Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 10 of 172
Found at i:2815355 original size:56 final size:53
Alignment explanation
Indices: 2815277--2815466 Score: 221
Period size: 50 Copynumber: 3.6 Consensus size: 53
2815267 GAGGATGAGA
2815277 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C-TTGAGA-TATGAGAGG
* *
2815333 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC-CGAG--ATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
*** * **
2815383 TCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACTT---ATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
* *
2815433 TCCCATGTAAGACCATATCTGGGATATGGCATTG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTG
2815467 ACAGTACAAG
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
50 75 0.65
53 3 0.03
55 1 0.01
56 36 0.31
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (53 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
Found at i:2818251 original size:21 final size:23
Alignment explanation
Indices: 2818201--2818252 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
2818191 GTGGCGTGAA
*
2818201 CTGTAAAAAATGTCTAGTAAGAT
1 CTGTAATAAATGTCTAGTAAGAT
* *
2818224 ATG-AATAAAT-TCTA-TTAGAT
1 CTGTAATAAATGTCTAGTAAGAT
2818244 CTGTAATAA
1 CTGTAATAA
2818253 GTATGGCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 7 0.29
21 9 0.38
22 6 0.25
23 2 0.08
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (23 bp):
CTGTAATAAATGTCTAGTAAGAT
Found at i:2818439 original size:13 final size:13
Alignment explanation
Indices: 2818421--2818449 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2818411 GTGATTGAAG
2818421 GATCTGTCATTGT
1 GATCTGTCATTGT
2818434 GATCTGTCATTGT
1 GATCTGTCATTGT
2818447 GAT
1 GAT
2818450 TCATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.45
Consensus pattern (13 bp):
GATCTGTCATTGT
Found at i:2819227 original size:16 final size:15
Alignment explanation
Indices: 2819206--2819235 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2819196 TGTTGTAAAG
2819206 TTATATATCAAGTTTA
1 TTATATAT-AAGTTTA
2819222 TTATATATAAGTTT
1 TTATATATAAGTTT
2819236 GTCATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
TTATATATAAGTTTA
Found at i:2819252 original size:56 final size:56
Alignment explanation
Indices: 2819171--2819282 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
2819161 GAATACGCCT
*
2819171 TATAAGTTTGTCATTATTAATTCTATGTTGTAAAGTTATATATCAAGTTTATTATA
1 TATAAGTTTGTCATTAATAATTCTATGTTGTAAAGTTATATATCAAGTTTATTATA
2819227 TATAAGTTTGTCATTAATAATTCTATGTTGTAAAGTTATATATCAAGTTTATTATA
1 TATAAGTTTGTCATTAATAATTCTATGTTGTAAAGTTATATATCAAGTTTATTATA
2819283 ACAAGTTATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (56 bp):
TATAAGTTTGTCATTAATAATTCTATGTTGTAAAGTTATATATCAAGTTTATTATA
Found at i:2819911 original size:34 final size:35
Alignment explanation
Indices: 2819872--2820138 Score: 132
Period size: 34 Copynumber: 7.8 Consensus size: 35
2819862 AAAATATTGT
2819872 AATATTGTAATATAATTTAATATAAAAA-AATAAA
1 AATATTGTAATATAATTTAATATAAAAATAATAAA
* * **
2819906 AATATTTTAATATAATTTAATATAAAATATTATTTCCA
1 AATATTGTAATATAATTTAATATAAAA-A-TA-ATAAA
* **
2819944 AAT-TTAGAAAATATAA---AA-ATAAAACAT--TTTA
1 AATATT-G-TAATATAATTTAATATAAAA-ATAATAAA
2819975 AATATTGTAATATAATTTAATATAAAAATAA-AAA
1 AATATTGTAATATAATTTAATATAAAAATAATAAA
* * * **
2820009 TATATTTTAATATAATTTAATATAAAATATTATTTCCA
1 AATATTGTAATATAATTTAATATAAAA-A-TA-ATAAA
* * * * * **
2820047 AAT-TT-CAA-AAAATATAA-AAATAAAATATTTTA
1 AATATTGTAATATAATTTAATATA-AAAATAATAAA
*
2820079 AATATTTTAATATAATTTAATATAAAAAT-A-AAA
1 AATATTGTAATATAATTTAATATAAAAATAATAAA
* * *
2820112 AATCTTTTGATATAATTTAATATAAAA
1 AATATTGTAATATAATTTAATATAAAA
2820139 TATCATTTAA
Statistics
Matches: 178, Mismatches: 33, Indels: 45
0.70 0.13 0.18
Matches are distributed among these distances:
30 7 0.04
31 6 0.03
32 8 0.04
33 34 0.19
34 64 0.36
35 31 0.17
36 8 0.04
37 5 0.03
38 8 0.04
39 7 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
AATATTGTAATATAATTTAATATAAAAATAATAAA
Found at i:2820105 original size:104 final size:102
Alignment explanation
Indices: 2819824--2820146 Score: 513
Period size: 103 Copynumber: 3.1 Consensus size: 102
2819814 AAATATAAAA
* * *
2819824 ATAAAATATTATTTCTAAATTTTAGAAATTATAAAAATAAAATATTGT-AATATTGTAATATAAT
1 ATAAAATATTATTTCCAAA-TTTAGAAAATATAAAAATAAAATATTTTAAATATTGTAATATAAT
*
2819888 TTAATATAAAAAAATAAAAATATTTTAATATAATTTAAT
65 TTAATATAAAAATA-AAAAATATTTTAATATAATTTAAT
*
2819927 ATAAAATATTATTTCCAAATTTAGAAAATATAAAAATAAAACATTTTAAATATTGTAATATAATT
1 ATAAAATATTATTTCCAAATTTAGAAAATATAAAAATAAAATATTTTAAATATTGTAATATAATT
2819992 TAATATAAAAATAAAAATATATTTTAATATAATTTAAT
66 TAATATAAAAATAAAAA-ATATTTTAATATAATTTAAT
* *
2820030 ATAAAATATTATTTCCAAATTTCAAAAAATATAAAAATAAAATATTTTAAATATTTTAATATAAT
1 ATAAAATATTATTTCCAAATTT-AGAAAATATAAAAATAAAATATTTTAAATATTGTAATATAAT
* *
2820095 TTAATATAAAAATAAAAAATCTTTTGATATAATTTAAT
65 TTAATATAAAAATAAAAAATATTTTAATATAATTTAAT
*
2820133 ATAAAATATCATTT
1 ATAAAATATTATTT
2820147 AAATATTATT
Statistics
Matches: 206, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
102 29 0.14
103 120 0.58
104 57 0.28
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (102 bp):
ATAAAATATTATTTCCAAATTTAGAAAATATAAAAATAAAATATTTTAAATATTGTAATATAATT
TAATATAAAAATAAAAAATATTTTAATATAATTTAAT
Found at i:2820141 original size:40 final size:37
Alignment explanation
Indices: 2820055--2820141 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 37
2820045 CAAATTTCAA
*
2820055 AAAATATAAAAATAAAATATTTTAAATATTTTAATAT
1 AAAATATAAAAATAAAATATTTTAAATAATTTAATAT
* *
2820092 AATTTAATATAAAAATAAAAAATCTTTTGATATAATTTAATAT
1 AA---AATATAAAAAT--AAAATATTTT-AAATAATTTAATAT
2820135 AAAATAT
1 AAAATAT
2820142 CATTTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
37 2 0.05
40 16 0.39
42 9 0.22
43 14 0.34
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (37 bp):
AAAATATAAAAATAAAATATTTTAAATAATTTAATAT
Found at i:2824021 original size:15 final size:15
Alignment explanation
Indices: 2824001--2824029 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2823991 CTCTTCTTAA
2824001 AGATTGTTATACAAT
1 AGATTGTTATACAAT
2824016 AGATTGTTATACAA
1 AGATTGTTATACAA
2824030 CATTAGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
AGATTGTTATACAAT
Found at i:2824203 original size:114 final size:113
Alignment explanation
Indices: 2824016--2824223 Score: 303
Period size: 114 Copynumber: 1.8 Consensus size: 113
2824006 GTTATACAAT
*
2824016 AGATTGTTATACAACATTAGTCATTACAATTTTTTTTTTTACAATTACTCTGTGATGTTCAAACA
1 AGATTGTTATACAACATTAGTCATTACAATTTTTTTTTTTACAATTACTCTATGATGTTCAAACA
* *
2824081 TACTTTTAATGTTTTGTGTCCTACATTAAGCTAAGGAATTGTAATTACTAG
66 TACCTTTAATG---TGTATCCTACATTAAGCTAAGGAATTGTAATTACTAG
* * * *
2824132 AGATTGTTATACTACCTTAGTCATTAC-A-TTTTTTTTTTGCAGTTACTCTATGATGTTCAAACA
1 AGATTGTTATACAACATTAGTCATTACAATTTTTTTTTTTACAATTACTCTATGATGTTCAAACA
*
2824195 TGCCTTTAATGTGTATCCTACATTAAGCT
66 TACCTTTAATGTGTATCCTACATTAAGCT
2824224 TTGACCATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
111 17 0.20
114 41 0.49
115 1 0.01
116 25 0.30
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (113 bp):
AGATTGTTATACAACATTAGTCATTACAATTTTTTTTTTTACAATTACTCTATGATGTTCAAACA
TACCTTTAATGTGTATCCTACATTAAGCTAAGGAATTGTAATTACTAG
Found at i:2830190 original size:19 final size:20
Alignment explanation
Indices: 2830150--2830190 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2830140 ATTAATTATT
*
2830150 TATAAACTTTAATTAGAATA
1 TATAAACTATAATTAGAATA
*
2830170 TATAAACTATATTTA-AATA
1 TATAAACTATAATTAGAATA
2830189 TA
1 TA
2830191 ACCATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAAACTATAATTAGAATA
Found at i:2832785 original size:9 final size:9
Alignment explanation
Indices: 2832767--2832797 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2832757 TTTGGTTAAA
2832767 AATTAACCG
1 AATTAACCG
*
2832776 AATTACCCG
1 AATTAACCG
2832785 AATTAACCG
1 AATTAACCG
2832794 AATT
1 AATT
2832798 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:2832919 original size:18 final size:18
Alignment explanation
Indices: 2832896--2832949 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
2832886 AATTTTTATG
2832896 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
2832914 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
2832932 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
2832950 TTAGGTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:2834201 original size:24 final size:24
Alignment explanation
Indices: 2834169--2834227 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
2834159 TTAAGTAGTG
* *
2834169 ATACATAATAAATTTAAAATAATA
1 ATACATAATAAACTTAAAATAAAA
* *
2834193 ATACGTAATAAACTTATAATAAAA
1 ATACATAATAAACTTAAAATAAAA
*
2834217 ATACATTATAA
1 ATACATAATAA
2834228 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (24 bp):
ATACATAATAAACTTAAAATAAAA
Found at i:2835338 original size:23 final size:22
Alignment explanation
Indices: 2835307--2835349 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2835297 ACTGCATAGG
*
2835307 GAAGACGTGACGTGTATGGAGAC
1 GAAGACGTG-CGCGTATGGAGAC
*
2835330 GAAGGCGTGCGCGTATGGAG
1 GAAGACGTGCGCGTATGGAG
2835350 GCTCGTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.26, C:0.14, G:0.44, T:0.16
Consensus pattern (22 bp):
GAAGACGTGCGCGTATGGAGAC
Found at i:2836251 original size:19 final size:19
Alignment explanation
Indices: 2836227--2836280 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2836217 AATCTTCAAG
2836227 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
2836246 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2836265 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
2836281 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2836256 original size:36 final size:36
Alignment explanation
Indices: 2836216--2836287 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
2836206 TATGGAAACA
2836216 TAATCTT-CA-AGGATATGCAATCTTAGATATGATATG
1 TAATCTTACATAGGATATGCAATCTTAGA-A-GATATG
* *
2836252 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTACATAGGATATGCAATCTTAGAAGATATG
2836288 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.41
37 2 0.06
38 17 0.53
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (36 bp):
TAATCTTACATAGGATATGCAATCTTAGAAGATATG
Found at i:2836271 original size:38 final size:40
Alignment explanation
Indices: 2836227--2836303 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
2836217 AATCTTCAAG
2836227 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
*
2836265 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
2836304 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 13 0.38
41 8 0.24
42 13 0.38
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:2836527 original size:23 final size:23
Alignment explanation
Indices: 2836483--2836527 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2836473 TCTCATTTTG
* *
2836483 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
2836506 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
2836528 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:2836727 original size:23 final size:23
Alignment explanation
Indices: 2836682--2836728 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2836672 TTATTTTAGT
* *
2836682 TTTTATTATTATTAAATTAATTA
1 TTTTAATATTATTAAACTAATTA
2836705 TTTTAATATTATTAATACT-ATTA
1 TTTTAATATTATTAA-ACTAATTA
2836728 T
1 T
2836729 GTGGCATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAATATTATTAAACTAATTA
Found at i:2836759 original size:3 final size:3
Alignment explanation
Indices: 2836751--2836794 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2836741 ATCTTGTATC
2836751 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2836795 ATTCATGTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2844622 original size:15 final size:16
Alignment explanation
Indices: 2844604--2844633 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2844594 TGTGATTATG
2844604 GTTTAATTAA-TTAAA
1 GTTTAATTAAGTTAAA
2844619 GTTTAATTAAGTTAA
1 GTTTAATTAAGTTAA
2844634 TTAAGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
GTTTAATTAAGTTAAA
Found at i:2844646 original size:8 final size:9
Alignment explanation
Indices: 2844606--2844646 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
2844596 TGATTATGGT
2844606 TTAA-TTAA
1 TTAAGTTAA
2844614 TTAAAGTTTAA
1 TT-AAG-TTAA
2844625 TTAAGTTAA
1 TTAAGTTAA
2844634 TTAAGTT-A
1 TTAAGTTAA
2844642 TTAAG
1 TTAAG
2844647 GATTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.27
9 13 0.43
10 3 0.10
11 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (9 bp):
TTAAGTTAA
Found at i:2853735 original size:331 final size:333
Alignment explanation
Indices: 2853131--2853790 Score: 1146
Period size: 331 Copynumber: 2.0 Consensus size: 333
2853121 ATCTTGATGA
* *
2853131 GGGTTTGAAGATTATTGATGCAAGATTCAACAATTTGGTGGAAGAATGATTTAATCGAGACATGA
1 GGGTTTGAAGATTATTGATGCAAAATTCAACAATTCGGTGGAAGAATGATTTAATCGAGACATGA
2853196 TTTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATAAAGGTAAAAAAATTTTATAAAAAGAA
66 TTTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATAAAGGTAAAAAAATTTTATAAAAAGAA
2853261 AAGAAGGAAAATAAAAAAAAAGAAAGGATTTTAAAGAGAAAAGAAAAGAATTCAATTTAGGGTTG
131 AAGAAGGAAAATAAAAAAAAAGAAAGGATTTTAAAGAGAAAAGAAAAGAATTCAATTTAGGGTTG
*
2853326 GAAAGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTAGGTTTTCAAAATTGGA
196 GAAAGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTACGTTTTCAAAATTGGA
*
2853391 GGGTTGATTGGGCAAATAACCCATCTACCGAAAATTAAGAAAATGGGAGGGGGAATGGCACGCTT
261 GGGTTGATTGGGCAAATAACCCATCTACCAAAAATTAAGAAAATGGGAGGGGGAATGGCACGCTT
2853456 TGAACATG
326 TGAACATG
* *
2853464 GGGTTTGAAGATTATTGATGCAAAATTCAACAATTC-GTGGGAAGAATGATTTAATCGGGACTTG
1 GGGTTTGAAGATTATTGATGCAAAATTCAACAATTCGGT-GGAAGAATGATTTAATCGAGACATG
* * * *
2853528 ATTTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATGAAGG-CAAAATATTTTATGAAAAGA
65 ATTTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATAAAGGTAAAAAAATTTTATAAAAAGA
* * * *
2853592 AAAGAGGGAAACT-AAAAGAAAGAAAGGATTTTAAAGAGAAGAGAAAAGAATTCAATTTAGGGTT
130 AAAGAAGGAAAATAAAAAAAAAGAAAGGATTTTAAAGAGAAAAGAAAAGAATTCAATTTAGGGTT
2853656 GGAAAGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTACGTTTTCAAAATTGG
195 GGAAAGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTACGTTTTCAAAATTGG
* *
2853721 AGGGTTGATTGGGCAAATAACCCATCTGCCAAAAATTAAGAAAATGGGAGGGGGAATGGCATGCT
260 AGGGTTGATTGGGCAAATAACCCATCTACCAAAAATTAAGAAAATGGGAGGGGGAATGGCACGCT
2853786 TTGAA
325 TTGAA
2853791 ACTGGAAGCA
Statistics
Matches: 310, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
331 180 0.58
332 30 0.10
333 100 0.32
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (333 bp):
GGGTTTGAAGATTATTGATGCAAAATTCAACAATTCGGTGGAAGAATGATTTAATCGAGACATGA
TTTCAATTTAGGATTCAAAAGATTAATTTTCCAGCAATAAAGGTAAAAAAATTTTATAAAAAGAA
AAGAAGGAAAATAAAAAAAAAGAAAGGATTTTAAAGAGAAAAGAAAAGAATTCAATTTAGGGTTG
GAAAGGATTCAAAATCATAGTATAACTAGGGGAAGTTAATAAATTCCTACGTTTTCAAAATTGGA
GGGTTGATTGGGCAAATAACCCATCTACCAAAAATTAAGAAAATGGGAGGGGGAATGGCACGCTT
TGAACATG
Found at i:2856710 original size:18 final size:19
Alignment explanation
Indices: 2856671--2856711 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2856661 GTAAAAAAAA
2856671 TAAATTTTAGAAAAAGTAT
1 TAAATTTTAGAAAAAGTAT
2856690 TAAATTTTA-ATAAAA-TAT
1 TAAATTTTAGA-AAAAGTAT
2856708 TAAA
1 TAAA
2856712 AAATTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAATTTTAGAAAAAGTAT
Found at i:2857056 original size:28 final size:27
Alignment explanation
Indices: 2857003--2857065 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2856993 TGTAAAATTG
* * * * *
2857003 TATACTTTTTTATATTTCTATTTATTT
1 TATATTTTTTTAGATTTATATATATTC
2857030 TATATTTTTTTACGATTTATATATATTC
1 TATATTTTTTTA-GATTTATATATATTC
2857058 TA-ATTTTT
1 TATATTTTT
2857066 AATATTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (27 bp):
TATATTTTTTTAGATTTATATATATTC
Found at i:2864691 original size:13 final size:13
Alignment explanation
Indices: 2864673--2864697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2864663 GTCCTGGTGA
2864673 TCTAGTAAAACAC
1 TCTAGTAAAACAC
2864686 TCTAGTAAAACA
1 TCTAGTAAAACA
2864698 AAAGTTACCA
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:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
TCTAGTAAAACAC
Found at i:2867390 original size:144 final size:145
Alignment explanation
Indices: 2867076--2867390 Score: 510
Period size: 144 Copynumber: 2.2 Consensus size: 145
2867066 GAGGCATGGG
* *
2867076 CCGCATCTCC-ATTTTCAGATTTTTTTGCCAACACTTTTTTTTTCTAATAAGAAATTTTATCTTT
1 CCGCATCTCCAATTTT-AGA-TTTTTTGCCAACACTTTTTTTTTCTAATAAGAAATCTTATCGTT
*
2867140 CAATGCTTCTAACACACAATGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAG
64 CAATGCTTCAAACACACAATGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAG
2867205 GCACGGGGTTCGATCCC
129 GCACGGGGTTCGATCCC
* *
2867222 CCGCATCTCCAACTTTAGACTTTTTGCCAACACTTTTTTTTTTCTAATAAGAAATCTTAT-GTT-
1 CCGCATCTCCAATTTTAGATTTTTTGCCAACAC-TTTTTTTTTCTAATAAGAAATCTTATCGTTC
* *
2867285 AATGCTTCAAACGCACAATGGGGATGTAGCTCAAATGGTAGAGTGCTCGCTTTGCATGCGAGAGG
65 AATGCTTCAAACACACAATGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGG
2867350 CACGGGGTTCGATCCC
130 CACGGGGTTCGATCCC
*
2867366 CCGCATCTCCAATTTTGGATTTTTT
1 CCGCATCTCCAATTTTAGATTTTTT
2867391 TTTGCCTAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
144 100 0.64
145 15 0.10
146 38 0.24
147 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (145 bp):
CCGCATCTCCAATTTTAGATTTTTTGCCAACACTTTTTTTTTCTAATAAGAAATCTTATCGTTCA
ATGCTTCAAACACACAATGGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATGCGAGAGGC
ACGGGGTTCGATCCC
Found at i:2868173 original size:21 final size:20
Alignment explanation
Indices: 2868134--2868173 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2868124 AAAAAAATCA
* *
2868134 ATTTTAAAATTTTTAACATT
1 ATTTTAAAAATTCTAACATT
2868154 ATTTTAAAAATTCTAGACAT
1 ATTTTAAAAATTCTA-ACAT
2868174 GAAAGAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTTAAAAATTCTAACATT
Found at i:2875876 original size:99 final size:99
Alignment explanation
Indices: 2875696--2875879 Score: 266
Period size: 99 Copynumber: 1.9 Consensus size: 99
2875686 AAGCAAAGCC
*
2875696 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCTAGTTATAGGAAATTG
1 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCAAGTTATAGGAAATTG
* **
2875761 AGTTATGATAGATCAGATGAAAGAGAAGAAGGAT
66 AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
* *
2875795 ATGGAGGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAGTCAAGTTATAGAAGAAA-
1 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCAAGTTATAG--GAAAT
2875859 TGA-TGACAAT-GATTCAGATGA
64 TGAGTGACAATAGA-TCAGATGA
2875880 TGAAAGGAGG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
98 2 0.03
99 67 0.88
100 3 0.04
101 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.33, T:0.22
Consensus pattern (99 bp):
ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCAAGTTATAGGAAATTG
AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
Found at i:2879787 original size:19 final size:18
Alignment explanation
Indices: 2879765--2879815 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
2879755 ATACAATCTT
2879765 TTAAAGAAAATAAAGAATA
1 TTAAAGAAAATAAA-AATA
* *
2879784 TTAATGAAAATTAAAATA
1 TTAAAGAAAATAAAAATA
2879802 TT-AAGAAAATAAAA
1 TTAAAGAAAATAAAA
2879816 TTGAGCAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 12 0.43
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (18 bp):
TTAAAGAAAATAAAAATA
Found at i:2879803 original size:18 final size:17
Alignment explanation
Indices: 2879768--2879816 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
2879758 CAATCTTTTA
*
2879768 AAGAAAATAAAGAATATT
1 AAGAAAATTAA-AATATT
2879786 AATGAAAATTAAAATATT
1 AA-GAAAATTAAAATATT
2879804 AAGAAAA-TAAAAT
1 AAGAAAATTAAAAT
2879817 TGAGCAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 5 0.17
18 10 0.34
19 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AAGAAAATTAAAATATT
Found at i:2886421 original size:16 final size:17
Alignment explanation
Indices: 2886384--2886421 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
2886374 AATTTTTAAG
2886384 TTTTAAAAATGATATTTA
1 TTTTAAAAATGATA-TTA
2886402 TTTTAAAAATGATA-TA
1 TTTTAAAAATGATATTA
2886418 TTTT
1 TTTT
2886422 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
18 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTTAAAAATGATATTA
Found at i:2892162 original size:16 final size:16
Alignment explanation
Indices: 2892141--2892171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2892131 ATAGTTGAAT
*
2892141 ATAATTAACGTATTTA
1 ATAATTAAAGTATTTA
2892157 ATAATTAAAGTATTT
1 ATAATTAAAGTATTT
2892172 CTAACATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
ATAATTAAAGTATTTA
Found at i:2896267 original size:19 final size:19
Alignment explanation
Indices: 2896243--2896334 Score: 166
Period size: 19 Copynumber: 4.8 Consensus size: 19
2896233 AATCATATCT
2896243 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2896262 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
2896281 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2896300 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
2896319 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
2896335 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2896292 original size:38 final size:38
Alignment explanation
Indices: 2896220--2896334 Score: 185
Period size: 38 Copynumber: 2.9 Consensus size: 38
2896210 AAATTAAATC
*
2896220 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
2896262 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
2896300 TCTAAGATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
2896335 CTTGAAGATT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 54 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2897218 original size:50 final size:50
Alignment explanation
Indices: 2897063--2897218 Score: 123
Period size: 50 Copynumber: 3.1 Consensus size: 50
2897053 TGCAATGTTG
* * * *
2897063 GGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAATAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCTA
* * * * * * * ** * * ** * *
2897113 AGGAAGTAAAATTCACCGTTTGTGGCTTTAATCTTTTTAATTGCAAAGTTG
1 GGGAAATAAGATTCACCG-TCGTAGCTTCAATCTGTTCCACTACACCGCTA
*
2897164 GGGAAATGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCTA
1 GGGAAATAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCTA
2897214 GGGAA
1 GGGAA
2897219 GTAAAATTTG
Statistics
Matches: 70, Mismatches: 35, Indels: 2
0.65 0.33 0.02
Matches are distributed among these distances:
50 38 0.54
51 32 0.46
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (50 bp):
GGGAAATAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCTA
Found at i:2897286 original size:100 final size:101
Alignment explanation
Indices: 2897050--2897308 Score: 387
Period size: 101 Copynumber: 2.6 Consensus size: 101
2897040 TTGCGGGTTC
* *
2897050 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAAG
1 AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAG
* * *
2897115 GAAGTAAAATTCACCGTTTGTGGCTTTAATCTTTTT
66 GAAGTAAAATTCACCGATTGCGGCTTCAATCTTTTT
* * * *
2897151 AATTGCAAAGTTGGGGAAA-TGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCTAG
1 AATTGCAATGTTGGGGAAACT-AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAA
**
2897215 GGAAGTAAAATTTGCC-ATTGCGGCTTCAATCTTTTT
65 GGAAGTAAAATTCACCGATTGCGGCTTCAATCTTTTT
*
2897251 AATTGCAATGTTGGGGAAACTAGATTCGCCATCGTAGCTTCAATCTGTTCCACTACAC
1 AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC
2897309 TATCAGGAGA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
100 70 0.49
101 72 0.51
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (101 bp):
AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAAG
GAAGTAAAATTCACCGATTGCGGCTTCAATCTTTTT
Found at i:2897322 original size:100 final size:100
Alignment explanation
Indices: 2897050--2897346 Score: 370
Period size: 100 Copynumber: 3.0 Consensus size: 100
2897040 TTGCGGGTTC
* * *
2897050 AATTGCAATGTTGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAAG
1 AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACA-CACCAAG
** * *
2897115 GA-AGTAAAATTCACCGTTTGTGGCTTTAATCTTTTT
65 GAGAGTAAAATTTGCC-ATTGCGGCTTTAATCTTTTT
* * *
2897151 AATTGCAAAGTTGGGGAAA-TGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACAC-CGCTA
1 AATTGCAATGTTGGGGAAACT-AGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACAC-CAA
*
2897214 GG-GAAGTAAAATTTGCCATTGCGGCTTCAATCTTTTT
64 GGAG-AGTAAAATTTGCCATTGCGGCTTTAATCTTTTT
* *
2897251 AATTGCAATGTTGGGGAAACTAGATTCGCCATCGTAGCTTCAATCTGTTCCACTACACTATC-AG
1 AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACAC-ACCAAG
* *
2897315 GAGAGTAAGATTTGCCGTTGCGGCTTTAATCT
65 GAGAGTAAAATTTGCCATTGCGGCTTTAATCT
2897347 GCTCGACTGT
Statistics
Matches: 171, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
99 1 0.01
100 104 0.61
101 66 0.39
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (100 bp):
AATTGCAATGTTGGGGAAACTAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACACCAAGG
AGAGTAAAATTTGCCATTGCGGCTTTAATCTTTTT
Found at i:2897711 original size:44 final size:44
Alignment explanation
Indices: 2897663--2897925 Score: 391
Period size: 44 Copynumber: 6.0 Consensus size: 44
2897653 AGTAAGATTC
* * * * *
2897663 ACAATCTTCAACCTATTCCACTACTAACCAGGGAGATACGACTC
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* * *
2897707 ACAATCTTCAACCTATTCCACTGTTGACCAGGGAGATAGGATTT
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* * *
2897751 ACAATTTTCAAACTATTCCACTGTTGACCAGGGAAATAGGACTT
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
*
2897795 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTT
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
* *
2897839 ACAGTTTTCAAACTATTCCACTGCTGACCAGGGAGATAGGACTT
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
*
2897883 ACAATTTTCAACCTATTCCACTACTGACCAGGGAGATAGGACT
1 ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACT
2897926 AGGGTCATCG
Statistics
Matches: 199, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 199 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (44 bp):
ACAATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT
Found at i:2900290 original size:11 final size:11
Alignment explanation
Indices: 2900271--2900323 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
2900261 AACATCGAAC
*
2900271 TTTTTGGGTAA
1 TTTTCGGGTAA
2900282 TTTTCGGGTAA
1 TTTTCGGGTAA
*
2900293 --TTCAGGTAA
1 TTTTCGGGTAA
*
2900302 TTTTTGGGTAA
1 TTTTCGGGTAA
2900313 --TTCGGGTAA
1 TTTTCGGGTAA
2900322 TT
1 TT
2900324 CAGTTAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 16 0.48
11 17 0.52
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:2900302 original size:20 final size:20
Alignment explanation
Indices: 2900277--2900323 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2900267 GAACTTTTTG
2900277 GGTAATTTTCGGGTAATTCA
1 GGTAATTTTCGGGTAATTCA
* *
2900297 GGTAATTTTTGGGTAATTCG
1 GGTAATTTTCGGGTAATTCA
2900317 GGTAATT
1 GGTAATT
2900324 CAGTTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (20 bp):
GGTAATTTTCGGGTAATTCA
Found at i:2900319 original size:9 final size:9
Alignment explanation
Indices: 2900284--2900385 Score: 107
Period size: 9 Copynumber: 11.2 Consensus size: 9
2900274 TTGGGTAATT
2900284 TTCGGGTAA
1 TTCGGGTAA
*
2900293 TTCAGGTAA
1 TTCGGGTAA
*
2900302 TTTTTGGGTAA
1 --TTCGGGTAA
2900313 TTCGGGTAA
1 TTCGGGTAA
* *
2900322 TTCAGTTAA
1 TTCGGGTAA
*
2900331 TTCGGTTAA
1 TTCGGGTAA
*
2900340 TTCGGTTAA
1 TTCGGGTAA
*
2900349 TTCGGTTAA
1 TTCGGGTAA
*
2900358 -TCGGATAA
1 TTCGGGTAA
2900366 TTCGGGTAA
1 TTCGGGTAA
2900375 TTCGGGTAA
1 TTCGGGTAA
2900384 TT
1 TT
2900386 TTTAACCAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.09
9 67 0.83
11 7 0.09
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:2900368 original size:26 final size:26
Alignment explanation
Indices: 2900310--2900384 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
2900300 AATTTTTGGG
* *
2900310 TAATTCGGGTAATTCAGTTAATTCGGT
1 TAATTCGGGTAATTCGGTTAA-TCGGA
*
2900337 TAATTCGGTTAATTCGGTTAATCGGA
1 TAATTCGGGTAATTCGGTTAATCGGA
*
2900363 TAATTCGGGTAATTCGGGTAAT
1 TAATTCGGGTAATTCGGTTAAT
2900385 TTTTAACCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 24 0.56
27 19 0.44
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (26 bp):
TAATTCGGGTAATTCGGTTAATCGGA
Found at i:2904659 original size:21 final size:23
Alignment explanation
Indices: 2904633--2904678 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2904623 TAAAAGGTAT
*
2904633 TTAC-AAATTAAATC-TCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
*
2904654 TTACAAAATCATATCTTCTAAGA
1 TTACAAAATCAAATCTTCTAAGA
2904677 TT
1 TT
2904679 GCATATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 9 0.43
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (23 bp):
TTACAAAATCAAATCTTCTAAGA
Found at i:2904677 original size:23 final size:22
Alignment explanation
Indices: 2904633--2904786 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 22
2904623 TAAAAGGTAT
* *
2904633 TTACAAATTAAATC-TCTAAGA
1 TTACAAATCATATCTTCTAAGA
2904654 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATCTTCTAAGA
* *
2904677 TTGCATATCATA---TCTAAGA
1 TTACAAATCATATCTTCTAAGA
* **
2904696 TTGCCTATCATA---TCTAAGA
1 TTACAAATCATATCTTCTAAGA
* *
2904715 TTGCATATCATA---TCTAAGA
1 TTACAAATCATATCTTCTAAGA
*
2904734 TTACATATCATA---TCTAAGA
1 TTACAAATCATATCTTCTAAGA
* *
2904753 TTGCATATCATA---TCTAAGA
1 TTACAAATCATATCTTCTAAGA
*
2904772 TTACATATCATATCT
1 TTACAAATCATATCT
2904787 AAGATTGCAT
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
19 90 0.76
21 4 0.03
22 15 0.13
23 10 0.08
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (22 bp):
TTACAAATCATATCTTCTAAGA
Found at i:2904694 original size:19 final size:19
Alignment explanation
Indices: 2904670--2904796 Score: 227
Period size: 19 Copynumber: 6.7 Consensus size: 19
2904660 AATCATATCT
2904670 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2904689 TCTAAGATTGCCTATCATA
1 TCTAAGATTGCATATCATA
2904708 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2904727 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
2904746 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2904765 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
2904784 TCTAAGATTGCAT
1 TCTAAGATTGCAT
2904797 GTCCTTCAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 102 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2904716 original size:38 final size:38
Alignment explanation
Indices: 2904647--2904796 Score: 237
Period size: 38 Copynumber: 3.8 Consensus size: 38
2904637 AAATTAAATC
*
2904647 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
* *
2904689 TCTAAGATTGCCTATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
2904727 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
2904765 TCTAAGATTACATATCATATCTAAGATTGCAT
1 TCTAAGATTACATATCATATCTAAGATTGCAT
2904797 GTCCTTCAAG
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 87 0.84
41 6 0.06
42 10 0.10
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2904741 original size:57 final size:57
Alignment explanation
Indices: 2904647--2904792 Score: 220
Period size: 57 Copynumber: 2.5 Consensus size: 57
2904637 AAATTAAATC
* * *
2904647 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATATCTAAGATTGCCTATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
2904708 TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
2904765 TCTAAGATTACATATCATATCTAAGATT
1 TCTAAGATTACATATCATATCTAAGATT
2904793 GCATGTCCTT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
57 63 0.79
60 7 0.09
61 10 0.12
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (57 bp):
TCTAAGATTACATATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2904917 original size:20 final size:19
Alignment explanation
Indices: 2904892--2904932 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2904882 AAATGATATA
2904892 ATTTTGGACTTTATTTTATT
1 ATTTTGG-CTTTATTTTATT
* *
2904912 ATTTTGGGTTTATTTTTTT
1 ATTTTGGCTTTATTTTATT
2904931 AT
1 AT
2904933 GAGCCTAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.68
Consensus pattern (19 bp):
ATTTTGGCTTTATTTTATT
Found at i:2906001 original size:69 final size:69
Alignment explanation
Indices: 2905769--2906002 Score: 297
Period size: 69 Copynumber: 3.4 Consensus size: 69
2905759 ACTTATAATG
* * *
2905769 TCAACTGGGAGCATAGGTCTGCTAGCTACTTTAGAGGTTGCGATCTTAAATCATCAAACCTTTAT
1 TCAACTGGGAGCATAGGTCCGCTAGCTACTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTAT
2905834 GACA
66 GACA
** * * * * * * *
2905838 TCAGTTGGGAACGTAGGTTCGTTAGCTGCTTTGGAGGTTGTGATCTTAAATTGTCAAACCTTTAT
1 TCAACTGGGAGCATAGGTCCGCTAGCTACTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTAT
2905903 GACA
66 GACA
** * **
2905907 TCAGTTGGGAGCGTAGGTCTACTAGCTACTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTAT
1 TCAACTGGGAGCATAGGTCCGCTAGCTACTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTAT
*
2905972 GGCA
66 GACA
*
2905976 TAAACTGGGAGCATAGGTCCGCTAGCT
1 TCAACTGGGAGCATAGGTCCGCTAGCT
2906003 GTGTCGGAGC
Statistics
Matches: 138, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 138 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (69 bp):
TCAACTGGGAGCATAGGTCCGCTAGCTACTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTAT
GACA
Found at i:2908409 original size:16 final size:15
Alignment explanation
Indices: 2908388--2908422 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2908378 TAAGATTTTG
2908388 TATATCTAGATAAAAA
1 TATATCTAGA-AAAAA
*
2908404 TATATCTATAAAAAA
1 TATATCTAGAAAAAA
2908419 TATA
1 TATA
2908423 GACAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATATCTAGAAAAAA
Found at i:2912768 original size:41 final size:40
Alignment explanation
Indices: 2912718--2912806 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 40
2912708 GTTTTTTTAC
* * * *
2912718 TTTATATATTAGGCTTTAAATTAGCTCTTTAAATTTTAGA
1 TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
* * * *
2912758 TTTTAAATATTAAGTTTTAAATTGGATTTTTAGATTCTAGA
1 -TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
2912799 TTTAAATA
1 TTTAAATA
2912807 CTATGTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 8 0.20
41 32 0.80
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (40 bp):
TTTAAATATTAAGCTTTAAATTAGATCTTTAAATTCTAGA
Found at i:2915227 original size:43 final size:42
Alignment explanation
Indices: 2915166--2915344 Score: 162
Period size: 43 Copynumber: 4.2 Consensus size: 42
2915156 TTTCAAGTCA
* * * * *
2915166 AAGCAAATAAACTGGCACACGATGTGCATCATCGGACGAATCG
1 AAGCAATTATACTAGCACA-GATGTGCATCATCGGACAAACCG
* *
2915209 AAGCAATTATACTAGCACAGAAAGTGCATCATCGGACAAACTG
1 AAGCAATTATACTAGCACAG-ATGTGCATCATCGGACAAACCG
* * * * *
2915252 AGGCAATTATACTAGCACACAAGGTACATCA-CTGGAAAAACCG
1 AAGCAATTATACTAGCACA-GATGTGCATCATC-GGACAAACCG
* * * *
2915295 AAGCAATCATACTAGCACAGATAGTGCTTCATTGGATAAACCG
1 AAGCAATTATACTAGCACAGAT-GTGCATCATCGGACAAACCG
2915338 AAGCAAT
1 AAGCAAT
2915345 CATATTGGTA
Statistics
Matches: 110, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.03
43 107 0.97
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGCAATTATACTAGCACAGATGTGCATCATCGGACAAACCG
Found at i:2915377 original size:43 final size:43
Alignment explanation
Indices: 2915207--2915379 Score: 136
Period size: 43 Copynumber: 4.0 Consensus size: 43
2915197 TCGGACGAAT
* * * *
2915207 CGAAGCAATTATACTAGCACAGA-AAGTGCATCATCGGACAAAC
1 CGAAGCAATCATACTAGCACACATAA-TGCATCATCGAATAAAC
* * * * * *
2915250 TGAGGCAATTATACTAGCACACA-AGGTACATCACTGGAA-AAAC
1 CGAAGCAATCATACTAGCACACATA-ATGCATCA-TCGAATAAAC
* * * * *
2915293 CGAAGCAATCATACTAGCACAGATAGTGCTTCATTGGATAAAC
1 CGAAGCAATCATACTAGCACACATAATGCATCATCGAATAAAC
* * *
2915336 CGAAGCAATCATATTGGTACACATAATGCATCATCGAATAAAC
1 CGAAGCAATCATACTAGCACACATAATGCATCATCGAATAAAC
2915379 C
1 C
2915380 AAAGTATAAA
Statistics
Matches: 103, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.03
43 96 0.93
44 4 0.04
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (43 bp):
CGAAGCAATCATACTAGCACACATAATGCATCATCGAATAAAC
Found at i:2917765 original size:27 final size:27
Alignment explanation
Indices: 2917713--2917767 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2917703 TAGTATTGGC
* **
2917713 GCCTATCTGGGAGGCGCCAATTGTGGT
1 GCCTACCTGGGAGGCGCCAACGGTGGT
2917740 GCCTACCTGGGAGGCGCCAACGGTGGT
1 GCCTACCTGGGAGGCGCCAACGGTGGT
2917767 G
1 G
2917768 TCATTCTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.40, T:0.20
Consensus pattern (27 bp):
GCCTACCTGGGAGGCGCCAACGGTGGT
Found at i:2917899 original size:22 final size:23
Alignment explanation
Indices: 2917847--2917899 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
2917837 CCAGAAACGA
*
2917847 AAGAAATAAGAAGGAAGGAAGCAG
1 AAGAAA-AAGAAGGAAGGAAGAAG
2917871 AAG-AAAAGAAGGAAGGAA-AAG
1 AAGAAAAAGAAGGAAGGAAGAAG
2917892 AAGAAAAA
1 AAGAAAAA
2917900 AATTAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 2 0.07
24 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (23 bp):
AAGAAAAAGAAGGAAGGAAGAAG
Found at i:2921238 original size:6 final size:6
Alignment explanation
Indices: 2921227--2921256 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2921217 AGTTCTTGTT
*
2921227 TGGCTC TGGCTC CGGCTC TGGCTC TGGCTC
1 TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC
2921257 CGGTGCATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (6 bp):
TGGCTC
Found at i:2922912 original size:16 final size:15
Alignment explanation
Indices: 2922881--2922922 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2922871 ACAAAATCAA
*
2922881 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
2922896 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
2922912 ATAAAAATTAA
1 ATAAAAGTTAA
2922923 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:2923002 original size:38 final size:38
Alignment explanation
Indices: 2922959--2923040 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
2922949 AAAAAGTCAG
2922959 TTATAATTAAACTTTTAACAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAACAAAATGATTTTTAATTTTT
**
2922997 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAACAAAATGATTTTTAATTTTT
2923035 TTATAA
1 TTATAA
2923041 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAACAAAATGATTTTTAATTTTT
Found at i:2923150 original size:60 final size:60
Alignment explanation
Indices: 2923074--2923195 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
2923064 ATACTAAACT
* * * * * *
2923074 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATT-AATTATAAAATAATTAC
*
2923134 AAACACAAAAATTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
2923194 AA
1 AA
2923196 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:2923293 original size:22 final size:22
Alignment explanation
Indices: 2923236--2923595 Score: 262
Period size: 22 Copynumber: 15.9 Consensus size: 22
2923226 ATATCCCCAC
2923236 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
*
2923263 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
2923285 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC-AAA--A-AA
2923311 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
* *
2923334 AATATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
2923361 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
2923383 ATTACAATATTCATACAAAACTATAA
1 ATTACAATATTCATAC-AAA--A-AA
2923409 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
* *
2923432 TTTATAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
2923451 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
* * *
2923472 ATTACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
2923493 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAAAA
*
2923515 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
2923534 ATTACAATATTCAT--AAAAAA
1 ATTACAATATTCATACAAAAAA
*
2923554 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
* *
2923576 GTTAAAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
2923596 TTCTAATCTA
Statistics
Matches: 274, Mismatches: 28, Indels: 67
0.74 0.08 0.18
Matches are distributed among these distances:
19 34 0.12
20 24 0.09
21 15 0.05
22 93 0.34
23 21 0.08
24 7 0.03
25 6 0.02
26 11 0.04
27 63 0.23
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:2923342 original size:30 final size:27
Alignment explanation
Indices: 2923236--2923461 Score: 195
Period size: 27 Copynumber: 9.1 Consensus size: 27
2923226 ATATCCCCAC
* * *
2923236 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAAATATAAT
*
2923263 ATTATAATATTCATAC--AAA-A-AA-
1 ATTACAATATTCATACAAAAATATAAT
* *
2923285 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAAATATAAT
2923312 ATTACAATATTCATACAAAAA-A-AAT
1 ATTACAATATTCATACAAAAATATAAT
* * *
2923337 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAAATATAAT
2923361 ATTACAATATTCATAC--AAA-A-AA-
1 ATTACAATATTCATACAAAAATATAAT
*
2923383 ATTACAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAATATAAT
2923410 ATTACAATATTCATAC--AAA-A-AAT
1 ATTACAATATTCATACAAAAATATAAT
* * *
2923433 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAATATAAT
2923459 ATT
1 ATT
2923462 CATACAAAAA
Statistics
Matches: 165, Mismatches: 14, Indels: 40
0.75 0.06 0.18
Matches are distributed among these distances:
22 59 0.36
23 8 0.05
24 13 0.08
25 14 0.08
26 8 0.05
27 63 0.38
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAAATATAAT
Found at i:2923460 original size:49 final size:49
Alignment explanation
Indices: 2923183--2923461 Score: 368
Period size: 49 Copynumber: 5.7 Consensus size: 49
2923173 AATTAATTAT
*
2923183 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-AT-C
1 AAAAAAATTACAATATTCATAC--AAAATTACAATATTACAATATTCATAC
*** * * *
2923231 -CCCACATTACAATATTCATACAAAATTACAAAATTATAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
2923279 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
2923328 AAAAAAAATATAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
2923377 AAAAAAATTACAATATTCATACAAAACTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
2923426 AAAAAATTTATAATATTCATACAAAATTACAATATT
1 AAAAAAATTACAATATTCATACAAAATTACAATATT
2923462 CATACAAAAA
Statistics
Matches: 198, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
45 18 0.09
46 1 0.01
47 18 0.09
48 1 0.01
49 160 0.81
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:2923497 original size:98 final size:91
Alignment explanation
Indices: 2923355--2923575 Score: 198
Period size: 103 Copynumber: 2.3 Consensus size: 91
2923345 CATACAAAAT
* * ** *
2923355 TACAAAATTACAATATTCATAC--AAAAAAATTACAATATTCATACAAAACTATAATATTACAAT
1 TACAAAATTACAATATTCATACAAAAAAAAATCAAAATATAAATACAAAATTATAATATTACAAT
2923418 ATTCATACAAAAAATTTATAATATTCA
66 ATTCATACAAAAAA-TTATAATATTCA
2923445 TACAAAATTACAATATTCATACAAAAAATTACTAATCCAAAACTATAAATACAAATTTAATTATA
1 TACAAAATTACAATATTCATACAAAAAA--A--AAT-CAAAA-TATAAATAC-AA---AATTAT-
* *
2923510 AAATAATTACAATATTCATAC--AACATTACAATATTCA
55 -AAT-ATTACAATATTCATACAAAAAATTATAATATTCA
* *
2923547 TAAAAAAATTATAATATTCATACAAAAAA
1 T-ACAAAATTACAATATTCATACAAAAAA
2923576 GTTAAAATAT
Statistics
Matches: 106, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
90 22 0.21
92 4 0.04
94 1 0.01
96 3 0.03
97 3 0.03
98 7 0.07
99 2 0.02
102 17 0.16
103 28 0.26
104 3 0.03
105 16 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (91 bp):
TACAAAATTACAATATTCATACAAAAAAAAATCAAAATATAAATACAAAATTATAATATTACAAT
ATTCATACAAAAAATTATAATATTCA
Found at i:2923764 original size:3 final size:3
Alignment explanation
Indices: 2923758--2923798 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
2923748 TTTTTTTTCT
* *
2923758 TTC TTC TTC TTC -TC TTC TTC TCC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2923799 CCTTTCTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:2923789 original size:20 final size:20
Alignment explanation
Indices: 2923760--2923802 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2923750 TTTTTTCTTT
*
2923760 CTTCTTCTTCTCTTCTTCTC
1 CTTCTCCTTCTCTTCTTCTC
2923780 CTTCTCCTTCTCTTCTTCTC
1 CTTCTCCTTCTCTTCTTCTC
2923800 CTT
1 CTT
2923803 TCTCTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (20 bp):
CTTCTCCTTCTCTTCTTCTC
Found at i:2923810 original size:14 final size:14
Alignment explanation
Indices: 2923761--2923810 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2923751 TTTTTCTTTC
*
2923761 TTCT-TCTTCTCTT
1 TTCTCTCTTCTCCT
2923774 CTTCTC-CTTCTCC-
1 -TTCTCTCTTCTCCT
2923787 TTCTCTTCTTCTCCT
1 TTCTC-TCTTCTCCT
2923802 TTCTCTCTT
1 TTCTCTCTT
2923811 TTTTTTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.16
14 21 0.68
15 5 0.16
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTCTCTTCTCCT
Found at i:2934717 original size:56 final size:56
Alignment explanation
Indices: 2934626--2934748 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
2934616 GAGATTGGCG
* * *
2934626 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
2934683 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
2934738 CTGAGTGTGCG
1 CTAAGTGTGCG
2934749 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:2934735 original size:27 final size:28
Alignment explanation
Indices: 2934626--2934748 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
2934616 GAGATTGGCG
* * * *
2934626 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
2934655 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
2934683 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
2934711 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
2934738 CTGAGTGTGCG
1 CTAAGTGTGCG
2934749 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:2934759 original size:27 final size:27
Alignment explanation
Indices: 2934651--2934761 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
2934641 TAAATTGTAC
* * *
2934651 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
2934679 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
2934707 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
2934734 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
2934761 A
1 A
2934762 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:2938081 original size:23 final size:23
Alignment explanation
Indices: 2938055--2938107 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2938045 ATAAGTGTCA
2938055 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2938078 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2938101 CACTGAT
1 CACTGAT
2938108 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2938359 original size:18 final size:17
Alignment explanation
Indices: 2938333--2938371 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2938323 ATTTTCCTTC
2938333 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
2938350 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
2938368 CACA
1 CACA
2938372 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:2948604 original size:43 final size:42
Alignment explanation
Indices: 2948522--2948605 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
2948512 TTTATCTTAG
* * * *
2948522 AAAAAGAATTTTAAAAAGGAGAAGACAATCTTGGGTTGTTGA
1 AAAAAGAATTTAAAAAAGGAGAAGAAAATCATGGATTGTTGA
2948564 AAAAAGAATTTAAAAAGAGGAGAAGATAAAT-ATGGATTGTTG
1 AAAAAGAATTTAAAAA-AGGAGAAGA-AAATCATGGATTGTTG
2948606 GATTTGCCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 15 0.42
43 18 0.50
44 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.25
Consensus pattern (42 bp):
AAAAAGAATTTAAAAAAGGAGAAGAAAATCATGGATTGTTGA
Found at i:2954111 original size:25 final size:25
Alignment explanation
Indices: 2954083--2954136 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
2954073 TCTGTAAATT
* *
2954083 CTTTATGGCGATCTCTCTAAAAAGC
1 CTTTATGGCAATCTATCTAAAAAGC
* **
2954108 CTTTGTGGCAATCTATCTGGAAAGC
1 CTTTATGGCAATCTATCTAAAAAGC
2954133 CTTT
1 CTTT
2954137 GTGGTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (25 bp):
CTTTATGGCAATCTATCTAAAAAGC
Found at i:2954137 original size:25 final size:25
Alignment explanation
Indices: 2954103--2954178 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
2954093 ATCTCTCTAA
2954103 AAAGCCTTTGTGGCAATCTATCTGG
1 AAAGCCTTTGTGGCAATCTATCTGG
*
2954128 AAAGCCTTTGTGGTATAT-TATCTGG
1 AAAGCCTTTGTGGCA-ATCTATCTGG
* * *
2954153 AGAGCCTTGGTGACAAGTC-ATCTGG
1 AAAGCCTTTGTGGCAA-TCTATCTGG
2954178 A
1 A
2954179 GAACCTATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 40 0.93
26 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (25 bp):
AAAGCCTTTGTGGCAATCTATCTGG
Found at i:2970378 original size:34 final size:35
Alignment explanation
Indices: 2970294--2970399 Score: 110
Period size: 34 Copynumber: 3.0 Consensus size: 35
2970284 ATAAGGAGAT
* * *
2970294 ACTTATGGGAGGTCCTGCTCCTAATATAT-GGAGGG
1 ACTTATGGGAGGTCCTGCTCCCAACACATAGG-GGG
2970329 CACTTATGAGG-GGTCCTGCTCCCAACACATAGGGGG
1 -ACTTATG-GGAGGTCCTGCTCCCAACACATAGGGGG
* * *
2970365 -CTTATGGGAGGTCCTACTCCCAGCACAAAGGGGG
1 ACTTATGGGAGGTCCTGCTCCCAACACATAGGGGG
2970399 A
1 A
2970400 GGCTTATAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
33 2 0.03
34 28 0.47
36 26 0.43
37 4 0.07
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.22
Consensus pattern (35 bp):
ACTTATGGGAGGTCCTGCTCCCAACACATAGGGGG
Found at i:2970464 original size:35 final size:36
Alignment explanation
Indices: 2970397--2970475 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
2970387 GCACAAAGGG
* *
2970397 GGAGGCTTATAAGAGGTCTTACTTCCAACACATGAC
1 GGAGGCTTATAAGAGATCTTACTCCCAACACATGAC
* * *
2970433 GGAGGCTTA-GAGAGATCTTGCTCCCAACACATGGC
1 GGAGGCTTATAAGAGATCTTACTCCCAACACATGAC
2970468 GGAGGCTT
1 GGAGGCTT
2970476 GCAAGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 29 0.76
36 9 0.24
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.23
Consensus pattern (36 bp):
GGAGGCTTATAAGAGATCTTACTCCCAACACATGAC
Found at i:2973952 original size:21 final size:21
Alignment explanation
Indices: 2973912--2973968 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2973902 GGTGGATCAA
* *
2973912 CTCTTATGAGCTTTTGTTCAG
1 CTCTTATGAGCTTCTATTCAG
* *
2973933 TTTTTATGAGCTTCTATTCAG
1 CTCTTATGAGCTTCTATTCAG
*
2973954 CTCTTATGAACTTCT
1 CTCTTATGAGCTTCT
2973969 GTTGGCGTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (21 bp):
CTCTTATGAGCTTCTATTCAG
Found at i:2974037 original size:40 final size:39
Alignment explanation
Indices: 2973950--2974042 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 39
2973940 GAGCTTCTAT
* *
2973950 TCAGCTCTTATGAACTTCTGTTGGCGTGTTTCAGATGGC
1 TCAGCTCTTATGAACTTCTGTTGGCGTATTTCAGATGGA
* * * * * *
2973989 CCAACTCTTATGAGCTTTTGTTTGGCGTATTTCGGTTGGA
1 TCAGCTCTTATGAACTTCTG-TTGGCGTATTTCAGATGGA
2974029 TCAGCTCTTATGAA
1 TCAGCTCTTATGAA
2974043 TTTATGTCTG
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
39 16 0.38
40 26 0.62
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (39 bp):
TCAGCTCTTATGAACTTCTGTTGGCGTATTTCAGATGGA
Found at i:2980908 original size:39 final size:40
Alignment explanation
Indices: 2980865--2980952 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
2980855 AGGTGTTACA
* *
2980865 TCTTATGAGCTTATG-TTGGCGTGTTTCGAG-TGGACCAGC
1 TCTTATGAGCTTATGTTTGGCATATTTC-AGTTGGACCAGC
* **
2980904 TCTTATGAGCTTTTGTTTGGCATATTTCAGTTGGATTAGC
1 TCTTATGAGCTTATGTTTGGCATATTTCAGTTGGACCAGC
2980944 TCTTATGAG
1 TCTTATGAG
2980953 TTTCTGTCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 16 0.38
40 26 0.62
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (40 bp):
TCTTATGAGCTTATGTTTGGCATATTTCAGTTGGACCAGC
Found at i:2990496 original size:2 final size:2
Alignment explanation
Indices: 2990489--2990534 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2990479 AGATAGCGAT
2990489 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2990530 AG AG A
1 AG AG A
2990535 TTGGGACAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2993705 original size:281 final size:282
Alignment explanation
Indices: 2993200--2993747 Score: 947
Period size: 281 Copynumber: 1.9 Consensus size: 282
2993190 ATGTGTCCAT
2993200 TTTTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGGAAAGCAAAG
1 TTTTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGG-AAGCAAAG
* * *
2993265 AGCAAAACTATCAGTAACAACATTGAAAACAGAACAGTTATATAAATCTTTAGCGCTCCATAGCT
65 AGCAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAACT
*
2993330 CAGCTTCACAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGT
130 CAGCTTCAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGT
*
2993395 TTATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGA
195 TCATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGA
2993460 CAATAAATCTTTAGCAATTTCTC
260 CAATAAATCTTTAGCAATTTCTC
* * * *
2993483 TTTTTTTTTTTTGGTCAAATAAGATATTTCCTCATAGCAATTTC-TCAAGAAAGTGG-AGCAAAT
1 TTTTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGT-AAGAAAGAGGAAGCAAAG
2993546 AGCAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAACT
65 AGCAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAACT
* * *
2993611 CAGCTTTAAAACTAGGCAAATTCAGAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGT
130 CAGCTTCAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGT
*
2993676 TCATCTTCTTCCATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGA
195 TCATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGA
2993741 CAATAAA
260 CAATAAA
2993748 GGGAAACCCA
Statistics
Matches: 251, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
281 199 0.79
282 1 0.00
283 51 0.20
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (282 bp):
TTTTTTTTTTTTGGTCAAATAAAATATTTACTCATAGCAATTTCGTAAGAAAGAGGAAGCAAAGA
GCAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAACTC
AGCTTCAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTT
CATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGAC
AATAAATCTTTAGCAATTTCTC
Found at i:2994465 original size:27 final size:28
Alignment explanation
Indices: 2994362--2994465 Score: 72
Period size: 27 Copynumber: 3.7 Consensus size: 28
2994352 TTAAGCCTGC
* *
2994362 TTTTATTAAAAATTATAAAAAATT-TAAA
1 TTTTAATAAAAATTA-AAAATATTATAAA
* * *
2994390 -ATCAATAAAAACTAAAAATATTATTAAA
1 TTTTAATAAAAATTAAAAATATTA-TAAA
*
2994418 TTTTAATAAAAGAATT-CAAATATTA-AAA
1 TTTTAAT-AAA-AATTAAAAATATTATAAA
* *
2994446 TTTTACTAAAAATTAGAAAT
1 TTTTAATAAAAATTAAAAAT
2994466 TTTTTTATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
26 11 0.19
27 17 0.29
28 13 0.22
29 4 0.07
30 11 0.19
31 3 0.05
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTTAATAAAAATTAAAAATATTATAAA
Found at i:2994503 original size:29 final size:28
Alignment explanation
Indices: 2994470--2994557 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
2994460 AGAAATTTTT
2994470 TTATAAAAATCGTAAAAAATTTATAAAA
1 TTATAAAAATCGTAAAAAATTTATAAAA
* * *
2994498 TATATAGAAAT-ATAAAAAAATTATAAAA
1 T-TATAAAAATCGTAAAAAATTTATAAAA
* * *
2994526 TTTTCTAAAGTCGTAAGAAAATTATATAAAA
1 TTAT-AAAAATCGTAA-AAAATT-TATAAAA
2994557 T
1 T
2994558 GTAAAGAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.04
28 20 0.43
29 11 0.24
30 5 0.11
31 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (28 bp):
TTATAAAAATCGTAAAAAATTTATAAAA
Found at i:2994771 original size:35 final size:35
Alignment explanation
Indices: 2994732--2994864 Score: 97
Period size: 35 Copynumber: 3.7 Consensus size: 35
2994722 AGTCATTAAT
*
2994732 TTTTTTATTATTTTTATAAAATTTTACAATTTTTA
1 TTTTTAATTATTTTTATAAAATTTTACAATTTTTA
* ** *
2994767 TTTTTTACGATTTTTATAAAAAATTT-CTAATTTTTAA
1 TTTTTAATTATTTTTAT-AAAATTTTAC-AATTTTT-A
* * * ** *
2994804 TAAATTTAATTAATTTTATAAAATTTAATTATTTTAA
1 T--TTTTAATTATTTTTATAAAATTTTACAATTTTTA
* *
2994841 ATTTTAATTATTTTTCTAAAATTT
1 TTTTTAATTATTTTTATAAAATTT
2994865 ATTATTTTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
35 36 0.48
36 14 0.19
37 3 0.04
38 11 0.15
39 11 0.15
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (35 bp):
TTTTTAATTATTTTTATAAAATTTTACAATTTTTA
Found at i:2994774 original size:16 final size:16
Alignment explanation
Indices: 2994753--2994783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2994743 TTTTATAAAA
2994753 TTTTACAATTTTTATT
1 TTTTACAATTTTTATT
*
2994769 TTTTACGATTTTTAT
1 TTTTACAATTTTTAT
2994784 AAAAAATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTACAATTTTTATT
Found at i:2994827 original size:19 final size:18
Alignment explanation
Indices: 2994794--2994875 Score: 80
Period size: 19 Copynumber: 4.5 Consensus size: 18
2994784 AAAAAATTTC
2994794 TAATTTTTAATAAATTTAAT
1 TAATTTTT-A-AAATTTAAT
2994814 TAATTTTATAAAATTTAAT
1 TAATTTT-TAAAATTTAAT
*
2994833 T-A-TTTTAAATTTTAAT
1 TAATTTTTAAAATTTAAT
*
2994849 TATTTTTCTAAAATTT-AT
1 TAATTTT-TAAAATTTAAT
*
2994867 TATTTTTTA
1 TAATTTTTA
2994876 CTTTTTAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.20
17 5 0.09
18 13 0.24
19 17 0.31
20 8 0.15
21 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATTTTTAAAATTTAAT
Found at i:2994833 original size:15 final size:16
Alignment explanation
Indices: 2994813--2994852 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2994803 ATAAATTTAA
2994813 TTAATT-TTATAAAAT
1 TTAATTATTATAAAAT
* *
2994828 TTAATTATTTTAAATT
1 TTAATTATTATAAAAT
2994844 TTAATTATT
1 TTAATTATT
2994853 TTTCTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAATTATTATAAAAT
Found at i:2994865 original size:35 final size:33
Alignment explanation
Indices: 2994804--2994872 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
2994794 TAATTTTTAA
2994804 TAAATTTAATTAATTTTATAAAATTTAATTATTT
1 TAAATTTAATTAATTTTATAAAATTT-ATTATTT
* *
2994838 TAAATTTTAATTATTTTTCTAAAATTTATTATTT
1 TAAA-TTTAATTAATTTTATAAAATTTATTATTT
2994872 T
1 T
2994873 TTACTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 12 0.38
35 20 0.62
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
TAAATTTAATTAATTTTATAAAATTTATTATTT
Found at i:2995022 original size:87 final size:86
Alignment explanation
Indices: 2994896--2995107 Score: 241
Period size: 87 Copynumber: 2.4 Consensus size: 86
2994886 AGAGCATGGG
* * *
2994896 CTTAATTGTTTTTTTGAAAATTTTTGA-GGTCTTTGTGATGCATTTTGAAAATTCAAATACTCAA
1 CTTAATTCTTTTTTTGAAAA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAATTCAAATACTCAA
* *
2994960 TTGAGTGGAAAAAAAA-AAGGA
65 TTAAGTGCAAAAAAAATAAGGA
* * *
2994981 CTTAATTACTTTTTTTGAAGAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTGCTCA
1 CTTAATT-CTTTTTTTGAA-AAGTTTGAGGGTCTTTTTGATGCATTTTGAAAATTCAAATACTCA
* *
2995046 ATTAAGTGCAAAAAAAATTGAGGGG
64 ATTAAGTGCAAAAAAAA-T-AAGGA
*
2995071 CTTGATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTT
1 CTTAATT-CTTTTTTTG-AAAAGTTTGAGGGTCTTTTT
2995108 ACACCATTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
85 7 0.06
86 15 0.14
87 49 0.45
89 6 0.06
90 29 0.27
91 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (86 bp):
CTTAATTCTTTTTTTGAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAATTCAAATACTCAAT
TAAGTGCAAAAAAAATAAGGA
Found at i:2995634 original size:20 final size:20
Alignment explanation
Indices: 2995595--2995634 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2995585 TAATATTTTC
** *
2995595 TCATAAAAGGATATTCAAAA
1 TCATAAAAAAATATTAAAAA
2995615 TCATAAAAAAATATTAAAAA
1 TCATAAAAAAATATTAAAAA
2995635 CTAAAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (20 bp):
TCATAAAAAAATATTAAAAA
Found at i:2995648 original size:9 final size:9
Alignment explanation
Indices: 2995636--2995773 Score: 50
Period size: 9 Copynumber: 14.9 Consensus size: 9
2995626 TATTAAAAAC
2995636 TAAAAATTA
1 TAAAAATTA
**
2995645 TAAATTTTA
1 TAAAAATTA
2995654 T-AAAATTAA
1 TAAAAATT-A
*
2995663 TAAAACATATT
1 TAAAA-AT-TA
* *
2995674 TAAAATTTTC
1 TAAAA-ATTA
*
2995684 TAAAATTATA
1 TAAAAAT-TA
2995694 TAAAAATCT-
1 TAAAAAT-TA
*
2995703 TAAAAGTTA
1 TAAAAATTA
* *
2995712 TAATAATCA
1 TAAAAATTA
* *
2995721 TAACAATCA
1 TAAAAATTA
2995730 TTAAAACA-TA
1 -TAAAA-ATTA
* *
2995740 TGAAAATCA
1 TAAAAATTA
2995749 TAAAAATTA
1 TAAAAATTA
2995758 T-AAAATTA
1 TAAAAATTA
*
2995766 TAATAATT
1 TAAAAATT
2995774 TGCAAAAATT
Statistics
Matches: 96, Mismatches: 23, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
8 14 0.15
9 50 0.52
10 22 0.23
11 9 0.09
12 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:2995817 original size:32 final size:29
Alignment explanation
Indices: 2995777--2995842 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
2995767 AATAATTTGC
*
2995777 AAAAATTTACAAATTTAATAAAAATATATTT
1 AAAAATTTA-AAATTTAATAAAAA-ATATAT
*
2995808 AAAATATTTAAAATTTTATAAAAAATATAT
1 AAAA-ATTTAAAATTTAATAAAAAATATAT
2995838 AAAAA
1 AAAAA
2995843 ATCATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 1 0.03
30 9 0.28
31 17 0.53
32 5 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAATTTAAAATTTAATAAAAAATATAT
Found at i:2995844 original size:32 final size:31
Alignment explanation
Indices: 2995777--2995852 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
2995767 AATAATTTGC
**
2995777 AAAA-ATTTACAAATTTAATAAAAATATATTT
1 AAAATATTTA-AAATTTAATAAAAATATATAA
*
2995808 AAAATATTTAAAATTTTATAAAAAATATATAA
1 AAAATATTTAAAATTTAAT-AAAAATATATAA
2995840 AAAATCATTTAAA
1 AAAAT-ATTTAAA
2995853 CCCCTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 12 0.31
32 20 0.51
33 7 0.18
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATATTTAAAATTTAATAAAAATATATAA
Found at i:2996020 original size:20 final size:21
Alignment explanation
Indices: 2995995--2996036 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2995985 GACAATTTCC
2995995 TTTTTATTGAT-AAATTTTTA
1 TTTTTATTGATAAAATTTTTA
**
2996015 TTTTTATTTTTAAAATTTTTA
1 TTTTTATTGATAAAATTTTTA
2996036 T
1 T
2996037 CTCCAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTATTGATAAAATTTTTA
Found at i:2997097 original size:37 final size:37
Alignment explanation
Indices: 2997024--2997097 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
2997014 TCGTCGCTAA
*
2997024 CTTTAGCGACACTTTTCCCACAAACGCCGACCAAGAT
1 CTTTAGCGACACTTTTCCCACAAACGCCGACAAAGAT
* * *
2997061 CTTTAGCGGCGCTTTTCCCACAAATGCCG-CTAAAGAT
1 CTTTAGCGACACTTTTCCCACAAACGCCGAC-AAAGAT
2997098 AATGACCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (37 bp):
CTTTAGCGACACTTTTCCCACAAACGCCGACAAAGAT
Found at i:2997184 original size:43 final size:43
Alignment explanation
Indices: 2997052--2997308 Score: 245
Period size: 43 Copynumber: 6.0 Consensus size: 43
2997042 CACAAACGCC
* * *
2997052 GACCAAGATCTTTAGCGGCGCTTTTCCCACAAATGCCGCTAAA
1 GACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
* * * *
2997095 GA-TAATGACCTTTAGCGGCGC--TTTCCCCCAACGCCACTAAA
1 GACCAA-GACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
* *
2997136 GACCAAGACCTTTAGCAGCGCTTTTTTCACAAACGCCGCTAAA
1 GACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
* * *
2997179 GACCAAGACATTTAGCGGCAC-TTTTCTCTCAAACGCCGCTAAA
1 GACCAAGACCTTTAGCGGCGCTTTTTC-CACAAACGCCGCTAAA
* * * **
2997222 AACTAAGACCTTTAGCGACGCTTTTTCCTA-AAGTGCCGCTAAA
1 GACCAAGACCTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTAAA
* * * * * *
2997265 AAACAAGACCTTTAGCGACGCTTTCTCCAAAAACGCCACTAAA
1 GACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
2997308 G
1 G
2997309 GTCACGAAAA
Statistics
Matches: 173, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
41 31 0.18
42 9 0.05
43 128 0.74
44 5 0.03
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
GACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAA
Found at i:2998073 original size:47 final size:46
Alignment explanation
Indices: 2998021--2998110 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 46
2998011 TGGTTGTGCA
*
2998021 AAATACTTCAACTTGCAGCACTTAAA-ACATCTCAATTTCCAGCAACT
1 AAATACTTCAACTTGCAGCACTTAAACAC-T-TCAATTTACAGCAACT
*
2998068 AAATACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCA
1 AAATACTTCAACTTGCAGCACTTAAACACTTCAATTTACAGCA
2998111 CTATCAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 12 0.30
47 26 0.65
48 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.29
Consensus pattern (46 bp):
AAATACTTCAACTTGCAGCACTTAAACACTTCAATTTACAGCAACT
Found at i:2998086 original size:23 final size:23
Alignment explanation
Indices: 2998021--2998112 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
2998011 TGGTTGTGCA
*
2998021 AAATACTTCAACTTGCAGCACTT
1 AAATACTTCAATTTGCAGCACTT
*
2998044 AAA-ACATCTCAATTTCCAGCAAC-T
1 AAATAC-T-TCAATTTGCAGC-ACTT
2998068 AAATACTTCAATTTGCAGCACTT
1 AAATACTTCAATTTGCAGCACTT
* *
2998091 AAACACTTCAATTTACAGCACT
1 AAATACTTCAATTTGCAGCACT
2998113 ATCAAATTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
22 4 0.07
23 36 0.61
24 15 0.25
25 4 0.07
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (23 bp):
AAATACTTCAATTTGCAGCACTT
Found at i:2998531 original size:41 final size:39
Alignment explanation
Indices: 2998448--2998531 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
2998438 GCACAATACA
* **
2998448 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
*
2998487 ATATAAAAAGCATATATAAATATATGTATGTCACAGAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAGAAA-T
2998528 ATAT
1 ATAT
2998532 TCATTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.77
40 4 0.10
41 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
Found at i:3001910 original size:146 final size:146
Alignment explanation
Indices: 3001608--3002339 Score: 1100
Period size: 146 Copynumber: 5.0 Consensus size: 146
3001598 CGTTTTGTTT
* * * *
3001608 TTGCTTATCTTTAGCAGCGCTTCTTGA-AAATCGCCGCAAAATTTTTTTATTTTGAACAAAATGA
1 TTGCTTACCTTTAGCGGCGCTTCTT-ATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGA
* *
3001672 CGCCGTTTTGCTATTCTACACA-TTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCAGCGTT
65 CGCCGTTTTGCTATTCTA-AAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGCGGCGTT
*
3001736 TTTCTGAAAAACGTCGCTA
128 TTTCTGAAAAACGCCGCTA
*
3001755 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCTGCAAAATTTTTTCATTTTGAACAAAATGAC
1 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGAC
* *
3001820 GCTGTTTTGTTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTT
66 GCCGTTTTGCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTT
3001885 CTGAAAAACGCCGCTA
131 CTGAAAAACGCCGCTA
* *
3001901 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGC-AATTTTTTTCATTTTGAACAAAACGA-
1 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGAC
* *
3001964 -CCGTTTTGCTATTCTAAATTTTTTTTATTTTTTTTTATAAATTGATTTATTCTTTGCGGCATTT
66 GCCGTTTTGCTATTCTAAAATTTTTTTA--TTTTTTTATAAATTGATTTATTCTTTGCGGCGTTT
*
3002028 TTCTGGAAAACGCCGCTA
129 TTCTGAAAAACGCCGCTA
**
3002046 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAATTTTTTTTCATTTTGAACAAAATGAC
1 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGAC
* *
3002111 GTCGTTTTGCTATTCT-AAATATTTTTTATTTTTTTATAAATTGATTTATCCTTTGCGGCGTTTT
66 GCCGTTTTGCTATTCTAAAAT-TTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTT
* *
3002175 TCTGGAAAACGCCTCTA
130 TCTGAAAAACGCCGCTA
* * * *
3002192 TTGCTTACCTTTAGCAGCGCTTCGTATAAAACGCCGTAAAATTTTTTCATTTTGAACAAAACGAC
1 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGAC
* *
3002257 GCCGTTTTGCCATTCTAAAATTTTTTTTATTTTTTTATAAATTGATTTATTTTTTGCGGCGTTTT
66 GCCGTTTTGCTATTCTAAAA-TTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTT
*
3002322 TGT-AAAAACGCCGCTA
130 TCTGAAAAACGCCGCTA
3002338 TT
1 TT
3002340 TCATTTTGAA
Statistics
Matches: 537, Mismatches: 38, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
143 24 0.04
145 112 0.21
146 250 0.47
147 129 0.24
148 22 0.04
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (146 bp):
TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAATGAC
GCCGTTTTGCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTT
CTGAAAAACGCCGCTA
Found at i:3002031 original size:291 final size:291
Alignment explanation
Indices: 3001608--3002339 Score: 1109
Period size: 291 Copynumber: 2.5 Consensus size: 291
3001598 CGTTTTGTTT
* * *
3001608 TTGCTTATCTTTAGCAGCGCTTCTTGA-AAATCGCCGCAAAATTTTTTT-ATTTTGAACAAAATG
1 TTGCTTACCTTTAGCAGCGCTTCTT-ATAAAACGCCGC--AATTTTTTTCATTTTGAACAAAACG
* ** *
3001671 ACGCCGTTTTGCTATTCTACACATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCAGCGTT
63 AC-CCGTTTTGCTATTCTAAATTTTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCGGCGTT
* *
3001736 TTTCTGAAAAACGTCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCTGCAAAATTTTT
127 TTTCTGAAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTT
*
3001801 TCATTTTGAACAAAATGACG-CTGTTTTGTTATTCTAAA-ATTTTTTTATTTTTTTATAAATTGA
192 TCATTTTGAACAAAATGACGTC-GTTTTGCTATTCTAAATA-TTTTTTATTTTTTTATAAATTGA
*
3001864 TTTATTCTTTGCGGCGTTTTTCTGAAAAACGCCGCTA
255 TTTATCCTTTGCGGCGTTTTTCTGAAAAACGCCGCTA
*
3001901 TTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAATTTTTTTCATTTTGAACAAAACGA-C
1 TTGCTTACCTTTAGCAGCGCTTCTTATAAAACGCCGCAATTTTTTTCATTTTGAACAAAACGACC
*
3001965 CGTTTTGCTATTCTAAATTTTTTTTATTTTTTTTTATAAATTGATTTATTCTTTGCGGCATTTTT
66 CGTTTTGCTATTCTAAATTTTTTTTA-TTTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTT
* **
3002030 CTGGAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAATTTTTTTTCA
130 CTGAAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCA
3002095 TTTTGAACAAAATGACGTCGTTTTGCTATTCTAAATATTTTTTATTTTTTTATAAATTGATTTAT
195 TTTTGAACAAAATGACGTCGTTTTGCTATTCTAAATATTTTTTATTTTTTTATAAATTGATTTAT
* *
3002160 CCTTTGCGGCGTTTTTCTGGAAAACGCCTCTA
260 CCTTTGCGGCGTTTTTCTGAAAAACGCCGCTA
* * *
3002192 TTGCTTACCTTTAGCAGCGCTTCGTATAAAACGCCGTAAAATTTTTTCATTTTGAACAAAACGAC
1 TTGCTTACCTTTAGCAGCGCTTCTTATAAAACGCCG-CAATTTTTTTCATTTTGAACAAAACGAC
* *
3002257 GCCGTTTTGCCATTCTAAAATTTTTTTTA-TTTTTTTATAAATTGATTTATTTTTTGCGGCGTTT
65 -CCGTTTTGCTATTCT-AAATTTTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCGGCGTTT
*
3002321 TTGT-AAAAACGCCGCTATT
128 TTCTGAAAAACGCCGCTATT
3002340 TCATTTTGAA
Statistics
Matches: 403, Mismatches: 27, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
290 24 0.06
291 228 0.57
292 57 0.14
293 68 0.17
294 14 0.03
295 12 0.03
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (291 bp):
TTGCTTACCTTTAGCAGCGCTTCTTATAAAACGCCGCAATTTTTTTCATTTTGAACAAAACGACC
CGTTTTGCTATTCTAAATTTTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTC
TGAAAAACGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCAT
TTTGAACAAAATGACGTCGTTTTGCTATTCTAAATATTTTTTATTTTTTTATAAATTGATTTATC
CTTTGCGGCGTTTTTCTGAAAAACGCCGCTA
Found at i:3003036 original size:21 final size:22
Alignment explanation
Indices: 3003010--3003085 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
3003000 CCTTGATCCC
3003010 TAAACCTTAAATCCCAAC-CCT
1 TAAACCTTAAATCCCAACTCCT
* * * *
3003031 TAAACCAT-AATCCCTACTTCA
1 TAAACCTTAAATCCCAACTCCT
* *
3003052 TAATCCCTAAAT-CCATACTCCT
1 TAAACCTTAAATCCCA-ACTCCT
3003074 TAAACCTTAAAT
1 TAAACCTTAAAT
3003086 ATGAACTCCT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 8 0.20
21 16 0.39
22 17 0.41
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAACCTTAAATCCCAACTCCT
Found at i:3003911 original size:114 final size:112
Alignment explanation
Indices: 3003641--3004013 Score: 556
Period size: 113 Copynumber: 3.3 Consensus size: 112
3003631 AGCTCAAGGT
3003641 TTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
1 TTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAA
* *
3003706 ACGCCGCTAAAT-CCCTAAAGCTCAGAAAACGG-AGTCGTGGGGCTTAGG
65 ACGCCGCTAAATCCCCGAAAGCTCA-AAAACGGCA-TCGTTGGGCTTAGG
* *
3003754 TTTTTTTGCGGCGCTTTCCCACAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTATAA
1 TTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTA-AA
3003819 ACGCCGCTAAATCCCCGAAAGCTCATAAAACGGCATCGTTGGGCTTAGG
65 ACGCCGCTAAATCCCCGAAAGCTCA-AAAACGGCATCGTTGGGCTTAGG
*
3003868 TTTTTTTGCGGCGCTTTTGCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
1 TTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* * * *
3003933 AGCCGCTAAATCCCCGAAAGCTCGAGAAACGACGTCGTTGGGCTTAGG
66 CGCCGCTAAATCCCCGAAAGCTC-AAAAACGGCATCGTTGGGCTTAGG
* *
3003981 -TTTTTTGTGGCGC-TTTCTCAAAAACGCCACTAA
1 TTTTTTTGCGGCGCTTTTC-CAAAAACGCCGCTAA
3004014 TGGTTATTTT
Statistics
Matches: 240, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
111 3 0.01
112 27 0.11
113 118 0.49
114 91 0.38
115 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (112 bp):
TTTTTTTGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
CGCCGCTAAATCCCCGAAAGCTCAAAAACGGCATCGTTGGGCTTAGG
Found at i:3004099 original size:12 final size:12
Alignment explanation
Indices: 3004082--3004107 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3004072 TTTTTTATCC
3004082 AAACGCCGCTAA
1 AAACGCCGCTAA
3004094 AAACGCCGCTAA
1 AAACGCCGCTAA
3004106 AA
1 AA
3004108 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:3006379 original size:31 final size:31
Alignment explanation
Indices: 3006355--3006413 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3006345 TGGTTATCTG
3006355 TGGGACTTAGAGGGATGTGGGTGGTTAATTA
1 TGGGACTTAGAGGGATGTGGGTGGTTAATTA
* **
3006386 TGGGACTTAGTGGGATGTGAATGGTTAA
1 TGGGACTTAGAGGGATGTGGGTGGTTAA
3006414 GAAATTATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.03, G:0.41, T:0.32
Consensus pattern (31 bp):
TGGGACTTAGAGGGATGTGGGTGGTTAATTA
Found at i:3012696 original size:11 final size:11
Alignment explanation
Indices: 3012682--3012727 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
3012672 GTTTTCTTGG
3012682 TTTTTTTTCTC
1 TTTTTTTTCTC
*
3012693 TTTTTTCTCT-
1 TTTTTTTTCTC
3012703 TTTTTTTTCTC
1 TTTTTTTTCTC
3012714 TCTATTTTTTCTC
1 T-T-TTTTTTCTC
3012727 T
1 T
3012728 ATATGCGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
12 1 0.03
13 10 0.33
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:3012698 original size:13 final size:13
Alignment explanation
Indices: 3012693--3012727 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
3012683 TTTTTTTCTC
*
3012693 TTTTTTCTCT-TT
1 TTTTTTCTCTCTA
3012705 TTTTTTCTCTCTA
1 TTTTTTCTCTCTA
3012718 TTTTTTCTCT
1 TTTTTTCTCT
3012728 ATATGCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTCTCTA
Found at i:3012721 original size:25 final size:22
Alignment explanation
Indices: 3012682--3012727 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 22
3012672 GTTTTCTTGG
3012682 TTTTTTTTCTCTTTTTTCTCTT
1 TTTTTTTTCTCTTTTTTCTCTT
3012704 TTTTTTTCTCTCTATTTTTTCTCT
1 TTTTTTT-TCTC--TTTTTTCTCT
3012728 ATATGCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 4 0.19
25 10 0.48
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTTCTCTTTTTTCTCTT
Found at i:3016612 original size:18 final size:18
Alignment explanation
Indices: 3016563--3016613 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3016553 CAAGTTTTCG
3016563 TTTTCATTTTCATTTCCA
1 TTTTCATTTTCATTTCCA
** **
3016581 TTCCCATTCCCATTTCCA
1 TTTTCATTTTCATTTCCA
3016599 TTTTCATTTTCATTT
1 TTTTCATTTTCATTT
3016614 TTGGAAACTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTCATTTTCATTTCCA
Found at i:3016615 original size:7 final size:6
Alignment explanation
Indices: 3016557--3016614 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
3016547 GAATTGCAAG
* * ** ** *
3016557 TTTTCG TTTTCA TTTTCA TTTCCA TTCCCA TTCCCA TTTCCA TTTTCA
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
3016605 TTTTCA TTTT
1 TTTTCA TTTT
3016615 TGGAAACTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.14, C:0.26, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTTCA
Found at i:3020273 original size:23 final size:22
Alignment explanation
Indices: 3020247--3020298 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
3020237 TTTTTTTGAA
*
3020247 AATATTTATATTATTTTTAATTT
1 AATATTTAT-TTATTTATAATTT
3020270 AATACTTTATTTATTTATAATTT
1 AATA-TTTATTTATTTATAATTT
3020293 ATATAT
1 A-ATAT
3020299 AGATATCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTATTTATTTATAATTT
Found at i:3023704 original size:29 final size:29
Alignment explanation
Indices: 3023662--3023732 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
3023652 ATTGAATTAA
*
3023662 TAAA-TTATTATCTAGATAAACATTAAAT
1 TAAATTTAATATCTAGATAAACATTAAAT
*
3023690 TAAATTTAATATCTAGATAAATATTAAAT
1 TAAATTTAATATCTAGATAAACATTAAAT
3023719 TAAATTTAATATCT
1 TAAATTTAATATCT
3023733 CATATTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 4 0.10
29 36 0.90
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAATTTAATATCTAGATAAACATTAAAT
Found at i:3023716 original size:24 final size:23
Alignment explanation
Indices: 3023688--3023763 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
3023678 TAAACATTAA
3023688 ATTAAATTTAATATCTAGATAAAT
1 ATTAAA-TTAATATCTAGATAAAT
*
3023712 ATTAAATTAA-ATTTA-AT--AT
1 ATTAAATTAATATCTAGATAAAT
* * *
3023731 CTCATATTAATATCTAGATAAAT
1 ATTAAATTAATATCTAGATAAAT
3023754 ATTAAATTAA
1 ATTAAATTAA
3023764 ATTCATTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
19 9 0.22
20 4 0.10
21 4 0.10
22 4 0.10
23 13 0.32
24 6 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (23 bp):
ATTAAATTAATATCTAGATAAAT
Found at i:3023780 original size:37 final size:41
Alignment explanation
Indices: 3023697--3023780 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
3023687 AATTAAATTT
* * **
3023697 AATATCTAGATAAATATTAAATTAAATTTAATATCTCATATT
1 AATATCTAGATAAATATTAAATTAAATTT-ACATCTCAAAAC
3023739 AATATCTAGATAAATATTAAATTAAA-TT-CAT-T-AAAAC
1 AATATCTAGATAAATATTAAATTAAATTTACATCTCAAAAC
3023776 AATAT
1 AATAT
3023781 TATCTTTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 7 0.18
38 1 0.03
39 2 0.05
41 2 0.05
42 26 0.68
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (41 bp):
AATATCTAGATAAATATTAAATTAAATTTACATCTCAAAAC
Found at i:3026892 original size:42 final size:42
Alignment explanation
Indices: 3026833--3026916 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
3026823 AATTTAAGTC
3026833 TAATAAACCTAAATTAAATTATAATTAA-ATTTAAATGTCAAT
1 TAATAAACCTAAATTAAATTATAA-TAATATTTAAATGTCAAT
* *
3026875 TAATAAATCTAAATTAAATTATAATAATATTTAGATGTCAAT
1 TAATAAACCTAAATTAAATTATAATAATATTTAAATGTCAAT
3026917 ACACTTTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (42 bp):
TAATAAACCTAAATTAAATTATAATAATATTTAAATGTCAAT
Found at i:3027619 original size:28 final size:27
Alignment explanation
Indices: 3027580--3027642 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
3027570 AATATTTTTA
*
3027580 TTTTTT-ATTTTTTTAACTTTAAAATACT
1 TTTTTTAATTTTTTTAAATTTAAAAT--T
*
3027608 TTTTTTAATTTTTTTAAATTTTAAATT
1 TTTTTTAATTTTTTTAAATTTAAAATT
3027635 TTTTTTAA
1 TTTTTTAA
3027643 AATACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 9 0.28
28 6 0.19
29 17 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTTTAATTTTTTTAAATTTAAAATT
Found at i:3027653 original size:41 final size:40
Alignment explanation
Indices: 3027597--3027719 Score: 183
Period size: 40 Copynumber: 3.0 Consensus size: 40
3027587 TTTTTTTAAC
* *
3027597 TTTAAAATACTTTTTTTAATTTTTTTAAATTTTAAATTTTT
1 TTTAAAATACTTTTTTTAATTTTTTT-AATTTTAAAATATT
3027638 TTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
1 TTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
3027678 TTTAAAATACTTTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTAAAATACTTTTTTTAA--TTT-TTTTAA-TTTTAAAATA
3027720 AATTTTTGGT
Statistics
Matches: 76, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
40 31 0.41
41 26 0.34
42 3 0.04
43 6 0.08
44 10 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATT
Found at i:3028283 original size:19 final size:19
Alignment explanation
Indices: 3028237--3028284 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3028227 AACTCTTTTA
* **
3028237 AATTCAAAAAATAAAAATG
1 AATTCAAAATATAAAAAAC
* *
3028256 ATTTTAAAATATAAAAAAC
1 AATTCAAAATATAAAAAAC
3028275 AATTCAAAAT
1 AATTCAAAAT
3028285 TCAATGTTAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (19 bp):
AATTCAAAATATAAAAAAC
Done.