Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005519.1 Hibiscus syriacus cultivar Beakdansim tig00012751_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: 71199
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3831 original size:31 final size:31
Alignment explanation
Indices: 3795--3857 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3785 CCCCGATCTA
3795 ACCATTCTTACAATTATGCCTTTCATTTCCG
1 ACCATTCTTACAATTATGCCTTTCATTTCCG
3826 ACCATTCTTACAATTATGCCTTTCATTTCCG
1 ACCATTCTTACAATTATGCCTTTCATTTCCG
3857 A
1 A
3858 AGCTCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (31 bp):
ACCATTCTTACAATTATGCCTTTCATTTCCG
Found at i:9860 original size:14 final size:14
Alignment explanation
Indices: 9841--9870 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9831 TAAACTTAAT
9841 AATAATAATATAAA
1 AATAATAATATAAA
9855 AATAATAATATAAA
1 AATAATAATATAAA
9869 AA
1 AA
9871 GAGTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATAATATAAA
Found at i:13588 original size:24 final size:24
Alignment explanation
Indices: 13556--13617 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
13546 GTTTTATCTT
13556 ATTTATGTTCTGATTTACGATATGA
1 ATTT-TGTTCTGATTTACGATATGA
* *
13581 ATTTTGTTCTGATTTTCGATCTGA
1 ATTTTGTTCTGATTTACGATATGA
* *
13605 ATTCTGTTATGAT
1 ATTTTGTTCTGAT
13618 ATTTGACCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.52
Consensus pattern (24 bp):
ATTTTGTTCTGATTTACGATATGA
Found at i:13628 original size:24 final size:24
Alignment explanation
Indices: 13578--13631 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
13568 ATTTACGATA
* * *
13578 TGAATTTTGTTCTGATTTTCGATC
1 TGAATTCTGTTATGATTTTCGACC
13602 TGAATTCTGTTATGATATTT-GACC
1 TGAATTCTGTTATGAT-TTTCGACC
13626 TGAATT
1 TGAATT
13632 ATCTTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTTCGACC
Found at i:14005 original size:15 final size:16
Alignment explanation
Indices: 13979--14009 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13969 GGGAGGGATT
13979 AATATGGTTTTAAAAA
1 AATATGGTTTTAAAAA
13995 AATAT-GTTTTAAAAA
1 AATATGGTTTTAAAAA
14010 GATCTGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
AATATGGTTTTAAAAA
Found at i:17078 original size:24 final size:24
Alignment explanation
Indices: 17019--17078 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
17009 TTTATTTGAT
17019 TTCTGTTATGATTTCCGATCTGAA
1 TTCTGTTATGATTTCCGATCTGAA
* *
17043 TTCTATTTTGATTTCCGATCTGAA
1 TTCTGTTATGATTTCCGATCTGAA
*
17067 TTCTGTTCTGAT
1 TTCTGTTATGAT
17079 ATTTAACCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.50
Consensus pattern (24 bp):
TTCTGTTATGATTTCCGATCTGAA
Found at i:17476 original size:16 final size:17
Alignment explanation
Indices: 17449--17480 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17439 TGGAGGAATT
17449 AATATGGTTTTAAAAAA
1 AATATGGTTTTAAAAAA
17466 AATAT-GTTTTAAAAA
1 AATATGGTTTTAAAAA
17481 GATCTGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
AATATGGTTTTAAAAAA
Found at i:20582 original size:14 final size:14
Alignment explanation
Indices: 20565--20637 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
20555 TATTTATGTT
20565 AATATTATTATTAA
1 AATATTATTATTAA
*
20579 AATATT-GTATCTAA
1 AATATTATTAT-TAA
* *
20593 AAT-TTATAAATAAA
1 AATATTAT-TATTAA
** *
20607 AATATTAAAATTAT
1 AATATTATTATTAA
20621 AATATT-TTATTAA
1 AATATTATTATTAA
20634 AATA
1 AATA
20638 AAAATATTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
13 13 0.29
14 27 0.60
15 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:20643 original size:19 final size:19
Alignment explanation
Indices: 20609--20645 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20599 TAAATAAAAA
* *
20609 TATTAAAATTATAATATTT
1 TATTAAAATAAAAATATTT
20628 TATTAAAATAAAAATATT
1 TATTAAAATAAAAATATT
20646 ATAAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTAAAATAAAAATATTT
Found at i:20645 original size:14 final size:15
Alignment explanation
Indices: 20591--20651 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
20581 TATTGTATCT
20591 AAAAT-TTATAAATA
1 AAAATATTATAAATA
20605 AAAATATTA-AAATTA
1 AAAATATTATAAA-TA
* *
20620 TAATATTTTATTAAAATA
1 -AAAATATTA-T-AAATA
20638 AAAATATTATAAAT
1 AAAATATTATAAAT
20652 TATTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
14 8 0.22
15 9 0.24
16 8 0.22
17 7 0.19
18 2 0.05
19 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATTATAAATA
Found at i:20714 original size:25 final size:25
Alignment explanation
Indices: 20686--20745 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
20676 ATTATTAATT
*
20686 ATATTAAATAATTTTTAAAATAAAA
1 ATATTAAAAAATTTTTAAAATAAAA
* *
20711 ATA-TAATAAAATTTTTAAAATTATA
1 ATATTAA-AAAATTTTTAAAATAAAA
20736 ATATTAAAAA
1 ATATTAAAAA
20746 TATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 24 0.80
26 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATTAAAAAATTTTTAAAATAAAA
Found at i:20813 original size:27 final size:25
Alignment explanation
Indices: 20782--20856 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
20772 TTTTAAATAT
20782 TAAATAATTTAATAATATTATTTTA
1 TAAATAATTTAATAATATTATTTTA
* *
20807 TAAA-AATAATAAATAAAATTAATTTTA
1 TAAATAAT--TTAATAATATT-ATTTTA
* *
20834 TTAATAATTTATTATATATTATT
1 TAAATAATTTAATA-ATATTATT
20857 AAAATAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
24 3 0.08
25 4 0.10
26 16 0.41
27 13 0.33
28 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATAATTTAATAATATTATTTTA
Found at i:20827 original size:26 final size:28
Alignment explanation
Indices: 20783--20834 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
20773 TTTAAATATT
* *
20783 AAATAATTTAATAATATT-ATTTTATAA
1 AAATAATTAAATAAAATTAATTTTATAA
20810 AAATAA-TAAATAAAATTAATTTTAT
1 AAATAATTAAATAAAATTAATTTTAT
20835 TAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATAATTAAATAAAATTAATTTTATAA
Found at i:23238 original size:16 final size:16
Alignment explanation
Indices: 23217--23257 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
23207 GGTTTCCTAA
23217 AAGGAAAAACATTCTC
1 AAGGAAAAACATTCTC
23233 AAGGAAAAACATTCTC
1 AAGGAAAAACATTCTC
*
23249 AAAGAAAAA
1 AAGGAAAAA
23258 ATCCCTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (16 bp):
AAGGAAAAACATTCTC
Found at i:28780 original size:2 final size:2
Alignment explanation
Indices: 28771--28804 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28761 TTAATAAAAA
28771 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28805 ATTCAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37316 original size:12 final size:12
Alignment explanation
Indices: 37301--37329 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
37291 TCCTTAAATT
37301 TGATGCTAAAAG
1 TGATGCTAAAAG
37313 TGATGCTAAAAG
1 TGATGCTAAAAG
37325 TGATG
1 TGATG
37330 AAGGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (12 bp):
TGATGCTAAAAG
Found at i:40730 original size:45 final size:46
Alignment explanation
Indices: 40681--40768 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
40671 GAACATCAAA
* * *
40681 TGCATTTTATGCATCGATGCA-TATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
40726 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
40769 CAGGCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:42203 original size:34 final size:32
Alignment explanation
Indices: 42150--42219 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
42140 ACCTTACAAC
* *
42150 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
42182 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
42216 TCCC
1 TCCC
42220 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:42673 original size:19 final size:19
Alignment explanation
Indices: 42649--42696 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42639 GAGCCGCAGG
*
42649 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
* *
42668 TTACTGTTCGAATAGTAAT
1 TTACTGTTCAAACAGTAAT
*
42687 TTACTATTCA
1 TTACTGTTCA
42697 TAAAAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:42795 original size:29 final size:31
Alignment explanation
Indices: 42763--42820 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
42753 ATTTTGAATA
42763 AATTCAATT-AAGT-CAAAATA-CATTTTGTG
1 AATTCAATTCAAGTCCAAAA-ACCATTTTGTG
42792 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
42821 CCTTAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.35
30 5 0.19
31 12 0.46
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTG
Found at i:52571 original size:19 final size:18
Alignment explanation
Indices: 52544--52579 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52534 ATCAAGGTCT
*
52544 TTGTTGATGCCATGAAATC
1 TTGTCGATGCCAT-AAATC
52563 TTGTCGATGCCATAAAT
1 TTGTCGATGCCATAAAT
52580 ACATGGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (18 bp):
TTGTCGATGCCATAAATC
Found at i:55735 original size:19 final size:20
Alignment explanation
Indices: 55706--55758 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
55696 TTTTAAGAAT
*
55706 TTTTATTTAAAATAAAAA-TA
1 TTTT-TTTAAAATAAAAACCA
*
55726 TTTTTTTAAAAAAAAAACCA
1 TTTTTTTAAAATAAAAACCA
*
55746 TTTTTTTCAAATA
1 TTTTTTTAAAATA
55759 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTTTTAAAATAAAAACCA
Found at i:55737 original size:20 final size:20
Alignment explanation
Indices: 55706--55752 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
55696 TTTTAAGAAT
* *
55706 TTTTATTTAAAATAAAAA-TA
1 TTTT-TTTAAAAAAAAAACCA
55726 TTTTTTTAAAAAAAAAACCA
1 TTTTTTTAAAAAAAAAACCA
55746 TTTTTTT
1 TTTTTTT
55753 CAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTTTAAAAAAAAAACCA
Found at i:62264 original size:26 final size:25
Alignment explanation
Indices: 62234--62289 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
62224 CTTATAAAAA
62234 TGATTGATATATATATG-AATTAAATT
1 TGATT-AT-TATATATGAAATTAAATT
* *
62260 TGATTATTATATTTGATAATTATATT
1 TGATTATTATATATGA-AATTAAATT
62286 TGAT
1 TGAT
62290 AAATGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 7 0.27
25 2 0.08
26 17 0.65
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (25 bp):
TGATTATTATATATGAAATTAAATT
Found at i:62273 original size:13 final size:13
Alignment explanation
Indices: 62251--62291 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
62241 TATATATATG
*
62251 AATTAAATTTGAT
1 AATTATATTTGAT
*
62264 TATTATATTTGAT
1 AATTATATTTGAT
62277 AATTATATTTGAT
1 AATTATATTTGAT
62290 AA
1 AA
62292 ATGGTTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (13 bp):
AATTATATTTGAT
Found at i:64381 original size:93 final size:93
Alignment explanation
Indices: 64222--65101 Score: 1147
Period size: 93 Copynumber: 9.5 Consensus size: 93
64212 AGTATTGACT
* * * *
64222 ATGCCATAAATATAGTGCATGAACGGATGGACTAAGGCATGAAAGGATACCATAAATAAAAATGC
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
64287 ATGAACGGATGCATTAAGGCATGAAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGG
* * *
64315 ATGCCATAACTAAAGTGCATGAACGAATGCACTAAGGCTTGAAAGAATGCCATAAATAAAAATGC
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
* *
64380 ATGAACGGATGCATTAATGCTTGAAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGG
* *
64408 ATGCCATAACTAAAGTGCATGAACAGATGCACTAAGGTATGAAAGGATGCCATAAATAAAAATGC
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
** * *
64473 ATGATTGGATGTATTAAGGCATAAAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGG
* * *
64501 ATGCCATAACTAAAGTTCATGAACGGATGAAATAAGGCATGAAAGGATGCCATAAATAAAAATGC
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
* *
64566 ATGAGCGGATGCATTAAGGCATGAAAGA
66 ATGAACGGATGCATTAAGGCATGAAAGG
* * * *
64594 ATGCCTTTACTAAACTGCATGAACGGATGCACTAAGGTATGAAAGGATGCCATAAATAAAAATGC
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
*
64659 ATGAACAGATGCATTAAGGCATGAAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGG
* *
64687 ATGCCATAACTAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGA
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
* *
64752 ATGAACAGATGCATTAAGTCATGAAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGG
* * *
64780 ATGCCATAACTAAAGCGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAACTAAAGCA--
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAA-AATG
*
64843 CATGAACGGATGCACTAAGGCATGAAAGG
65 CATGAACGGATGCATTAAGGCATGAAAGG
* * * * ** * * *
64872 ATGCCATAAATAAAAATGCATGAACGGACGCATTAAGGCATGAAATAATGTCATAACT-AAAGTG
1 ATGCCATAACT-AAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATG
* **
64936 CATGAAAGGATGCACCAAGGCATGAAAGG
65 CATGAACGGATGCATTAAGGCATGAAAGG
* * * * * * * * *
64965 ATGTCATAATTAAAAATGCATGAATGGATGCATTAAGGAATGAAATGATGCCATAACT-AAAGTG
1 ATGCCATAACT-AAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATG
* *
65029 CATGAACAGATACATTAAGGCATGAAAGG
65 CATGAACGGATGCATTAAGGCATGAAAGG
* * * * * *
65058 ATGCCATAACTAAAATGTATGAACGAATGTATTAATGCATGAAA
1 ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAA
65102 AGAGGCTATA
Statistics
Matches: 696, Mismatches: 87, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
92 64 0.09
93 631 0.91
94 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.21
Consensus pattern (93 bp):
ATGCCATAACTAAAGTGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
ATGAACGGATGCATTAAGGCATGAAAGG
Found at i:65100 original size:232 final size:232
Alignment explanation
Indices: 64222--65101 Score: 1152
Period size: 232 Copynumber: 3.8 Consensus size: 232
64212 AGTATTGACT
* * * *
64222 ATGCCATAAATATAGTGCATGAACGGATGGACTAAGGCATGAAAGGATACCATAAATAAAAATGC
1 ATGCCATAAATAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
*
64287 ATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAGTGCATGAACGAATGCACTAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAGTGCATGAACGGATGCACTAAGG
* * * * *
64352 CTTGAAAGAATGCCATAAATAAAAATGCATGAACGGATGCATTAATGCTTGAAAGGATGCCATAA
131 CATGAAAGAATGCCATAACT-AAAATGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAA
* * * *
64417 CT-AAAGTGCATGAACAGATGCACTAAGGTATGAAAGG
195 ATAAAAATGCATGAACAGATGCATTAAGGCATGAAAGG
* * * * * * * *
64454 ATGCCATAAATAAAAATGCATGATTGGATGTATTAAGGCATAAAAGGATGCCATAACT-AAAGTT
1 ATGCCATAAAT-AAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATG
* * * * * *
64518 CATGAACGGATGAAATAAGGCATGAAAGGATGCCATAAATAAAAATGCATGAGCGGATGCATTAA
65 CATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACT-AAAGTGCATGAACGGATGCACTAA
* * * *
64583 GGCATGAAAGAATGCCTTTACTAAACTGCATGAACGGATGCACTAAGGTATGAAAGGATGCCATA
129 GGCATGAAAGAATGCCATAACTAAAATGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATA
64648 AATAAAAATGCATGAACAGATGCATTAAGGCATGAAAGG
194 AATAAAAATGCATGAACAGATGCATTAAGGCATGAAAGG
* *
64687 ATGCCATAACTAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGA
1 ATGCCATAAATAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
* * *
64752 ATGAACAGATGCATTAAGTCATGAAAGGATGCCATAACTAAAGCGCATGAACGGATGCACTAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAGTGCATGAACGGATGCACTAAGG
* ***
64817 CATGAAAGGATGCCATAACTAAAGCACATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAA
131 CATGAAAGAATGCCATAACTAAAATGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAA
* * **
64882 TAAAAATGCATGAACGGACGCATTAAGGCATGAAATA
196 TAAAAATGCATGAACAGATGCATTAAGGCATGAAAGG
* * * * * *
64919 ATGTCATAACTAAAGTGCATGAAAGGATGCACCAAGGCATGAAAGGATGTCATAATTAAAAATGC
1 ATGCCATAAATAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
* * * * * *
64984 ATGAATGGATGCATTAAGGAATGAAATGATGCCATAACTAAAGTGCATGAACAGATACATTAAGG
66 ATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAGTGCATGAACGGATGCACTAAGG
* * * * * *
65049 CATGAAAGGATGCCATAACTAAAATGTATGAACGAATGTATTAATGCATGAAA
131 CATGAAAGAATGCCATAACTAAAATGCATGAACGGATGCACTAAGGCATGAAA
65102 AGAGGCTATA
Statistics
Matches: 560, Mismatches: 84, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
232 405 0.72
233 155 0.28
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.21
Consensus pattern (232 bp):
ATGCCATAAATAAAGTGCATGAATGGATGCACTAAGGCATGAAAGGATGCCATAAATAAAAATGC
ATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAGTGCATGAACGGATGCACTAAGG
CATGAAAGAATGCCATAACTAAAATGCATGAACGGATGCACTAAGGCATGAAAGGATGCCATAAA
TAAAAATGCATGAACAGATGCATTAAGGCATGAAAGG
Found at i:67500 original size:3 final size:3
Alignment explanation
Indices: 67492--67564 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
67482 TCATTTCATT
** **
67492 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA AAA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
67538 TTA TATA TTA -TA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA T-TA TTA TTA TTA TT
67565 TAATAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.03
3 47 0.81
4 9 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:68964 original size:15 final size:15
Alignment explanation
Indices: 68944--68993 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
68934 GATCCTATAG
68944 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
68959 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
68973 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
68989 TTTTA
1 TTTTA
68994 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:69913 original size:28 final size:27
Alignment explanation
Indices: 69882--69935 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
69872 TAATTCTTTC
*
69882 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
* *
69910 TTTTCATAGTATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
69936 TTATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:69956 original size:24 final size:24
Alignment explanation
Indices: 69899--69956 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
69889 AATTTTTATA
* *
69899 TATACTTATTATTTTCATAGTATT
1 TATATTTATTATTTTCATAATATT
*
69923 TATATATATTATTTT-ATTAATATT
1 TATATTTATTATTTTCA-TAATATT
69947 TCAT-TTTATT
1 T-ATATTTATT
69957 TGCAAGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATTTATTATTTTCATAATATT
Done.