Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004866.1 Hibiscus syriacus cultivar Beakdansim tig00010974_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: 66553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1866 original size:29 final size:29
Alignment explanation
Indices: 1815--1879 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 29
1805 TATGTCCCGA
1815 AGGTAAACATCCATATGTCCCGAAGAACAT
1 AGGTAAACATCCA-ATGTCCCGAAGAACAT
1845 AGGTAAACAGTCC-ATGTCCCGAAGAACAT
1 AGGTAAACA-TCCAATGTCCCGAAGAACAT
1874 AGGTAA
1 AGGTAA
1880 CCCTCGACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 22 0.65
30 9 0.26
31 3 0.09
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (29 bp):
AGGTAAACATCCAATGTCCCGAAGAACAT
Found at i:2755 original size:21 final size:21
Alignment explanation
Indices: 2731--2775 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2721 TTTTGTTCGT
* *
2731 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2752 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2773 TTG
1 TTG
2776 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:9102 original size:19 final size:19
Alignment explanation
Indices: 9075--9131 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
9065 ACGTTTTTCA
*
9075 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
9094 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
*
9113 AATTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
9132 TCAAAAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:10271 original size:29 final size:29
Alignment explanation
Indices: 10229--10285 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
10219 ATGGTTCTGG
* * *
10229 GTAGGTCGTCAGGGTATCCCAGCGACATT
1 GTAGGTCGCCAGGGCATCCCAACGACATT
10258 GTAGGTCGCCAGGGCATCCCAACGACAT
1 GTAGGTCGCCAGGGCATCCCAACGACAT
10286 GCATGCTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCAGGGCATCCCAACGACATT
Found at i:10613 original size:8 final size:9
Alignment explanation
Indices: 10583--10620 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
10573 GAGGTAAGTT
10583 TTTTAATTA
1 TTTTAATTA
10592 TTTTAATTA
1 TTTTAATTA
*
10601 CTTT-ATTA
1 TTTTAATTA
10609 TTTTAAATTA
1 TTTT-AATTA
10619 TT
1 TT
10621 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:0.03, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:10687 original size:39 final size:39
Alignment explanation
Indices: 10637--10721 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
10627 TTAGTTTATG
*
10637 GTTTAAGGTAAAACAATATTTTAGTTAATTAGTTAGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
*
10676 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTTGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
10715 GTTTAAG
1 GTTTAAG
10722 TTATATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (39 bp):
GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTAGTTA
Found at i:11103 original size:21 final size:21
Alignment explanation
Indices: 11078--11117 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11068 GTTAATTAGT
11078 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
11099 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
11118 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:11347 original size:29 final size:30
Alignment explanation
Indices: 11298--11387 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
11288 TAATTAATTT
* *
11298 TTTAGTAG-TAAA-TTATAATTAAA-AATCG
1 TTTATTAGTTAAAGTTAT-ATTAAAGAATAG
*
11326 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
11356 TTTATTAGTTAAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
11386 TT
1 TT
11388 AAAATTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.13
29 9 0.16
30 39 0.71
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTATTAGTTAAAGTTATATTAAAGAATAG
Found at i:11356 original size:22 final size:22
Alignment explanation
Indices: 11331--11411 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
11321 AATCGTTTAT
11331 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
11353 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
* *
11383 TAGTTAAAATTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
11405 TAGTTTA
1 TAGTTTA
11412 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 23 0.48
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 18 0.38
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:11359 original size:30 final size:29
Alignment explanation
Indices: 11310--11417 Score: 124
Period size: 30 Copynumber: 3.9 Consensus size: 29
11300 TAGTAGTAAA
*
11310 TTATAATTAAA-AATCGTTTATTAGTTTAAG
1 TTAT-ATTAAAGAATAGTTTATTAG-TTAAG
11340 TTATATTAAAGAATAGTTTATTAGTTAAAG
1 TTATATTAAAGAATAGTTTATTAGTT-AAG
11370 TTATATTAAAGAATAG-TTA--A---AA-
1 TTATATTAAAGAATAGTTTATTAGTTAAG
11392 TTATATTAAAGAATAGTTTATTAGTT
1 TTATATTAAAGAATAGTTTATTAGTT
11418 GTTTAAGGGA
Statistics
Matches: 69, Mismatches: 1, Indels: 18
0.78 0.01 0.20
Matches are distributed among these distances:
22 16 0.23
23 5 0.07
25 1 0.01
27 1 0.01
29 11 0.16
30 35 0.51
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (29 bp):
TTATATTAAAGAATAGTTTATTAGTTAAG
Found at i:11361 original size:15 final size:16
Alignment explanation
Indices: 11338--11388 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
11328 TATTAGTTTA
11338 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
***
11354 AGTT-TATTAGTTAA-
1 AGTTATATTAAAGAAT
11368 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
11384 AGTTA
1 AGTTA
11389 AAATTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:11770 original size:20 final size:20
Alignment explanation
Indices: 11745--11817 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
11735 CAATACAAAA
*
11745 TCGCAACGCGATACTAACTT
1 TCGCAACGCGATACTGACTT
*
11765 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
11785 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
*
11805 TCGCAACGAGATA
1 TCGCAACGCGATA
11818 ATACAGAATC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:12000 original size:12 final size:12
Alignment explanation
Indices: 11971--12011 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
11961 CTCTCTGGCG
11971 ACATCCGTTCCC
1 ACATCCGTTCCC
* *
11983 ATATCCGTTCCT
1 ACATCCGTTCCC
11995 ACATCC-TTCCC
1 ACATCCGTTCCC
12006 -CATCCG
1 ACATCCG
12012 GCAACAGGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.21
11 4 0.17
12 15 0.62
ACGTcount: A:0.17, C:0.46, G:0.07, T:0.29
Consensus pattern (12 bp):
ACATCCGTTCCC
Found at i:12178 original size:20 final size:20
Alignment explanation
Indices: 12153--12190 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12143 ATTCATTTGA
*
12153 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
12173 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
12191 CGCAATGCGA
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:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:12413 original size:14 final size:14
Alignment explanation
Indices: 12394--12430 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12384 CATCAATTAA
12394 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
12408 ACAAATCATCTTTT
1 ACAAATCAACATTT
12422 ACAAATCAA
1 ACAAATCAA
12431 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:14355 original size:19 final size:20
Alignment explanation
Indices: 14300--14367 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
14290 GAAACTTAAA
*
14300 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
14320 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* * **
14340 ATCGTAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
14359 ATCGCAACG
1 ATCGCAACG
14368 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:14375 original size:14 final size:14
Alignment explanation
Indices: 14356--14413 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
14346 ATGCGAAATG
14356 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
14370 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
14386 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
14402 AAAATCGCAACG
1 AAAATCGCAACG
14414 TGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:14398 original size:32 final size:33
Alignment explanation
Indices: 14340--14411 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
14330 GGAAATGGCT
*
14340 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
14373 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
14405 ATCGCAA
1 ATCGCAA
14412 CGTGAAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 23 0.61
33 15 0.39
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:14447 original size:19 final size:19
Alignment explanation
Indices: 14425--14521 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
14415 GAAACACAAA
14425 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
14444 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
14460 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
14477 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
14493 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
14510 TCGCATTGCGAT
1 TCGCATTGCGAT
14522 AGCCATTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:14466 original size:14 final size:14
Alignment explanation
Indices: 14447--14505 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
14437 TTTCATTTCG
14447 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
14461 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
14478 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
14494 CGTTGCGATTTT
1 CGTTGCGATTTT
14506 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:14541 original size:39 final size:33
Alignment explanation
Indices: 14430--14521 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
14420 ACAAATCGCA
*
14430 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
14463 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
14496 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
14522 AGCCATTTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:14557 original size:20 final size:20
Alignment explanation
Indices: 14508--14560 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
14498 GCGATTTTCA
*
14508 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
14528 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
14548 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
14561 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:15062 original size:18 final size:18
Alignment explanation
Indices: 15036--15080 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
15026 GTCGATCAGA
* *
15036 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
15054 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
15072 TGATGGCTC
1 TGATGGCTC
15081 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:16425 original size:20 final size:20
Alignment explanation
Indices: 16400--16442 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16390 AATAGTTTCT
16400 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* * *
16420 GAAAATGACAATCTCAACGC
1 GAAAATGAAAATCGCAACAC
16440 GAA
1 GAA
16443 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:16760 original size:22 final size:22
Alignment explanation
Indices: 16721--16764 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16711 GATGGAGATA
*
16721 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
16743 GACGGATTTTGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
16765 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:16982 original size:20 final size:20
Alignment explanation
Indices: 16952--17085 Score: 135
Period size: 20 Copynumber: 6.7 Consensus size: 20
16942 GATTATGTAT
*
16952 TATCACGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
16972 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
16992 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
17012 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* * *
17033 TATTGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
17053 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
17073 TATCGCATTGCGA
1 TATCGCGTTGCGA
17086 TTTTCCCAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.03
20 82 0.84
21 11 0.11
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:17086 original size:20 final size:20
Alignment explanation
Indices: 16932--17086 Score: 134
Period size: 20 Copynumber: 7.7 Consensus size: 20
16922 CGCTTAGAAA
*
16932 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * * *
16953 ATCACGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
16973 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
16993 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
17013 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
17034 ATTGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
17054 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
17074 ATCGCATTGCGAT
1 ATCGCATTGCGAT
17087 TTTCCCAATT
Statistics
Matches: 113, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
19 5 0.04
20 85 0.75
21 21 0.19
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:17105 original size:61 final size:61
Alignment explanation
Indices: 16974--17107 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
16964 AAAGTCAGAA
* * * * **
16974 TCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTAT
1 TCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCA-TAT
* *
17036 T-GCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCA-AT
1 TCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCATAT
17096 TCGCGTTGCGAT
1 TCGCGTTGCGAT
17108 TTACTTATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 3 0.05
61 56 0.92
62 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (61 bp):
TCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCATAT
Found at i:17197 original size:21 final size:21
Alignment explanation
Indices: 17157--17197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17147 ACTGTAGACC
** *
17157 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
17178 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
17198 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:19697 original size:59 final size:57
Alignment explanation
Indices: 19603--19729 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 57
19593 TTTTAGTATC
* *
19603 AAATCATTATTATAATTTCATTACTAGTAATCATTAGTATTAAATAATTAAATATTAATAA
1 AAATCATTATTATAA-TTAATTACTAG-AATCATTAGTATCAAATAATTAAATATT--TAA
*
19664 TAAATCATTATTATTAA-TAATTACTA-AATCATTAGTATCAAATCATTAAATATTTAA
1 -AAATCATTATTA-TAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATTTAA
19721 AAATCATTA
1 AAATCATTA
19730 ATAAATTCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 26 0.43
61 8 0.13
62 12 0.20
63 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (57 bp):
AAATCATTATTATAATTAATTACTAGAATCATTAGTATCAAATAATTAAATATTTAA
Found at i:19839 original size:14 final size:14
Alignment explanation
Indices: 19816--20072 Score: 113
Period size: 14 Copynumber: 19.6 Consensus size: 14
19806 TAGTAATAAT
19816 TATTAAATCATTAG
1 TATTAAATCATTAG
* *
19830 TATTATATCATTAT
1 TATTAAATCATTAG
*
19844 TATAAAATCA-T--
1 TATTAAATCATTAG
*
19855 TACTAAATCA-T--
1 TATTAAATCATTAG
*
19866 TATTAAATCATTAC
1 TATTAAATCATTAG
*
19880 TATTAAATCATTAT
1 TATTAAATCATTAG
* *
19894 TA-T-AATGATTAT
1 TATTAAATCATTAG
*
19906 TATTAAATCATTAT
1 TATTAAATCATTAG
* *
19920 TA-T-AATGATTAT
1 TATTAAATCATTAG
19932 TATTAAATCA-T--
1 TATTAAATCATTAG
*
19943 TATT--ATCATTAT
1 TATTAAATCATTAG
*
19955 TATTAAATCATTAT
1 TATTAAATCATTAG
* *
19969 TA-T-AATGATTAT
1 TATTAAATCATTAG
* *
19981 TACTAAATCATTAT
1 TATTAAATCATTAG
* *
19995 TA-TAATTTCATTAC
1 TATTAA-ATCATTAG
*
20009 TAGT-AATCATTAG
1 TATTAAATCATTAG
* *
20022 TATTAAATAATTAAA
1 TATTAAATCATT-AG
* * *
20037 TATT-AATAATAAA
1 TATTAAATCATTAG
*
20050 TACTAAATCATTAG
1 TATTAAATCATTAG
*
20064 TATCAAATC
1 TATTAAATC
20073 GTTAAATATT
Statistics
Matches: 196, Mismatches: 28, Indels: 38
0.75 0.11 0.15
Matches are distributed among these distances:
9 4 0.02
10 1 0.01
11 22 0.11
12 35 0.18
13 25 0.13
14 103 0.53
15 6 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:19911 original size:26 final size:26
Alignment explanation
Indices: 19801--20000 Score: 243
Period size: 26 Copynumber: 8.0 Consensus size: 26
19791 TTATTCCATA
* *
19801 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* * *
19825 ATTAGTATTATATCATTATTATAA-A
1 ATTATTATTAAATCATTATTATAATC
* *
19850 ATCATTACTAAATCATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
19875 ATTACTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
*
19901 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
19927 ATTATTATTAAATCATTA-T-T-ATC
1 ATTATTATTAAATCATTATTATAATC
*
19950 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
*
19976 ATTATTACTAAATCATTATTATAAT
1 ATTATTATTAAATCATTATTATAAT
20001 TTCATTACTA
Statistics
Matches: 151, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.13
24 11 0.07
25 46 0.30
26 74 0.49
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATC
Found at i:19997 original size:3 final size:3
Alignment explanation
Indices: 19889--19982 Score: 50
Period size: 3 Copynumber: 32.3 Consensus size: 3
19879 CTATTAAATC
* * * * * *
19889 ATT ATT ATA ATG ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
19936 A-A ATC ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19982 A
1 A
19983 CTAAATCATT
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
2 3 0.04
3 65 0.96
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (3 bp):
ATT
Found at i:20041 original size:21 final size:20
Alignment explanation
Indices: 20017--20082 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
20007 ACTAGTAATC
20017 ATTAGTATTAAATAATTAAAT
1 ATTAGTATTAAAT-ATTAAAT
* * *
20038 ATTAATAATAAATACTAAAT
1 ATTAGTATTAAATATTAAAT
* *
20058 CATTAGTATCAAATCGTTAAAT
1 -ATTAGTATTAAAT-ATTAAAT
20080 ATT
1 ATT
20083 TAAAAATCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 6 0.17
21 24 0.69
22 5 0.14
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTAGTATTAAATATTAAAT
Found at i:20200 original size:14 final size:14
Alignment explanation
Indices: 20179--20396 Score: 113
Period size: 14 Copynumber: 16.1 Consensus size: 14
20169 ATTAGTAATA
20179 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
20193 AGTATTAAATAATT
1 ATTATTAAATCATT
*
20207 ATTA-TAAA--ATA
1 ATTATTAAATCATT
* *
20218 ATTACTAAATAATT
1 ATTATTAAATCATT
*
20232 ACTATTAAATCATT
1 ATTATTAAATCATT
*
20246 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
20258 ATTACTAAATCATT
1 ATTATTAAATCATT
*
20272 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
20284 ATTATCAAATCATT
1 ATTATTAAATCATT
*
20298 ACTAAATCATAAAATCATT
1 A-T---T-ATTAAATCATT
* *
20317 AAATATTAAA--ATC
1 -ATTATTAAATCATT
*
20330 ATTATTAAATCGTT
1 ATTATTAAATCATT
*
20344 ATTA-TAATTTCATT
1 ATTATTAA-ATCATT
*
20358 ATTACT-AAT-A--
1 ATTATTAAATCATT
20368 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
20382 ACTATCAAATCATT
1 ATTATTAAATCATT
20396 A
1 A
20397 AATATTAATA
Statistics
Matches: 156, Mismatches: 27, Indels: 42
0.69 0.12 0.19
Matches are distributed among these distances:
10 5 0.03
11 9 0.06
12 34 0.22
13 13 0.08
14 75 0.48
15 7 0.04
16 1 0.01
18 1 0.01
19 10 0.06
20 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:20258 original size:26 final size:26
Alignment explanation
Indices: 20174--20298 Score: 135
Period size: 26 Copynumber: 4.8 Consensus size: 26
20164 TAATTATTAG
* *
20174 TAATAATTATTAAATCATTAGTATTAAA
1 TAATTATTATTAAATCATTATTA-T-AA
* * *
20202 TAATTATTATAAAATAATTACTA-AA
1 TAATTATTATTAAATCATTATTATAA
*
20227 TAATTACTATTAAATCATTATTATAA
1 TAATTATTATTAAATCATTATTATAA
* *
20253 TGATTATTACTAAATCATTATTATAA
1 TAATTATTATTAAATCATTATTATAA
* *
20279 TGATTATTATCAAATCATTA
1 TAATTATTATTAAATCATTA
20299 CTAAATCATA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
25 21 0.25
26 43 0.52
28 19 0.23
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTATTATTAAATCATTATTATAA
Found at i:20336 original size:19 final size:19
Alignment explanation
Indices: 20290--20340 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
20280 GATTATTATC
*
20290 AAATCATTACTAAATCATA
1 AAATCATTATTAAATCATA
20309 AAATC---ATTAAAT-ATTA
1 AAATCATTATTAAATCA-TA
20325 AAATCATTATTAAATC
1 AAATCATTATTAAATC
20341 GTTATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
19 12 0.46
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATCATTATTAAATCATA
Found at i:20384 original size:21 final size:20
Alignment explanation
Indices: 20357--20412 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
20347 ATAATTTCAT
20357 TATTACTAATAATTATTAAA
1 TATTACTAATAATTATTAAA
*
20377 TCATTACT-ATCAAATCATTAAA
1 T-ATTACTAAT--AATTATTAAA
*
20399 TATTAATAATAATT
1 TATTACTAATAATT
20413 TCATTATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 12 0.41
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTACTAATAATTATTAAA
Found at i:20426 original size:18 final size:17
Alignment explanation
Indices: 20399--20671 Score: 56
Period size: 18 Copynumber: 16.6 Consensus size: 17
20389 AATCATTAAA
*
20399 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
20417 TATTAC---TAA-TCAT
1 TATTACTAATAATTCAT
* * * *
20430 TACTACTAAATCATTAAA
1 TATTACT-AATAATTCAT
*
20448 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
20466 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
20482 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
20497 TATTAATAATAATT--T
1 TATTACTAATAATTCAT
* *
20512 TATTATTACTAA-TCAT
1 TATTACTAATAATTCAT
* * * * *
20528 AACTACTAAATCATTAAA
1 TATTACT-AATAATTCAT
*
20546 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
20564 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
20580 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
20595 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
20613 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
20629 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
20644 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
20662 TATTACTAAT
1 TATTACTAAT
20672 CATTACTAAA
Statistics
Matches: 178, Mismatches: 55, Indels: 44
0.64 0.20 0.16
Matches are distributed among these distances:
13 9 0.05
14 25 0.14
15 25 0.14
16 17 0.10
17 33 0.19
18 69 0.39
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTACTAATAATTCAT
Found at i:20428 original size:49 final size:49
Alignment explanation
Indices: 20368--20738 Score: 569
Period size: 49 Copynumber: 7.6 Consensus size: 49
20358 ATTACTAATA
20368 ATTATTA--AATCATTACTATCAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
20415 ATTATTACTAATCATTACTA-CTAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTATC-AAATCATTAAATATTAATAATAATTTC
*
20464 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTT
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
*
20513 ATTATTACTAATCATAACTA-CTAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTATC-AAATCATTAAATATTAATAATAATTTC
20562 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
20611 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
* * * *
20660 ATTATTACTAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAATTC
1 ATTATTACTAATCATTACTATCA-AATCATTA-AATATTAATA-ATAATTTC
* *
20710 ATTATTA--AATCATGATTATCAAATCATTA
1 ATTATTACTAATCATTACTATCAAATCATTA
20739 CTAAATCAAA
Statistics
Matches: 302, Mismatches: 12, Indels: 19
0.91 0.04 0.06
Matches are distributed among these distances:
47 7 0.02
48 19 0.06
49 253 0.84
50 23 0.08
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTC
Found at i:20431 original size:13 final size:14
Alignment explanation
Indices: 20413--20445 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20403 AATAATAATT
*
20413 TCATTATTACT-AA
1 TCATTACTACTAAA
20426 TCATTACTACTAAA
1 TCATTACTACTAAA
20440 TCATTA
1 TCATTA
20446 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
TCATTACTACTAAA
Found at i:24097 original size:17 final size:17
Alignment explanation
Indices: 24042--24102 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
24032 ATAATATAAA
*
24042 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
24059 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
24080 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
*
24097 TAAAAC
1 TTAAAC
24103 GGAAATTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 5 0.15
20 4 0.12
21 8 0.24
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:24645 original size:28 final size:28
Alignment explanation
Indices: 24607--24660 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
24597 TAAATATAAT
24607 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
24635 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
24661 ATTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:24667 original size:28 final size:28
Alignment explanation
Indices: 24602--24667 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
24592 ATATATAAAT
24602 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
24630 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
24658 ATAATTTATA
1 ATAATATATA
24668 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:24670 original size:21 final size:21
Alignment explanation
Indices: 24637--24685 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
24627 CTAATATAAT
24637 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
24658 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
24679 ATTAACT
1 A-TAACT
24686 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:25166 original size:29 final size:29
Alignment explanation
Indices: 25152--25225 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
25142 ATATCGCCGA
25152 GAGTGCATGGCGACCTCCTTGGTCGCCCG
1 GAGTGCATGGCGACCTCCTTGGTCGCCCG
*
25181 GAGTGCATGGCGACCTCCTTGGTCGTCCG
1 GAGTGCATGGCGACCTCCTTGGTCGCCCG
*
25210 GAGAGCATGGCGACCT
1 GAGTGCATGGCGACCT
25226 ATGGGTTGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.14, C:0.31, G:0.35, T:0.20
Consensus pattern (29 bp):
GAGTGCATGGCGACCTCCTTGGTCGCCCG
Found at i:30153 original size:7 final size:7
Alignment explanation
Indices: 30141--30199 Score: 118
Period size: 7 Copynumber: 8.4 Consensus size: 7
30131 GCTGGAAAAG
30141 CTAAACC
1 CTAAACC
30148 CTAAACC
1 CTAAACC
30155 CTAAACC
1 CTAAACC
30162 CTAAACC
1 CTAAACC
30169 CTAAACC
1 CTAAACC
30176 CTAAACC
1 CTAAACC
30183 CTAAACC
1 CTAAACC
30190 CTAAACC
1 CTAAACC
30197 CTA
1 CTA
30200 GGGTTCTTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:30401 original size:113 final size:113
Alignment explanation
Indices: 30203--30413 Score: 334
Period size: 113 Copynumber: 1.9 Consensus size: 113
30193 AACCCTAGGG
* * * *
30203 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGT
1 TTCTTCTCATTACGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGT
30268 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA
* * * *
30316 TTCTTCTCATTACGAACTTCCTCTGG-AAAGTTTGATCCATCAAGTGATGGTTTTGAATAAAAAG
1 TTCTTCTCATTACGAACTTCCTCTGGAAAAG-CTGATCCATCAAATGATGGATTTGAACAAAAAG
30380 TTGAACAAATTCTTCTCATTATGAATTTCTTCTT
65 TTGAACAAATTCTTCTCATTATGAATTTCTTCTT
30414 TCAGATGAGT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 4 0.04
113 85 0.96
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTACGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGT
TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAA
Found at i:30411 original size:17 final size:17
Alignment explanation
Indices: 30389--30477 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
30379 GTTGAACAAA
*
30389 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
* *
30406 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAC
30423 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
30440 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
30459 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
30476 TT
1 TT
30478 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 27 0.48
18 9 0.16
19 14 0.25
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:30427 original size:34 final size:36
Alignment explanation
Indices: 30389--30480 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
30379 GTTGAACAAA
30389 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
30423 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
30459 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
30481 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:30538 original size:143 final size:149
Alignment explanation
Indices: 30274--30591 Score: 461
Period size: 143 Copynumber: 2.1 Consensus size: 149
30264 AGGTTGAACA
30274 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTC
1 AATTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTC
* * *
30339 TGGAAAGTTTGATCCATCAAGTGATGGTTTTGAATAAAAAGTTGAACAAATTCTTCTCATTATGA
63 TGGAAAGTCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
30404 A-T-TTCTT-C-T-TTCAGATG
128 ACTCTTCTTCCTTCTTCAGATG
* * * *
30421 AGTTCTTCTCATTATGAACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 AATTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG
* *
30485 AAAAG-CTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAAC
66 -AAAGTCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC
30549 TTCTTCTTCCTTCTTCAGATG
130 -TCTTCTTCCTTCTTCAGATG
30570 AATTCTTCTCATTATGAACTTC
1 AATTCTTCTCATTATGAACTTC
30592 CTCTGGAAAG
Statistics
Matches: 154, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
143 90 0.58
144 10 0.06
145 1 0.01
146 5 0.03
147 18 0.12
148 1 0.01
149 29 0.19
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (149 bp):
AATTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG
AAAGTCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACT
CTTCTTCCTTCTTCAGATG
Found at i:30620 original size:113 final size:109
Alignment explanation
Indices: 30421--30625 Score: 313
Period size: 113 Copynumber: 1.8 Consensus size: 109
30411 CTTTCAGATG
* *
30421 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGGA
*
30486 AAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
66 AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
*
30530 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTC
1 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTC
*
30595 TGG-AAAGTTTGATCCATCAAATGATGGATTT
62 TGGAAAAG-CTGATCCATCAAATGATGGATTT
30626 TAATATTTGC
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
109 17 0.20
112 10 0.12
113 59 0.69
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (109 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGGA
AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
Found at i:31575 original size:93 final size:93
Alignment explanation
Indices: 31416--31617 Score: 345
Period size: 93 Copynumber: 2.2 Consensus size: 93
31406 CTTATTTCTA
* *
31416 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTGTGGGTTCATACCAAACCAGACCAG
31481 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
31509 CTATGAGCACATTCATC-TTCTAAATTCAATGATTGGTTTT-TGGGGTTCATACCAAACCAGACC
1 CTATGAGCACATTCATCTTTC-AAATCCAATGATTGGTTTTGT-GGGTTCATACCAAACCAGACC
31572 AGATAACTCAAAGAACACTTCCAGAAGATG
64 AGATAACTCAAAGAACACTTCCAGAAGATG
31602 CTATGAGCACATTCAT
1 CTATGAGCACATTCAT
31618 ACCAAACCAG
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
92 4 0.04
93 100 0.96
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTTCAAATCCAATGATTGGTTTTGTGGGTTCATACCAAACCAGACCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:31646 original size:59 final size:59
Alignment explanation
Indices: 31554--31676 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
31544 GTTTTTGGGG
31554 TTCATACCAAACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
1 TTCATACCAAACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
*
31613 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
1 TTCATACCAAACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
31672 TTCAT
1 TTCAT
31677 CTTCCAAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (59 bp):
TTCATACCAAACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
Found at i:31737 original size:152 final size:152
Alignment explanation
Indices: 31461--31764 Score: 590
Period size: 152 Copynumber: 2.0 Consensus size: 152
31451 GTTTTGTGGT
31461 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC
1 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC
*
31526 TTCTAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGACCAGATAACTCAAAGAACACT
66 TTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGACCAGATAACTCAAAGAACACT
31591 TCCAGAAGATGCTATGAGCACA
131 TCCAGAAGATGCTATGAGCACA
31613 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC
1 TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC
*
31678 TTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACT
66 TTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGACCAGATAACTCAAAGAACACT
31743 TCCAGAAGATGCTATGAGCACA
131 TCCAGAAGATGCTATGAGCACA
31765 CGGCACTTGT
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (152 bp):
TTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC
TTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGACCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATGAGCACA
Found at i:32763 original size:1 final size:1
Alignment explanation
Indices: 32759--32857 Score: 90
Period size: 1 Copynumber: 99.0 Consensus size: 1
32749 TGACCCCCCA
* * * * * * *
32759 TTTTTTTTCTTTTTTTCTTTCTTTCTCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
32824 TTCTTTCTTTTTTTTATTTTTTCTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32858 CTTCAAGAAT
Statistics
Matches: 74, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:32793 original size:20 final size:20
Alignment explanation
Indices: 32768--32860 Score: 114
Period size: 21 Copynumber: 4.5 Consensus size: 20
32758 ATTTTTTTTC
*
32768 TTTTTTTCTTTCTTTCTCTTT
1 TTTTTTTCTTTTTTTCTC-TT
* *
32789 TTTTTTTCTTTTTTTTTTTT
1 TTTTTTTCTTTTTTTCTCTT
*
32809 TTTTTTTCTTTTTTTTTCTT
1 TTTTTTTCTTTTTTTCTCTT
*
32829 TCTTTTTTTTATTTTTTCTCTT
1 T-TTTTTTCT-TTTTTTCTCTT
32851 TTTTTTTCTT
1 TTTTTTTCTT
32861 CAAGAATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
20 23 0.37
21 29 0.46
22 11 0.17
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTCTCTT
Found at i:32795 original size:30 final size:29
Alignment explanation
Indices: 32759--32857 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 29
32749 TGACCCCCCA
*
32759 TTTTTTTTCTTTTTTTCTTTCTTTCTCTTTT
1 TTTTTTTTCTTTTTTT-TTTTTTTCTC-TTT
* *
32790 TTTTTTCTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTT-TTCTTTTTTTTTTTTTTCTC-TTT
32821 TTTTTCTTTCTTTTTTTTATTTTTTCTCTTT
1 TTTTT-TTTCTTTTTTTT-TTTTTTCTCTTT
32852 TTTTTT
1 TTTTTT
32858 CTTCAAGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 41 0.68
32 18 0.30
ACGTcount: A:0.01, C:0.11, G:0.00, T:0.88
Consensus pattern (29 bp):
TTTTTTTTCTTTTTTTTTTTTTTCTCTTT
Found at i:32815 original size:41 final size:42
Alignment explanation
Indices: 32759--32860 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 42
32749 TGACCCCCCA
*
32759 TTTTTTTTCTTTTTTTCTTTCTTTCTCTTT-TTTTTTTCT-TT
1 TTTTTTTTTTTTTTTTCTTTCTTTCTCTTTCTTTTTTT-TATT
* *
32800 TTTTTTTTTTTTTTTTCTTTTTTTTTCTTTCTTTTTTTTATT
1 TTTTTTTTTTTTTTTTCTTTCTTTCTCTTTCTTTTTTTTATT
* *
32842 TTTTCTCTTTTTTTTTCTT
1 TTTTTTTTTTTTTTTTCTT
32861 CAAGAATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 28 0.52
42 26 0.48
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (42 bp):
TTTTTTTTTTTTTTTTCTTTCTTTCTCTTTCTTTTTTTTATT
Found at i:32858 original size:32 final size:31
Alignment explanation
Indices: 32759--32860 Score: 145
Period size: 32 Copynumber: 3.3 Consensus size: 31
32749 TGACCCCCCA
*
32759 TTTTT-TTTCTTTTTTTCTTTCTTTCTCTTTTT
1 TTTTTCTTTCTTTTTTT-TTTTTTTCTC-TTTT
*
32791 TTTTTCTTT-TTTTTTTTTTTTTTTTCTTTT
1 TTTTTCTTTCTTTTTTTTTTTTTTCTCTTTT
32821 TTTTTCTTTCTTTTTTTTATTTTTTCTCTTTT
1 TTTTTCTTTCTTTTTTTT-TTTTTTCTCTTTT
32853 TTTTTCTT
1 TTTTTCTT
32861 CAAGAATAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
30 13 0.20
31 16 0.25
32 32 0.50
33 3 0.05
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (31 bp):
TTTTTCTTTCTTTTTTTTTTTTTTCTCTTTT
Found at i:38104 original size:13 final size:13
Alignment explanation
Indices: 38086--38111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38076 GTACTCTGCG
38086 GGTATCCTTGTAT
1 GGTATCCTTGTAT
38099 GGTATCCTTGTAT
1 GGTATCCTTGTAT
38112 AGAAATGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
GGTATCCTTGTAT
Found at i:40237 original size:15 final size:17
Alignment explanation
Indices: 40198--40231 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40188 TGAATAATGA
40198 ATGTATGCCAAATATAT
1 ATGTATGCCAAATATAT
40215 ATGTATGCCAAATATAT
1 ATGTATGCCAAATATAT
40232 GTATGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
ATGTATGCCAAATATAT
Found at i:45735 original size:3 final size:3
Alignment explanation
Indices: 45729--45794 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
45719 TAATATTTAT
45729 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
45776 TAA TGA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
45795 TTTAAATGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52325 original size:183 final size:181
Alignment explanation
Indices: 51849--52328 Score: 719
Period size: 182 Copynumber: 2.6 Consensus size: 181
51839 GTATGTATCA
* * *
51849 ATACAAATAAAAAGGTATCAATCCATAACAATATAACAAGTAAAAATATGACAGAACCAGTTTCA
1 ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACA-AAACAGTTTCA
*
51914 TTATGACAAAATCGGTAAAGCGCTA-TCGGATATGTTGAATGTGTCGATACCATTGAAATAAGTA
65 TTATGACAAAATCGGTAAAGCGCTACT-GGATATGTTGAAAGTGTCGATACCATTGAAATAAGTA
51978 TCAACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
129 TCAACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
* * * *
52031 ATACAAATAAAAATGTATCGATCTATAATAATAAAACAAGTAAAAATATGACAAAACATGTATCA
1 ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACA-GTTTCA
** *
52096 TTATGACAAAATCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATTCCATTGAAATAAGTAT
65 TTATGACAAAATCGGTAAAGCGCTACTGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTAT
* * *
52161 CGACACTTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCG
130 CAACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
** * *
52213 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGATTTA
1 ATAC-AAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACAG-TTTC
* * *
52278 ATTATGAAAAAACCGGTAAAGCACTACTGGATATGTTGAAAGTGTCGATAC
64 ATTATGACAAAATCGGTAAAGCGCTACTGGATATGTTGAAAGTGTCGATAC
52329 TTTAATACGC
Statistics
Matches: 266, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
181 4 0.02
182 167 0.63
183 95 0.36
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (181 bp):
ATACAAATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAACAGTTTCAT
TATGACAAAATCGGTAAAGCGCTACTGGATATGTTGAAAGTGTCGATACCATTGAAATAAGTATC
AACACTTTTGGAATTTAAAAGAGAAGCAGAAATAGCGCATATAAAGTGTCG
Found at i:54414 original size:21 final size:21
Alignment explanation
Indices: 54388--54429 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54378 TTACGAAAGT
*
54388 CACTGTAGCA-GTGCATCGATG
1 CACTGTAG-AGGTACATCGATG
54409 CACTGTAGAGGTACATCGATG
1 CACTGTAGAGGTACATCGATG
54430 TACAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
CACTGTAGAGGTACATCGATG
Found at i:56680 original size:22 final size:24
Alignment explanation
Indices: 56630--56681 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
56620 GTTTTTTCTT
56630 TTTATATAAAATGATAGTATAATTA
1 TTTATATAAAATGATAG-ATAATTA
*
56655 -TTATATAAAATGATA-A-ATTTA
1 TTTATATAAAATGATAGATAATTA
56676 TTTATA
1 TTTATA
56682 AATTCATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
24 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (24 bp):
TTTATATAAAATGATAGATAATTA
Found at i:57443 original size:21 final size:22
Alignment explanation
Indices: 57412--57452 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57402 ACACCCAAGC
57412 AAAAGCAAAACGTAAGTTGAAT
1 AAAAGCAAAACGTAAGTTGAAT
* *
57434 AAAAG-AAAACTTAATTTGA
1 AAAAGCAAAACGTAAGTTGA
57453 TTTTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (22 bp):
AAAAGCAAAACGTAAGTTGAAT
Found at i:61759 original size:127 final size:126
Alignment explanation
Indices: 61409--61759 Score: 361
Period size: 127 Copynumber: 2.8 Consensus size: 126
61399 TTACTTTAAA
* ** * * *** * * *
61409 GTAATAGGTAAATTTGCAATGTAAGTGGTAAAAATACACATTTTTCATGACAAAATTA-GTAAAC
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAA-TAGGTCAAC
* * * * * * *
61473 ACAATGTATTGATA-ATTTTTAAAATTGTATCAATCCCAAAAATTGAAATCGATAATTATAAT
65 ATAAAGTATCGATACATTTTT-AAATTGTATCGATCCCAAAAAATCAAACCGATAATTATAAT
* *
61535 GTAATAGGTAAATTTACAATTTAACCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACA
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
* *
61600 TAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCAAACCGATAATTATAAT
66 TAAAGTATCGATACATTT-TTAAATTGTATCGATCCCAAAAA-ATCAAACCGATAATTATAAT
* * * *
61662 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAGAATAGGTCCACA
1 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
* *
61727 TAATGTATC-A-ACACTTTTTAAATTTGTGTCGAT
66 TAAAGTATCGATACA-TTTTTAAA-TTGTATCGAT
61760 ACTTTTGGTC
Statistics
Matches: 186, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
125 10 0.05
126 77 0.41
127 97 0.52
128 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (126 bp):
GTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGATTTAATGAGAAAATAGGTCAACA
TAAAGTATCGATACATTTTTAAATTGTATCGATCCCAAAAAATCAAACCGATAATTATAAT
Found at i:61857 original size:199 final size:198
Alignment explanation
Indices: 61598--62753 Score: 1523
Period size: 199 Copynumber: 5.8 Consensus size: 198
61588 AATAGGTCAA
* *
61598 CATAAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATC-AAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAAT-CCAAAAACATCGAAACCGATAATTATAA
* * * * *
61661 TGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAGAATAGGTCCAC
63 TATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAAC
* *
61726 ATAATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAACGAGG
128 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGG
61791 TGCACG
193 TGCACG
* * * * *
61797 CATAAAATGTCCATACATTTAAAATTGCATCGATCACAAAAACATCGAAACCAATAATTATAATA
1 CATAAAGTGTCGATACATTTAAAATTGTATCAATC-CAAAAACATCGAAACCGATAATTATAATA
* * * * *
61862 TAATAGGTAAATTTACAATTTAACCGGTAGAAATATATCGGTTTAATTAGAGAATA-GTCCACAA
65 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACAT
* *
61926 AATATATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCCAACGAGGTG
130 AATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTG
*
61991 CATG
195 CACG
* *
61995 CATAAAGTGTCGATACATTTATTAAA-AGTATCAATCCTAAAAACATCAAAACCGATAATTATAA
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAATCC-AAAAACATCGAAACCGATAATTATAA
* *
62059 TATAATAGGTAAATTGACAATGTAACCGGTAGAAAT-TAACCGG-TTAATTAGAAAATAGATCAA
63 TATAATAGGTAAATTTACAATGTAACCGGTAGAAATAT-ACCGGTTTAATTAGAAAATAGGTCAA
* * ** * * * *
62122 CATAATGTATCGATACATTTTAAAAATGTGTCGATACTTTTTGTCCATAATGAATG-TCAATGAG
127 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAG
*
62186 GTGCACA
192 GTGCACG
* * *
62193 CATAAAGTGTCGATACATTTATTAAA-AGTATCAAT-CAAAAATATCGAAACTGATAATTATAAT
1 CATAAAGTGTCGATACATTTA--AAATTGTATCAATCCAAAAACATCGAAACCGATAATTATAAT
* * * *
62256 ATAATA-GTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAAAATAGGTTAACA
64 ATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACA
* *
62320 TAATGTATTGACACTTTTTAAATTTGTGTCCATACATTTT-GTCCAGAATGAATGCCCAACGAGG
129 TAATGTATCGACACTTTTTAAATTTGTGTCGATAC-TTTTGGTCCAGAATGAATGCCCAACGAGG
62384 TGCACG
193 TGCACG
*
62390 CATAAAGTGTCGATACATTTAAAATTGTAT-ATATCCTAAAAGCATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTAAAATTGTATCA-ATCC-AAAAACATCGAAACCGATAATTATAAT
* * * *
62454 GTAATAGGTAAATTTAAAATGTAACCGGTAGAAATATACCAGTTTAATTAGAAAATAGGTTAACA
64 ATAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACA
*
62519 TAATGTATCGACAC-TTTTAAATTTGTGTCGATA-TTTTTGTCCAGAATGAATGCCCAACGAGGT
129 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGT
*
62582 ACACG
194 GCACG
* *
62587 CATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATTGAAACCGATAATTATAATG
1 CATAAAGTGTCGATACATTTAAAATTGTATCAAT-CCAAAAACATCGAAACCGATAATTATAATA
* * * ** *
62652 T-ATAGTTAAATTTACAATGTAACCAGTAAAAATATACATGTTTAATTAGAGAATAGGTCAACAT
65 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACAT
* * *
62716 AATGTATCGACACTTTTTAAATTTATATCGATATTTTT
130 AATGTATCGACACTTTTTAAATTTGTGTCGATACTTTT
62754 TAAATTACGT
Statistics
Matches: 851, Mismatches: 84, Indels: 45
0.87 0.09 0.05
Matches are distributed among these distances:
195 33 0.04
196 171 0.20
197 148 0.17
198 222 0.26
199 274 0.32
200 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTAAAATTGTATCAATCCAAAAACATCGAAACCGATAATTATAATAT
AATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATA
ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCCCAACGAGGTGC
ACG
Found at i:62400 original size:395 final size:394
Alignment explanation
Indices: 61598--62739 Score: 1615
Period size: 395 Copynumber: 2.9 Consensus size: 394
61588 AATAGGTCAA
* *
61598 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAACCGATAATTATAATG
1 CATAAAGTGTCGATACATTTATTAAAAGTATCAATCCTAAAAACATCAAACCGATAATTATAATG
* * * *
61663 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAGAATAGGTCCACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTCAACAT
* *
61728 AATGTATCAACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATGCACAACGAGGTG
130 AATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAACGAGGTG
* * * * *
61793 CACGCATAAAATGTCCATACATTTAAAATTGCATCGATCACAAAAACATCGAAACCAATAATTAT
194 CACGCATAAAGTGTCGATACATTTAAAATTGTATCAATC-CAAAAACATCGAAACCGATAATTAT
* * * *
61858 AATATAATAGGTAAATTTACAATTTAACCGGTAGAAATATATCGGTTTAATTAGAGAATA-GTCC
258 AATATAATA-GTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAGAATAGGTCA
* * *
61922 ACAAAATATATCGACACTTTTTAAATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCCAACGA
322 ACATAATGTATCGACACTTTTTAAATTTGTGTCCATACTTTTGGTCCAGAATAAATGCCCAACGA
*
61987 GGTGCATG
387 GGTGCACG
61995 CATAAAGTGTCGATACATTTATTAAAAGTATCAATCCTAAAAACATCAAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATTAAAAGTATCAATCCTAAAAACATC-AAACCGATAATTATAAT
* * *
62060 ATAATAGGTAAATTGACAATGTAACCGGTAGAAAT-TAACCGGTTAATTAGAAAATAGATCAACA
65 GTAATAGGTAAATTTACAATGTAACCGGTAGAAATAT-ACCGGTTAATTAGAAAATAGGTCAACA
* ** * * *
62124 TAATGTATCGATACATTTTAAAAATGTGTCGATACTTTTTGTCCATAATGAATG-TCAATGAGGT
129 TAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAACGAGGT
* * * *
62188 GCACACATAAAGTGTCGATACATTTATTAAA-AGTATCAAT-CAAAAATATCGAAACTGATAATT
193 GCACGCATAAAGTGTCGATACATTTA--AAATTGTATCAATCCAAAAACATCGAAACCGATAATT
* *
62251 ATAATATAATAGTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAAAATAGGTT
256 ATAATATAATAGTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAGAATAGGTC
* *
62316 AACATAATGTATTGACACTTTTTAAATTTGTGTCCATACATTTT-GTCCAGAATGAATGCCCAAC
321 AACATAATGTATCGACACTTTTTAAATTTGTGTCCATAC-TTTTGGTCCAGAATAAATGCCCAAC
62380 GAGGTGCACG
385 GAGGTGCACG
* *
62390 CATAAAGTGTCGATACATTTA--AAATTGTAT-ATATCCTAAAAGCATCGAAACCGATAATTATA
1 CATAAAGTGTCGATACATTTATTAAA-AGTATCA-ATCCTAAAAACATC-AAACCGATAATTATA
* * *
62452 ATGTAATAGGTAAATTTAAAATGTAACCGGTAGAAATATACCAGTTTAATTAGAAAATAGGTTAA
63 ATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACC-GGTTAATTAGAAAATAGGTCAA
*
62517 CATAATGTATCGACACTTTTAAATTTGTGTCGATA-TTTTTGTCCAGAATGAATGCCCAACGAGG
127 CATAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAACGAGG
* *
62581 TACACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACATTGAAACCGATAATT
192 TGCACGCATAAAGTGTCGATACATTTAAAATTGTATCAAT-CCAAAAACATCGAAACCGATAATT
* *
62646 ATAATGT-ATAGTTAAATTTACAATGTAACCAGTAAAAATATA-CATGTTTAATTAGAGAATAGG
256 ATAATATAATAG-TAAATTTACAATGTAACCAGTAGAAATATATCA-GTTTAATTAGAGAATAGG
62709 TCAACATAATGTATCGACACTTTTTAAATTT
319 TCAACATAATGTATCGACACTTTTTAAATTT
62740 ATATCGATAT
Statistics
Matches: 664, Mismatches: 65, Indels: 34
0.87 0.09 0.04
Matches are distributed among these distances:
392 3 0.00
393 30 0.05
394 170 0.26
395 252 0.38
396 35 0.05
397 116 0.17
398 58 0.09
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (394 bp):
CATAAAGTGTCGATACATTTATTAAAAGTATCAATCCTAAAAACATCAAACCGATAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCAACATA
ATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCACAACGAGGTGCA
CGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCAAAAACATCGAAACCGATAATTATAAT
ATAATAGTAAATTTACAATGTAACCAGTAGAAATATATCAGTTTAATTAGAGAATAGGTCAACAT
AATGTATCGACACTTTTTAAATTTGTGTCCATACTTTTGGTCCAGAATAAATGCCCAACGAGGTG
CACG
Found at i:62746 original size:21 final size:21
Alignment explanation
Indices: 62720--62759 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62710 CAACATAATG
62720 TATCGACACTTTTTAAATTTA
1 TATCGACACTTTTTAAATTTA
* *
62741 TATCGATATTTTTTAAATT
1 TATCGACACTTTTTAAATT
62760 ACGTATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TATCGACACTTTTTAAATTTA
Found at i:63090 original size:18 final size:16
Alignment explanation
Indices: 63047--63105 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
63037 CCTTCTCAAA
*
63047 CTTCTTCTCAACCAAG
1 CTTCTTCTCAACCAAC
*
63063 C-TCTTTTCAACGACAAC
1 CTTCTTCTCAAC--CAAC
63080 CTTCTTCTCAACCAATC
1 CTTCTTCTCAACCAA-C
63097 GCTTCTTCT
1 -CTTCTTCT
63106 GAACAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.26
16 4 0.11
17 5 0.14
18 17 0.49
ACGTcount: A:0.22, C:0.37, G:0.05, T:0.36
Consensus pattern (16 bp):
CTTCTTCTCAACCAAC
Found at i:63114 original size:18 final size:18
Alignment explanation
Indices: 63080--63114 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63070 CAACGACAAC
*
63080 CTTCTTCTCAACCAATCG
1 CTTCTTCTCAACAAATCG
*
63098 CTTCTTCTGAACAAATC
1 CTTCTTCTCAACAAATC
63115 AGGTCGTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (18 bp):
CTTCTTCTCAACAAATCG
Found at i:65698 original size:24 final size:23
Alignment explanation
Indices: 65667--65711 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
65657 TTCATTTCAT
65667 ATTTAATTGGAGTTTGAATTTAA
1 ATTTAATTGGAGTTTGAATTTAA
*
65690 ATTTCAATTTGAGTTTGAATTT
1 ATTT-AATTGGAGTTTGAATTT
65712 CGATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
ATTTAATTGGAGTTTGAATTTAA
Found at i:65722 original size:24 final size:24
Alignment explanation
Indices: 65671--65723 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
65661 TTTCATATTT
* * *
65671 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
**
65695 AATTTGAGTTTGAATTTCGATATA
1 AATTTGAGTTTGAATTTAAATATA
65719 AATTT
1 AATTT
65724 CGGCTCCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Done.