAAAAATAACAACCAAAAC
1 AATAACAAAAATAACACCAAAAACAACACAAAAATAACAACAAAAAC
*
169343 AGTAA-AAAAA-AACACC-AAAACAACA
1 AATAACAAAAATAACACCAAAAACAACA
169368 ATATAATTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
44 9 0.14
45 18 0.29
46 14 0.22
47 22 0.35
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (47 bp):
AATAACAAAAATAACACCAAAAACAACACAAAAATAACAACAAAAAC
Found at i:176054 original size:23 final size:22
Alignment explanation
Indices: 176011--176055 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
176001 AATCTCTTTT
*
176011 AATTTTTATATTAATTCTTTCA
1 AATTTTTATATGAATTCTTTCA
* *
176033 AATTTATTATATGATTTTTTTCA
1 AATTT-TTATATGAATTCTTTCA
176056 CCTACAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTTATATGAATTCTTTCA
Found at i:181074 original size:154 final size:154
Alignment explanation
Indices: 180898--181205 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
180888 CATAAAAAAT
180898 TTAGATGACCAAAATAGAAATACACTAATAATTGAGTGACTATCCGAAGAGTTTACCCATAACTT
1 TTAGATGACCAAAATAGAAATACACTAATAATTGAGTGACTATCCGAAGAGTTTACCCATAACTT
180963 TATACCAATAGCAGCAATAATAATAATAATTCATAAAAATAATTATAAATAAATAAAAGGAAAAA
66 TATACCAATAGCAGCAATAATAATAATAATTCATAAAAATAATTATAAATAAATAAAAGGAAAAA
181028 CCTGCAGAGAGCTTTCATCTCGTC
131 CCTGCAGAGAGCTTTCATCTCGTC
181052 TTAGATGACCAAAATAGAAATACACTAATAATTGAGTGACTATCCGAAGAGTTTACCCATAACTT
1 TTAGATGACCAAAATAGAAATACACTAATAATTGAGTGACTATCCGAAGAGTTTACCCATAACTT
*
181117 TATCCCAATAGCAGCAATAATAATAATAATTCATAAAAATAATTATAAATAAATAAAAGGAAAAA
66 TATACCAATAGCAGCAATAATAATAATAATTCATAAAAATAATTATAAATAAATAAAAGGAAAAA
181182 CCTGCAGAGAGCTTTCATCTCGTC
131 CCTGCAGAGAGCTTTCATCTCGTC
181206 AATCCAACCA
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.27
Consensus pattern (154 bp):
TTAGATGACCAAAATAGAAATACACTAATAATTGAGTGACTATCCGAAGAGTTTACCCATAACTT
TATACCAATAGCAGCAATAATAATAATAATTCATAAAAATAATTATAAATAAATAAAAGGAAAAA
CCTGCAGAGAGCTTTCATCTCGTC
Found at i:181456 original size:3 final size:3
Alignment explanation
Indices: 181448--181477 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
181438 TGTTTGTATT
181448 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
181478 ACGACTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:189001 original size:15 final size:14
Alignment explanation
Indices: 188975--189017 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
188965 TTTTTAAAAC
188975 ATATAAAAATTAAA
1 ATATAAAAATTAAA
188989 AT-TAACCAAATTAAA
1 ATATAA--AAATTAAA
189004 ATATAAAAATTAAA
1 ATATAAAAATTAAA
189018 TCTACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 10 0.38
15 10 0.38
16 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATAAAAATTAAA
Found at i:195882 original size:19 final size:18
Alignment explanation
Indices: 195829--195888 Score: 102
Period size: 18 Copynumber: 3.3 Consensus size: 18
195819 AATGTCAATG
195829 GTCAACAGGTCGATCAAA
1 GTCAACAGGTCGATCAAA
*
195847 GTTAACAGGTCGATCAAA
1 GTCAACAGGTCGATCAAA
195865 GTCAACAGGTCAGATCAAA
1 GTCAACAGGTC-GATCAAA
195884 GTCAA
1 GTCAA
195889 TGAGTCGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 27 0.69
19 12 0.31
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (18 bp):
GTCAACAGGTCGATCAAA
Found at i:196483 original size:10 final size:10
Alignment explanation
Indices: 196454--196483 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
196444 AGGCTGGTCG
*
196454 AAAAAGGAGG
1 AAAAAGGAGA
196464 AAAAAGGAGA
1 AAAAAGGAGA
196474 AAAAAGGAGA
1 AAAAAGGAGA
196484 GGTCGACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
AAAAAGGAGA
Found at i:198340 original size:16 final size:16
Alignment explanation
Indices: 198316--198382 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
198306 AATATTATTA
*
198316 AATTGTATTTAATAAT
1 AATTATATTTAATAAT
198332 AATTATA-TTAA-AAT
1 AATTATATTTAATAAT
** *
198346 ATGATTA-ATTTTTTATT
1 A--ATTATATTTAATAAT
198363 AAATTATATTTAATAAT
1 -AATTATATTTAATAAT
198380 AAT
1 AAT
198383 CTTATTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
14 4 0.11
15 5 0.13
16 19 0.50
17 9 0.24
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:199870 original size:16 final size:17
Alignment explanation
Indices: 199837--199873 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
199827 ATATCTATAA
*
199837 AAATTGTAAAAATATTT
1 AAATTATAAAAATATTT
199854 AAATTATAAAAAT-TTT
1 AAATTATAAAAATATTT
199870 AAAT
1 AAAT
199874 AATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAATTATAAAAATATTT
Found at i:199917 original size:19 final size:20
Alignment explanation
Indices: 199844--199922 Score: 57
Period size: 19 Copynumber: 4.3 Consensus size: 20
199834 TAAAAATTGT
*
199844 AAAAATATTT--AAAT-TAT
1 AAAAATATTTAAAAATATAA
*
199861 AAAAAT-TTTAAATAAT-T-G
1 AAAAATATTTAAA-AATATAA
*
199879 AAAAA-ATTTAAAAATGTAA
1 AAAAATATTTAAAAATATAA
*
199898 ACAAATATTTAAAAA-ATAA
1 AAAAATATTTAAAAATATAA
199917 AAAAAT
1 AAAAAT
199923 CCAAGATCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.06
17 9 0.18
18 13 0.26
19 16 0.32
20 9 0.18
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAATATTTAAAAATATAA
Found at i:201537 original size:7 final size:8
Alignment explanation
Indices: 201521--201546 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
201511 AAGCTTAAGC
201521 TTTTATTT
1 TTTTATTT
201529 TTTTATTT
1 TTTTATTT
201537 TTTTATTT
1 TTTTATTT
201545 TT
1 TT
201547 ACAGATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:208590 original size:21 final size:22
Alignment explanation
Indices: 208521--208620 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 22
208511 CACTAGCGCA
* * *
208521 CTCTCTGTTTAGCACGTCTCGTG
1 CTCTCTGATTAACACGTGT-GTG
*
208544 CTCTCTGTTATTATCACTTGTGTGTG
1 CTCTCTG--ATTAACAC--GTGTGTG
*
208570 CTCTCTGATTAATAC-TGTGTG
1 CTCTCTGATTAACACGTGTGTG
*
208591 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGATTAACAC-GTGTGTG
208614 CTCTCTG
1 CTCTCTG
208621 TTGCCCAGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
21 19 0.30
23 20 0.31
24 6 0.09
25 6 0.09
26 10 0.16
27 3 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (22 bp):
CTCTCTGATTAACACGTGTGTG
Found at i:208596 original size:23 final size:23
Alignment explanation
Indices: 208541--208620 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 23
208531 AGCACGTCTC
*
208541 GTGCTCTCTGTTATTATCACTTGTGT
1 GTGCTCTCTG--ATTAACAC-TGTGT
*
208567 GTGCTCTCTGATTAATAC--TGT
1 GTGCTCTCTGATTAACACTGTGT
*
208588 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAACACTGTGT
208611 GTGCTCTCTG
1 GTGCTCTCTG
208621 TTGCCCAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 19 0.40
23 13 0.27
24 6 0.12
26 10 0.21
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAACACTGTGT
Found at i:208654 original size:21 final size:21
Alignment explanation
Indices: 208564--208668 Score: 79
Period size: 21 Copynumber: 4.7 Consensus size: 21
208554 TTATCACTTG
**
208564 TGTGTGCTCTCTGATTAATAC-
1 TGTGTGCTCTCTG-TTAGCACT
208585 TGTGTGCTCTCTGATTAGCACT
1 TGTGTGCTCTCTG-TTAGCACT
208607 GTGTGTGCTCTCTGTTGCCCAGCACT
1 -TGTGTGCTCTCTGTT----AGCACT
* *
208633 TATGTGCTCTCTGTTAGTACT
1 TGTGTGCTCTCTGTTAGCACT
*
208654 T-TGGTACTCTCTGTT
1 TGT-GTGCTCTCTGTT
208669 TGTTCCGTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
20 1 0.01
21 36 0.50
22 2 0.03
23 13 0.18
25 14 0.19
26 6 0.08
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (21 bp):
TGTGTGCTCTCTGTTAGCACT
Found at i:211086 original size:12 final size:12
Alignment explanation
Indices: 211064--211134 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
211054 TTAAGATAAT
211064 TATTAAA-TTAA
1 TATTAAATTTAA
211075 TATTAAATTTAA
1 TATTAAATTTAA
211087 TA-TAATACTTATTAA
1 TATTAA-A--T-TTAA
*
211102 GA-TAAATATT-A
1 TATTAAAT-TTAA
*
211113 GATTAAATTTAA
1 TATTAAATTTAA
211125 TATTAAATTT
1 TATTAAATTT
211135 TATTAACTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 15 0.29
12 26 0.51
14 2 0.04
15 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (12 bp):
TATTAAATTTAA
Found at i:211086 original size:17 final size:16
Alignment explanation
Indices: 211065--211197 Score: 64
Period size: 17 Copynumber: 8.3 Consensus size: 16
211055 TAAGATAATT
211065 ATTAAATTAATATTAA
1 ATTAAATTAATATTAA
*
211081 ATTTAATATAATACTT--
1 ATTAAAT-TAATA-TTAA
* *
211097 ATTAAGATAAATATTAG
1 ATTAA-ATTAATATTAA
211114 ATTAAATTTAATATTAA
1 ATTAAA-TTAATATTAA
** *
211131 ATTTTATTAA-CTT-A
1 ATTAAATTAATATTAA
* *
211145 A-TAAATTATTTATTTAC
1 ATTAAATTA-ATA-TTAA
* *
211162 A--AAATAAACATTAA
1 ATTAAATTAATATTAA
211176 ATTAAATTTAATATTAA
1 ATTAAA-TTAATATTAA
211193 ATTAA
1 ATTAA
211198 TAAAATATTA
Statistics
Matches: 85, Mismatches: 19, Indels: 25
0.66 0.15 0.19
Matches are distributed among these distances:
13 5 0.06
14 6 0.07
15 5 0.06
16 29 0.34
17 38 0.45
18 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTAAATTAATATTAA
Found at i:211126 original size:33 final size:32
Alignment explanation
Indices: 211063--211126 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
211053 ATTAAGATAA
* *
211063 TTATTAAATTAATATTAAATTTAATATAATAC
1 TTATTAAATAAATATTAAATTAAATATAATAC
* *
211095 TTATTAAGATAAATATTAGATTAAATTTAATA
1 TTATTAA-ATAAATATTAAATTAAATATAATA
211127 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
TTATTAAATAAATATTAAATTAAATATAATAC
Found at i:211843 original size:21 final size:20
Alignment explanation
Indices: 211808--211847 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
211798 TATAATAAAA
211808 ATAAATTTAAAATAAAATAT
1 ATAAATTTAAAATAAAATAT
*
211828 ATAAATATTAATATAAAATA
1 ATAAAT-TTAAAATAAAATA
211848 CTATTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATTTAAAATAAAATAT
Found at i:217242 original size:2 final size:2
Alignment explanation
Indices: 217237--217261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
217227 ATTTTATTTA
217237 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 A
217262 AAATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:223379 original size:32 final size:32
Alignment explanation
Indices: 223343--223406 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
223333 TCTTCCTAGT
223343 ATAAATCATGCTCATTAACCACTTTCTCTTTC
1 ATAAATCATGCTCATTAACCACTTTCTCTTTC
223375 ATAAATCATGCTCATTAACCACTTTCTCTTTC
1 ATAAATCATGCTCATTAACCACTTTCTCTTTC
223407 TTAGTGGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (32 bp):
ATAAATCATGCTCATTAACCACTTTCTCTTTC
Found at i:230463 original size:29 final size:30
Alignment explanation
Indices: 230416--230495 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 30
230406 CCCTTCAATT
230416 TTTTTGTAAATTCTCATTAAGC-C-TCTAAAA
1 TTTTTG-AAATTCTCATTAAGCTCGTC-AAAA
* *
230446 -TTTTGAAAGTTCTAATTATGCTCGTCAAAA
1 TTTTTGAAA-TTCTCATTAAGCTCGTCAAAA
230476 TTTTTGAAAATTCTCATTAA
1 TTTTTG-AAATTCTCATTAA
230496 ATCCCCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 3 0.07
29 15 0.37
30 5 0.12
31 15 0.37
32 3 0.07
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (30 bp):
TTTTTGAAATTCTCATTAAGCTCGTCAAAA
Found at i:247555 original size:98 final size:97
Alignment explanation
Indices: 247384--247572 Score: 247
Period size: 98 Copynumber: 1.9 Consensus size: 97
247374 TGGAAAAAGA
* * *
247384 TATTCGATTACCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATC
1 TATTCGATTACCTCGATTTGAAGAAAAATCGCACCGAGTAAGTTAAGGCACAAATTTTCAAAATC
*
247449 AGAGAT-AAAGAAACATTGCCTCGATTAAAGGG
66 AGAAATAAAAG-AACATTGCCTCGATTAAAGGG
** * *
247481 TATTCGATTATTTCGATTTGAAGAAAAAATTGCGCCGAGTAAGTTAAGGCACAAATTTTCAAAAC
1 TATTCGATTACCTCGATTTGAAG-AAAAATCGCACCGAGTAAGTTAAGGCACAAATTTTCAAAA-
* *
247546 TC-GAAATAAAAGAATATTGCCTTGATT
64 TCAGAAATAAAAGAACATTGCCTCGATT
247573 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
97 21 0.27
98 52 0.66
99 6 0.08
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (97 bp):
TATTCGATTACCTCGATTTGAAGAAAAATCGCACCGAGTAAGTTAAGGCACAAATTTTCAAAATC
AGAAATAAAAGAACATTGCCTCGATTAAAGGG
Found at i:247929 original size:30 final size:29
Alignment explanation
Indices: 247892--248011 Score: 111
Period size: 30 Copynumber: 4.1 Consensus size: 29
247882 AAAATTTTAC
247892 ATTCGAGGGTAAAATGGTAATTTTTGAAA
1 ATTCGAGGGTAAAATGGTAATTTTTGAAA
* * *
247921 AGTTCGAGGTTTAACATGG-AATTTTT-AGAC
1 A-TTCGAGG-GTAAAATGGTAATTTTTGA-AA
* * *
247951 ATCCGAAGGTAAAATGGTAATTTTGGAAA
1 ATTCGAGGGTAAAATGGTAATTTTTGAAA
*
247980 AATCG-GGGTCAAAAATGGTAATTTTTGAAA
1 ATTCGAGGGT--AAAATGGTAATTTTTGAAA
248010 AT
1 AT
248012 AAATTTATAA
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
28 10 0.14
29 17 0.24
30 36 0.51
31 7 0.10
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (29 bp):
ATTCGAGGGTAAAATGGTAATTTTTGAAA
Found at i:247972 original size:59 final size:57
Alignment explanation
Indices: 247846--247996 Score: 169
Period size: 57 Copynumber: 2.6 Consensus size: 57
247836 CCCAGGGGCC
* * * *
247846 AAATGGTAATTTTGGGAAAGTTCGGGGTCAAAAATGAAAATTTTACATTCGAGGGTA
1 AAATGGTAATTTTGGAAAAGTTCGAGGTCAAAAATGAAAATTTTACATCCGAAGGTA
* ** * * *
247903 AAATGGTAATTTTTGAAAAGTTCGAGGTTTAACATGGAATTTTTAGACATCCGAAGGTA
1 AAATGGTAATTTTGGAAAAGTTCGAGGTCAAAAATGAAAATTTT--ACATCCGAAGGTA
* *
247962 AAATGGTAATTTTGGAAAA-ATCGGGGTCAAAAATG
1 AAATGGTAATTTTGGAAAAGTTCGAGGTCAAAAATG
247997 GTAATTTTTG
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
57 36 0.47
58 11 0.14
59 29 0.38
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (57 bp):
AAATGGTAATTTTGGAAAAGTTCGAGGTCAAAAATGAAAATTTTACATCCGAAGGTA
Found at i:248003 original size:59 final size:56
Alignment explanation
Indices: 247846--248005 Score: 176
Period size: 59 Copynumber: 2.8 Consensus size: 56
247836 CCCAGGGGCC
* * * * *
247846 AAATGGTAATTTTGGGAAAGTTCGGGGTCAAAAATGAAAATTTTACATTCGAGGGTA
1 AAATGGTAATTTT-GGAAAATTCGGGGTCAAAAATGGAATTTTTACATCCGAAGGTA
* * ** *
247903 AAATGGTAATTTTTGAAAAGTTCGAGGTTTAACATGGAATTTTTAGACATCCGAAGGTA
1 AAATGGTAATTTTGGAAAA-TTCGGGGTCAAAAATGGAATTTTT--ACATCCGAAGGTA
*
247962 AAATGGTAATTTTGGAAAAATCGGGGTCAAAAATGGTAATTTTT
1 AAATGGTAATTTTGGAAAATTCGGGGTCAAAAATGG-AATTTTT
248006 GAAAATAAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
56 4 0.05
57 31 0.37
58 12 0.14
59 36 0.43
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (56 bp):
AAATGGTAATTTTGGAAAATTCGGGGTCAAAAATGGAATTTTTACATCCGAAGGTA
Found at i:248074 original size:14 final size:13
Alignment explanation
Indices: 248054--248097 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
248044 ATTTTTAAAC
248054 TTTTTTTTCATTT
1 TTTTTTTTCATTT
248067 TTTATTTTTACAGTTT
1 TTT-TTTTT-CA-TTT
*
248083 TTTTTTTACATTT
1 TTTTTTTTCATTT
248096 TT
1 TT
248098 GTACTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 8 0.30
14 7 0.26
15 6 0.22
16 6 0.22
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCATTT
Found at i:248925 original size:20 final size:20
Alignment explanation
Indices: 248888--248926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
248878 TGATAAATGT
**
248888 TAACATATCATGTCATCAAC
1 TAACATATCACATCATCAAC
*
248908 TAACATATCACATTATCAA
1 TAACATATCACATCATCAA
248927 TAATGTGGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (20 bp):
TAACATATCACATCATCAAC
Found at i:252070 original size:53 final size:53
Alignment explanation
Indices: 251988--252094 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
251978 ATTTATAACC
*
251988 ATGGAAGTCTCAAAAGAAAATCACGCCCCTTCCCTCTCTATACATACCAGCTT
1 ATGGAAGTCTCAAAAGAAAATCACACCCCTTCCCTCTCTATACATACCAGCTT
*
252041 ATGGAAGTCTCAAAAGAAGATCACACCCCTTCCCTCTCTATACATACCAGCTT
1 ATGGAAGTCTCAAAAGAAAATCACACCCCTTCCCTCTCTATACATACCAGCTT
252094 A
1 A
252095 ATGCAAATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (53 bp):
ATGGAAGTCTCAAAAGAAAATCACACCCCTTCCCTCTCTATACATACCAGCTT
Found at i:263867 original size:47 final size:46
Alignment explanation
Indices: 263763--263869 Score: 115
Period size: 52 Copynumber: 2.2 Consensus size: 46
263753 TTTGTAACAA
* * *
263763 TTTTAATCCTCAACAGTTATACATTATATTAATTTTATTTTGATTT
1 TTTTAACCCTCAACAGTTATACATTATATTAATTTTATTTTCAGTT
*
263809 TAAAAAATTTAACCCTCAACATTTATACATTATATTAATTTTATTTTACAGTT
1 T------TTTAACCCTCAACAGTTATACATTATATTAATTTTATTTT-CAGTT
263862 TTTTAACC
1 TTTTAACC
263870 ATTTCACCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
46 1 0.02
47 7 0.14
52 38 0.76
53 4 0.08
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.50
Consensus pattern (46 bp):
TTTTAACCCTCAACAGTTATACATTATATTAATTTTATTTTCAGTT
Found at i:268646 original size:19 final size:20
Alignment explanation
Indices: 268624--268666 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
268614 TCTCTCAACA
268624 AATTAAAAAAAAATC-AAAT
1 AATTAAAAAAAAATCAAAAT
** *
268643 AATTTTAAAAAAGTCAAAAT
1 AATTAAAAAAAAATCAAAAT
268663 AATT
1 AATT
268667 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (20 bp):
AATTAAAAAAAAATCAAAAT
Found at i:268654 original size:20 final size:22
Alignment explanation
Indices: 268629--268673 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
268619 CAACAAATTA
268629 AAAAAAAATC-AAATAA-TTTT
1 AAAAAAAATCAAAATAATTTTT
*
268649 -AAAAAAGTCAAAATAATTTTT
1 AAAAAAAATCAAAATAATTTTT
268670 AAAA
1 AAAA
268674 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 4 0.19
22 3 0.14
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAAAAATCAAAATAATTTTT
Found at i:268687 original size:18 final size:19
Alignment explanation
Indices: 268639--268694 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
268629 AAAAAAAATC
* * *
268639 AAATAATTTTAAAAAAGTCA
1 AAATAATTTT-TAAAATTTA
268659 AAATAATTTTTAAAATTTA
1 AAATAATTTTTAAAATTTA
268678 AAAT-ATTTTTAAAATTT
1 AAATAATTTTTAAAATTT
268695 TCAAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 13 0.39
19 10 0.30
20 10 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATAATTTTTAAAATTTA
Found at i:272548 original size:45 final size:45
Alignment explanation
Indices: 272484--272575 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
272474 TTCGAGAGTA
272484 TGTCGAAAAATTACTATGGAAAAAAGAGTTGGCCTGTGAAAGAAT
1 TGTCGAAAAATTACTATGGAAAAAAGAGTTGGCCTGTGAAAGAAT
272529 TGTCGAAAAATTACTATGGAAAAAAGAGTTGGCCTGTGAAAGAAT
1 TGTCGAAAAATTACTATGGAAAAAAGAGTTGGCCTGTGAAAGAAT
272574 TG
1 TG
272576 GGCTTTTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (45 bp):
TGTCGAAAAATTACTATGGAAAAAAGAGTTGGCCTGTGAAAGAAT
Found at i:273095 original size:31 final size:29
Alignment explanation
Indices: 273059--273144 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 29
273049 GATTAAATCA
*
273059 AAATTAAAGTGTCAAGTATACATTTGAACC
1 AAATTAAAGT-TCAAGTATACAATTGAACC
* * * *
273089 ACAATTAGAGTTTCACGTATATAATTGCACC
1 A-AATTAAAG-TTCAAGTATACAATTGAACC
* *
273120 AAATTAAAATTCATGTATACAATTG
1 AAATTAAAGTTCAAGTATACAATTG
273145 CATATTAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
29 14 0.31
30 7 0.16
31 23 0.51
32 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (29 bp):
AAATTAAAGTTCAAGTATACAATTGAACC
Found at i:273137 original size:29 final size:30
Alignment explanation
Indices: 273100--273169 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
273090 CAATTAGAGT
* *
273100 TTCACGTATATAATTGCACCA-AATT-AAAA
1 TTCATGTATACAATTGCA-CATAATTCAAAA
*
273129 TTCATGTATACAATTGCATATTAATTCAAAA
1 TTCATGTATACAATTGCACA-TAATTCAAAA
273160 TTCATGTATA
1 TTCATGTATA
273170 ATTTAGAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 16 0.46
30 4 0.11
31 14 0.40
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (30 bp):
TTCATGTATACAATTGCACATAATTCAAAA
Found at i:276154 original size:40 final size:44
Alignment explanation
Indices: 276073--276154 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 44
276063 AATATATTTA
*
276073 TATTAAATTGTTTTAATATATAATAATTTTATATATTTTTTATT
1 TATTAAATTGTTTTAATATATAATAATCTTATATATTTTTTATT
*
276117 TATTAAA-T-TTTTAATATA-AA-CATCTTA-ATATTATTTTA
1 TATTAAATTGTTTTAATATATAATAATCTTATATATT-TTTTA
276155 ATATTTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 5 0.14
40 10 0.29
41 2 0.06
42 10 0.29
43 1 0.03
44 7 0.20
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (44 bp):
TATTAAATTGTTTTAATATATAATAATCTTATATATTTTTTATT
Found at i:277383 original size:14 final size:13
Alignment explanation
Indices: 277357--277381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277347 GCAGTGGTTT
277357 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
277370 TTTTTTTCTTTT
1 TTTTTTTCTTTT
277382 TCCATTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Done.