Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold266
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: 653600
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 22668 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:478 original size:6 final size:6
Alignment explanation
Indices: 467--495 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
457 TGGCATCTCC
467 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
496 ATCCTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:6522 original size:21 final size:21
Alignment explanation
Indices: 6498--6543 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6488 GGGCTTCTAC
* *
6498 ATTAATTATTTATAAAATTTA
1 ATTAAATATTAATAAAATTTA
* *
6519 ATTAAATATTAATACAATTTT
1 ATTAAATATTAATAAAATTTA
6540 ATTA
1 ATTA
6544 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAAATATTAATAAAATTTA
Found at i:11920 original size:36 final size:38
Alignment explanation
Indices: 11878--11959 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
11868 TATAGTATTA
* *
11878 TATATTATG-ATTTTCGTAAATT-TATATAAGAATAAT
1 TATATTAAGAATTTTAGTAAATTATATATAAGAATAAT
* * *
11914 TATATTAAGAATTTTATTAAATTATATTTAATAATAAT
1 TATATTAAGAATTTTAGTAAATTATATATAAGAATAAT
*
11952 TATGTTAA
1 TATATTAA
11960 AATATGATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 8 0.21
37 11 0.29
38 19 0.50
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (38 bp):
TATATTAAGAATTTTAGTAAATTATATATAAGAATAAT
Found at i:11950 original size:38 final size:37
Alignment explanation
Indices: 11894--11975 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
11884 ATGATTTTCG
* *
11894 TAAATT-TATATAAGAATAATTATATTAAGAATTTTAT
1 TAAATTATATATAAGAATAATTATATTAA-AATATGAT
* * *
11931 TAAATTATATTTAATAATAATTATGTTAAAATATGAT
1 TAAATTATATATAAGAATAATTATATTAAAATATGAT
11968 TAAATTAT
1 TAAATTAT
11976 TTATTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 20 0.51
38 19 0.49
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (37 bp):
TAAATTATATATAAGAATAATTATATTAAAATATGAT
Found at i:14285 original size:25 final size:23
Alignment explanation
Indices: 14257--14304 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
14247 ACACACACAT
14257 AAATTTTAAAAATGAAAAATAGAGG
1 AAATTTTAAAAAT-AAAAA-AGAGG
* *
14282 AAATTTTCAAACTAAAAAAGAGG
1 AAATTTTAAAAATAAAAAAGAGG
14305 GCTCAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (23 bp):
AAATTTTAAAAATAAAAAAGAGG
Found at i:14732 original size:132 final size:132
Alignment explanation
Indices: 14495--14744 Score: 387
Period size: 132 Copynumber: 1.9 Consensus size: 132
14485 AGAAAAATAG
* * * *
14495 ATAGAAGAGATGAACAAGAGAAGGCGGCGTCTATCGGTTGAGAGAGCCAGATATTTAAAGGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
*
14560 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATTATGACAAATTTAACCTTTTACCTCTTCTAT
66 GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
14625 CA
131 CA
* *
14627 ATAGAAGAGATGAACAGGAGAAGGCGGCGGAC-AACGGTTAAGATAGCCAGATATTTAAAGGGAA
1 ATAGAAGAGATGAACAAGAGAAGGCGGC-GACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAA
* *
14691 AGAAATGAGAAGGTATAGGGTTTAA-TATTAGGTGTAATGACAATTTTAACCTTT
65 AGAAATGAGAAGGTATAGGGTTTAAGT-TTAGGTATAATGACAAATTTAACCTTT
14745 AATTTTTACA
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
131 1 0.01
132 104 0.97
133 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.26
Consensus pattern (132 bp):
ATAGAAGAGATGAACAAGAGAAGGCGGCGACTAACGGTTAAGAGAGCCAGATATTTAAAGGGAAA
GAAATGAGAAGGTATAGGGTTTAAGTTTAGGTATAATGACAAATTTAACCTTTTACCTCTTCTAT
CA
Found at i:19184 original size:30 final size:27
Alignment explanation
Indices: 19127--19192 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 27
19117 AAAATTGATG
*
19127 TTTTTTTTTTTTTTGCTTTCTTGTTGT
1 TTTTTTTTTTTTTTGCTTTCTTCTTGT
19154 TTTTTTATTGTTTTGTTGCTATT-TTCTTGT
1 TTTTTT-TT-TTTT-TTGCT-TTCTTCTTGT
19184 TTTTTTTTT
1 TTTTTTTTT
19193 CACTATTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 3 0.09
29 6 0.18
30 17 0.50
31 2 0.06
ACGTcount: A:0.03, C:0.06, G:0.11, T:0.80
Consensus pattern (27 bp):
TTTTTTTTTTTTTTGCTTTCTTCTTGT
Found at i:19202 original size:34 final size:33
Alignment explanation
Indices: 19143--19218 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 33
19133 TTTTTTTTGC
* * * *
19143 TTTCTTGTTGTTTTTTTATTGTTTTGTTGCTAT
1 TTTCTTGTTGTTTTTTTACTATTTTGCTACTAT
*
19176 TTTCTTGTTTTTTTTTTCACTATTTTGCTACTAT
1 TTTCTTGTTGTTTTTTT-ACTATTTTGCTACTAT
*
19210 TTTGTTGTT
1 TTTCTTGTT
19219 ATTGTTTGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.44
34 20 0.56
ACGTcount: A:0.08, C:0.09, G:0.12, T:0.71
Consensus pattern (33 bp):
TTTCTTGTTGTTTTTTTACTATTTTGCTACTAT
Found at i:25195 original size:19 final size:20
Alignment explanation
Indices: 25171--25215 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
25161 TTGAATTCGT
*
25171 AAAAAACAACAAAAA-AGTA
1 AAAAAACAACAAAAATAATA
* *
25190 AAAAAATAATAAAAATAATA
1 AAAAAACAACAAAAATAATA
25210 AAAAAA
1 AAAAAA
25216 ACGTCAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAAACAACAAAAATAATA
Found at i:31838 original size:18 final size:17
Alignment explanation
Indices: 31805--31843 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31795 TTTTATAAAT
31805 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
31823 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
31840 TGTG
1 TGTG
31844 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:32096 original size:23 final size:23
Alignment explanation
Indices: 32069--32190 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
32059 AGTGTTATTG
32069 ATCAGTGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
32091 ATTCAGTGGTAGCTACGGCTCCAT
1 A-TCAGTGGTAGCTTCGGCTACAT
*
32115 ATCAGTGGTAGCTTCGGCTCCAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
32138 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
32161 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
32184 ATCAGTG
1 ATCAGTG
32191 TGGCACTTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
22 1 0.01
23 86 0.98
24 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:32122 original size:46 final size:46
Alignment explanation
Indices: 32069--32190 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
32059 AGTGTTATTG
*
32069 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTCCAT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
* * *
32115 ATCAGTGGTAGCTTCGGCTCCATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
32161 ATCAGTGGTAGCTTCGGCTAC-ATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACAAT-TCAGTG
32191 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 68 0.99
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGGCTACAT
Found at i:39312 original size:14 final size:15
Alignment explanation
Indices: 39283--39316 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
39273 ATATTTGGAA
*
39283 AAATACTCATAGGTG
1 AAATACTCATAAGTG
39298 AAATAC-CATAAGTG
1 AAATACTCATAAGTG
39312 AAATA
1 AAATA
39317 TGTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (15 bp):
AAATACTCATAAGTG
Found at i:39788 original size:31 final size:31
Alignment explanation
Indices: 39746--39808 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
39736 CACCAAAGTA
39746 AGTTACCTGTAAATAATAGCAATATATTTTT
1 AGTTACCTGTAAATAATAGCAATATATTTTT
*
39777 AGTTACTTGTAAATAATAGCAATATATTTTT
1 AGTTACCTGTAAATAATAGCAATATATTTTT
39808 A
1 A
39809 TAAATTGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTACCTGTAAATAATAGCAATATATTTTT
Found at i:40122 original size:22 final size:23
Alignment explanation
Indices: 40070--40144 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
40060 AGTATTATTG
40070 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
40093 TTCAGTGGTAGCTACGGCTAC-T
1 ATCAGTGGTAGCTTCGGCTACAT
40115 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40138 ATCAGTG
1 ATCAGTG
40145 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 20 0.43
23 27 0.57
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:45502 original size:19 final size:18
Alignment explanation
Indices: 45480--45515 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45470 ATAGTTTGAT
45480 ATTCGAATTATTCGAATTA
1 ATTCGAATTA-TCGAATTA
*
45499 ATTCGAGTTATCGAATT
1 ATTCGAATTATCGAATT
45516 CGAAAGCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (18 bp):
ATTCGAATTATCGAATTA
Found at i:45588 original size:9 final size:9
Alignment explanation
Indices: 45571--45601 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
45561 TCGAGTTGAT
45571 TCGAATAAC
1 TCGAATAAC
*
45580 TCGATTAAC
1 TCGAATAAC
45589 TCGAATAAC
1 TCGAATAAC
45598 TCGA
1 TCGA
45602 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:48730 original size:2 final size:2
Alignment explanation
Indices: 48723--48752 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48713 ATAGTTTCCT
48723 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48753 ACAAATCCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:60392 original size:23 final size:22
Alignment explanation
Indices: 60347--60394 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
60337 CAAGTATTAC
*
60347 TAAAATGTTAGAATGATAAATA
1 TAAAATGTTAAAATGATAAATA
* *
60369 TAAAATTTTAAAATTGATACATA
1 TAAAATGTTAAAA-TGATAAATA
60392 TAA
1 TAA
60395 TGTAACCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAAATGTTAAAATGATAAATA
Found at i:63198 original size:21 final size:21
Alignment explanation
Indices: 63174--63214 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
63164 TCATTAAGCC
63174 ATTAGATTAAA-AACTAATTAG
1 ATTA-ATTAAATAACTAATTAG
*
63195 ATTAATTAAATTACTAATTA
1 ATTAATTAAATAACTAATTA
63215 TTAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
ATTAATTAAATAACTAATTAG
Found at i:64971 original size:69 final size:69
Alignment explanation
Indices: 64860--64999 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
64850 GGAGAAGGGC
* * *
64860 TAATAGGGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGAGTATCTCATTGTATTGGGCA
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGAGCATCTCATTGTATTGAGCA
*
64925 TAAT
66 CAAT
* * * * * *
64929 TAATAGAGTGTGCTTCCCCTTATATGTATTATGATGGGGATTCGGGCCTTTCATTGTATTGAGCA
1 TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGAGCATCTCATTGTATTGAGCA
64994 CAAT
66 CAAT
64998 TA
1 TA
65000 TATGTGTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TAATAGAGTGTGATTCCCCTCATATGTATTATGATGAGGATTCGAGCATCTCATTGTATTGAGCA
CAAT
Found at i:76311 original size:4 final size:4
Alignment explanation
Indices: 76302--76328 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
76292 AAACTAAGTA
76302 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
76329 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:80215 original size:18 final size:18
Alignment explanation
Indices: 80192--80234 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
80182 ACCCAATCTA
**
80192 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
80210 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
80228 AACCCAA
1 AACCCAA
80235 TCATAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:83373 original size:17 final size:18
Alignment explanation
Indices: 83351--83387 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
83341 ATGAAGTGTA
83351 AAGTATATATATC-ATAT
1 AAGTATATATATCTATAT
*
83368 AAGTATTTATATCTATAT
1 AAGTATATATATCTATAT
83386 AA
1 AA
83388 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
AAGTATATATATCTATAT
Found at i:88372 original size:22 final size:21
Alignment explanation
Indices: 88339--88382 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
88329 CAAATATAAG
*
88339 TATTGTATTAACCAAATCATT
1 TATTGAATTAACCAAATCATT
88360 TATTGAATATAACCAAATCATT
1 TATTGAAT-TAACCAAATCATT
88382 T
1 T
88383 TCATATGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (21 bp):
TATTGAATTAACCAAATCATT
Found at i:88802 original size:13 final size:13
Alignment explanation
Indices: 88780--88830 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
88770 ACACTCAAAT
*
88780 TTCTCAAAAGCAG
1 TTCTCAAAAGCAC
*
88793 TTCTCCAAAGCAC
1 TTCTCAAAAGCAC
*
88806 TTCTCCAAAGCAC
1 TTCTCAAAAGCAC
88819 TTCTCAAAAGCA
1 TTCTCAAAAGCA
88831 ATAAAGAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:90661 original size:3 final size:3
Alignment explanation
Indices: 90653--90683 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
90643 CTGAAGTTGG
90653 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
90684 TTATTATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:104423 original size:44 final size:44
Alignment explanation
Indices: 104360--104476 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 44
104350 GGTCACGAAC
104360 CCTATTTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGATACAAGT
1 CCTATTTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGATACAAGT
* *
104404 CCTATTTCCCTGAAGTTGCAGTGGAGGAGGTTGAGGATACAAGT
1 CCTATTTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGATACAAGT
* *
104448 CTTATTTCCCTGAAGATGCAGTGGAGTAG
1 CCTATTTCCCTGAAGTTGCAGTGGAGTAG
104477 ACTGAAAACA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (44 bp):
CCTATTTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGATACAAGT
Found at i:106336 original size:15 final size:15
Alignment explanation
Indices: 106318--106372 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
106308 TATTATCATT
106318 TATTATTATTTATAA
1 TATTATTATTTATAA
*
106333 TATTATTATTTATAT
1 TATTATTATTTATAA
* *
106348 TATTTTTATTTATCA
1 TATTATTATTTATAA
*
106363 TACTATTATT
1 TATTATTATT
106373 ATATGATAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATTATTTATAA
Found at i:106357 original size:30 final size:29
Alignment explanation
Indices: 106308--106418 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 29
106298 TACTTTAATG
* *
106308 TATTATCAT-TTATTATTATTTATAATAT
1 TATTATTATATTATTATTATTTATAATAC
* *
106336 TATTATTTATATTATTTTTATTTATCATAC
1 TATTA-TTATATTATTATTATTTATAATAC
*
106366 TATTATTATATGA-TAGTT-TTGATATACATAC
1 TATTATTATATTATTA-TTATT--TATA-ATAC
*
106397 -ATGTATAATATTATTATTATTT
1 TAT-TATTATATTATTATTATTT
106419 CTTTTTTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
28 8 0.12
29 12 0.18
30 27 0.42
31 14 0.22
32 4 0.06
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (29 bp):
TATTATTATATTATTATTATTTATAATAC
Found at i:106508 original size:122 final size:123
Alignment explanation
Indices: 106366--106612 Score: 469
Period size: 122 Copynumber: 2.0 Consensus size: 123
106356 TTTATCATAC
*
106366 TATTATTATATGATAGTTTTGATATACATACATGTATAATATTATTATTATTTCTTTTTTAAAAG
1 TATTATTATAT-ATAGTTTTGATATACATACATGTATAAGATTATTATTATTTCTTTTTTAAAAG
106431 ACTTATCTAATAAACATAAATATCTTTTTATATATCTGTATAACCTTTTTCTTTTTTTT
65 ACTTATCTAATAAACATAAATATCTTTTTATATATCTGTATAACCTTTTTCTTTTTTTT
106490 TATTATTATAT-TAGTTTTGATATACATACATGTATAAGATTATTATTATTTCTTTTTTAAAAGA
1 TATTATTATATATAGTTTTGATATACATACATGTATAAGATTATTATTATTTCTTTTTTAAAAGA
106554 CTTATCTAATAAACATAAATATCTTTTTATATATCTGTATAACCTTTTTCTTTTTTTT
66 CTTATCTAATAAACATAAATATCTTTTTATATATCTGTATAACCTTTTTCTTTTTTTT
106612 T
1 T
106613 TCTCACGAAT
Statistics
Matches: 122, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
122 111 0.91
124 11 0.09
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (123 bp):
TATTATTATATATAGTTTTGATATACATACATGTATAAGATTATTATTATTTCTTTTTTAAAAGA
CTTATCTAATAAACATAAATATCTTTTTATATATCTGTATAACCTTTTTCTTTTTTTT
Found at i:116542 original size:26 final size:26
Alignment explanation
Indices: 116506--116557 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
116496 AAGCCCATGT
116506 ATGCAAATCAGACAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
116532 ATGCAAATCAGACAGAGTGTGAAGAA
1 ATGCAAATCAGACAGAGTGTGAAGAA
116558 CTTGATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.15
Consensus pattern (26 bp):
ATGCAAATCAGACAGAGTGTGAAGAA
Found at i:121464 original size:26 final size:22
Alignment explanation
Indices: 121419--121466 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
121409 TGTAAATCAG
121419 AAAATATCTCTAGAAATTTTCT
1 AAAATATCTCTAGAAATTTTCT
121441 AAAATAATCTCTTCAGAGAATTTTCT
1 AAAAT-ATCTC-T-AGA-AATTTTCT
121467 CTTTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 1 0.05
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (22 bp):
AAAATATCTCTAGAAATTTTCT
Found at i:121714 original size:25 final size:24
Alignment explanation
Indices: 121686--121735 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
121676 TAAATTTCTA
*
121686 TTAAGATAATCACT-TTAATATTAAG
1 TTAAGAAAAT-ACTATTAATA-TAAG
*
121711 TTAATAAAATACTATTAATATAAG
1 TTAAGAAAATACTATTAATATAAG
121735 T
1 T
121736 ATTGAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
TTAAGAAAATACTATTAATATAAG
Found at i:130238 original size:38 final size:38
Alignment explanation
Indices: 130136--130242 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 38
130126 TGTAATAGAA
* * * * *
130136 CAATTCAACACTACCAGTAAACATGTTTAACATGTATT
1 CAATTCAACATTAGCAATCAACATGCTTAACATGTATT
*
130174 CAATTCAACATTGGCAATCAACATGCTTAACATGTATT
1 CAATTCAACATTAGCAATCAACATGCTTAACATGTATT
* * * *
130212 CACTTTAACATTAGTAAT-AGATATGCTTAAC
1 CAATTCAACATTAGCAATCA-ACATGCTTAAC
130243 GTGCACTTCG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 1 0.02
38 56 0.98
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (38 bp):
CAATTCAACATTAGCAATCAACATGCTTAACATGTATT
Found at i:130687 original size:20 final size:21
Alignment explanation
Indices: 130650--130697 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
130640 CATGGTGCAC
*
130650 AAAAATAAATAAAAAAAGAAA
1 AAAAAGAAATAAAAAAAGAAA
* *
130671 AAAAAGAAA-AAACAAAGAGA
1 AAAAAGAAATAAAAAAAGAAA
*
130691 AAGAAGA
1 AAAAAGA
130698 GAGACTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAGAAATAAAAAAAGAAA
Found at i:131132 original size:21 final size:21
Alignment explanation
Indices: 131110--131159 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
131100 AAATAACTTA
*
131110 TATATTAATTAAA-A-TTTAC
1 TATATTTATTAAATATTTTAC
131129 TATATTTATTAAATATTTTAC
1 TATATTTATTAAATATTTTAC
131150 TAT-TTTATTA
1 TATATTTATTA
131160 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTATTAAATATTTTAC
Found at i:132003 original size:12 final size:12
Alignment explanation
Indices: 131986--132011 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
131976 CAAAACAGGC
131986 TTTTAGCGGCGT
1 TTTTAGCGGCGT
131998 TTTTAGCGGCGT
1 TTTTAGCGGCGT
132010 TT
1 TT
132012 GGACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:132045 original size:41 final size:38
Alignment explanation
Indices: 132000--132091 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 38
131990 AGCGGCGTTT
132000 TTAGCGGCGTTTGGACAAAAAACGCCGCTAAAAATGGAGCA
1 TTAGCGGCGTTT--ACAAAAAACGCCGCTAAAAAT-GAGCA
** *
132041 TTAGCGGCGCTTTACGTAAAGCGCCGCTAAAAATGAGCA
1 TTAGCGGCG-TTTACAAAAAACGCCGCTAAAAATGAGCA
*
132080 TTACCGGCGTTT
1 TTAGCGGCGTTT
132092 TTTGGAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.07
39 13 0.28
40 18 0.39
41 9 0.20
42 3 0.07
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (38 bp):
TTAGCGGCGTTTACAAAAAACGCCGCTAAAAATGAGCA
Found at i:132106 original size:40 final size:40
Alignment explanation
Indices: 132017--132113 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
132007 CGTTTGGACA
*
132017 AAAAACGCCGCTAAAAATGGAGCATTAGCGGCGCTTTACG
1 AAAAACGCCGCTAAAAATGGAGCATTACCGGCGCTTTACG
* * * **
132057 TAAAGCGCCGCTAAAAAT-GAGCATTACCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGGAGCATTACCGGCG-CTTTACG
132097 AAAAACGCCGCTAAAAA
1 AAAAACGCCGCTAAAAA
132114 CCTAAGCACA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 13 0.27
40 35 0.73
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATGGAGCATTACCGGCGCTTTACG
Found at i:132226 original size:41 final size:41
Alignment explanation
Indices: 132150--132299 Score: 219
Period size: 41 Copynumber: 3.6 Consensus size: 41
132140 CCTTTCGGGA
*
132150 CTTTAGCGGCGTTTTTAAAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTT-GAAAAAGCGCCGCTAATGCTCAGAT
* *
132192 CTTTAGCGGCGTTTTTGGAAAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
** * **
132233 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGG
1 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
132274 CTTTAGCGGCGTTTTTGAAAAAGCGC
1 CTTTAGCGGCGTTTTTGAAAAAGCGC
132300 TGCAAAAACA
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 82 0.84
42 16 0.16
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAT
Found at i:132447 original size:26 final size:26
Alignment explanation
Indices: 132399--132448 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
132389 AAAATGTATA
** *
132399 AATTTGAAATAATGACACGTAGAAGT
1 AATTTGAAATAAAAACACATAGAAGT
*
132425 AATTTGAAATAAAAATACATAGAA
1 AATTTGAAATAAAAACACATAGAA
132449 AAATATTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (26 bp):
AATTTGAAATAAAAACACATAGAAGT
Found at i:133270 original size:21 final size:20
Alignment explanation
Indices: 133217--133270 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
133207 TGTGATTTAA
* *
133217 GGTTTATGGGTTATGGGTTAG
1 GGTTTA-GGGTTAAGAGTTAG
*
133238 GGGTTAGAGGTTAAGAGTTAG
1 GGTTTAG-GGTTAAGAGTTAG
133259 GGATTTAGGGTT
1 GG-TTTAGGGTT
133271 TATGGATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAGTTAG
Found at i:133462 original size:89 final size:89
Alignment explanation
Indices: 133287--133451 Score: 242
Period size: 89 Copynumber: 1.9 Consensus size: 89
133277 TTCAGTGTTA
* *
133287 GGTTAGGGGTTAGGGTTTAGATTAATTAGTATGTTTTAATTTATATATTAAATAATGTTAAGGGG
1 GGTTAGGGGTTAGGATTTAGATTAATTAGTATGTTTTAATTTATATATTAAATAAGGTTAAGGGG
*
133352 TTAGGGGTTAGAGATTCGGGGTCG
66 TTAGGGGTCAGAGATTCGGGGTCG
* * * *
133376 GGTTAGGGTTTATGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAAGGTGT-AGGG
1 GGTTAGGGGTTAGGATTTAGATTAATTAGTATGTTTTAATTTATATATTAAATAAGGT-TAAGGG
*
133440 GTTAGTGGTCAG
65 GTTAGGGGTCAG
133452 GGGTTTGGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
89 66 0.99
90 1 0.01
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (89 bp):
GGTTAGGGGTTAGGATTTAGATTAATTAGTATGTTTTAATTTATATATTAAATAAGGTTAAGGGG
TTAGGGGTCAGAGATTCGGGGTCG
Found at i:134201 original size:147 final size:143
Alignment explanation
Indices: 133962--134249 Score: 445
Period size: 147 Copynumber: 2.0 Consensus size: 143
133952 GATTTTTAGC
* * *
133962 ATAGCAAAATAGTGTCGTTTTATTCCAAATGAAATAAGTTTTTGCGGCGTTTTTGATAAAAACGC
1 ATAGCAAAACAGAGTCGTTTTATTCAAAATGAAATAAGTTTTTGCGGCGTTTTTGATAAAAACGC
134027 CGCAAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTAC-TTTAAA
66 CGCAAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCAC--AAAA-AA-TTTACTTTTAAA
134091 AAAATAGCGCCATTTTAT
127 AAAATAG-GCCATTTTAT
* *
134109 ATAGCAAAACAGAGTCGTTTTATTCAAAATGAAATAATTTTTTGCGGCGTTTTT-CTGAAAAACG
1 ATAGCAAAACAGAGTCGTTTTATTCAAAATGAAATAAGTTTTTGCGGCGTTTTTGAT-AAAAACG
* *
134173 CCGCAAAAGGTAAGCAATAGCGGTGTTTTTATTAAAAACGCCACAAAAAATTTACTTTTAAAAAA
65 CCGCAAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATTTACTTTTAAAAAA
134238 ATAGGCCATTTT
130 ATAGGCCATTTT
134250 TTAAAATCCC
Statistics
Matches: 132, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
143 13 0.10
144 15 0.11
145 4 0.03
146 1 0.01
147 99 0.75
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (143 bp):
ATAGCAAAACAGAGTCGTTTTATTCAAAATGAAATAAGTTTTTGCGGCGTTTTTGATAAAAACGC
CGCAAAAGGTAAGCAATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATTTACTTTTAAAAAAA
TAGGCCATTTTAT
Found at i:134293 original size:22 final size:22
Alignment explanation
Indices: 134268--134325 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
134258 CCCTCCCCCC
134268 AAAATCCCCAACTTTCCCGCC-T
1 AAAATCCCCAACTTTCCC-CCTT
*
134290 AAAATCCCTAA-TTTCCCCCTT
1 AAAATCCCCAACTTTCCCCCTT
* *
134311 GAAACCCCCAACTTT
1 AAAATCCCCAACTTT
134326 ACAAACATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 15 0.50
22 13 0.43
ACGTcount: A:0.29, C:0.41, G:0.03, T:0.26
Consensus pattern (22 bp):
AAAATCCCCAACTTTCCCCCTT
Found at i:138584 original size:43 final size:43
Alignment explanation
Indices: 138479--138790 Score: 315
Period size: 43 Copynumber: 7.3 Consensus size: 43
138469 AGATTATGTT
** * *
138479 TTTAGCGGCGTTT-TGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
138520 TTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * **
138563 TATATCGGCGTTTGTGATAAAAGCACCGCTAAATATCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
138606 TTTAGTGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
138649 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
138692 TTTAGCGGCGTTTGTGGGGAAAGCACCGTTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
138735 TTTAGCAGCATTTGTG-GAAAAACCGCCGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAG-AAAAGCGCCGCTAAAGGTCTTGGTC
*
138778 TTTAGCGCCGTTT
1 TTTAGCGGCGTTT
138791 TTTCCGGCGC
Statistics
Matches: 229, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
41 12 0.05
42 20 0.09
43 197 0.86
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:138681 original size:129 final size:129
Alignment explanation
Indices: 138498--138790 Score: 363
Period size: 129 Copynumber: 2.3 Consensus size: 129
138488 GTTTTGCTAG
* * * *
138498 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAATGTCATGGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
* * * * ** *
138562 CTATATCGGCGTTTGTGATAAAAGCACCGCTAAATATCTTGGTCTTTAGTGGCATTTGTGGGAA
66 CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
* * * *
138626 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCTTGGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
* * * * *
138691 CTTTAGCGGCGTTTGTGGGGAAAGCACCGTTAAAGGTCATGGTCTTTAGCAGCATTTGTGGAAA
66 CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
* * * *
138755 AACCGCCGCTAAAGATCATGGTCTTTAGCGCCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
138791 TTTCCGGCGC
Statistics
Matches: 140, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
128 16 0.11
129 124 0.89
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (129 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
Found at i:138859 original size:21 final size:22
Alignment explanation
Indices: 138833--138877 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
138823 TTTAGCGGCG
*
138833 CTAAAAA-GCGCCGCTAAAGGC
1 CTAAAAAGGCGCCGCTAAAAGC
138854 CTAAAAAGGCGCCGCTAAAAGC
1 CTAAAAAGGCGCCGCTAAAAGC
138876 CT
1 CT
138878 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.38, C:0.29, G:0.22, T:0.11
Consensus pattern (22 bp):
CTAAAAAGGCGCCGCTAAAAGC
Found at i:143226 original size:18 final size:18
Alignment explanation
Indices: 143184--143226 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
143174 AAAGAAGAAA
143184 ATTT-TATTAAATTTAAT
1 ATTTATATTAAATTTAAT
**
143201 ATAAATATTAAATTTAAT
1 ATTTATATTAAATTTAAT
143219 ATTTATAT
1 ATTTATAT
143227 AATAACCCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATTAAATTTAAT
Found at i:143590 original size:21 final size:20
Alignment explanation
Indices: 143546--143599 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
143536 AAAATTCAAA
*
143546 AAAATTATAAAAATTAGTTTT
1 AAAATTAT-AAAATTAGTTGT
*
143567 AAAATTATAAAATTGGTTGGT
1 AAAATTATAAAATTAGTT-GT
143588 -AAATTAATAAAA
1 AAAATT-ATAAAA
143600 AGTAAGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAATTATAAAATTAGTTGT
Found at i:145458 original size:914 final size:915
Alignment explanation
Indices: 143680--145508 Score: 3651
Period size: 914 Copynumber: 2.0 Consensus size: 915
143670 ATTTTAATCT
143680 TATGAATATAATATTTTATATTATTTGGATAAAATTTAAATATAATAATCTGAAAACCTCATTTT
1 TATGAATATAATATTTTATATTATTTGGATAAAATTTAAATATAATAATCTGAAAACCTCATTTT
143745 ATTTTGAAAAATAATTTATTTTAATTAAAAAATTAGCATAATATTTTTACCATGAAGTGATAAAT
66 ATTTTGAAAAATAATTTATTTTAATTAAAAAATTAGCATAATATTTTTACCATGAAGTGATAAAT
143810 AGCTATCTACCTATTTATCTTATTCACTAAATTTTTTGTTGAGAATTTTATATTAAGTAAAAAGT
131 AGCTATCTACCTATTTATCTTATTCACTAAATTTTTTGTTGAGAATTTTATATTAAGTAAAAAGT
143875 TAAAATGGTTATCAAACATATTTAATGTCAAACACACCCTAAATTAAAAAAAAATAAAACATGTA
196 TAAAATGGTTATCAAACATATTTAATGTCAAACACACCCTAAATTAAAAAAAAATAAAACATGTA
143940 AAATCATGTACAACACGCATGACATTAGAAATTAGTAACAAACAATCGAATATATTTATTTGAGA
261 AAATCATGTACAACACGCATGACATTAGAAATTAGTAACAAACAATCGAATATATTTATTTGAGA
144005 AAAAGCTTAGGTGCTGTTTGTTAAACTGAAAAATAAGGTTGTGTTTGATAAACCATCGAAAATTT
326 AAAAGCTTAGGTGCTGTTTGTTAAACTGAAAAATAAGGTTGTGTTTGATAAACCATCGAAAATTT
144070 TCATTTCATTGAAAATGAAAATTTTTAAATGTGTTTGATAATCTTATTGATTTGTTAAAGTTGAT
391 TCATTTCATTGAAAATGAAAATTTTTAAATGTGTTTGATAATCTTATTGATTTGTTAAAGTTGAT
144135 TTTATTTTAAAAATAAAGCATCTCTTCCTCTTTTTTTGTTGTTGTTAAAAAGTTATTATATTTAT
456 TTTATTTTAAAAATAAAGCATCTCTTCCTCTTTTTTTGTTGTTGTTAAAAAGTTATTATATTTAT
144200 TGTTTTGAAAAATATACAAAATAAGATAAAACATTAATAAGATTAAATTTAAGAGATAAATAAAA
521 TGTTTTGAAAAATATACAAAATAAGATAAAACATTAATAAGATTAAATTTAAGAGATAAATAAAA
144265 AAAATCAAGATTAATTTTACTAAATAACATAATTACATTTAATACGCCAATAACCTCTTAGTTTA
586 AAAATCAAGATTAATTTTACTAAATAACATAATTACATTTAATACGCCAATAACCTCTTAGTTTA
144330 GTGACAAGGGCATTAAGTTGCGAGAAATGAAAGTGTGTTCGATCTCAAGTAATTTCTTTAAACAT
651 GTGACAAGGGCATTAAGTTGCGAGAAATGAAAGTGTGTTCGATCTCAAGTAATTTCTTTAAACAT
144395 GATATGATAAAAACATAATATAAAAAAGAACACAATACATATATACTTTAAAAATGATTATAATA
716 GATATGATAAAAACATAATATAAAAAAGAACACAATACATATATACTTTAAAAATGATTATAATA
144460 CAGAAAATAACACAAAATACCCTTAATAGAATAATTTTCCCTTTCAAACACTATAAGAAAAAAGA
781 CAGAAAATAACACAAAATACCCTTAATAGAATAATTTTCCCTTTCAAACACTATAAGAAAAAAGA
144525 GAGTAAAAGTTTAATAGAATCTTAAATTTTAAGTAGAAAGAAATAAGTTGATTAGGGATACATAT
846 GAGTAAAAGTTTAATAGAATCTTAAATTTTAAGTAGAAAGAAATAAGTTGATTAGGGATACATAT
144590 TTATG
911 TTATG
144595 TATGAATAT-ATATTTTATATTATTTGGATAAAATTTAAATATAATAATCTGAAAACCTCATTTT
1 TATGAATATAATATTTTATATTATTTGGATAAAATTTAAATATAATAATCTGAAAACCTCATTTT
144659 ATTTTGAAAAATAATTTATTTTAATTAAAAAATTAGCATAATATTTTTACCATGAAGTGATAAAT
66 ATTTTGAAAAATAATTTATTTTAATTAAAAAATTAGCATAATATTTTTACCATGAAGTGATAAAT
144724 AGCTATCTACCTATTTATCTTATTCACTAAATTTTTTGTTGAGAATTTTATATTAAGTAAAAAGT
131 AGCTATCTACCTATTTATCTTATTCACTAAATTTTTTGTTGAGAATTTTATATTAAGTAAAAAGT
144789 TAAAATGGTTATCAAACATATTTAATGTCAAACACACCCTAAATTAAAAAAAAATAAAACATGTA
196 TAAAATGGTTATCAAACATATTTAATGTCAAACACACCCTAAATTAAAAAAAAATAAAACATGTA
144854 AAATCATGTACAACACGCATGACATTAGAAATTAGTAACAAACAATCGAATATATTTATTTGAGA
261 AAATCATGTACAACACGCATGACATTAGAAATTAGTAACAAACAATCGAATATATTTATTTGAGA
144919 AAAAGCTTAGGTGCTGTTTGTTAAACTGAAAAATAAGGTTGTGTTTGATAAACCATCGAAAATTT
326 AAAAGCTTAGGTGCTGTTTGTTAAACTGAAAAATAAGGTTGTGTTTGATAAACCATCGAAAATTT
144984 TCATTTCATTGAAAATGAAAATTTTTAAATGTGTTTGATAATCTTATTGATTTGTTAAAGTTGAT
391 TCATTTCATTGAAAATGAAAATTTTTAAATGTGTTTGATAATCTTATTGATTTGTTAAAGTTGAT
145049 TTTATTTTAAAAATAAAGCATCTCTTCCTCTTTTTTTGTTGTTGTTAAAAAGTTATTATATTTAT
456 TTTATTTTAAAAATAAAGCATCTCTTCCTCTTTTTTTGTTGTTGTTAAAAAGTTATTATATTTAT
145114 TGTTTTGAAAAATATACAAAATAAGATAAAACATTAATAAGATTAAATTTAAGAGATAAATAAAA
521 TGTTTTGAAAAATATACAAAATAAGATAAAACATTAATAAGATTAAATTTAAGAGATAAATAAAA
145179 AAAATCAAGATTAATTTTACTAAATAACATAATTACATTTAATACGCCAATAACCTCTTAGTTTA
586 AAAATCAAGATTAATTTTACTAAATAACATAATTACATTTAATACGCCAATAACCTCTTAGTTTA
145244 GTGACAAGGGCATTAAGTTGCGAGAAATGAAAGTGTGTTCGATCTCAAGTAATTTCTTTAAACAT
651 GTGACAAGGGCATTAAGTTGCGAGAAATGAAAGTGTGTTCGATCTCAAGTAATTTCTTTAAACAT
145309 GATATGATAAAAACATAATATAAAAAAGAACACAATACATATATACTTTAAAAATGATTATAATA
716 GATATGATAAAAACATAATATAAAAAAGAACACAATACATATATACTTTAAAAATGATTATAATA
145374 CAGAAAATAACACAAAATACCCTTAATAGAATAATTTTCCCTTTCAAACACTATAAGAAAAAAGA
781 CAGAAAATAACACAAAATACCCTTAATAGAATAATTTTCCCTTTCAAACACTATAAGAAAAAAGA
145439 GAGTAAAAGTTTAATAGAATCTTAAATTTTAAGTAGAAAGAAATAAGTTGATTAGGGATACATAT
846 GAGTAAAAGTTTAATAGAATCTTAAATTTTAAGTAGAAAGAAATAAGTTGATTAGGGATACATAT
145504 TTATG
911 TTATG
145509 GGTCAGACAA
Statistics
Matches: 914, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
914 905 0.99
915 9 0.01
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (915 bp):
TATGAATATAATATTTTATATTATTTGGATAAAATTTAAATATAATAATCTGAAAACCTCATTTT
ATTTTGAAAAATAATTTATTTTAATTAAAAAATTAGCATAATATTTTTACCATGAAGTGATAAAT
AGCTATCTACCTATTTATCTTATTCACTAAATTTTTTGTTGAGAATTTTATATTAAGTAAAAAGT
TAAAATGGTTATCAAACATATTTAATGTCAAACACACCCTAAATTAAAAAAAAATAAAACATGTA
AAATCATGTACAACACGCATGACATTAGAAATTAGTAACAAACAATCGAATATATTTATTTGAGA
AAAAGCTTAGGTGCTGTTTGTTAAACTGAAAAATAAGGTTGTGTTTGATAAACCATCGAAAATTT
TCATTTCATTGAAAATGAAAATTTTTAAATGTGTTTGATAATCTTATTGATTTGTTAAAGTTGAT
TTTATTTTAAAAATAAAGCATCTCTTCCTCTTTTTTTGTTGTTGTTAAAAAGTTATTATATTTAT
TGTTTTGAAAAATATACAAAATAAGATAAAACATTAATAAGATTAAATTTAAGAGATAAATAAAA
AAAATCAAGATTAATTTTACTAAATAACATAATTACATTTAATACGCCAATAACCTCTTAGTTTA
GTGACAAGGGCATTAAGTTGCGAGAAATGAAAGTGTGTTCGATCTCAAGTAATTTCTTTAAACAT
GATATGATAAAAACATAATATAAAAAAGAACACAATACATATATACTTTAAAAATGATTATAATA
CAGAAAATAACACAAAATACCCTTAATAGAATAATTTTCCCTTTCAAACACTATAAGAAAAAAGA
GAGTAAAAGTTTAATAGAATCTTAAATTTTAAGTAGAAAGAAATAAGTTGATTAGGGATACATAT
TTATG
Found at i:148594 original size:44 final size:45
Alignment explanation
Indices: 148515--148646 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 45
148505 ACTTCCAATT
* * **
148515 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT-G
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTCG
** *
148559 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT-----CG
*
148609 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
148647 ATCCCAATGA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 36 0.51
50 35 0.49
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (45 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTCG
Found at i:148669 original size:56 final size:50
Alignment explanation
Indices: 148457--148690 Score: 162
Period size: 50 Copynumber: 4.7 Consensus size: 50
148447 TGATAATAAC
* * * *
148457 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGA--TGT-TTCCTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
* * * * * **
148504 TACTTCCAATTCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT----
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
** ** * *
148552 AT--CGGTGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
* *
148600 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCCCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTC---ATCCC---G
148656 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
148691 GGATCTCTTT
Statistics
Matches: 143, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
44 33 0.23
46 1 0.01
47 1 0.01
48 2 0.01
49 31 0.22
50 34 0.24
51 2 0.01
52 1 0.01
53 4 0.03
56 34 0.24
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
Found at i:151568 original size:61 final size:61
Alignment explanation
Indices: 151473--151594 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
151463 CCATTTTCAA
151473 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
1 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
151534 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
1 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
151595 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (61 bp):
AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
Found at i:156413 original size:20 final size:19
Alignment explanation
Indices: 156372--156415 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
156362 CTTTAAAACA
* **
156372 AATATATAATTATTCATTT
1 AATATATAACTATTCAAAT
156391 AATACTATAACTATTCAAAT
1 AATA-TATAACTATTCAAAT
156411 AATAT
1 AATAT
156416 TATTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATATAACTATTCAAAT
Found at i:160449 original size:21 final size:20
Alignment explanation
Indices: 160425--160479 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
160415 AAATAAAATA
160425 TTTTATATTTAAATATTATTC
1 TTTTATA-TTAAATATTATTC
**
160446 TTTTGATAGAAAATATTATTC
1 TTTT-ATATTAAATATTATTC
*
160467 TTTAATATTAAAT
1 TTTTATATTAAAT
160480 TGATGTGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTATATTAAATATTATTC
Found at i:160526 original size:25 final size:26
Alignment explanation
Indices: 160492--160543 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
160482 ATGTGAATAC
160492 TTATATTTAT-AGTTATTAAATTTTTA
1 TTATATTTATGA-TTATTAAATTTTTA
* *
160518 TTAT-TTTATGATTTTTATATTTTTA
1 TTATATTTATGATTATTAAATTTTTA
160543 T
1 T
160544 AAAACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (26 bp):
TTATATTTATGATTATTAAATTTTTA
Found at i:163924 original size:12 final size:13
Alignment explanation
Indices: 163907--163935 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
163897 ATTTTAATTT
163907 CTTTAA-TTTTAA
1 CTTTAATTTTTAA
163919 CTTTAATTTTTAA
1 CTTTAATTTTTAA
163932 CTTT
1 CTTT
163936 TTACTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTAATTTTTAA
Found at i:166558 original size:10 final size:11
Alignment explanation
Indices: 166519--166571 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
166509 ATCTACTTCT
166519 AAAAATTATAA
1 AAAAATTATAA
*
166530 AAAAATCTATGTGA
1 AAAAAT-TA--TAA
166544 AAAAATTATAA
1 AAAAATTATAA
*
166555 AAAAA-CATAA
1 AAAAATTATAA
166565 AAAAATT
1 AAAAATT
166572 TGGAAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 9 0.26
11 13 0.38
12 2 0.06
13 2 0.06
14 8 0.24
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:171120 original size:21 final size:20
Alignment explanation
Indices: 171067--171121 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
171057 TTCTAAGCAG
171067 TGCAAAGTTATTCTTTCCTT
1 TGCAAAGTTATTCTTTCCTT
171087 TGCAAAGTTATTCTTTCCTT
1 TGCAAAGTTATTCTTTCCTT
171107 TGCAAAGTTTATTCT
1 TGCAAAG-TTATTCT
171122 ATTTCCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.79
21 7 0.21
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (20 bp):
TGCAAAGTTATTCTTTCCTT
Found at i:171504 original size:23 final size:24
Alignment explanation
Indices: 171478--171530 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
171468 CAAAGTAAAC
171478 ATCAATTCATTCAAGCAATACCT-
1 ATCAATTCATTCAAGCAATACCTA
171501 ATCAATTCATTCAAGCAATACCTA
1 ATCAATTCATTCAAGCAATACCTA
171525 ATCAAT
1 ATCAAT
171531 ACCTAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (24 bp):
ATCAATTCATTCAAGCAATACCTA
Found at i:172128 original size:21 final size:21
Alignment explanation
Indices: 172102--172143 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
172092 GAACACGCCG
*
172102 ACAGAAGCTCATGAGAGCTGA
1 ACAGAAGCTCATAAGAGCTGA
* *
172123 ACAGAATCTCGTAAGAGCTGA
1 ACAGAAGCTCATAAGAGCTGA
172144 TCTACCGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (21 bp):
ACAGAAGCTCATAAGAGCTGA
Found at i:180867 original size:22 final size:23
Alignment explanation
Indices: 180832--180877 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
180822 NNNNNNAAAA
180832 ATATAACCATTACAAATTTAAAT
1 ATATAACCATTACAAATTTAAAT
*
180855 ATATAA-CATTACATATTTAAAT
1 ATATAACCATTACAAATTTAAAT
180877 A
1 A
180878 AATCCTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAACCATTACAAATTTAAAT
Found at i:182275 original size:147 final size:148
Alignment explanation
Indices: 182033--182336 Score: 520
Period size: 147 Copynumber: 2.0 Consensus size: 148
182023 GAGGAGGAAG
* *
182033 AGGAAGAGGTGGGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGTAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
*
182098 ATTGTGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTT-GAAGATGAAGACAAGGATTATG
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTAGAAGATGAAGACAAGGATTATG
182162 AGGAGGAAGAAGAAGAAA
131 AGGAGGAAGAAGAAGAAA
182180 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
* * * *
182245 ATTGCGGATAAAAAATCTGTCAAGCGGGAAAGCTTGTCTGTTGAAGAAGATGAAGACAAGGATTA
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTT--AGAAGATGAAGACAAGGATTA
182310 TGAGGAGGAAGAAGAAGAAA
129 TGAGGAGGAAGAAGAAGAAA
182330 AGGAAGA
1 AGGAAGA
182337 TGATGATGAG
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
147 100 0.68
150 47 0.32
ACGTcount: A:0.40, C:0.06, G:0.36, T:0.18
Consensus pattern (148 bp):
AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTAGAAGATGAAGACAAGGATTATG
AGGAGGAAGAAGAAGAAA
Found at i:182382 original size:36 final size:36
Alignment explanation
Indices: 182341--182457 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
182331 GGAAGATGAT
* * ** *
182341 GATGAGGAGTTCACTCCAGATTTAGAAGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
182377 GATGAGGAATTTACTCTGGATGAAGAGGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
182413 GATGAAGAATTCACTCCGGATGAAGAGGATTGTTTA
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
182449 GATGAGGAA
1 GATGAGGAA
182458 GAGGAATTGA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (36 bp):
GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
Found at i:184955 original size:33 final size:33
Alignment explanation
Indices: 184913--184977 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
184903 AGTCAATTTT
184913 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
184946 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
184978 GAGTTCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.18, T:0.46
Consensus pattern (33 bp):
CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
Found at i:184967 original size:17 final size:17
Alignment explanation
Indices: 184914--184968 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
184904 GTCAATTTTC
184914 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
* * ***
184931 TGCTT-TTACTGCTTCC
1 TGCTTCTCAGTGCTGAT
184947 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
184964 TGCTT
1 TGCTT
184969 TTACTGCTTG
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.09, C:0.25, G:0.20, T:0.45
Consensus pattern (17 bp):
TGCTTCTCAGTGCTGAT
Found at i:190141 original size:18 final size:17
Alignment explanation
Indices: 190108--190149 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
190098 AGCTTCTCAG
* *
190108 AAATACTTTTGGGATAA
1 AAATATTTTTGAGATAA
190125 AAAGTATTTTTGAGATAA
1 AAA-TATTTTTGAGATAA
190143 AAATATT
1 AAATATT
190150 GTTAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (17 bp):
AAATATTTTTGAGATAA
Found at i:192338 original size:15 final size:15
Alignment explanation
Indices: 192294--192340 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
192284 AAAAGTATGT
*
192294 ATAAAATCTAAAAAA
1 ATAAAATTTAAAAAA
*
192309 ATATAAA-TTATAAAA
1 ATA-AAATTTAAAAAA
192324 ATAAAATTTACAAAAA
1 ATAAAATTTA-AAAAA
192340 A
1 A
192341 ATTACGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
16 8 0.31
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAATTTAAAAAA
Found at i:192414 original size:21 final size:22
Alignment explanation
Indices: 192389--192432 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
192379 TATTATTACA
*
192389 AAAAAATT-TAACAAAAATTGT
1 AAAAAATTATAAAAAAAATTGT
192410 -AAAAATTATAAAAAAAATTGT
1 AAAAAATTATAAAAAAAATTGT
192431 AA
1 AA
192433 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 12 0.60
22 1 0.05
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAAAATTATAAAAAAAATTGT
Found at i:192716 original size:7 final size:7
Alignment explanation
Indices: 192681--192719 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
192671 TATTTAAATA
192681 TTTAATAT
1 TTTAAT-T
*
192689 TATAATT
1 TTTAATT
*
192696 TTTTATT
1 TTTAATT
192703 TTTAATT
1 TTTAATT
192710 TTTAATT
1 TTTAATT
192717 TTT
1 TTT
192720 TTAAACGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:194734 original size:29 final size:29
Alignment explanation
Indices: 194702--194758 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
194692 ACTCACTACA
*
194702 TTGTATTTAAACAAGCCCTTAACATATTC
1 TTGTAGTTAAACAAGCCCTTAACATATTC
* *
194731 TTGTAGTTAAATAAGCCCTTAACTTATT
1 TTGTAGTTAAACAAGCCCTTAACATATT
194759 ATTTTTACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (29 bp):
TTGTAGTTAAACAAGCCCTTAACATATTC
Found at i:195762 original size:20 final size:20
Alignment explanation
Indices: 195739--195779 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
195729 CTTAAACAAA
*
195739 TTAAGATTTATTTAA-TTAAT
1 TTAAG-TTTAATTAACTTAAT
195759 TTAAGTTTAATTAACTTAAT
1 TTAAGTTTAATTAACTTAAT
195779 T
1 T
195780 AACAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAAGTTTAATTAACTTAAT
Found at i:196374 original size:49 final size:50
Alignment explanation
Indices: 196302--196431 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 50
196292 TGCCTTAGGT
* * *
196302 TGAAAATCATCATTGTCGGGCTATCCGAGATGA-TAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
** *
196351 TGAAAACCATTGTTTTCGGGCTATCTGTGAT-AGTAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
*
196400 TGAAAACCATCATTTTCAGGCTATCCGTGATG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATG
196432 GTAAAATGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
49 68 0.99
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (50 bp):
TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
Found at i:196516 original size:23 final size:23
Alignment explanation
Indices: 196489--196535 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
196479 TGATAATGTA
*
196489 TTGTATAGTGCGAACCATTGTTG
1 TTGTATAGTGCGAACCATCGTTG
196512 TTGTATAGTGCGAACCATCGTTG
1 TTGTATAGTGCGAACCATCGTTG
196535 T
1 T
196536 CGGGCCACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (23 bp):
TTGTATAGTGCGAACCATCGTTG
Found at i:202815 original size:5 final size:6
Alignment explanation
Indices: 202802--202826 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
202792 ATCACAAAGT
202802 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
202827 GAACACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:203390 original size:14 final size:14
Alignment explanation
Indices: 203371--203399 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
203361 AGTTAACCCC
203371 ACAAAAATTTGAAT
1 ACAAAAATTTGAAT
203385 ACAAAAATTTGAAT
1 ACAAAAATTTGAAT
203399 A
1 A
203400 GGATTCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
ACAAAAATTTGAAT
Found at i:203828 original size:32 final size:32
Alignment explanation
Indices: 203792--203852 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
203782 TTTTTAGAGG
* * *
203792 TTGATTAATGCAAATCCTTAAAGAAATTAGAA
1 TTGATTAATACAAACCCCTAAAGAAATTAGAA
*
203824 TTGATTAATACAAACCCCTGAAGAAATTA
1 TTGATTAATACAAACCCCTAAAGAAATTA
203853 AGGTTGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (32 bp):
TTGATTAATACAAACCCCTAAAGAAATTAGAA
Found at i:205385 original size:4 final size:4
Alignment explanation
Indices: 205378--206367 Score: 1971
Period size: 4 Copynumber: 247.5 Consensus size: 4
205368 GTTAAAATAA
*
205378 ATGT ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205426 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205474 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205522 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205570 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205618 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205666 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205714 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205762 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205810 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205858 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205906 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
205954 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206002 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206050 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206098 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206146 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206194 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206242 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206290 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
206338 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
206368 ATGTTTGAAT
Statistics
Matches: 984, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 984 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:213574 original size:5 final size:5
Alignment explanation
Indices: 213564--213589 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
213554 TGAGCATTCG
213564 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
213590 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:214460 original size:9 final size:9
Alignment explanation
Indices: 214443--214473 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
214433 TCGAGTTGAT
214443 TCGAATAAC
1 TCGAATAAC
*
214452 TCGATTAAC
1 TCGAATAAC
214461 TCGAATAAC
1 TCGAATAAC
214470 TCGA
1 TCGA
214474 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:221996 original size:42 final size:42
Alignment explanation
Indices: 221857--222013 Score: 129
Period size: 42 Copynumber: 3.7 Consensus size: 42
221847 TCGTGTTTAC
* * * **
221857 TTTCCGTTTAGCTCTCACTAGCTTCTATTCAACTCA-TATAAG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAAC-CATTATGGG
**** * *
221899 TTTCTGTTTAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
* * * *
221941 TTT-TCGCTCAGCTCTTACGAGCTTCCGTTCAACCATTATGGG
1 TTTCT-GTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
* *
221983 TTTCTGTTTAGCTCTCATGAGCTTTTGTTCA
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCA
222014 GCCTTTGGGC
Statistics
Matches: 88, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.02
42 85 0.97
43 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
Found at i:229524 original size:42 final size:42
Alignment explanation
Indices: 229425--229581 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 42
229415 TCATGTTTAC
* * * * * *
229425 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* * * * *
229467 TTT-TCGTTTAACTCTTTTGAGCTTCTGTTTACCCCTTATGGG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* *
229509 TTTCTGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* *
229551 TTTTTGTTTAGCT-TTCATGAGCTTCTGTTCA
1 TTTCTGTTCAGCTCTT-ATGAGCTTCTGTTCA
229582 GGCTTCAGGC
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 3 0.03
42 88 0.96
43 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:229525 original size:21 final size:21
Alignment explanation
Indices: 229426--229582 Score: 84
Period size: 21 Copynumber: 7.5 Consensus size: 21
229416 CATGTTTACT
* * *
229426 TTCTGTTTAGCTCTCACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
229447 TTCTGTTCAACTCATATGAG-
1 TTCTGTTCAGCTCTTATGAGC
* * * *
229467 TTTTCGTTTAACTCTTTTGAGC
1 TTCT-GTTCAGCTCTTATGAGC
* * * * *
229489 TTCTGTTTACCCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
*
229510 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * * *
229531 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
* *
229552 TTTTGTTTAGCT-TTCATGAGC
1 TTCTGTTCAGCTCTT-ATGAGC
229573 TTCTGTTCAG
1 TTCTGTTCAG
229583 GCTTCAGGCT
Statistics
Matches: 97, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
20 5 0.05
21 89 0.92
22 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:229572 original size:84 final size:84
Alignment explanation
Indices: 229425--229579 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
229415 TCATGTTTAC
* * * *
229425 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACTCATATGAGTTTTCGTTTAACTCTTTTGAGCT
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTTATGAGCT
229490 TCTGTTTACCCCTTATGGG
66 TCTGTTTACCCCTTATGGG
* * * * *
229509 TTTCTGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTTTGTTTAGCT-TTCATGAGC
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTT-ATGAGC
229573 TTCTGTT
65 TTCTGTT
229580 CAGGCTTCAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.03
84 59 0.97
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (84 bp):
TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTTATGAGCT
TCTGTTTACCCCTTATGGG
Found at i:232021 original size:50 final size:50
Alignment explanation
Indices: 231899--232145 Score: 182
Period size: 50 Copynumber: 4.8 Consensus size: 50
231889 GATAATAACA
* * ** * * **
231899 TGCCAAAGTCATGTCCCAGAAATGGTCTTACATGGGATGTTTC-T-TGTAC
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCATATATGG
* * **
231948 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-TGG
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCATATATGG
* *
231998 TG-CACATGCCATGTCCCAAATATGGTCTTACGA-GGGACCTCTCATCT-CGG
1 TGCCA-ATGCCATGTCCCAAA-ATGGTCTTAC-ATGGGACCTCTCATATATGG
* * *
232048 TGTCAACGCCATGTCCCAGAAATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCAT-A--T--ATGG
*
232104 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAAA-ATGGTCTTACATGGGACCTCT
232146 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
49 40 0.25
50 75 0.47
51 6 0.04
53 1 0.01
55 2 0.01
56 37 0.23
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAAATGGTCTTACATGGGACCTCTCATATATGG
Found at i:239082 original size:49 final size:50
Alignment explanation
Indices: 238969--239165 Score: 209
Period size: 56 Copynumber: 3.8 Consensus size: 50
238959 TTTTTTGTAC
* **
238969 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
239019 TGTCC-ATGCCATGTCCCAGATATGGTCTTAC-GGGGACCTCTCATCTTGG
1 TG-CCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
239068 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
239124 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
239166 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.02
49 39 0.32
50 39 0.32
51 2 0.02
53 1 0.01
56 40 0.33
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
Found at i:239135 original size:56 final size:50
Alignment explanation
Indices: 238932--239165 Score: 208
Period size: 49 Copynumber: 4.6 Consensus size: 50
238922 CCAAAGCTAG
* * *
238932 GTCCCAGACATGGTCTTACATGGGA--TGT-TTTTTGTACTGCCAATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG-A-TGCCAATGCCAT
* * ** * * *
238981 ATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATG-CCAATGCCAT
* * * *
239031 GTCCCAGATATGGTCTTAC-GGGGACCTCTCATCTTGGTGCCAACGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATGCCAATGCCAT
239080 GTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TGATGCCAATGCCAT
* *
239136 GTCCCAAACATGGTCTTACATGGGATCTCT
1 GTCCCAGACATGGTCTTACATGGGACCTCT
239166 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
48 2 0.01
49 62 0.41
50 39 0.25
51 4 0.03
52 3 0.02
53 2 0.01
56 41 0.27
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATGCCAATGCCAT
Found at i:248155 original size:13 final size:13
Alignment explanation
Indices: 248139--248164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
248129 CCAATCCATC
248139 CCTCAACTCCAGT
1 CCTCAACTCCAGT
248152 CCTCAACTCCAGT
1 CCTCAACTCCAGT
248165 GCTGCAACAT
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:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CCTCAACTCCAGT
Found at i:252104 original size:6 final size:6
Alignment explanation
Indices: 252095--252124 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
252085 TTTTCTTTCC
252095 CATTTT CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
252125 GGAGAAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:257225 original size:13 final size:13
Alignment explanation
Indices: 257207--257231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257197 TGATATACCA
257207 AAAAAAAGTTCTC
1 AAAAAAAGTTCTC
257220 AAAAAAAGTTCT
1 AAAAAAAGTTCT
257232 TTCTATTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAAGTTCTC
Found at i:269657 original size:43 final size:42
Alignment explanation
Indices: 269590--269719 Score: 158
Period size: 43 Copynumber: 3.0 Consensus size: 42
269580 CATAGGATTT
269590 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
*
269633 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGCCA
1 TCGA-TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
269676 TCGATATGTGATTACATGTAAGACCACGTTTGGGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
269719 T
1 T
269720 TGTACGAGTT
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
42 3 0.04
43 66 0.88
44 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:270591 original size:23 final size:22
Alignment explanation
Indices: 270565--270687 Score: 113
Period size: 24 Copynumber: 5.3 Consensus size: 22
270555 TGAGTTGAAT
*
270565 CAATTTATTACATATATGCTGTC
1 CAATTT-TTACATAAATGCTGTC
* *
270588 CAATTTTGATGCATAAATGCTGCC
1 CAATTTT--TACATAAATGCTGTC
270612 CAATTTGTTACAT-AATGCTGTC
1 CAATTT-TTACATAAATGCTGTC
* * *
270634 CAATTTTGATGCTTAAATGCTGCC
1 CAATTTT--TACATAAATGCTGTC
*
270658 CAATTTGTTACATATATGCTGTC
1 CAATTT-TTACATAAATGCTGTC
270681 CAATTTT
1 CAATTTT
270688 GATGCTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.01
22 16 0.20
23 30 0.37
24 32 0.40
25 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (22 bp):
CAATTTTTACATAAATGCTGTC
Found at i:270638 original size:46 final size:47
Alignment explanation
Indices: 270565--270730 Score: 262
Period size: 47 Copynumber: 3.6 Consensus size: 47
270555 TGAGTTGAAT
* *
270565 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
270612 CAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
270658 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
** ** *
270705 CAAACTGTTTTATATATGCTGACCAA
1 CAATTTGTTACATATATGCTGTCCAA
270731 ATTCATGAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
46 45 0.41
47 66 0.59
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (47 bp):
CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
Found at i:271927 original size:9 final size:8
Alignment explanation
Indices: 271910--271934 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
271900 TTTAATTCTG
271910 TTATTTTT
1 TTATTTTT
271918 TTATTTTT
1 TTATTTTT
271926 TTATTTTT
1 TTATTTTT
271934 T
1 T
271935 CAAGAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:275043 original size:17 final size:16
Alignment explanation
Indices: 275006--275073 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
274996 CAACCCAATT
*
275006 TTTATTTTTATTATTTA
1 TTTATTTTT-TTCTTTA
275023 -TTATTTTTTTCTTTA
1 TTTATTTTTTTCTTTA
* *
275038 CTTTATTTATTACTTTA
1 -TTTATTTTTTTCTTTA
* *
275055 TTTTATTTTATTATTTA
1 -TTTATTTTTTTCTTTA
275072 TT
1 TT
275074 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.15
16 10 0.24
17 25 0.61
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTTTTCTTTA
Found at i:275052 original size:12 final size:12
Alignment explanation
Indices: 275016--275081 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
275006 TTTATTTTTA
275016 TTATTTATTA-T
1 TTATTTATTACT
* *
275027 TTTTTTCTTTACT
1 TTATTT-ATTACT
275040 TTATTTATTACT
1 TTATTTATTACT
*
275052 TTATTTTATT-TT
1 TTA-TTTATTACT
275064 ATTATTTATTAC-
1 -TTATTTATTACT
275076 TTATTT
1 TTATTT
275082 GGATATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 11 0.25
12 18 0.41
13 15 0.34
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTATTACT
Found at i:275244 original size:22 final size:22
Alignment explanation
Indices: 275216--275265 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
275206 GCCCAGAATG
* *
275216 CCTGCAGCCAAACTACCC-TATT
1 CCTGCAGCC-AACCACCCTTATC
275238 CCTGCAGCCAACCACCCTTATC
1 CCTGCAGCCAACCACCCTTATC
275260 CCTGCA
1 CCTGCA
275266 CCCTAGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.24, C:0.46, G:0.10, T:0.20
Consensus pattern (22 bp):
CCTGCAGCCAACCACCCTTATC
Found at i:275639 original size:25 final size:25
Alignment explanation
Indices: 275593--275644 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
275583 CTGTAATTTT
* *
275593 TTGCTGTGATTGGTTATTGTTGCTG
1 TTGCTGTGATTGATTATTGTTGATG
*
275618 TTGCTGTGATT-ATTTTTGGTTGATG
1 TTGCTGTGATTGATTATT-GTTGATG
275643 TT
1 TT
275645 ACTGCTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.10, C:0.06, G:0.29, T:0.56
Consensus pattern (25 bp):
TTGCTGTGATTGATTATTGTTGATG
Found at i:276362 original size:101 final size:100
Alignment explanation
Indices: 276172--276360 Score: 254
Period size: 101 Copynumber: 1.8 Consensus size: 100
276162 AAGAACATGT
* * *
276172 TGGGCTGAGTAACCAGGGTGGGGTGCTTGGCTGTCATCTCTTTTCGCATCAAAAGGTTCGATGTG
1 TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATG
* *
276237 TTCTTAAGAAAAAATTATAATAAATTAGGAGTCTGC
66 TCCTAAAGAAAAAA-TATAATAAATTAGGAGTCTGC
* *
276273 TGGGCTGAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATA
1 TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTC-G-ATA
276338 T-TCCTAAAGCATAAAAAATATAA
64 TGTCCTAAAG---AAAAAATATAA
276361 ATAATAAATA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 55 0.72
102 7 0.09
103 3 0.04
104 5 0.07
105 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (100 bp):
TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATG
TCCTAAAGAAAAAATATAATAAATTAGGAGTCTGC
Found at i:282545 original size:15 final size:14
Alignment explanation
Indices: 282520--282555 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
282510 GACTCTATTT
*
282520 TAATTATATTAGGA
1 TAATTATATTAAGA
282534 TAATTGATATTAAGA
1 TAATT-ATATTAAGA
282549 TAATTAT
1 TAATTAT
282556 TAAGGATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:286043 original size:13 final size:14
Alignment explanation
Indices: 286027--286113 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 14
286017 AGATGAATAA
286027 ATGAAAT-GATTAT
1 ATGAAATAGATTAT
* *
286040 ATG-AATCGGTTAT
1 ATGAAATAGATTAT
*
286053 ATGGAAGTAGA-TAT
1 AT-GAAATAGATTAT
*
286067 ATGAAAT-GGTTAT
1 ATGAAATAGATTAT
* *
286080 ATG-AATCGGTTAT
1 ATGAAATAGATTAT
*
286093 ATGGAACTAGA-TAT
1 AT-GAAATAGATTAT
286107 ATGAAAT
1 ATGAAAT
286114 GAAACATTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
12 7 0.12
13 32 0.56
14 12 0.21
15 6 0.11
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (14 bp):
ATGAAATAGATTAT
Found at i:286082 original size:40 final size:40
Alignment explanation
Indices: 286027--286115 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
286017 AGATGAATAA
*
286027 ATGAAATGATTATATGAATCGGTTATATGGAAGTAGATAT
1 ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
*
286067 ATGAAATGGTTATATGAATCGGTTATATGGAACTAGATAT
1 ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
286107 ATGAAATGA
1 ATGAAATGA
286116 AACATTGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (40 bp):
ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
Found at i:289808 original size:28 final size:28
Alignment explanation
Indices: 289776--289831 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
289766 CCCTTTTTAC
*
289776 GATTTAGTTTTTTTCACCTAATTAACCA
1 GATTTAGTCTTTTTCACCTAATTAACCA
289804 GATTTAGTCTTTTTCACCTAATTAACCA
1 GATTTAGTCTTTTTCACCTAATTAACCA
289832 TTTAAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.45
Consensus pattern (28 bp):
GATTTAGTCTTTTTCACCTAATTAACCA
Found at i:289887 original size:75 final size:75
Alignment explanation
Indices: 289797--289950 Score: 299
Period size: 75 Copynumber: 2.1 Consensus size: 75
289787 TTTCACCTAA
289797 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
1 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
289862 TAATACGACC
66 TAATACGACC
*
289872 TTAACCAGATTTAGTCTTTTTCTCCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
1 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
289937 TAATACGACC
66 TAATACGACC
289947 TTAA
1 TTAA
289951 TATAATCCCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (75 bp):
TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
TAATACGACC
Found at i:292479 original size:6 final size:6
Alignment explanation
Indices: 292468--292498 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
292458 AAGCCTTCCT
292468 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
292499 CATTTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:292907 original size:76 final size:76
Alignment explanation
Indices: 292827--292977 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
292817 AAGATTACTT
*
292827 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAATATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
292892 ACAAACAATTA
66 ACAAACAATTA
*
292903 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATTATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
292968 ACAAACAATT
66 ACAAACAATT
292978 CTGGCAAACC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (76 bp):
ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
ACAAACAATTA
Found at i:293991 original size:8 final size:8
Alignment explanation
Indices: 293978--294010 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
293968 AGTAAGCACT
293978 GTGGAGTC
1 GTGGAGTC
293986 GTGGAGTC
1 GTGGAGTC
293994 GTGGA--C
1 GTGGAGTC
294000 GTGGAGTC
1 GTGGAGTC
294008 GTG
1 GTG
294011 AATCGGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.26
8 17 0.74
ACGTcount: A:0.12, C:0.12, G:0.52, T:0.24
Consensus pattern (8 bp):
GTGGAGTC
Found at i:302449 original size:25 final size:25
Alignment explanation
Indices: 302421--302499 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
302411 GATAATCAAT
*
302421 TTAAGGATCCCTTGATGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
302446 TTAATAATCCCTTAAAGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
302471 TCAAGAATCCCCTGATGGATTTGAG
1 TTAAGAATCCCTTGATGGATTTGAA
302496 TTAA
1 TTAA
302500 TGATATTGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (25 bp):
TTAAGAATCCCTTGATGGATTTGAA
Found at i:303659 original size:31 final size:31
Alignment explanation
Indices: 303623--303685 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
303613 AAATAATGGC
303623 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
303654 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
303685 A
1 A
303686 TGTACATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
AGGACATATGATAATATTATTAACTCAGAAG
Found at i:308220 original size:23 final size:23
Alignment explanation
Indices: 308194--308237 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
308184 TCATATTATA
308194 CAATTAAAACAATTCATCTTGTG
1 CAATTAAAACAATTCATCTTGTG
308217 CAATTAAAACAATTCATCTTG
1 CAATTAAAACAATTCATCTTG
308238 CTAATGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (23 bp):
CAATTAAAACAATTCATCTTGTG
Found at i:318723 original size:21 final size:21
Alignment explanation
Indices: 318685--318724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
318675 CCTCTTTTTT
*
318685 TATGTATTCCGGCTTGTCCAG
1 TATGTATTCCGGCATGTCCAG
318706 TATGTA-TCCGGGCATGTCC
1 TATGTATTCC-GGCATGTCC
318725 GACGAGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTATTCCGGCATGTCCAG
Found at i:323394 original size:21 final size:21
Alignment explanation
Indices: 323368--323423 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
323358 AATAGCGGTG
*
323368 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
323389 GCGGTGAAATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
323410 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
323424 AACAATGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:326906 original size:39 final size:39
Alignment explanation
Indices: 326852--326932 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
326842 NNNNNNNNNN
326852 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
* *
326891 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
326930 TTT
1 TTT
326933 TCACTTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (39 bp):
TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
Found at i:327321 original size:30 final size:30
Alignment explanation
Indices: 327240--327428 Score: 351
Period size: 30 Copynumber: 6.2 Consensus size: 30
327230 GAATAAACTG
327240 AATACACTACATATATATTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
*
327271 AATACACTAAATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
327302 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
327332 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
327362 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
327392 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
327422 AATACAC
1 AATACAC
327429 AAATACAATG
Statistics
Matches: 155, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
30 112 0.72
31 42 0.27
32 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:327522 original size:43 final size:43
Alignment explanation
Indices: 327474--327606 Score: 212
Period size: 43 Copynumber: 3.0 Consensus size: 43
327464 CTTCTATCGA
* *
327474 TTCCCCTTTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
*
327517 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCTATTCCCAT
1 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
*
327560 TTCCCCTCTTCCATCGATTCCCCTCCTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCATCG--TGCCCTCCTCCCATTTCCCATTCCCAT
327605 TT
1 TT
327607 ACGGTTACTT
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 56 0.67
45 27 0.33
ACGTcount: A:0.10, C:0.50, G:0.04, T:0.37
Consensus pattern (43 bp):
TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
Found at i:329056 original size:19 final size:19
Alignment explanation
Indices: 329034--329092 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 19
329024 CTATTTTCGA
329034 GTTCCTTTCACTTTTTTCT
1 GTTCCTTTCACTTTTTTCT
* * *
329053 GTT-C--TAACTATTTTCGA
1 GTTCCTTTCACTTTTTTC-T
329070 GTTCCTTTCACTTTTTTCT
1 GTTCCTTTCACTTTTTTCT
329089 GTTC
1 GTTC
329093 TAACTTTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 2 0.07
19 7 0.23
20 9 0.30
ACGTcount: A:0.10, C:0.24, G:0.08, T:0.58
Consensus pattern (19 bp):
GTTCCTTTCACTTTTTTCT
Found at i:329070 original size:36 final size:36
Alignment explanation
Indices: 329023--329097 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
329013 CCTTTGAGGT
329023 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
1 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
329059 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
1 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
329095 ACT
1 ACT
329098 TTGAATCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.55
Consensus pattern (36 bp):
ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
Found at i:329440 original size:19 final size:19
Alignment explanation
Indices: 329412--329482 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
329402 TTCGAGGATC
*
329412 TGCAACCTTAGATATGATA
1 TGCAATCTTAGATATGATA
329431 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATG--ATA
329452 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
*
329471 TGTAATCTTAGA
1 TGCAATCTTAGA
329483 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 29 0.60
21 19 0.40
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
TGCAATCTTAGATATGATA
Done.