Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006330.1 Hibiscus syriacus cultivar Beakdansim tig00015129_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: 75996
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:9621 original size:12 final size:12
Alignment explanation
Indices: 9600--9632 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9590 CTGAAAGTGC
9600 AAAGGAAGAGGA
1 AAAGGAAGAGGA
9612 GAAA-GAAGAGGA
1 -AAAGGAAGAGGA
9624 AAAGGAAGA
1 AAAGGAAGA
9633 TGATGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 13 0.68
13 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AAAGGAAGAGGA
Found at i:11371 original size:135 final size:135
Alignment explanation
Indices: 11144--11394 Score: 396
Period size: 135 Copynumber: 1.9 Consensus size: 135
11134 ATTGTTTTTC
* ** * *
11144 CCTTGATGTGACAGCTCAATCTGACTTTGCAAAAATGGAAACAAAATCTAAACAAGCAATGGAGA
1 CCTTGATGTGACAGCTCAAGCTGACTCCGCAAAAACGGAAACAAAATCTAAACAAGCAAGGGAGA
*
11209 AGGGTGAGTGAATTTTCAAGTCTATTAGTTATGAGGGTCCTGCATGATTTTGGCCAATAATTTTT
66 AGGGTGAGTAAATTTTCAAGTCTATTAGTTATGAGGGTCCTGCATGATTTTGGCCAATAATTTTT
11274 TATTT
131 TATTT
* * *
11279 CCTTGATGTGGCAGCTCAAGCTGACTCCGCCAAAACGGAAAGAAAATCTAAA-ATAGCAAGGGAG
1 CCTTGATGTGACAGCTCAAGCTGACTCCGCAAAAACGGAAACAAAATCTAAACA-AGCAAGGGAG
*
11343 AGGGGTGAGTAAATTTTCAAGTCTATTAGTTATGAGGGTCCTGCATGATTTT
65 AAGGGTGAGTAAATTTTCAAGTCTATTAGTTATGAGGGTCCTGCATGATTTT
11395 CGCTGCCCAC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
134 1 0.01
135 104 0.99
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (135 bp):
CCTTGATGTGACAGCTCAAGCTGACTCCGCAAAAACGGAAACAAAATCTAAACAAGCAAGGGAGA
AGGGTGAGTAAATTTTCAAGTCTATTAGTTATGAGGGTCCTGCATGATTTTGGCCAATAATTTTT
TATTT
Found at i:18408 original size:2 final size:2
Alignment explanation
Indices: 18401--18439 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18391 AAAAGGCTGA
18401 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18440 TCATGAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27144 original size:20 final size:21
Alignment explanation
Indices: 27119--27211 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
27109 TTTTCCCAAT
*
27119 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27139 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
27160 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27180 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
27201 TCGCAATGCGA
1 TCGCAATGCGA
27212 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:27164 original size:41 final size:41
Alignment explanation
Indices: 27119--27211 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
27109 TTTTCCCAAT
27119 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
27160 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
27201 TCGCAATGCGA
1 TCGCAATGCGA
27212 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:27224 original size:41 final size:41
Alignment explanation
Indices: 27138--27272 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
27128 GAATAAGTAA
* *
27138 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
27179 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
27220 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
27261 TTCGCAACGCGA
1 ATCGCAACGCGA
27273 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:27225 original size:20 final size:20
Alignment explanation
Indices: 27200--27294 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
27190 AATTGGGAAA
*
27200 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
27220 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
27241 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
27261 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
27281 TTCGCAACGCGATA
1 ATCGCAACGCGATA
27295 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:27510 original size:22 final size:22
Alignment explanation
Indices: 27482--27525 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27472 CACTCTCTCA
27482 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
27504 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
27526 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:27814 original size:20 final size:20
Alignment explanation
Indices: 27789--27826 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27779 CGATTCTCTC
27789 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
27809 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
27827 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:28126 original size:21 final size:20
Alignment explanation
Indices: 28040--28196 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
28030 AAATGACTAA
**
28040 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
28059 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
28079 CATAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
28099 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
28120 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
28141 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
28161 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
28182 GAAAATCGCAACGCG
1 CAAAATCGCAACGCG
28197 TATCCGTAAA
Statistics
Matches: 103, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:28211 original size:20 final size:20
Alignment explanation
Indices: 28165--28373 Score: 224
Period size: 20 Copynumber: 10.4 Consensus size: 20
28155 GATTTTCAAG
* ** *
28165 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
28185 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
28205 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28225 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28245 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28265 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28285 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28305 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28325 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28345 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28365 AATCACAAC
1 AATCGCAAC
28374 ACTGAAATTT
Statistics
Matches: 160, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 159 0.99
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:29093 original size:24 final size:24
Alignment explanation
Indices: 29066--29112 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29056 AAATTTGGTC
29066 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
29090 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
29113 GATGTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:29304 original size:12 final size:12
Alignment explanation
Indices: 29287--29311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29277 ATATAATCCT
29287 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29299 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29311 G
1 G
29312 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31645 original size:33 final size:33
Alignment explanation
Indices: 31608--31735 Score: 116
Period size: 33 Copynumber: 3.7 Consensus size: 33
31598 GCAACGAGAG
31608 AATCGCAATGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAA
*
31641 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
* * * * *
31680 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
31713 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
31736 GCAATGCGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
31 1 0.01
32 6 0.08
33 27 0.36
34 15 0.20
36 1 0.01
38 2 0.03
39 22 0.29
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAA
Found at i:31671 original size:53 final size:52
Alignment explanation
Indices: 31608--31735 Score: 213
Period size: 53 Copynumber: 2.4 Consensus size: 52
31598 GCAACGAGAG
31608 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
31661 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
31713 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
31736 GCAATGCGAA
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
52 31 0.43
53 40 0.56
54 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:31677 original size:19 final size:19
Alignment explanation
Indices: 31608--31763 Score: 197
Period size: 19 Copynumber: 8.7 Consensus size: 19
31598 GCAACGAGAG
31608 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31627 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
31641 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
31661 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31680 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31694 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31713 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31732 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
31751 AATTGCATTGCGA
1 AATCGCAATGCGA
31764 TTCTCTCGTT
Statistics
Matches: 120, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
14 22 0.18
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 74 0.62
20 16 0.13
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:31866 original size:52 final size:53
Alignment explanation
Indices: 31755--31869 Score: 214
Period size: 53 Copynumber: 2.2 Consensus size: 53
31745 AATGAAAATT
31755 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
1 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
*
31808 GCATTGCGATTCTCTCGTTGTGATTTTCATTT-CGCATTGCGATTTTCATTTC
1 GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
31860 GCATTGCGAT
1 GCATTGCGAT
31870 AGTCATTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
GCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTC
Found at i:31877 original size:19 final size:19
Alignment explanation
Indices: 31772--31869 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
31762 GATTCTCTCG
31772 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31792 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31811 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
31825 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31844 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31863 TTGCGAT
1 TTGCGAT
31870 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31994 original size:14 final size:14
Alignment explanation
Indices: 31975--32011 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31965 GCATCAATAC
31975 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31989 ACAAATCATCTTTT
1 ACAAATCAACTTTT
32003 ACAAATCAA
1 ACAAATCAA
32012 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:33973 original size:19 final size:19
Alignment explanation
Indices: 33931--34103 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
33921 TAGTTTACTT
* *
33931 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
33951 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
33970 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
33989 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
34008 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34027 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
34041 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34060 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
34074 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34093 TCGCAATGCGA
1 TCGCAACGCGA
34104 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 82 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34044 original size:14 final size:14
Alignment explanation
Indices: 34025--34081 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
34015 GCGAAATGAA
*
34025 AATCGCAACGACAG
1 AATCGCAACGAAAG
34039 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
34056 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
34072 AATCGCAACG
1 AATCGCAACG
34082 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:34052 original size:33 final size:33
Alignment explanation
Indices: 34006--34098 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
33996 GCGAAACCAA
34006 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
34039 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
34072 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
34099 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:34095 original size:52 final size:52
Alignment explanation
Indices: 33965--34103 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
33955 AACGCGAAAT
* * * *
33965 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
34017 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
34069 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
34104 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:34121 original size:19 final size:17
Alignment explanation
Indices: 34099--34190 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 17
34089 AAAATCGCAA
34099 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTT-GCGT
*
34118 TGCGATATTG--T-CGT
1 TGCGATTTTGTTTGCGT
34132 TGCGATTTTGGTTTAGCGT
1 TGCGATTTT-GTTT-GCGT
*
34151 TGCGATTCTG--T-CGT
1 TGCGATTTTGTTTGCGT
*
34165 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTT-GCGT
34184 TGCGATT
1 TGCGATT
34191 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 22 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 29 0.50
ACGTcount: A:0.10, C:0.16, G:0.28, T:0.46
Consensus pattern (17 bp):
TGCGATTTTGTTTGCGT
Found at i:34141 original size:33 final size:33
Alignment explanation
Indices: 34099--34222 Score: 169
Period size: 33 Copynumber: 3.7 Consensus size: 33
34089 AAAATCGCAA
34099 TGCGATTTTGGTTTCGCGTTGCGATAT-TGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGAT-TCTGTCGT
*
34132 TGCGATTTTGGTTTAGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
34165 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
34198 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
34223 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
32 1 0.01
33 68 0.84
34 12 0.15
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:34167 original size:14 final size:14
Alignment explanation
Indices: 34148--34204 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
34138 TTTGGTTTAG
*
34148 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
34162 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
34181 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34195 CGTTGCGATT
1 CGTTGCGATT
34205 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:34443 original size:93 final size:93
Alignment explanation
Indices: 34319--34634 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
34309 TCAGGGTATT
34319 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
34384 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
34412 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
34477 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
* *
34505 AGTTTAACAGAATTGGCAGCAACCGGACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
34570 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
34598 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
34635 AAGCAATCTA
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 218 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:34507 original size:17 final size:17
Alignment explanation
Indices: 34485--34517 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34475 AATACTATTT
34485 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
34502 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
34518 TGGCAGCAAC
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:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:36364 original size:21 final size:21
Alignment explanation
Indices: 36308--36372 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
36298 TCTTTTGGTT
36308 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
36329 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
36349 GAAATGAAAATTGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
36370 GAA
1 GAA
36373 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:36433 original size:14 final size:14
Alignment explanation
Indices: 36414--36469 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
36404 TTTGGTTTCG
36414 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36428 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
36446 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36460 CGTTGCGATT
1 CGTTGCGATT
36470 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 20 0.56
15 3 0.08
17 3 0.08
18 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36448 original size:32 final size:33
Alignment explanation
Indices: 36398--36476 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
36388 AAAATCGCAA
**
36398 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
36431 TGCGA-TTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
36463 TGCGATTTTCATTT
1 TGCGATTTTCATTT
36477 TTCTCGTTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:36482 original size:21 final size:21
Alignment explanation
Indices: 36457--36529 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
36447 GTTGCGATTC
36457 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
36478 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
36499 TCACGTTGCGA-TTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
36519 TCTCGTTGCGA
1 TCTCGTTGCGA
36530 CTCTTATGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 20 0.47
22 6 0.14
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:36651 original size:33 final size:33
Alignment explanation
Indices: 36609--36679 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
36599 AATACTAACT
36609 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
36642 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
36675 TGAAA
1 TGAAA
36680 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:37079 original size:20 final size:20
Alignment explanation
Indices: 37054--37246 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
37044 CTTTAAAAAT
37054 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37074 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
37094 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
37115 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
37135 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
37155 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37175 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37195 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
37215 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
37235 CGCGTTGCGATT
1 CGCGTTGCGATT
37247 CTTGAAAATT
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38669 original size:18 final size:18
Alignment explanation
Indices: 38648--38692 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38638 TCCACTTCGG
*
38648 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
38666 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
38684 GAGCCATCA
1 GAGCCATCA
38693 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:39217 original size:19 final size:20
Alignment explanation
Indices: 39174--39229 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
39164 CGTAACACGA
39174 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
39194 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
39213 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
39230 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:39237 original size:14 final size:14
Alignment explanation
Indices: 39218--39275 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
39208 ATGCGAAATG
39218 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
39232 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
39248 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
39264 AAAATCGCAACG
1 AAAATCGCAACG
39276 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:39260 original size:32 final size:33
Alignment explanation
Indices: 39202--39292 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
39192 GGAAATGGCT
*
39202 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
39235 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
39267 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
39293 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:39286 original size:19 final size:19
Alignment explanation
Indices: 39182--39297 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
39172 GAAAATGACT
***
39182 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAA
*
39202 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
39221 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
39235 ATCGCAACGCGAAATG-AA
1 ATCGCAACGCGAAATGAAA
*
39253 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
39267 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
39286 ATCGCAATGCGA
1 ATCGCAACGCGA
39298 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.36
20 9 0.12
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:39328 original size:14 final size:14
Alignment explanation
Indices: 39309--39366 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
39299 TTGTGTTTCG
39309 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
39323 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
39339 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
39355 CGTTGCGATTTT
1 CGTTGCGATTTT
39367 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:39343 original size:32 final size:33
Alignment explanation
Indices: 39304--39382 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
39294 GCGATTTGTG
39304 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
39336 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
39369 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
39383 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:39381 original size:19 final size:19
Alignment explanation
Indices: 39323--39440 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
39313 GCGATTTTGT
39323 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
39341 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
39355 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
39374 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
39394 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
39413 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
39433 TGTTGCGA
1 CGTTGCGA
39441 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:41431 original size:19 final size:19
Alignment explanation
Indices: 41407--41443 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41397 GCAAAACAGA
41407 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
*
41426 CTATCGCAATGCGAAATG
1 CTATCGCAACGCGAAATG
41444 AAAATCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:41450 original size:19 final size:19
Alignment explanation
Indices: 41409--41458 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
41399 AAAACAGACT
* ***
41409 ATCGCAACGCGAAATGGCT
1 ATCGCAATGCGAAATGAAA
41428 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
41447 ATCGCAATGCGA
1 ATCGCAATGCGA
41459 TAACCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:42489 original size:24 final size:24
Alignment explanation
Indices: 42462--42515 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
42452 GTATTCGAAA
* *
42462 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
42486 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
42510 TTTGAT
1 TTTGAT
42516 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:42707 original size:12 final size:12
Alignment explanation
Indices: 42690--42714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42680 ATATAATCCT
42690 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42702 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42714 G
1 G
42715 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:45043 original size:33 final size:33
Alignment explanation
Indices: 45001--45127 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
44991 GGAAATTACT
*
45001 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
45034 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
45066 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
45100 ATCGCAATGGGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
45128 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:45084 original size:66 final size:66
Alignment explanation
Indices: 45002--45134 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
44992 GAAATTACTA
*
45002 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
45067 T
66 T
* * *
45068 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGGGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
45133 T
66 T
45134 T
1 T
45135 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:45149 original size:19 final size:20
Alignment explanation
Indices: 45127--45169 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
45117 AAATCGCAAC
45127 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
45146 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
45166 GCGA
1 GCGA
45170 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:45154 original size:14 final size:14
Alignment explanation
Indices: 45155--45188 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
45145 TGCGATTTTC
45155 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
45169 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
45183 ATTTTC
1 ATTTTC
45189 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:45329 original size:14 final size:14
Alignment explanation
Indices: 45310--45346 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
45300 CATCAATTAA
45310 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
45324 ACAAATCACCTTTT
1 ACAAATCAACTTTT
45338 ACAAATCAA
1 ACAAATCAA
45347 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46758 original size:21 final size:21
Alignment explanation
Indices: 46692--46758 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
46682 GTGAATCGGG
*
46692 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
46712 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
46734 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
46755 CTCT
1 CTCT
46759 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:46777 original size:42 final size:41
Alignment explanation
Indices: 46692--46814 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
46682 GTGAATCGGG
* * * * *
46692 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
46734 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
46776 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
46815 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:57914 original size:14 final size:14
Alignment explanation
Indices: 57895--57925 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
57885 TTAAATAATA
57895 AACGAACACAAACG
1 AACGAACACAAACG
*
57909 AACGAACATAAACG
1 AACGAACACAAACG
57923 AAC
1 AAC
57926 TCGAACGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:57950 original size:24 final size:24
Alignment explanation
Indices: 57892--57972 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
57882 CATTTAAATA
*
57892 ATAAACGAACACAAACGAACGAAC
1 ATAAACGAACTCAAACGAACGAAC
*
57916 ATAAACGAACTCGAACGAAC-ATAC
1 ATAAACGAACTCAAACGAACGA-AC
* *
57940 ATAAACGAACTGAATA--AAAGAAC
1 ATAAACGAACTCAA-ACGAACGAAC
57963 ATAAACGAAC
1 ATAAACGAAC
57973 AACACAAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
23 15 0.31
24 33 0.67
25 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.10
Consensus pattern (24 bp):
ATAAACGAACTCAAACGAACGAAC
Found at i:58346 original size:40 final size:40
Alignment explanation
Indices: 58296--58398 Score: 188
Period size: 40 Copynumber: 2.6 Consensus size: 40
58286 AACGAGCCTT
*
58296 TTGTTTATGTTCGTTCATTTAATTAAACGAACGCAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
*
58336 TTGTTCATGTTCGTTCATTTAATTAAATGAACGCAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
58376 TTGTTCATGTTCGTTCATTTAAT
1 TTGTTCATGTTCGTTCATTTAAT
58399 AAATAAACGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (40 bp):
TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
Found at i:62661 original size:39 final size:39
Alignment explanation
Indices: 62607--62690 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
62597 CATATTTTCG
62607 GATCGAATCATAGTAACATTCATGTCATAAACTATAACA
1 GATCGAATCATAGTAACATTCATGTCATAAACTATAACA
62646 GATCGAATCATAGTAACATTCATGTCATAAACTATAACA
1 GATCGAATCATAGTAACATTCATGTCATAAACTATAACA
62685 GATCGA
1 GATCGA
62691 TTAGTTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (39 bp):
GATCGAATCATAGTAACATTCATGTCATAAACTATAACA
Done.