Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 1 of 204
Found at i:2702 original size:17 final size:17
Alignment explanation
Indices: 2680--2713 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2670 ATCCACTAAT
*
2680 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2697 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2714 AATCCATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2794 original size:20 final size:20
Alignment explanation
Indices: 2769--2818 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2759 TGGCTTAAAA
2769 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2789 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2806 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2819 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:7432 original size:20 final size:20
Alignment explanation
Indices: 7407--7456 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
7397 TGGCTTAAAA
7407 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
7427 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
7444 GTGGTAGTGGATT
1 TTGGTAGTGGATT
7457 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:13619 original size:16 final size:17
Alignment explanation
Indices: 13598--13630 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13588 ATTGATTGAT
*
13598 AAAATT-ATTTAGTTAA
1 AAAATTAATTTAATTAA
13614 AAAATTAATTTAATTAA
1 AAAATTAATTTAATTAA
13631 TTAAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATTAATTTAATTAA
Found at i:20238 original size:6 final size:6
Alignment explanation
Indices: 20229--20284 Score: 85
Period size: 6 Copynumber: 8.8 Consensus size: 6
20219 CAGAAAACAG
20229 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAATAAA ATCAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT-A-AAA AT-AAAA
20280 ATAAA
1 ATAAA
20285 TTACAAACCC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 35 0.74
7 6 0.13
8 6 0.13
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:32356 original size:21 final size:22
Alignment explanation
Indices: 32327--32373 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
32317 CAGAAGGAGT
*
32327 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
32349 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
32370 GAGT
1 GAGT
32374 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:34357 original size:157 final size:157
Alignment explanation
Indices: 34071--34386 Score: 623
Period size: 157 Copynumber: 2.0 Consensus size: 157
34061 CATATTCCTT
34071 GCAATCAAATACATACAAATCAGGAGATTTCATACTGCAGTGGTGATGACAGTAGGGGCTTGTGA
1 GCAATCAAATACATACAAATCAGGAGATTTCATACTGCAGTGGTGATGACAGTAGGGGCTTGTGA
34136 TGGAGATAAGGCCAAGAAGAGGAGAAGAATCATGATCAGAACCGGTACGAAAAGAAGCATCGATG
66 TGGAGATAAGGCCAAGAAGAGGAGAAGAATCATGATCAGAACCGGTACGAAAAGAAGCATCGATG
34201 GCGGAGGCGGAAGCGACGGCAGAAGCA
131 GCGGAGGCGGAAGCGACGGCAGAAGCA
34228 GCAATCAAATACATACAAATCAGGAGATTTCATACTGCAGTGGTGATGACAGTAGGGGCTTGTGA
1 GCAATCAAATACATACAAATCAGGAGATTTCATACTGCAGTGGTGATGACAGTAGGGGCTTGTGA
*
34293 TGGAGATAAGGCCAAGAAGAGGAGGAGAATCATGATCAGAACCGGTACGAAAAGAAGCATCGATG
66 TGGAGATAAGGCCAAGAAGAGGAGAAGAATCATGATCAGAACCGGTACGAAAAGAAGCATCGATG
34358 GCGGAGGCGGAAGCGACGGCAGAAGCA
131 GCGGAGGCGGAAGCGACGGCAGAAGCA
34385 GC
1 GC
34387 GGCAAAACCA
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.15
Consensus pattern (157 bp):
GCAATCAAATACATACAAATCAGGAGATTTCATACTGCAGTGGTGATGACAGTAGGGGCTTGTGA
TGGAGATAAGGCCAAGAAGAGGAGAAGAATCATGATCAGAACCGGTACGAAAAGAAGCATCGATG
GCGGAGGCGGAAGCGACGGCAGAAGCA
Found at i:36976 original size:6 final size:7
Alignment explanation
Indices: 36943--36980 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
36933 TCTTGCATTT
36943 TTTAAAA
1 TTTAAAA
36950 TTTAAAA
1 TTTAAAA
36957 TTTAAAA
1 TTTAAAA
36964 TTTAAAA
1 TTTAAAA
36971 -TTAAAA
1 TTTAAAA
36977 TTTA
1 TTTA
36981 TTTTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:40012 original size:17 final size:17
Alignment explanation
Indices: 39978--40020 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39968 TAAAATAAAC
*
39978 TAAAATTATTTAATTTA
1 TAAAATTATATAATTTA
39995 TAAATATTATATAA-TTA
1 TAAA-ATTATATAATTTA
40012 TAATAATTA
1 TAA-AATTA
40021 ATTAGCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTATATAATTTA
Found at i:43334 original size:24 final size:24
Alignment explanation
Indices: 43286--43337 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
43276 TTTTTAGAAG
* ** *
43286 ATTTAGTATTTATTAGTATAGTAT
1 ATTTAGCATTTATTAACATAATAT
43310 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
43334 ATTT
1 ATTT
43338 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:67467 original size:3 final size:3
Alignment explanation
Indices: 67461--67498 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
67451 ATTCTCTTTG
67461 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TGTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TT
67499 TTCAATTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:67548 original size:114 final size:113
Alignment explanation
Indices: 67350--67699 Score: 479
Period size: 105 Copynumber: 3.1 Consensus size: 113
67340 CTCTGCTGCA
* * *
67350 TCTT-TTCTTTTTCTT-TTCTTCTTTTTCTTCTTTTCAGTTTCATC-CTCAGCCCCTGCATCAAT
1 TCTTCTTCTTCTTCTTCTTCTTC-TTTTCTTCTTTTCAATTTCATCACT----CCCTACATCAAT
*
67412 TGCACCGTCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
61 TGCACCATCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
* *
67465 TCTTCTTCTTCTTCTTCTTCTTCTTTGTCTTCTTTTCAATTTCATCACTCTCTACATCCATTGCA
1 TCTTCTTCTTCTTCTTCTTCTTCTTT-TCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCA
* * *
67530 CCATCAACAACAGCAATAGCCTCAATAGCATCCTCATTTTCATTG----
65 CCATCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
67575 -C-TCTTCTTCTTCTTCTTC-T-TTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC
1 TCTTCTTCTTCTTCTTCTTCTTCTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC
67636 CATCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
66 CATCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
*
67684 TCTTCTTTTTCTTCTT
1 TCTTCTTCTTCTTCTT
67700 TTCAATTTCA
Statistics
Matches: 210, Mismatches: 15, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
105 78 0.37
106 3 0.01
107 1 0.00
108 17 0.08
109 1 0.00
110 1 0.00
111 12 0.06
114 54 0.26
115 4 0.02
116 13 0.06
117 24 0.11
118 2 0.01
ACGTcount: A:0.18, C:0.31, G:0.06, T:0.45
Consensus pattern (113 bp):
TCTTCTTCTTCTTCTTCTTCTTCTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC
CATCAACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTGTTCT
Found at i:67693 original size:96 final size:96
Alignment explanation
Indices: 67479--68775 Score: 1701
Period size: 96 Copynumber: 13.2 Consensus size: 96
67469 CTTCTTCTTC
* * *
67479 TTCTTCTTCTTTGTCTTCTTTTCAATTTCATCACTCTCTACATCCATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
*
67544 AATAGCCTCAATAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
67575 CTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATC
1 ---------TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATC
* *
67640 AACAACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTG
57 AACAACAGCAATAGCCTCAATAGCATCCTCATTCTCATTG
* *
67680 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCACTATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
* * *
67745 AACAG---CAATAGCCTCCTCATTCTCTTTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
67773 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
1 ---TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
*
67838 AGCAATAGCCTCAATAGCATCCTCATTTTCATTG
63 AGCAATAGCCTCAATAGCATCCTCATTCTCATTG
* *
67872 CTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTTCATCAATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
* *
67937 AATAGCCTCAACAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
67968 CTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACC
1 ------------TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACC
* * ** *
68033 ATCAACAACGGCAATAGCCTC-CT--CATTCTCTTTGTTCTTC-TTC
54 ATCAACAACAGCAATAGCCTCAATAGCA-TC-C-TCATTC-TCATTG
* *
68076 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTGCATCAATTGCACTATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-A-C
* *
68141 AACAGCAATAGCCTCAATAGCCTCCTCATTCTCTTTG
60 AACAGCAATAGCCTCAATAGCATCCTCATTCTCATTG
*
68178 TTCTTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACACCAATTGCACCATCAACAAC
1 ---TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAAC
*
68243 AGCAATAGCCTCAATAGCATCCTCATTTTCATTG
63 AGCAATAGCCTCAATAGCATCCTCATTCTCATTG
*
68277 CTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
*
68342 AATAGCCTCAATAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
*
68373 CTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
*
68438 AATAGCCTCAATAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
*
68469 --C-TCTTCTTCTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
*
68531 AATAGCCTCAATAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
* *
68562 --C-TCTTCTTCTTCTTCTTTTCAAGTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
*
68624 AATAGCCTCAATAGCATCCTCATTTTCATTG
66 AATAGCCTCAATAGCATCCTCATTCTCATTG
* * *
68655 --C-TCTTCTTCTTCTTCTTTTCAATTTCATTACTCCCTACATCAATTGCACTATCAACAACAGC
1 TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCAC---CATC-A-A-C
68717 AACAGCAATAGCCTCAATAGCAT-CTACATTCTCATTG
60 AACAGCAATAGCCTCAATAGCATCCT-CATTCTCATTG
* * *
68754 CTCTTCTTCTTCTTCTTATTTT
1 TTCTTCTTCTTTTTCTTCTTTT
68776 TCTTTGTTTC
Statistics
Matches: 1097, Mismatches: 50, Indels: 93
0.88 0.04 0.08
Matches are distributed among these distances:
93 253 0.23
94 1 0.00
96 471 0.43
97 1 0.00
98 3 0.00
99 92 0.08
100 2 0.00
101 5 0.00
102 41 0.04
103 2 0.00
104 2 0.00
105 143 0.13
106 2 0.00
107 1 0.00
108 76 0.07
109 2 0.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.40
Consensus pattern (96 bp):
TTCTTCTTCTTTTTCTTCTTTTCAATTTCATCACTCCCTACATCAATTGCACCATCAACAACAGC
AATAGCCTCAATAGCATCCTCATTCTCATTG
Found at i:67977 original size:3 final size:3
Alignment explanation
Indices: 67969--67999 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
67959 TTTTCATTGC
*
67969 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
68000 TTCAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:68963 original size:3 final size:3
Alignment explanation
Indices: 68955--69002 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
68945 ATCCTCTTTA
* * * *
68955 TTC TTC TTC TTC TTC TTC TTT TTC TTT TTC TTT TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
69003 ACTTGAACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:68985 original size:18 final size:18
Alignment explanation
Indices: 68958--69002 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
68948 CTCTTTATTC
68958 TTCTTCTTCTTCTTCTTT
1 TTCTTCTTCTTCTTCTTT
* *
68976 TTCTTTTTCTTTTTCTTT
1 TTCTTCTTCTTCTTCTTT
68994 TTCTTCTTC
1 TTCTTCTTC
69003 ACTTGAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TTCTTCTTCTTCTTCTTT
Found at i:72984 original size:235 final size:234
Alignment explanation
Indices: 72632--73296 Score: 848
Period size: 235 Copynumber: 2.9 Consensus size: 234
72622 CAACAATTTC
* * *
72632 AATTC-AATTCATTTTCAGCAACTTTTCATTCACTTTCTCACCAACCAAAAAACAGATCAAACCA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
* * * * *
72696 AAAAGAAAAGCAGATGAAATTTTGACTTCGCAAAAACATGACCATGCAAGCTTAAGGATCTTTAA
66 AAAAGAAAAACAGATGAAATTTAGACTTCACAAATACATGA-CATGTAAGCTTAAGGATCTTTAA
* *
72761 GATCAAATTCCCGTTTGTTGACCGAGAAAACGGATGACAAGAAGTATTTACTACTCATACATGTA
130 GATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAGT-TTTACTACTCATACATGTA
* *
72826 AACCTAACATCGTAATTCATATTTTAATTTTACATC-AATA
194 AACCTAACATCATAATTCATATTTTAATGTTACATCAAATA
** * *
72866 AATTCAAATTCAAATTCCGCAACTTTCCCTTCACTTTCTCACTAACCAAACAACAGATCAAACCA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
* * * * *
72931 AAAAGAAAAACAGATGAAATTTAGACTTTACAAATACATAATCATATAAGCTTAAAGACCTTTAA
66 AAAAGAAAAACAGATGAAATTTAGACTTCACAAATACATGA-CATGTAAGCTTAAGGATCTTTAA
* *
72996 GATCAAATTCCCGTTTATTTATCGAGAAAACGGATGAAAAGAAGCTTTTACTACTCATACATGTA
130 GATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAG-TTTTACTACTCATACATGTA
*
73061 AACCTAACATCATAATTTATATTTTAATGTTACATCAATTAATA
194 AACCTAACATCATAATTCATATTTTAATGTTACATC-A--AATA
* *
73105 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTTTCACCAACC-AACAACAGATC-AAGCA
1 AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
* * ** * * ** *
73168 AAAA-AAAAA-AAAGGAAA-ACAGA--TGA-AACT-TTTGACTTGTAAGCTTAAGGATCTTTAAG
66 AAAAGAAAAACAGATGAAATTTAGACTTCACAAATACATGACATGTAAGCTTAAGGATCTTTAAG
* *
73226 ATCAAATTCCCGTTTGTTTACCGAGAAAATGGATGAAAAGAAGTTTTTACTCCTCATACATGTAA
131 ATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAG-TTTTACTACTCATACATGTAA
73291 ACCTAA
195 ACCTAA
73297 TAAATTCAAA
Statistics
Matches: 376, Mismatches: 49, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
229 86 0.23
230 2 0.01
231 3 0.01
232 2 0.01
234 8 0.02
235 204 0.54
236 6 0.02
237 8 0.02
238 11 0.03
239 46 0.12
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (234 bp):
AATTCAAATTCATTTTCCGCAACTTTTCCTTCACTTTCTCACCAACCAAACAACAGATCAAACCA
AAAAGAAAAACAGATGAAATTTAGACTTCACAAATACATGACATGTAAGCTTAAGGATCTTTAAG
ATCAAATTCCCGTTTGTTTACCGAGAAAACGGATGAAAAGAAGTTTTACTACTCATACATGTAAA
CCTAACATCATAATTCATATTTTAATGTTACATCAAATA
Found at i:75663 original size:17 final size:17
Alignment explanation
Indices: 75638--75670 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75628 ATATATTTTA
*
75638 TTTTTAATCAAATATAC
1 TTTTCAATCAAATATAC
75655 TTTTCAATCAAATATA
1 TTTTCAATCAAATATA
75671 TATTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTCAATCAAATATAC
Found at i:76303 original size:13 final size:13
Alignment explanation
Indices: 76285--76316 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
76275 TCGTGGGCCC
76285 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
76298 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
*
76311 GTCTTT
1 TTCTTT
76317 CAGCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:78844 original size:48 final size:48
Alignment explanation
Indices: 78777--78868 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
78767 GATAAAAAAG
78777 AAGAGGGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAATATAA
1 AAGAGGGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAATATAA
* * * *
78825 AAGAGGGGAAGGGGGTTAATGGGCTAAAAACACTAATTGGAAAT
1 AAGAGGGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAAT
78869 GGGCTAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.47, C:0.07, G:0.30, T:0.16
Consensus pattern (48 bp):
AAGAGGGAAAGGAGGTTAATGGGCTAAAAACACAAATAGGAAATATAA
Found at i:80566 original size:20 final size:20
Alignment explanation
Indices: 80513--80568 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
80503 GCTTTTACCA
*
80513 ATTGGT-AAATTTATTTTTT
1 ATTGGTAAAATTAATTTTTT
80532 ATT-GTATGAATATTAATTTTTT
1 ATTGGTA--AA-ATTAATTTTTT
80554 ATTGGTAAAATTAAT
1 ATTGGTAAAATTAAT
80569 ATATGATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
19 3 0.10
20 6 0.19
21 4 0.13
22 13 0.42
23 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTGGTAAAATTAATTTTTT
Found at i:84296 original size:18 final size:18
Alignment explanation
Indices: 84273--84311 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
84263 TTTATACGAG
84273 AAAATATATAATAAAAAT
1 AAAATATATAATAAAAAT
* *
84291 AAAATATATATTTAAAAT
1 AAAATATATAATAAAAAT
84309 AAA
1 AAA
84312 TGATAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATATAATAAAAAT
Found at i:84390 original size:22 final size:23
Alignment explanation
Indices: 84355--84399 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
84345 ATAAACTTTA
84355 ATTTTGTACAAATTTATATATAT
1 ATTTTGTACAAATTTATATATAT
*
84378 ATTTTTTA-AAATTTATATATAT
1 ATTTTGTACAAATTTATATATAT
84400 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTGTACAAATTTATATATAT
Found at i:84407 original size:24 final size:23
Alignment explanation
Indices: 84353--84409 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
84343 AAATAAACTT
84353 TAATTTTGTACAAATTTATATATA
1 TAATTTT-TACAAATTTATATATA
*
84377 TATTTTTTA-AAATTTATATATA
1 TAATTTTTACAAATTTATATATA
84399 TGGAATTTTTA
1 T--AATTTTTA
84410 TTTGATCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 14 0.48
23 2 0.07
24 13 0.45
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
TAATTTTTACAAATTTATATATA
Found at i:86387 original size:3 final size:3
Alignment explanation
Indices: 86379--86404 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
86369 AAGGGTCGCT
86379 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
86405 TTTCCTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:87445 original size:11 final size:12
Alignment explanation
Indices: 87423--87465 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
87413 TTTAACTCAC
87423 AAATTAATATTT
1 AAATTAATATTT
*
87435 AAATTATATTTTTT
1 AAATTA-A-TATTT
*
87449 ATATTAATATTT
1 AAATTAATATTT
87461 AAATT
1 AAATT
87466 TTGGTACCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 14 0.56
13 2 0.08
14 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTAATATTT
Found at i:98479 original size:22 final size:22
Alignment explanation
Indices: 98453--98499 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
98443 AGTTTCAATA
* * *
98453 TTCAATTTGGTACTTGATCTTT
1 TTCAATTTGATACATGAGCTTT
98475 TTCAATTTGATACATGAGCTTT
1 TTCAATTTGATACATGAGCTTT
98497 TTC
1 TTC
98500 TTTTTGTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (22 bp):
TTCAATTTGATACATGAGCTTT
Found at i:99009 original size:8 final size:8
Alignment explanation
Indices: 98993--99094 Score: 52
Period size: 8 Copynumber: 12.1 Consensus size: 8
98983 ATGAAAAATT
*
98993 ATTAAAAA
1 ATTATAAA
99001 ATTATAAA
1 ATTATAAA
99009 A--ATAAA
1 ATTATAAA
*
99015 A-TATTAA
1 ATTATAAA
99022 A-TATTAAA
1 ATTA-TAAA
99030 ATTGATATAA
1 ATT-ATA-AA
99040 ACTTATTAAA
1 A-TTA-TAAA
99050 ATTATAAA
1 ATTATAAA
99058 AGTATATAAA
1 A-T-TATAAA
*
99068 AATATAAAA
1 ATTAT-AAA
99077 ATCTA-ATAA
1 AT-TATA-AA
99086 ATTATAAA
1 ATTATAAA
99094 A
1 A
99095 AGAATTATAA
Statistics
Matches: 76, Mismatches: 5, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
6 6 0.08
7 7 0.09
8 26 0.34
9 16 0.21
10 17 0.22
11 4 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (8 bp):
ATTATAAA
Found at i:99091 original size:18 final size:17
Alignment explanation
Indices: 98997--99095 Score: 57
Period size: 18 Copynumber: 5.8 Consensus size: 17
98987 AAAATTATTA
98997 AAAAATTAT-AAAA-AT
1 AAAAATTATAAAAATAT
*
99012 -AAAA-TAT-TAAATAT
1 AAAAATTATAAAAATAT
* *
99026 TAAAATTGATATAAACTTAT
1 AAAAATT-ATA-AAA-ATAT
*
99046 TAAAATTATAAAAGTATAT
1 AAAAATTATAAAA--ATAT
*
99065 AAAAA-TATAAAAATCT
1 AAAAATTATAAAAATAT
99081 AATAAATTATAAAAA
1 AA-AAATTATAAAAA
99096 GAATTATAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
13 6 0.09
14 6 0.09
15 4 0.06
16 6 0.09
17 5 0.07
18 18 0.27
19 12 0.18
20 10 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAATTATAAAAATAT
Found at i:99124 original size:38 final size:37
Alignment explanation
Indices: 99024--99124 Score: 86
Period size: 37 Copynumber: 2.7 Consensus size: 37
99014 AATATTAAAT
* *
99024 ATTA-AAATTGATATAAACTTAT-TAAAATTATAAAAGT
1 ATTATAAATTAATA-AAACTTATAT-AAATTATAAAAGA
* *
99061 A-TATAAA-AATATAAAAATCTA-ATAAATTATAAAAAGA
1 ATTATAAATTA-ATAAAACT-TATATAAATTAT-AAAAGA
99098 ATTATAAATTAATAAAACTTATATAAA
1 ATTATAAATTAATAAAACTTATATAAA
99125 ATATTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
36 13 0.26
37 18 0.36
38 18 0.36
39 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (37 bp):
ATTATAAATTAATAAAACTTATATAAATTATAAAAGA
Found at i:99135 original size:29 final size:28
Alignment explanation
Indices: 99045--99166 Score: 83
Period size: 29 Copynumber: 4.3 Consensus size: 28
99035 TATAAACTTA
99045 TTAAAATT-ATAAAAGTATATAAAA-AT
1 TTAAAATTAATAAAAGTATATAAAATAT
* * * *
99071 ATAAAAATCTAAT-AAATTATA-AAAAGAA
1 -TTAAAAT-TAATAAAAGTATATAAAATAT
*
99099 TTATAAATTAATAAAACTTATATAAAATAT
1 TTA-AAATTAATAAAA-GTATATAAAATAT
* * *
99129 TTAAAATTAAAAAAACGTAT-TAGAATTT
1 TTAAAATTAATAAAA-GTATATAAAATAT
99157 TTATAAATTA
1 TTA-AAATTA
99167 CGAAATATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 16 0.21
28 25 0.32
29 28 0.36
30 8 0.10
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
TTAAAATTAATAAAAGTATATAAAATAT
Found at i:108041 original size:28 final size:29
Alignment explanation
Indices: 108009--108077 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
107999 ATTAGACCTG
108009 AATTTCAAATTTTAAAAAAATAG-GACTA
1 AATTTCAAATTTTAAAAAAATAGAGACTA
** *
108037 AATTTCTAAA-AATAAAAATATAGAGACTA
1 AATTTC-AAATTTTAAAAAAATAGAGACTA
108066 AATTAT-AAATTT
1 AATT-TCAAATTT
108078 ATGAAAAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
28 19 0.59
29 12 0.38
30 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (29 bp):
AATTTCAAATTTTAAAAAAATAGAGACTA
Found at i:108313 original size:30 final size:30
Alignment explanation
Indices: 108283--108340 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
108273 TTAAATATTA
*
108283 AAATAATAAA-AAAATTTAAGTATTAAATT
1 AAATAATAAACAAAATTTAAGTATCAAATT
* *
108312 AAATATTAAACTAAATTTAAGTATCAAAT
1 AAATAATAAACAAAATTTAAGTATCAAAT
108341 GATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATAATAAACAAAATTTAAGTATCAAATT
Found at i:109578 original size:5 final size:5
Alignment explanation
Indices: 109570--109601 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
109560 CCCTTAAATT
109570 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
109602 AATTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:110151 original size:3 final size:3
Alignment explanation
Indices: 110137--110189 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
110127 AGGAGACTCA
* * * *
110137 GAT GAG GAT GAT GAT GAT GAT AAT GAT GAT GAT GAT GGT GAT GAT GGT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
110185 GAT GA
1 GAT GA
110190 AGGTGAGGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:110194 original size:9 final size:9
Alignment explanation
Indices: 110143--110195 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
110133 CTCAGATGAG
*
110143 GATGATGAT
1 GATGGTGAT
* *
110152 GATGATAAT
1 GATGGTGAT
*
110161 GATGATGAT
1 GATGGTGAT
110170 GATGGTGAT
1 GATGGTGAT
110179 GATGGTGAT
1 GATGGTGAT
*
110188 GAAGGTGA
1 GATGGTGA
110196 GGCTATGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (9 bp):
GATGGTGAT
Found at i:113952 original size:19 final size:19
Alignment explanation
Indices: 113928--113964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
113918 AAGATAAGAT
113928 TTTTTTGAGATAATATCTG
1 TTTTTTGAGATAATATCTG
*
113947 TTTTTTTAGATAATATCT
1 TTTTTTGAGATAATATCT
113965 AAAATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTTTGAGATAATATCTG
Found at i:119548 original size:24 final size:24
Alignment explanation
Indices: 119493--119551 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
119483 TTAAGATAAT
* *
119493 AAAAA-TATAATTTTATTATTTTA
1 AAAAATTATATTTTTATCATTTTA
* **
119516 ATAGTTTATATTTTTATCATTTTA
1 AAAAATTATATTTTTATCATTTTA
119540 AAAAATTATATT
1 AAAAATTATATT
119552 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
AAAAATTATATTTTTATCATTTTA
Found at i:134524 original size:11 final size:11
Alignment explanation
Indices: 134508--134635 Score: 72
Period size: 11 Copynumber: 12.9 Consensus size: 11
134498 ATAAAAAATT
134508 TATTTTAAAAA
1 TATTTTAAAAA
134519 TATTTT--AAA
1 TATTTTAAAAA
134528 -A--TTAAAAA
1 TATTTTAAAAA
** *
134536 -AAATTAAAAG
1 TATTTTAAAAA
134546 TATTTTAAAAA
1 TATTTTAAAAA
134557 TATTTT--AAA
1 TATTTTAAAAA
*
134566 -A--TTAAAAG
1 TATTTTAAAAA
134574 TATTTTAAAAA
1 TATTTTAAAAA
134585 TATTTT--AAA
1 TATTTTAAAAA
134594 -A--TTAAAAA
1 TATTTTAAAAA
*
134602 AATTTTAAAAAA
1 TATTTT-AAAAA
*
134614 GTATTTTAAAAG
1 -TATTTTAAAAA
134626 TATTTTAAAA
1 TATTTTAAAA
134636 TTTAAAAAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 34
0.69 0.06 0.25
Matches are distributed among these distances:
6 6 0.07
8 12 0.13
9 11 0.12
10 6 0.07
11 43 0.47
12 9 0.10
13 5 0.05
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:134534 original size:17 final size:17
Alignment explanation
Indices: 134512--134611 Score: 77
Period size: 17 Copynumber: 6.0 Consensus size: 17
134502 AAAATTTATT
134512 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* * *
134529 TTAAAAAAAATTAAAAGTA
1 TTAAAAATATTTTAAA--A
134548 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
*
134567 TTAAAAGTA--TT----
1 TTAAAAATATTTTAAAA
134578 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
134595 TTAAAAAAATTTTAAAA
1 TTAAAAATATTTTAAAA
134612 AAGTATTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
11 8 0.12
13 2 0.03
15 2 0.03
17 37 0.58
19 2 0.03
21 13 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:134536 original size:38 final size:37
Alignment explanation
Indices: 134477--134648 Score: 148
Period size: 41 Copynumber: 4.6 Consensus size: 37
134467 CCAAAAAATT
*
134477 TATTTTAAAAATTAAACAAAAATAAAAAATTTATTTTAAAAA
1 TATTTT-AAAATTAAA-AAAAAT--AAAA-GTATTTTAAAAA
134519 TATTTTAAAATTAAAAAAAATTAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAA-TAAAAGTATTTTAAAAA
134557 TATTTTAAAA-T--------TAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATAAAAGTATTTTAAAAA
* *
134585 TATTTTAAAATTAAAAAAATTTTAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA----ATAAAAGTATTTTAAAAA
*
134626 TATTTTAAAATT-TAAAAAATAAA
1 TATTTTAAAATTAAAAAAAATAAA
134649 TAAAAAAATA
Statistics
Matches: 111, Mismatches: 5, Indels: 34
0.74 0.03 0.23
Matches are distributed among these distances:
28 27 0.24
29 1 0.01
36 4 0.04
37 1 0.01
38 21 0.19
39 4 0.04
40 10 0.09
41 37 0.33
42 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (37 bp):
TATTTTAAAATTAAAAAAAATAAAAGTATTTTAAAAA
Found at i:134566 original size:28 final size:28
Alignment explanation
Indices: 134535--134624 Score: 144
Period size: 28 Copynumber: 3.1 Consensus size: 28
134525 AAAATTAAAA
134535 AAAATTAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAGTATTTTAAAAATATTTT
134563 AAAATTAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAGTATTTTAAAAATATTTT
**
134591 AAAATTAAAAAAATTTTAAAAAAGTATTTT
1 AAAATTAAAAGTATTTT-AAAAA-TATTTT
134621 AAAA
1 AAAA
134625 GTATTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
28 43 0.74
29 5 0.09
30 10 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTAAAAGTATTTTAAAAATATTTT
Found at i:144430 original size:3 final size:3
Alignment explanation
Indices: 144422--144461 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
144412 TTTAGCAACT
144422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
144462 CATTGCTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:145889 original size:55 final size:57
Alignment explanation
Indices: 145825--145937 Score: 160
Period size: 56 Copynumber: 2.0 Consensus size: 57
145815 CTGAATCTGC
* *
145825 AAAACTATAAATATCCA-TTT-TCATGAGACTCTTCTCTTTCATCAATC-ACCTTCTT
1 AAAACTATAAATATCCATTTTCTCAT-AAACTCTTCTCATTCATCAATCGACCTTCTT
* *
145880 AAAACTATAAATATCCATTTTCTCATAAATTCTTCTCATTCATCAATCGACTTTCTT
1 AAAACTATAAATATCCATTTTCTCATAAACTCTTCTCATTCATCAATCGACCTTCTT
145937 A
1 A
145938 CCAAACAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 17 0.33
56 22 0.43
57 12 0.24
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.41
Consensus pattern (57 bp):
AAAACTATAAATATCCATTTTCTCATAAACTCTTCTCATTCATCAATCGACCTTCTT
Found at i:150177 original size:15 final size:15
Alignment explanation
Indices: 150132--150239 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
150122 CCAATATCTC
150132 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
150147 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
150162 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
150177 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
150192 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
150207 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
150222 GATACCCATATCTTT
1 GATACCCATATCTTT
150237 GAT
1 GAT
150240 TTTCCATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:150246 original size:30 final size:30
Alignment explanation
Indices: 150122--150245 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
150112 TTTTATTATG
*
150122 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
150153 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
150183 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
150213 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
150243 CCA
1 CCA
150246 TAAATATGGA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 83 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:154865 original size:30 final size:30
Alignment explanation
Indices: 154814--154907 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
154804 TTTTATTATG
* *
154814 CCAATATCTCGATACCTATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
154845 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
154875 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
154905 CCA
1 CCA
154908 TAAATATGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 52 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:154869 original size:15 final size:15
Alignment explanation
Indices: 154824--154901 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
154814 CCAATATCTC
*
154824 GATACCTATATCTTT
1 GATACCCATATCTTT
** *
154839 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
154854 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
154869 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
154884 GATACCCATATCTTT
1 GATACCCATATCTTT
154899 GAT
1 GAT
154902 TTTCCATAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 9 0.20
15 29 0.63
16 8 0.17
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:161160 original size:27 final size:27
Alignment explanation
Indices: 161130--161188 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
161120 TTATTGAGGA
* *
161130 GGAGTGTATTGATGCTACTACTAAGGG
1 GGAGTCTATTGATGCTACAACTAAGGG
* * *
161157 GGAGTCTGTTGATGCTACAATTATGGG
1 GGAGTCTATTGATGCTACAACTAAGGG
161184 GGAGT
1 GGAGT
161189 TTTCTTCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (27 bp):
GGAGTCTATTGATGCTACAACTAAGGG
Found at i:165898 original size:15 final size:16
Alignment explanation
Indices: 165872--165901 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
165862 TTGATAAATT
165872 GAAAAGTTAAGTACTG
1 GAAAAGTTAAGTACTG
165888 GAAAA-TTAAGTACT
1 GAAAAGTTAAGTACT
165902 AAATTTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
GAAAAGTTAAGTACTG
Found at i:172973 original size:21 final size:20
Alignment explanation
Indices: 172935--172978 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
172925 AACTTTGCTT
* *
172935 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGAA
*
172955 AAATTTATGAATAAAAAAGAA
1 AAATTTAAG-ATAAAAAAGAA
172976 AAA
1 AAA
172979 GAGTCCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGAA
Found at i:172977 original size:20 final size:20
Alignment explanation
Indices: 172935--172977 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
172925 AACTTTGCTT
*
172935 AAATTTAAGATAACAAAGCA
1 AAATTTAAGATAAAAAAGCA
*
172955 AAATTTATGAATAAAAAAG-A
1 AAATTTAAG-ATAAAAAAGCA
172975 AAA
1 AAA
172978 AGAGTCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (20 bp):
AAATTTAAGATAAAAAAGCA
Found at i:188705 original size:18 final size:17
Alignment explanation
Indices: 188677--188715 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
188667 TTCTTTTCTT
*
188677 ATTAGATTAAAGTAGAA
1 ATTAGATTAAAATAGAA
*
188694 ATTAGTATTAAAATAGAG
1 ATTAG-ATTAAAATAGAA
188712 ATTA
1 ATTA
188716 TGCACAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTAGATTAAAATAGAA
Found at i:196552 original size:20 final size:20
Alignment explanation
Indices: 196529--196566 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
196519 TGTAACTTTA
196529 TAATA-ATTTTATAATTTTTT
1 TAATATATTTTA-AATTTTTT
196549 TAATATATTTTAAATTTT
1 TAATATATTTTAAATTTT
196567 AAAAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATATATTTTAAATTTTTT
Found at i:196878 original size:22 final size:21
Alignment explanation
Indices: 196842--196901 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
196832 GGCCTGGCCC
*
196842 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA-AAAAA
196864 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
**
196886 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
196902 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:196930 original size:37 final size:38
Alignment explanation
Indices: 196874--196952 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 38
196864 ATTTATTTTA
196874 AAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATT
*
196912 AAAATT-AAAAAAAGTATTTTGAAAATATTTTAAAATT
1 AAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATT
196949 AAAA
1 AAAA
196953 AATTTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 34 0.85
38 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (38 bp):
AAAATTAAAAAAAAGTATTTTAAAAATATTTTAAAATT
Found at i:196974 original size:17 final size:16
Alignment explanation
Indices: 196933--196974 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
196923 AAGTATTTTG
*
196933 AAAATATTTTAAAATT
1 AAAATATTTTAAAAAT
*
196949 AAAAAATTTTAAAAAT
1 AAAATATTTTAAAAAT
196965 AAATATATTT
1 AAA-ATATTT
196975 ATTATATCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATATTTTAAAAAT
Found at i:207228 original size:56 final size:56
Alignment explanation
Indices: 207166--207277 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
207156 CTCAATCACG
207166 ATACTATAGTAGAATGACTTCGTGACTAAATGAGATTATAATTAATAGGCGAAAAA
1 ATACTATAGTAGAATGACTTCGTGACTAAATGAGATTATAATTAATAGGCGAAAAA
207222 ATACTATAGTAGAATGACTTCGTGACTAAATGAGATTATAATTAATAGGCGAAAAA
1 ATACTATAGTAGAATGACTTCGTGACTAAATGAGATTATAATTAATAGGCGAAAAA
207278 CTGGAACTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (56 bp):
ATACTATAGTAGAATGACTTCGTGACTAAATGAGATTATAATTAATAGGCGAAAAA
Found at i:220769 original size:12 final size:12
Alignment explanation
Indices: 220752--220776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220742 ATTTTATAAC
220752 ATAAATATTGTT
1 ATAAATATTGTT
220764 ATAAATATTGTT
1 ATAAATATTGTT
220776 A
1 A
220777 ATAGCCTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:225125 original size:23 final size:24
Alignment explanation
Indices: 225091--225143 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
225081 TCAAGGTTCG
225091 TTTC-TTTTCTACCAAACA-GGTT
1 TTTCTTTTTCTACCAAACAGGGTT
225113 TTTCTTTTTCTACCAAACAGGGTT
1 TTTCTTTTTCTACCAAACAGGGTT
225137 TGTTCTT
1 T-TTCTT
225144 ATACTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.14
23 14 0.50
24 5 0.18
25 5 0.18
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCTTTTTCTACCAAACAGGGTT
Found at i:227207 original size:22 final size:22
Alignment explanation
Indices: 227160--227212 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
227150 AATAATATTA
* * *
227160 ATAAATCATAATATTAATATGC
1 ATAAATAATAATATGAAAATGC
227182 ATAAATAATAATTATGAAAATG-
1 ATAAATAATAA-TATGAAAATGC
227204 ATAATATAA
1 ATAA-ATAA
227213 ATAACAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.34
Consensus pattern (22 bp):
ATAAATAATAATATGAAAATGC
Found at i:227250 original size:16 final size:18
Alignment explanation
Indices: 227206--227251 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
227196 TGAAAATGAT
227206 AATATAAATAACAATAAC
1 AATATAAATAACAATAAC
227224 AATATATAATAAC-ATAA-
1 AATATA-AATAACAATAAC
*
227241 ATTATAAATAA
1 AATATAAATAA
227252 TCTAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
18 10 0.38
19 6 0.23
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (18 bp):
AATATAAATAACAATAAC
Found at i:227306 original size:23 final size:25
Alignment explanation
Indices: 227279--227337 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
227269 TCATAAAAAG
227279 TAATAAATAAATAA-ATAATGG-AA
1 TAATAAATAAATAAGATAATGGCAA
227302 TAAT-AATAAA-AATGATAATGGCAA
1 TAATAAATAAATAA-GATAATGGCAA
*
227326 -AATAAAAAAATA
1 TAATAAATAAATA
227338 CAAAAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 2 0.07
22 6 0.20
23 14 0.47
24 7 0.23
25 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (25 bp):
TAATAAATAAATAAGATAATGGCAA
Found at i:227442 original size:18 final size:18
Alignment explanation
Indices: 227419--227454 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
227409 TTAAAAATTG
227419 AAAATAAATAAAT-AAATA
1 AAAAT-AATAAATGAAATA
227437 AAAATAATAAATGAAATA
1 AAAATAATAAATGAAATA
227455 GTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAATAATAAATGAAATA
Found at i:227466 original size:21 final size:20
Alignment explanation
Indices: 227419--227473 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
227409 TTAAAAATTG
227419 AAAATAAATAAATAAATAAA
1 AAAATAAATAAATAAATAAA
** *
227439 AATAATAAATGAAATAGTTTAA
1 AA-AATAAAT-AAATAAATAAA
*
227461 AAAATAAAAAAAT
1 AAAATAAATAAAT
227474 TGAAGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 13 0.45
22 10 0.34
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAATAAATAAATAAATAAA
Found at i:228753 original size:17 final size:17
Alignment explanation
Indices: 228731--228768 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
228721 TTGTCTCCAC
228731 TCAAATTCTCCATATTT
1 TCAAATTCTCCATATTT
228748 TCAAATTCTCCATATTT
1 TCAAATTCTCCATATTT
228765 TCAA
1 TCAA
228769 GATCCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TCAAATTCTCCATATTT
Found at i:235120 original size:9 final size:9
Alignment explanation
Indices: 235108--235176 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
235098 AAATATATTT
235108 ATTTTTTAA
1 ATTTTTTAA
235117 ATTTTTTAA
1 ATTTTTTAA
*
235126 A-TTTTAAA
1 ATTTTTTAA
235134 ATATTTTTAAAA
1 AT-TTTTT--AA
*
235146 TACTTTTTTTA
1 -A-TTTTTTAA
*
235157 ATTTTTTTA
1 ATTTTTTAA
*
235166 ATTTTTAAA
1 ATTTTTTAA
235175 AT
1 AT
235177 AAATTTTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.14
9 27 0.55
10 5 0.10
11 1 0.02
12 2 0.04
13 6 0.12
14 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:235140 original size:18 final size:17
Alignment explanation
Indices: 235110--235144 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
235100 ATATATTTAT
*
235110 TTTTTAAATTTTTTAAA
1 TTTTAAAATTTTTTAAA
235127 TTTTAAAATATTTTTAAA
1 TTTTAAAAT-TTTTTAAA
235145 ATACTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAAATTTTTTAAA
Found at i:235192 original size:31 final size:30
Alignment explanation
Indices: 235136--235197 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
235126 ATTTTAAAAT
** * *
235136 ATTTTTAAAATACTTTTTTTAATTTTTTTA
1 ATTTTTAAAATAAATTTTTGAATTTTATTA
235166 ATTTTTAAAATAAATTTTTGATATTTTATTA
1 ATTTTTAAAATAAATTTTTGA-ATTTTATTA
235197 A
1 A
235198 AAATGGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (30 bp):
ATTTTTAAAATAAATTTTTGAATTTTATTA
Found at i:238079 original size:55 final size:56
Alignment explanation
Indices: 237971--238083 Score: 167
Period size: 55 Copynumber: 2.0 Consensus size: 56
237961 TATTGTTTGG
*
237971 TAAGAAAGTCGATTGATGAATGAGAAGAATTTATGAGAAAATGGATATTTATAGTTT
1 TAAGAAAGTCGATTGATGAATGAGAAGAATTCAT-AGAAAATGGATATTTATAGTTT
* *
238028 TAAGAAGGT-GATTGATGAATGAGAAGAGTCTCAT-GAAAATGGATATTTATAGTTT
1 TAAGAAAGTCGATTGATGAATGAGAAGAAT-TCATAGAAAATGGATATTTATAGTTT
238083 T
1 T
238084 GCAGATTAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 22 0.42
56 19 0.37
57 11 0.21
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.34
Consensus pattern (56 bp):
TAAGAAAGTCGATTGATGAATGAGAAGAATTCATAGAAAATGGATATTTATAGTTT
Found at i:242753 original size:29 final size:26
Alignment explanation
Indices: 242709--242763 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
242699 TTTGATTCTT
242709 TTTAATATAGGGACTAA-ATTGATCCA
1 TTTAATATAGGGACTAACA-TGATCCA
242735 TTTAATAATAGAGGTACTAACATGATCCA
1 TTTAAT-ATAG-GG-ACTAACATGATCCA
242764 GCCCCTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.24
27 4 0.16
28 2 0.08
29 12 0.48
30 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (26 bp):
TTTAATATAGGGACTAACATGATCCA
Found at i:251865 original size:93 final size:93
Alignment explanation
Indices: 251702--251891 Score: 353
Period size: 93 Copynumber: 2.0 Consensus size: 93
251692 TATTTGTTCA
* *
251702 GTAAAGGAGACAAAATGCAATTTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTTT
1 GTAAAGGAGACAAAATACAAATTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTTT
251767 CACCACCGAAGAATAATGAGAAGACACT
66 CACCACCGAAGAATAATGAGAAGACACT
251795 GTAAAGGAGACAAAATACAAATTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTTT
1 GTAAAGGAGACAAAATACAAATTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTTT
*
251860 TACCACCGAAGAATAATGAGAAGACACT
66 CACCACCGAAGAATAATGAGAAGACACT
251888 GTAA
1 GTAA
251892 CACCATAAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (93 bp):
GTAAAGGAGACAAAATACAAATTAAATCTTAGTATATTTTAATATAAAGGCCTCCATGATGCTTT
CACCACCGAAGAATAATGAGAAGACACT
Found at i:267641 original size:22 final size:24
Alignment explanation
Indices: 267589--267641 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
267579 TAAAATATTA
267589 AAATTTAATATTTTGAATTAATTC
1 AAATTTAATATTTTGAATTAATTC
* *
267613 AAATTTATTATTTT-AA-TAATTT
1 AAATTTAATATTTTGAATTAATTC
267635 AAATTTA
1 AAATTTA
267642 GGTTTGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 12 0.44
23 2 0.07
24 13 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATTTAATATTTTGAATTAATTC
Found at i:271755 original size:31 final size:31
Alignment explanation
Indices: 271714--271784 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
271704 TAAATATATC
* * * *
271714 ATTTGATATTTGAGTTTAGTTTTAATGTTTA
1 ATTTGATATTTGAATTTAGCTTCAATGTTCA
*
271745 ATTTGGTATTTGAATTTAGCTTCAATGTTCA
1 ATTTGATATTTGAATTTAGCTTCAATGTTCA
*
271776 ATTTTATAT
1 ATTTGATAT
271785 AAAATAGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (31 bp):
ATTTGATATTTGAATTTAGCTTCAATGTTCA
Found at i:279840 original size:14 final size:16
Alignment explanation
Indices: 279816--279851 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
279806 TTTTAAAAAA
279816 TTAATATATAT-ATTT
1 TTAATATATATAATTT
279831 TTAA-ATATATAATTT
1 TTAATATATATAATTT
279846 TTAATA
1 TTAATA
279852 ATTTACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATATATATAATTT
Found at i:291604 original size:73 final size:74
Alignment explanation
Indices: 291469--291617 Score: 273
Period size: 73 Copynumber: 2.0 Consensus size: 74
291459 TTATATGGCT
*
291469 TTCTCTTTTTCCCTCTTTTCTACAGTTCATTTTTTTAATGAAAATAACTTTGGATGTCACGAATT
1 TTCTCTTTTTCCCTCTCTTCTACAGTTCATTTTTTTAATGAAAATAACTTTGGATGTCACGAATT
291534 TGTGAATCA
66 TGTGAATCA
*
291543 TTCTCTTTTTTCCTCTCTTCTACAGTTCA-TTTTTTAATGAAAATAACTTTGGATGTCACGAATT
1 TTCTCTTTTTCCCTCTCTTCTACAGTTCATTTTTTTAATGAAAATAACTTTGGATGTCACGAATT
291607 TGTGAATCA
66 TGTGAATCA
291616 TT
1 TT
291618 GTACCAATCG
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 46 0.63
74 27 0.37
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (74 bp):
TTCTCTTTTTCCCTCTCTTCTACAGTTCATTTTTTTAATGAAAATAACTTTGGATGTCACGAATT
TGTGAATCA
Found at i:298728 original size:17 final size:17
Alignment explanation
Indices: 298706--298749 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
298696 GTTGGACATA
*
298706 TATTTATATTTATATTG
1 TATTTATAATTATATTG
298723 TATTTATAATTATATTG
1 TATTTATAATTATATTG
*
298740 TATTTGTAAT
1 TATTTATAAT
298750 AGTAATTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (17 bp):
TATTTATAATTATATTG
Found at i:298735 original size:23 final size:23
Alignment explanation
Indices: 298704--298747 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
298694 TGGTTGGACA
*
298704 TATATTTATATT-TATATTGTATT
1 TATAATTATATTGTAT-TTGTATT
298727 TATAATTATATTGTATTTGTA
1 TATAATTATATTGTATTTGTA
298748 ATAGTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TATAATTATATTGTATTTGTATT
Found at i:302730 original size:24 final size:23
Alignment explanation
Indices: 302677--302730 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
302667 TATAGATATC
* * *
302677 TTTAATATTTTTTAATGTTTACA
1 TTTAATATTATTTAATATTTAAA
*
302700 TTATAATATTATTTATTATTATAAA
1 TT-TAATATTATTTAATATT-TAAA
302725 TTTAAT
1 TTTAAT
302731 TTTTGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 18 0.72
25 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTAATATTATTTAATATTTAAA
Found at i:303751 original size:22 final size:22
Alignment explanation
Indices: 303717--303760 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
303707 TTTTTAAAAT
*
303717 TTTTATATTATTTAATTTTTTTA
1 TTTTATATTATTT-ATGTTTTTA
303740 TTTTA-ATTATTTATGTTTTTA
1 TTTTATATTATTTATGTTTTTA
303761 AATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTATATTATTTATGTTTTTA
Found at i:306750 original size:16 final size:17
Alignment explanation
Indices: 306719--306752 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
306709 CATTGTATTT
*
306719 AATTTCTATAATTTTAA
1 AATTTATATAATTTTAA
306736 AATTTATAT-ATTTTAA
1 AATTTATATAATTTTAA
306752 A
1 A
306753 CTAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATATAATTTTAA
Found at i:312440 original size:51 final size:51
Alignment explanation
Indices: 312358--312573 Score: 344
Period size: 51 Copynumber: 4.3 Consensus size: 51
312348 ACTTCTGATC
*
312358 AGTGATAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
312409 AGTGGCAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTAATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
312460 AATGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATTTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
312511 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTATACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
312561 AGTGATAAGTGAT
1 AGTGACAAGTGAT
312574 CATACGTAAG
Statistics
Matches: 151, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 34 0.23
51 117 0.77
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:322882 original size:17 final size:17
Alignment explanation
Indices: 322850--322911 Score: 70
Period size: 17 Copynumber: 3.4 Consensus size: 17
322840 TTAAAGCTAT
322850 TTTTTTATATTTTATTTA
1 TTTTTTA-ATTTTATTTA
* *
322868 TTTTTTAATTGTATTTG
1 TTTTTTAATTTTATTTA
322885 TTGTTGTCTAATTTTATTTA
1 TT-TT-T-TAATTTTATTTA
322905 TTTTTTA
1 TTTTTTA
322912 TATATTCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
17 12 0.32
18 10 0.27
19 3 0.08
20 12 0.32
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTTTAATTTTATTTA
Found at i:323831 original size:25 final size:26
Alignment explanation
Indices: 323778--323831 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
323768 CATACTAAGG
323778 AAGATTTTCTTAGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
*
323804 AAGATTTTCTTGGCCTGA-TTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
323829 AAG
1 AAG
323832 TATTCTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (26 bp):
AAGATTTTCTTAGCCTGATTTTCTTT
Found at i:324348 original size:55 final size:55
Alignment explanation
Indices: 324264--324373 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
324254 AGATAACTAG
324264 TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTA-TATAACGAATATTGATGTAC
1 TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTACT-TAACGAATATTGATGTAC
324319 TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
1 TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
324374 GATAATGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 53 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (55 bp):
TATATTTTTCTCTTTATTCCTTGTTTTGTGGATTACTTAACGAATATTGATGTAC
Found at i:327455 original size:21 final size:21
Alignment explanation
Indices: 327429--327469 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
327419 AGACGAGCAA
* *
327429 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
327450 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
327470 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:336752 original size:25 final size:27
Alignment explanation
Indices: 336694--336752 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
336684 AAAATAAAGT
336694 CCCAAAATTACAACAAACAAAACCAGG
1 CCCAAAATTACAACAAACAAAACCAGG
* **
336721 CCTAAAATTA-AACAAACCCAA-CAGG
1 CCCAAAATTACAACAAACAAAACCAGG
336746 CCCAAAA
1 CCCAAAA
336753 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 9 0.32
27 9 0.32
ACGTcount: A:0.54, C:0.31, G:0.07, T:0.08
Consensus pattern (27 bp):
CCCAAAATTACAACAAACAAAACCAGG
Found at i:336753 original size:26 final size:27
Alignment explanation
Indices: 336697--336755 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
336687 ATAAAGTCCC
*
336697 AAAATTACAACAAACAAAACCAGGCCT
1 AAAATTACAACAAACAAAACCAGGCCA
**
336724 AAAATTA-AACAAACCCAA-CAGGCCCA
1 AAAATTACAACAAACAAAACCAGG-CCA
336750 AAAATT
1 AAAATT
336756 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 17 0.61
27 7 0.25
ACGTcount: A:0.56, C:0.25, G:0.07, T:0.12
Consensus pattern (27 bp):
AAAATTACAACAAACAAAACCAGGCCA
Found at i:338050 original size:3 final size:3
Alignment explanation
Indices: 338042--338087 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
338032 ACTTTTTGCC
338042 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
338088 TTATTATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:338094 original size:3 final size:3
Alignment explanation
Indices: 338088--338225 Score: 159
Period size: 3 Copynumber: 46.0 Consensus size: 3
338078 TCTTCTTCTT
* *
338088 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * * *
338136 TTG TTG TTG TGG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
338184 TTG TGG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
338226 CTACTGGCAC
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:338165 original size:42 final size:42
Alignment explanation
Indices: 338106--338218 Score: 217
Period size: 42 Copynumber: 2.7 Consensus size: 42
338096 ATTATTATTA
*
338106 TTATTATTATTATTATTATTATTATTGTTGTTGTTGTTGTGG
1 TTATTATTATTATTATTATTATTATTATTGTTGTTGTTGTGG
338148 TTATTATTATTATTATTATTATTATTATTGTTGTTGTTGTGG
1 TTATTATTATTATTATTATTATTATTATTGTTGTTGTTGTGG
338190 TTATTATTATTATTATTATTATTATTATT
1 TTATTATTATTATTATTATTATTATTATT
338219 ATTATTACTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (42 bp):
TTATTATTATTATTATTATTATTATTATTGTTGTTGTTGTGG
Found at i:354281 original size:25 final size:27
Alignment explanation
Indices: 354223--354281 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
354213 AAAATAAAGT
354223 CCCAAAATTACAACAAACAAAACCAGG
1 CCCAAAATTACAACAAACAAAACCAGG
* **
354250 CCTAAAATTA-AACAAACCCAA-CAGG
1 CCCAAAATTACAACAAACAAAACCAGG
354275 CCCAAAA
1 CCCAAAA
354282 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 9 0.32
27 9 0.32
ACGTcount: A:0.54, C:0.31, G:0.07, T:0.08
Consensus pattern (27 bp):
CCCAAAATTACAACAAACAAAACCAGG
Found at i:354282 original size:26 final size:27
Alignment explanation
Indices: 354226--354284 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
354216 ATAAAGTCCC
*
354226 AAAATTACAACAAACAAAACCAGGCCT
1 AAAATTACAACAAACAAAACCAGGCCA
**
354253 AAAATTA-AACAAACCCAA-CAGGCCCA
1 AAAATTACAACAAACAAAACCAGG-CCA
354279 AAAATT
1 AAAATT
354285 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 17 0.61
27 7 0.25
ACGTcount: A:0.56, C:0.25, G:0.07, T:0.12
Consensus pattern (27 bp):
AAAATTACAACAAACAAAACCAGGCCA
Found at i:355578 original size:3 final size:3
Alignment explanation
Indices: 355570--355614 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
355560 ACTTTTTGCC
355570 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
355615 ATTATTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:355619 original size:3 final size:3
Alignment explanation
Indices: 355613--355759 Score: 186
Period size: 3 Copynumber: 49.0 Consensus size: 3
355603 CTTCTTCTTC
355613 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * **
355661 TTA TTG TTG TTG TTG TTG TGG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * **
355709 TTG TTG TTG TGG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
355757 TTA
1 TTA
355760 CTACTGGCAC
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 136 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:355686 original size:39 final size:39
Alignment explanation
Indices: 355613--355749 Score: 211
Period size: 39 Copynumber: 3.5 Consensus size: 39
355603 CTTCTTCTTC
* * * **
355613 TTATTATTATTATTATTATTATTATTATTATTATTATTA
1 TTATTATTATTATTATTATTGTTGTTGTGGTTATTATTA
* *
355652 TTATTATTATTATTGTTGTTGTTGTTGTGGTTATTATTA
1 TTATTATTATTATTATTATTGTTGTTGTGGTTATTATTA
355691 TTATTATTATTATTATTATTGTTGTTGTGGTTATTATTA
1 TTATTATTATTATTATTATTGTTGTTGTGGTTATTATTA
355730 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
355750 ATTATTATTA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (39 bp):
TTATTATTATTATTATTATTGTTGTTGTGGTTATTATTA
Found at i:372855 original size:170 final size:172
Alignment explanation
Indices: 372534--372881 Score: 522
Period size: 170 Copynumber: 2.0 Consensus size: 172
372524 TTTAATTTTA
*
372534 GCCTAAAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTT
1 GCCTCAAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTT
* * *
372599 TAAAATTTACGGAAATAAGCTCGGTATTTTATTATTTACTGGAATGAGTCATTTTCCCCAAAATC
66 TAAAATTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTCATTTTCCCCAAAATC
* * * *
372664 GCGTCTACGTTAGCGCGATGTCAGGGGACGTCAGCAAATCGC
131 GCGTCTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGC
*
372706 GCCTCAAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCCTT-TTTTTT
1 GCCTCAAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTT
* * * *
372770 TTAAATTTACCGAAATAGGCCCGGTA-TTTATTATTTACCGGAATG-GGCTATTTTTCCCAAAAT
66 TAAAATTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTC-ATTTTCCCCAAAAT
* *
372833 TGCTTCTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGC
130 CGCGTCTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGC
372876 GTCCTC
1 G-CCTC
372882 GTAGGCACAA
Statistics
Matches: 159, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
169 2 0.01
170 69 0.43
171 32 0.20
172 56 0.35
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (172 bp):
GCCTCAAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTT
TAAAATTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTCATTTTCCCCAAAATC
GCGTCTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGC
Found at i:374439 original size:15 final size:15
Alignment explanation
Indices: 374414--374448 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
374404 AGACTCTATT
*
374414 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
374428 TAATTAATATTAAGA
1 TAATTAATATTAAGA
374443 TAATTA
1 TAATTA
374449 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:376887 original size:30 final size:30
Alignment explanation
Indices: 376841--376931 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 30
376831 TTTTATTATG
*
376841 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
376872 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
376901 --ATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
376929 CCA
1 CCA
376932 TAAATATGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 23 0.43
28 2 0.04
29 2 0.04
30 20 0.37
31 7 0.13
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:381570 original size:27 final size:29
Alignment explanation
Indices: 381498--381585 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 29
381488 TTTATTATGC
* *
381498 CAATATCTCGATACCCATATATTTGACTTT
1 CAATAT-TTGATACCCATATCTTTGACTTT
381528 CCAATATTTGATACCCATATCTTTGAC-TT
1 -CAATATTTGATACCCATATCTTTGACTTT
* *
381557 -ATTATTTGATACCCATATCTTTGATTTT
1 CAATATTTGATACCCATATCTTTGACTTT
381585 C
1 C
381586 CATAAATATG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
27 23 0.45
28 2 0.04
29 2 0.04
30 18 0.35
31 6 0.12
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (29 bp):
CAATATTTGATACCCATATCTTTGACTTT
Found at i:385564 original size:18 final size:18
Alignment explanation
Indices: 385541--385600 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
385531 AGATGTTCGA
385541 CTTGGATTTTTCCGAAAC
1 CTTGGATTTTTCCGAAAC
* * *
385559 CTTGGA-CTTCCCTGAGAC
1 CTTGGATTTTTCC-GAAAC
* * *
385577 ATTGGATTTCTCTGAAAC
1 CTTGGATTTTTCCGAAAC
385595 CTTGGA
1 CTTGGA
385601 GATCCTCAGG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 4 0.13
18 24 0.80
19 2 0.07
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (18 bp):
CTTGGATTTTTCCGAAAC
Found at i:391114 original size:36 final size:36
Alignment explanation
Indices: 391062--391148 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
391052 CCCAACTACT
*
391062 GTATACGTGAACAGTACTATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTATATACGTGAATAGTGCC
* *
391098 GTATACGTAAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTATATACGTGAATAGTGCC
391134 GTATACGTGAATAGT
1 GTATACGTGAATAGT
391149 GCCGTAAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACTATATACGTGAATAGTGCC
Found at i:391149 original size:18 final size:18
Alignment explanation
Indices: 391062--391154 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
391052 CCCAACTACT
* * *
391062 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTGCC
*
391080 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
* * *
391098 GTATACGTAAATAGTACT
1 GTATACGTGAATAGTGCC
391116 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
391134 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
391152 GTA
1 GTA
391155 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:393050 original size:54 final size:53
Alignment explanation
Indices: 392937--393102 Score: 278
Period size: 54 Copynumber: 3.1 Consensus size: 53
392927 GATACCAAGT
*
392937 ATATTTTTCTCTTTATTCCTTGTTTTGTGGATTATATAACGAATATTGATGTACT
1 ATATTTTTCTCTTTATTCCTTGTTTT-TGGATTAT-TAACGAATATTGATGTACG
392992 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTACTTAACGAATATTGATGTACG
1 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTA-TTAACGAATATTGATGTACG
*
393046 ATATTTTTCTCTTTATTCCTTATTTTTGGATTATTTAACGAATATTGATGTACG
1 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTA-TTAACGAATATTGATGTACG
393100 ATA
1 ATA
393103 ATACTTTGGT
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
54 80 0.75
55 27 0.25
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.52
Consensus pattern (53 bp):
ATATTTTTCTCTTTATTCCTTGTTTTTGGATTATTAACGAATATTGATGTACG
Found at i:393946 original size:22 final size:22
Alignment explanation
Indices: 393921--393989 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
393911 TTTTTTGTAA
393921 TTCAATTGTTAAAGTATGTAGT
1 TTCAATTGTTAAAGTATGTAGT
*** * *
393943 TTC-ATACAT-AATTATTGTTGT
1 TTCAATTGTTAAAGTA-TGTAGT
393964 TTCAATTGTTAAAGTATGTAGT
1 TTCAATTGTTAAAGTATGTAGT
393986 TTCA
1 TTCA
393990 TACATAATTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 15 0.44
23 4 0.12
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (22 bp):
TTCAATTGTTAAAGTATGTAGT
Found at i:393965 original size:21 final size:21
Alignment explanation
Indices: 393941--394007 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
393931 AAAGTATGTA
393941 GTTTCATACATAATTATTGTT
1 GTTTCATACATAATTATTGTT
*** * *
393962 GTTTCAATTGTTAAAGTA-TGTA
1 GTTTC-ATACAT-AATTATTGTT
393984 GTTTCATACATAATTATTGTT
1 GTTTCATACATAATTATTGTT
394005 GTT
1 GTT
394008 AATTTAGAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 11 0.33
23 4 0.12
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.51
Consensus pattern (21 bp):
GTTTCATACATAATTATTGTT
Found at i:393968 original size:43 final size:43
Alignment explanation
Indices: 393921--394007 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
393911 TTTTTTGTAA
393921 TTCAATTGTTAAAGTATGTAGTTTCATACATAATTATTGTTGT
1 TTCAATTGTTAAAGTATGTAGTTTCATACATAATTATTGTTGT
393964 TTCAATTGTTAAAGTATGTAGTTTCATACATAATTATTGTTGT
1 TTCAATTGTTAAAGTATGTAGTTTCATACATAATTATTGTTGT
394007 T
1 T
394008 AATTTAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (43 bp):
TTCAATTGTTAAAGTATGTAGTTTCATACATAATTATTGTTGT
Found at i:396862 original size:20 final size:20
Alignment explanation
Indices: 396837--396886 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
396827 TGGCTTAAAA
396837 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
396857 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
396874 GTGGTAGTGGATT
1 TTGGTAGTGGATT
396887 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:401501 original size:20 final size:20
Alignment explanation
Indices: 401476--401525 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
401466 TGGCTTAAAA
401476 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
401496 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
401513 GTGGTAGTGGATT
1 TTGGTAGTGGATT
401526 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:402825 original size:171 final size:172
Alignment explanation
Indices: 402537--402879 Score: 523
Period size: 171 Copynumber: 2.0 Consensus size: 172
402527 TTTAGCCTAA
402537 AAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTTTAAAA
1 AAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTTTAAAA
* *
402602 TTTACGGAAATAAGCCCGGTATTTTATTATTTACTGGAATGAGTCATTTTCCCCAAAATCGCGTC
66 TTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTCATTTT-CCCAAAATCGCGTC
* * * *
402667 TACGTTAGCGCGATGTCAGGGGA-GTCAGCAAATCGCG-CCTC
130 TACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGCGTCCTC
* *
402708 AAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCCTTATTTTTTTTAAA
1 AAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTTTAAAA
* * * *
402773 TTTACCGAAATAGGCCCGGTA-TTTATTATTTACCGGAATG-GGCTATTTTTCCCAAAATTGCTT
66 TTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTC-A-TTTTCCCAAAATCGCGT
402836 CTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGCGTCCTC
129 CTACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGCGTCCTC
402880 GTAGGCACAA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
169 2 0.01
170 51 0.33
171 99 0.63
172 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (172 bp):
AAAAAAAAAATCTTGACTTGGTCCCTTTCGGGCAAATTACACATAAAAGCATTATTTTTTTAAAA
TTTACCGAAATAAGCCCGGTATTTTATTATTTACCGGAATGAGTCATTTTCCCAAAATCGCGTCT
ACATCAGCGCGATGTCAAGGGACGTCAGAAAATCGCGTCCTC
Found at i:404438 original size:15 final size:15
Alignment explanation
Indices: 404413--404447 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
404403 GACTCTATTT
*
404413 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
404427 TAATTAATATTAAGA
1 TAATTAATATTAAGA
404442 TAATTA
1 TAATTA
404448 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:406937 original size:27 final size:27
Alignment explanation
Indices: 406903--407080 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
406893 TAAATTGTAC
406903 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
406930 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
406956 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* * *
406984 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
407012 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
407039 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
407066 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
407081 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 104 0.83
28 21 0.17
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:407020 original size:82 final size:81
Alignment explanation
Indices: 406904--407059 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
406894 AAATTGTACA
* * * *
406904 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
406968 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
406985 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
407050 TGCGAGTTGA
65 TGCGAATTGA
407060 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:407071 original size:82 final size:81
Alignment explanation
Indices: 406900--407080 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
406890 GAGTAAATTG
* * * *
406900 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
406965 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
406981 TGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
407045 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
407063 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
407081 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:407091 original size:27 final size:27
Alignment explanation
Indices: 406985--407091 Score: 81
Period size: 27 Copynumber: 3.9 Consensus size: 27
406975 TGACCATGCG
*
406985 GCACTAAGTGTGCGAG-TCTAACTATGTA
1 GCACTAAGTGTGCGAGCTC-AA-TATATA
** * * **
407013 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
407040 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
407067 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
407092 CATTCGTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 49 0.74
28 16 0.24
29 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:413176 original size:21 final size:21
Alignment explanation
Indices: 413144--413184 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
413134 GAACATTTGG
413144 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
413165 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
413185 CTCGAGCCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:418650 original size:18 final size:18
Alignment explanation
Indices: 418627--418686 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
418617 AGATGTTCGA
418627 CTTGGATTTTTCCGAAAC
1 CTTGGATTTTTCCGAAAC
** * *
418645 CTTGGA-CCTCCCTGAGAC
1 CTTGGATTTTTCC-GAAAC
* *
418663 CTTGGATTTCTCTGAAAC
1 CTTGGATTTTTCCGAAAC
418681 CTTGGA
1 CTTGGA
418687 GATCCTCAGG
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 3 0.10
18 26 0.87
19 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (18 bp):
CTTGGATTTTTCCGAAAC
Found at i:420953 original size:54 final size:54
Alignment explanation
Indices: 420791--420956 Score: 296
Period size: 54 Copynumber: 3.1 Consensus size: 54
420781 GATACCAAGT
*
420791 ATATTTTTCTCTTTATTCCTTGTTTTGTGGATTATATAACGAATATTGATGTACT
1 ATATTTTTCTCTTTATTCCTTGTTTT-TGGATTATATAACGAATATTGATGTACG
420846 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTATATAACGAATATTGATGTACG
1 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTATATAACGAATATTGATGTACG
* *
420900 ATATTTTTCTCTTTATTCCTTATTTTTGGATTATTTAACGAATATTGATGTACG
1 ATATTTTTCTCTTTATTCCTTGTTTTTGGATTATATAACGAATATTGATGTACG
420954 ATA
1 ATA
420957 ATACTTTGGT
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
54 82 0.76
55 26 0.24
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (54 bp):
ATATTTTTCTCTTTATTCCTTGTTTTTGGATTATATAACGAATATTGATGTACG
Found at i:421800 original size:22 final size:22
Alignment explanation
Indices: 421775--421843 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
421765 TTTTTTGTAA
421775 TTCAATTGTTAAAGTATGTAGT
1 TTCAATTGTTAAAGTATGTAGT
*** * *
421797 TTC-ATACAT-AATTATTGTTGT
1 TTCAATTGTTAAAGTA-TGTAGT
421818 TTCAATTGTTAAAGTATGTAGT
1 TTCAATTGTTAAAGTATGTAGT
421840 TTCA
1 TTCA
421844 TACATAATTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 15 0.44
23 4 0.12
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (22 bp):
TTCAATTGTTAAAGTATGTAGT
Found at i:421819 original size:21 final size:21
Alignment explanation
Indices: 421795--421861 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
421785 AAAGTATGTA
421795 GTTTCATACATAATTATTGTT
1 GTTTCATACATAATTATTGTT
*** * *
421816 GTTTCAATTGTTAAAGTA-TGTA
1 GTTTC-ATACAT-AATTATTGTT
421838 GTTTCATACATAATTATTGTT
1 GTTTCATACATAATTATTGTT
421859 GTT
1 GTT
421862 AATTTAGAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 14 0.42
22 11 0.33
23 4 0.12
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.51
Consensus pattern (21 bp):
GTTTCATACATAATTATTGTT
Done.