Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008439.1 Hibiscus syriacus cultivar Beakdansim tig00111238_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: 2703160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:2521135 original size:60 final size:58
Alignment explanation
Indices: 2521020--2521164 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 58
2521010 ATCCTTAAGC
* *
2521020 TTTTGAATATTTCAATTTCAT-CACAAACTATGATTCATTATAAATTAATCCTCAAAA
1 TTTTGAATATTCCAATTTCATCCACAAACTAGGATTCATTATAAATTAATCCTCAAAA
* * * * *
2521077 TTTTGAAAATTCCAATTTCATCCATAAACTAGGACTCTTATTATAAATTAATCTTCAAAC
1 TTTTGAATATTCCAATTTCATCCACAAACTAGGA-T-TCATTATAAATTAATCCTCAAAA
* * *
2521137 TTTTTAATCTTCCAATTTCATCCCCAAA
1 TTTTGAATATTCCAATTTCATCCACAAA
2521165 TTCATCCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 19 0.26
58 10 0.14
59 1 0.01
60 43 0.59
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.40
Consensus pattern (58 bp):
TTTTGAATATTCCAATTTCATCCACAAACTAGGATTCATTATAAATTAATCCTCAAAA
Found at i:2521409 original size:60 final size:60
Alignment explanation
Indices: 2521316--2521434 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
2521306 TGAAACGTTC
* * * *
2521316 AAAAGTTTAAGGACTAATTTAGAATAAGTGTCATAGTTT-GGGTATGTAATTGGAATATTT
1 AAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTTAGGG-ATGAAATTGGAATATTT
* * * *
2521376 AAAAGTTTGAGGATTAATTCAAAATGAGGGTCATAGTTTATGGATGAAATTGGAATATT
1 AAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTTAGGGATGAAATTGGAATATT
2521435 CAAATATTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
60 48 0.96
61 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTTAGGGATGAAATTGGAATATTT
Found at i:2521460 original size:60 final size:60
Alignment explanation
Indices: 2521313--2521475 Score: 147
Period size: 60 Copynumber: 2.7 Consensus size: 60
2521303 AATTGAAACG
* * * * * *
2521313 TTCAAAAGTTTAAGGA-CTAATTTAGAATAAGTGTCATAGTTTGGGTATGTAATTGGAATA
1 TTCAAAAGTTTGAGGATC-AATTCAAAATGAGAGTCATAGTTTGGGTATGAAATTGGAATA
* * * *
2521373 TTTAAAAGTTTGAGGATTAATTCAAAATGAGGGTCATAGTTTATGG-ATGAAATTGGAATA
1 TTCAAAAGTTTGAGGATCAATTCAAAATGAGAGTCATAGTTT-GGGTATGAAATTGGAATA
*
2521433 TTCAAATA-TTT-AGGTATCAATAT-AAAATGAGATTCATAGTTTG
1 TTCAAA-AGTTTGAGG-ATCAAT-TCAAAATGAGAGTCATAGTTTG
2521476 AGGATATGTG
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
59 3 0.04
60 77 0.92
61 4 0.05
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (60 bp):
TTCAAAAGTTTGAGGATCAATTCAAAATGAGAGTCATAGTTTGGGTATGAAATTGGAATA
Found at i:2531815 original size:2 final size:2
Alignment explanation
Indices: 2531808--2531838 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2531798 TACCACACCA
2531808 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2531839 TCTGCTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2538339 original size:40 final size:41
Alignment explanation
Indices: 2538292--2538387 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
2538282 ACAGGTTCCA
2538292 AAATCGCAACGCGAA-AGTCAAATTCGCAACGATAA-A-GTC
1 AAATCGCAACGCGAATAGTCAAA-TCGCAACGATAATATGTC
*
2538331 AAATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT-
1 AAA-TCGCAACGCGAATAGTCAAATCGCAACGATAATATGTC
2538372 AAATCGCAACGCGAAT
1 AAATCGCAACGCGAAT
2538388 TTCGTTTTCG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
39 3 0.06
40 37 0.71
41 10 0.19
42 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGCGAATAGTCAAATCGCAACGATAATATGTC
Found at i:2538368 original size:20 final size:19
Alignment explanation
Indices: 2538292--2538382 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 19
2538282 ACAGGTTCCA
*
2538292 AAATCGCAACGCGAAAGTC
1 AAATCGCAACGAGAAAGTC
*
2538311 AAATTCGCAACGATAAAGTC
1 AAA-TCGCAACGAGAAAGTC
* *
2538331 AAATTCGCAACGCGAATAGTT
1 AAA-TCGCAACGAGAA-AGTC
*
2538352 AAATCGCAACGATAATATGT-
1 AAATCGCAACGAGAA-A-GTC
2538372 AAATCGCAACG
1 AAATCGCAACG
2538383 CGAATTTCGT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.05
20 51 0.82
21 8 0.13
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (19 bp):
AAATCGCAACGAGAAAGTC
Found at i:2538603 original size:20 final size:20
Alignment explanation
Indices: 2538580--2538652 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
2538570 AAAGTCAAAT
2538580 TCGCAACGCGAATAGTTAAA
1 TCGCAACGCGAATAGTTAAA
** *
2538600 TCGCAACGATAATA-TGTAAT
1 TCGCAACGCGAATAGT-TAAA
* * *
2538620 TCTCAATGCGAATAGGTAAA
1 TCGCAACGCGAATAGTTAAA
*
2538640 TCGCAACGTGAAT
1 TCGCAACGCGAAT
2538653 TCTCCAAATT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATAGTTAAA
Found at i:2538870 original size:22 final size:21
Alignment explanation
Indices: 2538836--2538934 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 21
2538826 TTAGCGTTGC
*
2538836 GAAATTCGAGTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
*
2538857 GAGAATTCGCGTTGCAAATTT-
1 GA-AATTCGCGTTGCGAATTTG
** * *
2538878 GACTTTCGCATTGCGATTTTG
1 GAAATTCGCGTTGCGAATTTG
* *
2538899 GAACA-T-GTGTTGCGAAATTG
1 GAA-ATTCGCGTTGCGAATTTG
*
2538919 G-AGTTCGCGTTGCGAA
1 GAAATTCGCGTTGCGAA
2538935 CTTGTTGGTC
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.03
20 33 0.57
21 7 0.12
22 16 0.28
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.33
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:2543261 original size:23 final size:23
Alignment explanation
Indices: 2543235--2543282 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2543225 TATTTGTTTG
2543235 TTAAGAT-CATTTAATAAATTTAA
1 TTAAGATCCATTTAA-AAATTTAA
*
2543258 TTAATATCCATTTAAAAATTTAA
1 TTAAGATCCATTTAAAAATTTAA
2543281 TT
1 TT
2543283 GAATCGACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAAGATCCATTTAAAAATTTAA
Found at i:2546055 original size:15 final size:15
Alignment explanation
Indices: 2546035--2546134 Score: 55
Period size: 15 Copynumber: 6.9 Consensus size: 15
2546025 GAGCGGTGAA
2546035 GAGGATGATGAAGAT
1 GAGGATGATGAAGAT
*
2546050 GAGGATGATG-ACA-
1 GAGGATGATGAAGAT
*
2546063 G-GGATGA-CAATGAT
1 GAGGATGATGAA-GAT
* * * *
2546077 GATGATGACGAGGAG
1 GAGGATGATGAAGAT
* * *
2546092 GAGGATGAAGTAGAG
1 GAGGATGATGAAGAT
* * *
2546107 GAGAACGAAGAAGAT
1 GAGGATGATGAAGAT
2546122 GAGGATGATGAAG
1 GAGGATGATGAAG
2546135 TTCCTCAGCC
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
12 7 0.11
13 2 0.03
14 3 0.05
15 49 0.79
16 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.41, T:0.15
Consensus pattern (15 bp):
GAGGATGATGAAGAT
Found at i:2554955 original size:37 final size:36
Alignment explanation
Indices: 2554914--2554987 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
2554904 TTTAAAAAAT
*
2554914 ATTTATA-AATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAAATTAAAAT-ATAAA
*
2554951 ATTTATATAATTTTTTTACAAAAATTAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAAATTAAAATATAAA
2554987 A
1 A
2554988 ATGTTTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 22 0.65
38 6 0.18
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAAATTAAAATATAAA
Found at i:2565407 original size:16 final size:17
Alignment explanation
Indices: 2565370--2565413 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
2565360 GTTTATGAGA
2565370 GAATTGAAATCTGTGAAG
1 GAATTGAAATCTGT-AAG
2565388 GAATTGAAATCTGT-AG
1 GAATTGAAATCTGTAAG
2565404 GAATTGAAAT
1 GAATTGAAAT
2565414 TCAATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (17 bp):
GAATTGAAATCTGTAAG
Found at i:2566036 original size:37 final size:37
Alignment explanation
Indices: 2565984--2566076 Score: 141
Period size: 37 Copynumber: 2.5 Consensus size: 37
2565974 TTTTCACCCT
*
2565984 AAACCCGAACCCGACCTGACACGAATATCACACTTAAA
1 AAACCCG-ACCCGACCCGACACGAATATCACACTTAAA
* **
2566022 AAACCCGACCCGACCCGACCCGAATATCATGCTTAAA
1 AAACCCGACCCGACCCGACACGAATATCACACTTAAA
2566059 AAACCCGACCCGACCCGA
1 AAACCCGACCCGACCCGA
2566077 ACAAAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 44 0.86
38 7 0.14
ACGTcount: A:0.38, C:0.39, G:0.13, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACACGAATATCACACTTAAA
Found at i:2566539 original size:32 final size:33
Alignment explanation
Indices: 2566462--2566540 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 33
2566452 TTTTCACCCT
*
2566462 AAACCCGATCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
* *
2566495 AAACCCCAACCCGACCTGAATATCACACTT-AAA
1 AAA-CCCGACCCGACCCGAATATCACACTTAAAA
2566528 AAACCCGACCCGA
1 AAACCCGACCCGA
2566541 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
32 9 0.22
33 9 0.22
34 23 0.56
ACGTcount: A:0.42, C:0.37, G:0.09, T:0.13
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:2566682 original size:239 final size:244
Alignment explanation
Indices: 2566245--2566743 Score: 765
Period size: 239 Copynumber: 2.0 Consensus size: 244
2566235 TTTTCACCCT
*
2566245 AAACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAAGTT
1 AAACCCCAACCCGACCCGAATATCACACTT-AAAAAA--C-ACCCGACCCGAACAAAATAAAGTT
* *
2566310 TCATCCGATCTGACCCGAATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAA
62 TCATCCGACCCGACCCGAATATATGAATTAGAAAT----CCCGACCCGACCCGAAATAATAAAAA
2566375 AATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGG
123 AATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGG
*
2566440 TCGGTCAGATTTTTTTCACCCT-A-AACCCGATCCGACCCGAATATCACACTTAAAA
188 TCGGTCAGATTTTTTTCACCCTAACAACCCGACCCGACCCGAATATCACACTTAAAA
*
2566495 AAACCCCAACCCGACCTGAATATCACACTT-AAAAA-ACCCGACCCGAACAAAATAAAGTTTCAT
1 AAACCCCAACCCGACCCGAATATCACACTTAAAAAACACCCGACCCGAACAAAATAAAGTTTCAT
2566558 CCGACCCGACCCGAATATATGAATTAGAAAT-CCGACCCGACCCGAAATAATAAAAAAATATTTT
66 CCGACCCGACCCGAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAATATTTT
* * * *
2566622 TATTTAATAAAAACAGTGACTTAATCCGACTCGACCTGAATTATATATATTTTCGGGTCGGTCCG
131 TATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCAG
*
2566687 GTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
196 ATTTTTTTCACCCT-AA--C-AACCCGACCCGACCCGAATATCACACTTAAAA
2566740 AAAC
1 AAAC
2566744 TGATCTGACC
Statistics
Matches: 233, Mismatches: 10, Indels: 17
0.90 0.04 0.07
Matches are distributed among these distances:
239 107 0.46
241 1 0.00
244 57 0.24
245 35 0.15
248 5 0.02
250 28 0.12
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (244 bp):
AAACCCCAACCCGACCCGAATATCACACTTAAAAAACACCCGACCCGAACAAAATAAAGTTTCAT
CCGACCCGACCCGAATATATGAATTAGAAATCCCGACCCGACCCGAAATAATAAAAAAATATTTT
TATTTAATAAAAACAATGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCAG
ATTTTTTTCACCCTAACAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:2567915 original size:21 final size:21
Alignment explanation
Indices: 2567891--2567935 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2567881 TTGCCTCCCA
2567891 TTGTTCCTAAACTCCCTCCAG
1 TTGTTCCTAAACTCCCTCCAG
*
2567912 TTGTTCCTAAACTCCCTCCGG
1 TTGTTCCTAAACTCCCTCCAG
2567933 TTG
1 TTG
2567936 AGCTCCCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.36, G:0.13, T:0.36
Consensus pattern (21 bp):
TTGTTCCTAAACTCCCTCCAG
Found at i:2571277 original size:60 final size:60
Alignment explanation
Indices: 2571211--2571361 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 60
2571201 ACATATGAAA
* *
2571211 AGTCGGGTGACTATTTTGTAATTTTTAATAGTCTATGGACTCAACAAAACAACACCATAT
1 AGTCGGGTGACTATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAACAACACCATAT
* *
2571271 AGTCGGGTGA-TCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAACACCTTAT
1 AGTCGGGTGACT-ATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAACAACACCATAT
* * * *
2571331 AAT-AGG-GACTATTGTGTAACTTGTAATAGTC
1 AGTCGGGTGACTATTTTGTAACTTTTAATAGTC
2571362 GGAGATTCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
58 21 0.26
59 4 0.05
60 56 0.69
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (60 bp):
AGTCGGGTGACTATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAACAACACCATAT
Found at i:2574437 original size:22 final size:22
Alignment explanation
Indices: 2574409--2574451 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2574399 TTTTTGGTTA
* *
2574409 ATTATAAGATAATATCTGTTTG
1 ATTATAAAATAATATATGTTTG
*
2574431 ATTATAAAATGATATATGTTT
1 ATTATAAAATAATATATGTTT
2574452 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (22 bp):
ATTATAAAATAATATATGTTTG
Found at i:2576276 original size:15 final size:15
Alignment explanation
Indices: 2576256--2576434 Score: 214
Period size: 15 Copynumber: 11.5 Consensus size: 15
2576246 TAATAAGGTT
2576256 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2576271 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2576286 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2576301 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
2576316 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
2576331 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
2576346 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
2576361 ATTTATTTTAGAATA
1 ATTTATTTTAAAATA
* *
2576376 AATTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
2576395 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
* *
2576413 ATTTATTTTTAATTA
1 ATTTATTTTAAAATA
2576428 ATTTATT
1 ATTTATT
2576435 AATATGGATT
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
15 124 0.87
16 3 0.02
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 4 0.03
22 6 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:2576403 original size:22 final size:22
Alignment explanation
Indices: 2576378--2576479 Score: 96
Period size: 22 Copynumber: 4.5 Consensus size: 22
2576368 TTAGAATAAA
*
2576378 TTATTATAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
** * *
2576400 TTATTTTAAAATAATTTATTTTTAA
1 TTATTTTAAAAT-A--TAGATTGAT
* * *
2576425 TTAATTTATTAATATGGATTGAT
1 TTATTTTA-AAATATAGATTGAT
2576448 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
2576470 TTATTTTAAA
1 TTATTTTAAA
2576480 TAATTTATTA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
22 33 0.54
23 12 0.20
25 13 0.21
26 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
TTATTTTAAAATATAGATTGAT
Found at i:2576434 original size:52 final size:51
Alignment explanation
Indices: 2576256--2576612 Score: 222
Period size: 52 Copynumber: 7.1 Consensus size: 51
2576246 TAATAAGGTT
* * *
2576256 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAA-AT--A---
1 ATTTATTTTAAAATAATTTATTTTTAAATAATTTATTTAAAATATAGATTG
* *
2576301 ATTTATTATAAAATAATTTATTTTAAAATAATTTA-TTATAAA-AT--A---
1 ATTTATTTTAAAATAATTTATTTTTAAATAATTTATTTA-AAATATAGATTG
* *
2576346 ATTTATTATAAAATAATTTA-TTTTAGAATAAATTATTATAAAATATAGATTG
1 ATTTATTTTAAAATAATTTATTTTTA-AATAATTTATT-TAAAATATAGATTG
* *
2576398 ATTTATTTTAAAATAATTTATTTTTAATTAATTTA-TT--AATATGGATTG
1 ATTTATTTTAAAATAATTTATTTTTAAATAATTTATTTAAAATATAGATTG
* *
2576446 ATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TT--AGTATAGATTG
1 ATTTATTTT-AAA-ATA-ATT--TAT-TTTTAAATAATTTATTTAAAATATAGATTG
** * *
2576500 ATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT--ATTG
1 ATTTATTTTAAAATAATTTATT--T-TTAAATAATTTA-TTTAAAATATAGATTG
* * * *
2576552 ATTTATTTT-AAATAATTTATTTGTATGGACTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTT-T-T-AAATAATTTA-TTTAAAATATAGATTG
2576606 ATTTATT
1 ATTTATT
2576613 ATTGTAGTTG
Statistics
Matches: 262, Mismatches: 22, Indels: 47
0.79 0.07 0.14
Matches are distributed among these distances:
44 6 0.02
45 67 0.26
46 4 0.02
47 5 0.02
48 21 0.08
49 5 0.02
50 17 0.06
51 7 0.03
52 75 0.29
53 7 0.03
54 48 0.18
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.52
Consensus pattern (51 bp):
ATTTATTTTAAAATAATTTATTTTTAAATAATTTATTTAAAATATAGATTG
Found at i:2576487 original size:14 final size:14
Alignment explanation
Indices: 2576468--2576520 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2576458 ATATAGATTG
2576468 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2576482 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
2576500 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2576514 ATTTATT
1 ATTTATT
2576521 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2576497 original size:32 final size:32
Alignment explanation
Indices: 2576459--2576685 Score: 173
Period size: 32 Copynumber: 7.0 Consensus size: 32
2576449 TATTTTAAAA
2576459 TATAGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
2576491 TATAGATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
* * *
2576523 TATGGATTGATTTATTTTAAAATATATTGATTTAT
1 TATAGATTGATTTATTTT-AAATA-ATTTA-TTAG
* * * * * *
2576558 TTTA-AATAATTTATTTGTATGGACTGATTTATT-T
1 TATAGATTGATTTATTT-TA---AATAATTTATTAG
* * *
2576592 TA-AAATATGGATTGA-TTT--ATTATTGTAGTT-G
1 TATAGAT-T-GATTTATTTTAAATAATT-TA-TTAG
*
2576623 TATAAATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
2576655 TAT-GAATTGATTTATTTTAAATAATTTATTA
1 TATAG-ATTGATTTATTTTAAATAATTTATTA
2576686 TTGTAGTTAT
Statistics
Matches: 157, Mismatches: 20, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
29 4 0.03
30 7 0.04
31 10 0.06
32 85 0.54
33 11 0.07
34 19 0.12
35 11 0.07
36 8 0.05
37 2 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TATAGATTGATTTATTTTAAATAATTTATTAG
Found at i:2576505 original size:18 final size:18
Alignment explanation
Indices: 2576482--2576538 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
2576472 ATTTTAAATA
2576482 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
2576500 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
*
2576514 ATTTATTAGTATGGATTG
1 ATTTATTAGTATAGATTG
2576532 ATTTATT
1 ATTTATT
2576539 TTAAAATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:2576651 original size:14 final size:14
Alignment explanation
Indices: 2576632--2576684 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
2576622 GTATAAATTG
2576632 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
2576646 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
2576664 ATTTATTTTAAATA
1 ATTTATTTTAAATA
2576678 ATTTATT
1 ATTTATT
2576685 ATTGTAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:2579792 original size:6 final size:6
Alignment explanation
Indices: 2579781--2579807 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2579771 TATAATCAAG
2579781 TTCCAA TTCCAA TTCCAA TTCCAA TTC
1 TTCCAA TTCCAA TTCCAA TTCCAA TTC
2579808 TAGCCCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCCAA
Found at i:2581584 original size:17 final size:18
Alignment explanation
Indices: 2581545--2581595 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
2581535 CAACCCCTCC
2581545 ATAAGTATCACCTCTAAT
1 ATAAGTATCACCTCTAAT
*
2581563 GTAAGTATCACC-CTAAT
1 ATAAGTATCACCTCTAAT
*
2581580 ATAAGTGTCACCTCTA
1 ATAAGTATCACCTCTA
2581596 GGACTTTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (18 bp):
ATAAGTATCACCTCTAAT
Found at i:2582160 original size:21 final size:21
Alignment explanation
Indices: 2582135--2582185 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
2582125 ATCTCATTCT
2582135 AAATTATAATAAATGTGACAA
1 AAATTATAATAAATGTGACAA
2582156 AAATTTATAATAAATGTGACAA
1 AAA-TTATAATAAATGTGACAA
*
2582178 AAAATATA
1 AAATTATA
2582186 TTTTACATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (21 bp):
AAATTATAATAAATGTGACAA
Found at i:2582163 original size:22 final size:22
Alignment explanation
Indices: 2582138--2582180 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2582128 TCATTCTAAA
2582138 TTATAATAAATGTGACAAAAAT
1 TTATAATAAATGTGACAAAAAT
2582160 TTATAATAAATGTGACAAAAA
1 TTATAATAAATGTGACAAAAA
2582181 ATATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
TTATAATAAATGTGACAAAAAT
Found at i:2590565 original size:34 final size:34
Alignment explanation
Indices: 2590522--2590589 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2590512 ATAAATTTCA
2590522 TTTCCCCATTATCTAATCATATGCAATCCTCTTG
1 TTTCCCCATTATCTAATCATATGCAATCCTCTTG
2590556 TTTCCCCATTATCTAATCATATGCAATCCTCTTG
1 TTTCCCCATTATCTAATCATATGCAATCCTCTTG
2590590 GCAGCAGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (34 bp):
TTTCCCCATTATCTAATCATATGCAATCCTCTTG
Found at i:2599558 original size:60 final size:60
Alignment explanation
Indices: 2599494--2599618 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 60
2599484 TTCAAAAGGA
* *
2599494 AAAATATAAAAACATGTTAAATACATAAATTTCAA-TTCTT-AAGTCACATGTAAACTTCTC
1 AAAATATAAAAACATGTTAAACACAT-AATTTCAAGCTCTTCAA-TCACATGTAAACTTCTC
* * *
2599554 AAAATATAAAAACATGTTACACACATAATTTTAAGCTCTTCAATCTCATGTAAACTTCTC
1 AAAATATAAAAACATGTTAAACACATAATTTCAAGCTCTTCAATCACATGTAAACTTCTC
2599614 AAAAT
1 AAAAT
2599619 GATCCTTACA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
59 7 0.12
60 49 0.84
61 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.33
Consensus pattern (60 bp):
AAAATATAAAAACATGTTAAACACATAATTTCAAGCTCTTCAATCACATGTAAACTTCTC
Found at i:2599709 original size:2 final size:2
Alignment explanation
Indices: 2599704--2599734 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2599694 TAAAAAAACA
2599704 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2599735 TATTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2601643 original size:2 final size:2
Alignment explanation
Indices: 2601636--2601664 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2601626 TCCTTCTCCG
2601636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2601665 CATACAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2607482 original size:29 final size:29
Alignment explanation
Indices: 2607440--2607498 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2607430 ATTTTCACCT
2607440 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2607469 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2607498 A
1 A
2607499 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2622160 original size:23 final size:22
Alignment explanation
Indices: 2622134--2622205 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
2622124 GGGGAAACGA
2622134 GTTTATGAAAGAAGAAGGAATG
1 GTTTATGAAAGAAGAAGGAATG
* *
2622156 CGTTTATGGAAGAAGAAGAAATG
1 -GTTTATGAAAGAAGAAGGAATG
2622179 TGTTTAT-AGAAGAAGAA-GAATG
1 -GTTTATGA-AAGAAGAAGGAATG
2622201 GTTTA
1 GTTTA
2622206 GATTCATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 5 0.12
22 4 0.09
23 34 0.79
ACGTcount: A:0.43, C:0.01, G:0.29, T:0.26
Consensus pattern (22 bp):
GTTTATGAAAGAAGAAGGAATG
Found at i:2622170 original size:46 final size:44
Alignment explanation
Indices: 2622118--2622205 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 44
2622108 CAAACAAATT
**
2622118 GAAGAAGGGGAAACGAGTTTAT-GAAAGAAGAAGGAATGCGTTTATG
1 GAAGAAGAAGAAACGAGTTTATAG-AAGAAGAA-GAATG-GTTTATG
* *
2622164 GAAGAAGAAGAAATGTGTTTATAGAAGAAGAAGAATGGTTTA
1 GAAGAAGAAGAAACGAGTTTATAGAAGAAGAAGAATGGTTTA
2622206 GATTCATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 5 0.14
45 5 0.14
46 26 0.70
47 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.22
Consensus pattern (44 bp):
GAAGAAGAAGAAACGAGTTTATAGAAGAAGAAGAATGGTTTATG
Found at i:2631305 original size:60 final size:60
Alignment explanation
Indices: 2631198--2631346 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 60
2631188 AGACCGAGAC
* * * *
2631198 CAATTTAAGAAT-AGAGTCATAGTTTAGGGATGGAATTAGAATGTTCAAACGTTTAAGGA-
1 CAATTTAA-AATGTGAGTCATAGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAT
* * * *
2631257 CTAATTTAGAATGTGAGTCATTGTTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGAT
1 C-AATTTAAAATGTGAGTCATAGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAT
* * *
2631318 CAATTTAAAATGAGGGTTATAGTTTAGGG
1 CAATTTAAAATGTGAGTCATAGTTTAGGG
2631347 GTAATATGCA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
59 4 0.05
60 68 0.93
61 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (60 bp):
CAATTTAAAATGTGAGTCATAGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAT
Found at i:2636773 original size:5 final size:6
Alignment explanation
Indices: 2636744--2636772 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2636734 TACTAAGTTG
2636744 ATTTAA ATTTAA ATTTAA ATTT-A ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
2636773 TCATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:2636780 original size:13 final size:11
Alignment explanation
Indices: 2636744--2636782 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
2636734 TACTAAGTTG
2636744 ATTTAAATTTAA
1 ATTTAAATTT-A
2636756 ATTTAAATTTA
1 ATTTAAATTTA
2636767 ATTTAATCATTTA
1 ATTTAA--ATTTA
2636780 ATT
1 ATT
2636783 AGATGATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 7 0.28
12 10 0.40
13 8 0.32
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:2637347 original size:2 final size:2
Alignment explanation
Indices: 2637340--2637367 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2637330 AATAAATTAC
2637340 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
2637368 TCATGATTCA
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:2637671 original size:20 final size:20
Alignment explanation
Indices: 2637642--2637679 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2637632 TTTTAAATAT
* *
2637642 AATTTTAAAAATATATTTAA
1 AATTTAAAAAATAAATTTAA
2637662 AATTTAAAAAATAAATTT
1 AATTTAAAAAATAAATTT
2637680 TGAAAATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTAAAAAATAAATTTAA
Found at i:2643534 original size:29 final size:29
Alignment explanation
Indices: 2643492--2643550 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2643482 ATTTTCACCT
*
2643492 AACTAAATTAATGTAAGCAATGACGTCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
*
2643521 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
2643550 A
1 A
2643551 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:2648534 original size:400 final size:399
Alignment explanation
Indices: 2647795--2648595 Score: 1557
Period size: 400 Copynumber: 2.0 Consensus size: 399
2647785 CCCTGACAAT
2647795 AATCTTAAGAAATCTTTTCTGATGTGGAAGATCAGTTAACAACTGCAGCCACAGAGCATACTCGG
1 AATCTTAAGAAATCTTTTCTGATGTGGAAGATCAGTTAACAACTGCAGCCACAGAGCATACTCGG
*
2647860 AATTTCAAGAGACCTTAAAAACGTGGCTTGAATACCAATTGTTGAATCAAAATAGAGTAAAAACT
66 AATTTCAAGAGACCTTAAAAACGTGGCTCGAATACCAATTGTTGAATCAAAATAGAGTAAAAACT
2647925 CTAATTGATCGAGAAGAAAAAAAACTCTCTTTAGAATAATCTCACAAAATTGCAAAAGGGGAGAA
131 CTAATTGATCGAGAAGAAAAAAAACTCTCTTTAGAATAATCTCACAAAATTGCAAAAGGGGAGAA
2647990 CTCTTAAGAAAGCTTTCAAATACTTATAATTAAGCTTTGATTGTTGGATGATAAAACTCAAATAC
196 CTCTTAAGAAAGCTTTCAAATACTTATAATTAAGCTTTGATTGTTGGATGATAAAACTCAAATAC
2648055 AAGTAAGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAAGCACTAAATAAT
261 AAGTAAGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAAGCACTAAATAAT
*
2648120 ATAAACCATTGAAATTAAAACATGAGAAAAATACTTAATTTTCACCTAACTAAATTGATGTAAAC
326 ATAAACCATTGAAATTAAAACATAAGAAAAATACTTAATTTTCACCTAACTAAATTGATGTAAAC
2648185 AATGACATC
391 AATGACATC
2648194 AATCTTAAGAAATCTTTTCTGATGTGGAAGATCAGTTAACAACTGCAGCCACAGAGCATACTCGG
1 AATCTTAAGAAATCTTTTCTGATGTGGAAGATCAGTTAACAACTGCAGCCACAGAGCATACTCGG
*
2648259 AATTTCAAGAGACTTTAAAAACGTGGCTCGAATACCAATTGTTGAATCAAAATAGAGTAAAAACT
66 AATTTCAAGAGACCTTAAAAACGTGGCTCGAATACCAATTGTTGAATCAAAATAGAGTAAAAACT
2648324 CTAATTGATCGAGAAGAAAAAAAAACTCTCTTTAGAATAATCTCACAAAATTGCAAAAGGGGAGA
131 CTAATTGATCGAGAAG-AAAAAAAACTCTCTTTAGAATAATCTCACAAAATTGCAAAAGGGGAGA
2648389 ACTCTTAAGAAAGCTTTCAAATACTTATAATTAAGCTTTGATTGTTGGATGATAAAACTCAAATA
195 ACTCTTAAGAAAGCTTTCAAATACTTATAATTAAGCTTTGATTGTTGGATGATAAAACTCAAATA
2648454 CAAGTAAGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAAGCACTAAATAA
260 CAAGTAAGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAAGCACTAAATAA
*
2648519 TCTAAACCATTGAAATTAAAACATAAGAAAAATACTTAATTTTCACCTAACTAAATTGATGTAAA
325 TATAAACCATTGAAATTAAAACATAAGAAAAATACTTAATTTTCACCTAACTAAATTGATGTAAA
2648584 CAATGACATC
390 CAATGACATC
2648594 AA
1 AA
2648596 AACTAAATTG
Statistics
Matches: 397, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
399 144 0.36
400 253 0.64
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (399 bp):
AATCTTAAGAAATCTTTTCTGATGTGGAAGATCAGTTAACAACTGCAGCCACAGAGCATACTCGG
AATTTCAAGAGACCTTAAAAACGTGGCTCGAATACCAATTGTTGAATCAAAATAGAGTAAAAACT
CTAATTGATCGAGAAGAAAAAAAACTCTCTTTAGAATAATCTCACAAAATTGCAAAAGGGGAGAA
CTCTTAAGAAAGCTTTCAAATACTTATAATTAAGCTTTGATTGTTGGATGATAAAACTCAAATAC
AAGTAAGGTATTTATAGGTTACAAGAAACAATCTAAACCACTCATTAAAATAAGCACTAAATAAT
ATAAACCATTGAAATTAAAACATAAGAAAAATACTTAATTTTCACCTAACTAAATTGATGTAAAC
AATGACATC
Found at i:2648609 original size:29 final size:29
Alignment explanation
Indices: 2648567--2648625 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2648557 ATTTTCACCT
2648567 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
*
2648596 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
2648625 A
1 A
2648626 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:2669867 original size:33 final size:33
Alignment explanation
Indices: 2669793--2669869 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
2669783 TCATAACCAA
* *
2669793 AATGAGGGCAGACTTAGCTATGTGTAGAAAGTT
1 AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
*
2669826 AATGAGGGTAGACTTTGCTATGCGTAGAAAGTT
1 AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
2669859 AATGAGGGTAG
1 AATGAGGGTAG
2669870 TACAAATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (33 bp):
AATGAGGGTAGACTTAGCTATGCGTAGAAAGTT
Found at i:2683380 original size:2 final size:2
Alignment explanation
Indices: 2683373--2683397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2683363 ATCAATTAAT
2683373 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2683398 TATGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2688168 original size:21 final size:21
Alignment explanation
Indices: 2688144--2688189 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2688134 GTATGTAACA
2688144 GTGAAGACAGTACTTTGGTAT
1 GTGAAGACAGTACTTTGGTAT
2688165 GTGAAGACAGTACTTTGGTAT
1 GTGAAGACAGTACTTTGGTAT
2688186 GTGA
1 GTGA
2688190 GAAGTCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (21 bp):
GTGAAGACAGTACTTTGGTAT
Found at i:2691524 original size:2 final size:2
Alignment explanation
Indices: 2691517--2691549 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2691507 CATGAAAAGT
2691517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2691550 TATGATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2693178 original size:33 final size:33
Alignment explanation
Indices: 2693130--2693196 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2693120 TTATTTCAAC
*
2693130 TTTAAGAATAAAATAATTTATTTGTAATATTAT
1 TTTAAGAATAAAATAATTTATTTGGAATATTAT
**
2693163 TTTAAGAATGGAATAATTTATTTGGAATATTAT
1 TTTAAGAATAAAATAATTTATTTGGAATATTAT
2693196 T
1 T
2693197 GGAATAGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (33 bp):
TTTAAGAATAAAATAATTTATTTGGAATATTAT
Found at i:2695663 original size:23 final size:23
Alignment explanation
Indices: 2695635--2695680 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2695625 TTTTGCTCGA
*
2695635 CTCGTTAAGTTCGATGCTCGTTG
1 CTCGTTAAGCTCGATGCTCGTTG
2695658 CTCGTTAAGCTCGATGCTCGTTG
1 CTCGTTAAGCTCGATGCTCGTTG
2695681 TTCGCCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (23 bp):
CTCGTTAAGCTCGATGCTCGTTG
Found at i:2695669 original size:16 final size:16
Alignment explanation
Indices: 2695650--2695739 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 16
2695640 TAAGTTCGAT
2695650 GCTCGTTGCTCGTTAA
1 GCTCGTTGCTCGTTAA
* **
2695666 GCTCGATGCTCGTTGTTC
1 GCTCGTTGCTCG-T-TAA
* *
2695684 GCCTTGTTACTCGTTAA
1 G-CTCGTTGCTCGTTAA
* **
2695701 GCTCGATGCTCGTTGCTT
1 GCTCGTTGCTCGTT--AA
2695719 GTCTCGTTGCTCGTTAA
1 G-CTCGTTGCTCGTTAA
2695736 GCTC
1 GCTC
2695740 ACTGAAATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
16 24 0.46
17 4 0.08
18 4 0.08
19 20 0.38
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (16 bp):
GCTCGTTGCTCGTTAA
Found at i:2695703 original size:35 final size:35
Alignment explanation
Indices: 2695651--2695739 Score: 126
Period size: 35 Copynumber: 2.5 Consensus size: 35
2695641 AAGTTCGATG
*
2695651 CTCGTTGCTCGTTAAGCTCGATGCTCGTTG-TTCGC
1 CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTT-GC
* *
2695686 CTTGTTACTCGTTAAGCTCGATGCTCGTTGCTTGT
1 CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTTGC
*
2695721 CTCGTTGCTCGTTAAGCTC
1 CTCGTTACTCGTTAAGCTC
2695740 ACTGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 46 0.96
36 2 0.04
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (35 bp):
CTCGTTACTCGTTAAGCTCGATGCTCGTTGCTTGC
Found at i:2697210 original size:36 final size:36
Alignment explanation
Indices: 2697143--2697224 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
2697133 TATGTATCAT
*
2697143 GAAAATAAAATTATTAAAAAATAAAAAAAATATAAA
1 GAAAATAAAATTATTAAAAAATAAAAAAAATAGAAA
* *
2697179 GAAAATTAAATT-TT-ATAAATAAAAAGTAAATAGAAA
1 GAAAATAAAATTATTAAAAAATAAAAA--AAATAGAAA
*
2697215 GTAAA-AAAAT
1 GAAAATAAAAT
2697225 ACATACCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 10 0.26
35 6 0.15
36 23 0.59
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (36 bp):
GAAAATAAAATTATTAAAAAATAAAAAAAATAGAAA
Done.