Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006420.1 Hibiscus syriacus cultivar Beakdansim tig00015487_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: 133378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1889 original size:2 final size:2
Alignment explanation
Indices: 1882--1909 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1872 GTAATTGTAT
1882 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
1910 GGTTATAGGC
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):
TA
Found at i:2039 original size:27 final size:28
Alignment explanation
Indices: 2006--2060 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1996 AAAGTTTATA
2006 GAGTTTAGGATATAATTTATA-GGTTTT
1 GAGTTTAGGATATAATTTATAGGGTTTT
* *
2033 GAGTTTATGATGTAATTTATAGGGTTTT
1 GAGTTTAGGATATAATTTATAGGGTTTT
2061 AATTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (28 bp):
GAGTTTAGGATATAATTTATAGGGTTTT
Found at i:6267 original size:2 final size:2
Alignment explanation
Indices: 6260--6290 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6250 AGATAAATAG
6260 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 A
6291 ATTGTTTATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9110 original size:31 final size:31
Alignment explanation
Indices: 9075--9169 Score: 127
Period size: 31 Copynumber: 3.1 Consensus size: 31
9065 AGTAGGCACA
* * * * *
9075 TAAAAATGTAACAGATAAAACATTAGGCATC
1 TAAAAGTGTAACGGAGAAAACGTTAGACATC
* *
9106 TAAAAGTGTAATGGAGAAAACGTTAGACATT
1 TAAAAGTGTAACGGAGAAAACGTTAGACATC
9137 TAAAAGTGTAACGGAGAAAACGTTAGACATC
1 TAAAAGTGTAACGGAGAAAACGTTAGACATC
9168 TA
1 TA
9170 TTTTTTAACG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (31 bp):
TAAAAGTGTAACGGAGAAAACGTTAGACATC
Found at i:18123 original size:22 final size:22
Alignment explanation
Indices: 18098--18148 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
18088 ACGTGAGAAT
*
18098 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
18120 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
18142 CACGGGT
1 CACGGGT
18149 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:18191 original size:23 final size:23
Alignment explanation
Indices: 18165--18208 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
18155 TCCTGCAAGG
18165 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
18188 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
18209 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:18215 original size:23 final size:23
Alignment explanation
Indices: 18166--18215 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
18156 CCTGCAAGGC
* *
18166 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGGGCA
18189 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCTGCATGTGGGGGGCA
18212 TGCA
1 TGCA
18216 ACTGATGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGGGCA
Found at i:18418 original size:30 final size:30
Alignment explanation
Indices: 18384--18444 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
18374 CAATTACAGA
18384 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
1 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
18414 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
1 AGCAGTGAGAGCTTGAGAGGGAGATTGATC
18444 A
1 A
18445 CAAAGCATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.39, T:0.20
Consensus pattern (30 bp):
AGCAGTGAGAGCTTGAGAGGGAGATTGATC
Found at i:21246 original size:14 final size:14
Alignment explanation
Indices: 21224--21729 Score: 120
Period size: 14 Copynumber: 36.5 Consensus size: 14
21214 CTATTATTAT
*
21224 ATCAGTAAATATAA
1 ATCATTAAATATAA
*
21238 ATCATTAAAGT-CAA
1 ATCATTAAA-TATAA
* * *
21252 GTAATT-ATTATTAA
1 ATCATTAAATA-TAA
21266 ATCATTAAA-ATAAA
1 ATCATTAAATAT-AA
21280 ATCATTAAA-ATTAA
1 ATCATTAAATA-TAA
* * *
21294 GTAATT-ATTATTAA
1 ATCATTAAATA-TAA
*
21308 ATTATTAAA-ATTAA
1 ATCATTAAATA-TAA
*
21322 ATCATTAAA-GT-A
1 ATCATTAAATATAA
*
21334 ATTATT--AT-TAA
1 ATCATTAAATATAA
21345 ATCATTAAAT-TAA
1 ATCATTAAATATAA
21358 ATCATTAAA-ATTAA
1 ATCATTAAATA-TAA
* * *
21372 GTAATT-ATTATTAA
1 ATCATTAAATA-TAA
*
21386 ATTATTAAA-ATTAA
1 ATCATTAAATA-TAA
*
21400 ATCATTAAAGTA-ATT
1 ATCATTAAA-TATA-A
*
21415 ATTATTAAATCATTAA
1 ATCATTAAAT-A-TAA
21431 ATCATTAAATCATTAA
1 ATCATTAAAT-A-TAA
21447 ATCATTAAA-ATAA
1 ATCATTAAATATAA
*
21460 TTATTATTAAATCATTAA
1 --ATCATTAAAT-A-TAA
21478 ATCATTAAATCATTAA
1 ATCATTAAAT-A-TAA
* *
21494 AGTAATT-ATTATTAA
1 A-TCATTAAATA-TAA
21509 ATCATTAAAGT-TAA
1 ATCATTAAA-TATAA
*
21523 ATCATTAAA-GT-A
1 ATCATTAAATATAA
*
21535 ATTATT--AT-TAA
1 ATCATTAAATATAA
21546 ATCATTAAATCATTAA
1 ATCATTAAAT-A-TAA
21562 ATCATTAAATCATTAA
1 ATCATTAAAT-A-TAA
* *
21578 AGTAATT-ATTATTAA
1 A-TCATTAAATA-TAA
21593 ATCATTAAAGT-TAA
1 ATCATTAAA-TATAA
*
21607 ATCATTAAA-GT-A
1 ATCATTAAATATAA
*
21619 ATTATT--AT-TAA
1 ATCATTAAATATAA
21630 ATCATTAAAGT-TAA
1 ATCATTAAA-TATAA
*
21644 ATCATTAAA-GT-A
1 ATCATTAAATATAA
*
21656 ATTATT--AT-TAA
1 ATCATTAAATATAA
21667 ATCATTAAAGT-TAA
1 ATCATTAAA-TATAA
* *
21681 ATAATT-ATTATTAA
1 ATCATTAAATA-TAA
21695 ATCATTAAAGT-TAA
1 ATCATTAAA-TATAA
* *
21709 ATAATTAAATTTAA
1 ATCATTAAATATAA
*
21723 ATAATTA
1 ATCATTA
21730 TTATTAAATA
Statistics
Matches: 383, Mismatches: 51, Indels: 116
0.70 0.09 0.21
Matches are distributed among these distances:
10 8 0.02
11 24 0.06
12 26 0.07
13 31 0.08
14 176 0.46
15 37 0.10
16 68 0.18
17 10 0.03
18 3 0.01
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (14 bp):
ATCATTAAATATAA
Found at i:21324 original size:84 final size:79
Alignment explanation
Indices: 21250--21687 Score: 602
Period size: 84 Copynumber: 5.5 Consensus size: 79
21240 CATTAAAGTC
* *
21250 AAGTAATTATTATTAAATCATTAAAATAAAATCATTAAAATTAAGTAATTATTATTAAATTATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATTAAATCATTA
21315 AAATTAAATCATTA
66 AAATTAAATCATTA
*
21329 AAGTAATTATTATTAAATCATT-AAATTAAATCATTAAAATTAAGTAATTATTATTAAATTATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATTAAATCATTA
21393 AAATTAAATCATTA
66 AAATTAAATCATTA
*
21407 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTAAAATAATTATTATTAAAT
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAA--ATT-AAGTAATTATTATTAAAT
21472 CATTAAATCATTAAATCATTA
61 CATTAAA--ATTAAATCATTA
* * * *
21493 AAGTAATTATTATTAAATCATTAAAGTTAAATCATT-AAAGTAATTATTATTAAATCATTAAATC
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTA--ATT--ATTATTAAATC
21557 ATTAAATCATTAAATCATTA
62 ATTAAA--ATTAAATCATTA
*
21577 AAGTAATTATTATTAAATCATTAAAGTTAAATCATT---A--AAGTAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATTAAATCATTA
*
21637 AAGTTAAATCATTA
66 AAATTAAATCATTA
* *
21651 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
21688 TTATTAAATC
Statistics
Matches: 335, Mismatches: 11, Indels: 30
0.89 0.03 0.08
Matches are distributed among these distances:
74 46 0.14
76 16 0.05
78 80 0.24
79 24 0.07
80 8 0.02
81 16 0.05
82 4 0.01
83 5 0.01
84 99 0.30
86 37 0.11
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (79 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATTAAATCATTA
AAATTAAATCATTA
Found at i:21333 original size:37 final size:37
Alignment explanation
Indices: 21292--21717 Score: 241
Period size: 37 Copynumber: 11.1 Consensus size: 37
21282 CATTAAAATT
21292 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
*
21329 AAGTAATTATTATTAAATCATT-AAATTAAATCATTAAAA
1 AAGTAATTATTATTAAATTATTAAAATTAAATCATT---A
21368 TTAAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 --AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
*
21407 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATTATTAAA--ATTAAATCATTA
* * *
21446 AA-TCATTA-AAATAATTATTATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAA--ATTATTAAA--ATTAAATCATTA
* * *
21485 AA-TCATTA-AAGT-AATTATT---ATTAAATCATTA
1 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
* *
21516 AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTA
1 AAG-T-AATTATT--ATTAA--ATTATTAAA--ATTAAATCATTA
* * * **
21561 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAA-TTATTAAAATTAAATCATTA
* * **
21600 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATTATTAAA-TTATTAAAATTAAATCATTA
* * **
21637 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATTATTAAA-TTATTAAAATTAAATCATTA
* * *
21674 AAGTTAAATAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAG-----TAATTATTATTAAATTATTAAAATTAAATCATTA
21716 AA
1 AA
21718 TTTAAATAAT
Statistics
Matches: 328, Mismatches: 26, Indels: 65
0.78 0.06 0.16
Matches are distributed among these distances:
31 14 0.04
33 1 0.00
34 3 0.01
36 19 0.06
37 122 0.37
38 7 0.02
39 63 0.19
40 7 0.02
41 31 0.09
42 36 0.11
43 9 0.03
44 2 0.01
45 14 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (37 bp):
AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
Found at i:21718 original size:8 final size:8
Alignment explanation
Indices: 21261--21703 Score: 234
Period size: 8 Copynumber: 59.8 Consensus size: 8
21251 AGTAATTATT
21261 ATTAAATC
1 ATTAAATC
21269 ATTAAA--
1 ATTAAATC
*
21275 ATAAAATC
1 ATTAAATC
21283 ATTAAA--
1 ATTAAATC
* *
21289 ATTAAGTA
1 ATTAAATC
*
21297 ATT--ATT
1 ATTAAATC
*
21303 ATTAAATT
1 ATTAAATC
21311 ATTAAA--
1 ATTAAATC
21317 ATTAAATC
1 ATTAAATC
*
21325 ATTAAAGTA
1 ATTAAA-TC
*
21334 ATT--ATT
1 ATTAAATC
21340 ATTAAATC
1 ATTAAATC
21348 ATT-AA--
1 ATTAAATC
21353 ATTAAATC
1 ATTAAATC
21361 ATTAAA--
1 ATTAAATC
* *
21367 ATTAAGTA
1 ATTAAATC
*
21375 ATT--ATT
1 ATTAAATC
*
21381 ATTAAATT
1 ATTAAATC
21389 ATTAAA--
1 ATTAAATC
21395 ATTAAATC
1 ATTAAATC
*
21403 ATTAAAGTA
1 ATTAAA-TC
*
21412 ATT--ATT
1 ATTAAATC
21418 ATTAAATC
1 ATTAAATC
21426 ATTAAATC
1 ATTAAATC
21434 ATTAAATC
1 ATTAAATC
21442 ATTAAATC
1 ATTAAATC
*
21450 ATTAAAATA
1 ATT-AAATC
*
21459 ATT--ATT
1 ATTAAATC
21465 ATTAAATC
1 ATTAAATC
21473 ATTAAATC
1 ATTAAATC
21481 ATTAAATC
1 ATTAAATC
*
21489 ATTAAAGTA
1 ATTAAA-TC
*
21498 ATT--ATT
1 ATTAAATC
21504 ATTAAATC
1 ATTAAATC
21512 ATTAAA--
1 ATTAAATC
*
21518 GTTAAATC
1 ATTAAATC
*
21526 ATTAAAGTA
1 ATTAAA-TC
*
21535 ATT--ATT
1 ATTAAATC
21541 ATTAAATC
1 ATTAAATC
21549 ATTAAATC
1 ATTAAATC
21557 ATTAAATC
1 ATTAAATC
21565 ATTAAATC
1 ATTAAATC
*
21573 ATTAAAGTA
1 ATTAAA-TC
*
21582 ATT--ATT
1 ATTAAATC
21588 ATTAAATC
1 ATTAAATC
21596 ATTAAA--
1 ATTAAATC
*
21602 GTTAAATC
1 ATTAAATC
*
21610 ATTAAAGTA
1 ATTAAA-TC
*
21619 ATT--ATT
1 ATTAAATC
21625 ATTAAATC
1 ATTAAATC
21633 ATTAAA--
1 ATTAAATC
*
21639 GTTAAATC
1 ATTAAATC
*
21647 ATTAAAGTA
1 ATTAAA-TC
*
21656 ATT--ATT
1 ATTAAATC
21662 ATTAAATC
1 ATTAAATC
21670 ATTAAA--
1 ATTAAATC
* *
21676 GTTAAATA
1 ATTAAATC
*
21684 ATT--ATT
1 ATTAAATC
21690 ATTAAATC
1 ATTAAATC
21698 ATTAAA
1 ATTAAA
21704 GTTAAATAAT
Statistics
Matches: 342, Mismatches: 42, Indels: 102
0.70 0.09 0.21
Matches are distributed among these distances:
5 3 0.01
6 95 0.28
7 9 0.03
8 200 0.58
9 35 0.10
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:25111 original size:18 final size:18
Alignment explanation
Indices: 25088--25122 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
25078 ACCAACTTGC
25088 TTCAGACGAATCTCACGT
1 TTCAGACGAATCTCACGT
25106 TTCAGACGAATCTCACG
1 TTCAGACGAATCTCACG
25123 CTTCGGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (18 bp):
TTCAGACGAATCTCACGT
Found at i:25755 original size:22 final size:22
Alignment explanation
Indices: 25727--25768 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25717 AATAGTACCA
*
25727 TAACATTATAATTATTTACTAT
1 TAACATTATAAATATTTACTAT
*
25749 TAACATTATAAATGTTTACT
1 TAACATTATAAATATTTACT
25769 TTTTACTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (22 bp):
TAACATTATAAATATTTACTAT
Found at i:27243 original size:20 final size:20
Alignment explanation
Indices: 27220--27257 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27210 CCTATTATCT
27220 CTGGTAATCCTATATTCCTG
1 CTGGTAATCCTATATTCCTG
*
27240 CTGGTAATCTTATATTCC
1 CTGGTAATCCTATATTCC
27258 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (20 bp):
CTGGTAATCCTATATTCCTG
Found at i:28194 original size:40 final size:35
Alignment explanation
Indices: 28114--28189 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
28104 AAAACAATCA
*
28114 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* *
28149 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
28184 TCAATT
1 TCAATT
28190 CAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
Found at i:28731 original size:130 final size:130
Alignment explanation
Indices: 28585--28832 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
28575 TATTTATATA
* **
28585 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
28650 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
28715 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
28780 TTAACACATGATCATGATATATGTTATTGGTGACACGTGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
28833 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:28863 original size:130 final size:129
Alignment explanation
Indices: 28599--28863 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
28589 ATTTGGTCCT
* ** *
28599 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
28664 TGACATGTGTCATTGGTGACACATGTCACCGCCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
28729 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
28794 TGATATATGTTATTGGTGACACGTGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
28858 -A
128 CA
28859 AAATT
1 AAATT
28864 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:29191 original size:28 final size:27
Alignment explanation
Indices: 29160--29222 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
29150 AGTTGATACA
*
29160 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
29188 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
29216 ATATTTT
1 ATATTTT
29223 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:29325 original size:16 final size:18
Alignment explanation
Indices: 29304--29337 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
29294 ATTTCTTATT
29304 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
29320 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
29338 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:30164 original size:13 final size:13
Alignment explanation
Indices: 30146--30170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30136 AACAACTCTT
30146 AACTTTTGGTTCA
1 AACTTTTGGTTCA
30159 AACTTTTGGTTC
1 AACTTTTGGTTC
30171 CGATTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
AACTTTTGGTTCA
Found at i:32288 original size:23 final size:23
Alignment explanation
Indices: 32252--32297 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32242 AATATCTATA
*
32252 TCAATCCGTGAAGTGTTAAAATT
1 TCAATCCATGAAGTGTTAAAATT
*
32275 TCAATCCATTAAGTGTTAAAATT
1 TCAATCCATGAAGTGTTAAAATT
32298 AGTGTGTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
TCAATCCATGAAGTGTTAAAATT
Found at i:33971 original size:30 final size:31
Alignment explanation
Indices: 33936--34020 Score: 138
Period size: 30 Copynumber: 2.8 Consensus size: 31
33926 AGTTGGAAGT
33936 GTCTTATTAAAGACATGTTTAACTGAAA-AC
1 GTCTTATTAAAGACATGTTTAACTGAAAGAC
33966 GTCTTATTAAAGACATGTTTAACT-AAAGAC
1 GTCTTATTAAAGACATGTTTAACTGAAAGAC
* *
33996 GTCTTATTAAAGGCATGCTTAACTG
1 GTCTTATTAAAGACATGTTTAACTG
34021 GAGGCGTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
29 3 0.06
30 48 0.94
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (31 bp):
GTCTTATTAAAGACATGTTTAACTGAAAGAC
Found at i:33994 original size:16 final size:16
Alignment explanation
Indices: 33943--33995 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
33933 AGTGTCTTAT
33943 TAAAGACATGTTTAAC
1 TAAAGACATGTTTAAC
*
33959 TGAAA-AC--GTCTT-AT
1 T-AAAGACATGT-TTAAC
33973 TAAAGACATGTTTAAC
1 TAAAGACATGTTTAAC
33989 TAAAGAC
1 TAAAGAC
33996 GTCTTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 3 0.10
14 6 0.21
15 4 0.14
16 13 0.45
17 3 0.10
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (16 bp):
TAAAGACATGTTTAAC
Found at i:40433 original size:89 final size:89
Alignment explanation
Indices: 40277--40439 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
40267 ACATTTTCAC
* * *
40277 CTTTTCACCTTTCTACCGTCGAGATTCTCCTATACTATGGTTAGATCACAATGATATTGAGATAT
1 CTTTCCACCTTTCTACCATCGAGATTCTCCTATACTACGGTTAGATCACAATGATATTGAGATAT
40342 ATTGTTCTCCTCATTAACGTCTAT
66 ATTGTTCTCCTCATTAACGTCTAT
* * *
40366 CTTTCCACCTTTCTACCATTGAGATTCTCTTATA-TCACGGTTAGATCACAATGATTTTGAGATA
1 CTTTCCACCTTTCTACCATCGAGATTCTCCTATACT-ACGGTTAGATCACAATGATATTGAGATA
40430 TATTGTTCTC
65 TATTGTTCTC
40440 TTCACCAACG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
88 1 0.01
89 66 0.99
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (89 bp):
CTTTCCACCTTTCTACCATCGAGATTCTCCTATACTACGGTTAGATCACAATGATATTGAGATAT
ATTGTTCTCCTCATTAACGTCTAT
Found at i:47422 original size:19 final size:17
Alignment explanation
Indices: 47388--47420 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47378 TTGTAATTAT
47388 GAGAGAGAATTATTTTG
1 GAGAGAGAATTATTTTG
*
47405 GAGAGAGAATCATTTT
1 GAGAGAGAATTATTTT
47421 TTAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (17 bp):
GAGAGAGAATTATTTTG
Found at i:48518 original size:23 final size:22
Alignment explanation
Indices: 48492--48548 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
48482 TTGTATTGTT
*
48492 AATATACACGTTCCTACCCTGAA
1 AATATA-ACGTTACTACCCTGAA
* *
48515 AATATATCGTTAGTACCCTGAA
1 AATATAACGTTACTACCCTGAA
*
48537 AATATATCGTTA
1 AATATAACGTTA
48549 GATCTGCCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (22 bp):
AATATAACGTTACTACCCTGAA
Found at i:48531 original size:22 final size:22
Alignment explanation
Indices: 48506--48549 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48496 TACACGTTCC
48506 TACCCTGAAAATATATCGTTAG
1 TACCCTGAAAATATATCGTTAG
48528 TACCCTGAAAATATATCGTTAG
1 TACCCTGAAAATATATCGTTAG
48550 ATCTGCCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
TACCCTGAAAATATATCGTTAG
Found at i:52355 original size:10 final size:10
Alignment explanation
Indices: 52342--52366 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52332 AGAATGAAGA
52342 AGAAGGTAGC
1 AGAAGGTAGC
52352 AGAAGGTAGC
1 AGAAGGTAGC
52362 AGAAG
1 AGAAG
52367 AAGCAAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.40, T:0.08
Consensus pattern (10 bp):
AGAAGGTAGC
Found at i:52987 original size:2 final size:2
Alignment explanation
Indices: 52980--53061 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
52970 AAAGTATTAG
52980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53062 TGATTTTAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58858 original size:2 final size:2
Alignment explanation
Indices: 58851--58877 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58841 AGATCTACAA
58851 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 A
58878 ACATTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64796 original size:16 final size:17
Alignment explanation
Indices: 64764--64797 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
64754 AAAGATAATC
*
64764 AAACAAGCATACTCATA
1 AAACAAGCATACACATA
64781 AAACAA-CATACACATA
1 AAACAAGCATACACATA
64797 A
1 A
64798 TGCACCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.24, G:0.03, T:0.15
Consensus pattern (17 bp):
AAACAAGCATACACATA
Found at i:76971 original size:24 final size:24
Alignment explanation
Indices: 76924--76995 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
76914 GGTTTGACCC
*
76924 GACCCGACCCGACC--CGACCGTT
1 GACCCGACCCGACCATTGACCGTT
76946 GACCCGACCCGACCATTGACCGTT
1 GACCCGACCCGACCATTGACCGTT
76970 GACCCGACCCGACCATTGACCGTT
1 GACCCGACCCGACCATTGACCGTT
76994 GA
1 GA
76996 TCGTTGACCG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 14 0.30
24 33 0.70
ACGTcount: A:0.21, C:0.43, G:0.22, T:0.14
Consensus pattern (24 bp):
GACCCGACCCGACCATTGACCGTT
Found at i:76978 original size:5 final size:5
Alignment explanation
Indices: 76919--76959 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
76909 AAACCGGTTT
*
76919 GACCC GACCC GACCC GACCC GACCGTT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
76960 ATTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:76983 original size:17 final size:17
Alignment explanation
Indices: 76929--76966 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
76919 GACCCGACCC
*
76929 GACCCGACCCGACCGTT
1 GACCCGACCCGACCATT
76946 GACCCGACCCGACCATT
1 GACCCGACCCGACCATT
76963 GACC
1 GACC
76967 GTTGACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCATT
Found at i:76995 original size:7 final size:7
Alignment explanation
Indices: 76980--77020 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
76970 GACCCGACCC
*
76980 GACCATT
1 GACCGTT
76987 GACCGTT
1 GACCGTT
*
76994 GATCGTT
1 GACCGTT
77001 GACCG-T
1 GACCGTT
77007 GACCGTT
1 GACCGTT
77014 GACCGTT
1 GACCGTT
77021 TACTTCCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:77015 original size:13 final size:13
Alignment explanation
Indices: 76980--77019 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
76970 GACCCGACCC
*
76980 GACCATTGACCGTT
1 GACCGTTGACCG-T
*
76994 GATCGTTGACCGT
1 GACCGTTGACCGT
77007 GACCGTTGACCGT
1 GACCGTTGACCGT
77020 TTACTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:83199 original size:122 final size:122
Alignment explanation
Indices: 82979--83219 Score: 446
Period size: 122 Copynumber: 2.0 Consensus size: 122
82969 ATTTTTCAGG
82979 AATTTACTTATCATCATTCAGTGCTTCTCTCAATTCAGGTTTGTTTATATGTGTAACTTGTGCTA
1 AATTTACTTATCATCATTCAGTGCTTCTCTCAATTCAGGTTTGTTTATATGTGTAACTTGTGCTA
* *
83044 ATTGATTTGTCACTCATATAGTATGAGTTAGTTGTTTGATTCTGGTTTAATAATAAA
66 ATTGATTTGTCACTCATATAATATGAGTGAGTTGTTTGATTCTGGTTTAATAATAAA
*
83101 AATTTACTTATCATCATTCAGTGCTTCTCTCAATTCAGGTTTGTTTATATGTGTAACTTGTGTTA
1 AATTTACTTATCATCATTCAGTGCTTCTCTCAATTCAGGTTTGTTTATATGTGTAACTTGTGCTA
*
83166 ATTGATTTGTCACTCATATAATATGAGTGAGTTGTTTGATTTTGGTTTAATAAT
66 ATTGATTTGTCACTCATATAATATGAGTGAGTTGTTTGATTCTGGTTTAATAAT
83220 CTTCTCGTTA
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (122 bp):
AATTTACTTATCATCATTCAGTGCTTCTCTCAATTCAGGTTTGTTTATATGTGTAACTTGTGCTA
ATTGATTTGTCACTCATATAATATGAGTGAGTTGTTTGATTCTGGTTTAATAATAAA
Found at i:90560 original size:37 final size:37
Alignment explanation
Indices: 90510--90581 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
90500 ATGGAATGAA
** *
90510 TTAGGGATAAAATGTTATACATACCCATAATAAAAAT
1 TTAGGGATAAAATGCGATACATAACCATAATAAAAAT
* *
90547 TTAGGGCTAAAATGCGATACATAACTATAATAAAA
1 TTAGGGATAAAATGCGATACATAACCATAATAAAA
90582 TATAAATTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (37 bp):
TTAGGGATAAAATGCGATACATAACCATAATAAAAAT
Found at i:90729 original size:22 final size:22
Alignment explanation
Indices: 90686--90729 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
90676 AAGAAAACTA
* *
90686 TAAAAAAATAATTTTTTGAATT
1 TAAAAAAATAATTTTCTCAATT
90708 TAAAAAAAT-ATTTATCTCAATT
1 TAAAAAAATAATTT-TCTCAATT
90730 GATTGTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAAAATAATTTTCTCAATT
Found at i:94046 original size:39 final size:39
Alignment explanation
Indices: 93987--94067 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
93977 CTAAAATGAC
*
93987 AGAGGCTTTCACCATGTACTTGTGAGTGATGGCTGAGGA
1 AGAGGCTTTCACCATGTACTTGTGAGTGATGGCTAAGGA
* *
94026 AGAGGCTTTCACCATTTACTTGTGAGTGATGGTTAAGGA
1 AGAGGCTTTCACCATGTACTTGTGAGTGATGGCTAAGGA
94065 AGA
1 AGA
94068 AGAACCCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.30
Consensus pattern (39 bp):
AGAGGCTTTCACCATGTACTTGTGAGTGATGGCTAAGGA
Found at i:95935 original size:2 final size:2
Alignment explanation
Indices: 95928--95971 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
95918 TGTAATTGAA
95928 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
95970 AT
1 AT
95972 TGCTTCAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117170 original size:2 final size:2
Alignment explanation
Indices: 117163--117194 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117153 TAATTCTATT
117163 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
117195 CACTATTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:118510 original size:5 final size:5
Alignment explanation
Indices: 118500--118524 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
118490 CAGAGAAAAC
118500 CCACA CCACA CCACA CCACA CCACA
1 CCACA CCACA CCACA CCACA CCACA
118525 ATTGCCCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.60, G:0.00, T:0.00
Consensus pattern (5 bp):
CCACA
Found at i:129910 original size:26 final size:26
Alignment explanation
Indices: 129881--129944 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
129871 GAATTACGTC
129881 ATGTCAGGTTAAATTGGATATAAATT
1 ATGTCAGGTTAAATTGGATATAAATT
*
129907 ATGTCAGGTTAAATTGGATATAAGTT
1 ATGTCAGGTTAAATTGGATATAAATT
*
129933 ATGTCAAGTTAA
1 ATGTCAGGTTAA
129945 TTGAATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (26 bp):
ATGTCAGGTTAAATTGGATATAAATT
Found at i:131776 original size:41 final size:42
Alignment explanation
Indices: 131661--131777 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 42
131651 AAAGTGAATT
* *
131661 AAAAATTAGGGTCATCAATTATAAATATAAAAAGTGAGATGGAA
1 AAAAATTAGGG-CCTCAATTATAAATAT-AAAAGTGAGATGCAA
* * * * *
131705 AAAAACTAATGGTCC-CGATTATAAAGATAAAAGT-ATGAT-CAC
1 AAAAA-TTA-GGGCCTCAATTATAAATATAAAAGTGA-GATGCAA
131747 AAAAATTAGGGCCTCAATTATAAATATAAAA
1 AAAAATTAGGGCCTCAATTATAAATATAAAA
131778 AATAAAATTG
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
40 4 0.07
41 17 0.29
42 7 0.12
43 9 0.16
44 16 0.28
45 3 0.05
46 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (42 bp):
AAAAATTAGGGCCTCAATTATAAATATAAAAGTGAGATGCAA
Found at i:131811 original size:85 final size:86
Alignment explanation
Indices: 131661--131821 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 86
131651 AAAGTGAATT
* * * * * *
131661 AAAAATTAGGGTCATCAATTATAAATATAAAAAGTGAGATGGAAAAAAACTAATGGTCCCGATTA
1 AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACTAAAGGACCCAATTA
*
131726 TAAAGATAAAAGTATGATCAC
66 TAAAAATAAAAGTATGATCAC
* * * *
131747 AAAAATTAGGG-CCTCAATTATAAATATAAAAAATAAAATTGAAGAAAA-TGAAAGGACTCAATT
1 AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACT-AAAGGACCCAATT
131810 ATAAAAATAAAA
65 ATAAAAATAAAA
131822 AATATAATAG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.02
85 51 0.81
86 11 0.17
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24
Consensus pattern (86 bp):
AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACTAAAGGACCCAATTA
TAAAAATAAAAGTATGATCAC
Found at i:131836 original size:85 final size:86
Alignment explanation
Indices: 131661--131839 Score: 193
Period size: 85 Copynumber: 2.1 Consensus size: 86
131651 AAAGTGAATT
* * * * * *
131661 AAAAATTAGGGTCATCAATTATAAATATAAAAAGTGAGATGGAAAAAAACTAATGGTCCCGATTA
1 AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACTAAAGGACCCAATTA
* * *
131726 TAAAGATAAAAGTATGATCAC
66 TAAAAATAAAAATATAATCAC
* * * *
131747 AAAAATTAGGG-CCTCAATTATAAATATAAAAAATAAAATTGAAGAAAA-TGAAAGGACTCAATT
1 AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACT-AAAGGACCCAATT
*
131810 ATAAAAATAAAAAATATAAT-AG
65 ATAAAAAT-AAAAATATAATCAC
131832 AAAAATTA
1 AAAAATTA
131840 AGGATCCTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
84 1 0.01
85 56 0.73
86 20 0.26
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (86 bp):
AAAAATTAGGGTCATCAATTATAAATATAAAAAATAAAATGGAAAAAAACTAAAGGACCCAATTA
TAAAAATAAAAATATAATCAC
Done.