Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002367.1 Hibiscus syriacus cultivar Beakdansim tig00004836_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: 42612
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:212 original size:22 final size:22
Alignment explanation
Indices: 168--212 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
158 ATTACATAAC
*
168 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGATACTT
* * *
190 TTTATAAAAAGTATGGGTACTT
1 TTTAAAAAAAGTATCGATACTT
212 T
1 T
213 CAATATAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGATACTT
Found at i:261 original size:23 final size:23
Alignment explanation
Indices: 230--302 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
220 ATAGGTAAAA
*
230 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
253 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
276 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
299 ATAT
1 ATAT
303 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:788 original size:23 final size:23
Alignment explanation
Indices: 718--790 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
708 ATAGGTAAAA
*
718 ATATGATGTAATAGGTAGAGCTT
1 ATATAATGTAATAGGTAGAGCTT
* * * * *
741 AAATAATATAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGAGCTT
*
764 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGAGCTT
787 ATAT
1 ATAT
791 TGTAAAGTAT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGAGCTT
Found at i:1009 original size:488 final size:490
Alignment explanation
Indices: 8--2161 Score: 3662
Period size: 488 Copynumber: 4.4 Consensus size: 490
1 ACATTTA
*
8 TATTA-TATCTTTGGTTAATATTGTTAAATTTAAA-ATCTAAATAATATTTTATAAAATATCAAA
1 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
71 ACAATCAAATAATTTTTTGTGTAAATGAAATTATT-AATTAATATTGTAGGTGGAAAACATGAAA
66 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
135 CACTGTT--AAAAAA-TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
131 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
**
197 AAAGTATGGGTACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
196 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
262 AATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATA
261 AATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATA
*
327 AAAGTGTCTATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
326 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
392 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGGTATATATTATTA
391 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGG-ATATATTATTA
457 TTAAATTAAAAACAATAAAC--ATATATTACATATT
455 TTAAATTAAAAACAATAAACATATATATTACATATT
* *
491 TATTATTATATTTGGTTAATATTGTTAAATTTAAA-ATCTAAATAATATTTTATAAAATATCAAA
1 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
555 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
66 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
* *
620 CACTGTTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCATTTTTAT-
131 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTATA
* * * *
684 AAAAGTATGGGCACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGAGCTTAAATAATA
195 AAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATG
* *
749 TAATATGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATTCTTTTTAT
260 TAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTAT
814 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
325 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
879 AAGATATTAATTTAGT-ATTATAGGCGTCTAATGA-TTATTTTTTACGTTACGG-TATATTATTA
390 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGGATATATTATTA
941 TTAAATTAAAAACAATAAACATATATA-TACATATT
455 TTAAATTAAAAACAATAAACATATATATTACATATT
976 TATTA-TATCTTT-GTTAATA-TGTTAAATTTAAA-TTCT--A-AATATTTTATAAAATATCAAA
1 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
* *
1034 ACAATCAAATAATTTTTTATGTAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
66 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
1099 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
131 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
*
1164 AAAGTATGGACACTTTCAATATAATATGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
196 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
**
1229 AATAGGTATTGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATA
261 AATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATA
*
1294 AAAGTGTCCATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
326 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
* *
1359 AGATATTAATTTAGTAATTATATGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTA
391 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACG-GATATATTATTA
1424 TTAAATTAAAAACAATAAACATATATATTACATATT
455 TTAAATTAAAAACAATAAACATATATATTACATATT
1460 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTT-TAAATAATATTTTATAAAATATCAAA
1 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
1524 ACAATCAAATAA-TTTTTGTGTAAATG-AATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
66 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
1587 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
131 CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
*
1652 AAAGGATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
196 AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
* *
1717 AATAAGTAGCGCTTATATAATGTAATAGGTA-TCGCTTATATTGTAAAGTATCTATCCTTTTTAT
261 AATAGGTAGCGTTTATATAATGTAATAGGTAGT-GCTTATATTGTAAAGTATCTATCCTTTTTAT
* * *
1781 AGAAGTGTCAATACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
325 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
* * ** ** * *
1846 AAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTGACGGTATATATTATC
390 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGG-ATATATTATT
*
1911 ATTAAATTAAAAACAATAAACATATATATTACATACT
454 ATTAAATTAAAAACAATAAACATATATATTACATATT
*
1948 TATTATTATCTTTGGTTAATATTGTTAAATTTAAA-TTCTAAATATTATTTTATAAAATATCAAA
1 TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
*
2012 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAACATGAA
66 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG-AAAACATGAA
2077 ACACTATT--AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTAT
130 ACACTATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTAT
2140 AAAAAAGTATGGACACTTTCAA
194 -AAAAAGTATGGACACTTTCAA
2162 CATATTATAA
Statistics
Matches: 1587, Mismatches: 55, Indels: 50
0.94 0.03 0.03
Matches are distributed among these distances:
478 23 0.01
479 323 0.20
480 18 0.01
481 16 0.01
482 16 0.01
483 49 0.03
484 141 0.09
485 56 0.04
486 29 0.02
487 41 0.03
488 676 0.43
489 79 0.05
490 82 0.05
491 38 0.02
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (490 bp):
TATTATTATCTTTGGTTAATATTGTTAAATTTAAATTTCTAAATAATATTTTATAAAATATCAAA
ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
CACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGT
AATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATA
AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGGATATATTATTAT
TAAATTAAAAACAATAAACATATATATTACATATT
Found at i:1228 original size:23 final size:23
Alignment explanation
Indices: 1197--1269 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1187 ATATGTAAAA
* *
1197 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
1220 ATATAATGTAATAGGTATTGTTT
1 ATATAATGTAATAGGTAGTGCTT
1243 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGTGCTT
1266 ATAT
1 ATAT
1270 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:1716 original size:23 final size:23
Alignment explanation
Indices: 1685--1757 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1675 ATAGGTAAAA
*
1685 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1708 ATATAATGTAATAAGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1731 ATATAATGTAATAGGTATCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1754 ATAT
1 ATAT
1758 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:4565 original size:15 final size:15
Alignment explanation
Indices: 4532--4584 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
4522 TAGTCGAGAT
*
4532 GAGTCAACTC-ACT-
1 GAGTCAACTCGAGTA
4545 GAGTCAACTCGAGTA
1 GAGTCAACTCGAGTA
4560 GAGTCAACTCGAGTA
1 GAGTCAACTCGAGTA
4575 GAGTCAACTC
1 GAGTCAACTC
4585 ATTGACTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
15 25 0.68
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (15 bp):
GAGTCAACTCGAGTA
Found at i:5563 original size:26 final size:27
Alignment explanation
Indices: 5503--5569 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
5493 CCCTAAAGTG
5503 TAAAATGATCTAAAGTACCTTCAAGCCC
1 TAAAATGA-CTAAAGTACCTTCAAGCCC
**
5531 TGGAATGACTAAA-TACCTTCAAGCTCC
1 TAAAATGACTAAAGTACCTTCAAGC-CC
*
5558 -AAAATGAATAAA
1 TAAAATGACTAAA
5570 ACAACTTCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 20 0.61
27 7 0.21
28 6 0.18
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (27 bp):
TAAAATGACTAAAGTACCTTCAAGCCC
Found at i:8909 original size:2 final size:2
Alignment explanation
Indices: 8902--8940 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8892 AAACATTGTC
8902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8941 GACACTGATA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13573 original size:28 final size:27
Alignment explanation
Indices: 13542--13598 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
13532 TATTTTATAT
* *
13542 TTTATAATTAATAAAA-AGTATTATATTA
1 TTTAAAATCAATAAAATA-TATTA-ATTA
*
13570 TTTAAAATCATTAAAATATATTAATTA
1 TTTAAAATCAATAAAATATATTAATTA
13597 TT
1 TT
13599 CTGACAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 6 0.24
28 18 0.72
29 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTTAAAATCAATAAAATATATTAATTA
Found at i:18549 original size:45 final size:45
Alignment explanation
Indices: 18485--18639 Score: 145
Period size: 45 Copynumber: 3.5 Consensus size: 45
18475 TTGAATTTGC
18485 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTA
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTA
* ** * * * ** * *
18530 TTCCACTATTCTTTTGTGGAG-TTCAGA-TTT-ATGATTGAATTTGC
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGA-AAAATCT-A
* *
18574 TTCCACTACTCTTCTGTGGAGTTTGATACTTTGCTGAAAAATCTG
1 TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTA
* *
18619 TTCCACCACTCTTTCGTGGAG
1 TTCCACTACTCTTCCGTGGAG
18640 CTCAGACTTT
Statistics
Matches: 83, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
42 3 0.04
43 7 0.08
44 23 0.28
45 40 0.48
46 7 0.08
47 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (45 bp):
TTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTA
Found at i:18595 original size:89 final size:89
Alignment explanation
Indices: 18475--18645 Score: 288
Period size: 89 Copynumber: 1.9 Consensus size: 89
18465 AAATTCAAAG
* *
18475 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTATTCCACTATT
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTATTCCACCACT
* *
18540 CTTTTGTGGAGTTCAGATTTATGA
66 CTTTCGTGGAGCTCAGATTTATGA
* *
18564 TTGAATTTGCTTCCACTACTCTTCTGTGGAGTTTGATACTTTGCTGAAAAATCTGTTCCACCACT
1 TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTATTCCACCACT
18629 CTTTCGTGGAGCTCAGA
66 CTTTCGTGGAGCTCAGA
18646 CTTTGGTCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (89 bp):
TTGAATTTGCTTCCACTACTCTTCCGTGGAGTTTGATACTTTGCTGAAAAATCTATTCCACCACT
CTTTCGTGGAGCTCAGATTTATGA
Found at i:27074 original size:12 final size:12
Alignment explanation
Indices: 27028--27075 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
27018 TGAATATTTT
27028 ATCTG-ATTACTG
1 ATCTGAATT-CTG
*
27040 ATCTGAATTATG
1 ATCTGAATTCTG
* *
27052 CTCTGATTTCTG
1 ATCTGAATTCTG
27064 ATCTGAATTCTG
1 ATCTGAATTCTG
27076 TTATGATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (12 bp):
ATCTGAATTCTG
Found at i:27082 original size:24 final size:24
Alignment explanation
Indices: 27031--27113 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
27021 ATATTTTATC
* * * *
27031 TGATTACTGATCTGAATTATGCTC
1 TGATTTCTGATCTGAATTCTGTTA
27055 TGATTTCTGATCTGAATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTA
* * * * *
27079 TGATATATGATATGAATTCTATTT
1 TGATTTCTGATCTGAATTCTGTTA
27103 TGATTTCTGAT
1 TGATTTCTGAT
27114 ATCTCTGTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTA
Found at i:30194 original size:14 final size:14
Alignment explanation
Indices: 30175--30211 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
30165 TTTGTGTAAA
30175 ACTGTTGACCGTTG
1 ACTGTTGACCGTTG
30189 ACTGTTGACCGTTG
1 ACTGTTGACCGTTG
30203 ACT-TTGACC
1 ACTGTTGACC
30212 AAAAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.35
Consensus pattern (14 bp):
ACTGTTGACCGTTG
Found at i:32739 original size:24 final size:24
Alignment explanation
Indices: 32669--32775 Score: 92
Period size: 24 Copynumber: 4.5 Consensus size: 24
32659 ATATTTTATC
* * * *
32669 TGATTTCCGATTTGAAATATGTTC
1 TGATTTCTGATCTGAATTATGTTT
*
32693 TGATTTCTGATCT-AATTTCTGTTT
1 TGATTTCTGATCTGAA-TTATGTTT
* *
32717 TGATTTCTGATCTGGATTATGTTA
1 TGATTTCTGATCTGAATTATGTTT
* *
32741 TGATATT-TGATATGAATTCTGTTT
1 TGAT-TTCTGATCTGAATTATGTTT
*
32765 TGATTTTTGAT
1 TGATTTCTGAT
32776 ATCTCCATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.06
24 60 0.90
25 3 0.04
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.53
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:40683 original size:21 final size:21
Alignment explanation
Indices: 40657--40697 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40647 ACCAACTAAG
40657 AAGAGCTAATGTTAGGTCATA
1 AAGAGCTAATGTTAGGTCATA
*
40678 AAGAGCTGATGTTAGGTCAT
1 AAGAGCTAATGTTAGGTCAT
40698 GGAAAGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
AAGAGCTAATGTTAGGTCATA
Done.