Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 13 of 27
Found at i:1950179 original size:36 final size:36
Alignment explanation
Indices: 1950139--1950215 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
1950129 TTTGAAATTT
1950139 GATTTCAA-TTTAATGATTTTTGGATTTTTT-TTTTTC
1 GATTTCAATTTTAA-GATTTTT-GATTTTTTATTTTTC
* * * *
1950175 GATTTTAATTTTCAGATTTTTTATTTTTTATTTTTG
1 GATTTCAATTTTAAGATTTTTGATTTTTTATTTTTC
1950211 GATTT
1 GATTT
1950216 ATGAAAGTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 7 0.20
36 24 0.69
37 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.66
Consensus pattern (36 bp):
GATTTCAATTTTAAGATTTTTGATTTTTTATTTTTC
Found at i:1952223 original size:27 final size:27
Alignment explanation
Indices: 1952193--1952247 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1952183 GCCCATGGCA
** *
1952193 GATCCGAAGAGGGATTTGCGAGGGGCG
1 GATCCGAAGAGGGAGCTACGAGGGGCG
* *
1952220 GATCTGAGGAGGGAGCTACGAGGGGCG
1 GATCCGAAGAGGGAGCTACGAGGGGCG
1952247 G
1 G
1952248 CTCGAGAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.51, T:0.13
Consensus pattern (27 bp):
GATCCGAAGAGGGAGCTACGAGGGGCG
Found at i:1952523 original size:26 final size:27
Alignment explanation
Indices: 1952494--1952544 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1952484 ATGTGTACAT
*
1952494 ATTTTTATTATATA-ATATATATTAAG
1 ATTTTTAATATATATATATATATTAAG
1952520 ATTTTTAATATATATATATATATTA
1 ATTTTTAATATATATATATATATTA
1952545 TTTATTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTTTTAATATATATATATATATTAAG
Found at i:1954222 original size:2 final size:2
Alignment explanation
Indices: 1954217--1954264 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1954207 TTTATGAATG
*
1954217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1954259 TA TA TA
1 TA TA TA
1954265 AAAAAAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1954364 original size:21 final size:21
Alignment explanation
Indices: 1954338--1954382 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1954328 AAAATTTTTG
* *
1954338 AATCTTATTTGAATTTTATAA
1 AATCTTATTTGAACTTCATAA
1954359 AATCTTATTTGAACTTCATAA
1 AATCTTATTTGAACTTCATAA
1954380 AAT
1 AAT
1954383 TTAAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (21 bp):
AATCTTATTTGAACTTCATAA
Found at i:1954524 original size:15 final size:16
Alignment explanation
Indices: 1954504--1954534 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1954494 ATAATGTATC
1954504 AAATATAA-ATATTTA
1 AAATATAATATATTTA
1954519 AAATATAATATATTTA
1 AAATATAATATATTTA
1954535 TATAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATATTTA
Found at i:1954540 original size:20 final size:21
Alignment explanation
Indices: 1954517--1954559 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1954507 TATAAATATT
1954517 TAAAATATAATA-TATTTATA
1 TAAAATATAATATTATTTATA
* *
1954537 TAAATTTTAATATTTATTTATA
1 TAAAATATAATA-TTATTTATA
1954559 T
1 T
1954560 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAATATAATATTATTTATA
Found at i:1954792 original size:6 final size:6
Alignment explanation
Indices: 1954781--1954834 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
1954771 TTTTTATAAA
1954781 TTATAT TTATAT TTATAT TTATAT TTATA- -T-TAT TTATAT TT-TAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1954825 TTAT-T TTATA
1 TTATAT TTATA
1954835 ATAAATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 11 0.26
6 29 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:1954804 original size:18 final size:18
Alignment explanation
Indices: 1954781--1954834 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 18
1954771 TTTTTATAAA
1954781 TTATATTTATATTTATAT
1 TTATATTTATATTTATAT
1954799 TTATATTTATA--T-TAT
1 TTATATTTATATTTATAT
1954814 TTATATTT-TATTTAT-T
1 TTATATTTATATTTATAT
1954830 TTATA
1 TTATA
1954835 ATAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 8 0.24
17 1 0.03
18 11 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTTATATTTATAT
Found at i:1954819 original size:27 final size:25
Alignment explanation
Indices: 1954784--1954834 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
1954774 TTATAAATTA
1954784 TATTTATATTTATATTTATATTTATAT
1 TATTTATATTT-TATTTAT-TTTATAT
1954811 TATTTATATTTTATTTATTTTATA
1 TATTTATATTTTATTTATTTTATA
1954835 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.25
26 7 0.29
27 11 0.46
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTATATTTTATTTATTTTATAT
Found at i:1955113 original size:23 final size:24
Alignment explanation
Indices: 1955086--1955153 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
1955076 TTATTTATAT
1955086 TTAATTATAAA-AATATATAAATA
1 TTAATTATAAATAATATATAAATA
* *
1955109 TTAATATATAAATTATATTTAAATA
1 TTAAT-TATAAATAATATATAAATA
*
1955134 TT-ATTTTAAATAATATATAA
1 TTAATTATAAATAATATATAA
1955154 TTTTTAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 18 0.47
24 8 0.21
25 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATTATAAATAATATATAAATA
Found at i:1955175 original size:17 final size:18
Alignment explanation
Indices: 1955110--1955200 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 18
1955100 ATATAAATAT
* **
1955110 TAATATATAAATTATATT
1 TAATATATAAATTTTAAA
*
1955128 TAA-ATAT-TATTTTAAA
1 TAATATATAAATTTTAAA
*
1955144 TAATATATAATTTTTAAA
1 TAATATATAAATTTTAAA
1955162 TTAAT-T-TAAATTTTGATAAA
1 -TAATATATAAA-TTT--TAAA
* *
1955182 TAAAATAAAAATTTTAAA
1 TAATATATAAATTTTAAA
1955200 T
1 T
1955201 TATAATTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
16 8 0.14
17 11 0.20
18 19 0.34
19 7 0.12
20 8 0.14
21 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAATATATAAATTTTAAA
Found at i:1955207 original size:40 final size:42
Alignment explanation
Indices: 1955117--1955210 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 42
1955107 TATTAATATA
** * * *
1955117 TAAATTAT-ATTTAAATATTATTTTAAATAATATATAATTTT
1 TAAATTATAATTTAAATATTATGATAAATAAAATAAAAATTT
1955158 TAAA-T-TAATTTAAAT-TT-TGATAAATAAAATAAAAATTT
1 TAAATTATAATTTAAATATTATGATAAATAAAATAAAAATTT
1955196 TAAATTATAATTTAA
1 TAAATTATAATTTAA
1955211 TTTAATTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
38 20 0.44
39 4 0.09
40 17 0.38
41 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (42 bp):
TAAATTATAATTTAAATATTATGATAAATAAAATAAAAATTT
Found at i:1959094 original size:25 final size:22
Alignment explanation
Indices: 1959050--1959114 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
1959040 ATTATTTAAA
*
1959050 TAATAAAAATTATTTTAAATAT
1 TAATAAAAATAATTTTAAATAT
1959072 TAATATAAAATAATTTTTAAA-AT
1 TAATA-AAAATAA-TTTTAAATAT
* * *
1959095 T-TTAAATATTATTTTAAATA
1 TAATAAAAATAATTTTAAATA
1959115 ATAAAACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 7 0.19
21 6 0.17
22 7 0.19
23 9 0.25
24 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAAAAATAATTTTAAATAT
Found at i:1959113 original size:12 final size:12
Alignment explanation
Indices: 1959053--1959114 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
1959043 ATTTAAATAA
*
1959053 TAAAAATTATTT
1 TAAATATTATTT
* *
1959065 TAAATATTAATA
1 TAAATATTATTT
*
1959077 TAAA-ATAATTT
1 TAAATATTATTT
*
1959088 TTAA-A--ATTT
1 TAAATATTATTT
1959097 TAAATATTATTT
1 TAAATATTATTT
1959109 TAAATA
1 TAAATA
1959115 ATAAAACTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 8 0.21
12 23 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTATTT
Found at i:1960951 original size:34 final size:34
Alignment explanation
Indices: 1960902--1961155 Score: 202
Period size: 34 Copynumber: 7.5 Consensus size: 34
1960892 GGTAAAAACC
*
1960902 ACCATTTAATCAACAATGACAACCTACCAAATCT
1 ACCATTTAATCAACAATGATAACCTACCAAATCT
* * *
1960936 ACCATTTAGTTAACAATGGTAAGCC-ACCAAATC-
1 ACCATTTAATCAACAATGATAA-CCTACCAAATCT
* * * *
1960969 ACCCATTTAATCAATAATGGTAAGCTACCAAATTT
1 A-CCATTTAATCAACAATGATAACCTACCAAATCT
* *
1961004 ATCATTTAATCAACAAT-AGTAAGCTACCAAATCT
1 ACCATTTAATCAACAATGA-TAACCTACCAAATCT
* *
1961038 -CTCATTTAGTCAACAATGGCA-AAGC-ACCAAATC-
1 AC-CATTTAATCAACAAT-G-ATAACCTACCAAATCT
* * * *
1961071 ACCCATTTAATCAATAATGGTAAACTACTAAATC-
1 A-CCATTTAATCAACAATGATAACCTACCAAATCT
* * *
1961105 ACCCATTTAATCAATAATGGTAAACTACCAAATC-
1 A-CCATTTAATCAACAATGATAACCTACCAAATCT
1961139 ACCATTTAATCAACAAT
1 ACCATTTAATCAACAAT
1961156 TCTCCCACTT
Statistics
Matches: 185, Mismatches: 22, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
33 21 0.11
34 155 0.84
35 8 0.04
37 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
ACCATTTAATCAACAATGATAACCTACCAAATCT
Found at i:1961019 original size:68 final size:67
Alignment explanation
Indices: 1960903--1961155 Score: 292
Period size: 68 Copynumber: 3.7 Consensus size: 67
1960893 GTAAAAACCA
** * * * *
1960903 CCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTTAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATC-ACCATTTAATCAACAATGGTAAGCTACCAAAT
1960968 CAC
65 CAC
* * * *
1960971 CCATTTAATCAATAATGGTAAGCTACCAAATTTATCATTTAATCAACAATAGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAA-TCACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1961036 CTC
65 CAC
* * * * * *
1961039 TCATTTAGTCAACAATGGCAAAGC-ACCAAATCACCCATTTAATCAATAATGGTAAACTACTAAA
1 CCATTTAATCAACAATGG-TAAGCTACCAAATCA-CCATTTAATCAACAATGGTAAGCTACCAAA
1961103 TCAC
64 TCAC
* *
1961107 CCATTTAATCAATAATGGTAAACTACCAAATCACCATTTAATCAACAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCACCATTTAATCAACAAT
1961156 TCTCCCACTT
Statistics
Matches: 153, Mismatches: 28, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
67 20 0.13
68 128 0.84
69 5 0.03
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (67 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1961046 original size:102 final size:100
Alignment explanation
Indices: 1960903--1961155 Score: 323
Period size: 102 Copynumber: 2.5 Consensus size: 100
1960893 GTAAAAACCA
* *
1960903 CCATTTAATCAACAATG-ACAACCTACCAAATCTACCATTTAGTTAACAATGG-TAAGCCACCAA
1 CCATTTAATCAACAATGTA-AA-CTACCAAATCT-CCATTTAGTCAACAATGGCAAAG-CACCAA
* *
1960966 ATCACCCATTTAATCAATAATGGTAAGCTACCAAATTTA-
62 ATCACCCATTTAATCAATAATGGTAAACTACCAAA-TCAC
* *
1961005 TCATTTAATCAACAATAGTAAGCTACCAAATCTCTCATTTAGTCAACAATGGCAAAGCACCAAAT
1 CCATTTAATCAACAAT-GTAAACTACCAAATCTC-CATTTAGTCAACAATGGCAAAGCACCAAAT
*
1961070 CACCCATTTAATCAATAATGGTAAACTACTAAATCAC
64 CACCCATTTAATCAATAATGGTAAACTACCAAATCAC
* * *
1961107 CCATTTAATCAATAATGGTAAACTACCAAATCACCATTTAATCAACAAT
1 CCATTTAATCAACAAT-GTAAACTACCAAATCTCCATTTAGTCAACAAT
1961156 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
101 17 0.13
102 110 0.83
103 5 0.04
104 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (100 bp):
CCATTTAATCAACAATGTAAACTACCAAATCTCCATTTAGTCAACAATGGCAAAGCACCAAATCA
CCCATTTAATCAATAATGGTAAACTACCAAATCAC
Found at i:1965601 original size:34 final size:33
Alignment explanation
Indices: 1965558--1965779 Score: 257
Period size: 34 Copynumber: 6.6 Consensus size: 33
1965548 GATTTGGTAA
* *
1965558 AAATCACCATTTAATCAACAATGGCAACCTACC
1 AAATCACCATTTAATCAACAATGGTAAGCTACC
* *
1965591 AAATCTACCATTTAGTCAACAATGGTAAGCCACC
1 AAATC-ACCATTTAATCAACAATGGTAAGCTACC
* * *
1965625 AAATCACCTATTTAATTAATAATGGTAAGCTACT
1 AAATCACC-ATTTAATCAACAATGGTAAGCTACC
**
1965659 AAATTTCTCATTTAATCAACAATGGTAAGCTACC
1 AAATCAC-CATTTAATCAACAATGGTAAGCTACC
* * *
1965693 AAATCTCTTATTTAGTCAACAATGGTAAAGC-ACC
1 AAATCAC-CATTTAATCAACAATGGT-AAGCTACC
* *
1965727 AAATCACCCATTTAATCAATAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGGTAAGCTACC
1965761 AAATCACCATTTAATCAAC
1 AAATCACCATTTAATCAAC
1965780 CCAAATGACG
Statistics
Matches: 160, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGGTAAGCTACC
Found at i:1965741 original size:102 final size:101
Alignment explanation
Indices: 1965558--1965779 Score: 322
Period size: 102 Copynumber: 2.2 Consensus size: 101
1965548 GATTTGGTAA
1965558 AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
1 AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
* * * *
1965623 CCAAATCACCTATTTAATTAATAATGGTAAGCTACT
66 CCAAATCACCCATTTAATCAATAATGGTAAACTACC
** * * *
1965659 AAATTTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CTTATTTAGTCAACAATGGTAAAG
1 AAATCAC-CATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGT-AAG
1965723 -CACCAAATCACCCATTTAATCAATAATGGTAAACTACC
63 CCACCAAATCACCCATTTAATCAATAATGGTAAACTACC
1965761 AAATCACCATTTAATCAAC
1 AAATCACCATTTAATCAAC
1965780 CCAAATGACG
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
101 18 0.17
102 86 0.80
103 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (101 bp):
AAATCACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCA
CCAAATCACCCATTTAATCAATAATGGTAAACTACC
Found at i:1967967 original size:12 final size:12
Alignment explanation
Indices: 1967950--1967974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1967940 GTATTTTTTG
1967950 TTTTATATAATT
1 TTTTATATAATT
1967962 TTTTATATAATT
1 TTTTATATAATT
1967974 T
1 T
1967975 AAAAATTATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATATAATT
Found at i:1970475 original size:29 final size:30
Alignment explanation
Indices: 1970432--1970493 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
1970422 TCATTGAGCA
*
1970432 TTAAATATAAGTTTT-ATATTTTATATAAAT
1 TTAAATATAAATTTTAATATTTT-TATAAAT
*
1970462 TTAAA-ATAAATTTTAATATTTTTATATAT
1 TTAAATATAAATTTTAATATTTTTATAAAT
1970491 TTA
1 TTA
1970494 TTTGTGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTAAATATAAATTTTAATATTTTTATAAAT
Found at i:1970521 original size:18 final size:17
Alignment explanation
Indices: 1970481--1970523 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1970471 ATTTTAATAT
*
1970481 TTTTATATATTTATTTG
1 TTTTATATATTTATTTA
* *
1970498 TGTTATATCATTTTTTTA
1 TTTTATAT-ATTTATTTA
1970516 TTTTATAT
1 TTTTATAT
1970524 TTATATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTATATATTTATTTA
Found at i:1971116 original size:18 final size:19
Alignment explanation
Indices: 1971093--1971129 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1971083 GTTGAGTAAC
1971093 AAAATTCAATTA-AAAATT
1 AAAATTCAATTATAAAATT
*
1971111 AAAATTTAATTATAAAATT
1 AAAATTCAATTATAAAATT
1971130 CAATCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAATTATAAAATT
Found at i:1971750 original size:2 final size:2
Alignment explanation
Indices: 1971743--1971780 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1971733 CACATCTGAA
1971743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1971781 TGTGAGTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1973123 original size:38 final size:38
Alignment explanation
Indices: 1973081--1973196 Score: 93
Period size: 38 Copynumber: 3.1 Consensus size: 38
1973071 TTAAATTAAA
*
1973081 AAATATATATAATAAATAATTAAAATTATATTTTTATT
1 AAATATATATAATAAATAAATAAAATTATATTTTTATT
1973119 AAATACTA-A-AAT--ATAAATAAAATTATATTTATTA-T
1 AAATA-TATATAATAAATAAATAAAATTATATTT-TTATT
* * * * *
1973154 GAATA-ATAATTAA-AAGTTAGTAAAATTATATTTGTATT
1 AAATATAT-A-TAATAAATAAATAAAATTATATTTTTATT
1973192 AAATA
1 AAATA
1973197 ATAAAATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
33 1 0.02
35 23 0.37
36 3 0.05
37 7 0.11
38 26 0.42
39 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (38 bp):
AAATATATATAATAAATAAATAAAATTATATTTTTATT
Found at i:1973143 original size:35 final size:35
Alignment explanation
Indices: 1973096--1973203 Score: 112
Period size: 35 Copynumber: 3.0 Consensus size: 35
1973086 TATATAATAA
* *
1973096 ATAATTAAAATTATATTTTTATTAAATACTAAAAT
1 ATAAATAAAATTATATTTTTATTAAATAATAAAAT
*
1973131 ATAAATAAAATTATATTTATTATGAATAATAATTAAAAGT
1 ATAAATAAAATTATATTT-TTAT-TA-AATAA-TAAAA-T
* *
1973171 -T-AGTAAAATTATATTTGTATTAAATAATAAAAT
1 ATAAATAAAATTATATTTTTATTAAATAATAAAAT
1973204 TATATTATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.02
34 5 0.08
35 22 0.35
36 5 0.08
37 4 0.06
38 18 0.29
39 6 0.10
40 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.43
Consensus pattern (35 bp):
ATAAATAAAATTATATTTTTATTAAATAATAAAAT
Found at i:1973218 original size:40 final size:38
Alignment explanation
Indices: 1973099--1973242 Score: 97
Period size: 40 Copynumber: 3.8 Consensus size: 38
1973089 ATAATAAATA
*
1973099 ATTAAAATTATATTTTTATTAAATACTAAAA-TATA-A-
1 ATTAAAATTATA-TTTTATTAAATAATAAAATTATATAT
*
1973135 A-TAAAATTATA-TTTATT--ATGAATAATAATTA-AAAGTT
1 ATTAAAATTATATTTTATTAAAT-AATAA-AATTATATA--T
*
1973172 AGTAAAATTATATTTGTATTAAATAATAAAATTATATTAT
1 ATTAAAATTATATTT-TATTAAATAATAAAATTATA-TAT
* * * *
1973212 ATTAAAAATAAATTAATATAAAATAATAAAA
1 ATTAAAATTATATT-TTATTAAATAATAAAA
1973243 AAAAAAGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
31 2 0.02
32 4 0.05
33 9 0.10
34 3 0.03
35 10 0.12
36 1 0.01
37 1 0.01
38 10 0.12
39 2 0.02
40 35 0.41
41 6 0.07
42 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.41
Consensus pattern (38 bp):
ATTAAAATTATATTTTATTAAATAATAAAATTATATAT
Found at i:1973230 original size:22 final size:23
Alignment explanation
Indices: 1973174--1973242 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 23
1973164 TAAAAGTTAG
*
1973174 TAAAATTATATTTGTATTAAATAA
1 TAAAATTATA-TTATATTAAATAA
1973198 TAAAATTATATTATATTAAA-AA
1 TAAAATTATATTATATTAAATAA
1973220 T-AAATTA-A-TATA--AAATAA
1 TAAAATTATATTATATTAAATAA
1973238 TAAAA
1 TAAAA
1973243 AAAAAAGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 7 0.17
20 1 0.02
21 6 0.14
22 3 0.07
23 9 0.21
24 10 0.24
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
TAAAATTATATTATATTAAATAA
Found at i:1973231 original size:24 final size:25
Alignment explanation
Indices: 1973176--1973231 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
1973166 AAAGTTAGTA
*
1973176 AAATT-ATAT-TTGTATTAAATAAT
1 AAATTAATATATTATATTAAATAAT
*
1973199 AAA--ATTATATTATATTAAA-AAT
1 AAATTAATATATTATATTAAATAAT
1973221 AAATTAATATA
1 AAATTAATATA
1973232 AAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
22 9 0.35
23 12 0.46
24 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATTAATATATTATATTAAATAAT
Found at i:1982274 original size:18 final size:17
Alignment explanation
Indices: 1982251--1982314 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
1982241 TTTATACGCA
*
1982251 TAAATATAATATAATTAT
1 TAAATATAATATAAAT-T
*
1982269 TAAATATATTA-AAATT
1 TAAATATAATATAAATT
* *
1982285 TAAATAAAATATATAATA
1 TAAATATAATATA-AATT
*
1982303 TAAATATTATAT
1 TAAATATAATAT
1982315 CTATCGTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 10 0.27
17 4 0.11
18 23 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAATATAAATT
Found at i:1983016 original size:3 final size:3
Alignment explanation
Indices: 1983002--1983042 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1982992 CTTTTTCCAC
*
1983002 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1983043 GAAAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1983483 original size:2 final size:2
Alignment explanation
Indices: 1983476--1983513 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1983466 CCAATAACAA
1983476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1983514 GGATAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1984056 original size:3 final size:3
Alignment explanation
Indices: 1984048--1984076 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1984038 AAGGAGTCTT
1984048 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1984077 TGTAATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1984723 original size:17 final size:16
Alignment explanation
Indices: 1984703--1984747 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1984693 TTCTCTTCAA
1984703 ATTTTTTTAAAAATATT
1 ATTTTTTTAAAAAT-TT
**
1984720 ATTTTTTTATTGAATTT
1 ATTTTTTTA-AAAATTT
1984737 ATTTTTTTAAA
1 ATTTTTTTAAA
1984748 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
ATTTTTTTAAAAATTT
Found at i:1984763 original size:14 final size:14
Alignment explanation
Indices: 1984721--1984763 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1984711 AAAAATATTA
*
1984721 TTTTTTTATTGAAT
1 TTTTTTTATTAAAT
1984735 TTATTTTT-TTAAAT
1 TT-TTTTTATTAAAT
*
1984749 TTTTTTTATTTAAT
1 TTTTTTTATTAAAT
1984763 T
1 T
1984764 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTTTATTAAAT
Found at i:2000148 original size:14 final size:15
Alignment explanation
Indices: 2000119--2000151 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2000109 AAATTATTTA
*
2000119 AAATTTAATTTAAAT
1 AAATTAAATTTAAAT
2000134 AAATTAAATTT-AAT
1 AAATTAAATTTAAAT
2000148 AAAT
1 AAAT
2000152 AACTTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTAAATTTAAAT
Found at i:2000523 original size:26 final size:27
Alignment explanation
Indices: 2000475--2000527 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2000465 TGTTCTAAAT
* *
2000475 ATTTTTTGAATTTGAATTAATTTTTAA
1 ATTTTTTAAATTTAAATTAATTTTTAA
2000502 ATTTTTTAAATTTAAATT-ATTTTTAA
1 ATTTTTTAAATTTAAATTAATTTTTAA
2000528 CTTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
ATTTTTTAAATTTAAATTAATTTTTAA
Found at i:2000524 original size:16 final size:16
Alignment explanation
Indices: 2000497--2000594 Score: 85
Period size: 16 Copynumber: 6.2 Consensus size: 16
2000487 TGAATTAATT
2000497 TTTAAATT-TTTTAAA
1 TTTAAATTATTTTAAA
*
2000512 TTTAAATTATTTTTAA
1 TTTAAATTATTTTAAA
* *
2000528 CTTAAATTTTTTTAAA
1 TTTAAATTATTTTAAA
* *
2000544 TTTAATTTATTTTAGA
1 TTTAAATTATTTTAAA
* *
2000560 -TT-ATTTTTTTTCAAA
1 TTTAAATTATTTT-AAA
* *
2000575 TTTAAATCATTTTAAT
1 TTTAAATTATTTTAAA
2000591 TTTA
1 TTTA
2000595 GTTCTTTTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
14 8 0.12
15 12 0.18
16 39 0.60
17 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:2000588 original size:31 final size:30
Alignment explanation
Indices: 2000498--2000589 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
2000488 GAATTAATTT
2000498 TTAAATTTTTTAAATTTAAATTATTTTTAAC
1 TTAAATTTTTTAAATTTAAATTA-TTTTAAC
*
2000529 TTAAATTTTTTTAAATTTAATTTATTTTAGA-
1 TTAAA-TTTTTTAAATTTAAATTATTTTA-AC
** *
2000560 TTATTTTTTTTCAAATTTAAATCATTTTAA
1 TTAAATTTTTT-AAATTTAAATTATTTTAA
2000590 TTTTAGTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
30 7 0.13
31 28 0.53
32 18 0.34
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (30 bp):
TTAAATTTTTTAAATTTAAATTATTTTAAC
Found at i:2000603 original size:16 final size:14
Alignment explanation
Indices: 2000584--2000622 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
2000574 ATTTAAATCA
2000584 TTTTAATTTTAGTTCT
1 TTTTAATTTTA-TT-T
2000600 TTTTAAATTTTATTT
1 TTTT-AATTTTATTT
2000615 TTTTAATT
1 TTTTAATT
2000623 AAATTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 5 0.23
16 6 0.27
17 7 0.32
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTAATTTTATTT
Found at i:2000610 original size:17 final size:15
Alignment explanation
Indices: 2000503--2000620 Score: 69
Period size: 15 Copynumber: 7.5 Consensus size: 15
2000493 AATTTTTAAA
*
2000503 TTTTTTAAATTTAAAT
1 TTTTTTAAATTT-TAT
* **
2000519 TATTTTTAACTTAAAT
1 T-TTTTTAAATTTTAT
*
2000535 TTTTTTAAATTTAAT
1 TTTTTTAAATTTTAT
*
2000550 TTATTTTAGATTATT-T
1 TT-TTTTAAATT-TTAT
* *
2000566 TTTTTCAAATTTAAAT
1 TTTTTTAAATTT-TAT
**
2000582 CATTTT-AATTTTAGT
1 TTTTTTAAATTTTA-T
2000597 TCTTTTTAAATTTTAT
1 T-TTTTTAAATTTTAT
2000613 TTTTTTAA
1 TTTTTTAA
2000621 TTAAATTGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
14 2 0.03
15 34 0.43
16 26 0.33
17 17 0.22
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTTTAAATTTTAT
Found at i:2000634 original size:15 final size:15
Alignment explanation
Indices: 2000623--2000652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2000613 TTTTTTAATT
2000623 AAATTGAATTTAAAA
1 AAATTGAATTTAAAA
*
2000638 AAATTTAATTTAAAA
1 AAATTGAATTTAAAA
2000653 TTTTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
AAATTGAATTTAAAA
Found at i:2002224 original size:3 final size:3
Alignment explanation
Indices: 2002218--2002252 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2002208 AAAAAAAATG
*
2002218 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2002253 CCAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2004160 original size:318 final size:317
Alignment explanation
Indices: 2003584--2004839 Score: 2361
Period size: 318 Copynumber: 4.0 Consensus size: 317
2003574 ATTTTTTTTT
2003584 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
1 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
* *
2003649 TTTTGGTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTATTATTTTTTTAACGA
66 TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACGA
* *
2003714 ATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGTTGTATTGGATTAATGCTGTCAGTATCTT
131 ATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCTT
2003779 CAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAATT
196 CAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAATT
* *
2003844 GGTTTTGTTACCTGTTAAGATCCTTAGTCTGGAAACATAAATTTTGATTTTGTTACC
261 GGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACC
2003901 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
1 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
2003966 GTTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACG
66 -TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACG
2004031 AATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCT
130 AATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCT
*
2004096 TCAAAGGCTTGCGTGTCTGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAAT
195 TCAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAAT
2004161 TGGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACC
260 TGGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACC
2004219 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
1 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
2004284 GTTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACG
66 -TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACG
2004349 AATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCT
130 AATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCT
*
2004414 TCAAAGGCTTGCGTGTCTGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAAT
195 TCAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAAT
*
2004479 TGGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACA
260 TGGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACC
2004537 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGA-TTT
1 TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
* *
2004601 TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTATTATTTTTTTAATGA
66 TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACGA
*
2004666 ATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTATATTGGATTAATGTTGTCAGTATCTT
131 ATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCTT
*
2004731 CAAAGGCTTGCATGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAATT
196 CAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAATT
*
2004796 GGTTTTGTTACCTGTTAAGATCCTTAGTCTGGAAACATAAATTT
261 GGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTT
2004840 TTATAGTGAA
Statistics
Matches: 924, Mismatches: 14, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
316 233 0.25
317 68 0.07
318 623 0.67
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (317 bp):
TCTTTTTACATTGCTGTTTGATTGGTTAACTTGTTTGTGTTGTTTCAGTTATGAATTTTGATTTT
TTTTGTTTTCGGTTCAATGTTCATGAACACTGTGGGATAAAAAAACACTACTATTTTTTTAACGA
ATGTAGTGACAATGTTTTTAATAAGTATTCTGTTTGGTGTATTGGATTAATGTTGTCAGTATCTT
CAAAGGCTTGCGTGTCCGGAATAAAACCTCCTTTTCAATGCAGAACCTTGTCCTGTTGTTAAATT
GGTTTTGTTACCCGTTAAGATCCTTAGTCTGGAAACATAAATTTAGATTTTGTTACC
Found at i:2008750 original size:31 final size:30
Alignment explanation
Indices: 2008692--2008750 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2008682 TCACACACAT
* * * *
2008692 ATTAAATATATTTTTTAATTTTTTTATTAA
1 ATTAAAAAAATTTTTTAATTATATTATTAA
2008722 ATTAAAAAAATTTTATTAATTATATTATT
1 ATTAAAAAAATTTT-TTAATTATATTATT
2008751 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTAAAAAAATTTTTTAATTATATTATTAA
Found at i:2008761 original size:16 final size:17
Alignment explanation
Indices: 2008730--2008769 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2008720 AAATTAAAAA
*
2008730 AATTTTATTAATTATAT
1 AATTTTATTAAATATAT
*
2008747 TATTTT-TTAAATATAT
1 AATTTTATTAAATATAT
2008763 AATTTTA
1 AATTTTA
2008770 ACTATATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTTATTAAATATAT
Found at i:2020923 original size:2 final size:2
Alignment explanation
Indices: 2020910--2020941 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2020900 ATTCTTTGGA
*
2020910 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2020942 CAACTTCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2020978 original size:3 final size:3
Alignment explanation
Indices: 2020970--2021012 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2020960 AGCAAAATTG
2020970 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2021013 GCCTAATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2021987 original size:20 final size:20
Alignment explanation
Indices: 2021964--2022005 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2021954 AATATTTAAA
*
2021964 TATTATATTAAATAATTTTT
1 TATTATATTAAATAAATTTT
* *
2021984 TATTTTATTATATAAATTTT
1 TATTATATTAAATAAATTTT
2022004 TA
1 TA
2022006 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATATTAAATAAATTTT
Found at i:2022299 original size:3 final size:3
Alignment explanation
Indices: 2022291--2022325 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2022281 TATTTCTTAT
2022291 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2022326 CAAAATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2024986 original size:21 final size:21
Alignment explanation
Indices: 2024956--2025008 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2024946 TCCCTTTTCC
*
2024956 ATTTCCATTTGCACTTGTTTTT
1 ATTTCTATTTGCA-TTGTTTTT
* *
2024978 ATTT-TATTTTTCATTTTTTTT
1 ATTTCTA-TTTGCATTGTTTTT
2024999 ATTTCTATTT
1 ATTTCTATTT
2025009 CTGTTGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (21 bp):
ATTTCTATTTGCATTGTTTTT
Found at i:2025734 original size:19 final size:19
Alignment explanation
Indices: 2025706--2025742 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2025696 TAAGTGATCG
2025706 AAATAAAATG-TTAAAATA
1 AAATAAAATGTTTAAAATA
2025724 AAATAAAAATGTTTAAAAT
1 AAAT-AAAATGTTTAAAAT
2025743 GATAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATAAAATGTTTAAAATA
Found at i:2026037 original size:16 final size:19
Alignment explanation
Indices: 2026000--2026035 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2025990 TTTAAATATG
2026000 ATATGATTATACAAAATAA
1 ATATGATTATACAAAATAA
2026019 ATATGA-TATA-AAAATAA
1 ATATGATTATACAAAATAA
2026036 TACAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (19 bp):
ATATGATTATACAAAATAA
Found at i:2031074 original size:15 final size:15
Alignment explanation
Indices: 2031056--2031102 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2031046 TTTTTATTTA
2031056 TTTATTTTTATAAAT
1 TTTATTTTTATAAAT
*
2031071 TTTATATTTA-ATAAT
1 TTTATTTTTATA-AAT
* *
2031086 TATATTTTTATATAT
1 TTTATTTTTATAAAT
2031101 TT
1 TT
2031103 ATACATAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTTTTATAAAT
Found at i:2031116 original size:29 final size:29
Alignment explanation
Indices: 2031054--2031130 Score: 68
Period size: 30 Copynumber: 2.6 Consensus size: 29
2031044 ATTTTTTATT
* * *
2031054 TATT-TATTTTTATAAATTTTATATTTAA
1 TATTATATTTTTATATATTTTATAATAAA
2031082 TAATTATATTTTTATATA-TTTATACATAAA
1 T-ATTATATTTTTATATATTTTATA-ATAAA
*
2031112 TATTAAATATTTTTTTATA
1 TATT--ATATTTTTATATA
2031131 AAATTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 12 0.30
30 15 0.38
31 12 0.30
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTATATTTTTATATATTTTATAATAAA
Found at i:2031138 original size:20 final size:24
Alignment explanation
Indices: 2031107--2031153 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
2031097 ATATTTATAC
2031107 ATAAATATT-AAA-TATTTTT-TT
1 ATAAATATTAAAAGTATTTTTATT
2031128 ATAAA-ATTAAAAGTATTTTTATT
1 ATAAATATTAAAAGTATTTTTATT
2031151 ATA
1 ATA
2031154 TTACGACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 8 0.35
22 7 0.30
23 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAAATATTAAAAGTATTTTTATT
Found at i:2036960 original size:21 final size:22
Alignment explanation
Indices: 2036936--2036981 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2036926 ACCGATAACA
* *
2036936 TTTATTTTAAATT-AATTTGAT
1 TTTATATTAAATTCAATTTAAT
*
2036957 TTTATATTACATTCAATTTAAT
1 TTTATATTAAATTCAATTTAAT
2036979 TTT
1 TTT
2036982 TAAAAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTATATTAAATTCAATTTAAT
Found at i:2040872 original size:3 final size:3
Alignment explanation
Indices: 2040864--2040907 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
2040854 TTATTCCTTT
*
2040864 TTA TTA TTA TT- TTAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2040908 CTTTGCAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.92
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2041018 original size:6 final size:6
Alignment explanation
Indices: 2041007--2041051 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
2040997 ACAATTGTAT
* *
2041007 AATATA AATAT- AATATA AAAAT- AATATA AACAT- AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
2041052 TTAATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.41
6 19 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:2041020 original size:11 final size:11
Alignment explanation
Indices: 2041004--2041051 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
2040994 AATACAATTG
2041004 TATAATATAAA
1 TATAATATAAA
2041015 TATAATATAAA
1 TATAATATAAA
*
2041026 AATAATATAAA
1 TATAATATAAA
*
2041037 CATAATATAAA
1 TATAATATAAA
2041048 TATA
1 TATA
2041052 TTAATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAATATAAA
Found at i:2041065 original size:37 final size:37
Alignment explanation
Indices: 2041024--2041098 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
2041014 ATATAATATA
*
2041024 AAAATAATATAA-AC-ATAATATAAATATATTAATTTTT
1 AAAAT-ATATAATACGA-AATATAAATATATTAAATTTT
* *
2041061 AAAATATATAATACGAATTATTAATATATTAAATTTT
1 AAAATATATAATACGAAATATAAATATATTAAATTTT
2041098 A
1 A
2041099 TTAAAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 6 0.18
37 26 0.79
38 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (37 bp):
AAAATATATAATACGAAATATAAATATATTAAATTTT
Found at i:2041106 original size:20 final size:20
Alignment explanation
Indices: 2041011--2041138 Score: 63
Period size: 20 Copynumber: 6.4 Consensus size: 20
2041001 TTGTATAATA
2041011 TAAATATAATATAAAA-ATAAT
1 TAAATATAAT-TAAAATAT-AT
*
2041032 ATAAACATAA-TATAAATATAT
1 -TAAATATAATTA-AAATATAT
*
2041053 T-AAT-T-TTTAAAATATA-
1 TAAATATAATTAAAATATAT
* *
2041069 T-AATACGAATTATTAATATAT
1 TAAATA-TAATTA-AAATATAT
* * *
2041090 TAAATTTTATTAAAATATTT
1 TAAATATAATTAAAATATAT
*
2041110 TAAATATAATTATAATATAAT
1 TAAATATAATTAAAATAT-AT
*
2041131 AAAATATA
1 TAAATATA
2041139 TAAAAATAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
16 4 0.05
17 7 0.09
18 3 0.04
19 5 0.06
20 30 0.38
21 18 0.22
22 13 0.16
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (20 bp):
TAAATATAATTAAAATATAT
Found at i:2041128 original size:11 final size:11
Alignment explanation
Indices: 2041004--2041130 Score: 54
Period size: 11 Copynumber: 12.0 Consensus size: 11
2040994 AATACAATTG
*
2041004 TATAATATAAA
1 TATAATATAAT
*
2041015 TATAATATAAA
1 TATAATATAAT
* *
2041026 AATAATATAAA
1 TATAATATAAT
* *
2041037 CATAATATAAA
1 TATAATATAAT
2041048 TAT-AT-TAAT
1 TATAATATAAT
* *
2041057 T-T-TTAAAAT
1 TATAATATAAT
*
2041066 ATATAATACGAAT
1 -TATAATA-TAAT
2041079 TATTAATAT-AT
1 TA-TAATATAAT
* *
2041090 TA-AATTTTAT
1 TATAATATAAT
* *
2041100 TAAAATAT-TT
1 TATAATATAAT
2041110 TA-AATATAAT
1 TATAATATAAT
2041120 TATAATATAAT
1 TATAATATAAT
2041131 AAAATATATA
Statistics
Matches: 93, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
8 2 0.02
9 16 0.17
10 13 0.14
11 50 0.54
12 4 0.04
13 8 0.09
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (11 bp):
TATAATATAAT
Found at i:2043257 original size:3 final size:3
Alignment explanation
Indices: 2043249--2043280 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2043239 TTTTTCACTA
2043249 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2043281 GTTAGCAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2044282 original size:3 final size:3
Alignment explanation
Indices: 2044276--2044317 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2044266 GGTAATTGGA
2044276 ATT ATT 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
2044318 GTGGACTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2045485 original size:26 final size:27
Alignment explanation
Indices: 2045456--2045508 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2045446 ATATCAATCA
*
2045456 ATAAATTAATCA-CTTAAA-AATATTTC
1 ATAAATT-ATCATATTAAATAATATTTC
2045482 ATAAATTATCATATTAAATAATATTTC
1 ATAAATTATCATATTAAATAATATTTC
2045509 TTTATTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 12 0.50
27 8 0.33
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (27 bp):
ATAAATTATCATATTAAATAATATTTC
Found at i:2046642 original size:15 final size:14
Alignment explanation
Indices: 2046624--2046671 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
2046614 TTAATTTTTT
2046624 TTAATTATATTTAAA
1 TTAATT-TATTTAAA
2046639 TTAAATTTTATTTAAA
1 TT-AA-TTTATTTAAA
2046655 TTAATTTAATTTAAA
1 TTAATTT-ATTTAAA
2046670 TT
1 TT
2046672 TTAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.10
15 13 0.43
16 12 0.40
17 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTTATTTAAA
Found at i:2046645 original size:16 final size:16
Alignment explanation
Indices: 2046626--2046671 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2046616 AATTTTTTTT
2046626 AATTATATTTAAATTA
1 AATTATATTTAAATTA
*
2046642 AATTTTATTTAAATTA
1 AATTATATTTAAATTA
*
2046658 ATTTA-ATTTAAATT
1 AATTATATTTAAATT
2046672 TTAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTATATTTAAATTA
Found at i:2046652 original size:26 final size:26
Alignment explanation
Indices: 2046616--2046674 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2046606 TAAAAATTTT
*
2046616 AATTTT-TTTTAATTATATTTAAATTA
1 AATTTTATTTAAATTA-ATTTAAATTA
*
2046642 AATTTTATTTAAATTAATTTAATTTA
1 AATTTTATTTAAATTAATTTAAATTA
2046668 AATTTTA
1 AATTTTA
2046675 ATATATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
AATTTTATTTAAATTAATTTAAATTA
Found at i:2047164 original size:3 final size:3
Alignment explanation
Indices: 2047156--2047181 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2047146 AACAAAAGGA
2047156 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2047182 CAAAAAGGAC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2048053 original size:19 final size:20
Alignment explanation
Indices: 2048009--2048053 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2047999 TAATCTTTAC
*
2048009 AATTAATAAATGATAATAAT
1 AATTAATAAATGATAATAAA
*
2048029 AA-TAATAAAT-ATATTAAA
1 AATTAATAAATGATAATAAA
2048047 AATTAAT
1 AATTAAT
2048054 GAACTGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 12 0.55
20 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTAATAAATGATAATAAA
Found at i:2048935 original size:3 final size:3
Alignment explanation
Indices: 2048927--2048954 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2048917 AATTCTTTTA
2048927 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2048955 TTGTCCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2058778 original size:28 final size:29
Alignment explanation
Indices: 2058723--2058780 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
2058713 TTTAATATGT
* *
2058723 TTTTTAATTCAATTTTTAATATTTTAATA
1 TTTTTAATTCAATTTTTAAAATTATAATA
2058752 TTTTT-ATT-AATTTTTAAAATATATAATA
1 TTTTTAATTCAATTTTTAAAAT-TATAATA
2058780 T
1 T
2058781 AATATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 11 0.42
28 10 0.38
29 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTAATTCAATTTTTAAAATTATAATA
Found at i:2058804 original size:16 final size:17
Alignment explanation
Indices: 2058782--2058823 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2058772 ATATAATATA
* *
2058782 ATATATTTTTTATTGTT
1 ATATATTTTATATTATT
2058799 -TATATTATTATATTATT
1 ATATATT-TTATATTATT
2058816 ATATATTT
1 ATATATTT
2058824 ATTCTTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.29
17 9 0.43
18 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATATATTTTATATTATT
Found at i:2059500 original size:22 final size:20
Alignment explanation
Indices: 2059465--2059505 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2059455 AAATACTTTT
*
2059465 ACTTTTTAAAAAAATTTATC
1 ACTTTTTAAAAAAAATTATC
2059485 ACTTTTATAAAAAAAAATTAT
1 ACTTTT-T-AAAAAAAATTAT
2059506 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
ACTTTTTAAAAAAAATTATC
Found at i:2065909 original size:21 final size:22
Alignment explanation
Indices: 2065879--2065920 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2065869 TATTTTATAA
* *
2065879 ATTTTTTATTTTTA-AAATATG
1 ATTTTATATTTATATAAATATG
2065900 ATTTTATATTTATATAAATAT
1 ATTTTATATTTATATAAATAT
2065921 AAATCAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTATATTTATATAAATATG
Found at i:2067117 original size:2 final size:2
Alignment explanation
Indices: 2067112--2067146 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2067102 AGTGTGTGTG
2067112 TA TA TA 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 TA TA TA T
2067147 GCTTTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2074968 original size:12 final size:13
Alignment explanation
Indices: 2074945--2074985 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2074935 TTTGATGTTG
* *
2074945 TTTAAAATTAATT
1 TTTATAATTAATA
2074958 TTTAT-ATTAATA
1 TTTATAATTAATA
2074970 TTTATAATTAA-A
1 TTTATAATTAATA
2074982 TTTA
1 TTTA
2074986 AATAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:2075268 original size:31 final size:35
Alignment explanation
Indices: 2075219--2075299 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 35
2075209 TATGTTTAAA
*
2075219 ATATTTATA-TATATATAAA-TTAAAAATATTA-TT
1 ATATTTATATTATATA-AAATTTAAAAATAATATTT
*
2075252 A-ATTTATATTATATAAAATTTAAATATAATATTT
1 ATATTTATATTATATAAAATTTAAAAATAATATTT
2075286 ATATTT-TATTATAT
1 ATATTTATATTATAT
2075300 TTTTAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 10 0.24
33 17 0.40
34 11 0.26
35 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
ATATTTATATTATATAAAATTTAAAAATAATATTT
Found at i:2075301 original size:16 final size:15
Alignment explanation
Indices: 2075280--2075349 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 15
2075270 TTTAAATATA
2075280 ATATTTATATTTTATT
1 ATATTTA-ATTTTATT
2075296 ATATTTTTAATTTATATT
1 ATA--TTTAATTT-TATT
* * *
2075314 ATATTTAA-ATAATG
1 ATATTTAATTTTATT
2075328 ATATTTAATTTTATT
1 ATATTTAATTTTATT
*
2075343 AAATTTA
1 ATATTTA
2075350 CTCCAATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.23
15 10 0.23
16 8 0.19
17 4 0.09
18 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (15 bp):
ATATTTAATTTTATT
Found at i:2078065 original size:22 final size:22
Alignment explanation
Indices: 2078027--2078068 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2078017 GTAATTACTA
*
2078027 AAATTTTAATATTATAAATATT
1 AAATTTTAATATAATAAATATT
2078049 AAATATTTAATA-AATAAATA
1 AAAT-TTTAATATAATAAATA
2078069 AATAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTTTAATATAATAAATATT
Found at i:2078165 original size:24 final size:22
Alignment explanation
Indices: 2078128--2078183 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2078118 GATCATTACA
*
2078128 TAAAAAATATTAAAATAAATTTT
1 TAAAAAATAAT-AAATAAATTTT
2078151 TAAAAAATCAATAAATAAATTTT
1 TAAAAAAT-AATAAATAAATTTT
* *
2078174 TTATAAATAA
1 TAAAAAATAA
2078184 AATAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAATAATAAATAAATTTT
Found at i:2078181 original size:23 final size:24
Alignment explanation
Indices: 2078140--2078194 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
2078130 AAAAATATTA
*
2078140 AAATAAATTTTTAAAAAAT-CAAT
1 AAATAAATTTTTAAAAAATAAAAT
* *
2078163 AAATAAATTTTTTATAAATAAAAT
1 AAATAAATTTTTAAAAAATAAAAT
2078187 AAA-AAATT
1 AAATAAATT
2078195 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAAATTTTTAAAAAATAAAAT
Found at i:2078261 original size:16 final size:15
Alignment explanation
Indices: 2078242--2078276 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2078232 ATTCGATATA
2078242 ATAAATATAAATCAAT
1 ATAAATATAAAT-AAT
*
2078258 ATAAATTTAAATAAT
1 ATAAATATAAATAAT
2078273 ATAA
1 ATAA
2078277 TATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAATATAAATAAT
Found at i:2078285 original size:16 final size:15
Alignment explanation
Indices: 2078239--2078283 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2078229 CAAATTCGAT
2078239 ATAATA-AATA-TAA
1 ATAATATAATATTAA
2078252 ATCAATATAA-ATTTAA
1 AT-AATATAATA-TTAA
2078268 ATAATATAATATTAA
1 ATAATATAATATTAA
2078283 A
1 A
2078284 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.07
14 5 0.19
15 14 0.52
16 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATATAATATTAA
Found at i:2078811 original size:20 final size:19
Alignment explanation
Indices: 2078743--2078810 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
2078733 TTAATATGAT
2078743 AATAT-AAATATTATATAA
1 AATATAAAATATTATATAA
* *
2078761 AA-ATAAAAAATAATAATAA
1 AATATAAAATATTAT-ATAA
2078780 TAA-ATAAAAT-TTATATAA
1 -AATATAAAATATTATATAA
2078798 AATATAAAATATT
1 AATATAAAATATT
2078811 TTAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.10
18 20 0.49
19 9 0.22
20 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATAAAATATTATATAA
Found at i:2080372 original size:23 final size:22
Alignment explanation
Indices: 2080346--2080393 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
2080336 TTTAAAATAA
2080346 TTATTT-AATTAATAAAAATTATT
1 TTATTTAAATT-AT-AAAATTATT
*
2080369 TTATTTAAATTATTAAATTATT
1 TTATTTAAATTATAAAATTATT
2080391 TTA
1 TTA
2080394 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTAAATTATAAAATTATT
Found at i:2082461 original size:16 final size:16
Alignment explanation
Indices: 2082437--2082493 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
2082427 TTAAAAAATC
2082437 AAATATAATTATTTTT
1 AAATATAATTATTTTT
* * * *
2082453 AAATTTAATAAATATT
1 AAATATAATTATTTTT
* *
2082469 AAATAAAATTATTTAT
1 AAATATAATTATTTTT
*
2082485 AAATTTAAT
1 AAATATAAT
2082494 AAGTATTAAA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATAATTATTTTT
Found at i:2082479 original size:32 final size:32
Alignment explanation
Indices: 2082419--2082504 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
2082409 TCGATATTGA
* *
2082419 TTATAAATTTAA-AAA-ATCAAATATAATTAT
1 TTATAAATTTAATAAATATTAAATAAAATTAT
*
2082449 TTTTAAATTTAATAAATATTAAATAAAATTAT
1 TTATAAATTTAATAAATATTAAATAAAATTAT
*
2082481 TTATAAATTTAATAAGTATTAAAT
1 TTATAAATTTAATAAATATTAAAT
2082505 TTTATTACGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 11 0.22
31 3 0.06
32 35 0.71
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
TTATAAATTTAATAAATATTAAATAAAATTAT
Found at i:2082518 original size:32 final size:32
Alignment explanation
Indices: 2082420--2082522 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 32
2082410 CGATATTGAT
* * **
2082420 TATAAATTTAA-AAA-ATCAAATATAATTATT
1 TATAAATTTAATAAATATTAAATAAAATTACG
* **
2082450 TTTAAATTTAATAAATATTAAATAAAATTATT
1 TATAAATTTAATAAATATTAAATAAAATTACG
* ***
2082482 TATAAATTTAATAAGTATTAAATTTTATTACG
1 TATAAATTTAATAAATATTAAATAAAATTACG
2082514 TATAAATTT
1 TATAAATTT
2082523 GAAAATTACT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 10 0.16
31 3 0.05
32 48 0.79
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (32 bp):
TATAAATTTAATAAATATTAAATAAAATTACG
Found at i:2082672 original size:19 final size:20
Alignment explanation
Indices: 2082645--2082684 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2082635 TAATTTTATT
*
2082645 TATTTTATAT-TTAAAAATA
1 TATTATATATATTAAAAATA
*
2082664 TATTATATATATTTAAAATA
1 TATTATATATATTAAAAATA
2082684 T
1 T
2082685 TTAAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATATATATTAAAAATA
Found at i:2083783 original size:26 final size:26
Alignment explanation
Indices: 2083754--2083812 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
2083744 TTAAATATTT
2083754 TTATTAAAAAAATATTATA-AATTATA
1 TTATTAAAAAAATATTATATAA-TATA
* * *
2083780 TTATTTATAAAATTTTATATAATATA
1 TTATTAAAAAAATATTATATAATATA
*
2083806 TTTTTAA
1 TTATTAA
2083813 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTATTAAAAAAATATTATATAATATA
Found at i:2084185 original size:2 final size:2
Alignment explanation
Indices: 2084178--2084202 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2084168 TATGCAGCCT
2084178 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
2084203 TTATTATGTT
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:2084528 original size:12 final size:12
Alignment explanation
Indices: 2084511--2084546 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2084501 TTGAGTGGAA
*
2084511 AAATTTTTATTT
1 AAATTTTAATTT
2084523 AAATTTTAATTT
1 AAATTTTAATTT
*
2084535 AAATATTAATTT
1 AAATTTTAATTT
2084547 TTTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AAATTTTAATTT
Found at i:2084633 original size:63 final size:61
Alignment explanation
Indices: 2084566--2084684 Score: 143
Period size: 64 Copynumber: 1.9 Consensus size: 61
2084556 TAAATTTATA
* *
2084566 TAAAAAT-ATTTTTTAATAAATAATAATATTAATT-AAATTAATTTAAATTATAATATATAAAAT
1 TAAAAATAATTTTTAAATAAAT-ATAATATGAATTCAAATT-A-TTAAATTAT-ATATATAAAAT
* * *
2084629 TAAAATTAATTTTTAAATAAATTTAATATGAATTCAAATTATTATATTATATATAT
1 TAAAAATAATTTTTAAATAAATATAATATGAATTCAAATTATTAAATTATATATAT
2084685 TTAATTTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 6 0.12
62 8 0.16
63 17 0.35
64 18 0.37
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (61 bp):
TAAAAATAATTTTTAAATAAATATAATATGAATTCAAATTATTAAATTATATATATAAAAT
Found at i:2084736 original size:19 final size:19
Alignment explanation
Indices: 2084709--2084756 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
2084699 GGCTAATTTA
*
2084709 ATTTTTTATTAAATTATAT
1 ATTTTTTATTAAATTAAAT
*
2084728 ATTTATTATTAAATTAAAT
1 ATTTTTTATTAAATTAAAT
2084747 ATTTTTTATT
1 ATTTTTTATT
2084757 GATAATATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTATTAAATTAAAT
Found at i:2085632 original size:9 final size:8
Alignment explanation
Indices: 2085563--2085634 Score: 56
Period size: 9 Copynumber: 8.2 Consensus size: 8
2085553 CTGATTTACG
2085563 TATATAAA
1 TATATAAA
2085571 TATA-AATA
1 TATATAA-A
2085579 TATATACTAA
1 TATATA--AA
*
2085589 TATATGAAG
1 TATAT-AAA
2085598 TATTATAAA
1 TA-TATAAA
*
2085607 TAAATATAA
1 TATATA-AA
2085616 TATATAAA
1 TATATAAA
2085624 TATATTAAA
1 TATA-TAAA
2085633 TA
1 TA
2085635 ATTGATAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 18 0.35
9 21 0.40
10 9 0.17
11 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (8 bp):
TATATAAA
Found at i:2085635 original size:13 final size:13
Alignment explanation
Indices: 2085566--2085635 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
2085556 ATTTACGTAT
*
2085566 ATAAATATAA-AT
1 ATAAATATAATAA
* *
2085578 ATATATACTAATAT
1 ATAAATA-TAATAA
* *
2085592 ATGAAGTATTATAA
1 AT-AAATATAATAA
*
2085606 ATAAATATAATAT
1 ATAAATATAATAA
*
2085619 ATAAATATATTAA
1 ATAAATATAATAA
2085632 ATAA
1 ATAA
2085636 TTGATAACGT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
12 6 0.13
13 26 0.58
14 10 0.22
15 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (13 bp):
ATAAATATAATAA
Found at i:2085642 original size:27 final size:27
Alignment explanation
Indices: 2085571--2085635 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 27
2085561 CGTATATAAA
*
2085571 TATAAATATATATACTAATATATGAAGTAT
1 TATAAATA-A-ATA-TAATATATGAAATAT
2085601 TATAAATAAATATAATATAT-AAATA-
1 TATAAATAAATATAATATATGAAATAT
2085626 TATTAAATAA
1 TA-TAAATAA
2085636 TTGATAACGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 11 0.33
27 8 0.24
28 3 0.09
29 1 0.03
30 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (27 bp):
TATAAATAAATATAATATATGAAATAT
Found at i:2086878 original size:18 final size:19
Alignment explanation
Indices: 2086835--2086884 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
2086825 AAAATAATAA
*
2086835 ATAAATAATTTAAATTAATT
1 ATAAAT-ATTTAAATAAATT
2086855 -TAAAATATTTAAA-AAATT
1 AT-AAATATTTAAATAAATT
2086873 ATAAATATTTAA
1 ATAAATATTTAA
2086885 TCTATTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.52
19 9 0.33
20 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATATTTAAATAAATT
Found at i:2087159 original size:3 final size:3
Alignment explanation
Indices: 2087151--2087188 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2087141 AAAAGAACAA
2087151 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2087189 GCATGCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2088572 original size:22 final size:22
Alignment explanation
Indices: 2088524--2088566 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2088514 TTGATTAAAT
*
2088524 AAAAAATATATATTTTTGAATG
1 AAAAAATATATATTTTTGAATA
2088546 AAAAAATATA-ATTTTT-AATA
1 AAAAAATATATATTTTTGAATA
2088566 A
1 A
2088567 TTAAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AAAAAATATATATTTTTGAATA
Found at i:2094515 original size:53 final size:52
Alignment explanation
Indices: 2094418--2094689 Score: 174
Period size: 53 Copynumber: 4.9 Consensus size: 52
2094408 AATCAATTAA
* * * * *
2094418 ATTAATAAAAATT-AAGTTTAAACTTATTTTTAATTTTATTTTAAAAATATTTT
1 ATTAATAAAATTTAAAATTTTAACTTA--TTTAATTTTATATTAAAAAAATTTT
* *
2094471 ATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTG
1 AT-TAATAAAATTTAAAATTTTAACTTATTTAATTTTATATT---AAAA-A-AATTTT
** * **
2094529 ATTAAATATATTTTTATTAAATATTT-A-TTAAATTTAATATTTAAATTAAAAAAAATTAA
1 ATT-AATA-AAATTTA--AAAT-TTTAACTT--ATTTAAT-TTTATATT-AAAAAAATTTT
* * * * *
2094588 ATTAATAAAAATT-AAGTTTAAACTTATTTTTAATTTTATTTTAAAAATATTTT
1 ATTAATAAAATTTAAAATTTTAACTTA--TTTAATTTTATATTAAAAAAATTTT
*
2094641 ATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAA
1 AT-TAATAAAATTTAAAATTTTAACTTATTTAATTTTATATTAAAAAAA
2094690 CACAATTTGA
Statistics
Matches: 169, Mismatches: 29, Indels: 42
0.70 0.12 0.17
Matches are distributed among these distances:
53 45 0.27
54 30 0.18
55 30 0.18
56 4 0.02
57 5 0.03
58 14 0.08
59 12 0.07
60 3 0.02
61 10 0.06
62 10 0.06
63 6 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (52 bp):
ATTAATAAAATTTAAAATTTTAACTTATTTAATTTTATATTAAAAAAATTTT
Found at i:2094589 original size:15 final size:15
Alignment explanation
Indices: 2094569--2094602 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2094559 AATTTAATAT
2094569 TTAAATTAAAAAAAA
1 TTAAATTAAAAAAAA
*
2094584 TTAAATTAATAAAAA
1 TTAAATTAAAAAAAA
2094599 TTAA
1 TTAA
2094603 GTTTAAACTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAATTAAAAAAAA
Found at i:2094599 original size:170 final size:171
Alignment explanation
Indices: 2094403--2094742 Score: 664
Period size: 170 Copynumber: 2.0 Consensus size: 171
2094393 TAAAAACCCG
2094403 TAAAAAATCAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATTTTAAAAATAT
1 TAAAAAA-CAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATTTTAAAAATAT
2094468 TTTATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTGATTA
65 TTTATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTGATTA
2094533 AATATATTTTTATTAAATATTTATTAAATTTAATATTTAAAT
130 AATATATTTTTATTAAATATTTATTAAATTTAATATTTAAAT
2094575 TAAAAAA-AATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATTTTAAAAATATT
1 TAAAAAACAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATTTTAAAAATATT
2094639 TTATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTGATTAA
66 TTATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTGATTAA
2094704 ATATATTTTTATTAAATATTTATTAAATTTAATATTTAA
131 ATATATTTTTATTAAATATTTATTAAATTTAATATTTAA
2094743 TTTTTTTTAA
Statistics
Matches: 168, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
170 161 0.96
172 7 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (171 bp):
TAAAAAACAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATTTTAAAAATATT
TTATGTAATAAAATTTAAAATTTTAACTTATTTAATCTTATATTAAAAAAACACAATTTGATTAA
ATATATTTTTATTAAATATTTATTAAATTTAATATTTAAAT
Found at i:2094632 original size:54 final size:54
Alignment explanation
Indices: 2094403--2094689 Score: 158
Period size: 54 Copynumber: 5.1 Consensus size: 54
2094393 TAAAAACCCG
2094403 TAAAAAATCAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTAT-T
1 TAAAAAA--AATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATAT
* * ** * * * *
2094458 TTAAAAATATTTTATGTAATAAAATTTAAAATTTTAACTTA--TTTAATCTTATAT
1 TAAAAAAAATTAAAT-TAATAAAAATT-AAGTTTAAACTTATTTTTAATTTTATAT
* * * * * * *
2094512 TAAAAAAACA-CAATTTGATTAAATATATTTTTA-TTAAATATTTATTAAATTTAATATTTAAAT
1 TAAAAAAA-ATTAAATT-AATAAA-A-A--TTAAGTTTAA-ACTTATT---TTTAAT-TTTATAT
2094575 TAAAAAAAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTAT-T
1 TAAAAAAAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATAT
* * ** * * * *
2094628 TTAAAAATATTTTATGTAATAAAATTTAAAATTTTAACTTA--TTTAATCTTATAT
1 TAAAAAAAATTAAAT-TAATAAAAATT-AAGTTTAAACTTATTTTTAATTTTATAT
2094682 TAAAAAAA
1 TAAAAAAA
2094690 CACAATTTGA
Statistics
Matches: 172, Mismatches: 39, Indels: 43
0.68 0.15 0.17
Matches are distributed among these distances:
53 38 0.22
54 44 0.26
55 36 0.21
56 3 0.02
57 5 0.03
58 11 0.06
59 4 0.02
60 1 0.01
61 1 0.01
62 12 0.07
63 17 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (54 bp):
TAAAAAAAATTAAATTAATAAAAATTAAGTTTAAACTTATTTTTAATTTTATAT
Found at i:2094887 original size:2 final size:2
Alignment explanation
Indices: 2094880--2094918 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2094870 TTAACATAAA
2094880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2094919 GATTGACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2103280 original size:12 final size:13
Alignment explanation
Indices: 2103251--2103324 Score: 59
Period size: 13 Copynumber: 5.7 Consensus size: 13
2103241 AGATGTTTTT
*
2103251 AAATTACTTTAACCA
1 AAATTAATTTAA--A
2103266 AAACTTAA-TTAAA
1 AAA-TTAATTTAAA
2103279 AAATTAATTTAAA
1 AAATTAATTTAAA
2103292 ATAA--AATTT--A
1 A-AATTAATTTAAA
2103302 AAATTAATTTAAA
1 AAATTAATTTAAA
2103315 ATAATTAATT
1 A-AATTAATT
2103325 ATTAATTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
9 2 0.04
10 2 0.04
11 5 0.10
12 9 0.18
13 12 0.24
14 10 0.20
15 7 0.14
16 3 0.06
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAATTTAAA
Found at i:2103292 original size:11 final size:11
Alignment explanation
Indices: 2103278--2103320 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
2103268 ACTTAATTAA
2103278 AAAATTAATTT
1 AAAATTAATTT
*
2103289 AAAATAAAATTT
1 AAAAT-TAATTT
2103301 AAAATTAATTT
1 AAAATTAATTT
2103312 AAAA-TAATT
1 AAAATTAATT
2103321 AATTATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATTAATTT
Found at i:2105442 original size:24 final size:24
Alignment explanation
Indices: 2105414--2105478 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
2105404 TTTCGTAAAG
2105414 ATATAATATATTTAAAAATA-ATT
1 ATATAATATATTTAAAAATATATT
*
2105437 AATATAATATTTTTAATAAATATATT
1 -ATATAATATATTTAA-AAATATATT
*
2105463 ATAT-ATGTATTTAAAA
1 ATATAATATATTTAAAA
2105479 TTTTAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 2 0.06
24 22 0.61
25 9 0.25
26 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATAATATATTTAAAAATATATT
Found at i:2105625 original size:18 final size:18
Alignment explanation
Indices: 2105604--2105670 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
2105594 AAGATATTTC
2105604 ATATTTTTATAAATTTTG
1 ATATTTTTATAAATTTTG
* *
2105622 ATATGTTAAT-AA--TTG
1 ATATTTTTATAAATTTTG
* *
2105637 ATA-TTATATAAATTTTA
1 ATATTTTTATAAATTTTG
* *
2105654 ATATATTTATATATTTT
1 ATATTTTTATAAATTTT
2105671 TATTATATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
17 7 0.19
18 18 0.50
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATATTTTTATAAATTTTG
Found at i:2105687 original size:25 final size:27
Alignment explanation
Indices: 2105654--2105710 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
2105644 ATAAATTTTA
*
2105654 ATATATTT-ATATATTTTTATTATA-TT
1 ATATATTTAAT-TATTTTTATCATATTT
*
2105680 ATATT-TTAATTATTTTTATCATATTT
1 ATATATTTAATTATTTTTATCATATTT
2105706 ATATA
1 ATATA
2105711 ATTATATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATATTTAATTATTTTTATCATATTT
Found at i:2105692 original size:19 final size:19
Alignment explanation
Indices: 2105638--2105738 Score: 58
Period size: 19 Copynumber: 5.5 Consensus size: 19
2105628 TAATAATTGA
*
2105638 TATTATA-TAAATTTTAA-
1 TATTATATTATATTTTAAT
2105655 TA-TAT-TTATATATTT--T
1 TATTATATTATAT-TTTAAT
2105671 TATTATATTATATTTTAAT
1 TATTATATTATATTTTAAT
2105690 TATT-T-TTATCATATTTATAT
1 TATTATATTAT-AT-TTTA-AT
* *
2105710 AATTATATCTA-ATATTAAT
1 TATTATAT-TATATTTTAAT
*
2105729 TATTAAATTA
1 TATTATATTA
2105739 AAAAATATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
16 9 0.14
17 15 0.23
18 11 0.17
19 17 0.26
20 8 0.12
21 3 0.05
22 1 0.02
23 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATATTATATTTTAAT
Found at i:2105707 original size:34 final size:34
Alignment explanation
Indices: 2105638--2105717 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
2105628 TAATAATTGA
* *
2105638 TATTATA-TAAATTTTAATATATTTATATATTTT
1 TATTATATTATATTTTAATATATTTATATATATT
*
2105671 TATTATATTATATTTTAAT-TATTTTTATCATATT
1 TATTATATTATATTTTAATATATTTATAT-ATATT
2105705 TA-TATAATTATAT
1 TATTAT-ATTATAT
2105718 CTAATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 18 0.44
34 23 0.56
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (34 bp):
TATTATATTATATTTTAATATATTTATATATATT
Found at i:2105924 original size:18 final size:19
Alignment explanation
Indices: 2105901--2105938 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2105891 ATTTAAATTA
2105901 TTATTTA-ATAATTATTTT
1 TTATTTATATAATTATTTT
2105919 TTATTTATTATAATTATTTT
1 TTATTTA-TATAATTATTTT
2105939 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTATATAATTATTTT
Found at i:2106251 original size:17 final size:17
Alignment explanation
Indices: 2106229--2106261 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2106219 GTTGAGCTGA
2106229 AAAAGAAAGAAAGAAAT
1 AAAAGAAAGAAAGAAAT
*
2106246 AAAAGAAATAAAGAAA
1 AAAAGAAAGAAAGAAA
2106262 GAAAGGAGAA
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:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAGAAAGAAAGAAAT
Found at i:2106279 original size:21 final size:20
Alignment explanation
Indices: 2106227--2106282 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
2106217 ACGTTGAGCT
* *
2106227 GAAAAAGAAAGAAAGAAATA
1 GAAAAAAAAAGAAAGAAAGA
2106247 -AAAGAAATAAAGAAAGAAAGGA
1 GAAA-AAA-AAAGAAAGAAA-GA
2106269 GAAAAAAAAAGAAA
1 GAAAAAAAAAGAAA
2106283 AAAATTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 18 0.60
22 4 0.13
23 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
GAAAAAAAAAGAAAGAAAGA
Found at i:2106332 original size:26 final size:27
Alignment explanation
Indices: 2106302--2106369 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 27
2106292 GTATTTGTAT
*
2106302 TTATATTATTTTTTATATTTAA-AATA
1 TTATATTATTTTATATATTTAATAATA
*
2106328 TTATA--ATTTTATATA-TTAATAATT
1 TTATATTATTTTATATATTTAATAATA
*
2106352 TTATTTTATTTTATATAT
1 TTATATTATTTTATATAT
2106370 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 4 0.11
24 16 0.46
26 15 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTATATATTTAATAATA
Found at i:2106343 original size:15 final size:16
Alignment explanation
Indices: 2106325--2106355 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2106315 TATATTTAAA
2106325 ATATT-ATAATTTTAT
1 ATATTAATAATTTTAT
2106340 ATATTAATAATTTTAT
1 ATATTAATAATTTTAT
2106356 TTTATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTAATAATTTTAT
Done.