Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007050.1 Hibiscus syriacus cultivar Beakdansim tig00018276_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: 90602
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5319 original size:21 final size:21
Alignment explanation
Indices: 5269--5319 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5259 TACAAAAAAA
*
5269 TTATATATATTTTTAGTAATT
1 TTATATTTATTTTTAGTAATT
* *
5290 TGT-TTTTTATTTTTGGTAATT
1 T-TATATTTATTTTTAGTAATT
5311 TTATATTTA
1 TTATATTTA
5320 AAATTTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TTATATTTATTTTTAGTAATT
Found at i:5336 original size:24 final size:23
Alignment explanation
Indices: 5309--5370 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
5299 TTTTTGGTAA
**
5309 TTTTATATTTAAAATTTTGAATAT
1 TTTTATATTTAAAA-TTAAAATAT
5333 TTTTATATTTTAAAATTAAAATAT
1 TTTTATA-TTTAAAATTAAAATAT
*
5357 TTTTATTTTTAAAA
1 TTTTATATTTAAAA
5371 GAAACCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.21
24 20 0.59
25 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTATATTTAAAATTAAAATAT
Found at i:11560 original size:2 final size:2
Alignment explanation
Indices: 11553--11578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11543 TGTTCAAATG
11553 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11579 AAGAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17263 original size:25 final size:25
Alignment explanation
Indices: 17217--17289 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
17207 CTCATATAAA
** *
17217 TTGCACCGAAGTGTCGCGTAGAATT
1 TTGCACCGAAGTACCGCATAGAATT
*
17242 TTGCACCGAAGTACCGTATAGAATT
1 TTGCACCGAAGTACCGCATAGAATT
* *
17267 TTGTC-CCGAAGGACCACATAGAA
1 TTG-CACCGAAGTACCGCATAGAA
17290 ATTCCTTAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (25 bp):
TTGCACCGAAGTACCGCATAGAATT
Found at i:28194 original size:25 final size:25
Alignment explanation
Indices: 28150--28207 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
28140 ATAATCTGTT
*
28150 TTCACCCCCCTAAAATTTTTATAAG
1 TTCACCCCACTAAAATTTTTATAAG
*
28175 TTCACCCCACTGAAAA-TTTTATATG
1 TTCACCCCACT-AAAATTTTTATAAG
*
28200 TTCGCCCC
1 TTCACCCC
28208 CAACATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (25 bp):
TTCACCCCACTAAAATTTTTATAAG
Found at i:28208 original size:26 final size:25
Alignment explanation
Indices: 28154--28219 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
28144 TCTGTTTTCA
28154 CCCCC-CTAAAATTTTTATAAGTTC
1 CCCCCACTAAAATTTTTATAAGTTC
* *
28178 ACCCCACTGAAAA-TTTTATATGTTC
1 CCCCCACT-AAAATTTTTATAAGTTC
28203 GCCCCCAACATAAAATT
1 -CCCCC-AC-TAAAATT
28220 ATTTGTTCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 8 0.24
27 6 0.18
28 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (25 bp):
CCCCCACTAAAATTTTTATAAGTTC
Found at i:34397 original size:23 final size:26
Alignment explanation
Indices: 34360--34428 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
34350 TTCTCTTGTG
34360 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
34384 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
34409 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
34429 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:34410 original size:12 final size:12
Alignment explanation
Indices: 34393--34428 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
34383 TATCATGTTC
34393 TCATATCACATG
1 TCATATCACATG
*
34405 TCATATCACATA
1 TCATATCACATG
34417 TCATATCACATG
1 TCATATCACATG
34429 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:34914 original size:45 final size:45
Alignment explanation
Indices: 34819--34918 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
34809 TGCACTCCTT
* *
34819 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
34864 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
34908 AGTGCATCGAT
1 A-TGCATCGAT
34919 ACACTTTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 2 0.04
45 40 0.83
46 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:38493 original size:21 final size:21
Alignment explanation
Indices: 38451--38493 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
38441 TTTTTGGGCT
* * *
38451 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
38472 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
38493 A
1 A
38494 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:39210 original size:149 final size:150
Alignment explanation
Indices: 39023--39330 Score: 564
Period size: 150 Copynumber: 2.1 Consensus size: 150
39013 GGGTAGAGGG
* *
39023 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
39087 TACTTGATCCCTAATATATGTATATGATTTTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
39152 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
39172 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
39237 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
39302 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
39322 TCTACGCGG
1 TCTACGCGG
39331 CACTACGGTG
Statistics
Matches: 153, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
149 51 0.33
150 102 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:39373 original size:23 final size:23
Alignment explanation
Indices: 39306--39363 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
39296 ATCATTATAT
39306 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
39329 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
39352 GGCACTTCGGTG
1 GGCACTACGGTG
39364 TATTTATACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.22
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:46187 original size:149 final size:150
Alignment explanation
Indices: 45998--46313 Score: 573
Period size: 150 Copynumber: 2.1 Consensus size: 150
45988 GGGTAGAGGG
* *
45998 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
46062 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
46127 ATATGGCACTACAGTGCAAT
131 ATATGGCACTACAGTGCAAT
*
46147 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
46212 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
*
46277 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACAGTGCAAT
46297 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
46314 TGCATTTATA
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 52 0.32
150 109 0.68
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACAGTGCAAT
Found at i:46325 original size:23 final size:23
Alignment explanation
Indices: 46281--46325 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46271 ATCATTATAT
*
46281 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
46304 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
46326 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:50442 original size:23 final size:26
Alignment explanation
Indices: 50405--50457 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
50395 TTCTCTTGTG
50405 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
50429 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
50454 ATCA
1 ATCA
50458 CATGAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:50877 original size:64 final size:63
Alignment explanation
Indices: 50769--50947 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 63
50759 TAATGAAGGT
* * * ** * **
50769 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-GAATTGCATTCGATGT-TTCATTATTAATGGG
50833 ATGCATCGATGCACT-CTTTATGCATCGATGCAGCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTAC-TTATGCATCGATGCAG-AATTGCATTCGATGTTTCATTATTAATGGG
50897 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT
1 ATGCATCGATGCACTACTTATGCATCGATGCA-GAATTGCATTCGATGTTT
50948 TTGTTTTAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
63 3 0.03
64 97 0.95
65 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCAGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:51031 original size:21 final size:21
Alignment explanation
Indices: 51005--51060 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
50995 TTAATCTTGA
51005 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
51026 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
51047 TGCATCGATGCACT
1 TGCATCGATGCACT
51061 CTGCCCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:52713 original size:31 final size:31
Alignment explanation
Indices: 52675--52737 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
52665 GTTAACTCGG
52675 AGTGACCACATCTTAATTAAACAAAAAAGAA
1 AGTGACCACATCTTAATTAAACAAAAAAGAA
* *
52706 AGTGACCACATCTTAGTTAAATAAAAAAGAA
1 AGTGACCACATCTTAATTAAACAAAAAAGAA
52737 A
1 A
52738 ATGGTCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (31 bp):
AGTGACCACATCTTAATTAAACAAAAAAGAA
Found at i:58588 original size:24 final size:24
Alignment explanation
Indices: 58556--58603 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
58546 CTCAAATACT
58556 TACCACCAACGGTGCCCCTTCACC
1 TACCACCAACGGTGCCCCTTCACC
58580 TACCACCAACGGTGCCCCTTCACC
1 TACCACCAACGGTGCCCCTTCACC
58604 ATTTCTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.50, G:0.12, T:0.17
Consensus pattern (24 bp):
TACCACCAACGGTGCCCCTTCACC
Found at i:67120 original size:21 final size:21
Alignment explanation
Indices: 67096--67135 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
67086 ATAAATTTGA
67096 GATTAGGGTAAGAGATTTAGG
1 GATTAGGGTAAGAGATTTAGG
* * *
67117 GATTTGGGTTAGGGATTTA
1 GATTAGGGTAAGAGATTTA
67136 TGTTTAGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.35
Consensus pattern (21 bp):
GATTAGGGTAAGAGATTTAGG
Found at i:67128 original size:13 final size:14
Alignment explanation
Indices: 67112--67152 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
67102 GGTAAGAGAT
67112 TTAGGGATTT-GGG
1 TTAGGGATTTAGGG
* *
67125 TTAGGGATTTATGT
1 TTAGGGATTTAGGG
67139 TTAGGGATTTAGGG
1 TTAGGGATTTAGGG
67153 GGATTGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (14 bp):
TTAGGGATTTAGGG
Found at i:67765 original size:14 final size:15
Alignment explanation
Indices: 67734--67769 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
67724 TGGCGGCCAC
67734 TTTAATTTCAAATAA
1 TTTAATTTCAAATAA
*
67749 TTTAATTT-AAATCA
1 TTTAATTTCAAATAA
67763 TTTAATT
1 TTTAATT
67770 AATCAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTTCAAATAA
Found at i:69848 original size:26 final size:24
Alignment explanation
Indices: 69805--69856 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
69795 TCTCTTCTAA
69805 TTTTAAATTTAAATATTAAATGAAT
1 TTTTAAATTTAAATATTAAAT-AAT
69830 TTTTATAATTATAAA-ATTAAATAAT
1 TTTTA-AATT-TAAATATTAAATAAT
69855 TT
1 TT
69857 GACATCTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.40
26 11 0.44
27 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTAAATTTAAATATTAAATAAT
Found at i:71529 original size:2 final size:2
Alignment explanation
Indices: 71522--71549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
71512 AAAATATCAA
71522 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
71550 TACTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72219 original size:78 final size:78
Alignment explanation
Indices: 72090--72241 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
72080 AGGATGTAAT
* * *
72090 ATTTGTTTAGAATTTTTCTTCGTCATTAAGATCGTATACATATATTGTAGACATATCTGTCTTAA
1 ATTTGTTTAGAAATTTTCTTCGTCATTAAGATCGTATACATATATGGTAGACATATCCGTCTTAA
72155 CCCGAATCTGTAC
66 CCCGAATCTGTAC
72168 ATTTGTTTAGAAATTTTCTTCGTCATTAAGATCGTATACATATATGGTAGACATATCCGTCTTAA
1 ATTTGTTTAGAAATTTTCTTCGTCATTAAGATCGTATACATATATGGTAGACATATCCGTCTTAA
72233 CCCGAATCT
66 CCCGAATCT
72242 TTTAGAGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (78 bp):
ATTTGTTTAGAAATTTTCTTCGTCATTAAGATCGTATACATATATGGTAGACATATCCGTCTTAA
CCCGAATCTGTAC
Found at i:79572 original size:16 final size:16
Alignment explanation
Indices: 79548--79579 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
79538 TATCGCCGAT
*
79548 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
79564 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
79580 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:83645 original size:6 final size:6
Alignment explanation
Indices: 83634--83667 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
83624 GTTTTATTAT
83634 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAG
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG GGAG
83668 GAAAGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.68, T:0.15
Consensus pattern (6 bp):
GGAGTG
Found at i:86622 original size:13 final size:13
Alignment explanation
Indices: 86604--86649 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
86594 TTTTTTATCA
86604 AAAATAAAGAGAT
1 AAAATAAAGAGAT
* * *
86617 AAAATATATGATAA
1 AAAATA-AAGAGAT
86631 AAAATAAAGAGAT
1 AAAATAAAGAGAT
86644 AAAATA
1 AAAATA
86650 TATGATCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.20
Consensus pattern (13 bp):
AAAATAAAGAGAT
Found at i:86640 original size:27 final size:28
Alignment explanation
Indices: 86603--86664 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
86593 TTTTTTTATC
86603 AAAAATAAAGAGATAAAATATATGAT-A
1 AAAAATAAAGAGATAAAATATATGATCA
86630 AAAAATAAAGAGATAAAATATATGATCA
1 AAAAATAAAGAGATAAAATATATGATCA
*
86658 ATAAATA
1 AAAAATA
86665 TGCAATCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.23
Consensus pattern (28 bp):
AAAAATAAAGAGATAAAATATATGATCA
Done.