Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000274.1 Hibiscus syriacus cultivar Beakdansim tig00000508_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: 91748
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:487 original size:14 final size:14
Alignment explanation
Indices: 468--514 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
458 TATCAGAATA
*
468 ATTTATTTAATATT
1 ATTTATTAAATATT
*
482 ATTTATGTCAATATT
1 ATTTAT-TAAATATT
497 A-TTATTAAAATATT
1 ATTTATT-AAATATT
511 ATTT
1 ATTT
515 CTGTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 1 0.04
14 17 0.61
15 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:526 original size:28 final size:29
Alignment explanation
Indices: 476--539 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
466 TAATTTATTT
* *
476 AATATTATTTATGTCAATATTATTATTAA
1 AATATTATTTATGTCAATATTATAAATAA
* *
505 AATATTATTTCTGT-AATTTTATAAATAA
1 AATATTATTTATGTCAATATTATAAATAA
533 AATATTA
1 AATATTA
540 ATATTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
AATATTATTTATGTCAATATTATAAATAA
Found at i:561 original size:28 final size:27
Alignment explanation
Indices: 476--564 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 27
466 TAATTTATTT
*
476 AATATTATTTATGTCAATATTATTATTAA
1 AATATTATTTATGT--ATATTTTTATTAA
* *
505 AATATTATTTCTGTA-ATTTTATAAATAA
1 AATATTATTTATGTATATTTT-T-ATTAA
533 AATATTAATATTAT-TATATTTTTATTAA
1 AATATT-AT-TTATGTATATTTTTATTAA
561 AATA
1 AATA
565 AAACACTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 18 0.36
29 18 0.36
30 8 0.16
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
AATATTATTTATGTATATTTTTATTAA
Found at i:722 original size:29 final size:31
Alignment explanation
Indices: 648--723 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
638 TATAATATAT
* *
648 TATATTATTAATAAATATATGTTAAAAATAA
1 TATATTATTATTAAATATATATTAAAAATAA
679 TAT-TT-TTATTAAA-ATTATATT-AAAATAA
1 TATATTATTATTAAATA-TATATTAAAAATAA
*
707 TATATTAATATTAAATA
1 TATATTATTATTAAATA
724 GAAAAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 11 0.29
29 14 0.37
30 9 0.24
31 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TATATTATTATTAAATATATATTAAAAATAA
Found at i:9856 original size:22 final size:20
Alignment explanation
Indices: 9807--9872 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 20
9797 GCAAAAATGG
*
9807 ATCGATACCAT-GGAAG-GT
1 ATCGATACCATAGTAAGAGT
9825 ATCG-TACCATAGTATAGTAGT
1 ATCGATACCATAGTA-AG-AGT
*
9846 ATCGATACCATAGTAAGGGT
1 ATCGATACCATAGTAAGAGT
9866 ATCGATA
1 ATCGATA
9873 TAAGGCAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 2 0.05
20 9 0.22
21 8 0.20
22 10 0.24
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
ATCGATACCATAGTAAGAGT
Found at i:10445 original size:34 final size:34
Alignment explanation
Indices: 10407--10627 Score: 147
Period size: 34 Copynumber: 5.9 Consensus size: 34
10397 ACATAGCTGA
*
10407 AATGCATATGGGTGAATTATTGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
*
10441 AATGCTTATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATTGGCAT-AAA--A-G--A-A--T
* *
10484 AAAATGCATATGGGTGCA-TATCGGCATAAAATAAT
1 --AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* *
10519 AATGCATATGGGTGCATTATTAGCATGAAAGGATGCCAT
1 AATGCATATGGGTGCATTATTGGCAT-AAA--A-G-AAT
* * * *
10558 AGCTGAAACACATAGGGTGCATTATCGACATAAAAGAAT
1 A-ATG---CATAT-GGGTGCATTATTGGCATAAAAGAAT
*
10597 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGGCATAAAAG
10628 GATGCCAAAG
Statistics
Matches: 145, Mismatches: 20, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
33 16 0.11
34 50 0.34
35 11 0.08
37 3 0.02
38 4 0.03
39 6 0.04
40 4 0.03
41 3 0.02
43 11 0.08
44 22 0.15
45 15 0.10
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:10554 original size:78 final size:79
Alignment explanation
Indices: 10352--10671 Score: 500
Period size: 78 Copynumber: 4.1 Consensus size: 79
10342 GAACGAATGA
*
10352 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* * *
10417 GGTGAATTATTGGC
66 GGTGCATTATCGAC
* *
10431 ATAAAAGAATAATGCTTATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
10496 GGTGCA-TATCGGC
66 GGTGCATTATCGAC
* * **
10509 ATAAAATAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCATAGCTGAAACACATA-G
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
10573 GGTGCATTATCGAC
66 GGTGCATTATCGAC
* *
10587 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
10652 GGTGCATTATCAAC
66 GGTGCATTATCGAC
10666 ATAAAA
1 ATAAAA
10672 TTATGCTATA
Statistics
Matches: 220, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
77 7 0.03
78 126 0.57
79 87 0.40
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGAC
Found at i:10687 original size:45 final size:46
Alignment explanation
Indices: 10597--10713 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 46
10587 ATAAAAGAAT
*** *
10597 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTG-A
1 AATGCATATGGGTGCATTATAAACATAAAAGGATGCCAAAGTTGAA
* ** *
10642 AATGCATATGGGTGCATTATCAACATAAAATTATGCTATAA-TTGAA
1 AATGCATATGGGTGCATTATAAACATAAAAGGATGCCA-AAGTTGAA
*
10688 AATGCATAAT-GGTGCATGATAAACAT
1 AATGCAT-ATGGGTGCATTATAAACAT
10714 GAATGAATGT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 34 0.57
46 24 0.40
47 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (46 bp):
AATGCATATGGGTGCATTATAAACATAAAAGGATGCCAAAGTTGAA
Found at i:14067 original size:20 final size:20
Alignment explanation
Indices: 14042--14093 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
14032 CACCACATGT
*
14042 ATCTATATGCTCCTAAATGC
1 ATCTATATGATCCTAAATGC
14062 ATCTATATGATCCTAAATGC
1 ATCTATATGATCCTAAATGC
14082 ATCTATATGATC
1 ATCTATATGATC
14094 TTATACGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCTATATGATCCTAAATGC
Found at i:20010 original size:18 final size:17
Alignment explanation
Indices: 19990--20023 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19980 AAAAACCATA
19990 AAAATATGAATTTTTAG
1 AAAATATGAATTTTTAG
* *
20007 AAAATTTGACTTTTTAG
1 AAAATATGAATTTTTAG
20024 TCAAAGTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAATATGAATTTTTAG
Found at i:20078 original size:30 final size:30
Alignment explanation
Indices: 20028--20087 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
20018 TTTTAGTCAA
20028 AGTTAACGGTCAAAGTCAAAGTCAATGGGT
1 AGTTAACGGTCAAAGTCAAAGTCAATGGGT
*
20058 AGTTCAACGGTC-ATGTCAAAGTCAATGGGT
1 AGTT-AACGGTCAAAGTCAAAGTCAATGGGT
20088 TAGACTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (30 bp):
AGTTAACGGTCAAAGTCAAAGTCAATGGGT
Found at i:20136 original size:20 final size:20
Alignment explanation
Indices: 20098--20150 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
20088 TAGACTAGTT
* *
20098 CGGGTTGACCCAGGCCGGTT
1 CGGGTTGACTCAGGCCGGTA
* **
20118 TGGGTTGACTCAGTTCGGTA
1 CGGGTTGACTCAGGCCGGTA
*
20138 CGAGTTGACTCAG
1 CGGGTTGACTCAG
20151 ACTGGTCCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (20 bp):
CGGGTTGACTCAGGCCGGTA
Found at i:26426 original size:20 final size:20
Alignment explanation
Indices: 26389--26426 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26379 AAGTAATAGT
**
26389 CAAACACTTAATCTTTAACA
1 CAAACACTTAATAATTAACA
26409 CAAACACTTAATAATTAA
1 CAAACACTTAATAATTAA
26427 ATTTGAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAACACTTAATAATTAACA
Found at i:26596 original size:22 final size:22
Alignment explanation
Indices: 26570--26615 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
26560 TATAAAAATC
*
26570 TTTTTCTTTCTTCAATGCT-TTAA
1 TTTTT-TTCCTTCAA-GCTCTTAA
26593 TTTTTTTCCTTCAAGCTCTTAA
1 TTTTTTTCCTTCAAGCTCTTAA
26615 T
1 T
26616 CTTTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.62
23 5 0.24
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTTTTCCTTCAAGCTCTTAA
Found at i:26600 original size:21 final size:21
Alignment explanation
Indices: 26571--26624 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
26561 ATAAAAATCT
26571 TTTTCTTTCTTCAATGCT-TTAA
1 TTTT-TTTCTTCAA-GCTCTTAA
26593 TTTTTTTCCTTCAAGCTCTTAA
1 TTTTTTT-CTTCAAGCTCTTAA
* *
26615 TCTTTATCTT
1 TTTTTTTCTT
26625 TAATTCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTTTCTTCAAGCTCTTAA
Found at i:28737 original size:44 final size:44
Alignment explanation
Indices: 28668--28754 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
28658 TGCATTATGT
28668 CTAAAATTTATAAATAAACCATATATATAT-TAAAAATTAGTTGC
1 CTAAAATTTATAAATAAACCATATATATATAT-AAAATTAGTTGC
* * * *
28712 CTAACATTTATAGATAAGCCCTATATATATATAAAATTAGTTG
1 CTAAAATTTATAAATAAACCATATATATATATAAAATTAGTTG
28755 ATAGTAAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (44 bp):
CTAAAATTTATAAATAAACCATATATATATATAAAATTAGTTGC
Found at i:32218 original size:12 final size:12
Alignment explanation
Indices: 32183--32227 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
32173 CAATCCAGGC
32183 GACATACGGGGT
1 GACATACGGGGT
32195 GA-ATACGGGGGGT
1 GACATAC--GGGGT
32208 GACATACGGGGT
1 GACATACGGGGT
32220 GACATACG
1 GACATACG
32228 AGCCATACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.13
12 15 0.50
13 7 0.23
14 4 0.13
ACGTcount: A:0.27, C:0.16, G:0.42, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:32267 original size:13 final size:13
Alignment explanation
Indices: 32249--32274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32239 CCAATGGGGA
32249 GAGGTCGCCATGC
1 GAGGTCGCCATGC
32262 GAGGTCGCCATGC
1 GAGGTCGCCATGC
32275 AGTCCTATAC
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:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
GAGGTCGCCATGC
Found at i:32346 original size:29 final size:29
Alignment explanation
Indices: 32296--32375 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
32286 AGGAATAGAG
* *
32296 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
32325 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
32354 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
32376 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:32583 original size:25 final size:25
Alignment explanation
Indices: 32554--32605 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
32544 TGTACAATTA
32554 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
32579 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
32604 TT
1 TT
32606 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:32646 original size:23 final size:23
Alignment explanation
Indices: 32618--32663 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
32608 AAAAGAAAGA
32618 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
32641 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
32664 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:32678 original size:25 final size:23
Alignment explanation
Indices: 32618--32678 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
32608 AAAAGAAAGA
**
32618 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
32641 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
32664 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
32679 AGGGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:32692 original size:21 final size:21
Alignment explanation
Indices: 32668--32720 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
32658 TTGCAGCCGA
32668 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
32689 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
32710 GAAAGTAAGAA
1 GAAAGAAAGAA
32721 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:32714 original size:17 final size:16
Alignment explanation
Indices: 32666--32697 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
32656 GATTGCAGCC
32666 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
32682 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
32698 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:33210 original size:16 final size:16
Alignment explanation
Indices: 33178--33224 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
33168 TTTAAAAAGT
*
33178 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
33194 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
33210 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
33225 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:33219 original size:15 final size:14
Alignment explanation
Indices: 33199--33229 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
33189 GTTTATTAGT
33199 TTATTATATTATAAG
1 TTATTATATTA-AAG
33214 TTATTATATTAAAG
1 TTATTATATTAAAG
33228 TT
1 TT
33230 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:35400 original size:17 final size:17
Alignment explanation
Indices: 35378--35410 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35368 CAATGATTTT
*
35378 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
35395 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
35411 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:35427 original size:24 final size:22
Alignment explanation
Indices: 35395--35463 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
35385 AAATCATTAC
35395 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
35417 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
35442 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
35464 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:35680 original size:35 final size:37
Alignment explanation
Indices: 35599--35685 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
35589 TTAGTATTCT
* * *
35599 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
35637 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
35672 ATAATTATTATAAA
1 ATAATTATTATAAA
35686 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:35706 original size:12 final size:13
Alignment explanation
Indices: 35615--35842 Score: 120
Period size: 14 Copynumber: 17.1 Consensus size: 13
35605 ATTAGTAATA
35615 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
35629 AGTATTAAATCATT
1 ATTA-TAAATCATT
35643 ATTATAAAT-A--
1 ATTATAAATCATT
35653 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
35664 ATAACTAAATAATT
1 ATTA-TAAATCATT
35678 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
35692 ATTAT-AATGATT
1 ATTATAAATCATT
35704 ATTATCAAATCATT
1 ATTAT-AAATCATT
35718 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
35737 AAATATTTAAATCATT
1 --AT-TATAAATCATT
35753 A-T-TAAATCATT
1 ATTATAAATCATT
* *
35764 TTTAT-AATGATT
1 ATTATAAATCATT
35776 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
35790 ATTAT-AATGATT
1 ATTATAAATCATT
35802 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
35816 ACTAT-AATGATT
1 ATTATAAATCATT
35828 ATTATCAAATCATT
1 ATTAT-AAATCATT
35842 A
1 A
35843 CTAAATCATC
Statistics
Matches: 174, Mismatches: 18, Indels: 44
0.74 0.08 0.19
Matches are distributed among these distances:
10 4 0.02
11 24 0.14
12 45 0.26
13 9 0.05
14 66 0.38
15 1 0.01
16 8 0.05
17 1 0.01
18 3 0.02
19 11 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:35713 original size:26 final size:26
Alignment explanation
Indices: 35615--35842 Score: 174
Period size: 26 Copynumber: 9.2 Consensus size: 26
35605 ATTAGTAATA
* * *
35615 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
35640 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
35664 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
35689 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
35715 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
35738 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
35761 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
35787 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
35813 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
35839 ATTA
1 ATTA
35843 CTAAATCATC
Statistics
Matches: 158, Mismatches: 31, Indels: 27
0.73 0.14 0.12
Matches are distributed among these distances:
21 4 0.03
22 2 0.01
23 16 0.10
24 20 0.13
25 28 0.18
26 87 0.55
27 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:35839 original size:124 final size:123
Alignment explanation
Indices: 35631--35900 Score: 445
Period size: 124 Copynumber: 2.2 Consensus size: 123
35621 AAATCATTAG
* * *
35631 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
35694 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * * * *
35752 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
35817 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
35876 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
35901 ATAAATACAT
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 103 0.75
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:38803 original size:26 final size:24
Alignment explanation
Indices: 38743--38803 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
38733 TACTAATATT
*
38743 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
38767 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
38794 ATTTAATAAT
1 A-TTAATAAT
38804 ATGATTTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:39188 original size:14 final size:14
Alignment explanation
Indices: 39169--39195 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39159 CACATACACA
39169 ACAACAAAAAATAG
1 ACAACAAAAAATAG
39183 ACAACAAAAAATA
1 ACAACAAAAAATA
39196 ATAAATTACT
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):
ACAACAAAAAATAG
Found at i:39188 original size:17 final size:17
Alignment explanation
Indices: 39166--39198 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39156 TTACACATAC
39166 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
39183 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
39199 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:39630 original size:21 final size:21
Alignment explanation
Indices: 39597--39645 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
39587 AATATAATAT
*
39597 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* * *
39618 ATAATTTATACTAGCAAACTA
1 ATAACTTAAACTAACAAACTA
39639 ATTAACT
1 A-TAACT
39646 AGATTTTAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:40073 original size:35 final size:35
Alignment explanation
Indices: 40033--40100 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
40023 TGGATGCAAC
40033 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
40068 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
40101 CGATGCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:40157 original size:12 final size:12
Alignment explanation
Indices: 40140--40164 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40130 TCCATGGCGA
40140 CCTACCACCTAC
1 CCTACCACCTAC
40152 CCTACCACCTAC
1 CCTACCACCTAC
40164 C
1 C
40165 ATGTCGTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:40191 original size:29 final size:29
Alignment explanation
Indices: 40158--40228 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
40148 CTACCCTACC
40158 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
40187 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
40216 ACCTACCATGTCG
1 ACCTACCATGTCG
40229 CCGGCAACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.21
Consensus pattern (29 bp):
ACCTACCATGTCGTCGGGACTCCATGGCG
Found at i:40426 original size:31 final size:31
Alignment explanation
Indices: 40391--40455 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
40381 CCCATGCATA
40391 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
*
40422 GCACCAAAGCAGCATCAGTGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
40453 GCA
1 GCA
40456 AAGAACCAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.31, G:0.29, T:0.05
Consensus pattern (31 bp):
GCACCAAAGCAGCATCAGCGAGCAACAGCGG
Found at i:41884 original size:2 final size:2
Alignment explanation
Indices: 41877--41904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41867 AAATAAATAA
41877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41905 TATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43652 original size:25 final size:25
Alignment explanation
Indices: 43579--43671 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
43569 TATTATACTA
*
43579 TATTATATTTATTTCATATAGCATATAT
1 TATTATA--TATTT-ATATAGCATATAG
*
43607 TATATAGTATGGTTTTATATAGCATATA-
1 TAT-TA-TAT--ATTTATATAGCATATAG
*
43635 TATTATAATATTTATATAGTATATAG
1 TATTAT-ATATTTATATAGCATATAG
43661 TATTATATATT
1 TATTATATATT
43672 ATGTTTATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
25 19 0.34
26 7 0.12
27 4 0.07
28 7 0.12
29 14 0.25
30 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (25 bp):
TATTATATATTTATATAGCATATAG
Found at i:44740 original size:2 final size:2
Alignment explanation
Indices: 44714--44869 Score: 108
Period size: 2 Copynumber: 83.5 Consensus size: 2
44704 ACCCTATGTT
*
44714 TA TA T- TA TA TA T- TA TA -A TA TT TA TA TA GTA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
44752 TA TA TA T- TA TA GTA TA TT TA TA T- TA TA TA T- TA GTC TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
44793 T- TA TA T- TA TA TA TA TA TA TA TA TA TT TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
44831 TA T- TA TA GCA TA TT TA AA T- TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44870 TACATTATTT
Statistics
Matches: 121, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
1 15 0.12
2 100 0.83
3 6 0.05
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:44769 original size:35 final size:36
Alignment explanation
Indices: 44714--44871 Score: 123
Period size: 33 Copynumber: 4.8 Consensus size: 36
44704 ACCCTATGTT
*
44714 TATATTATATATTATA-ATATTTA-TATAGTATA-T
1 TATATTATATATTATATATATATATTATAGTATATT
* *
44747 TAT-TATATATATTATA-GTATAT-TTATATTATATAT
1 TATAT-TATATATTATATATATATATTATAGTATAT-T
*
44782 TAGT-CTATATATTATAT-TATATA-TATA-TATA--
1 TA-TATTATATATTATATATATATATTATAGTATATT
*
44813 TATATT-TAT-T-ATATAT-TATATTATAGCATATT
1 TATATTATATATTATATATATATATTATAGTATATT
*
44845 TAAATTATATATTATATATATATATTA
1 TATATTATATATTATATATATATATTA
44872 CATTATTTAT
Statistics
Matches: 101, Mismatches: 7, Indels: 31
0.73 0.05 0.22
Matches are distributed among these distances:
28 8 0.08
29 6 0.06
30 7 0.07
31 3 0.03
32 6 0.06
33 29 0.29
34 5 0.05
35 29 0.29
36 8 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
TATATTATATATTATATATATATATTATAGTATATT
Found at i:44815 original size:47 final size:51
Alignment explanation
Indices: 44714--44865 Score: 153
Period size: 47 Copynumber: 3.1 Consensus size: 51
44704 ACCCTATGTT
*
44714 TATATTATATATTATA-A-TATTTATATAGTATATTATTATATATATTATAG
1 TATATT-TATATTATATATTATCTATATAGTATATTATTATATATATTATAG
*
44764 TATATTTATATTATATATTAGTCTATATATTATATTA-TATATATA-TATA-
1 TATATTTATATTATATATTA-TCTATATAGTATATTATTATATATATTATAG
* * *
44813 TATA-TT-TATTATATATTATAT-TATAGCATATT-TAAATTATATATTATA-
1 TATATTTATATTATATATTATCTATATAGTATATTAT-TA-TATATATTATAG
44861 TATAT
1 TATAT
44866 ATATTACATT
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
45 9 0.10
46 3 0.03
47 18 0.20
48 10 0.11
49 13 0.15
50 11 0.12
51 10 0.11
52 14 0.16
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (51 bp):
TATATTTATATTATATATTATCTATATAGTATATTATTATATATATTATAG
Found at i:44825 original size:52 final size:53
Alignment explanation
Indices: 44712--44870 Score: 163
Period size: 52 Copynumber: 3.0 Consensus size: 53
44702 TTACCCTATG
* * *
44712 TTTATATTATATATTATAATAT-TTATATAGTATATTAT-TATATATAT-TATA
1 TTTAT-TTATATATTATATTATACTATATATTATATTATATATATATATATATA
*
44763 GTATATTTATAT-TATATATTAGT-CTATATATTATATTATATATATATATATATA
1 -TTTATTTATATAT-TATATTA-TACTATATATTATATTATATATATATATATATA
*
44817 TTTA-TTATATATTATATTATAGC-ATAT-TTAAATTATATATTATATATATATA
1 TTTATTTATATATTATATTATA-CTATATATTATATTATATA-TATATATATATA
44869 TT
1 TT
44871 ACATTATTTA
Statistics
Matches: 93, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
50 1 0.01
51 24 0.26
52 50 0.54
53 14 0.15
54 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (53 bp):
TTTATTTATATATTATATTATACTATATATTATATTATATATATATATATATA
Found at i:45873 original size:14 final size:14
Alignment explanation
Indices: 45851--45888 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
45841 CAAATGCATG
*
45851 TACATATCATGTAA
1 TACACATCATGTAA
45865 TACACATCATGTAA
1 TACACATCATGTAA
45879 TACACATCAT
1 TACACATCAT
45889 ACTTATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (14 bp):
TACACATCATGTAA
Found at i:45963 original size:17 final size:18
Alignment explanation
Indices: 45923--45964 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
45913 ATTAATATGC
*
45923 TTATCATTACTTATTTTA
1 TTATCATTAATTATTTTA
*
45941 TTATCATTAATTCTTTT-
1 TTATCATTAATTATTTTA
45958 TTATCAT
1 TTATCAT
45965 ATGAGCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATCATTAATTATTTTA
Found at i:46784 original size:2 final size:2
Alignment explanation
Indices: 46777--46831 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
46767 TAACTTCTAG
46777 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
46819 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
46832 TATATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46836 original size:2 final size:2
Alignment explanation
Indices: 46831--46859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46821 ACACACACAC
46831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46860 CTCATGTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47230 original size:22 final size:20
Alignment explanation
Indices: 47205--47253 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
47195 AGCACAGTAC
47205 CGATACCACTACTCTAGGGTAT
1 CGATACCACTAC-CTA-GGTAT
*
47227 CGATACC-CTTCCTAGGTAT
1 CGATACCACTACCTAGGTAT
47246 CGATACCA
1 CGATACCA
47254 AAATTAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 3 0.12
22 7 0.28
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
CGATACCACTACCTAGGTAT
Found at i:47325 original size:22 final size:22
Alignment explanation
Indices: 47275--47328 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
47265 GATGTTCCCC
47275 TGGTATCGATACACTCCACATA
1 TGGTATCGATACACTCCACATA
47297 -GGTATCGATAC-CTCTTC-CATA
1 TGGTATCGATACACTC--CACATA
47318 TGGTATCGATA
1 TGGTATCGATA
47329 TTGTTCATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 11 0.38
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (22 bp):
TGGTATCGATACACTCCACATA
Found at i:48960 original size:19 final size:19
Alignment explanation
Indices: 48938--48992 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
48928 ATACTAGAAG
48938 AGGGTATCGATACCATAGC
1 AGGGTATCGATACCATAGC
* *
48957 AGGGTAGCATTGACACCATAGC
1 AGGGT---ATCGATACCATAGC
48979 AGGGGTATCGATAC
1 A-GGGTATCGATAC
48993 TGAAGGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 5 0.18
20 6 0.21
22 13 0.46
23 4 0.14
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (19 bp):
AGGGTATCGATACCATAGC
Found at i:49473 original size:45 final size:45
Alignment explanation
Indices: 49422--49727 Score: 348
Period size: 45 Copynumber: 6.8 Consensus size: 45
49412 AGGATGCCAT
**
49422 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
* *
49467 GGTTGAAATGTATAT-GGTACATTATCAACAGAAAAGTATGCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * *
49511 AGTTGAAATGCATATGGGTGCATTATCAACAGAAATGTATGCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * * * *
49556 AGTTAAAATGCATATGTGTGCATTATCAACA-AAAGAGCATGCTAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAA-AGTATACTAG
** * *
49601 AGTTGAAATGTATATGAATACATTATCAACATAAAAATATACTATG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTA-G
* * *
49647 -GTTGAAATGTATATGGGTACATTGTCAACATAAAAGTATACTAT
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
* * * *
49691 AGTTGAAGTGCATATGAGTGCATTATCAACAGAAAAG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
49728 ATGTTATGTT
Statistics
Matches: 225, Mismatches: 31, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
44 42 0.19
45 179 0.80
46 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (45 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAG
Found at i:49676 original size:135 final size:134
Alignment explanation
Indices: 49422--49726 Score: 389
Period size: 135 Copynumber: 2.3 Consensus size: 134
49412 AGGATGCCAT
* * * * *
49422 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTAGGGTTGAAATGTATATGGTAC
1 AGTTGAAATGCATATGAGTGCATTATCAACAGAAAAACATACTAGAGTTGAAATGTATATGATAC
* * * * *
49487 ATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAATGTATG
66 ATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATA
49552 CTAG
131 CTAG
* * * *
49556 AGTTAAAATGCATATGTGTGCATTATCAACA-AAAGAGCATGCTAGAGTTGAAATGTATATGAAT
1 AGTTGAAATGCATATGAGTGCATTATCAACAGAAA-AACATACTAGAGTTGAAATGTATATG-AT
* * * *
49620 ACATTATCAACATAAAAATATACTATG-GTTGAAATGTATATGGGTACATTGTCAACATAAAAGT
64 ACATTATCAACAGAAAAATATACTA-GAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGT
*
49684 ATACTAT
128 ATACTAG
*
49691 AGTTGAAGTGCATATGAGTGCATTATCAACAGAAAA
1 AGTTGAAATGCATATGAGTGCATTATCAACAGAAAA
49727 GATGTTATGT
Statistics
Matches: 146, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
133 3 0.02
134 50 0.34
135 89 0.61
136 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (134 bp):
AGTTGAAATGCATATGAGTGCATTATCAACAGAAAAACATACTAGAGTTGAAATGTATATGATAC
ATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATA
CTAG
Found at i:58999 original size:31 final size:31
Alignment explanation
Indices: 58961--59020 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
58951 AATAAAAAAT
*
58961 GTCTGCTGTTACTTACAGTTATCAAACACAC
1 GTCTGCTGTTACATACAGTTATCAAACACAC
58992 GTCTGCTGTTACATACAGTTATCAAACAC
1 GTCTGCTGTTACATACAGTTATCAAACAC
59021 GAGCACATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (31 bp):
GTCTGCTGTTACATACAGTTATCAAACACAC
Found at i:61784 original size:11 final size:11
Alignment explanation
Indices: 61768--61799 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
61758 TAAGAATGCA
61768 TAAGGTGCGAG
1 TAAGGTGCGAG
61779 TAAGGTGCGAG
1 TAAGGTGCGAG
61790 TAAGGTGCGA
1 TAAGGTGCGA
61800 TTCCGTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.44, T:0.19
Consensus pattern (11 bp):
TAAGGTGCGAG
Found at i:69918 original size:20 final size:20
Alignment explanation
Indices: 69872--69964 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
69862 ATCAGAGTTA
*
69872 TGGTATTCATACCAGAGGAC
1 TGGTATCCATACCAGAGGAC
69892 T-GTATCCATACCAGAGGAC
1 TGGTATCCATACCAGAGGAC
69911 TGGTATCCATACCAGAGGAC
1 TGGTATCCATACCAGAGGAC
69931 TGGTATCCATACCAGAGGAC
1 TGGTATCCATACCAGAGGAC
*
69951 TGGAATCCATACCA
1 TGGTATCCATACCA
69965 AAGGCTTAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
19 18 0.26
20 52 0.74
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (20 bp):
TGGTATCCATACCAGAGGAC
Found at i:69983 original size:40 final size:40
Alignment explanation
Indices: 69879--69983 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 40
69869 TTATGGTATT
* * * *
69879 CATACCAGAGGACT-GTATCCATACCAGAGGACTGGTATC
1 CATACCAAAGGACTAATATCAATACCAGAGGACTGGAATC
* ** *
69918 CATACCAGAGGACTGGTATCCATACCAGAGGACTGGAATC
1 CATACCAAAGGACTAATATCAATACCAGAGGACTGGAATC
*
69958 CATACCAAAGG-CTTAATATTAATACC
1 CATACCAAAGGAC-TAATATCAATACC
69984 CAAAGGGGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.26
40 43 0.74
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (40 bp):
CATACCAAAGGACTAATATCAATACCAGAGGACTGGAATC
Found at i:70947 original size:27 final size:29
Alignment explanation
Indices: 70909--70975 Score: 68
Period size: 31 Copynumber: 2.3 Consensus size: 29
70899 CTTATTTTTT
* *
70909 CTTCTTTC-TTTT-GTC-TACTTGTGTTG
1 CTTCATTCATTTTCGTCTTACTTGTATTG
*
70935 CTTCATTCATTTTTTCTTCTTACTTGTATTG
1 CTTCATTCA--TTTTCGTCTTACTTGTATTG
70966 CTTCATTCAT
1 CTTCATTCAT
70976 GCATAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 7 0.21
29 5 0.15
30 2 0.06
31 19 0.58
ACGTcount: A:0.10, C:0.21, G:0.09, T:0.60
Consensus pattern (29 bp):
CTTCATTCATTTTCGTCTTACTTGTATTG
Done.