Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007709.1 Hibiscus syriacus cultivar Beakdansim tig00109924_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: 657132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:568185 original size:24 final size:24
Alignment explanation
Indices: 568132--568186 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
568122 ATTTTGTTAG
*
568132 TATTTTTTTAATTATTTTATTATT
1 TATTTTTTTAATTATTTTATTAAT
568156 TAATTTTTTT-ATTATTTTATTTAAT
1 T-ATTTTTTTAATTATTTTA-TTAAT
568181 TATTTT
1 TATTTT
568187 ATTTTTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (24 bp):
TATTTTTTTAATTATTTTATTAAT
Found at i:568194 original size:8 final size:8
Alignment explanation
Indices: 568132--568176 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
568122 ATTTTGTTAG
*
568132 TATTTTTT
1 TATTATTT
568140 TAATTATTT
1 T-ATTATTT
568149 TATTATTT
1 TATTATTT
* *
568157 AATTTTTT
1 TATTATTT
568165 TATTATTT
1 TATTATTT
568173 TATT
1 TATT
568177 TAATTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 24 0.77
9 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:568460 original size:8 final size:8
Alignment explanation
Indices: 568444--568482 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
568434 TATTACTGTA
*
568444 AAAAAAAT
1 AAAATAAT
568452 AAAATAAT
1 AAAATAAT
568460 AAAATAAT
1 AAAATAAT
*
568468 ACAATAAT
1 AAAATAAT
*
568476 TAAATAA
1 AAAATAA
568483 AATACTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:585161 original size:12 final size:12
Alignment explanation
Indices: 585140--585176 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
585130 CCTCCCTCCC
585140 TCTCTCTCTCTG
1 TCTCTCTCTCTG
*
585152 TCTCTGTCTCTG
1 TCTCTCTCTCTG
585164 TCTCTCTCTCTG
1 TCTCTCTCTCTG
585176 T
1 T
585177 GTTAGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.38, G:0.11, T:0.51
Consensus pattern (12 bp):
TCTCTCTCTCTG
Found at i:585656 original size:24 final size:25
Alignment explanation
Indices: 585619--585665 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
585609 ACAATAATAT
* **
585619 TTAATTTTTTAATTCTATTAATTAA
1 TTAATTTTTAAATTAAATTAATTAA
585644 TTAA-TTTTAAATTAAATTAATT
1 TTAATTTTTAAATTAAATTAATT
585666 GATAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATTTTTAAATTAAATTAATTAA
Found at i:589481 original size:19 final size:19
Alignment explanation
Indices: 589454--589490 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
589444 GATACTTTTT
*
589454 AAAATATTTTACTAATTAA
1 AAAACATTTTACTAATTAA
589473 AAAACATTTTACTAATTA
1 AAAACATTTTACTAATTA
589491 TTATATACAA
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:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAACATTTTACTAATTAA
Found at i:598276 original size:22 final size:22
Alignment explanation
Indices: 598250--598294 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
598240 CTTAGTAAAC
*
598250 TTATATAAAAT-TTATAAAAATT
1 TTATAGAAAATATT-TAAAAATT
*
598272 TTATAGAAAGTATTTAAAAATT
1 TTATAGAAAATATTTAAAAATT
598294 T
1 T
598295 GTTAGATCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TTATAGAAAATATTTAAAAATT
Found at i:599840 original size:22 final size:21
Alignment explanation
Indices: 599812--599856 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
599802 TTCGAACTCC
*
599812 TAATAATCA-AAATATTATAAAA
1 TAATAAT-ATAAATAAT-TAAAA
599834 TAATAATATAAATAATTAAAA
1 TAATAATATAAATAATTAAAA
599855 TA
1 TA
599857 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATATAAATAATTAAAA
Found at i:601145 original size:20 final size:20
Alignment explanation
Indices: 601108--601145 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
601098 TATTATTATT
*
601108 TTAAATTAATAAAAAAAATA
1 TTAAATTAAAAAAAAAAATA
*
601128 TTAATTTAAAAAAAAAAA
1 TTAAATTAAAAAAAAAAA
601146 CCATTTTTGT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAATTAAAAAAAAAAATA
Found at i:631720 original size:19 final size:20
Alignment explanation
Indices: 631696--631738 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
631686 AATAATAATT
631696 TATTAAAATTAT-TAA-AAAA
1 TATTAAAATT-TCTAATAAAA
*
631715 TATTAATATTTCTAATAAAA
1 TATTAAAATTTCTAATAAAA
631735 TATT
1 TATT
631739 TCTTTAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTAAAATTTCTAATAAAA
Found at i:635230 original size:25 final size:25
Alignment explanation
Indices: 635202--635261 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
635192 TTGAGTCGTA
*
635202 TTTAGGGTTTAGGATTCGAGTCAAG
1 TTTAGGGTTTAAGATTCGAGTCAAG
* * * **
635227 TTTAGAGTTTAAGATTTGGGTCGGG
1 TTTAGGGTTTAAGATTCGAGTCAAG
635252 TTTAGGGTTT
1 TTTAGGGTTT
635262 TTTTAAGTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (25 bp):
TTTAGGGTTTAAGATTCGAGTCAAG
Found at i:638297 original size:20 final size:20
Alignment explanation
Indices: 638272--638338 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
638262 AATTCGTAAT
638272 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
638292 GCGAATTGGGAAATTCGCAAT
1 GCGAATAAGTAAA-TCGCAAC
638313 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
638333 GCGAAT
1 GCGAAT
638339 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:638307 original size:41 final size:41
Alignment explanation
Indices: 638262--638357 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
638252 CGATTTTCTC
*
638262 AATTCGTAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
638303 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
638344 AAATCGCAATGCGA
1 AATTCGCAATGCGA
638358 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:638311 original size:21 final size:20
Alignment explanation
Indices: 638282--638357 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
638272 GCGAATAAGT
638282 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
638302 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
638323 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
*
638343 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
638358 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:638370 original size:41 final size:41
Alignment explanation
Indices: 638284--638418 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
638274 GAATAAGTAA
* * *
638284 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
638325 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
638366 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
638407 TTCGCAACGCGA
1 ATCGCAACGCGA
638419 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:638371 original size:20 final size:20
Alignment explanation
Indices: 638346--638439 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
638336 AATTGGGAAA
*
638346 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
638366 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
638387 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
638407 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
638427 TTCGCAACGCGAT
1 ATCGCAACGCGAT
638440 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:639016 original size:19 final size:19
Alignment explanation
Indices: 638992--639036 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
638982 GCAACGAGAT
*
638992 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
639011 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
639030 AATCGCA
1 AATCGCA
639037 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:639080 original size:20 final size:19
Alignment explanation
Indices: 639032--639197 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
639022 GAAACCAAAA
*
639032 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
639051 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
639070 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
639090 TCGTGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
639106 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
639123 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
639137 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
639156 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
639176 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
639196 TC
1 TC
639198 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:639122 original size:33 final size:33
Alignment explanation
Indices: 639085--639172 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
639075 GTTGCGATTT
* * *
639085 TCATTTCGTGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
639118 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
639151 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
639173 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:641249 original size:42 final size:42
Alignment explanation
Indices: 641189--641311 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
641179 GCCCGACTCG
* * *
641189 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
641231 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
641273 ACTGTCATCGTTGAAGAAGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAG-AGTCCACTCCCACCGTTCAAGAG
641312 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 61 0.92
43 5 0.08
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:641269 original size:21 final size:21
Alignment explanation
Indices: 641245--641311 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
641235 TCATTCCTCG
641245 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
641266 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
641287 AGAAGT-CCCTCCCACCATTCA
1 AG-AGTCCCCTCCCACCGTTCA
641308 AGAG
1 AGAG
641312 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:642687 original size:14 final size:14
Alignment explanation
Indices: 642668--642703 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
642658 ATTGTTTAAT
642668 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
642682 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
642696 TGATTTGT
1 TGATTTGT
642704 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:642904 original size:19 final size:19
Alignment explanation
Indices: 642882--642999 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
642872 CGAAATTAAA
642882 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
642901 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
642916 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
642934 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
642949 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
642967 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
642986 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
643000 GGACATTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
14 18 0.24
16 6 0.08
17 6 0.08
19 35 0.47
20 10 0.13
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:642926 original size:14 final size:14
Alignment explanation
Indices: 642907--642961 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
642897 TCATTTCGCA
642907 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
642921 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
642938 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
642954 TTGCGATT
1 TTGCGATT
642962 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:642928 original size:33 final size:33
Alignment explanation
Indices: 642886--642979 Score: 188
Period size: 33 Copynumber: 2.8 Consensus size: 33
642876 ATTAAATTCG
642886 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
642919 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
642952 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
642980 AGTAATTTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:645288 original size:12 final size:12
Alignment explanation
Indices: 645271--645295 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
645261 TCTTCGGGGA
645271 CTTTTTCTTCTT
1 CTTTTTCTTCTT
645283 CTTTTTCTTCTT
1 CTTTTTCTTCTT
645295 C
1 C
645296 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:646782 original size:14 final size:14
Alignment explanation
Indices: 646763--646799 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
646753 CATCAATTAA
646763 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
646777 ACAAATCATCTTTT
1 ACAAATCAACATTT
646791 ACAAATCAA
1 ACAAATCAA
646800 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:647187 original size:20 final size:20
Alignment explanation
Indices: 647162--647212 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
647152 ATTCATTTGA
*
647162 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
647182 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
647202 TTATCGCAACG
1 CTATCGCAACG
647213 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:647262 original size:14 final size:15
Alignment explanation
Indices: 647242--647314 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
647232 TGAAAATCGC
647242 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
647257 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
647274 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
647292 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
647308 -TTGCGAT
1 ATTGCGAT
647315 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:647279 original size:19 final size:19
Alignment explanation
Indices: 647238--647304 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
647228 GAAATGAAAA
647238 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
647254 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
647271 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
647289 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
647305 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:649328 original size:20 final size:19
Alignment explanation
Indices: 649293--649359 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
649283 GAAACTTAAA
*
649293 ATCGCAATGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
649312 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
649332 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
649351 ATCGCAACG
1 ATCGCAACG
649360 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:649354 original size:19 final size:19
Alignment explanation
Indices: 649274--649391 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
649264 TAGTTTACTT
* *
649274 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
649294 TCGCAATGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
649313 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
649333 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
649352 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
649366 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
649384 TCGCAACG
1 TCGCAACG
649392 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 28 0.35
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:649367 original size:14 final size:14
Alignment explanation
Indices: 649348--649405 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
649338 ATGCGAAATG
649348 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
649362 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
649378 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
649394 AAAATCGCAACG
1 AAAATCGCAACG
649406 CGAACACAAA
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:649390 original size:32 final size:33
Alignment explanation
Indices: 649332--649409 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 33
649322 GGAAATGGCT
*
649332 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
649365 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
649397 ATCGCAACGCGAA
1 ATCGCAACGCGAA
649410 CACAAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:649417 original size:32 final size:32
Alignment explanation
Indices: 649332--649420 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
649322 GGAAATGGCT
* *
649332 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAT-CAAATCGCAACGACAAA
*
649365 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATCAAATCGCAACGACAAA
649397 ATCGCAACGCGAACA-CAAATCGCA
1 ATCGCAACGCGAA-ATCAAATCGCA
649421 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 37 0.71
33 15 0.29
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATCAAATCGCAACGACAAA
Found at i:649418 original size:18 final size:17
Alignment explanation
Indices: 649348--649420 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 17
649338 ATGCGAAATG
649348 AAAATCGCAA--CG-AC
1 AAAATCGCAACGCGAAC
649362 AAAATCGCAACGCGAA-
1 AAAATCGCAACGCGAAC
649378 ATGAAATCGCAA--CG-AC
1 A--AAATCGCAACGCGAAC
649394 AAAATCGCAACGCGAAC
1 AAAATCGCAACGCGAAC
649411 ACAAATCGCA
1 A-AAATCGCA
649421 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
14 19 0.39
15 1 0.02
16 8 0.16
17 4 0.08
18 17 0.35
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAATCGCAACGCGAAC
Found at i:649443 original size:19 final size:19
Alignment explanation
Indices: 649416--649517 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 19
649406 CGAACACAAA
* *
649416 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
*
649435 TCGCGTTGCG--ATT--TG
1 TCGCGTTGCGATATTCATT
*
649450 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATATTCATT
* **
649467 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATATTCATT
*
649486 TCCGCGTTGCGATAGTCATTT
1 T-CGCGTTGCGATATTCA-TT
*
649507 TCGTGTTGCGA
1 TCGCGTTGCGA
649518 AAGTAAACTA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
13 7 0.11
15 4 0.06
17 4 0.06
19 22 0.35
20 23 0.37
21 3 0.05
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATATTCATT
Found at i:649497 original size:20 final size:19
Alignment explanation
Indices: 649463--649517 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
649453 TTGCGATTTT
*
649463 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
649482 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
649502 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
649518 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:650026 original size:36 final size:36
Alignment explanation
Indices: 649985--650065 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
649975 GTCGAATAGA
649985 TGATGGCTCTAGGTGAGGTGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGTGAGGTGATAGCTCTGGGCGAGG
650021 TGATGGCTCTAGGTGAGGTGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGTGAGGTGATAGCTCTGGGCGAGG
650057 -GATGGCTCT
1 TGATGGCTCT
650066 CGAAGTGGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 9 0.20
36 36 0.80
ACGTcount: A:0.16, C:0.15, G:0.43, T:0.26
Consensus pattern (36 bp):
TGATGGCTCTAGGTGAGGTGATAGCTCTGGGCGAGG
Found at i:650056 original size:18 final size:18
Alignment explanation
Indices: 649985--650065 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
649975 GTCGAATAGA
*
649985 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
650003 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
*
650021 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
650039 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
650057 -GATGGCTCT
1 TGATGGCTCT
650066 CGAAGTGGAG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
17 8 0.15
18 45 0.85
ACGTcount: A:0.16, C:0.15, G:0.43, T:0.26
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:651389 original size:20 final size:20
Alignment explanation
Indices: 651364--651417 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
651354 AATAGTTTCT
651364 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
651384 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
651404 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
651418 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:651890 original size:20 final size:21
Alignment explanation
Indices: 651865--651970 Score: 89
Period size: 20 Copynumber: 5.3 Consensus size: 21
651855 TGAAAAAGCA
* *
651865 TTGCGATATGT-ATTATCGCG
1 TTGCGATAAGTCAGTATCGCG
651885 TTGCGA-AAGTCAGTATCGCG
1 TTGCGATAAGTCAGTATCGCG
* *
651905 TTGCGA-AAGTAAGTATCTCG
1 TTGCGATAAGTCAGTATCGCG
* * * *
651925 TTGCGAT--TTTATTATCGCA
1 TTGCGATAAGTCAGTATCGCG
*
651944 TTGCGAT-AGTCAGTATCGCA
1 TTGCGATAAGTCAGTATCGCG
651964 TTGCGAT
1 TTGCGAT
651971 TTTCCCAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.24
20 54 0.76
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (21 bp):
TTGCGATAAGTCAGTATCGCG
Found at i:651959 original size:39 final size:39
Alignment explanation
Indices: 651898--651973 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
651888 CGAAAGTCAG
* * *
651898 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTAT
* *
651937 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
651974 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTAT
Found at i:651988 original size:21 final size:21
Alignment explanation
Indices: 651959--652033 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
651949 ATAGTCAGTA
651959 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
651980 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
652000 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
652021 TCGCGTTGCGATT
1 TCGCATTGCGATT
652034 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:652047 original size:40 final size:41
Alignment explanation
Indices: 651959--652053 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
651949 ATAGTCAGTA
*
651959 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
652000 TCGCATTGCGAATTTCCCAATTCGCGTTGCGA-TTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
652040 TCGCATTGCGAATT
1 TCGCATTGCGAATT
652054 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 22 0.42
41 31 0.58
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Done.