Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001904.1 Hibiscus syriacus cultivar Beakdansim tig00003855_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: 140145
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4639 original size:23 final size:23
Alignment explanation
Indices: 4593--4663 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
4583 TAAAACGTTA
* *
4593 AATTAAAAAGTAATT-AAATGTAT
1 AATTATAAATTAATTAAAAT-TAT
*
4616 AATTATAAATTAGTTAAAATTAT
1 AATTATAAATTAATTAAAATTAT
* * *
4639 AAATGTAATTTAATTAAAA-TAT
1 AATTATAAATTAATTAAAATTAT
4661 AAT
1 AAT
4664 ATCAACAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 5 0.13
23 30 0.77
24 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (23 bp):
AATTATAAATTAATTAAAATTAT
Found at i:4653 original size:17 final size:17
Alignment explanation
Indices: 4613--4663 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
4603 TAATTAAATG
*
4613 TATAATTATAAATTAGT
1 TATAATTATAAATTAAT
*
4630 TAAAATTATAAATGTAAT
1 TATAATTATAAAT-TAAT
4648 T-TAATTA-AAATATAAT
1 TATAATTATAAAT-TAAT
4664 ATCAACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 8 0.28
17 17 0.59
18 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TATAATTATAAATTAAT
Found at i:4997 original size:18 final size:17
Alignment explanation
Indices: 4974--5007 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4964 TTAGATATTT
*
4974 TTTAATATATTTATTTAA
1 TTTAATAAATTT-TTTAA
4992 TTTAATAAATTTTTTA
1 TTTAATAAATTTTTTA
5008 TCCAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATAAATTTTTTAA
Found at i:6352 original size:15 final size:16
Alignment explanation
Indices: 6319--6355 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6309 TTAAAAACTA
6319 ATATTTTATAAATATT
1 ATATTTTATAAATATT
*
6335 ATATTTTTTAAA-ATT
1 ATATTTTATAAATATT
6350 ATATTT
1 ATATTT
6356 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTTATAAATATT
Found at i:8577 original size:35 final size:35
Alignment explanation
Indices: 8538--8606 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
8528 AACAGTAAGG
*
8538 CCCTGAGCACAAAGCCGA-GAAGCCTGCAAGTAATT
1 CCCTGAGCACAAAGCCGATG-AGCCTCCAAGTAATT
*
8573 CCCTGAGCATAAAGCCGATGAGCCTCCAAGTAAT
1 CCCTGAGCACAAAGCCGATGAGCCTCCAAGTAAT
8607 CTTCCTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (35 bp):
CCCTGAGCACAAAGCCGATGAGCCTCCAAGTAATT
Found at i:8743 original size:23 final size:23
Alignment explanation
Indices: 8683--8772 Score: 126
Period size: 23 Copynumber: 3.8 Consensus size: 23
8673 CATAATTCAA
*
8683 GTCAAGTATCATATCAGAATCCAT
1 GTCAA-TATCAGATCAGAATCCAT
*
8707 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAT
8731 GTCAATATCAGATCAGAATCCAT
1 GTCAATATCAGATCAGAATCCAT
* *
8754 GTCAATATCATAACAGAAT
1 GTCAATATCAGATCAGAAT
8773 TCAAATCAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
23 35 0.58
24 25 0.42
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAT
Found at i:15854 original size:60 final size:58
Alignment explanation
Indices: 15686--15856 Score: 220
Period size: 57 Copynumber: 2.9 Consensus size: 58
15676 ACGCAGAGTT
* * * *
15686 AAAAGGCAGTCGGGATAACTGGCTAATTGGCAGTAGCAGATCAAACAGGTCA-TTTCC
1 AAAAGGCGGTAGGGATGACTGGCTAATTGGTAGTAGCAGATCAAACAGGTCATTTTCC
* * *
15743 AAAAGGTGGTAGGGATGACTGGCTAATCGGTAGTAGCAGATCAAACAGGTCATTTTCG
1 AAAAGGCGGTAGGGATGACTGGCTAATTGGTAGTAGCAGATCAAACAGGTCATTTTCC
**
15801 AAAA-GCGGTAGGGATGACTGGCTAATTGGTGGTAGTAGCAGATCTGACAGGTCATT
1 AAAAGGCGGTAGGGATGACTGGCTAA-T--TGGTAGTAGCAGATCAAACAGGTCATT
15857 CTCCCGTGAC
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
57 66 0.67
58 9 0.09
60 24 0.24
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.23
Consensus pattern (58 bp):
AAAAGGCGGTAGGGATGACTGGCTAATTGGTAGTAGCAGATCAAACAGGTCATTTTCC
Found at i:19688 original size:22 final size:23
Alignment explanation
Indices: 19654--19696 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19644 ATATAATATA
19654 TAATAATATTTATTATAAAAACT
1 TAATAATATTTATTATAAAAACT
* *
19677 TAATATTA-TTATTTTAAAAA
1 TAATAATATTTATTATAAAAA
19697 TATTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATAATATTTATTATAAAAACT
Found at i:19874 original size:8 final size:8
Alignment explanation
Indices: 19821--19888 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
19811 AATAGTATCA
19821 TATATTAT
1 TATATTAT
*
19829 TATAATA-
1 TATATTAT
*
19836 TA-ATTGAG
1 TATATT-AT
19844 TATATTAT
1 TATATTAT
* *
19852 TGTAGTAT
1 TATATTAT
19860 TATTATTAT
1 TA-TATTAT
19869 TATATTATAT
1 TATA-T-TAT
19879 TATATTAT
1 TATATTAT
19887 TA
1 TA
19889 ACAATATTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 23 0.49
9 12 0.26
10 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (8 bp):
TATATTAT
Found at i:19984 original size:19 final size:18
Alignment explanation
Indices: 19938--19988 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
19928 ATATTTTGAT
*
19938 TAAAATGATATTAAAATA
1 TAAAATAATATTAAAATA
* *
19956 TCATATTAATATTAAATATA
1 T-AAAATAATATTAAA-ATA
19976 TAAAATAATATTA
1 TAAAATAATATTA
19989 TTTTGAGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 21 0.81
20 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATAATATTAAAATA
Found at i:21544 original size:15 final size:15
Alignment explanation
Indices: 21524--21552 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21514 GTGATATGTT
21524 GAAGGGTTTTGTCCA
1 GAAGGGTTTTGTCCA
21539 GAAGGGTTTTGTCC
1 GAAGGGTTTTGTCC
21553 CTTCATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.34
Consensus pattern (15 bp):
GAAGGGTTTTGTCCA
Found at i:40318 original size:23 final size:23
Alignment explanation
Indices: 40292--40360 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
40282 CACCACAGCT
*
40292 CGTATAATTACATCGAAGTGCCA
1 CGTAGAATTACATCGAAGTGCCA
* * * *
40315 CGTAGAATTGCATCGTAGTACCG
1 CGTAGAATTACATCGAAGTGCCA
* *
40338 CGTAGAAATACACCGAAGTGCCA
1 CGTAGAATTACATCGAAGTGCCA
40361 TATAAGATGT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACATCGAAGTGCCA
Found at i:42287 original size:6 final size:6
Alignment explanation
Indices: 42276--42316 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
42266 ATTCTGTTAC
42276 TACTAT TACTAT TACTAT TACTAT TACTAT TACTAT TACTA
1 TACTAT TACTAT TACTAT TACTAT TACTAT TACTAT TACTA
42317 CTATTGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (6 bp):
TACTAT
Found at i:49242 original size:23 final size:23
Alignment explanation
Indices: 49216--49260 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49206 CACCACAGCT
*
49216 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
49239 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
49261 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:75360 original size:22 final size:21
Alignment explanation
Indices: 75335--75377 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
75325 GTTTGCAGTT
75335 CATTAATG-TTGTATGAGCTTAG
1 CATT-ATGATTGTA-GAGCTTAG
*
75357 CATTATGATTGTAGAGTTTAG
1 CATTATGATTGTAGAGCTTAG
75378 TGTTTCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (21 bp):
CATTATGATTGTAGAGCTTAG
Found at i:85538 original size:20 final size:20
Alignment explanation
Indices: 85513--85580 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
85503 GAAGTTCGCA
85513 TTGCGATTCATTCCAAATCG
1 TTGCGATTCATTCCAAATCG
* * *
85533 TTGCGA-T-AGTCGAAGTTCGCG
1 TTGCGATTCATTCCAA-AT--CG
85554 TTGCGATTCATTCCAAATCG
1 TTGCGATTCATTCCAAATCG
85574 TTGCGAT
1 TTGCGAT
85581 AGGCGAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.14
19 2 0.05
20 15 0.41
21 8 0.22
22 2 0.05
23 5 0.14
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TTGCGATTCATTCCAAATCG
Found at i:85539 original size:41 final size:41
Alignment explanation
Indices: 85494--85831 Score: 568
Period size: 41 Copynumber: 8.2 Consensus size: 41
85484 GATTCGCAAC
* *
85494 GCGATAGGTGAAGTTCGCATTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
85535 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
85576 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
85617 GCGATAGGCGAAGTTCGAGTTGCGATTCATTTCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
85658 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
85699 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
85741 GCGATAGGCGAAGTTCACGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
85783 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
85825 GCGATAG
1 GCGATAG
85832 TCCAAATATT
Statistics
Matches: 284, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
41 190 0.67
42 94 0.33
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:85924 original size:6 final size:6
Alignment explanation
Indices: 85908--85946 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
85898 AGACACGTAT
* *
85908 GACCAC TACCAC GACCAC GACCAC GACCCC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
85947 CAAGACGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.28, C:0.54, G:0.15, T:0.03
Consensus pattern (6 bp):
GACCAC
Found at i:86656 original size:12 final size:11
Alignment explanation
Indices: 86614--86656 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
86604 CCGTCCCGTC
86614 TCGGGTCG-GG
1 TCGGGTCGTGG
*
86624 TCGGGTCGGGG
1 TCGGGTCGTGG
86635 TCGGGGTCGTGG
1 TC-GGGTCGTGG
86647 TCGTGGTCGT
1 TCG-GGTCGT
86657 ACGTGTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 8 0.28
11 5 0.17
12 16 0.55
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.26
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:86748 original size:19 final size:19
Alignment explanation
Indices: 86724--86955 Score: 58
Period size: 21 Copynumber: 11.3 Consensus size: 19
86714 CAAATGCAAT
*
86724 ATTTGGGCTATCGCAACGA
1 ATTTGGACTATCGCAACGA
*
86743 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * *
86766 ACTTCGCCTATCGCAACGA
1 ATTTGGACTATCGCAACGA
*
86785 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * * *
86808 ACTTCGCCTGTCGCAACGA
1 ATTTGGACTATCGCAACGA
*
86827 A-TTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
*
86849 ACTTT-GCCTATCGCAACGA
1 A-TTTGGACTATCGCAACGA
* *
86868 A-TTGGAATGAATCACAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * *
86890 ACTTCGCCTATCGCAACG-
1 ATTTGGACTATCGCAACGA
*
86908 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * *
86931 ACTTCGACTATCACAACGA
1 ATTTGGACTATCGCAACGA
86950 ATTTGG
1 ATTTGG
86956 GATGAATCGC
Statistics
Matches: 150, Mismatches: 38, Indels: 50
0.63 0.16 0.21
Matches are distributed among these distances:
17 2 0.01
18 11 0.07
19 32 0.21
20 19 0.13
21 46 0.31
22 10 0.07
23 28 0.19
24 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (19 bp):
ATTTGGACTATCGCAACGA
Found at i:86844 original size:41 final size:42
Alignment explanation
Indices: 86731--86985 Score: 426
Period size: 41 Copynumber: 6.1 Consensus size: 42
86721 AATATTTGGG
86731 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
86773 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
86815 CTGTCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTTGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
86856 CTATCGCAACGAA-TTGGAATGAATCACAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
86897 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
86938 CTATCACAACGAATTTGGGATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
86980 CTATCG
1 CTATCG
86986 TGTTGCGAAT
Statistics
Matches: 201, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 1 0.00
41 112 0.56
42 88 0.44
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:99075 original size:21 final size:22
Alignment explanation
Indices: 99051--99091 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
99041 TTTTCTCTAG
*
99051 CACGCTGAAGGA-TTTCTTCAA
1 CACGATGAAGGATTTTCTTCAA
*
99072 CACGATGCAGGATTTTCTTC
1 CACGATGAAGGATTTTCTTC
99092 TGCAGATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (22 bp):
CACGATGAAGGATTTTCTTCAA
Found at i:100946 original size:220 final size:220
Alignment explanation
Indices: 100528--100957 Score: 835
Period size: 220 Copynumber: 2.0 Consensus size: 220
100518 CCTTGACGAC
100528 ATAGGGATGATCTGTCCCGTTTAACCTCAGAAACATTAGTAGCATCCTCAGTTTCCACCTGCACA
1 ATAGGGATGATCTGTCCCGTTTAACCTCAGAAACATTAGTAGCATCCTCAGTTTCCACCTGCACA
*
100593 TCAATATGAACAATATAGGTATCAGTTCAATCATCTAAAAGCAAAATTCGCTGACAAGTTGAAAC
66 TCAATATGAACAATATAGGTATCAGTTCAATCATCTAAAAGCAAAATTCACTGACAAGTTGAAAC
100658 GAAGATTCACACGAAAAAGGAAATTTAAATTCATGATTTGCTAATTTTCACTTTAAGCGGTGCAT
131 GAAGATTCACACGAAAAAGGAAATTTAAATTCATGATTTGCTAATTTTCACTTTAAGCGGTGCAT
100723 ATATATATATATATACATACCTATG
196 ATATATATATATATACATACCTATG
100748 ATAGGGATGATCTGTCCCGTTTAACCTCAGAAACATTAGTAGCATCCTCAGTTTCCACCTGCACA
1 ATAGGGATGATCTGTCCCGTTTAACCTCAGAAACATTAGTAGCATCCTCAGTTTCCACCTGCACA
100813 TCAATATGAACAATATAGGTATCAGTTCAATCATCTAAAAGCAAAATTCACTGACAAGTTGAAAC
66 TCAATATGAACAATATAGGTATCAGTTCAATCATCTAAAAGCAAAATTCACTGACAAGTTGAAAC
100878 GAAGATTCACACGAAAAAGGAAATTT-AATTCATGATTTGCTAATTTTCACTTTAAGCGGTGCCA
131 GAAGATTCACACGAAAAAGGAAATTTAAATTCATGATTTGCTAATTTTCACTTTAAGCGGTG-CA
100942 TATATATATATATATA
195 TATATATATATATATA
100958 TATATATTTA
Statistics
Matches: 208, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
219 35 0.17
220 173 0.83
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (220 bp):
ATAGGGATGATCTGTCCCGTTTAACCTCAGAAACATTAGTAGCATCCTCAGTTTCCACCTGCACA
TCAATATGAACAATATAGGTATCAGTTCAATCATCTAAAAGCAAAATTCACTGACAAGTTGAAAC
GAAGATTCACACGAAAAAGGAAATTTAAATTCATGATTTGCTAATTTTCACTTTAAGCGGTGCAT
ATATATATATATATACATACCTATG
Found at i:100948 original size:2 final size:2
Alignment explanation
Indices: 100941--100975 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
100931 AAGCGGTGCC
* *
100941 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
100976 CCTATGATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:101425 original size:15 final size:16
Alignment explanation
Indices: 101407--101436 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
101397 ATTCTTCTTC
101407 CTCCTCC-CCTTCCCT
1 CTCCTCCTCCTTCCCT
101422 CTCCTCCTCCTTCCC
1 CTCCTCCTCCTTCCC
101437 GCAATAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (16 bp):
CTCCTCCTCCTTCCCT
Found at i:102552 original size:22 final size:23
Alignment explanation
Indices: 102521--102570 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
102511 ATGAAAACTT
102521 CAATTCTTTT-GTTATTAGATAA
1 CAATTCTTTTAGTTATTAGATAA
* *
102543 CAATTTTTTTAACTTTATTAGATAA
1 CAATTCTTTT-A-GTTATTAGATAA
102568 CAA
1 CAA
102571 ATTTGATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
25 14 0.61
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (23 bp):
CAATTCTTTTAGTTATTAGATAA
Found at i:106830 original size:29 final size:29
Alignment explanation
Indices: 106793--106887 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
106783 AGGGCGCAGG
106793 ACAAGGTCGCCCAACGTGCATGGCGACCT
1 ACAAGGTCGCCCAACGTGCATGGCGACCT
* * * ***
106822 ACCATGTCGTCTGGCGTGCATGGCGACCT
1 ACAAGGTCGCCCAACGTGCATGGCGACCT
*** * *
106851 ACAAGGTCGCCTGGCGTGCATGACGACTT
1 ACAAGGTCGCCCAACGTGCATGGCGACCT
106880 ACAAGGTC
1 ACAAGGTC
106888 ACCCGGAAGG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (29 bp):
ACAAGGTCGCCCAACGTGCATGGCGACCT
Found at i:116424 original size:11 final size:10
Alignment explanation
Indices: 116398--116458 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 10
116388 CCAGGAAAAA
116398 GTCAACTGTCG
1 GTCAAC-GTCG
*
116409 TTCAACGTCCG
1 GTCAACGT-CG
116420 GTCAACGTCG
1 GTCAACGTCG
*
116430 GTCAAAGTTCTG
1 GTCAACG-TC-G
* *
116442 GTCCATGTCG
1 GTCAACGTCG
116452 GTCAACG
1 GTCAACG
116459 ATCAACGTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 16 0.40
11 18 0.45
12 6 0.15
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (10 bp):
GTCAACGTCG
Found at i:116565 original size:52 final size:52
Alignment explanation
Indices: 116484--116583 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
116474 CGGTCAACAG
* * *
116484 TTTTACACAAATGTCACCCTAACAGAAATTAATTACAAAATTAACACCTGAA
1 TTTTACACAAATATCACACTAACAAAAATTAATTACAAAATTAACACCTGAA
*
116536 TTTTACACAAATATCACATTAACAAAAATTAATTACAAAATTAACACC
1 TTTTACACAAATATCACACTAACAAAAATTAATTACAAAATTAACACC
116584 CTCTACGCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (52 bp):
TTTTACACAAATATCACACTAACAAAAATTAATTACAAAATTAACACCTGAA
Found at i:126128 original size:135 final size:135
Alignment explanation
Indices: 125886--126377 Score: 957
Period size: 135 Copynumber: 3.6 Consensus size: 135
125876 GATAATCCTA
125886 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
1 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
125951 GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
66 GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
126016 TGCTG
131 TGCTG
126021 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
1 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
*
126086 ACAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
66 GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
126151 TGCTG
131 TGCTG
126156 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
1 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
126221 GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
66 GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
126286 TGCTG
131 TGCTG
*
126291 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTCGATTCAAGAGCCTAAGGATAAT
1 GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
*
126356 GCAAGTTTTAGGATTGTGCTGC
66 GCAAGTTTTAGGATCGTGCTGC
126378 AAGTTGTAGA
Statistics
Matches: 353, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 353 1.00
ACGTcount: A:0.28, C:0.11, G:0.35, T:0.26
Consensus pattern (135 bp):
GGTGCTTGAGAGAAAATGAGGTGATTGAGAGGTTGAAAGCTTTGATTCAAGAGCCTAAGGATAAT
GCAAGTTTTAGGATCGTGCTGCTTTCAAGTGGTGGGCGTGGTGGCTCACATAGGAGGAAGAAGGA
TGCTG
Found at i:126554 original size:14 final size:15
Alignment explanation
Indices: 126523--126555 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
126513 TTTTGAAGGG
*
126523 TTTAATTTTAACATA
1 TTTAATTATAACATA
126538 TTTAATTATAA-ATA
1 TTTAATTATAACATA
126552 TTTA
1 TTTA
126556 TAATATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTATAACATA
Found at i:129113 original size:13 final size:15
Alignment explanation
Indices: 129095--129126 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
129085 GTTAGACTGT
129095 AAAAATAAA-AT-AA
1 AAAAATAAATATGAA
129108 AAAAATAAATATGAA
1 AAAAATAAATATGAA
129123 AAAA
1 AAAA
129127 GGGAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAAATAAATATGAA
Found at i:129274 original size:26 final size:25
Alignment explanation
Indices: 129226--129303 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 25
129216 AAAATAGGGT
* ** *
129226 TAAATATAAAAAAAATGTTAAGAAGA
1 TAAATATTAAAAAAAT-AAAAGAAAA
129252 TAAATATTAAAAAAATCAAAAGAAAA
1 TAAATATTAAAAAAAT-AAAAGAAAA
*
129278 TAAAATAAATAAAATAAATAAAAGAA
1 T-AAAT-ATTAAAA-AAATAAAAGAA
129304 CCAAATTGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 22 0.51
27 4 0.09
28 13 0.30
29 4 0.09
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (25 bp):
TAAATATTAAAAAAATAAAAGAAAA
Found at i:129287 original size:9 final size:9
Alignment explanation
Indices: 129275--129300 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
129265 AATCAAAAGA
129275 AAATAAAAT
1 AAATAAAAT
129284 AAATAAAAT
1 AAATAAAAT
129293 AAATAAAA
1 AAATAAAA
129301 GAACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:130240 original size:13 final size:13
Alignment explanation
Indices: 130222--130250 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
130212 ATAATAATAA
130222 AATATATATGTAT
1 AATATATATGTAT
130235 AATATATATGTAT
1 AATATATATGTAT
130248 AAT
1 AAT
130251 GAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
AATATATATGTAT
Found at i:131077 original size:84 final size:85
Alignment explanation
Indices: 130874--131083 Score: 251
Period size: 85 Copynumber: 2.5 Consensus size: 85
130864 ATTTGGTTTG
* * * * *
130874 CCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGACTTAAG
1 CCTCAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
130939 ATATCCTGTAAATTATGTGC
66 ATATCCTGCAAATGATGCGC
* * * * *
130959 CCTCAAAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCTTTTTAGCCTTAAG
1 CCTCAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* *
131024 TTATGCTGCAAATGATGCG-
66 ATATCCTGCAAATGATGCGC
**
131043 CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGTT
1 CCTCAGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-TGTT
131084 TCAAGAGAAA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 32 0.30
85 73 0.70
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (85 bp):
CCTCAGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
ATATCCTGCAAATGATGCGC
Found at i:131119 original size:32 final size:32
Alignment explanation
Indices: 131076--131192 Score: 155
Period size: 33 Copynumber: 3.6 Consensus size: 32
131066 CTCGAAGGTC
*
131076 TTTGTGTTTCAAGAGAAACATTTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAACA-GTTCAAAGGTTT
* *
131109 TTTGTG-TTCAAGAGAAATGAGTTCAAAGGTAT
1 TTTGTGTTTCAAGAGAAA-CAGTTCAAAGGTTT
**
131141 TTTGTGTTTCAAGAGAAACGAGTAAAAAGGTTT
1 TTTGTGTTTCAAGAGAAAC-AGTTCAAAGGTTT
131174 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
131193 TGTCTCCAGG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
32 27 0.36
33 47 0.64
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (32 bp):
TTTGTGTTTCAAGAGAAACAGTTCAAAGGTTT
Found at i:131312 original size:17 final size:17
Alignment explanation
Indices: 131252--131312 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
131242 TGGTGTTTCA
131252 AGAGAAACTGTCTCAAG
1 AGAGAAACTGTCTCAAG
*
131269 AGAGACAAAACTTTGTTTCAAG
1 AGAG---AAAC--TGTCTCAAG
131291 -G-GAAACTGTCTCAAG
1 AGAGAAACTGTCTCAAG
131306 AGAGAAA
1 AGAGAAA
131313 AAATTTGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 8 0.23
16 1 0.03
17 12 0.34
20 5 0.14
21 1 0.03
22 8 0.23
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.20
Consensus pattern (17 bp):
AGAGAAACTGTCTCAAG
Found at i:131332 original size:36 final size:36
Alignment explanation
Indices: 131245--131847 Score: 571
Period size: 36 Copynumber: 17.2 Consensus size: 36
131235 CAAATATTGG
131245 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
131282 TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
131318 TGTTTCAAGAGAAACTATCTCGAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
131355 AGTTTCAAAATAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
131391 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
131420 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
131456 TGTTTCAAGGGAAACTGTCTCAAGATAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
131492 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
131529 AGTTCCAAAAGAAACTGTCTCAATAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
131565 TGTTTCAAG-GAAAAC-ATAT-ACA-A-AG----ATTT
1 TGTTTCAAGAG-AAACTGTCTCA-AGAGAGACAAAATT
*
131594 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
131630 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
131666 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
131703 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
131739 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
131768 TGTTTTAAG-GGAACTGTCTCAAGAGTGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
131803 TGTTTCAAGGGAAACTGTCACAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
131839 TGTTTCAAG
1 TGTTTCAAG
131848 TAAATTAGTC
Statistics
Matches: 468, Mismatches: 59, Indels: 79
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.00
28 8 0.02
29 44 0.09
30 9 0.02
31 4 0.01
32 4 0.01
33 6 0.01
34 2 0.00
35 19 0.04
36 242 0.52
37 128 0.27
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:131434 original size:102 final size:102
Alignment explanation
Indices: 131246--131505 Score: 301
Period size: 101 Copynumber: 2.5 Consensus size: 102
131236 AAATATTGGT
* * *
131246 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAG-GGAAAC-TGTCTCAAGAGA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAAACATAT-TC-A-A-A
* *
131309 GAAAAAATTTGTTTCAAGAGAAACTATCTCGAGAGAGACAAAACTTA
61 G----ATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTA
* *
131356 GTTTCAAAATAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG-GAAAACATATTCAAAGATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATATTCAAAGATTT
* *
131420 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
66 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTA
** *
131457 GTTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTGTTTCAAGAGAAA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
131506 CTGTCTCAAG
Statistics
Matches: 134, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
101 41 0.31
102 39 0.29
106 2 0.01
107 1 0.01
108 1 0.01
109 18 0.13
110 32 0.24
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (102 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACATATTCAAAGATTT
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTA
Found at i:131479 original size:174 final size:174
Alignment explanation
Indices: 131187--131847 Score: 1040
Period size: 174 Copynumber: 3.8 Consensus size: 174
131177 GTGTTTCAAG
* * * * * *
131187 AGAAACTGTCTCCAGGGAGGCAAATTTTTTTTTCAA-GAGAAACATATTCAAATATTGGTGTTTC
1 AGAAACTGTCTCAAGGGAGACAAA-ATTTGTTTCAAGGA-AAACATATTCAAAGATT-TTGTTTC
* *
131251 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
63 AAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
131316 TTTGTTTCAAGAGAAACTATCTCGAGAGAGACAAAACTTAGTTTCAAA
127 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
*
131364 ATAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
* *
131429 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAATTTG
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
131494 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
131 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
** * *
131538 AGAAACTGTCTCAATAGAGACGAAATTTGTTTCAAGGAAAACATATACAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
131603 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*
131668 TTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAA
131 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* * *
131712 AGAAACTGTCTCAAGGGAGACGAAATTTGTTT-AATGTAAAACATATTCAAAGATTTTGTTTTAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAA
* *
131776 GGG-AACTGTCTCAAGAGTGACAAAATTTGTTTCAAGGGAAACTGTCACAAGAGAGACAAAATTT
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
131840 GTTTCAAG
130 GTTTCAAG
131848 TAAATTAGTC
Statistics
Matches: 453, Mismatches: 29, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
173 69 0.15
174 304 0.67
175 32 0.07
176 25 0.06
177 23 0.05
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (174 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:131625 original size:102 final size:102
Alignment explanation
Indices: 131490--131679 Score: 301
Period size: 101 Copynumber: 1.9 Consensus size: 102
131480 ATAGACAAAA
*
131490 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAATAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAG
*
131555 AGACGAAATTTGTTTCAAG-GAAAACATATACAAAGAT
65 AGACAAAATTTGTTTCAAGAGAAAACATATACAAAGAT
* * * **
131592 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
131657 GACAAAATTTGTTTCAAGAGAAA
66 GACAAAATTTGTTTCAAGAGAAA
131680 CTGTCTCAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 41 0.51
102 39 0.49
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTGTTTCAAGAGAAAACATATACAAAGAT
Found at i:131675 original size:21 final size:21
Alignment explanation
Indices: 131613--131677 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
131603 GGAAACTGTC
131613 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
131634 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
131649 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
131670 TCAAGAGA
1 TCAAGAGA
131678 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:131839 original size:100 final size:102
Alignment explanation
Indices: 131664--131851 Score: 247
Period size: 100 Copynumber: 1.9 Consensus size: 102
131654 AGAGACAAAA
* * *
131664 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAG
*
131729 AGACGAAATTTGTTT-AATGTAAAACATATTCAAAGAT
66 AGACAAAATTTGTTTCAA-GTAAAACATATTCAAAGAT
* * * * * **
131766 TTTGTTTTAAG-GGAACTGTCTCAAGAGTGACAAAA-TTTGTTTCAAGGGAAACTGTCACAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAG
131829 AGACAAAATTTGTTTCAAGTAAA
66 AGACAAAATTTGTTTCAAGTAAA
131852 TTAGTCTCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
100 41 0.55
101 23 0.31
102 10 0.14
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCACAAGAG
AGACAAAATTTGTTTCAAGTAAAACATATTCAAAGAT
Found at i:133393 original size:95 final size:94
Alignment explanation
Indices: 133230--133413 Score: 280
Period size: 95 Copynumber: 1.9 Consensus size: 94
133220 ATGTAAATAC
* * *
133230 CTTTATCAGGTTAGCTTAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGGAC
*
133295 AACTCAAGCTTTATTTTATAGTATAATCAT
66 AACTCAAGCTTTATTGTATA-TATAATCAT
* * *
133325 CTTTATCATGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTG-CTCTAGAGGGA
1 CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCT-TAGAGGGA
133389 CAACTCAAGCTTTATTGTATATATA
65 CAACTCAAGCTTTATTGTATATATA
133414 TTATAATTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
94 6 0.07
95 75 0.93
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (94 bp):
CTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCGTTTAACCAATTGCCTTAGAGGGAC
AACTCAAGCTTTATTGTATATATAATCAT
Found at i:134997 original size:16 final size:16
Alignment explanation
Indices: 134976--135019 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
134966 AATAAAAGTC
*
134976 CTACCCCGCATGATAT
1 CTACCCCACATGATAT
134992 CTACCCCACATGATAT
1 CTACCCCACATGATAT
135008 CTACCCCACATG
1 CTACCCCACATG
135020 CTCATTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.41, G:0.09, T:0.23
Consensus pattern (16 bp):
CTACCCCACATGATAT
Found at i:137138 original size:17 final size:17
Alignment explanation
Indices: 137084--137139 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
137074 TCATAGACTG
*
137084 TAAAATAATAATAATAA
1 TAAAATAATAAAAATAA
137101 -ATAAATATATAATATATATAA
1 TA-AAATA-ATAA-A-A-ATAA
137122 TAAAATAATAAAAATAA
1 TAAAATAATAAAAATAA
137139 T
1 T
137140 TGTAGGACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
16 1 0.03
17 10 0.31
18 5 0.16
19 1 0.03
20 5 0.16
21 9 0.28
22 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATAATAAAAATAA
Found at i:137750 original size:15 final size:16
Alignment explanation
Indices: 137730--137760 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
137720 AATTAAAAAA
137730 TTATTATTA-TTAATT
1 TTATTATTATTTAATT
137745 TTATTATTATTTAATT
1 TTATTATTATTTAATT
137761 AATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTTAATT
Found at i:138261 original size:21 final size:22
Alignment explanation
Indices: 138218--138263 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
138208 TCAAGATCAT
*
138218 TTTAATTTAAAATATTATTATA
1 TTTAATTTAAAATATTATAATA
*
138240 TTTAATTTAAAA-CTTATAATA
1 TTTAATTTAAAATATTATAATA
138261 TTT
1 TTT
138264 TTAATTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATTTAAAATATTATAATA
Done.