Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000497.1 Hibiscus syriacus cultivar Beakdansim tig00000947_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: 67348
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3913 original size:22 final size:21
Alignment explanation
Indices: 3871--3910 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3861 GATTTTATTT
*
3871 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3892 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3911 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:19363 original size:135 final size:135
Alignment explanation
Indices: 19112--19393 Score: 395
Period size: 135 Copynumber: 2.1 Consensus size: 135
19102 ATAAACGATC
* * * *
19112 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTTATCCGATATAGGGAGAAGAAGTTCGTAA
1 AACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAAAAAGTTCGCAA
* * ** *
19177 TGAGAATAACTTGTTCAACCTTTGCTCAATTCACGGCATTTTGAATCAGCAACACCTCACTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCAATTCACAGCATTTCAAATCAGCAAAACCTCACTTGAG
19242 GGATT
131 GGATT
* *
19247 AACATTTCTAATGGAGATTTCATAATGAGAAGAACTCATCCTATATAGGGAGAAAAAGTTTC-CA
1 AACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAAAAAG-TTCGCA
* ** * * *
19311 ATGAGAAGAACTTGTTCAACCTTTGCTCGATTCTTAGTATTTCAAATTAGCAAAATCTCACTTGA
65 ATGAGAAGAACTTGTTCAACCTTTGCTCAATTCACAGCATTTCAAATCAGCAAAACCTCACTTGA
19376 GGGATT
130 GGGATT
19382 AACATTTCTAAT
1 AACATTTCTAAT
19394 CTCGTTTCAC
Statistics
Matches: 129, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
135 126 0.98
136 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (135 bp):
AACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATATAGGGAGAAAAAGTTCGCAA
TGAGAAGAACTTGTTCAACCTTTGCTCAATTCACAGCATTTCAAATCAGCAAAACCTCACTTGAG
GGATT
Found at i:21062 original size:11 final size:10
Alignment explanation
Indices: 21025--21084 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
21015 TTGATCCTGA
21025 TATTTATGTTT
1 TATTTAT-TTT
21036 T-TTTAATTTT
1 TATTT-ATTTT
21046 T-TTTATTTT
1 TATTTATTTT
*
21055 TATGTTATGTT
1 TAT-TTATTTT
21066 T-TTTATTTTT
1 TATTTA-TTTT
21076 TATTTATTT
1 TATTTATTT
21085 AATTAGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.21
10 19 0.45
11 14 0.33
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (10 bp):
TATTTATTTT
Found at i:24343 original size:29 final size:29
Alignment explanation
Indices: 24299--24379 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
24289 AGTGAGTTGT
* * *
24299 AGGTCGCCATGCCATCCGGGCGAGCTTGG
1 AGGTCGACATGGCATCCGGGCGAGCTTAG
* *
24328 AGGTTGACATGGCATCTGGGCGAGCTTAG
1 AGGTCGACATGGCATCCGGGCGAGCTTAG
*
24357 AGGTCGCCATGGCATCCGGGCGA
1 AGGTCGACATGGCATCCGGGCGA
24380 CCTGTGTGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.17, C:0.26, G:0.38, T:0.19
Consensus pattern (29 bp):
AGGTCGACATGGCATCCGGGCGAGCTTAG
Found at i:24404 original size:25 final size:25
Alignment explanation
Indices: 24374--24425 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
24364 CATGGCATCC
*
24374 GGGCGACCTGTGTGGTGTTCTGCAT
1 GGGCGACCTATGTGGTGTTCTGCAT
*
24399 GGGCGACCTATGTGGTGTTGTGCAT
1 GGGCGACCTATGTGGTGTTCTGCAT
24424 GG
1 GG
24426 CTCATGCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.10, C:0.17, G:0.42, T:0.31
Consensus pattern (25 bp):
GGGCGACCTATGTGGTGTTCTGCAT
Found at i:24460 original size:38 final size:38
Alignment explanation
Indices: 24409--24481 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
24399 GGGCGACCTA
24409 TGTGGTGTTGTGCATGGCTCATGCAATGTTCGGTGTTG
1 TGTGGTGTTGTGCATGGCTCATGCAATGTTCGGTGTTG
24447 TGTGGTGTTGTGCATGGCTCATGCAATGTTCGGTG
1 TGTGGTGTTGTGCATGGCTCATGCAATGTTCGGTG
24482 CACATGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.11, C:0.14, G:0.37, T:0.38
Consensus pattern (38 bp):
TGTGGTGTTGTGCATGGCTCATGCAATGTTCGGTGTTG
Found at i:24663 original size:23 final size:23
Alignment explanation
Indices: 24638--24717 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 23
24628 ATTCATCTGT
*
24638 ATTATTGCAGCACTTATTGTTGT
1 ATTATTGCAGCACTTATTGTTGC
* *
24661 ATTATTGCAACACTTATTGCTGC
1 ATTATTGCAGCACTTATTGTTGC
*
24684 ATTATTCCAGCACTTATTGTTGC
1 ATTATTGCAGCACTTATTGTTGC
24707 ATTATTGCAGC
1 ATTATTGCAGC
24718 CCTTCAGCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (23 bp):
ATTATTGCAGCACTTATTGTTGC
Found at i:24926 original size:8 final size:9
Alignment explanation
Indices: 24896--24933 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
24886 GAGGTAAGTT
24896 TTTTAATTA
1 TTTTAATTA
24905 TTTTAATTA
1 TTTTAATTA
*
24914 GTTT-ATTA
1 TTTTAATTA
24922 TTTTAAATTA
1 TTTT-AATTA
24932 TT
1 TT
24934 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:24974 original size:38 final size:35
Alignment explanation
Indices: 24926--25015 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 35
24916 TTATTATTTT
24926 AAATTATTAGTTTGTTAGTTTATGGTTTAAGGTAAAACA
1 AAATT-TTAG-TTGTTAGTTTA--GTTTAAGGTAAAACA
24965 AAATTTTA---GTTAG-TTAGTTTAAGGTAAAACA
1 AAATTTTAGTTGTTAGTTTAGTTTAAGGTAAAACA
*
24996 AAATTTTAGTTAATTAGTTT
1 AAATTTTAGTT-GTTAGTTT
25016 GTTAGTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
31 23 0.51
33 3 0.07
34 5 0.11
35 4 0.09
36 2 0.04
38 3 0.07
39 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (35 bp):
AAATTTTAGTTGTTAGTTTAGTTTAAGGTAAAACA
Found at i:24987 original size:31 final size:31
Alignment explanation
Indices: 24950--25015 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
24940 TTAGTTTATG
*
24950 GTTTAAGGTAAAACAAAATTTTAGTTAGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTA
24981 GTTTAAGGTAAAACAAAATTTTAGTTAATTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTA
25012 GTTT
1 GTTT
25016 GTTAGTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (31 bp):
GTTTAAGGTAAAACAAAATTTTAGTTAATTA
Found at i:25038 original size:21 final size:21
Alignment explanation
Indices: 25014--25074 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
25004 GTTAATTAGT
*
25014 TTGTTAGTTTAAGCTATATTA
1 TTGTTAGTTTAAGTTATATTA
25035 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
25056 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
25075 CATACATACA
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:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:25169 original size:28 final size:27
Alignment explanation
Indices: 25130--25182 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
25120 TATATTAAAA
25130 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
25158 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
25183 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:25188 original size:27 final size:29
Alignment explanation
Indices: 25129--25193 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
25119 ATATATTAAA
25129 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
25158 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
25184 AAATAGTTAA
1 AAATAATTAA
25194 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:25243 original size:8 final size:8
Alignment explanation
Indices: 25230--25260 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
25220 TTATATAAAA
25230 AATTAGTT
1 AATTAGTT
25238 AATTAGTT
1 AATTAGTT
25246 AATTAGTT
1 AATTAGTT
*
25254 TATTAGT
1 AATTAGT
25261 AGTTTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
AATTAGTT
Found at i:25245 original size:54 final size:56
Alignment explanation
Indices: 25178--25309 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 56
25168 TAGTTTGTAG
* * *
25178 TTAGTTAAATAGTTAAGTTATATT-TTGGTTGTTGAA-TTTATATTAT-ATAAAAAA
1 TTAGTTAATTAGTTAAGTTATATTATTAGTAGTTGAAGTTT-TATTATAATAAAAAA
*
25232 TTAGTTAATTAGTTAA-TTAGT-TTATTAGTAGTTTAAGTTTTATTATAATAAAAAA
1 TTAGTTAATTAGTTAAGTTA-TATTATTAGTAGTTGAAGTTTTATTATAATAAAAAA
*
25287 -TAGTTTATTAGTTTAAGTTATAT
1 TTAGTTAATTAG-TTAAGTTATAT
25310 AAAAGAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
53 5 0.08
54 41 0.62
55 16 0.24
56 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (56 bp):
TTAGTTAATTAGTTAAGTTATATTATTAGTAGTTGAAGTTTTATTATAATAAAAAA
Found at i:25436 original size:21 final size:21
Alignment explanation
Indices: 25407--25446 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25397 GTTAATTAGT
*
25407 TTGTTAGTTTAAGTTATATTA
1 TTGTAAGTTTAAGTTATATTA
25428 TTGTAAGTTTAAGTTATAT
1 TTGTAAGTTTAAGTTATAT
25447 CATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (21 bp):
TTGTAAGTTTAAGTTATATTA
Found at i:25665 original size:30 final size:30
Alignment explanation
Indices: 25624--25718 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
25614 TTTAGTTAAT
*
25624 TAGTTTTTTAGTAGTAAATTATAATT-AA-AA
1 TAGTTTATTAGT-GTAAATTAT-ATTAAAGAA
* * *
25654 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTGTAAATTATATTAAAGAA
* *
25684 TAGTTTATTAGT-TAGAGTTATATTAGAGAA
1 TAGTTTATTAGTGTA-AATTATATTAAAGAA
25714 TAGTT
1 TAGTT
25719 AAAGTTATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.05
29 11 0.20
30 42 0.75
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTGTAAATTATATTAAAGAA
Found at i:25690 original size:22 final size:22
Alignment explanation
Indices: 25662--25742 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
25652 AATCGTTTAT
25662 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
*
25684 TAGTTTATTAGTTAGAGTTATATTAGAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
*
25714 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
25736 TAGTTTA
1 TAGTTTA
25743 TTAGTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
22 23 0.49
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 17 0.36
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:28310 original size:26 final size:26
Alignment explanation
Indices: 28232--28610 Score: 204
Period size: 26 Copynumber: 14.7 Consensus size: 26
28222 TTATTCCATA
* *
28232 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
28256 ATTATTATAAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
28281 ATTACTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
28307 ATTATTATTAAATCATTATTATTATT
1 ATTATTATTAAATCATTATTATAATC
* * *
28333 ATTATTATTATTATTATCATTA-AATC
1 ATTATTATTA-AATCATTATTATAATC
*
28359 ATTATTA-T-AATGATTATTACTAAATC
1 ATTATTATTAAATCATTATTA-T-AATC
*
28385 ATTATTA-T-AATGATTATTATCAAATC
1 ATTATTATTAAATCATTATTAT--AATC
* * *
28411 ATTACTAAATCATCAAATCATTAAATATTAA-A
1 ATTA-T---T-ATTAAATCATT-ATTA-TAATC
* *
28443 ATCATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
28469 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
28495 ATTATTATCAAATCATTAATA-AAT-
1 ATTATTATTAAATCATTATTATAATC
*
28519 ATTCAAATCATTAAAT-ATTA--A-AATC
1 ATT---ATTATTAAATCATTATTATAATC
28544 ---ATTATTAAATCATTATTATAATTTC
1 ATTATTATTAAATCATTATTATAA--TC
* * *
28569 ATTATTAGT-AATAATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* **
28593 ATTACTACCAAATCATTA
1 ATTATTATTAAATCATTA
28611 AATATTAATA
Statistics
Matches: 282, Mismatches: 42, Indels: 61
0.73 0.11 0.16
Matches are distributed among these distances:
19 9 0.03
20 4 0.01
22 1 0.00
23 10 0.04
24 22 0.08
25 48 0.17
26 128 0.45
27 36 0.13
28 6 0.02
30 1 0.00
31 2 0.01
32 3 0.01
33 8 0.03
34 3 0.01
35 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATC
Found at i:28313 original size:3 final size:3
Alignment explanation
Indices: 28295--28404 Score: 73
Period size: 3 Copynumber: 37.7 Consensus size: 3
28285 CTATTAAATC
* * * *
28295 ATT ATT ATA ATG ATT ATT ATT A-A ATC ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
28342 ATT ATT ATC ATT A-A ATC ATT ATT ATA ATG ATT ATT ACT A-A ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
28388 ATT ATA ATG ATT ATT AT
1 ATT ATT ATT ATT ATT AT
28405 CAAATCATTA
Statistics
Matches: 83, Mismatches: 21, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
2 3 0.04
3 80 0.96
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (3 bp):
ATT
Found at i:28455 original size:35 final size:35
Alignment explanation
Indices: 28406--28556 Score: 99
Period size: 35 Copynumber: 4.5 Consensus size: 35
28396 GATTATTATC
*
28406 AAATCATTACTAAATCATCAAATCATTAAATATTA
1 AAATCATTATTAAATCATCAAATCATTAAATATTA
* * * * *
28441 AAATCATTATTAAATCATTATTAT-AATGATTATTA
1 AAATCATTATTAAATCATCA-AATCATTAAATATTA
* * *
28476 CTAAATCATTA-T---T-AT--AATGATT-ATTA-TC
1 --AAATCATTATTAAATCATCAAATCATTAAATATTA
*
28504 AAATCATTAATAAAT-ATTCAAATCATTAAATATTA
1 AAATCATTATTAAATCA-TCAAATCATTAAATATTA
28539 AAATCATTATTAAATCAT
1 AAATCATTATTAAATCAT
28557 TATTATAATT
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
26 9 0.10
27 1 0.01
28 1 0.01
29 6 0.07
30 4 0.04
31 1 0.01
32 2 0.02
33 7 0.08
34 3 0.03
35 42 0.47
36 4 0.04
37 9 0.10
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.40
Consensus pattern (35 bp):
AAATCATTATTAAATCATCAAATCATTAAATATTA
Found at i:28535 original size:16 final size:16
Alignment explanation
Indices: 28514--28547 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28504 AAATCATTAA
*
28514 TAAATATTCAAATCAT
1 TAAATATTAAAATCAT
28530 TAAATATTAAAATCAT
1 TAAATATTAAAATCAT
28546 TA
1 TA
28548 TTAAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTAAAATCAT
Found at i:28594 original size:49 final size:49
Alignment explanation
Indices: 28245--29042 Score: 232
Period size: 49 Copynumber: 15.7 Consensus size: 49
28235 ATTAGTAATA
** *
28245 ATTATTAAATCATTATTATAAAATCATTACTA--AATCATTACTATTAAATC
1 ATTATTAAATCATTATTATAATTTCATTATTACTAATCATTAC---TAAATC
* * * * * * *
28295 ATTATTATAATGATTATTATTAA-ATCATTATTATTATTATTATTATTATTATT
1 ATTATTA-AATCATTATTA-TAATTTCATTATTACTA--ATCATTACTA-AATC
* * * *
28348 ATCATTAAATCATTATTATAA--TGATTATTACTAAATCATTATTATAATG
1 ATTATTAAATCATTATTATAATTTCATTATTACT-AATCATTACTA-AATC
* * *
28397 ATTATTATCAAATCATTACTA-AATCATCAAATCATTA--AAT-ATTA--AAATC
1 ATTA-T-T-AAATCATTATTATAAT-TTC--ATTATTACTAATCATTACTAAATC
* * *
28446 ATTATTAAATCATTATTATAA--TGATTATTACTAAATCATTATTATAATG
1 ATTATTAAATCATTATTATAATTTCATTATTACT-AATCATTACTA-AATC
* *
28495 ATTATTATCAAATCATTAATA-AATATTCAAATCATTA--AAT-ATTA--AAATC
1 ATTA-T-T-AAATCATTATTATAAT-TTC--ATTATTACTAATCATTACTAAATC
* *
28544 ATTATTAAATCATTATTATAATTTCATTATTAGTAATAATTACTAAATC
1 ATTATTAAATCATTATTATAATTTCATTATTACTAATCATTACTAAATC
*
28593 ATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTACCAA--
1 ATTA-T--TAAATCA-T---TA-T--T-ATAATTTCATTATTACTAATCATTACTA--AATC
* * *
28653 ATCATTAAAT-ATTAATAATAATTTAATTATTACTAATCATTACTACCAA--
1 ATTATTAAATCATT-ATTATAATTTCATTATTACTAATCATTACTA--AATC
* * *
28702 ATCATTAAAT-ATTAATAATAATTTCATTATTACTAATCATTACTAAATA
1 ATTATTAAATCATT-ATTATAATTTCATTATTACTAATCATTACTAAATC
* * * * * *
28751 ATTATTATAAT-TTTAAATATAAATTCATTATTAAATCATGATTA-TCAAATC
1 ATTATTA-AATCATT-ATTATAATTTCATTATT-ACTAATCATTACT-AAATC
* * * * * *
28802 ATTACTAAATCAAATCATTACTAA-ATCA-AATCA-T-ATCATTATTACAAATC
1 ATTATTAAATC--ATTATTA-TAATTTCATTATTACTAATCATTACT--AAATC
*
28852 ATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTACCAA--
1 ATTA-T--TAAATCA-T---TA-T--T-ATAATTTCATTATTACTAATCATTACTA--AATC
* * *
28912 ATCATTAAAT-ATTAATAATAATTTAATTATTACTAATCATTACTACCAA--
1 ATTATTAAATCATT-ATTATAATTTCATTATTACTAATCATTACTA--AATC
* * *
28961 ATCATTAAAT-ATTAATAATAATTTCATTATTACTAATCATTACTAAATA
1 ATTATTAAATCATT-ATTATAATTTCATTATTACTAATCATTACTAAATC
* * *
29010 ATTATTATAAT-TTTAAATATAAATTCATTATTA
1 ATTATTA-AATCATT-ATTATAATTTCATTATTA
29043 AATCATGATT
Statistics
Matches: 594, Mismatches: 70, Indels: 168
0.71 0.08 0.20
Matches are distributed among these distances:
42 6 0.01
44 7 0.01
45 3 0.01
46 32 0.05
47 15 0.03
48 9 0.02
49 209 0.35
50 77 0.13
51 50 0.08
52 62 0.10
53 27 0.05
54 2 0.00
55 9 0.02
56 17 0.03
57 9 0.02
58 4 0.01
59 7 0.01
60 36 0.06
61 1 0.00
62 12 0.02
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (49 bp):
ATTATTAAATCATTATTATAATTTCATTATTACTAATCATTACTAAATC
Found at i:28611 original size:98 final size:98
Alignment explanation
Indices: 28245--28565 Score: 414
Period size: 98 Copynumber: 3.2 Consensus size: 98
28235 ATTAGTAATA
* * * *
28245 ATTATTAAATCATTATTATAA-AATCATTACTAAATCATTACTATTAAATCATTATTAT-AATGA
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTA-T-AATGATTATTATCAA--A
* * * * * * ** *
28308 TTATTATTAAATCATTATTATTATTATTATTATTATTATT
62 TCATTAATAAATCATCA-AATCATTA--AATATTAAAATC
*
28348 ATCATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
*
28413 TACTAAATCATCAAATCATTAAATATTAAAATC
66 TAATAAATCATCAAATCATTAAATATTAAAATC
28446 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
28511 TAATAAAT-ATTCAAATCATTAAATATTAAAATC
66 TAATAAATCA-TCAAATCATTAAATATTAAAATC
28544 ATTATTAAATCATTATTATAAT
1 ATTATTAAATCATTATTATAAT
28566 TTCATTATTA
Statistics
Matches: 199, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
97 1 0.01
98 124 0.62
100 6 0.03
101 15 0.08
102 11 0.06
103 23 0.12
104 19 0.10
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (98 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
TAATAAATCATCAAATCATTAAATATTAAAATC
Found at i:28642 original size:98 final size:97
Alignment explanation
Indices: 28442--28763 Score: 311
Period size: 98 Copynumber: 3.3 Consensus size: 97
28432 TAAATATTAA
* * * * * *
28442 AATCATTATTAAATCATTATTATAA--TGATTATTACTAAATCATTATTATAATGATTATTATCA
1 AATCATTATTAAATCATTATTATAATTTAATTATTA-T-AATAATTACTA-AATCATTACTACCA
* * * * *
28505 AATCATTAATAAATATTCA-AATCA-TTAAATATTA-A
63 AATCA-T--TAAATATTAATAATAATTTCATTATTACT
*
28540 AATCATTATTAAATCATTATTATAATTTCATTATTAGTAATAATTACTAAATCATTACTACCAAA
1 AATCATTATTAAATCATTATTATAATTTAATTATTA-TAATAATTACTAAATCATTACTACCAAA
28605 TCATTAAATATTAATAATAATTTCATTATTACT
65 TCATTAAATATTAATAATAATTTCATTATTACT
* * * *
28638 AATCATTACTACCAAATCATTA-AAT-ATTAATAATAATT-TAATTATTACT-AATCATTACTAC
1 AATCATTA-T--TAAATCATTATTATAATT--TAATTATTATAATAATTACTAAATCATTACTAC
28699 CAAATCATTAAATATTAATAATAATTTCATTATTACT
61 CAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
28736 AATCATTACTAAATAATTATTATAATTT
1 AATCATTATTAAATCATTATTATAATTT
28764 TAAATATAAA
Statistics
Matches: 191, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
95 18 0.09
96 6 0.03
97 12 0.06
98 106 0.55
99 23 0.12
100 11 0.06
101 15 0.08
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.43
Consensus pattern (97 bp):
AATCATTATTAAATCATTATTATAATTTAATTATTATAATAATTACTAAATCATTACTACCAAAT
CATTAAATATTAATAATAATTTCATTATTACT
Found at i:28815 original size:16 final size:16
Alignment explanation
Indices: 28794--28835 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
28784 AATCATGATT
28794 ATCAAATCATTACTAA
1 ATCAAATCATTACTAA
28810 ATCAAATCATTACTAA
1 ATCAAATCATTACTAA
28826 ATCAAATCAT
1 ATCAAATCAT
28836 ATCATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ATCAAATCATTACTAA
Found at i:28854 original size:13 final size:14
Alignment explanation
Indices: 28836--28869 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28826 ATCAAATCAT
*
28836 ATCATTATTA-CAA
1 ATCATTACTACCAA
28849 ATCATTACTACCAA
1 ATCATTACTACCAA
28863 ATCATTA
1 ATCATTA
28870 AATATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
ATCATTACTACCAA
Found at i:28879 original size:259 final size:259
Alignment explanation
Indices: 28582--29111 Score: 1051
Period size: 259 Copynumber: 2.0 Consensus size: 259
28572 ATTAGTAATA
28582 ATTACTAAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTAC-AAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
28647 TACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTACCAAATCATTAAAT
65 TACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTACCAAATCATTAAAT
28712 ATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTATTATAATTTTAAATATAAATTC
130 ATTAATAATAATTTCATTATTACTAATCATTACTAAATAATTATTATAATTTTAAATATAAATTC
28777 ATTATTAAATCATGATTATCAAATCATTACTAAATCAAATCATTACTAAATCAAATCATATCATT
195 ATTATTAAATCATGATTATCAAATCATTACTAAATCAAATCATTACTAAATCAAATCATATCATT
28842 ATTACAAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACAAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
28907 ACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTACCAAATCATTAAATA
66 ACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTACCAAATCATTAAATA
28972 TTAATAATAATTTCATTATTACTAATCATTACTAAATAATTATTATAATTTTAAATATAAATTCA
131 TTAATAATAATTTCATTATTACTAATCATTACTAAATAATTATTATAATTTTAAATATAAATTCA
29037 TTATTAAATCATGATTATCAAATCATTACTAAATCAAATCATTACTAAATCAAATCATATCATT
196 TTATTAAATCATGATTATCAAATCATTACTAAATCAAATCATTACTAAATCAAATCATATCATT
29101 ATTACAAATCA
1 ATTACAAATCA
29112 AACAAGTGTT
Statistics
Matches: 270, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
259 265 0.98
260 5 0.02
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (259 bp):
ATTACAAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
ACCAAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTACCAAATCATTAAATA
TTAATAATAATTTCATTATTACTAATCATTACTAAATAATTATTATAATTTTAAATATAAATTCA
TTATTAAATCATGATTATCAAATCATTACTAAATCAAATCATTACTAAATCAAATCATATCATT
Found at i:29074 original size:16 final size:16
Alignment explanation
Indices: 29053--29094 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
29043 AATCATGATT
29053 ATCAAATCATTACTAA
1 ATCAAATCATTACTAA
29069 ATCAAATCATTACTAA
1 ATCAAATCATTACTAA
29085 ATCAAATCAT
1 ATCAAATCAT
29095 ATCATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ATCAAATCATTACTAA
Found at i:31961 original size:13 final size:13
Alignment explanation
Indices: 31924--31954 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
31914 AAATAAAAAA
31924 ATAAAAAAATTTAG
1 ATAAAAAAA-TTAG
31938 ATAAAAAAATTAG
1 ATAAAAAAATTAG
31951 ATAA
1 ATAA
31955 GATAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (13 bp):
ATAAAAAAATTAG
Found at i:32109 original size:22 final size:22
Alignment explanation
Indices: 32084--32126 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32074 TAATCTAATA
32084 TAAATTAA-ACAAAATATTTTTT
1 TAAA-TAACACAAAATATTTTTT
*
32106 TAAATAACACTAAATATTTTT
1 TAAATAACACAAAATATTTTT
32127 AAACACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATAACACAAAATATTTTTT
Found at i:32142 original size:17 final size:17
Alignment explanation
Indices: 32088--32148 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
32078 CTAATATAAA
*
32088 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
*
32105 TTAAATAACACTAA-ATATTT
1 TT--A-AACAC-AATATTTTT
32125 TTAAACACAATATTTTTT
1 TTAAACACAATA-TTTTT
32143 TTAAAC
1 TTAAAC
32149 GTGAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.23
18 11 0.31
19 1 0.03
20 11 0.31
21 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:32207 original size:84 final size:83
Alignment explanation
Indices: 32107--32280 Score: 276
Period size: 84 Copynumber: 2.1 Consensus size: 83
32097 ATATTTTTTT
* * *
32107 AAATAACACTAAATATTTTTAAACACAATATTTTTTTTAAACGTGAATAAATTAAACAAATTAAT
1 AAATAACACTAAATATTTTTAAACAAAATATGTTTTTTAAACGGGAATAAATTAAACAAATTAAT
32172 TTTATATAATCTAATATA
66 TTTATATAATCTAATATA
**
32190 AAATAAACACTAAATATTTTTAAACAAAATATGTTTTTTAAACGGGAATAAATTAAACACGTTAA
1 AAAT-AACACTAAATATTTTTAAACAAAATATGTTTTTTAAACGGGAATAAATTAAACAAATTAA
*
32255 TTTTATATACTCTAATATA
65 TTTTATATAATCTAATATA
*
32274 AACTAAC
1 AAATAAC
32281 TAACTAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 7 0.08
84 76 0.92
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (83 bp):
AAATAACACTAAATATTTTTAAACAAAATATGTTTTTTAAACGGGAATAAATTAAACAAATTAAT
TTTATATAATCTAATATA
Found at i:32324 original size:14 final size:14
Alignment explanation
Indices: 32305--32331 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32295 ACACATACAC
32305 AACAACAAAAAATG
1 AACAACAAAAAATG
32319 AACAACAAAAAAT
1 AACAACAAAAAAT
32332 AATAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:32755 original size:28 final size:28
Alignment explanation
Indices: 32724--32777 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
32714 ATAATCTAAT
*
32724 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
32752 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
32778 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:32784 original size:28 final size:28
Alignment explanation
Indices: 32720--32784 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
32710 TTATATAATC
*
32720 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
32748 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
32776 TAATTTATA
1 TAATATATA
32785 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:32787 original size:21 final size:21
Alignment explanation
Indices: 32754--32818 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
32744 TTAATATAAT
* *
32754 ATAACTTAAACTAACAAACTA
1 ATAATTTATACTAACAAACTA
32775 ATAATTTATACTAACAAACTA
1 ATAATTTATACTAACAAACTA
32796 ATAATTTATACTAACAAACTA
1 ATAATTTATACTAACAAACTA
32817 AT
1 AT
32819 TAACTAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATTTATACTAACAAACTA
Found at i:33345 original size:21 final size:21
Alignment explanation
Indices: 33321--33380 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
33311 GCTGCAAGAT
*
33321 GAATCACGCGAGGAGCAGGAG
1 GAATCACGCGAGGAGCAGCAG
* * ** *
33342 GAAT-AGGTGCAGTTGCAACAG
1 GAATCACGCG-AGGAGCAGCAG
33363 GAATCACGCGAGGAGCAG
1 GAATCACGCGAGGAGCAG
33381 AAGTGCACGG
Statistics
Matches: 26, Mismatches: 11, Indels: 4
0.63 0.27 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.33, C:0.18, G:0.38, T:0.10
Consensus pattern (21 bp):
GAATCACGCGAGGAGCAGCAG
Found at i:33415 original size:29 final size:29
Alignment explanation
Indices: 33382--33455 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
33372 GAGGAGCAGA
* *
33382 AGTGCACGGCGACCTACAAGGTCGTCCGG
1 AGTGCATGGCGACCTACAAGGTCGCCCGG
* *
33411 AGTGCTTGACGACCTACAAGGTCGCCCGG
1 AGTGCATGGCGACCTACAAGGTCGCCCGG
33440 AGTGCATGGCGACCTA
1 AGTGCATGGCGACCTA
33456 TGGTTGGGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (29 bp):
AGTGCATGGCGACCTACAAGGTCGCCCGG
Found at i:34013 original size:56 final size:55
Alignment explanation
Indices: 33927--34036 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 55
33917 GACGGGCCTG
33927 CTTTTAATGTTTATGCAGATTGGAAAGGAAAAAAGAAACAAATTTGAACGAACCCA
1 CTTTTAATGTTTATGCAGATTGGAAAGG-AAAAAGAAACAAATTTGAACGAACCCA
* *
33983 CTTTTAATGTTTATGCAGATTGGGAAGGAAAAAGAAACAACTTTGAACGAACCC
1 CTTTTAATGTTTATGCAGATTGGAAAGGAAAAAGAAACAAATTTGAACGAACCC
34037 GAATCGGTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 25 0.48
56 27 0.52
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (55 bp):
CTTTTAATGTTTATGCAGATTGGAAAGGAAAAAGAAACAAATTTGAACGAACCCA
Found at i:35961 original size:34 final size:33
Alignment explanation
Indices: 35896--35976 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 33
35886 AAATCAAGGG
* *
35896 AATAATTTATTTCATAATAATTGTATTTCCATCC
1 AATAATTT-TTTTATAATAATTGTATCTCCATCC
*
35930 AATAGATTTTTTTATAGTAATTGTATCTCCATCC
1 AATA-ATTTTTTTATAATAATTGTATCTCCATCC
35964 AATACATTTTTTT
1 AATA-ATTTTTTT
35977 GGCAACCAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 38 0.90
35 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (33 bp):
AATAATTTTTTTATAATAATTGTATCTCCATCC
Found at i:43370 original size:51 final size:49
Alignment explanation
Indices: 43315--43425 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 49
43305 GCTCCCTGCC
**
43315 CCGCGCTATATGCTGATTTGGC-ACCACGTGGGGTATAGCGCGCCCCCTGTA
1 CCGCGCTATATGCTGACATGGCTA-CACGT-GGGTATAGCGCG-CCCCTGTA
* * *
43366 CCGCGTTATATGTTGACATGGCTTACACGTGGGTATAGCGCGCCCCTGTT
1 CCGCGCTATATGCTGACATGGC-TACACGTGGGTATAGCGCGCCCCTGTA
43416 CCGCGCTATA
1 CCGCGCTATA
43426 GTTGTTTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
50 16 0.31
51 30 0.58
52 5 0.10
53 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (49 bp):
CCGCGCTATATGCTGACATGGCTACACGTGGGTATAGCGCGCCCCTGTA
Found at i:45716 original size:15 final size:15
Alignment explanation
Indices: 45696--45730 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45686 ACCTTCTCAG
45696 GATGACGAAGACAAC
1 GATGACGAAGACAAC
* *
45711 GATGACGACGACGAC
1 GATGACGAAGACAAC
45726 GATGA
1 GATGA
45731 TGATGACAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.31, T:0.09
Consensus pattern (15 bp):
GATGACGAAGACAAC
Found at i:45922 original size:26 final size:24
Alignment explanation
Indices: 45851--45922 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
45841 TTACATTTGT
45851 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
45876 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
45898 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
45923 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:45990 original size:35 final size:33
Alignment explanation
Indices: 45950--46034 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
45940 TGTATATAGT
*
45950 TAATTTTGTT-TATTACGATTTAATATCATTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
45985 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
46020 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
46035 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:49800 original size:30 final size:29
Alignment explanation
Indices: 49739--49800 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
49729 ACTGCAACGA
*
49739 GTGTTAGATCGAGAAATATAATCTGACCG
1 GTGTTAGATCGAGAAATATAATCTCACCG
49768 GTGTTAGATCG-GTAAATAT-ATCGGTCACCG
1 GTGTTAGATCGAG-AAATATAATC--TCACCG
49798 GTG
1 GTG
49801 ATTTTTCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 8 0.28
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (29 bp):
GTGTTAGATCGAGAAATATAATCTCACCG
Found at i:50453 original size:80 final size:80
Alignment explanation
Indices: 50320--50501 Score: 346
Period size: 80 Copynumber: 2.3 Consensus size: 80
50310 GCTGCGGTTG
50320 TAGTCTTTCTCTTCCTCTTCTTCTTCCTCCTCCTCGCATTCACTTCTGCTTCCCTGAAGCTGTTG
1 TAGTCTTTCTCTTCCTCTTCTTCTTCCTCCTCCTCGCATTCACTTCTGCTTCCCTGAAGCTGTTG
50385 TTTTGCAAATCTCCT
66 TTTTGCAAATCTCCT
50400 TAGTCTTTCTCTTCCTCTTCTTCTTCCTCCTCCTCGCATTCACTTCTGCTTCCCTGAAGCTGTTG
1 TAGTCTTTCTCTTCCTCTTCTTCTTCCTCCTCCTCGCATTCACTTCTGCTTCCCTGAAGCTGTTG
50465 TTTTGCAAATCTCCT
66 TTTTGCAAATCTCCT
*
50480 TAGTCTTCTCTGTTCCTCTTCT
1 TAGTCTT-TCTCTTCCTCTTCT
50502 GCATTGTTAT
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 87 0.87
81 13 0.13
ACGTcount: A:0.09, C:0.35, G:0.10, T:0.46
Consensus pattern (80 bp):
TAGTCTTTCTCTTCCTCTTCTTCTTCCTCCTCCTCGCATTCACTTCTGCTTCCCTGAAGCTGTTG
TTTTGCAAATCTCCT
Found at i:65203 original size:50 final size:50
Alignment explanation
Indices: 65098--65204 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
65088 TCACACTCCA
* * * *
65098 ATTTGTCTTTTCATCGCGACTAGGAGGGTTGGATAGAGCCATATTATTTT
1 ATTTTTCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATTCT
* *
65148 GTTTTTCTTTTCATTGCGACTAGGAGGGCTT-GATAG-GACATTATCCA-TCT
1 ATTTTTCTTTTCATCGCGACTAGGAGGG-TTGGATAGAGACA-TAT-CATTCT
65198 ATTTTTC
1 ATTTTTC
65205 GCAAATCCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
49 3 0.06
50 41 0.87
51 3 0.06
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (50 bp):
ATTTTTCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATTCT
Done.