Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000771.1 Hibiscus syriacus cultivar Beakdansim tig00001496_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: 52959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:116 original size:46 final size:45
Alignment explanation
Indices: 61--299 Score: 219
Period size: 46 Copynumber: 5.4 Consensus size: 45
51 CCAGCCGTCC
61 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATCTCT
1 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGA-CTCT
* * ** * *
107 TCATCACGTAGGAGCCGTG---TCACC-ATAGATAACCAGCCGTCC
1 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAC-TCT
149 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATCTCT
1 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGA-CTCT
* * * * **
195 TCATCACGTATGAGCCGTGTCA--ACC-ATAGATAACCAG-C-CGT
1 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACTC-T
* * *
236 CCATCACGTAGGAACCGTGTTATCACCTTTAGGTGGCCAGAGT-T
1 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACTCT
* *
280 TCATCAGGTATGAACCGTGT
1 TCATCACGTAGGAACCGTGT
300 CATCCCCAGA
Statistics
Matches: 151, Mismatches: 30, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
40 1 0.01
41 21 0.14
42 29 0.19
43 17 0.11
44 29 0.19
45 5 0.03
46 48 0.32
47 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACTCT
Found at i:158 original size:88 final size:89
Alignment explanation
Indices: 18--301 Score: 463
Period size: 88 Copynumber: 3.2 Consensus size: 89
8 CCAGACTTCC
18 TCATCACGTAGGAGCCGTGTCAACCATAG-TAAACCAGCCGTCCTCATCACGTAGGAACCGTGTT
1 TCATCACGTAGGAGCCGTGTCAACCATAGAT-AACCAGCCGTCCTCATCACGTAGGAACCGTGTT
82 ATCACCTTTAGATGGCCAGATCTCT
65 ATCACCTTTAGATGGCCAGATCTCT
107 TCATCACGTAGGAGCCGTGTC-ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
171 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGATCTCT
*
195 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGT-C-CATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
* *
258 TCACCTTTAGGTGGCCAGA-GT-T
66 TCACCTTTAGATGGCCAGATCTCT
* * *
280 TCATCAGGTATGAACCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
302 TCCCCAGACC
Statistics
Matches: 188, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
85 21 0.11
86 1 0.01
87 39 0.21
88 86 0.46
89 41 0.22
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (89 bp):
TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAGATGGCCAGATCTCT
Found at i:642 original size:3 final size:3
Alignment explanation
Indices: 631--680 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
621 TTTTTTTCCG
** * *
631 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTT TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
678 TTA
1 TTA
681 ATTAATTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1159 original size:19 final size:19
Alignment explanation
Indices: 1132--1169 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1122 GAGAGATTTC
*
1132 GAAACAAAAA-AAAACAGAA
1 GAAA-AAAAAGAAAAAAGAA
1151 GAAAAAAAAGAAAAAAGAA
1 GAAAAAAAAGAAAAAAGAA
1170 AAGTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAGAAAAAAGAA
Found at i:9513 original size:30 final size:29
Alignment explanation
Indices: 9477--9542 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
9467 AAAGGACGAG
9477 TTTGTAACATATGAATAGTCGAG-TGACTAT
1 TTTGTAAC-TATGAATAGTCG-GTTGACTAT
* *
9507 TTTGTAACTTTTAATAGTCGGTTGACTAT
1 TTTGTAACTATGAATAGTCGGTTGACTAT
9536 TTTGTAA
1 TTTGTAA
9543 ATTTTAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.73
30 8 0.24
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (29 bp):
TTTGTAACTATGAATAGTCGGTTGACTAT
Found at i:9526 original size:29 final size:29
Alignment explanation
Indices: 9490--9553 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
9480 GTAACATATG
*
9490 AATAGTCGAG-TGACTATTTTGTAACTTTT
1 AATAGTCG-GTTGACTATTTTGTAAATTTT
9519 AATAGTCGGTTGACTATTTTGTAAATTTT
1 AATAGTCGGTTGACTATTTTGTAAATTTT
9548 AATAGT
1 AATAGT
9554 TAAAGGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (29 bp):
AATAGTCGGTTGACTATTTTGTAAATTTT
Found at i:11304 original size:15 final size:17
Alignment explanation
Indices: 11284--11317 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
11274 TTAACTCGAG
11284 CTCAAAA-ATTAT-AAA
1 CTCAAAATATTATCAAA
11299 CTCAAAATATTATCAAA
1 CTCAAAATATTATCAAA
11316 CT
1 CT
11318 TAGTTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCAAAATATTATCAAA
Found at i:11957 original size:29 final size:30
Alignment explanation
Indices: 11899--11959 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
11889 ATTGAAAGGG
* *
11899 TATTAAAAATTTGAGGACTCAATTAAAATA
1 TATTAAAAATTTAACGACTCAATTAAAATA
*
11929 TATT-AAAATTTAACGAC-CAATTTAGAATA
1 TATTAAAAATTTAACGACTCAA-TTAAAATA
11958 TA
1 TA
11960 AGTATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 20 0.74
30 4 0.15
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
TATTAAAAATTTAACGACTCAATTAAAATA
Found at i:15033 original size:12 final size:12
Alignment explanation
Indices: 15018--15063 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
15008 CGGTTTTTTT
*
15018 ACCGGATAAAAA
1 ACCGGTTAAAAA
15030 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
15045 ACCGGTTAAAAA
1 ACCGGTTAAAAA
15057 ACCGGTT
1 ACCGGTT
15064 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:15045 original size:15 final size:13
Alignment explanation
Indices: 15024--15064 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
15014 TTTTACCGGA
15024 TAAAAAACCGGTT
1 TAAAAAACCGGTT
15037 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
15051 TAAAAAACCGGTT
1 TAAAAAACCGGTT
15064 T
1 T
15065 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:17437 original size:33 final size:33
Alignment explanation
Indices: 17390--17484 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
17380 TTTCAATTAG
17390 CGAACTT-GAAGTTTTTAAGTATTTGAATTTAT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
17422 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
* * *
17455 CAAACTTGGAAGTATTTAAGTATTTCAATT
1 CGAACTTGGAAGTTTTTAAGTATTTGAATT
17485 ATGTTGAGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 7 0.12
33 52 0.88
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (33 bp):
CGAACTTGGAAGTTTTTAAGTATTTGAATTTAT
Found at i:17513 original size:13 final size:13
Alignment explanation
Indices: 17470--17524 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
17460 TTGGAAGTAT
17470 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
17483 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
17497 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
17510 TTAAGTATTTGAA
1 TTAAGTATTTCAA
17523 TT
1 TT
17525 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:17746 original size:21 final size:21
Alignment explanation
Indices: 17720--17776 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
17710 TGGAGCGTGG
*
17720 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
17741 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
17762 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
17777 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:17993 original size:15 final size:15
Alignment explanation
Indices: 17940--17993 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
17930 ATCTGGAATA
17940 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
17955 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
17970 TTAAAAAAATCGGTTTTT
1 TT---AAAATCGGTTTTT
17988 TTAAAA
1 TTAAAA
17994 CCGAAACCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 19 0.59
18 13 0.41
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:20406 original size:21 final size:21
Alignment explanation
Indices: 20382--20421 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20372 TTTATTTTAT
20382 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
20403 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
20422 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:20469 original size:33 final size:33
Alignment explanation
Indices: 20416--20514 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
20406 TTTGTTTCAA
20416 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
20448 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
20481 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
20514 T
1 T
20515 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:20543 original size:13 final size:13
Alignment explanation
Indices: 20500--20554 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
20490 TTGGAAGTAT
20500 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
20513 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
20527 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
20540 TTAAGTATTTGAA
1 TTAAGTATTTCAA
20553 TT
1 TT
20555 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:20779 original size:21 final size:21
Alignment explanation
Indices: 20750--20806 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
20740 TGGAGCGTGG
*
20750 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
* * *
20771 GGGATTCGGTTTCCTCTCATC
1 GGGAATCGGTTCCCTCTCATA
20792 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
20807 AAGTGTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:21011 original size:17 final size:18
Alignment explanation
Indices: 20991--21024 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20981 TTTTTTTTAT
20991 AACC-GGTTTTTTAAAAA
1 AACCAGGTTTTTTAAAAA
*
21008 AACCAGTTTTTTTAAAA
1 AACCAGGTTTTTTAAAA
21025 CCGAAACCGG
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:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCAGGTTTTTTAAAAA
Found at i:21144 original size:15 final size:17
Alignment explanation
Indices: 21118--21149 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21108 TTCTATGGGA
21118 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
21134 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
21150 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:24638 original size:44 final size:44
Alignment explanation
Indices: 24575--24670 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
24565 TTAATTATAC
* *
24575 ATCCAAAAGTAAAAAGAAATAAAGGAAAATGGAATCGGAAACTT
1 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
24619 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
1 ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
*
24663 ACCCAAAA
1 ATCCAAAA
24671 TCGATCGGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (44 bp):
ATCCAAAAGTAAAAAGAAATAAACGAAAAAGGAATCGGAAACTT
Found at i:50428 original size:21 final size:20
Alignment explanation
Indices: 50402--50454 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 20
50392 AAATTACATA
50402 ACTTTCAACAAAGTATCGAT
1 ACTTTCAACAAAGTATCGAT
* *
50422 ACATTTCTATAAAAAGTATCTAT
1 AC-TTTC-A-ACAAAGTATCGAT
50445 ACTTTCAACA
1 ACTTTCAACA
50455 TATCAGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 5 0.19
23 13 0.48
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (20 bp):
ACTTTCAACAAAGTATCGAT
Found at i:50710 original size:87 final size:87
Alignment explanation
Indices: 50559--50864 Score: 468
Period size: 87 Copynumber: 3.5 Consensus size: 87
50549 ATAGGTAAAA
* * *
50559 ATATGATGTAATAGGTAGCACTTATCTAATAAAATAAGTTAATTACTAGAAACATTATCAAGCAC
1 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
* *
50624 AATAACATATTAGTTACCACTT
66 AATAACATATTAGGTACCGCTT
* * *
50646 ATATAATGTAATATGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCAC
1 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
50711 AATAACATATTAGGTACCGCTT
66 AATAACATATTAGGTACCGCTT
* ** *
50733 ATATAATGTAATATGTATAACATATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
1 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
*
50798 AATAACATATTAGGTAACGCTT
66 AATAACATATTAGGTACCGCTT
* **
50820 ATATAACGTAATAGGTAGCGTTTATATAATAAAATAGGTTAATTA
1 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTA
50865 TTTAATTTGC
Statistics
Matches: 198, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 198 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (87 bp):
ATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCAC
AATAACATATTAGGTACCGCTT
Found at i:50825 original size:23 final size:23
Alignment explanation
Indices: 50799--50858 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
50789 ATCAAGCACA
*
50799 ATAACATATTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* * *
50822 ATAACGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
50845 ATAATAAAATAGGT
1 ATAACATAATAGGT
50859 TAATTATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:51175 original size:20 final size:21
Alignment explanation
Indices: 51137--51176 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
51127 ACAAAATAAT
51137 AATAATATTTTTGAATATTAG
1 AATAATATTTTTGAATATTAG
51158 AATAAT-TTATTT-AATATTA
1 AATAATATT-TTTGAATATTA
51177 TTTATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AATAATATTTTTGAATATTAG
Found at i:51181 original size:14 final size:14
Alignment explanation
Indices: 51162--51206 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
51152 TATTAGAATA
*
51162 ATTTATTTAATATT
1 ATTTATTAAATATT
51176 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
51191 -TTTATTAAAATATT
1 ATTTATT-AAATATT
51205 AT
1 AT
51207 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:51903 original size:24 final size:24
Alignment explanation
Indices: 51876--51944 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
51866 AACATCAAAT
51876 AAAATAAAATAATATTATTTATTA
1 AAAATAAAATAATATTATTTATTA
51900 AAAA-AATAATAATATTATTT-TTA
1 AAAATAA-AATAATATTATTTATTA
*
51923 AAATATTAGAATAAT-TTATTTA
1 AAA-A-TAAAATAATATTATTTA
51945 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 8 0.21
24 24 0.62
25 6 0.15
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
AAAATAAAATAATATTATTTATTA
Found at i:51974 original size:14 final size:14
Alignment explanation
Indices: 51938--51980 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
51928 TTAGAATAAT
51938 TTATTT-AATATTA
1 TTATTTAAATATTA
*
51951 TTTATGTAAATATTA
1 -TTATTTAAATATTA
*
51966 TTATTTAAATGTTA
1 TTATTTAAATATTA
51980 T
1 T
51981 ATCTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TTATTTAAATATTA
Found at i:52051 original size:31 final size:31
Alignment explanation
Indices: 51988--52056 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
51978 TATATCTATA
*
51988 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
52018 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
52049 A-TTTATTA
1 ATTTTATTA
52057 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:52536 original size:198 final size:199
Alignment explanation
Indices: 52157--52825 Score: 877
Period size: 199 Copynumber: 3.4 Consensus size: 199
52147 CACATATGTT
* *
52157 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAAACAGTATAAATATACCGG
1 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT-ACCAGTATAAATATACCGG
* * ** **** * *
52222 TTTTATGAGAGAATAGGTCTACATAATGTATCGACACAAATTAAAAAAGTGTCGATACATTTTGT
65 TTTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTT
* * *
52287 CCATAATGAATGCCAAACGAGGTGCACGCATAAATTGTCGATACATTTATTAAAAGTATCGATCC
130 CCAGAATGAATGCCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCC
52352 AAAAA
195 AAAAA
* * * *
52357 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTATAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTAC-CAGTATAAATATACCGG
*
52422 -TTT-TGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGAGACTTTTTTT
65 TTTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTT
* *
52485 CCAGAATGAATGTTC-AACGAAGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATCGATC
130 CCAGAATGAATG-CCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATC
52549 CAAAAA
194 CAAAAA
** * *
52555 A-ATCGAAACCGGTAATTACAATGTAATATGTAAATTTACAATGTACCTAGTATAAATATACCGG
1 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTACC-AGTATAAATATACCGG
* * **
52619 TTTTATGAGAAAATAGGTCTACATAATGTATTGACTCATTTTAAGTTTGTGTATATACTTTTTTT
65 TTTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTT
* * *
52684 CCAGAATGAATGCCTAAC-AAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATTGAT
130 CCAGAATGAATGCCAAACGAA-GTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGA-
52746 TCC-AAAA
192 TCCAAAAA
* * * *
52753 ACATCGAAACCAATAATTATAATGTAATAAGTAAATTTGCAATGTTACCGGTATAAATATATCGG
1 ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATG-TACCAGTATAAATATACCGG
52818 TTTTATGA
65 TTTTATGA
52826 TAGAATATGT
Statistics
Matches: 412, Mismatches: 46, Indels: 23
0.86 0.10 0.05
Matches are distributed among these distances:
196 1 0.00
197 56 0.14
198 130 0.32
199 164 0.40
200 61 0.15
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (199 bp):
ACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTACCAGTATAAATATACCGGT
TTTATGAGAAAATAGGTCTACATAATGTATAGACACATTTTAAGTTTGTGTCGATACTTTTTTTC
CAGAATGAATGCCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCA
AAAA
Done.