Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_pilon, whole genome shotgun sequence
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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 25
Found at i:2923769 original size:6 final size:6
Alignment explanation
Indices: 2923739--2923796 Score: 53
Period size: 6 Copynumber: 8.7 Consensus size: 6
2923729 CAAATATATA
*
2923739 AAATTT AGATTT AAATACTT AAAATTT AAATTT AAATACTT AAAATTT
1 AAATTT AAATTT AAAT--TT -AAATTT AAATTT AAAT--TT -AAATTT
2923787 AAATTT AAAT
1 AAATTT AAAT
2923797 AACTGAATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
6 28 0.64
7 4 0.09
8 4 0.09
9 8 0.18
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (6 bp):
AAATTT
Found at i:2923812 original size:27 final size:21
Alignment explanation
Indices: 2923737--2923797 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
2923727 TTCAAATATA
*
2923737 TAAAATTTAGATTTAAATACT
1 TAAAATTTAAATTTAAATACT
2923758 TAAAATTTAAATTTAAATACT
1 TAAAATTTAAATTTAAATACT
2923779 TAAAATTTAAATTTAAATA
1 TAAAATTTAAATTTAAATA
2923798 ACTGAATTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAAATTTAAATTTAAATACT
Found at i:2927316 original size:46 final size:46
Alignment explanation
Indices: 2927263--2927355 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
2927253 TGAAGATGGC
2927263 TTTTGTTATAAAAATTATTTAAATAAACTAAATTGTAGCAATAAAT
1 TTTTGTTATAAAAATTATTTAAATAAACTAAATTGTAGCAATAAAT
2927309 TTTTGTTATAAAAATTATTTAAATAAACTAAATTGTAGCAATAAAT
1 TTTTGTTATAAAAATTATTTAAATAAACTAAATTGTAGCAATAAAT
2927355 T
1 T
2927356 GATTAAGTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (46 bp):
TTTTGTTATAAAAATTATTTAAATAAACTAAATTGTAGCAATAAAT
Found at i:2929295 original size:24 final size:25
Alignment explanation
Indices: 2929266--2929317 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2929256 TTTAAAACAT
2929266 AATAT-TTAA-ACTGAT-ATATAAA
1 AATATATTAATACTGATAATATAAA
2929288 AATATATTAATACTGATAATATAAA
1 AATATATTAATACTGATAATATAAA
2929313 AATAT
1 AATAT
2929318 TAAATCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.19
23 4 0.15
24 6 0.22
25 12 0.44
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
AATATATTAATACTGATAATATAAA
Found at i:2929317 original size:23 final size:22
Alignment explanation
Indices: 2929266--2929321 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 22
2929256 TTTAAAACAT
2929266 AATATTTAAACTGATATATAAAA
1 AATA-TTAAACTGATATATAAAA
2929289 ATATATTAATACTGATA-ATATAAA
1 A-ATATTAA-ACTGATATATA-AAA
2929313 AATATTAAA
1 AATATTAAA
2929322 TCAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 14 0.47
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (22 bp):
AATATTAAACTGATATATAAAA
Found at i:2942325 original size:17 final size:17
Alignment explanation
Indices: 2942297--2942355 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
2942287 GTATTAATTT
*
2942297 TGACATCTCTATGTCAA
1 TGACAACTCTATGTCAA
*
2942314 TGAAAACTCTATGTCAA
1 TGACAACTCTATGTCAA
* *
2942331 TGACAACTCTTTGCCAA
1 TGACAACTCTATGTCAA
2942348 TGACAACT
1 TGACAACT
2942356 TTTTGTCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (17 bp):
TGACAACTCTATGTCAA
Found at i:2945419 original size:22 final size:20
Alignment explanation
Indices: 2945372--2945419 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
2945362 AAAGTAAGAA
* *
2945372 AGAAATGAATCTTTATGTGT
1 AGAAATGAATATTTATGTAT
2945392 ATGAAATGGAATATTTACTGTAT
1 A-GAAAT-GAATATTTA-TGTAT
2945415 AGAAA
1 AGAAA
2945420 ATGCAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 5 0.22
22 12 0.52
23 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (20 bp):
AGAAATGAATATTTATGTAT
Found at i:2947112 original size:44 final size:43
Alignment explanation
Indices: 2947063--2947189 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
2947053 TTAAACATTA
2947063 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTA-TTTAAATATGTTTTAG
**
2947107 TATTTTAAT-TAAGTTTTAGG-A---TA--T---TAT-TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTATTTAAATATGTTTTAG
*
2947139 TATTTTATCTTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTA-TTTAAATATGTTTTAG
2947183 TATTTTA
1 TATTTTA
2947190 ATTAGGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
31 2 0.03
32 15 0.23
33 6 0.09
34 3 0.05
36 2 0.03
37 1 0.02
39 1 0.02
40 2 0.03
42 2 0.03
43 6 0.09
44 22 0.34
45 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (43 bp):
TATTTTATCTTTGTTTTAGGTATTTTATTTAAATATGTTTTAG
Found at i:2947171 original size:76 final size:76
Alignment explanation
Indices: 2947060--2947213 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
2947050 ATTTTAAACA
* *
2947060 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
2947125 GGATATTATTT
66 GAATATTATTT
* *
2947136 TTATATTTTATCTTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
2947201 GAATATTATTT
66 GAATATTATTT
2947212 TT
1 TT
2947214 GTTTTAGGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GAATATTATTT
Found at i:2947188 original size:19 final size:19
Alignment explanation
Indices: 2947164--2947201 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2947154 TTAGGTATTT
*
2947164 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAGGATTTAG
*
2947183 TATTTTAATTAGGATTTAG
1 TATTTTAAATAGGATTTAG
2947202 AATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
TATTTTAAATAGGATTTAG
Found at i:2947225 original size:63 final size:63
Alignment explanation
Indices: 2947143--2947263 Score: 199
Period size: 63 Copynumber: 1.9 Consensus size: 63
2947133 TTTTTATATT
*
2947143 TTATCTTTGTTTTAGGTATTTTATTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGAATA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAGAATA
* *
2947206 TTATTTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
2947264 AGATGATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 5 0.09
63 49 0.91
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.57
Consensus pattern (63 bp):
TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGAATA
Found at i:2947880 original size:9 final size:9
Alignment explanation
Indices: 2947866--2947899 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2947856 TATATACCAA
2947866 TTTATTTAT
1 TTTATTTAT
2947875 TTTATTTAT
1 TTTATTTAT
*
2947884 TTTTTTTAT
1 TTTATTTAT
*
2947893 TTAATTT
1 TTTATTT
2947900 TTATCTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2947883 original size:13 final size:13
Alignment explanation
Indices: 2947865--2947895 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2947855 CTATATACCA
2947865 ATTTATTTATTTT
1 ATTTATTTATTTT
*
2947878 ATTTATTTTTTTT
1 ATTTATTTATTTT
2947891 ATTTA
1 ATTTA
2947896 ATTTTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:2948001 original size:21 final size:22
Alignment explanation
Indices: 2947966--2948017 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2947956 TTTTAATTCA
* * *
2947966 TTATTTATTATTTTATTATT-T
1 TTATTTTTTAATTTATAATTAT
*
2947987 TTCTTTTTTAATTTATAATTAT
1 TTATTTTTTAATTTATAATTAT
2948009 TTATTTTTT
1 TTATTTTTT
2948018 TATACCTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTTTAATTTATAATTAT
Found at i:2952349 original size:2 final size:2
Alignment explanation
Indices: 2952342--2952380 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2952332 TTTTTAAAAC
2952342 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
2952381 CCCCCATCCC
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:2952567 original size:12 final size:12
Alignment explanation
Indices: 2952542--2952611 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
2952532 ACGAAGATAT
* *
2952542 CAGAAATCAAAA
1 CAGAATTCAGAA
2952554 CAGAATTCAGAA
1 CAGAATTCAGAA
2952566 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
2952578 CAGAATCCAGAT
1 CAGAATTCAGAA
*
2952590 CAGAAATCAGAA
1 CAGAATTCAGAA
2952602 CAGAATTCAG
1 CAGAATTCAG
2952612 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2952611 original size:48 final size:47
Alignment explanation
Indices: 2952540--2952648 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
2952530 AAACGAAGAT
*
2952540 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
2952587 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
2952635 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
2952649 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:2952646 original size:24 final size:25
Alignment explanation
Indices: 2952540--2952648 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
2952530 AAACGAAGAT
*
2952540 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
2952564 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
2952588 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
2952612 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
2952637 -TCGGAAATCAGA
1 ATCAGAAATCAGA
2952649 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:2954278 original size:63 final size:63
Alignment explanation
Indices: 2954179--2954301 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
2954169 TGCTTTCTTG
2954179 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
2954242 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
2954302 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:2955242 original size:15 final size:15
Alignment explanation
Indices: 2955222--2955252 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2955212 GGTCAACTCC
2955222 GGTCAACGATCAACG
1 GGTCAACGATCAACG
*
2955237 GGTCAACGGTCAACG
1 GGTCAACGATCAACG
2955252 G
1 G
2955253 CTCGGGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.13
Consensus pattern (15 bp):
GGTCAACGATCAACG
Found at i:2955279 original size:13 final size:13
Alignment explanation
Indices: 2955244--2955282 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2955234 ACGGGTCAAC
*
2955244 GGTCAACGGCTCG
1 GGTCAACGGGTCG
2955257 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2955270 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2955283 AGTCGGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.26, G:0.44, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2957179 original size:2 final size:2
Alignment explanation
Indices: 2957172--2957210 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2957162 TTTTTAAAAC
2957172 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
2957211 CCCCCATCCC
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:2957397 original size:12 final size:12
Alignment explanation
Indices: 2957372--2957441 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
2957362 ACGAAGATAT
* *
2957372 CAGAAATCAAAA
1 CAGAATTCAGAA
2957384 CAGAATTCAGAA
1 CAGAATTCAGAA
2957396 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
2957408 CAGAATCCAGAT
1 CAGAATTCAGAA
*
2957420 CAGAAATCAGAA
1 CAGAATTCAGAA
2957432 CAGAATTCAG
1 CAGAATTCAG
2957442 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2957441 original size:48 final size:47
Alignment explanation
Indices: 2957370--2957478 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
2957360 AAACGAAGAT
*
2957370 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
2957417 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
2957465 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
2957479 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:2957476 original size:24 final size:25
Alignment explanation
Indices: 2957370--2957478 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
2957360 AAACGAAGAT
*
2957370 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
2957394 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
2957418 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
2957442 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
2957467 -TCGGAAATCAGA
1 ATCAGAAATCAGA
2957479 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:2960110 original size:13 final size:13
Alignment explanation
Indices: 2960077--2960128 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
2960067 ACGGGTCAAC
* *
2960077 GGTCAACAGCTCG
1 GGTCAACGGGTCG
2960090 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2960103 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
2960116 GGTAAACGGGTCG
1 GGTCAACGGGTCG
2960129 AGTCGGGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2963147 original size:24 final size:24
Alignment explanation
Indices: 2963120--2963191 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
2963110 GTAAACGGAA
*
2963120 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
*
2963144 ATATCA-AATATCAGAACAGAATCC
1 ATATCAGAA-ATCAGAACAGAATTC
*
2963168 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
2963191 A
1 A
2963192 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 17 0.40
24 25 0.60
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:2963175 original size:12 final size:11
Alignment explanation
Indices: 2963153--2963212 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
2963143 CATATCAAAT
2963153 ATCAGAACAGA
1 ATCAGAACAGA
*
2963164 ATCCAGATCAGA
1 AT-CAGAACAGA
2963176 ATCAGAACAGA
1 ATCAGAACAGA
*
2963187 ATTCAGGTAAC-GT
1 A-TCA-G-AACAGA
2963200 ATCAGAACAGA
1 ATCAGAACAGA
2963211 AT
1 AT
2963213 TTAATTCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.08
11 15 0.38
12 16 0.40
13 3 0.08
14 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (11 bp):
ATCAGAACAGA
Found at i:2967618 original size:2 final size:2
Alignment explanation
Indices: 2967574--2967599 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2967564 CAGTAAAAAG
2967574 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
2967600 TTTAAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2967808 original size:24 final size:23
Alignment explanation
Indices: 2967781--2967852 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
2967771 GTAAACGGAG
*
2967781 ATATCAGAAATCAAAACAGAATTC
1 ATATCA-AAATCAGAACAGAATTC
2967805 ATATCAAATATCAGAACAGAA-TC
1 ATATCAAA-ATCAGAACAGAATTC
*
2967828 TAGATCAAAATCAGAACAGAATTC
1 -ATATCAAAATCAGAACAGAATTC
2967852 A
1 A
2967853 GGTAACGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 17 0.40
24 26 0.60
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.21
Consensus pattern (23 bp):
ATATCAAAATCAGAACAGAATTC
Found at i:2968994 original size:18 final size:18
Alignment explanation
Indices: 2968973--2969007 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2968963 TGCCATCCGG
*
2968973 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2968991 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2969008 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2972367 original size:2 final size:2
Alignment explanation
Indices: 2972320--2972347 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2972310 CAGTAAAAAG
2972320 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
2972348 TTTAAAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2972555 original size:24 final size:23
Alignment explanation
Indices: 2972528--2972599 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
2972518 GTAAACGAAG
*
2972528 ATATCATAAATCAAAACAGAATTC
1 ATATCA-AAATCAGAACAGAATTC
* *
2972552 ATATCAAATAACAGAACAGAATCC
1 ATATCAAA-ATCAGAACAGAATTC
* *
2972576 AGATCAGAATCAGAACAGAATTC
1 ATATCAAAATCAGAACAGAATTC
2972599 A
1 A
2972600 GGTAACGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (23 bp):
ATATCAAAATCAGAACAGAATTC
Found at i:2972583 original size:12 final size:11
Alignment explanation
Indices: 2972563--2972620 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
2972553 TATCAAATAA
2972563 CAGAACAGAAT
1 CAGAACAGAAT
*
2972574 CCAGATCAGAAT
1 -CAGAACAGAAT
2972586 CAGAACAGAATT
1 CAGAACAGAA-T
*
2972598 CAGGTAAC-GTAT
1 CA-G-AACAGAAT
2972610 CAGAACAGAAT
1 CAGAACAGAAT
2972621 TTAATTCGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 3 0.08
11 13 0.34
12 16 0.42
13 3 0.08
14 3 0.08
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (11 bp):
CAGAACAGAAT
Found at i:2973738 original size:18 final size:18
Alignment explanation
Indices: 2973717--2973754 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2973707 TCCTACCATC
2973717 CAATCTTATTATTTAATT
1 CAATCTTATTATTTAATT
*
2973735 CAATCTTATTATTTACTT
1 CAATCTTATTATTTAATT
2973753 CA
1 CA
2973755 GTCCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (18 bp):
CAATCTTATTATTTAATT
Found at i:2975041 original size:13 final size:13
Alignment explanation
Indices: 2975023--2975062 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2975013 CGCCAGTACA
2975023 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2975036 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
2975049 CGAGTCAACAGGT
1 CGGGTCAACGGGT
2975062 C
1 C
2975063 AGGTTGGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2978090 original size:18 final size:18
Alignment explanation
Indices: 2978069--2978104 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2978059 CTTTCATCCG
*
2978069 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2978087 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2978105 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2979417 original size:7 final size:7
Alignment explanation
Indices: 2979405--2979435 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
2979395 GGTCAACTAA
2979405 GGTCAAC
1 GGTCAAC
2979412 GGTCAAC
1 GGTCAAC
2979419 GGGTCAAC
1 -GGTCAAC
2979427 GGTCAAC
1 GGTCAAC
2979434 GG
1 GG
2979436 GTCGGGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2979425 original size:15 final size:15
Alignment explanation
Indices: 2979405--2979452 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2979395 GGTCAACTAA
2979405 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2979420 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
**
2979435 GGTC-GGGGTCAACG
1 GGTCAACGGTCAACG
2979449 GGTC
1 GGTC
2979453 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.25, G:0.40, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:2979446 original size:14 final size:15
Alignment explanation
Indices: 2979412--2979504 Score: 66
Period size: 18 Copynumber: 6.0 Consensus size: 15
2979402 TAAGGTCAAC
***
2979412 GGTCAACGGGTCAAC
1 GGTCAACGGGTCGGG
2979427 GGTCAACGGGTC-GG
1 GGTCAACGGGTCGGG
2979441 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTC-GG--G
2979459 GGTCAACGGGTC--G
1 GGTCAACGGGTCGGG
* *
2979472 GGTAAACGGGTGGGTCG
1 GGTCAACGGGTCGG--G
2979489 GGTCAAACGGGTCGGG
1 GGTC-AACGGGTCGGG
2979505 TCGGGTTGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.17
14 12 0.19
15 12 0.19
16 2 0.03
17 4 0.06
18 22 0.35
ACGTcount: A:0.17, C:0.20, G:0.47, T:0.15
Consensus pattern (15 bp):
GGTCAACGGGTCGGG
Found at i:2979463 original size:18 final size:18
Alignment explanation
Indices: 2979433--2979510 Score: 87
Period size: 19 Copynumber: 4.6 Consensus size: 18
2979423 CAACGGTCAA
2979433 CGGGTCGGGGTCAACGGGT
1 CGGGTC-GGGTCAACGGGT
2979452 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
2979465 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
2979483 -GGGTCGGGTCAAACGGGT
1 CGGGTCGGGTC-AACGGGT
2979501 CGGGTCGGGT
1 CGGGTCGGGT
2979511 TGTGACTGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 12 0.24
17 9 0.18
18 14 0.28
19 15 0.30
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2979470 original size:8 final size:8
Alignment explanation
Indices: 2979405--2979452 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
2979395 GGTCAACTAA
2979405 GGTCAAC-
1 GGTCAACG
2979412 GGTCAACG
1 GGTCAACG
2979420 GGTCAAC-
1 GGTCAACG
2979427 GGTCAACG
1 GGTCAACG
*
2979435 GGTC--GG
1 GGTCAACG
2979441 GGTCAACG
1 GGTCAACG
2979449 GGTC
1 GGTC
2979453 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:2979479 original size:13 final size:13
Alignment explanation
Indices: 2979452--2979486 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2979442 GTCAACGGGT
*
2979452 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
2979465 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2979478 CGGGT-GGGT
1 CGGGTCGGGT
2979487 CGGGTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.14, C:0.17, G:0.51, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2979498 original size:31 final size:31
Alignment explanation
Indices: 2979427--2979505 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 31
2979417 ACGGGTCAAC
*
2979427 GGTCAACGGGTCGGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTC-GGGTAAACGGGTCGGGTCG
2979459 GGTCAACGGGTCGGGTAAACGGGT-GGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
2979489 GGTCAAACGGGTCGGGT
1 GGTC-AACGGGTCGGGT
2979506 CGGGTTGTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 10 0.22
31 23 0.51
32 12 0.27
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:2982628 original size:18 final size:18
Alignment explanation
Indices: 2982605--2982640 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2982595 CCTTCATCCG
*
2982605 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2982623 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2982641 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2983760 original size:7 final size:7
Alignment explanation
Indices: 2983748--2983777 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2983738 GGTCAACTCC
2983748 GTCAACG
1 GTCAACG
2983755 GTCAACGG
1 GTCAAC-G
2983763 GTCAACG
1 GTCAACG
2983770 GTCAACG
1 GTCAACG
2983777 G
1 G
2983778 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.27, G:0.33, T:0.13
Consensus pattern (7 bp):
GTCAACG
Found at i:2983767 original size:8 final size:8
Alignment explanation
Indices: 2983748--2983793 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
2983738 GGTCAACTCC
2983748 GTCAAC-G
1 GTCAACGG
2983755 GTCAACGG
1 GTCAACGG
2983763 GTCAAC-G
1 GTCAACGG
2983770 GTCAACGG
1 GTCAACGG
2983778 GT---CGG
1 GTCAACGG
2983783 GTCAACGG
1 GTCAACGG
2983791 GTC
1 GTC
2983794 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.15
7 13 0.38
8 16 0.47
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (8 bp):
GTCAACGG
Found at i:2983768 original size:15 final size:15
Alignment explanation
Indices: 2983748--2983793 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2983738 GGTCAACTCC
2983748 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
2983763 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
*
2983778 GTC--GGGTCAACGG
1 GTCAACGGTCAACGG
2983791 GTC
1 GTC
2983794 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:2983798 original size:18 final size:18
Alignment explanation
Indices: 2983775--2983850 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
2983765 CAACGGTCAA
2983775 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2983793 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
2983806 C-GGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
2983823 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2983841 CGGGTCGGGT
1 CGGGTCGGGT
2983851 TGTGACTGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.20
13 1 0.02
17 1 0.02
18 38 0.76
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2983813 original size:30 final size:31
Alignment explanation
Indices: 2983769--2983846 Score: 140
Period size: 30 Copynumber: 2.5 Consensus size: 31
2983759 ACGGGTCAAC
2983769 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
2983800 GGTCAAC-GGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
2983830 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
2983847 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.66
31 15 0.34
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:2983819 original size:12 final size:13
Alignment explanation
Indices: 2983793--2983827 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2983783 GTCAACGGGT
*
2983793 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
2983806 C-GGTCGGGTAAA
1 CGGGTCGGGTAAA
2983818 CGGGTCGGGT
1 CGGGTCGGGT
2983828 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:2983846 original size:13 final size:13
Alignment explanation
Indices: 2983754--2983798 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
2983744 CTCCGTCAAC
*
2983754 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
2983769 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2983782 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2983795 GGTC
1 GGTC
2983799 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2986129 original size:76 final size:75
Alignment explanation
Indices: 2986022--2986236 Score: 281
Period size: 76 Copynumber: 2.9 Consensus size: 75
2986012 ATTTTAAACA
* * *
2986022 TTATATTTTATCTTTATTTTAGGTATTTTAGTTCAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
*
2986087 GGATATTATTT
66 GAATATTA-TT
* * *
2986098 TTATATTTTATCATTGTTTTAGGTATTTTAGTTTAAATAGGTTTTCGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
2986163 GAATATTATT
66 GAATATTATT
* * * * * *
2986173 TTAAATATTATTTTTGTTTTAAG-ATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTT
2986236 A
65 A
2986237 AGATGTTTTA
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
73 5 0.04
74 33 0.27
75 20 0.16
76 66 0.53
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.57
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
GAATATTATT
Found at i:2986876 original size:24 final size:21
Alignment explanation
Indices: 2986833--2986877 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2986823 TTTACCCCAA
*
2986833 TTTATTTATTTTACTTATTAT
1 TTTATTTATTTTACTCATTAT
2986854 TTTATTTAATATTTATCTCATTAT
1 TTTATTT-AT-TTTA-CTCATTAT
2986878 ACTTCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 4 0.20
24 7 0.35
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTATTTTACTCATTAT
Found at i:2990948 original size:12 final size:12
Alignment explanation
Indices: 2990928--2990997 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
2990918 GATACATTAC
*
2990928 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2990940 ATGATTTCTGTT
1 CTGATTTCTGTT
2990952 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
2990964 CTAATATCTGAT
1 CTGATTTCTGTT
*
2990976 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2990988 TTGATTTCTG
1 CTGATTTCTG
2990998 ATATCTTCAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2990959 original size:24 final size:24
Alignment explanation
Indices: 2990928--2990999 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
2990918 GATACATTAC
*
2990928 CTGAATTCTGTTATGATTTCTGTT
1 CTGAATTCTGTTATGATTTCTGAT
* * * *
2990952 CTGGATTCTGTTCTAATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
2990976 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
2991000 ATCTTCATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:2993984 original size:17 final size:18
Alignment explanation
Indices: 2993949--2993985 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2993939 GGATTAATAA
2993949 ATCTGAAAAGACATATTG
1 ATCTGAAAAGACATATTG
2993967 ATCTGATAAA-AC-TATTG
1 ATCTGA-AAAGACATATTG
2993984 AT
1 AT
2993986 GTGCATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (18 bp):
ATCTGAAAAGACATATTG
Found at i:2995620 original size:24 final size:24
Alignment explanation
Indices: 2995593--2995640 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2995583 GATACATTAA
2995593 CTGAATTCTATTCTGATTTCTGAT
1 CTGAATTCTATTCTGATTTCTGAT
* *
2995617 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTATTCTGATTTCTGAT
2995641 ATCTCAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (24 bp):
CTGAATTCTATTCTGATTTCTGAT
Found at i:2996582 original size:101 final size:99
Alignment explanation
Indices: 2996477--2996766 Score: 271
Period size: 102 Copynumber: 2.8 Consensus size: 99
2996467 TTTGTTGTAC
* * * * *
2996477 ATATAAACCTATTTTGTCTTACTTTTTTAGAATAAAAAATGTTAAAAATATATAACGTAAAAGGT
1 ATATAAACATATTTTGTCTTACATTTTCATAATAAAAAA-GTTGAAAATATATAACGTAAAAGGT
*
2996542 TGATCATTTTAGAAAAGGCTATATTTGTATTCTTATAT-
65 TGA-CATTTTA-AAAAGGCTATA--TATATTCTTATATA
* * * * * * * **
2996580 ATATAAACATATTTTATATTACATTTACATAA-AAAAAAGATGGCAAACATATAACTTAATTGGT
1 ATATAAACATATTTTGTCTTACATTTTCATAATAAAAAAG-TTGAAAATATATAACGTAAAAGGT
* * *
2996644 TGACTGTTTTAAAAAGATGCTACATATATTCTTATA-C
65 TGAC-ATTTTAAAAAG--GCTATATATATTCTTATATA
* *
2996681 ATATGAACATGTTTTGTCTTACATTTTCATAATAAAAAAGGTTGAAAATATATAACGTAAAAGGT
1 ATATAAACATATTTTGTCTTACATTTTCATAATAAAAAA-GTTGAAAATATATAACGTAAAAGGT
*
2996746 TGACCATTTCAAAAAGGCTAT
65 TGA-CATTTTAAAAAGGCTAT
2996767 CATAATAAAA
Statistics
Matches: 148, Mismatches: 31, Indels: 19
0.75 0.16 0.10
Matches are distributed among these distances:
100 4 0.03
101 45 0.30
102 67 0.45
103 32 0.22
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (99 bp):
ATATAAACATATTTTGTCTTACATTTTCATAATAAAAAAGTTGAAAATATATAACGTAAAAGGTT
GACATTTTAAAAAGGCTATATATATTCTTATATA
Found at i:3007956 original size:102 final size:101
Alignment explanation
Indices: 3007845--3008124 Score: 239
Period size: 101 Copynumber: 2.8 Consensus size: 101
3007835 TTTAATTAGA
* * *
3007845 AACCATTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAATAGTACA-ACAAAATAGGTTGAC
1 AACCGTTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAA-AATA-AGACAAAACAGGTTGAC
* * * *
3007909 AAGTGTAACATTACAGG-TAGCGCCTTTTTT-AATTGTC
64 AAGTATAACATTACAGGAT-GCACATTTTTTAAACTGTC
* * * * *
3007946 AACCGTTTAAG-TTATATGTTTTAAA-CATTTTATATTATGGAAAAATAAGACAAAACATGTTTA
1 AACCG-TTAAGATTATTTGTTTCAAACCATTTT-TATTA-AGAAAAATAAGACAAAACAGGTTGA
* * *
3008009 TAAGTATAACATTATATGATGCACATTTTTTAAACTGTC
63 CAAGTATAACATTACAGGATGCACATTTTTTAAACTGTC
* * * * * * *
3008048 AACCGTTAATATT-TTATGTTTCAAACCATTTTTATTATGAAACATTAAGAGAAAACAAGTTTAT
1 AACCGTTAAGATTATT-TGTTTCAAACCATTTTTATTAAGAAA-AATAAGACAAAACAGGTTGAC
*
3008112 AAGTCTAACATTA
64 AAGTATAACATTA
3008125 TAGGTTGTGT
Statistics
Matches: 146, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
100 7 0.05
101 67 0.46
102 66 0.45
103 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (101 bp):
AACCGTTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAAAATAAGACAAAACAGGTTGACAA
GTATAACATTACAGGATGCACATTTTTTAAACTGTC
Found at i:3008019 original size:101 final size:102
Alignment explanation
Indices: 3007704--3008129 Score: 327
Period size: 102 Copynumber: 4.2 Consensus size: 102
3007694 GGGATTTTTT
* * * * * * * * * *
3007704 TAAGTATAACATTATATGTGGCGCCTTTTTTATTTATCCATCATTTACGTTTTATGTTTGAAACC
1 TAAGTATAACATTATAGGTAGCGCCTTTTTTAATTGTCAACCGTTTAAGTTATATGTTTCAAACC
* *
3007769 -TTTTATATTGTA-AAAAAAGTAAGACAAAACATGTTTA
66 ATTTT-TATTATAGAAACAA-TAAGACAAAACATGTTTA
* * * * * *
3007806 TAAG-ATTACCATTGTAGGTTGCGCCTTCTTTTAATTAG-AAACC-ATTAAGATTATTTGTTTCA
1 TAAGTA-TAACATTATAGGTAGCGCCTT-TTTTAATT-GTCAACCGTTTAAG-TTATATGTTTCA
* * * * *
3007868 AACCATTTTTATTA-AGAAATAGTACA-ACAAAATAGGTTGA
62 AACCATTTTTATTATAGAAACAATA-AGACAAAACATGTTTA
* * * *
3007908 CAAGTGTAACATTACAGGTAGCGCCTTTTTTAATTGTCAACCGTTTAAGTTATATGTTTTAAA-C
1 TAAGTATAACATTATAGGTAGCGCCTTTTTTAATTGTCAACCGTTTAAGTTATATGTTTCAAACC
*
3007972 ATTTTATATTATGGAAA-AATAAGACAAAACATGTTTA
66 ATTTT-TATTATAGAAACAATAAGACAAAACATGTTTA
* * * * * *
3008009 TAAGTATAACATTATATG-ATGCACATTTTTTAAACTGTCAACCG-TTAATATTTTATGTTTCAA
1 TAAGTATAACATTATAGGTA-GCGCCTTTTTT-AATTGTCAACCGTTTAA-GTTATATGTTTCAA
* * *
3008072 ACCATTTTTATTAT-GAAACATTAAGAGAAAACAAGTTTA
63 ACCATTTTTATTATAGAAACAATAAGACAAAACATGTTTA
*
3008111 TAAGTCTAACATTATAGGT
1 TAAGTATAACATTATAGGT
3008130 TGTGTCTTTT
Statistics
Matches: 255, Mismatches: 50, Indels: 37
0.75 0.15 0.11
Matches are distributed among these distances:
100 9 0.04
101 75 0.29
102 130 0.51
103 37 0.15
104 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (102 bp):
TAAGTATAACATTATAGGTAGCGCCTTTTTTAATTGTCAACCGTTTAAGTTATATGTTTCAAACC
ATTTTTATTATAGAAACAATAAGACAAAACATGTTTA
Found at i:3008077 original size:203 final size:204
Alignment explanation
Indices: 3007705--3008089 Score: 456
Period size: 203 Copynumber: 1.9 Consensus size: 204
3007695 GGATTTTTTT
* * * * * * * * *
3007705 AAGTATAACATTATATGTGGCGCCTTTTTTATTTATCCATCATTTACGTTTTATGTTTGAAACCT
1 AAGTATAACATTACAGGTAGCGCCTTTTTTAATTATCAACCATTTAAGTTATATGTTTGAAACAT
* * * * * *
3007770 TTTATATTGTAAAAAAAGTAAGACAAAACATGTTTATAAGATTACCATTGTAGGTTGCGCCTTCT
66 TTTATATTATAAAAAAAGTAAGACAAAACATGTTTATAAGATTAACATTATAGGATGCACATTCT
*
3007835 TTTAATTAGAAACCATTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAATAGTACAACAAAA
131 TTTAACTAGAAACCATTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAATAGTACAACAAAA
3007900 TAGGTTGAC
196 TAGGTTGAC
* * * *
3007909 AAGTGTAACATTACAGGTAGCGCCTTTTTTAATTGTCAACCGTTTAAGTTATATGTTTTAAACAT
1 AAGTATAACATTACAGGTAGCGCCTTTTTTAATTATCAACCATTTAAGTTATATGTTTGAAACAT
** *
3007974 TTTATATTATGGAAAAA-TAAGACAAAACATGTTTATAAG-TATAACATTATATGATGCACATT-
66 TTTATATTATAAAAAAAGTAAGACAAAACATGTTTATAAGAT-TAACATTATAGGATGCACATTC
* * * *
3008036 TTTTAAACT-GTCAACCGTTAATATT-TTATGTTTCAAACCATTTTTATTATGAAA
130 TTTT-AACTAG-AAACCATTAAGATTATT-TGTTTCAAACCATTTTTATTAAGAAA
3008090 CATTAAGAGA
Statistics
Matches: 150, Mismatches: 27, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
202 8 0.05
203 76 0.51
204 66 0.44
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (204 bp):
AAGTATAACATTACAGGTAGCGCCTTTTTTAATTATCAACCATTTAAGTTATATGTTTGAAACAT
TTTATATTATAAAAAAAGTAAGACAAAACATGTTTATAAGATTAACATTATAGGATGCACATTCT
TTTAACTAGAAACCATTAAGATTATTTGTTTCAAACCATTTTTATTAAGAAATAGTACAACAAAA
TAGGTTGAC
Found at i:3011322 original size:29 final size:28
Alignment explanation
Indices: 3011267--3011322 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
3011257 TTCCCATTGG
*
3011267 TCATCCTAAACCCTAAAAAAACTTCCAA
1 TCATCCTAAACCCTAAAAAAACATCCAA
* * *
3011295 TCATCCTTAAAGCCTAGAATAACATCCA
1 TCATCC-TAAACCCTAAAAAAACATCCA
3011323 TTTGTAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.43, C:0.30, G:0.04, T:0.23
Consensus pattern (28 bp):
TCATCCTAAACCCTAAAAAAACATCCAA
Found at i:3013429 original size:11 final size:11
Alignment explanation
Indices: 3013413--3013437 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3013403 ACACTTCTCC
3013413 CTTTTAAAACA
1 CTTTTAAAACA
3013424 CTTTTAAAACA
1 CTTTTAAAACA
3013435 CTT
1 CTT
3013438 AACATTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
CTTTTAAAACA
Found at i:3016943 original size:30 final size:29
Alignment explanation
Indices: 3016866--3016944 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 29
3016856 GTCAATAACT
* * *
3016866 AAAATGT-ATTTTTTAAAGTTTAGTGACT
1 AAAATGTAATTTTTAAAAGTTTAGGGACA
* * **
3016894 AAAGTATACATTTGGAAAAGTTTAGGGACCA
1 AAAATGTA-ATTTTTAAAAGTTTAGGGA-CA
3016925 AAAATGTAATTTTTAAAAGT
1 AAAATGTAATTTTTAAAAGT
3016945 AATATTTTTG
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
28 5 0.14
30 25 0.68
31 7 0.19
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAAAAGTTTAGGGACA
Found at i:3021595 original size:45 final size:45
Alignment explanation
Indices: 3021541--3021755 Score: 308
Period size: 45 Copynumber: 4.7 Consensus size: 45
3021531 ATTATTCATT
3021541 ATTTCCATTTATGGCATCCTTTCATGCCTTTAATGTC-CCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATG-CACCGTTATGC
* *
3021587 ATTTCATTTATGACATCCGTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
3021632 ATTTCATTTATGGCATCCTTTCCTGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* ** *
3021677 ATTTCATTTATTGCATCCTTTCCATAACTTTAATGCATTC-TTATGC
1 ATTTCATTTATGGCATCCTTT-CATGCCTTTAATGCA-CCGTTATGC
*
3021723 ATTTCATTTATGACATCCTTTCATGCCTTTAAT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAAT
3021756 ATCCTTTTCA
Statistics
Matches: 152, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.01
45 109 0.72
46 41 0.27
47 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:3021676 original size:90 final size:91
Alignment explanation
Indices: 3021541--3021755 Score: 312
Period size: 91 Copynumber: 2.4 Consensus size: 91
3021531 ATTATTCATT
3021541 ATTTCCATTTATGGCATCCTTTCATGCCTTTAATGTCCCGTTATGCATTTCATTTA-TGACATCC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGTCCCGTTATGCATTTCATTTATTG-CATCC
**
3021605 GTT-CATGCCTTTAATGCA-CCGTTATGC
64 GTTCCATAACTTTAATGCATCC-TTATGC
* *
3021632 ATTTCATTTATGGCATCCTTTCCTGCCTTTAATG-CACCGTTATGCATTTCATTTATTGCATCCT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTC-CCGTTATGCATTTCATTTATTGCATCCG
*
3021696 TTCCATAACTTTAATGCATTCTTATGC
65 TTCCATAACTTTAATGCATCCTTATGC
*
3021723 ATTTCATTTATGACATCCTTTCATGCCTTTAAT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAAT
3021756 ATCCTTTTCA
Statistics
Matches: 113, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
89 1 0.01
90 55 0.49
91 56 0.50
92 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (91 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTCCCGTTATGCATTTCATTTATTGCATCCGT
TCCATAACTTTAATGCATCCTTATGC
Found at i:3022303 original size:95 final size:95
Alignment explanation
Indices: 3022133--3022332 Score: 237
Period size: 95 Copynumber: 2.1 Consensus size: 95
3022123 CCCTTACCAT
* * * *
3022133 GTATCGATACTTCTATACTATGGTATCGATATCCCCTTTCAGTATCGATACCATTTCTATATTCT
1 GTATCGATACTACTAAACTATGGTATCGATATCCCCTTTCAGTATCGATACCATTTCTACATTAT
* *
3022198 ATAATTCATGGTATCGATACCTTT-CTCTCA
66 AGAATACATGGTATCGATA-CTTTCCTCTCA
* *
3022228 GTATCGATGCTACTAAACTATGGTA-CTGATA-CTCCCTTTCAGTATCGATATCATTT-TAGCAT
1 GTATCGATACTACTAAACTATGGTATC-GATATC-CCCTTTCAGTATCGATACCATTTCTA-CAT
* * *
3022290 TATGGAATACATGGTATCGATACTTTCCTTTTA
63 TATAGAATACATGGTATCGATACTTTCCTCTCA
3022323 GTATCGATAC
1 GTATCGATAC
3022333 CCCATAAGTA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
94 8 0.09
95 81 0.91
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (95 bp):
GTATCGATACTACTAAACTATGGTATCGATATCCCCTTTCAGTATCGATACCATTTCTACATTAT
AGAATACATGGTATCGATACTTTCCTCTCA
Found at i:3023456 original size:49 final size:48
Alignment explanation
Indices: 3023380--3023486 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 48
3023370 TACATTGGGC
*
3023380 TATGAAAAT-AAATGTGAAAGTTCTGAAAAGTATCTGAAAAGAAAAGTA
1 TATG-AAATGAAATCTGAAAGTTCTGAAAAGTATCTGAAAAGAAAAGTA
* * * * **
3023428 TATGATAATGAAATCTGAAAGTTTTGAAATGTGTCTGTATGGAAAAGTA
1 TATGA-AATGAAATCTGAAAGTTCTGAAAAGTATCTGAAAAGAAAAGTA
3023477 TATGAAATGA
1 TATGAAATGA
3023487 TATTTTTGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.02
48 12 0.24
49 37 0.74
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.30
Consensus pattern (48 bp):
TATGAAATGAAATCTGAAAGTTCTGAAAAGTATCTGAAAAGAAAAGTA
Found at i:3025408 original size:14 final size:15
Alignment explanation
Indices: 3025391--3025420 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3025381 TATTATTTAT
3025391 TTATTTTTA-ATATC
1 TTATTTTTATATATC
3025405 TTATTTTTATATATC
1 TTATTTTTATATATC
3025420 T
1 T
3025421 AATTGTCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTTATATATC
Found at i:3028380 original size:94 final size:94
Alignment explanation
Indices: 3028219--3028408 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
3028209 TGTTTTATCT
3028219 TATATTAAAATGTTGTCTTTGTTTTTCAAACAAAGTTTTATGAGTGCTACAAATAAGAAAATGTT
1 TATATTAAAATGTTGTCTTTGTTTTTCAAACAAAGTTTTATGAGTGCTACAAATAAGAAAATGTT
3028284 TTTAAGTCATGTGATACTCGTGACTTGTA
66 TTTAAGTCATGTGATACTCGTGACTTGTA
3028313 TATATTAAAATGTTGTCTTTGTTTTTCAAACAAAGTTTTATGAGTGCTACAAATAAGAAAATGTT
1 TATATTAAAATGTTGTCTTTGTTTTTCAAACAAAGTTTTATGAGTGCTACAAATAAGAAAATGTT
3028378 TTTAAGTCATGTGATACTCGTGACTTGTA
66 TTTAAGTCATGTGATACTCGTGACTTGTA
3028407 TA
1 TA
3028409 CGAGAACATA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (94 bp):
TATATTAAAATGTTGTCTTTGTTTTTCAAACAAAGTTTTATGAGTGCTACAAATAAGAAAATGTT
TTTAAGTCATGTGATACTCGTGACTTGTA
Found at i:3053058 original size:2 final size:2
Alignment explanation
Indices: 3053051--3053078 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3053041 CTTGATAGGA
3053051 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
3053079 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3057801 original size:23 final size:24
Alignment explanation
Indices: 3057766--3057811 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3057756 GTCAGACCGG
3057766 TCAACAGTCAACGAGTTGACTCGA
1 TCAACAGTCAACGAGTTGACTCGA
*
3057790 TCAA-AGTTAACGAGTTGACTCG
1 TCAACAGTCAACGAGTTGACTCG
3057812 GCGACTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (24 bp):
TCAACAGTCAACGAGTTGACTCGA
Found at i:3059843 original size:18 final size:18
Alignment explanation
Indices: 3059799--3059846 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3059789 TTATTAAGCT
*
3059799 ATGTCTGATAACTGTAAA
1 ATGTCTGATAACTGAAAA
**
3059817 ACATCTGATAACTGAAAA
1 ATGTCTGATAACTGAAAA
*
3059835 ATGTATGATAAC
1 ATGTCTGATAAC
3059847 AATAAACTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
ATGTCTGATAACTGAAAA
Found at i:3067498 original size:20 final size:21
Alignment explanation
Indices: 3067461--3067500 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3067451 TCTCATGATT
3067461 TTATCAAAAATCATATAAATCA
1 TTATCAAAAATCA-ATAAATCA
*
3067483 TTATCAAATATC-ATAAAT
1 TTATCAAAAATCAATAAAT
3067501 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TTATCAAAAATCAATAAATCA
Found at i:3070517 original size:14 final size:13
Alignment explanation
Indices: 3070498--3070542 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3070488 ATATGTTCGC
3070498 TTATGTTCATTCAT
1 TTATGTTC-TTCAT
3070512 TTATG---TTCAT
1 TTATGTTCTTCAT
3070522 TTATGTTCGTTCAT
1 TTATGTTC-TTCAT
3070536 TTATGTT
1 TTATGTT
3070543 TGAAAAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 10 0.37
14 17 0.63
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (13 bp):
TTATGTTCTTCAT
Found at i:3070518 original size:24 final size:24
Alignment explanation
Indices: 3070489--3070542 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3070479 TGTTTGATTA
*
3070489 TATGTTCGCTTATGTTCATTCATT
1 TATGTTCACTTATGTTCATTCATT
* *
3070513 TATGTTCATTTATGTTCGTTCATT
1 TATGTTCACTTATGTTCATTCATT
3070537 TATGTT
1 TATGTT
3070543 TGAAAAGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (24 bp):
TATGTTCACTTATGTTCATTCATT
Found at i:3070820 original size:13 final size:12
Alignment explanation
Indices: 3070806--3070851 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3070796 TATGTTTGTG
3070806 TTGTTCGTTTA-
1 TTGTTCGTTTAT
3070817 -TGTTCGTTTAT
1 TTGTTCGTTTAT
3070828 TGTGTTCGTTTAT
1 T-TGTTCGTTTAT
3070841 GTTCGTTCGTT
1 -TT-GTTCGTT
3070852 CGTGTTCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.33
13 12 0.40
14 8 0.27
ACGTcount: A:0.07, C:0.11, G:0.22, T:0.61
Consensus pattern (12 bp):
TTGTTCGTTTAT
Found at i:3070822 original size:10 final size:10
Alignment explanation
Indices: 3070794--3070847 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
3070784 ATAAGTTTTT
*
3070794 TTTATGTTTG
1 TTTATGTTCG
*
3070804 TGT-TGTTCG
1 TTTATGTTCG
3070813 TTTATGTTCG
1 TTTATGTTCG
3070823 TTTATTGTGTTCG
1 TTTA---TGTTCG
3070836 TTTATGTTCG
1 TTTATGTTCG
3070846 TT
1 TT
3070848 CGTTCGTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.19
10 20 0.54
13 10 0.27
ACGTcount: A:0.07, C:0.07, G:0.22, T:0.63
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:3070825 original size:23 final size:23
Alignment explanation
Indices: 3070807--3070862 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3070797 ATGTTTGTGT
3070807 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCGTTTATGTTCGTTTATTG
**
3070830 TGTTCGTTTATGTTCGTTCGTTCG
1 TGTTCGTTTATGTTCGTTTATT-G
3070854 TGTTCGTTT
1 TGTTCGTTT
3070863 TTTAAATCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.05, C:0.12, G:0.23, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTATGTTCGTTTATTG
Found at i:3077060 original size:20 final size:21
Alignment explanation
Indices: 3077035--3077076 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3077025 TTGTGAATAG
*
3077035 TGGGGGATTCGGTT-CCCTTT
1 TGGGGGAATCGGTTCCCCTTT
3077055 TGGGGGAATCGGTTCCCCTTT
1 TGGGGGAATCGGTTCCCCTTT
3077076 T
1 T
3077077 ATATTCTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.07, C:0.21, G:0.33, T:0.38
Consensus pattern (21 bp):
TGGGGGAATCGGTTCCCCTTT
Found at i:3077788 original size:59 final size:59
Alignment explanation
Indices: 3077670--3077791 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
3077660 CAATCTCGAG
* * ** * *
3077670 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTCTCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCATTAAGTACAGTCCCGAA
* ** *
3077729 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCATTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCATTAAGTACAGTCCCGAA
3077788 TATG
1 TATG
3077792 CAGCATGCTG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCATTAAGTACAGTCCCGAA
Found at i:3086638 original size:22 final size:25
Alignment explanation
Indices: 3086613--3086665 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
3086603 ACCTATTATT
3086613 TAAAATTATTT-AAT-AAAATT-AA
1 TAAAATTATTTAAATGAAAATTAAA
*
3086635 TAAAATTATTTAAATGTAAATTAAA
1 TAAAATTATTTAAATGAAAATTAAA
3086660 TAAAAT
1 TAAAAT
3086666 ATTATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.41
23 3 0.11
24 5 0.19
25 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TAAAATTATTTAAATGAAAATTAAA
Found at i:3086726 original size:23 final size:24
Alignment explanation
Indices: 3086686--3086735 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3086676 ATGCAAAATA
3086686 AAATTAATATAATGTAATTTATAT
1 AAATTAATATAATGTAATTTATAT
* *
3086710 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAATGTAATTTATAT
3086733 AAA
1 AAA
3086736 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTAATATAATGTAATTTATAT
Found at i:3088998 original size:13 final size:14
Alignment explanation
Indices: 3088972--3089004 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3088962 CTATCACAGT
3088972 GAAAAATTATAAAA
1 GAAAAATTATAAAA
3088986 GAAAAATTA-AAAA
1 GAAAAATTATAAAA
3088999 GCAAAA
1 G-AAAA
3089005 CCTCAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (14 bp):
GAAAAATTATAAAA
Found at i:3090064 original size:18 final size:18
Alignment explanation
Indices: 3089994--3090192 Score: 115
Period size: 18 Copynumber: 11.1 Consensus size: 18
3089984 ATTAATAAAT
3089994 TAATATATAGTTTATATA
1 TAATATATAGTTTATATA
* *
3090012 TATTGTATAGTTTATATA
1 TAATATATAGTTTATATA
* *
3090030 TACTA-AT-G--AACTATA
1 TAATATATAGTTTA-TATA
*
3090045 TAATATATAGTTTGTATA
1 TAATATATAGTTTATATA
** * *
3090063 TACCATATACTATATAGGT-
1 TAATATATAGTTTATA--TA
* **
3090082 TATATATACTAATGAACTATA
1 TA-ATATA-TAGTTTA-TATA
*
3090103 TAATATAGAGTTTATATA
1 TAATATATAGTTTATATA
* * *
3090121 TACTATATAATTTATGTA
1 TAATATATAGTTTATATA
*
3090139 TAATGTATAGTTTATATA
1 TAATATATAGTTTATATA
** *
3090157 TACCATATAGTCTATATA
1 TAATATATAGTTTATATA
3090175 T-A-ATATAGTTTATATA
1 TAATATATAGTTTATATA
3090191 TA
1 TA
3090193 CTAATAAACT
Statistics
Matches: 133, Mismatches: 36, Indels: 25
0.69 0.19 0.13
Matches are distributed among these distances:
14 1 0.01
15 8 0.06
16 17 0.13
17 3 0.02
18 81 0.61
19 5 0.04
20 10 0.08
21 6 0.05
22 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (18 bp):
TAATATATAGTTTATATA
Found at i:3090076 original size:25 final size:25
Alignment explanation
Indices: 3090042--3090090 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3090032 CTAATGAACT
* *
3090042 ATATAATATATAGTTTGTATATACC
1 ATATAATATATAGGTTATATATACC
*
3090067 ATATACTATATAGGTTATATATAC
1 ATATAATATATAGGTTATATATAC
3090091 TAATGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAATATATAGGTTATATATACC
Found at i:3090085 original size:58 final size:58
Alignment explanation
Indices: 3090017--3090129 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
3090007 ATATATATTG
* * *
3090017 TATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACCATATACTA
1 TATAGGTTATATATACTAATGAACTATATAATATAGAGTTTATATATACCATATACTA
*
3090075 TATAGGTTATATATACTAATGAACTATATAATATAGAGTTTATATATACTATATA
1 TATAGGTTATATATACTAATGAACTATATAATATAGAGTTTATATATACCATATA
3090130 ATTTATGTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (58 bp):
TATAGGTTATATATACTAATGAACTATATAATATAGAGTTTATATATACCATATACTA
Found at i:3090151 original size:36 final size:35
Alignment explanation
Indices: 3090075--3090207 Score: 134
Period size: 36 Copynumber: 3.9 Consensus size: 35
3090065 CCATATACTA
*
3090075 TATAGGTTATATATACTA-ATGAA-C--TATATAAT
1 TATAGTTTATATATACTATAT-AATCTATATATAAT
* * *
3090107 ATAGAGTTTATATATACTATATAATTTATGTATAAT
1 -TATAGTTTATATATACTATATAATCTATATATAAT
* *
3090143 GTATAGTTTATATATACCATATAGTCTATATATAA-
1 -TATAGTTTATATATACTATATAATCTATATATAAT
*
3090178 TATAGTTTATATATACTA-ATAAACTATATA
1 TATAGTTTATATATACTATATAATCTATATA
3090208 ATGTATAATT
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
33 28 0.34
34 19 0.23
36 36 0.43
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (35 bp):
TATAGTTTATATATACTATATAATCTATATATAAT
Found at i:3090279 original size:2 final size:2
Alignment explanation
Indices: 3090268--3090333 Score: 55
Period size: 2 Copynumber: 32.0 Consensus size: 2
3090258 TAAATTACAC
*
3090268 TA TA TA -A TA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
3090310 AA TA TA AA CTA TA GTA TA TA TA TA
1 TA TA TA TA -TA TA -TA TA TA TA TA
3090334 GGTCATATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 2 0.04
2 44 0.85
3 6 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3090293 original size:20 final size:19
Alignment explanation
Indices: 3090268--3090333 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
3090258 TAAATTACAC
*
3090268 TATATA-ATATATATAGTT
1 TATATATATATATATAGTA
3090286 TATATATATAATATATAGTA
1 TATATATAT-ATATATAGTA
* *
3090306 TATAAATATAAACTATAGTA
1 TATATATATATA-TATAGTA
3090326 TATATATA
1 TATATATA
3090334 GGTCATATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.15
19 4 0.10
20 31 0.76
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (19 bp):
TATATATATATATATAGTA
Found at i:3090314 original size:22 final size:22
Alignment explanation
Indices: 3090268--3090329 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
3090258 TAAATTACAC
* *
3090268 TATATAATATATA-TAGTTTATA
1 TATATAATATATAGTA-TATAAA
3090290 TATATAATATATAGTATATAAA
1 TATATAATATATAGTATATAAA
*
3090312 TATA-AA-CTATAGTATATA
1 TATATAATATATAGTATATA
3090330 TATAGGTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 11 0.31
21 2 0.06
22 21 0.58
23 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
TATATAATATATAGTATATAAA
Found at i:3090332 original size:51 final size:50
Alignment explanation
Indices: 3090258--3090381 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 50
3090248 AGTTCATATG
* * *
3090258 TAAAT-TACACTATATAATATATATAGTTTATATATATAA-TATATAGTATA
1 TAAATATAAACTATAT-ATATATATAGGTCATATATA-AACTATATAGTATA
*
3090308 TAAATATAAACTATAGTATATATATAGGTCATATGTAAACTATATAGTATA
1 TAAATATAAACTATA-TATATATATAGGTCATATATAAACTATATAGTATA
*
3090359 TAAATATCAACTATA-ATATATAT
1 TAAATATAAACTATATATATATAT
3090382 GTAAATATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
49 8 0.12
50 7 0.11
51 50 0.76
52 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (50 bp):
TAAATATAAACTATATATATATATAGGTCATATATAAACTATATAGTATA
Found at i:3090386 original size:24 final size:24
Alignment explanation
Indices: 3090349--3090410 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
3090339 TATGTAAACT
*
3090349 ATATAGTATATAAATATCAACTATA
1 ATATA-TATGTAAATATCAACTATA
*
3090374 ATATATATGTAAATATTAACTATA
1 ATATATATGTAAATATCAACTATA
* *
3090398 TTTTATATGTAAA
1 ATATATATGTAAA
3090411 CTATAGTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (24 bp):
ATATATATGTAAATATCAACTATA
Found at i:3090448 original size:20 final size:20
Alignment explanation
Indices: 3090424--3090497 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
3090414 TAGTTCATAT
*
3090424 ATATAGTATATAAACATAAA
1 ATATAGTATATAAATATAAA
* *
3090444 CTATAGTTTATGTAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
3090469 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
3090489 TTATAGTAT
1 ATATAGTAT
3090498 GTAGTTTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 19 0.44
21 1 0.02
22 6 0.14
23 6 0.14
24 1 0.02
25 10 0.23
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:3090448 original size:24 final size:23
Alignment explanation
Indices: 3090296--3090448 Score: 65
Period size: 24 Copynumber: 6.1 Consensus size: 23
3090286 TATATATATA
*
3090296 ATATATAGTATATAAATATAAACT
1 ATATATA-TATATAAACATAAACT
**
3090320 ATAGTATATATATAGGTCATATGTAAACT
1 ATA-TATATATATA----A-ACATAAACT
* * *
3090349 ATATA-GTATATAAATATCAACT
1 ATATATATATATAAACATAAACT
* * *
3090371 ATAATATATATGTAAATATTAACT
1 AT-ATATATATATAAACATAAACT
* * **
3090395 ATATTTTATATGTAAACTATAGTTCAT
1 ATA-TATATATATAAAC-ATA-AAC-T
3090422 ATATATAGTATATAAACATAAACT
1 ATATATA-TATATAAACATAAACT
3090446 ATA
1 ATA
3090449 GTTTATGTAA
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
22 9 0.09
23 5 0.05
24 40 0.40
25 7 0.07
26 7 0.07
27 18 0.18
28 3 0.03
29 11 0.11
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATATATATAAACATAAACT
Found at i:3090531 original size:13 final size:13
Alignment explanation
Indices: 3090515--3090552 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3090505 ATATAAATAC
3090515 AAACCCTAAACCT
1 AAACCCTAAACCT
**
3090528 AAACATTAAACCT
1 AAACCCTAAACCT
3090541 AAACCCTAAACC
1 AAACCCTAAACC
3090553 CCACACATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:3090590 original size:22 final size:22
Alignment explanation
Indices: 3090562--3090611 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
3090552 CCCACACATA
3090562 TATATATATATAAACTATATAATT
1 TATAT-TA-ATAAACTATATAATT
3090586 TATATTAATAAACTATATAATT
1 TATATTAATAAACTATATAATT
3090608 TATA
1 TATA
3090612 AAATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 19 0.73
23 2 0.08
24 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTAATAAACTATATAATT
Found at i:3090661 original size:17 final size:17
Alignment explanation
Indices: 3090566--3090684 Score: 62
Period size: 17 Copynumber: 6.5 Consensus size: 17
3090556 CACATATATA
3090566 TATATATAAACTATATAATT
1 TATATATAAA-TATA-AA-T
3090586 TATATTAATAAACTATATAAT
1 TATA-T-ATAAA-TATA-AAT
*
3090607 T-TATA-AAATATATAT
1 TATATATAAATATAAAT
* * *
3090622 TATTTATAATTATACAT
1 TATATATAAATATAAAT
*
3090639 AATATATAAATATAAAT
1 TATATATAAATATAAAT
* **
3090656 TGTATAGTTTATATATAAT
1 TATATA-TAAATATA-AAT
3090675 TCATATATAA
1 T-ATATATAA
3090685 TTTATATATA
Statistics
Matches: 77, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.04
16 7 0.09
17 28 0.36
18 7 0.09
19 6 0.08
20 10 0.13
21 3 0.04
22 13 0.17
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
TATATATAAATATAAAT
Found at i:3090673 original size:20 final size:20
Alignment explanation
Indices: 3090648--3090750 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
3090638 TAATATATAA
*
3090648 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
3090668 ATATAATTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
3090690 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* *
3090710 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
*
3090729 ATATAAACTATATAGTATTAT
1 ATATAAATTATATAGT-TTAT
3090750 A
1 A
3090751 GTTTATACAT
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
19 13 0.21
20 28 0.46
21 4 0.07
22 16 0.26
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:3090693 original size:13 final size:11
Alignment explanation
Indices: 3090577--3090695 Score: 66
Period size: 11 Copynumber: 10.6 Consensus size: 11
3090567 ATATATAAAC
3090577 TATATAATTTA
1 TATATAATTTA
**
3090588 TAT-TAATAAA
1 TATATAATTTA
3090598 CTATATAATTTA
1 -TATATAATTTA
*
3090610 TAAAATATATATTA
1 T-ATATA-AT-TTA
*
3090624 TTTATAA-TTA
1 TATATAATTTA
*
3090634 TACATAATATATA
1 TATATAAT-T-TA
* *
3090647 AATATAA-AT-
1 TATATAATTTA
* *
3090656 TGTATAGTTTA
1 TATATAATTTA
*
3090667 TATATAATTCA
1 TATATAATTTA
3090678 TATATAATTTA
1 TATATAATTTA
3090689 TATATAA
1 TATATAA
3090696 ACTATGTAGT
Statistics
Matches: 78, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
9 4 0.05
10 15 0.19
11 32 0.41
12 11 0.14
13 12 0.15
14 4 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (11 bp):
TATATAATTTA
Found at i:3090783 original size:27 final size:28
Alignment explanation
Indices: 3090737--3090797 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
3090727 ATATATAAAC
* **
3090737 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
3090765 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
3090792 TATATA
1 TATATA
3090798 TAAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:3090796 original size:2 final size:2
Alignment explanation
Indices: 3090789--3090859 Score: 99
Period size: 2 Copynumber: 35.0 Consensus size: 2
3090779 TTTATACATA
* *
3090789 AT AT AT AT AT AA ACT AT AT AGT TT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
3090832 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
3090860 TAGTTGTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 1 0.02
2 59 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3090826 original size:18 final size:18
Alignment explanation
Indices: 3090763--3090858 Score: 76
Period size: 16 Copynumber: 5.4 Consensus size: 18
3090753 TTATACATGG
* *
3090763 TATATATAGT-TTATACTT
1 TATATATAGTATAATA-TA
* *
3090781 TATACATAATATATATATA
1 TATATATAGTATA-ATATA
* *
3090800 AACTATATAGTTTAATATA
1 TA-TATATAGTATAATATA
3090819 TATATATA-TAT-ATATA
1 TATATATAGTATAATATA
3090835 TATATATA-TAT-ATATA
1 TATATATAGTATAATATA
3090851 TATATATA
1 TATATATA
3090859 TTAGTTGTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
16 29 0.45
17 2 0.03
18 14 0.22
19 9 0.14
20 11 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (18 bp):
TATATATAGTATAATATA
Found at i:3091318 original size:209 final size:212
Alignment explanation
Indices: 3090884--3091697 Score: 1176
Period size: 216 Copynumber: 3.8 Consensus size: 212
3090874 TTTTTTCTCA
* * * *
3090884 ACTTATTACTTATTTATATTTATT-AATTGGCCCATAATTTTTTAAATGAGTATAATTTAGTACA
1 ACTTATTACTTATTTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
3090948 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-T-TTGTGATGTT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATTGTGTTGTT
* * ** * *
3091011 TAATATATTTTATTTTTTATTTTTAATTTCATATTTGTTGAATTTAGTCCTCCAAAATTTATTTG
130 TAATATATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
*
3091076 CACCTGAAATTGACCCAT
195 CATCTGAAATTGACCCAT
*
3091094 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACCT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
3091159 TTTTGTATTAATTTTAACCTCAAAATTTAAAATTATTTCGATTTGAT-CCT-T-TTTTGTTGTTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATTGTGTTGTTT
3091221 AATATATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
131 AATATATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
3091286 ATCTGAAATTGACCCAT
196 ATCTGAAATTGACCCAT
* *
3091303 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAATTTTTTAAATGGGTACAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * * *
3091368 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTTGATTTGATCCCTCATCAAAGTGTGTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT---ATTGTGTT
* * *
3091433 GTTTAATTTATTTAAATTTTTATTT-ATAATTTCATACTTGTTCAATTTAGTCATCCAAATTTTA
127 GTTTAATATATTTAAATTTTTATTTGA-AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
* *
3091497 TTTGCATATGAAATTGATCCAT
191 TTTGCATCTGAAATTGACCCAT
* * *
3091519 ACTTATTACTTAATTCTATTTTTGTAATTGGCACATAACTTTTTAAATGGGTATAATTTAGTA-T
1 ACTTATTACTTATTTCTATTTTT-AAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
* *
3091583 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTTGATTTGATCCCTCATCAATGTGTGT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT--AT-TGTGT
* *
3091648 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
126 TGTTTAATATATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTA
3091698 ATTCTTAAAT
Statistics
Matches: 554, Mismatches: 38, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
209 195 0.35
210 107 0.19
212 1 0.00
215 3 0.01
216 213 0.38
217 35 0.06
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (212 bp):
ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATTGTGTTGTTT
AATATATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
ATCTGAAATTGACCCAT
Found at i:3094516 original size:22 final size:22
Alignment explanation
Indices: 3094488--3094534 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3094478 TGAAGCGTGA
3094488 TGCATTGGCAAAAGGCATAAGT
1 TGCATTGGCAAAAGGCATAAGT
*
3094510 TGCATTGGCAAAAGGTATAAGT
1 TGCATTGGCAAAAGGCATAAGT
3094532 TGC
1 TGC
3094535 CTTTCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (22 bp):
TGCATTGGCAAAAGGCATAAGT
Found at i:3096491 original size:10 final size:10
Alignment explanation
Indices: 3096453--3096484 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3096443 TTTATAAAAT
3096453 TCAAGTCGAG
1 TCAAGTCGAG
3096463 TCAAGTCGAG
1 TCAAGTCGAG
*
3096473 TCTAGTCGAG
1 TCAAGTCGAG
3096483 TC
1 TC
3096485 CATTCGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (10 bp):
TCAAGTCGAG
Found at i:3097046 original size:5 final size:5
Alignment explanation
Indices: 3097036--3097062 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3097026 TCATAGCCCT
3097036 TTCTC TTCTC TTCTC TTCTC TTCTC TT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TT
3097063 GTCATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TTCTC
Found at i:3101613 original size:13 final size:13
Alignment explanation
Indices: 3101597--3101630 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3101587 CAATGCGCGT
3101597 CATAAATGAGCAC
1 CATAAATGAGCAC
**
3101610 CATAAATGAGCGT
1 CATAAATGAGCAC
3101623 CATAAATG
1 CATAAATG
3101631 TATGTCGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (13 bp):
CATAAATGAGCAC
Found at i:3101614 original size:85 final size:85
Alignment explanation
Indices: 3101451--3101616 Score: 192
Period size: 85 Copynumber: 2.0 Consensus size: 85
3101441 ATACAATCAC
* * * * *
3101451 GACACACGAATGTGTGTCATCTTTTTTAAGGACGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTATTTAAGGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
***
3101516 AATACGTGTCATAAATTTAT
66 AATACGCACCATAAATTTAT
* * **
3101536 GACACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACGCGCAATGCGCGTCAT
1 GACACACAAATGTGTGTCATCTT-ATTTAAGGACGGGGGCTTCAATGACACGCAATGCAAGTCAT
3101600 AAATGA-GCACCATAAAT
65 AAAT-ACGCACCATAAAT
3101617 GAGCGTCATA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 63 0.94
86 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAAGGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
AATACGCACCATAAATTTAT
Found at i:3105012 original size:21 final size:21
Alignment explanation
Indices: 3104986--3105037 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3104976 TTTGATGATC
*
3104986 AGTATCGATACTGATTTGAAG
1 AGTATCGATACTGATGTGAAG
* *
3105007 AGTATCGATAATGATGTGGAG
1 AGTATCGATACTGATGTGAAG
3105028 -GTATCGATAC
1 AGTATCGATAC
3105038 CAAGAGGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTGATGTGAAG
Found at i:3105742 original size:23 final size:23
Alignment explanation
Indices: 3105712--3105786 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
3105702 TCGAGGGTTT
3105712 TATGTGGTCCTTTAGGACAAACA
1 TATGTGGTCCTTTAGGACAAACA
* * *
3105735 TATGTGGTCCTTTGGGGCAAACC
1 TATGTGGTCCTTTAGGACAAACA
**
3105758 TATGTGGTTATTTAGGAC-AA-A
1 TATGTGGTCCTTTAGGACAAACA
3105779 TATGTGGT
1 TATGTGGT
3105787 ACTTCGGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 8 0.18
22 2 0.05
23 34 0.77
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (23 bp):
TATGTGGTCCTTTAGGACAAACA
Found at i:3105799 original size:44 final size:46
Alignment explanation
Indices: 3105712--3105799 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 46
3105702 TCGAGGGTTT
* * *
3105712 TATGTGGTCCTTTAGGACAAACATATGTGGTCCTTTGGGGCAAACC
1 TATGTGGTCATTTAGGACAAACATATGTGGTACTTCGGGGCAAACC
* *
3105758 TATGTGGTTATTTAGGAC-AA-ATATGTGGTACTTCGGTGCAAA
1 TATGTGGTCATTTAGGACAAACATATGTGGTACTTCGGGGCAAA
3105800 TTATGTGAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 19 0.51
45 2 0.05
46 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (46 bp):
TATGTGGTCATTTAGGACAAACATATGTGGTACTTCGGGGCAAACC
Found at i:3112353 original size:2 final size:2
Alignment explanation
Indices: 3112296--3112338 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3112286 TCAATTAAAT
3112296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
3112338 T
1 T
3112339 CAAATATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3128799 original size:41 final size:41
Alignment explanation
Indices: 3128754--3128838 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
3128744 ATAGTTCATT
*
3128754 ATTC-GATCAAATTCAAGAATAATAACATACAATAATTCACC
1 ATTCGGATC-AATTCAACAATAATAACATACAATAATTCACC
* * * *
3128795 ATTCGGTTCAATTCAACCATGATAGCATACAATAATTCACC
1 ATTCGGATCAATTCAACAATAATAACATACAATAATTCACC
3128836 ATT
1 ATT
3128839 TAACTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 35 0.92
42 3 0.08
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (41 bp):
ATTCGGATCAATTCAACAATAATAACATACAATAATTCACC
Found at i:3128895 original size:40 final size:41
Alignment explanation
Indices: 3128783--3128906 Score: 135
Period size: 41 Copynumber: 3.0 Consensus size: 41
3128773 TAATAACATA
** * * *
3128783 CAATAATTCACCATTC-GGTTCAATTCAACCATGATAGCATA
1 CAATAATTCACCATTCAACTT-GATTCAATCATGATAGCATG
* *
3128824 CAATAATTCACCATTTAACTTGATTCGATCATGATAGCATG
1 CAATAATTCACCATTCAACTTGATTCAATCATGATAGCATG
* * *
3128865 GAATAATTCACCA-TCAACTTGGTTCAATCATGGTAGCATG
1 CAATAATTCACCATTCAACTTGATTCAATCATGATAGCATG
3128905 CA
1 CA
3128907 TTAAATTACA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 24 0.35
41 43 0.62
42 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (41 bp):
CAATAATTCACCATTCAACTTGATTCAATCATGATAGCATG
Found at i:3135845 original size:45 final size:43
Alignment explanation
Indices: 3135796--3135956 Score: 116
Period size: 44 Copynumber: 3.7 Consensus size: 43
3135786 TGCTTGTTTT
* * *
3135796 CATCACATAAGAAGTTGGAGC-AGCATTAACCTTTTTGCTAGATTC
1 CATCACATAAGAAGTTGGA-CAAGCATCAA--TATTCGCTAGATTC
* * *
3135841 CATCACTTAAGGAGTTGGACAAGCATCAATATTCGCTCGATTC
1 CATCACATAAGAAGTTGGACAAGCATCAATATTCGCTAGATTC
* * *
3135884 CATCACATAA-AGAGTTAGATCAA-CATCAA-ACTTTCACTTGATTC
1 CATCACATAAGA-AGTTGGA-CAAGCATCAATA--TTCGCTAGATTC
* *
3135928 CATCAAATAATAAGTTGGATCAA-CATCAA
1 CATCACATAAGAAGTTGGA-CAAGCATCAA
3135957 CATATCGTGC
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 32 0.33
44 39 0.40
45 25 0.26
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (43 bp):
CATCACATAAGAAGTTGGACAAGCATCAATATTCGCTAGATTC
Found at i:3135899 original size:43 final size:43
Alignment explanation
Indices: 3135836--3135956 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
3135826 CTTTTTGCTA
* * *
3135836 GATTCCATCACTTAAGGAGTTGGA-CAAGCATCAATA-TTCGCTC
1 GATTCCATCACATAAAGAGTTGGATCAA-CATCAA-ACTTCACTC
* *
3135879 GATTCCATCACATAAAGAGTTAGATCAACATCAAACTTTCACTT
1 GATTCCATCACATAAAGAGTTGGATCAACATCAAAC-TTCACTC
*
3135923 GATTCCATCAAATAATA-AGTTGGATCAACATCAA
1 GATTCCATCACATAA-AGAGTTGGATCAACATCAA
3135957 CATATCGTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
42 1 0.01
43 27 0.40
44 38 0.57
45 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (43 bp):
GATTCCATCACATAAAGAGTTGGATCAACATCAAACTTCACTC
Found at i:3145770 original size:14 final size:13
Alignment explanation
Indices: 3145737--3145777 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3145727 TATAGGCGTG
* *
3145737 AATGGTGATAGAG
1 AATGGTGATGGAA
3145750 AATGGTGATGGAA
1 AATGGTGATGGAA
3145763 AGATGGTGATGGAA
1 A-ATGGTGATGGAA
3145777 A
1 A
3145778 TGTAGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:3149707 original size:28 final size:27
Alignment explanation
Indices: 3149676--3149730 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3149666 TTTGAGGGTA
3149676 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTCTTTTT
* *
3149704 CTTTGAATTTTTCTTCTTTTTCTTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTTT
3149731 TTCTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (27 bp):
CTTTGAATCTTTCTTCCTTTTCTTTTT
Done.