Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005068.1 Hibiscus syriacus cultivar Beakdansim tig00011373_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: 48941
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:2730 original size:10 final size:10
Alignment explanation
Indices: 2715--2765 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
2705 AGCTATCTAA
*
2715 TAATTATTTT
1 TAATAATTTT
* *
2725 TAATTACTATT
1 TAA-TAATTTT
2736 TAATAATTTT
1 TAATAATTTT
2746 TAATAATTTT
1 TAATAATTTT
2756 TAATAATTTT
1 TAATAATTTT
2766 ATTTTGATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 28 0.80
11 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TAATAATTTT
Found at i:2739 original size:24 final size:26
Alignment explanation
Indices: 2684--2743 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
2674 AATGAACTTT
*
2684 TTTAATAATTGTAGTTTAATTAGCTA
1 TTTAATAATTATAGTTTAATTAGCTA
* *
2710 TCTAATAATTAT-TTTTAATTA-CTA
1 TTTAATAATTATAGTTTAATTAGCTA
2734 TTTAATAATT
1 TTTAATAATT
2744 TTTAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.40
25 8 0.27
26 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTAATAATTATAGTTTAATTAGCTA
Found at i:2752 original size:24 final size:25
Alignment explanation
Indices: 2700--2753 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2690 AATTGTAGTT
*
2700 TAATTAGCTATCTAATAATTATTTT
1 TAATTAGCTATCTAATAATTATTTA
*
2725 TAATTA-CTATTTAATAATT-TTTAA
1 TAATTAGCTATCTAATAATTATTT-A
2749 TAATT
1 TAATT
2754 TTTAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 17 0.65
25 6 0.23
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (25 bp):
TAATTAGCTATCTAATAATTATTTA
Found at i:4299 original size:21 final size:21
Alignment explanation
Indices: 4273--4318 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4263 GCTGCAAGAT
4273 ACCTAAGAGGGAACATCTGAC
1 ACCTAAGAGGGAACATCTGAC
*
4294 ACCTAAGAGGGAACATCTGCC
1 ACCTAAGAGGGAACATCTGAC
4315 ACCT
1 ACCT
4319 GGGTCGGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (21 bp):
ACCTAAGAGGGAACATCTGAC
Found at i:28141 original size:23 final size:21
Alignment explanation
Indices: 28115--28164 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
28105 TTTTTAAAAG
* *
28115 TTTAGATAATAATAAAATATTTT
1 TTTAAATAAAAAT-AAAT-TTTT
28138 TTTAAATAAAAATAAA-TTTT
1 TTTAAATAAAAATAAATTTTT
28158 TTTAAAT
1 TTTAAAT
28165 TAAGTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
22 3 0.12
23 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAATAAAAATAAATTTTT
Found at i:28149 original size:18 final size:19
Alignment explanation
Indices: 28128--28164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
28118 AGATAATAAT
28128 AAAAT-ATTTTTTTAAATA
1 AAAATAATTTTTTTAAATA
28146 AAAATAAATTTTTTTAAAT
1 AAAAT-AATTTTTTTAAAT
28165 TAAGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATAATTTTTTTAAATA
Found at i:28199 original size:25 final size:24
Alignment explanation
Indices: 28121--28226 Score: 85
Period size: 25 Copynumber: 4.3 Consensus size: 24
28111 AAAGTTTAGA
* *
28121 TAATAATAAAATATTTTT-TTAA-A
1 TAATAATAAAAT-TTTTTAATAAGT
* *
28144 TAAAAATAAATTTTTTTAAATTAAGT
1 TAATAATAAAATTTTTT-AA-TAAGT
28170 TAATAATAAAATTTATTTAATAAGT
1 TAATAATAAAATTT-TTTAATAAGT
*
28195 TAAT-ATAAAAATATTTTTTA-AAGT
1 TAATAAT-AAAAT-TTTTTAATAAGT
28219 TAATAATA
1 TAATAATA
28227 TATAATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
22 5 0.07
23 10 0.15
24 11 0.16
25 23 0.34
26 16 0.24
27 3 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (24 bp):
TAATAATAAAATTTTTTAATAAGT
Found at i:28526 original size:31 final size:32
Alignment explanation
Indices: 28462--28526 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
28452 TGGTGACTAC
*
28462 ATCTTAATTAAAGAAAAAACAAAAGTGATCAT
1 ATCTTAATTAAAGAAAAAACAAAAGTGACCAT
* * *
28494 ATCTTAATTAAA-TAAAACCGAAAGTGACCAT
1 ATCTTAATTAAAGAAAAAACAAAAGTGACCAT
28525 AT
1 AT
28527 GTTATGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.26
Consensus pattern (32 bp):
ATCTTAATTAAAGAAAAAACAAAAGTGACCAT
Found at i:33435 original size:18 final size:18
Alignment explanation
Indices: 33412--33462 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
33402 GGATTATCAT
33412 TGGTCCTTCGGTACATAG
1 TGGTCCTTCGGTACATAG
33430 TGGTCCTTCAGG-ACATAG
1 TGGTCCTTC-GGTACATAG
*
33448 TGGTCATTCGGTACA
1 TGGTCCTTCGGTACA
33463 AATATTCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (18 bp):
TGGTCCTTCGGTACATAG
Found at i:34288 original size:10 final size:10
Alignment explanation
Indices: 34270--34332 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
34260 GATTTTATTA
34270 AAATAAAATC
1 AAATAAAATC
* *
34280 AAATGAAATG
1 AAATAAAATC
* *
34290 AAATCACATC
1 AAATAAAATC
34300 AAATAAAATC
1 AAATAAAATC
34310 AAACT-AAATC
1 AAA-TAAAATC
34320 AAA-ACAAATC
1 AAATA-AAATC
34330 AAA
1 AAA
34333 GCAAAACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 42 0.98
11 1 0.02
ACGTcount: A:0.65, C:0.14, G:0.03, T:0.17
Consensus pattern (10 bp):
AAATAAAATC
Found at i:34293 original size:15 final size:15
Alignment explanation
Indices: 34270--34347 Score: 72
Period size: 15 Copynumber: 5.2 Consensus size: 15
34260 GATTTTATTA
*
34270 AAATAAAATCAAATG
1 AAATAAAATCAAATC
* *
34285 AAATGAAATCACATC
1 AAATAAAATCAAATC
34300 AAATAAAATCAAA-C
1 AAATAAAATCAAATC
34314 TAAATCAAAA-CAAATC
1 -AAAT-AAAATCAAATC
*
34330 AAAGCAAAA-CAAATC
1 AAA-TAAAATCAAATC
34345 AAA
1 AAA
34348 ACAAAACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.02
15 47 0.89
16 5 0.09
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.15
Consensus pattern (15 bp):
AAATAAAATCAAATC
Found at i:34327 original size:5 final size:5
Alignment explanation
Indices: 34319--34357 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
34309 CAAACTAAAT
* * *
34319 CAAAA CAAAT CAAAG CAAAA CAAAT CAAAA CAAAA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
34358 CTAAACAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.05
Consensus pattern (5 bp):
CAAAA
Found at i:34337 original size:10 final size:10
Alignment explanation
Indices: 34305--34357 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
34295 ACATCAAATA
34305 AAATC-AAAC
1 AAATCAAAAC
34314 TAAATCAAAAC
1 -AAATCAAAAC
*
34325 AAATCAAAGC
1 AAATCAAAAC
* *
34335 AAAACAAATC
1 AAATCAAAAC
*
34345 AAAACAAAAC
1 AAATCAAAAC
34355 AAA
1 AAA
34358 CTAAACAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 34 0.89
11 4 0.11
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (10 bp):
AAATCAAAAC
Found at i:34352 original size:15 final size:15
Alignment explanation
Indices: 34319--34357 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
34309 CAAACTAAAT
*
34319 CAAAACAAATCAAAG
1 CAAAACAAATCAAAA
34334 CAAAACAAATCAAAA
1 CAAAACAAATCAAAA
34349 CAAAACAAA
1 CAAAACAAA
34358 CTAAACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.72, C:0.21, G:0.03, T:0.05
Consensus pattern (15 bp):
CAAAACAAATCAAAA
Found at i:38593 original size:31 final size:31
Alignment explanation
Indices: 38506--38632 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
38496 AGAGTCGAGG
38506 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
38537 GAATTACCTATG-TCTTTC-GAGACATATAGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
38569 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
38600 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
38631 GT
1 GT
38633 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.67
32 26 0.33
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:38674 original size:30 final size:30
Alignment explanation
Indices: 38620--38691 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
38610 GTTCTTCGGA
* * *
38620 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
*
38650 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
38680 ACCTCTGGATAG
1 ACCTCTGGATAG
38692 GTCCTTCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:43390 original size:63 final size:62
Alignment explanation
Indices: 43312--43438 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 62
43302 AGAGTCGAGG
* * *
43312 GTATACCTATGTTCTACGGAGCATATGGACAGAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAG-ATTACCTAGGTTCTTTCGA-ACATATGGACA
* * *
43375 GTATACCTATGTTCTAAGGAACATATGGACAGTTTACCTAGGTTCTTTGGAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGATTACCTAGGTTCTTTCGAACATATGGACA
43437 GT
1 GT
43439 TGCCAAGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 20 0.35
63 37 0.65
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (62 bp):
GTATACCTATGTTCTAAGGAACATATGGACAGATTACCTAGGTTCTTTCGAACATATGGACA
Found at i:43439 original size:31 final size:31
Alignment explanation
Indices: 43315--43439 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
43305 GTCGAGGGTA
** * *
43315 TACCTATGTTCTACGGAGCATATGGACAGAAT
1 TACCTATGTTCTTTGGAACATATGGACAG-TT
* *
43347 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTTTGGA-ACATATGGACAGTT
**
43378 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTTTGGAACATATGGACAGTT
* *
43409 TACCTAGGTTCTTTGGAACCTATGGACAGTT
1 TACCTATGTTCTTTGGAACATATGGACAGTT
43440 GCCAAGGATC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
31 53 0.69
32 24 0.31
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTTTGGAACATATGGACAGTT
Found at i:45301 original size:36 final size:36
Alignment explanation
Indices: 45260--45329 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
45250 TCTATCTCGT
45260 ATCATATAACATATATACTTTCATCTATTCATATGA
1 ATCATATAACATATATACTTTCATCTATTCATATGA
* * *
45296 ATCATATAACATGTGTACTTTCATTTATTCATAT
1 ATCATATAACATATATACTTTCATCTATTCATAT
45330 CATATAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (36 bp):
ATCATATAACATATATACTTTCATCTATTCATATGA
Found at i:45337 original size:32 final size:33
Alignment explanation
Indices: 45259--45339 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 33
45249 ATCTATCTCG
45259 TATCATATAACATATATACTTTCATCTATTCATA
1 TATCATATAACATATATACTTTCATCTATTCA-A
* * *
45293 TGAATCATATAACATGTGTACTTTCATTTATTC-A
1 T--ATCATATAACATATATACTTTCATCTATTCAA
45327 TATCATATAACAT
1 TATCATATAACAT
45340 TTATCAATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.29
34 3 0.07
36 27 0.64
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (33 bp):
TATCATATAACATATATACTTTCATCTATTCAA
Found at i:45356 original size:19 final size:20
Alignment explanation
Indices: 45317--45356 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
45307 TGTGTACTTT
45317 CATTTATTCATATCATATAA
1 CATTTATTCATATCATATAA
45337 CATTTA-TCA-ATCACTATAA
1 CATTTATTCATATCA-TATAA
45356 C
1 C
45357 TTATGCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (20 bp):
CATTTATTCATATCATATAA
Found at i:46989 original size:17 final size:18
Alignment explanation
Indices: 46948--46990 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
46938 ACCAACATAG
*
46948 ATAGATGATGGAGAAATAA
1 ATAGATGATGAAGAAAT-A
46967 ATTAGATGATGAAGAAAT-
1 A-TAGATGATGAAGAAATA
46985 ATAGAT
1 ATAGAT
46991 AAATGGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 1 0.05
19 1 0.05
20 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (18 bp):
ATAGATGATGAAGAAATA
Found at i:47660 original size:24 final size:25
Alignment explanation
Indices: 47601--47675 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
47591 TATTAAGTTA
47601 TAATATATGTAATTATTATAAAAGT
1 TAATATATGTAATTATTATAAAAGT
47626 TAATATATGTAATTATTATAAAAGT
1 TAATATATGTAATTATTATAAAAGT
47651 T-ATATATGTAATTATTATAAAAGT
1 TAATATATGTAATTATTATAAAAGT
47675 T
1 T
47676 CAATTCGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 24 0.48
25 26 0.52
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (25 bp):
TAATATATGTAATTATTATAAAAGT
Found at i:48574 original size:15 final size:15
Alignment explanation
Indices: 48556--48586 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48546 AAATTCTAAA
48556 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
48571 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
48586 T
1 T
48587 TTATCCGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Done.