Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001085.1 Hibiscus syriacus cultivar Beakdansim tig00002146_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: 62882
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3039 original size:30 final size:30
Alignment explanation
Indices: 3003--3071 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
2993 TTATATCAGT
*
3003 TATGTGATAAAGGTAT-AGAAATGATATGTC
1 TATGTGATAAAGGTATGA-AAATAATATGTC
3033 TATGTGATAAAGGTATGAAAATAATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
3063 TACGTGATA
1 TATGTGATA
3072 CAAATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:3350 original size:23 final size:23
Alignment explanation
Indices: 3290--3358 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3280 CATTATTATA
*
3290 TGGCACTAT-GGTGCAATTCTACA
1 TGGCACT-TCGGTGCAATTCTACG
* * **
3313 CGGCACTCCAATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3336 TGGCACTTCGGTGCAATTATACG
1 TGGCACTTCGGTGCAATTCTACG
3359 AGCTGTAGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:8934 original size:23 final size:22
Alignment explanation
Indices: 8908--8976 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
8898 CATTATTATA
8908 TGGCACCATGGTGCAATTCTACG
1 TGGCACC-TGGTGCAATTCTACG
8931 TGGCACTCTGGTGCAATTCTACG
1 TGGCAC-CTGGTGCAATTCTACG
* *
8954 TGGCACTTCGGTGCAATTATACG
1 TGGCACCT-GGTGCAATTCTACG
8977 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (22 bp):
TGGCACCTGGTGCAATTCTACG
Found at i:11715 original size:29 final size:29
Alignment explanation
Indices: 11666--11724 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
11656 ATTTTCACCT
11666 AACTAAATTGATATAACCAATGACATCAA
1 AACTAAATTGATATAACCAATGACATCAA
* *
11695 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAACCAATGACATCAA
11724 A
1 A
11725 TGAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAACCAATGACATCAA
Found at i:15737 original size:22 final size:21
Alignment explanation
Indices: 15681--15737 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
15671 AAATTAGTAC
* *
15681 TAATTATTAATTAAGTATATTT
1 TAATTATTAATT-AGTAAATTG
*
15703 TTATTATCT-ATTAGTAAATTAG
1 TAATTAT-TAATTAGTAAATT-G
15725 TAATTATTAATTA
1 TAATTATTAATTA
15738 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TAATTATTAATTAGTAAATTG
Found at i:16762 original size:26 final size:26
Alignment explanation
Indices: 16731--16783 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
16721 AAAACATAAC
16731 AAGGCATCATATATCATAAAAATTAT
1 AAGGCATCATATATCATAAAAATTAT
16757 AAGGCATCATATATCATAAAAATTAT
1 AAGGCATCATATATCATAAAAATTAT
16783 A
1 A
16784 TAGCTCAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (26 bp):
AAGGCATCATATATCATAAAAATTAT
Found at i:20013 original size:2 final size:2
Alignment explanation
Indices: 20006--20035 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19996 TTGTTCCAAC
20006 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20036 TTGTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:20265 original size:35 final size:35
Alignment explanation
Indices: 20226--20292 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
20216 ATGATGCGGA
*
20226 CAAAATGACGTCATTTTGGCGCAACTATTGATTTC
1 CAAAACGACGTCATTTTGGCGCAACTATTGATTTC
* * *
20261 CAAAACGACGTCGTTTTGGTGCACCTATTGAT
1 CAAAACGACGTCATTTTGGCGCAACTATTGAT
20293 GCCCATAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (35 bp):
CAAAACGACGTCATTTTGGCGCAACTATTGATTTC
Found at i:20312 original size:35 final size:35
Alignment explanation
Indices: 20273--20347 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
20263 AAACGACGTC
20273 GTTTTGGTGCACCTATTGATGCCCATA-ATGACATT
1 GTTTTGGTGCACCTATTGATGCCCA-AGATGACATT
* * *
20308 GTTTTGGTGCAGCTATTGATGCTCAAGATGATATT
1 GTTTTGGTGCACCTATTGATGCCCAAGATGACATT
20343 GTTTT
1 GTTTT
20348 AGGCACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (35 bp):
GTTTTGGTGCACCTATTGATGCCCAAGATGACATT
Found at i:28571 original size:2 final size:2
Alignment explanation
Indices: 28564--28593 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28554 CTAAAATGTA
28564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28594 TATTGTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29079 original size:14 final size:14
Alignment explanation
Indices: 29060--29088 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29050 AATTTGCTTC
29060 ATTGGTAAACGTCA
1 ATTGGTAAACGTCA
29074 ATTGGTAAACGTCA
1 ATTGGTAAACGTCA
29088 A
1 A
29089 GGGTCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (14 bp):
ATTGGTAAACGTCA
Found at i:30686 original size:3 final size:3
Alignment explanation
Indices: 30678--30707 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30668 TCTTATGTTA
30678 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30708 TCATATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:34257 original size:131 final size:131
Alignment explanation
Indices: 34084--34333 Score: 333
Period size: 131 Copynumber: 1.9 Consensus size: 131
34074 CAATTAGAGT
* * *
34084 AATAAATGATTGCTTTAAGGCATGAGAGGTAATTTATTCTCGATTGAAAATTATTAGATATTA-T
1 AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
** *
34148 CGTTTTCTTTCAAATCAATATTGATTTTTAAGAAAG-AATAGTGATATATCTTCATCTCGATTGG
66 -GTTTTCACTCAAATCAATATTGAATTTTAA-AAAGAAATAGTGATATATCTTCATCTCGATTGG
34212 AGC
129 AGC
* * * *
34215 AATAAATGACTGCTTTAGGGTATGAGAGGTCATTTATGCTCGATTGGAAATCATTAGATATTACT
1 AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
* * * * *
34280 GTTTTCACTCGAATCGATATTGAATTTTAATACGAAATAGTGATATCTCTTCAT
66 GTTTTCACTCAAATCAATATTGAATTTTAAAAAGAAATAGTGATATATCTTCAT
34334 TTAGATTAGA
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
130 2 0.02
131 99 0.97
132 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (131 bp):
AATAAATGACTGCTTTAAGGCATGAGAGGTAATTTATGCTCGATTGAAAATCATTAGATATTACT
GTTTTCACTCAAATCAATATTGAATTTTAAAAAGAAATAGTGATATATCTTCATCTCGATTGGAG
C
Found at i:35262 original size:14 final size:14
Alignment explanation
Indices: 35243--35270 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35233 CTTGAACCCA
35243 CAAGAAGAAGAAAG
1 CAAGAAGAAGAAAG
35257 CAAGAAGAAGAAAG
1 CAAGAAGAAGAAAG
35271 AAAGCTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.29, T:0.00
Consensus pattern (14 bp):
CAAGAAGAAGAAAG
Found at i:42522 original size:6 final size:6
Alignment explanation
Indices: 42511--42554 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
42501 TTATCACAAA
42511 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TG
42555 AGAAAGAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
TGGGAT
Found at i:47263 original size:42 final size:41
Alignment explanation
Indices: 47217--47329 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 41
47207 CCCCGAATTT
* * * *
47217 CCGTGTTTATTTTACGTAATTCGTTTTTCGGAAAATATTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAT-GTTTC
*
47259 CCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAATGTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTC
*
47300 CTCGTGTTTGTTTCACGTAATTGGTTTTCC
1 C-CGTGTTTGTTTCACGTAATTCGTTTTCC
47330 AGAACGTAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 5 0.08
42 59 0.92
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.49
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTC
Found at i:47554 original size:22 final size:23
Alignment explanation
Indices: 47524--47567 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
47514 TTTATTTAGT
47524 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
47547 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
47568 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:47642 original size:54 final size:52
Alignment explanation
Indices: 47533--47643 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 52
47523 TTATTAATAT
* ** *
47533 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAAAAA
*
47585 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAAAAAAA
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAAAAAAA
47639 TTATA
1 TTATA
47644 TATTTAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
52 16 0.32
53 7 0.14
54 27 0.54
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAAAAA
Found at i:47652 original size:28 final size:28
Alignment explanation
Indices: 47620--47683 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
47610 TTTATTTTAA
47620 TAATATAT-AATAAAAAAAATTATATATT
1 TAATA-ATGAATAAAAAAAATTATATATT
* ** *
47648 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAAAAAATTATATATT
47676 TAAATAAT
1 T-AATAAT
47684 ATTTTAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 22 0.73
29 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATAATGAATAAAAAAAATTATATATT
Found at i:47663 original size:19 final size:19
Alignment explanation
Indices: 47618--47693 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
47608 TTTTTATTTT
* *
47618 AATAATATATAATAA-AAAA
1 AATAATATAT-TTAATAATA
* *
47637 AATTATATATTTAATAATG
1 AATAATATATTTAATAATA
*
47656 AATAATATTATTTATATATTTA
1 AATAATA-TATTTA-ATA-ATA
47678 AATAATAT-TTTAATAA
1 AATAATATATTTAATAA
47694 AGATATTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
18 3 0.07
19 20 0.44
20 10 0.22
21 4 0.09
22 8 0.18
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
AATAATATATTTAATAATA
Found at i:47714 original size:23 final size:23
Alignment explanation
Indices: 47688--47732 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47678 AATAATATTT
47688 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
47711 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
47733 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:48052 original size:14 final size:14
Alignment explanation
Indices: 48033--48073 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
48023 AAATGTAATT
*
48033 CATTTTACAGAAAA
1 CATTTTTCAGAAAA
*
48047 CATTTTTCGGAAAA
1 CATTTTTCAGAAAA
48061 CATTTTTCAGAAA
1 CATTTTTCAGAAA
48074 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (14 bp):
CATTTTTCAGAAAA
Found at i:48117 original size:15 final size:15
Alignment explanation
Indices: 48075--48120 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
48065 TTTCAGAAAT
48075 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
48090 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
48104 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
48119 GT
1 GT
48121 TCCAGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:48138 original size:21 final size:21
Alignment explanation
Indices: 48099--48141 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48089 AGAATTCAAA
* **
48099 TTCCAGTAATTTATTTTCCAG
1 TTCCAGTAATTCAAATTCCAG
48120 TTCCAGTAATTCAAATTCCAG
1 TTCCAGTAATTCAAATTCCAG
48141 T
1 T
48142 AATTCATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:51550 original size:16 final size:16
Alignment explanation
Indices: 51529--51559 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51519 TAATAAATAG
51529 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51545 ACGAACATAAACGAA
1 ACGAACATAAACGAA
51560 TAAAACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:51642 original size:10 final size:10
Alignment explanation
Indices: 51627--51701 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
51617 CATTTAATAA
51627 ATAAACGAAC
1 ATAAACGAAC
51637 ATAAACGAAC
1 ATAAACGAAC
51647 ----ACGAAC
1 ATAAACGAAC
51653 ATAAACGAAC
1 ATAAACGAAC
* *
51663 ATGAAC-ATAA
1 ATAAACGA-AC
51673 ATGAACACGAAC
1 AT-AA-ACGAAC
51685 ATAAACGAAC
1 ATAAACGAAC
51695 ATAAACG
1 ATAAACG
51702 TTGGAGACCT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.11
9 1 0.02
10 37 0.70
11 3 0.06
12 5 0.09
13 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:51652 original size:16 final size:16
Alignment explanation
Indices: 51631--51695 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
51621 TAATAAATAA
51631 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51647 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
51663 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
51679 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51695 A
1 A
51696 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:52464 original size:14 final size:14
Alignment explanation
Indices: 52447--52502 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
52437 AATGAACATA
52447 AACGAACATAATCG
1 AACGAACATAATCG
52461 AACGAACAT-A---
1 AACGAACATAATCG
* *
52471 AACAAACATAACCG
1 AACGAACATAATCG
52485 AACGAACATAATCG
1 AACGAACATAATCG
52499 AACG
1 AACG
52503 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:52467 original size:24 final size:24
Alignment explanation
Indices: 52427--52501 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
52417 GATTGAGTTA
*
52427 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
52451 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
52475 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
52499 AAC
1 AAC
52502 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:55163 original size:3 final size:3
Alignment explanation
Indices: 55155--55207 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
55145 GAGCCACGTG
55155 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55202 TAT TAT
1 TAT TAT
55208 GTTGAAGGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56647 original size:2 final size:2
Alignment explanation
Indices: 56640--56695 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
56630 TCCTAATTTG
56640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56681 AT AT AT AT AT CAT AT
1 AT AT AT AT AT -AT AT
56696 CAAGAGAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.