Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold502
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: 119424
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 1264 characters in sequence are not A, C, G, or T
Found at i:495 original size:3 final size:3
Alignment explanation
Indices: 478--537 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
468 TTTAGGTTTA
* *
478 ATT ATT AAT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
526 ATT ATT ATT ATT
1 ATT ATT ATT ATT
538 TTGTTAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2590 original size:32 final size:32
Alignment explanation
Indices: 2526--2596 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
2516 CTATTCTGAA
* *
2526 AATAGTTATTTTGGACATAACTATTCTCAAAC
1 AATAGTTATTTTGAACACAACTATTCTCAAAC
* *
2558 AATAGTTATTTTGAACAACAATTGTTCT-AAAC
1 AATAGTTATTTTGAAC-ACAACTATTCTCAAAC
*
2590 AAGAGTT
1 AATAGTT
2597 GTTATTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (32 bp):
AATAGTTATTTTGAACACAACTATTCTCAAAC
Found at i:6888 original size:35 final size:35
Alignment explanation
Indices: 6849--6961 Score: 81
Period size: 35 Copynumber: 3.1 Consensus size: 35
6839 ATTTTCATAA
6849 TCTATACAATGTAAGTGAGAGGATACCTTTCACTC
1 TCTATACAATGTAAGTGAGAGGATACCTTTCACTC
* * * * * *
6884 TCTATTTAAGCTATG-AA-TTACACG-TTCCATTTTCA-TAA
1 TCTA--T-A-CAATGTAAGTGAGAGGATACC--TTTCACT-C
6922 TCTATACAATGTAAGTGAGAGGATACCTTTCACTC
1 TCTATACAATGTAAGTGAGAGGATACCTTTCACTC
6957 TCTAT
1 TCTAT
6962 TTAAGCTATG
Statistics
Matches: 55, Mismatches: 12, Indels: 22
0.62 0.13 0.25
Matches are distributed among these distances:
34 4 0.07
35 17 0.31
36 9 0.16
37 9 0.16
38 12 0.22
39 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (35 bp):
TCTATACAATGTAAGTGAGAGGATACCTTTCACTC
Found at i:6950 original size:73 final size:73
Alignment explanation
Indices: 6831--6975 Score: 290
Period size: 73 Copynumber: 2.0 Consensus size: 73
6821 GACTTGTTGT
6831 CACGTTCCATTTTCATAATCTATACAATGTAAGTGAGAGGATACCTTTCACTCTCTATTTAAGCT
1 CACGTTCCATTTTCATAATCTATACAATGTAAGTGAGAGGATACCTTTCACTCTCTATTTAAGCT
6896 ATGAATTA
66 ATGAATTA
6904 CACGTTCCATTTTCATAATCTATACAATGTAAGTGAGAGGATACCTTTCACTCTCTATTTAAGCT
1 CACGTTCCATTTTCATAATCTATACAATGTAAGTGAGAGGATACCTTTCACTCTCTATTTAAGCT
6969 ATGAATT
66 ATGAATT
6976 CCACTAGTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (73 bp):
CACGTTCCATTTTCATAATCTATACAATGTAAGTGAGAGGATACCTTTCACTCTCTATTTAAGCT
ATGAATTA
Found at i:11209 original size:24 final size:24
Alignment explanation
Indices: 11182--11235 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
11172 TAGGGGTAGG
**
11182 ATCTGTGGCTACATTTGTATATGA
1 ATCTGTGGCTACATTTACATATGA
* * *
11206 ATCTGTGTCTGCATTTACATCTGA
1 ATCTGTGGCTACATTTACATATGA
11230 ATCTGT
1 ATCTGT
11236 ATAAGTATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
ATCTGTGGCTACATTTACATATGA
Found at i:11792 original size:20 final size:19
Alignment explanation
Indices: 11757--11804 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
11747 CAATCACGAA
11757 ATTTCATTCCATATATATATT
1 ATTTCATT--ATATATATATT
11778 ATTATCATTATATATATATT
1 ATT-TCATTATATATATATT
11798 ATTTCAT
1 ATTTCAT
11805 AAATTAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 3 0.12
22 5 0.19
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTCATTATATATATATT
Found at i:17136 original size:43 final size:44
Alignment explanation
Indices: 17032--17139 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
17022 TGTGTTGTCG
* * *
17032 TGTAAGACCACGTCTGGGACGTTGGTATTGACTTGTGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTACA
17076 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGA-TTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTTACA
17119 TGTAAGACCACGTCTGGGACG
1 TGTAAGACCACGTCTGGGACG
17140 ATGACATTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
42 1 0.02
43 24 0.42
44 31 0.54
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTTACA
Found at i:17958 original size:23 final size:23
Alignment explanation
Indices: 17928--18123 Score: 176
Period size: 23 Copynumber: 8.4 Consensus size: 23
17918 TTCGATTCAA
* * *
17928 GTCCAATTCGATGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* * **
17951 GTCCAATTTTGGTGTAAAAATATT
1 GTCCAA-TTTGGTGTATATATGCT
*
17975 GTCCAATTTGGTATATATATGCT
1 GTCCAATTTGGTGTATATATGCT
* *
17998 GCCCAATTTGGTGTCTATATGCT
1 GTCCAATTTGGTGTATATATGCT
* * *
18021 ATCCAATTTTGGTGTAAAAATGCT
1 GTCCAA-TTTGGTGTATATATGCT
*
18045 GTCCAATTTGGTATATATATGCT
1 GTCCAATTTGGTGTATATATGCT
** * *
18068 ACCCAATTTGGTGTCTATATGTT
1 GTCCAATTTGGTGTATATATGCT
* * *
18091 GTCCAATTTTGGTGTAAAAATGAT
1 GTCCAA-TTTGGTGTATATATGCT
18115 GTCCAATTT
1 GTCCAATTT
18124 AATATATATA
Statistics
Matches: 135, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
23 81 0.60
24 54 0.40
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (23 bp):
GTCCAATTTGGTGTATATATGCT
Found at i:17997 original size:47 final size:46
Alignment explanation
Indices: 17943--18134 Score: 152
Period size: 47 Copynumber: 4.1 Consensus size: 46
17933 ATTCGATGTC
* *
17943 TATATGCTGTCCAATTTTGGTGTAAAAATATTGTCCAATTTGGTATA
1 TATATGCTGTCCAA-TTTGGTGTAAAAATACTATCCAATTTGGTATA
* ** * * *
17990 TATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTA
1 TATATGCTGTCCAATTTGGTGTAAAAATACTATCCAA-TTTGGTATA
* * * * * * * * *
18037 AAAATGCTGTCCAATTTGGTATATATATGCTACCCAATTTGGTGTC
1 TATATGCTGTCCAATTTGGTGTAAAAATACTATCCAATTTGGTATA
* * **
18083 TATATGTTGTCCAATTTTGGTGTAAAAATGA-TGTCCAATTTAATATA
1 TATATGCTGTCCAA-TTTGGTGTAAAAAT-ACTATCCAATTTGGTATA
18130 TATAT
1 TATAT
18135 ATATATATAT
Statistics
Matches: 114, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
46 36 0.32
47 78 0.68
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (46 bp):
TATATGCTGTCCAATTTGGTGTAAAAATACTATCCAATTTGGTATA
Found at i:18004 original size:70 final size:70
Alignment explanation
Indices: 17930--18281 Score: 452
Period size: 70 Copynumber: 4.9 Consensus size: 70
17920 CGATTCAAGT
* * ** *
17930 CCAATTCGATGTCTATATGCTGTCCAATTTTGGTGTAAAAATATTGTCCAATTTGGTATATATAT
1 CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATAT
17995 GCTGC
66 GCTGC
* *
18000 CCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTATATATAT
1 CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATAT
*
18065 GCTAC
66 GCTGC
* * *
18070 CCAATTTGGTGTCTATATGTTGTCCAATTTTGGTGTAAAAATGATGTCCAATTTAATATATATAT
1 CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCC------A-AT-T-T-G
18135 ATATATATATGCTGC
56 ATATATATATGCTGC
*
18150 CCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATAT
1 CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATAT
18215 GCTGC
66 GCTGC
* * * * * *
18220 CCATTTTGGTGTATAAATGTTGTCCAATTTTGGTGTATAAATGCTGTCCAATTTGATGTATA
1 CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATA
18282 AGAGCTGTCC
Statistics
Matches: 249, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
70 180 0.72
71 1 0.00
72 1 0.00
73 2 0.01
74 1 0.00
76 1 0.00
77 2 0.01
78 1 0.00
79 1 0.00
80 59 0.24
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (70 bp):
CCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATAT
GCTGC
Found at i:18162 original size:150 final size:150
Alignment explanation
Indices: 17986--18273 Score: 513
Period size: 150 Copynumber: 1.9 Consensus size: 150
17976 TCCAATTTGG
17986 TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
1 TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
* * *
18051 TTTGGTATATATATGCTACCCAATTTGGTGTCTATATGTTGTCCAATTTTGGTGTAAAAATGATG
66 TTTGATATATATATGCTACCCAATTTGGTGTATAAATGTTGTCCAATTTTGGTGTAAAAATGATG
18116 TCCAATTTAATATATATATA
131 TCCAATTTAATATATATATA
18136 TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
1 TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
* * * *
18201 TTTGATATATATATGCTGCCCATTTTGGTGTATAAATGTTGTCCAATTTTGGTGTATAAATGCTG
66 TTTGATATATATATGCTACCCAATTTGGTGTATAAATGTTGTCCAATTTTGGTGTAAAAATGATG
18266 TCCAATTT
131 TCCAATTT
18274 GATGTATAAG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 131 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (150 bp):
TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
TTTGATATATATATGCTACCCAATTTGGTGTATAAATGTTGTCCAATTTTGGTGTAAAAATGATG
TCCAATTTAATATATATATA
Found at i:18189 original size:80 final size:80
Alignment explanation
Indices: 18056--18214 Score: 273
Period size: 80 Copynumber: 2.0 Consensus size: 80
18046 TCCAATTTGG
* *
18056 TATATATATGCTACCCAATTTGGTGTCTATATGTTGTCCAATTTTGGTGTAAAAATGATGTCCAA
1 TATATATATGCTACCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGATGTCCAA
18121 TTTAATATATATATA
66 TTTAATATATATATA
* *
18136 TATATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGCTGTCCAA
1 TATATATATGCTACCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGATGTCCAA
*
18201 TTTGATATATATAT
66 TTTAATATATATAT
18215 GCTGCCCATT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (80 bp):
TATATATATGCTACCCAATTTGGTGTCTATATGCTATCCAATTTTGGTGTAAAAATGATGTCCAA
TTTAATATATATATA
Found at i:18279 original size:23 final size:23
Alignment explanation
Indices: 18138--18293 Score: 161
Period size: 23 Copynumber: 6.7 Consensus size: 23
18128 TATATATATA
* *
18138 TATATATGCTGCCCAATTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
* * *
18161 TCTATATGCTATCCAATTTTGGTG
1 TATAAATGCTGTCCAA-TTTGGTG
* * *
18185 TAAAAATGCTGTCCAATTTGATA
1 TATAAATGCTGTCCAATTTGGTG
* * *
18208 TATATATGCTGCCCATTTTGGTG
1 TATAAATGCTGTCCAATTTGGTG
*
18231 TATAAATGTTGTCCAATTTTGGTG
1 TATAAATGCTGTCCAA-TTTGGTG
*
18255 TATAAATGCTGTCCAATTTGATG
1 TATAAATGCTGTCCAATTTGGTG
18278 TATAAGA-GCTGTCCAA
1 TATAA-ATGCTGTCCAA
18294 ACAGGGTAGA
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
23 67 0.61
24 42 0.39
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (23 bp):
TATAAATGCTGTCCAATTTGGTG
Found at i:18282 original size:47 final size:46
Alignment explanation
Indices: 18138--18293 Score: 170
Period size: 47 Copynumber: 3.3 Consensus size: 46
18128 TATATATATA
* * * *
18138 TATATATGCTGCCCAATTTGGTGTCTATATGCTATCCAATTTTGGTG
1 TATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAA-TTTGGTG
* * * * *
18185 TAAAAATGCTGTCCAATTTGATATATATATGCTGCCCATTTTGGTG
1 TATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTG
* * *
18231 TATAAATGTTGTCCAATTTTGGTGTATAAATGCTGTCCAATTTGATG
1 TATAAATGCTGTCCAA-TTTGGTGTATATATGCTGTCCAATTTGGTG
18278 TATAAGA-GCTGTCCAA
1 TATAA-ATGCTGTCCAA
18294 ACAGGGTAGA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
46 21 0.24
47 67 0.75
48 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (46 bp):
TATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTGGTG
Found at i:20605 original size:13 final size:13
Alignment explanation
Indices: 20589--20613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20579 ATTAGACTCG
20589 TAAATATTTATAT
1 TAAATATTTATAT
20602 TAAATATTTATA
1 TAAATATTTATA
20614 GAGTTATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATATTTATAT
Found at i:22038 original size:18 final size:19
Alignment explanation
Indices: 22015--22057 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
22005 TGATTTTGAT
22015 ATGGAAATAG-AATGGGAA
1 ATGGAAATAGAAATGGGAA
*
22033 ATGG-AATTGAAATGGGAA
1 ATGGAAATAGAAATGGGAA
22051 AT-GAAAT
1 ATGGAAAT
22058 GTGAAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (19 bp):
ATGGAAATAGAAATGGGAA
Found at i:22533 original size:2 final size:2
Alignment explanation
Indices: 22526--22550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22516 GAAGGCTATG
22526 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22551 GTAAGAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22883 original size:28 final size:28
Alignment explanation
Indices: 22818--22885 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
22808 GTTTAGTGAA
*
22818 TTGGTGTTTGGATGTAATTAATATGGAT
1 TTGGTGTTTTGATGTAATTAATATGGAT
*
22846 TTGGTTTTTTGATGTAATTAATATGGAT
1 TTGGTGTTTTGATGTAATTAATATGGAT
22874 TTGGTGTTTTGA
1 TTGGTGTTTTGA
22886 ATGGAATGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.51
Consensus pattern (28 bp):
TTGGTGTTTTGATGTAATTAATATGGAT
Found at i:29950 original size:10 final size:10
Alignment explanation
Indices: 29924--29957 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
29914 CTGAAACGAC
29924 AATAAAAATACA
1 AATAAAAAT--A
29936 AATAAAAATA
1 AATAAAAATA
29946 AATAAAAATA
1 AATAAAAATA
29956 AA
1 AA
29958 ATCGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
12 9 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (10 bp):
AATAAAAATA
Found at i:39032 original size:19 final size:20
Alignment explanation
Indices: 38994--39032 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38984 AATAGGTAGA
38994 ATTCCTAGAAAATAGAATTT
1 ATTCCTAGAAAATAGAATTT
*
39014 ATTCCTAGAATAT-GAATTT
1 ATTCCTAGAAAATAGAATTT
39033 CCACTACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTCCTAGAAAATAGAATTT
Found at i:42219 original size:45 final size:44
Alignment explanation
Indices: 42152--42321 Score: 191
Period size: 45 Copynumber: 3.8 Consensus size: 44
42142 ATGTACTGAG
42152 TATCATTGATTATAAAGGTGGTTGCTATGAGCTGATTCCACCAGA
1 TATCATTGATTATAAAGGTGGTTGCTATGAGCTGATTCCACC-GA
* *
42197 TACCATTGATTATAAAGGTGGTTGCTATGAGCTGACTCCACCGGA
1 TATCATTGATTATAAAGGTGGTTGCTATGAGCTGATTCCACC-GA
* * ** * *
42242 AATTATTGAAAATAAAGGTGGTTGATAT-ATGTTGATTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGA-GCTGATTCCACCG-A
* * *
42287 TATAATTGATTATAAGGGTGGTT-CTATGTGCTGAT
1 TATCATTGATTATAAAGGTGGTTGCTATGAGCTGAT
42322 CAACCATGTA
Statistics
Matches: 103, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
44 10 0.10
45 93 0.90
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (44 bp):
TATCATTGATTATAAAGGTGGTTGCTATGAGCTGATTCCACCGA
Found at i:44781 original size:27 final size:27
Alignment explanation
Indices: 44751--44802 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
44741 TTTCATCTCC
*
44751 TAGGGTTATAACGGTCATTTTACCCTA
1 TAGGGTTATAACGGTAATTTTACCCTA
**
44778 TAGGGTTATTTCGGTAATTTTACCC
1 TAGGGTTATAACGGTAATTTTACCC
44803 ATCGAGGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (27 bp):
TAGGGTTATAACGGTAATTTTACCCTA
Found at i:44814 original size:27 final size:27
Alignment explanation
Indices: 44762--44905 Score: 132
Period size: 27 Copynumber: 5.3 Consensus size: 27
44752 AGGGTTATAA
*
44762 CGGTCATTTTACCCTAT--AGGGTTATTT
1 CGGTAATTTTACCC-ATCGAGGG-TATTT
44789 CGGTAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
** * *
44816 TAGTAATTTTACACATCAAGGGTATTT
1 CGGTAATTTTACCCATCGAGGGTATTT
* *
44843 CAGTAATTTTACCCATTTG-GGGTATTT
1 CGGTAATTTTACCCA-TCGAGGGTATTT
* * * *
44870 CGATAATCTTACCCATCGGGGGTCTTT
1 CGGTAATTTTACCCATCGAGGGTATTT
*
44897 CGGTCATTT
1 CGGTAATTT
44906 AATAACCTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.04
27 87 0.91
28 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
CGGTAATTTTACCCATCGAGGGTATTT
Found at i:45917 original size:26 final size:27
Alignment explanation
Indices: 45871--45923 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
45861 GAGAGGAGAG
45871 GAGAAGAAAGAAGTATTCGGCCAACAA
1 GAGAAGAAAGAAGTATTCGGCCAACAA
45898 GAGAAGAGAAG-AG-ATTCGGCCAACAA
1 GAGAAGA-AAGAAGTATTCGGCCAACAA
45924 CCAAAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.52
27 9 0.36
28 3 0.12
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.09
Consensus pattern (27 bp):
GAGAAGAAAGAAGTATTCGGCCAACAA
Found at i:46370 original size:25 final size:25
Alignment explanation
Indices: 46341--46394 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
46331 TGAACCTCTG
*
46341 ACCTCATTACCACACTTGTGAT-GCC
1 ACCTCATTACCACACCTGTG-TCGCC
* *
46366 ACCTCCTTGCCACACCTGTGTCGCC
1 ACCTCATTACCACACCTGTGTCGCC
46391 ACCT
1 ACCT
46395 TGCCACTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.19, C:0.43, G:0.13, T:0.26
Consensus pattern (25 bp):
ACCTCATTACCACACCTGTGTCGCC
Found at i:50536 original size:16 final size:17
Alignment explanation
Indices: 50505--50537 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50495 ATACACATAA
50505 ACCAAAACCTATTCAAG
1 ACCAAAACCTATTCAAG
*
50522 ACCAAAATC-ATTCAAG
1 ACCAAAACCTATTCAAG
50538 TATGACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (17 bp):
ACCAAAACCTATTCAAG
Found at i:60251 original size:17 final size:18
Alignment explanation
Indices: 60231--60269 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
60221 AAAGGTAATT
60231 AGGAATT-GAAG-GTCAAA
1 AGGAATTAGAAGAG-CAAA
60248 AGGAATTAGAAGAGCAAA
1 AGGAATTAGAAGAGCAAA
60266 AGGA
1 AGGA
60270 GAGTAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 12 0.60
19 1 0.05
ACGTcount: A:0.51, C:0.05, G:0.31, T:0.13
Consensus pattern (18 bp):
AGGAATTAGAAGAGCAAA
Found at i:61012 original size:19 final size:19
Alignment explanation
Indices: 60990--61031 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
60980 CATATACCCG
*
60990 ATATCATATAGCATAATTC
1 ATATCAAATAGCATAATTC
* *
61009 ATATCAAATATCATATTTC
1 ATATCAAATAGCATAATTC
61028 ATAT
1 ATAT
61032 ATCAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATCAAATAGCATAATTC
Found at i:69991 original size:27 final size:27
Alignment explanation
Indices: 69952--70052 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
69942 ACGTGTCATA
* *
69952 AAAATGAAACCTTTGTGGCAATTTATG
1 AAAATGAAGCCTTTGTGGCAATCTATG
* *
69979 AAAATGAAGCCTTGGTGGTAATCTATG
1 AAAATGAAGCCTTTGTGGCAATCTATG
*
70006 AAAAGGAAGCCTTTGTGGCAATCTATG
1 AAAATGAAGCCTTTGTGGCAATCTATG
* *
70033 AAAAAAGAAGCTTTTGTGGC
1 -AAAATGAAGCCTTTGTGGC
70053 GATTTATCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
27 47 0.73
28 17 0.27
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (27 bp):
AAAATGAAGCCTTTGTGGCAATCTATG
Found at i:70048 original size:28 final size:27
Alignment explanation
Indices: 69951--70080 Score: 127
Period size: 27 Copynumber: 4.7 Consensus size: 27
69941 AACGTGTCAT
* *
69951 AAAAATGAAACCTTTGTGGCAATTTATG
1 AAAAA-GAAGCCTTTGTGGCAATCTATG
* * *
69979 AAAATGAAGCCTTGGTGGTAATCTATG
1 AAAAAGAAGCCTTTGTGGCAATCTATG
*
70006 AAAAGGAAGCCTTTGTGGCAATCTATG
1 AAAAAGAAGCCTTTGTGGCAATCTATG
* * * *
70033 AAAAAAGAAGCTTTTGTGGCGATTTATC
1 -AAAAAGAAGCCTTTGTGGCAATCTATG
*
70061 ATAAAA-AAGCCTCTGTGGCA
1 A-AAAAGAAGCCTTTGTGGCA
70081 CCCTCTAATG
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
27 54 0.64
28 30 0.36
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (27 bp):
AAAAAGAAGCCTTTGTGGCAATCTATG
Found at i:77491 original size:25 final size:25
Alignment explanation
Indices: 77449--77501 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
77439 AAATACATAA
*
77449 AAATAACCTAAAATTAAAAATAAAT
1 AAATAACCAAAAATTAAAAATAAAT
* *
77474 AAAT-ACCAAAAATATAAAACTTAAT
1 AAATAACCAAAAAT-TAAAAATAAAT
77499 AAA
1 AAA
77502 CTAATATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (25 bp):
AAATAACCAAAAATTAAAAATAAAT
Found at i:80636 original size:17 final size:17
Alignment explanation
Indices: 80614--80648 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
80604 CATGAATGGT
80614 TTAAAGAATGTTCAAGC
1 TTAAAGAATGTTCAAGC
80631 TTAAAGAATGTTCAAGC
1 TTAAAGAATGTTCAAGC
80648 T
1 T
80649 CAGTTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (17 bp):
TTAAAGAATGTTCAAGC
Found at i:82113 original size:26 final size:26
Alignment explanation
Indices: 82078--82129 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
82068 AATGTGAAAG
*
82078 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
82104 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
82130 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:82161 original size:103 final size:103
Alignment explanation
Indices: 81939--82264 Score: 541
Period size: 103 Copynumber: 3.2 Consensus size: 103
81929 AATTGATACG
81939 AGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGG
1 AGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCGAGGG
* *
82004 GTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTG
65 GTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTA
82043 AGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGG
1 AGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGG
82108 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTA
66 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTA
* *
82146 AGTGCGAT-ATCCACCATATCTTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTTCTCCGAGG
1 AGTGCG-TGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGA-TTCCCCGAGG
* *
82209 GGTTGCTAAGTGTTGATTCCCCGATTCAGTGGTGGTGCTA
64 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTA
82249 AGTGCAG-GATCCACCA
1 AGTGC-GTGATCCACCA
82265 ATAACGGTTA
Statistics
Matches: 212, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
102 22 0.10
103 133 0.63
104 57 0.27
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCGAGGGG
TTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTA
Found at i:83740 original size:25 final size:25
Alignment explanation
Indices: 83712--83770 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
83702 CTTCTCCTAG
* **
83712 TTAAACTCTGTTTTTAGTTTTTCAC
1 TTAAACTCTATTTTTAGTTTCACAC
83737 TTAAACTCTATTTTTAGTTTCACAC
1 TTAAACTCTATTTTTAGTTTCACAC
83762 TTAAACTCT
1 TTAAACTCT
83771 TATTAGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (25 bp):
TTAAACTCTATTTTTAGTTTCACAC
Found at i:83776 original size:23 final size:24
Alignment explanation
Indices: 83725--83777 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
83715 AACTCTGTTT
** *
83725 TTAGTTTTTCACTTAAACTCTATTT
1 TTAGTTTCACACTTAAACTC-ATTA
83750 TTAGTTTCACACTTAAACTC-TTA
1 TTAGTTTCACACTTAAACTCATTA
83773 TTAGT
1 TTAGT
83778 GTAGGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
25 18 0.72
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (24 bp):
TTAGTTTCACACTTAAACTCATTA
Found at i:85598 original size:124 final size:125
Alignment explanation
Indices: 85441--85690 Score: 493
Period size: 124 Copynumber: 2.0 Consensus size: 125
85431 TTTAAATCCA
85441 ACTAAAAATGTTAAAAATCAAGAGGAAAAATTTGATTTGTCATTCTCCTATTAGAAAAGGATAGA
1 ACTAAAAATGTTAAAAATCAAGAGGAAAAATTTGATTTGTCATTCTCCTATTAGAAAAGGATAGA
85506 GATGACATGGAATCACAGTTTCATACAATCCCTTCTCAATATACATAGAGAGGAAAATAT
66 GATGACATGGAATCACAGTTTCATACAATCCCTTCTCAATATACATAGAGAGGAAAATAT
85566 ACTAAAAATG-TAAAAATCAAGAGGAAAAATTTGATTTGTCATTCTCCTATTAGAAAAGGATAGA
1 ACTAAAAATGTTAAAAATCAAGAGGAAAAATTTGATTTGTCATTCTCCTATTAGAAAAGGATAGA
85630 GATGACATGGAATCACAGTTTCATACAATCCCTTCTCAATATACATAGAGAGGAAAATAT
66 GATGACATGGAATCACAGTTTCATACAATCCCTTCTCAATATACATAGAGAGGAAAATAT
85690 A
1 A
85691 ATAGGGATCA
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
124 115 0.92
125 10 0.08
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (125 bp):
ACTAAAAATGTTAAAAATCAAGAGGAAAAATTTGATTTGTCATTCTCCTATTAGAAAAGGATAGA
GATGACATGGAATCACAGTTTCATACAATCCCTTCTCAATATACATAGAGAGGAAAATAT
Found at i:86008 original size:2 final size:2
Alignment explanation
Indices: 86001--86029 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
85991 ATCAAACTCG
86001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86030 TTCTATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87569 original size:17 final size:17
Alignment explanation
Indices: 87539--87595 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
87529 ATTTTTATCT
*
87539 AATAT-TTATTAATTAA
1 AATATATTATAAATTAA
*
87555 AATATATTATAAATTTA
1 AATATATTATAAATTAA
* * *
87572 TATGTATGATAAACTTAA
1 AATATATTATAAA-TTAA
87590 AATATA
1 AATATA
87596 ACTAATTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
16 5 0.16
17 19 0.61
18 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATATATTATAAATTAA
Found at i:94388 original size:16 final size:16
Alignment explanation
Indices: 94363--94395 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
94353 ACGGTATTCT
*
94363 ATATTTTATAGTAGCA
1 ATATTCTATAGTAGCA
94379 ATATTCTATAGTAGCA
1 ATATTCTATAGTAGCA
94395 A
1 A
94396 AGGAATAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
ATATTCTATAGTAGCA
Found at i:94984 original size:322 final size:322
Alignment explanation
Indices: 94399--95039 Score: 1219
Period size: 322 Copynumber: 2.0 Consensus size: 322
94389 GTAGCAAAGG
*
94399 AATAAGAAATACGAATAATAAATTTTTAAAAAAGAAAAGTCTGAATAGACCAAAAGAGGGGGGAG
1 AATAAGAAAAACGAATAATAAATTTTTAAAAAAGAAAAGTCTGAATAGACCAAAAGAGGGGGGAG
94464 GAAATAATAAAGAAAAATTTATACAAAGCTAGATATGAATCATCCACACCCTCTTTTTTGGATTT
66 GAAATAATAAAGAAAAATTTATACAAAGCTAGATATGAATCATCCACACCCTCTTTTTTGGATTT
* *
94529 CATTAAGTGAATTTTGTTTGATTAAGAGTAAGTTCTGTAAAAACCCCCGCCTTCTTTAAAATATC
131 CATTAAGTGAATTTTGTTTGATTAAGACTAAGTTCTGTAAAAACACCCGCCTTCTTTAAAATATC
94594 ATGAACAGTTGCTGTGGGTTGAGCTCCTTTTTCAAGGAAATAGAGAATGGCGGGAACATTTAAAT
196 ATGAACAGTTGCTGTGGGTTGAGCTCCTTTTTCAAGGAAATAGAGAATGGCGGGAACATTTAAAT
94659 AGGTTTGATTATTTATCGGATCATAAAAACCCACTTTTCGAAGATCTCTTCCCTCTCTTAGC
261 AGGTTTGATTATTTATCGGATCATAAAAACCCACTTTTCGAAGATCTCTTCCCTCTCTTAGC
** *
94721 AATAAGAAAAACGAATAATAAATTTTTTTAAAATAAAAGTCTGAATAGACCAAAAGAGGGGGGAG
1 AATAAGAAAAACGAATAATAAATTTTTAAAAAAGAAAAGTCTGAATAGACCAAAAGAGGGGGGAG
94786 GAAATAATAAAGAAAAATTTATACAAAGCTAGATATGAATCATCCACACCCTCTTTTTTGGATTT
66 GAAATAATAAAGAAAAATTTATACAAAGCTAGATATGAATCATCCACACCCTCTTTTTTGGATTT
*
94851 CATTAATTGAATTTTGTTTGATTAAGACTAAGTTCTGTAAAAACACCCGCCTTCTTTAAAATATC
131 CATTAAGTGAATTTTGTTTGATTAAGACTAAGTTCTGTAAAAACACCCGCCTTCTTTAAAATATC
94916 ATGAACAGTTGCTGTGGGTTGAGCTCCTTTTTCAAGGAAATAGAGAATGGCGGGAACATTTAAAT
196 ATGAACAGTTGCTGTGGGTTGAGCTCCTTTTTCAAGGAAATAGAGAATGGCGGGAACATTTAAAT
94981 AGGTTTGATTATTTATCGGATCATAAAAACCCACTTTTCGAAGATCTCTTCCCTCTCTT
261 AGGTTTGATTATTTATCGGATCATAAAAACCCACTTTTCGAAGATCTCTTCCCTCTCTT
95040 CGGGATCGAA
Statistics
Matches: 312, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 312 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (322 bp):
AATAAGAAAAACGAATAATAAATTTTTAAAAAAGAAAAGTCTGAATAGACCAAAAGAGGGGGGAG
GAAATAATAAAGAAAAATTTATACAAAGCTAGATATGAATCATCCACACCCTCTTTTTTGGATTT
CATTAAGTGAATTTTGTTTGATTAAGACTAAGTTCTGTAAAAACACCCGCCTTCTTTAAAATATC
ATGAACAGTTGCTGTGGGTTGAGCTCCTTTTTCAAGGAAATAGAGAATGGCGGGAACATTTAAAT
AGGTTTGATTATTTATCGGATCATAAAAACCCACTTTTCGAAGATCTCTTCCCTCTCTTAGC
Found at i:95199 original size:15 final size:15
Alignment explanation
Indices: 95179--95212 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
95169 AGTTATGTCT
*
95179 ATGTATGTAATTAGA
1 ATGTATGGAATTAGA
95194 ATGTATGGAATTAGA
1 ATGTATGGAATTAGA
95209 ATGT
1 ATGT
95213 CAAAAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTATGGAATTAGA
Found at i:96235 original size:19 final size:19
Alignment explanation
Indices: 96213--96253 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
96203 TTAAACTTTT
* *
96213 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCGATTCTA
96232 ATTAAACTTTTCGATTCTA
1 ATTAAACTTTTCGATTCTA
96251 ATT
1 ATT
96254 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTAAACTTTTCGATTCTA
Found at i:97058 original size:20 final size:20
Alignment explanation
Indices: 97033--97072 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
97023 AATTAAGAAA
97033 AATTGCTAAAGTATCAATAC
1 AATTGCTAAAGTATCAATAC
* *
97053 AATTGCTTAGGTATCAATAC
1 AATTGCTAAAGTATCAATAC
97073 CTCAGAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (20 bp):
AATTGCTAAAGTATCAATAC
Found at i:110028 original size:18 final size:18
Alignment explanation
Indices: 109969--110029 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 18
109959 ATTTTATAAC
109969 ATTTTTTATAAATAA-TT
1 ATTTTTTATAAATAAGTT
109986 ATTTTTTCATAACTTTATAAAGTT
1 ATTTTTT-ATAA----AT-AAGTT
110010 ATTTTTTATAAATAAGTT
1 ATTTTTTATAAATAAGTT
110028 AT
1 AT
110030 GGAAAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
17 7 0.19
18 11 0.30
19 2 0.05
22 2 0.05
23 6 0.16
24 9 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTTTTTATAAATAAGTT
Found at i:111788 original size:3 final size:3
Alignment explanation
Indices: 111780--111815 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
111770 TTGTTTACCC
111780 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
111816 CAATCCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:112278 original size:174 final size:174
Alignment explanation
Indices: 111981--112328 Score: 534
Period size: 174 Copynumber: 2.0 Consensus size: 174
111971 ATATAGATAC
* * *
111981 TTAGGGTATGTTTGGTTGGCTGTAATACCAATACATTACAGCTTAATTCAGTGGGCCCATCACTA
1 TTAGGGCATGTTTGGTTGGCTATAATACCAATACATTACAGCTCAATTCAGTGGGCCCATCACTA
* * *
112046 AGCCATTGTTTGGTTGGTTGCAATGAGCTATTACAACCTTATTCCTTACGGGCTTATTCAGGGAA
66 AGCCATTGTTTGGTTGGCTGCAATGAGCTATTACAACCCTATTCCATACGGGCTTATTCAGGGAA
*
112111 AAAATGTTGTTTACCATTCGGTGGTATCCCCACGAAATGATGAT
131 AAAATGTTGTTTACCATTCAGTGGTATCCCCACGAAATGATGAT
*
112155 TTAGGGCATGTTTGGTTGGTTATAATACCAATACATTACAGCTCAATTCAGTGGGCCCATCACTA
1 TTAGGGCATGTTTGGTTGGCTATAATACCAATACATTACAGCTCAATTCAGTGGGCCCATCACTA
* * * * * *
112220 AGCTATTGTTTGGTTGGCTGTAATGTGCTATTACAGCCCTATTCCATACTGGCTTATTCAGGGCA
66 AGCCATTGTTTGGTTGGCTGCAATGAGCTATTACAACCCTATTCCATACGGGCTTATTCAGGGAA
* * * *
112285 AAAATGTTGTTTACCATTTAGTGGTCTCCCCATGGAATGATGAT
131 AAAATGTTGTTTACCATTCAGTGGTATCCCCACGAAATGATGAT
112329 GCAAGGAATG
Statistics
Matches: 156, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
174 156 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (174 bp):
TTAGGGCATGTTTGGTTGGCTATAATACCAATACATTACAGCTCAATTCAGTGGGCCCATCACTA
AGCCATTGTTTGGTTGGCTGCAATGAGCTATTACAACCCTATTCCATACGGGCTTATTCAGGGAA
AAAATGTTGTTTACCATTCAGTGGTATCCCCACGAAATGATGAT
Found at i:116103 original size:15 final size:15
Alignment explanation
Indices: 116066--116108 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
116056 TAAAACTATT
* *
116066 TTTATTTTTGATATG
1 TTTATTTTTGTTATA
*
116081 TTTAATTTATGTTATA
1 TTT-ATTTTTGTTATA
116097 TTTATTTTTGTT
1 TTTATTTTTGTT
116109 CTTTAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (15 bp):
TTTATTTTTGTTATA
Found at i:119021 original size:23 final size:23
Alignment explanation
Indices: 118973--119022 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
118963 TAAATTACGT
* *
118973 TATATATTATTTTTATAATGTTA
1 TATATATGATTTTTATAATGTCA
*
118996 TATATTATGATTTTTTTAAT-TCA
1 TATA-TATGATTTTTATAATGTCA
119019 TATA
1 TATA
119023 ATAATAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATGTCA
Done.