Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007564.1 Hibiscus syriacus cultivar Beakdansim tig00021500_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: 71931
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5251 original size:42 final size:42
Alignment explanation
Indices: 5205--5416 Score: 150
Period size: 41 Copynumber: 5.1 Consensus size: 42
5195 CTAATATATC
* *
5205 GCGGCGTTTACTTAAAAAACACCACTACTGTCCAACTGTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
* * * * * *
5247 GCGGCGTTT--GTACGAAAATGCCTCTA-TAGTGCAACTCTATC
1 GCGGCGTTTACTTA-AAAAACGCCACTACT-GTCCAACTCTATA
***
5288 GCAATGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
* * * ** *
5330 GCGGCGTTT--GTACGAAAACGCCTCTA-TAGTGTAACTCTATC
1 GCGGCGTTTACTTA-AAAAACGCCACTACT-GTCCAACTCTATA
* * * *
5371 GTGGCGTTTAC-TAAAAAATGCCACAACTGTTCAACTCTATA
1 GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
5412 GCGGC
1 GCGGC
5417 TTTTGTACGA
Statistics
Matches: 125, Mismatches: 35, Indels: 21
0.69 0.19 0.12
Matches are distributed among these distances:
40 6 0.05
41 77 0.62
42 39 0.31
43 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTACTTAAAAAACGCCACTACTGTCCAACTCTATA
Found at i:5366 original size:41 final size:41
Alignment explanation
Indices: 5238--5463 Score: 131
Period size: 41 Copynumber: 5.5 Consensus size: 41
5228 ACTACTGTCC
* * *
5238 AACTGTATAGCGGCGTTTGTACGAAAATGCCTCTATAGTGC
1 AACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTGT
* *** * * * **
5279 AACTCTATCGCAATGTTTACTTA-AAAAACGCCACTACT-GTCC
1 AACTCTATAGCGGCGTTT--GTACGAAAACGCCTCTA-TAGTGT
5321 AACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTGT
1 AACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTGT
* * * * * * *
5362 AACTCTATCGTGGCGTTTACTA-AAAAATGCCAC-A-ACTGTT
1 AACTCTATAGCGGCGTTT-GTACGAAAACGCCTCTATAGTG-T
* *
5402 CAACTCTATAGCGGCTTTTGTACGAAAACGGCTCTATAGT-T
1 -AACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTGT
* * *
5443 CAACTATGTTGCGGCGTTTGT
1 -AACTCTATAGCGGCGTTTGT
5464 TGAAGAAAAA
Statistics
Matches: 135, Mismatches: 39, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
39 3 0.02
40 7 0.05
41 90 0.67
42 30 0.22
43 5 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (41 bp):
AACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTGT
Found at i:5459 original size:82 final size:83
Alignment explanation
Indices: 5167--5461 Score: 389
Period size: 83 Copynumber: 3.6 Consensus size: 83
5157 ATAAGTTTGA
* *
5167 GGCGTTTGTA-AAAAACGCCTCTATAGTGCTAA-TATATCGCGGCGTTTACTTAAAAAACACCAC
1 GGCGTTTGTACGAAAACGCCTCTATAGTGC-AACTATATCGCGGCGTTTACTTAAAAAACGCCAC
*
5230 TACTGTCCAACTGTATAGC
65 TACTGTCCAACTCTATAGC
* * ***
5249 GGCGTTTGTACGAAAATGCCTCTATAGTGCAACTCTATCGCAATGTTTACTTAAAAAACGCCACT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTATATCGCGGCGTTTACTTAAAAAACGCCACT
5314 ACTGTCCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
* * * * *
5332 GGCGTTTGTACGAAAACGCCTCTATAGTGTAACTCTATCGTGGCGTTTAC-TAAAAAATGCCACA
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTATATCGCGGCGTTTACTTAAAAAACGCCACT
*
5396 ACTGTTCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
* * * * *
5414 GGCTTTTGTACGAAAACGGCTCTATAGTTCAACTATGTTGCGGCGTTT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTATATCGCGGCGTTT
5462 GTTGAAGAAA
Statistics
Matches: 186, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
82 81 0.44
83 105 0.56
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (83 bp):
GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTATATCGCGGCGTTTACTTAAAAAACGCCACT
ACTGTCCAACTCTATAGC
Found at i:15028 original size:32 final size:31
Alignment explanation
Indices: 14992--15068 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
14982 TGGGGCCACG
* *
14992 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
15024 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
15055 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
15069 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:20748 original size:32 final size:31
Alignment explanation
Indices: 20711--20787 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
20701 CGAGGCCACG
* *
20711 GGGCCTACCTAAGAAT-ACTTCTTAGGGCCGTA
1 GGGCCTACCTAAGAATGA--TCTCAGGGCCGCA
*
20743 GGGCCTACCTGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATGATCTCAGGGCCGCA
*
20774 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
20788 GTCACATTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.59
32 15 0.38
33 1 0.03
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.19
Consensus pattern (31 bp):
GGGCCTACCTAAGAATGATCTCAGGGCCGCA
Found at i:25845 original size:20 final size:20
Alignment explanation
Indices: 25771--25845 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
25761 CCAGAACCCC
* * *
25771 ATGGGGGTATCGATTCCCCT
1 ATGGGGGAATCGGTTCCCTT
**
25791 ACAGGGGAATCGGTTCCCATT
1 ATGGGGGAATCGGTTCCC-TT
*
25812 CAAAGGGGGAATCGGTTCCCTT
1 --ATGGGGGAATCGGTTCCCTT
*
25834 ATGGGGGTATCG
1 ATGGGGGAATCG
25846 ATTACTTCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 24 0.56
21 1 0.02
22 2 0.05
23 16 0.37
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.25
Consensus pattern (20 bp):
ATGGGGGAATCGGTTCCCTT
Found at i:34818 original size:21 final size:19
Alignment explanation
Indices: 34780--34824 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
34770 TTAGTTGTAC
34780 TTTTATATTTTTATTTTAT
1 TTTTATATTTTTATTTTAT
*
34799 TTTTATCTTTTTAAATTTTAT
1 TTTTATATTTTT--ATTTTAT
34820 TTTTA
1 TTTTA
34825 GATTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATATTTTTATTTTAT
Found at i:39567 original size:154 final size:154
Alignment explanation
Indices: 39287--39596 Score: 593
Period size: 154 Copynumber: 2.0 Consensus size: 154
39277 AATATTTACA
*
39287 TAATCGCCAAGGACAACGTTAAACACCTACCTGTTCACAATCATCTCCTCCCCCAAGCCAGTTGC
1 TAATCGCCAAGAACAACGTTAAACACCTACCTGTTCACAATCATCTCCTCCCCCAAGCCAGTTGC
39352 TAGACAAAGTGAACCAGCAACCCTTGCAGCCATTTTCTCAAGAGGTAGTGTCACCATAGGTAGAC
66 TAGACAAAGTGAACCAGCAACCCTTGCAGCCATTTTCTCAAGAGGTAGTGTCACCATAGGTAGAC
39417 CAACCCATAACACATCCGTGCCAG
131 CAACCCATAACACATCCGTGCCAG
*
39441 TAATCGCCAAGAACAACGTTAAACAGCTACCTGTTCACAATCATCTCCTCCCCCAAGCCAGTTGC
1 TAATCGCCAAGAACAACGTTAAACACCTACCTGTTCACAATCATCTCCTCCCCCAAGCCAGTTGC
39506 TAGACAAAGTGAACCAGCAACCCTTGCAGCCATTTTCTCAAGAGGTAGTGTCACCATAGGTAGAC
66 TAGACAAAGTGAACCAGCAACCCTTGCAGCCATTTTCTCAAGAGGTAGTGTCACCATAGGTAGAC
*
39571 CAGCCCATAACACATCCGTGCCAG
131 CAACCCATAACACATCCGTGCCAG
39595 TA
1 TA
39597 GAATGTGAAT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.20
Consensus pattern (154 bp):
TAATCGCCAAGAACAACGTTAAACACCTACCTGTTCACAATCATCTCCTCCCCCAAGCCAGTTGC
TAGACAAAGTGAACCAGCAACCCTTGCAGCCATTTTCTCAAGAGGTAGTGTCACCATAGGTAGAC
CAACCCATAACACATCCGTGCCAG
Found at i:45215 original size:13 final size:13
Alignment explanation
Indices: 45197--45221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45187 GTAAACGGTA
45197 AACGGGTCGGGTT
1 AACGGGTCGGGTT
45210 AACGGGTCGGGT
1 AACGGGTCGGGT
45222 CGGTCAACGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:45232 original size:17 final size:18
Alignment explanation
Indices: 45199--45234 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
45189 AAACGGTAAA
*
45199 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
45217 CGGGTC-GGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
45234 C
1 C
45235 AGGTTGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:51763 original size:9 final size:9
Alignment explanation
Indices: 51749--51784 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
51739 ATTGGAAACC
51749 TAATATAAA
1 TAATATAAA
51758 TAATATAAA
1 TAATATAAA
51767 TAATATTTAAA
1 TAATA--TAAA
51778 TAATATA
1 TAATATA
51785 CGAAAACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TAATATAAA
Found at i:52387 original size:29 final size:30
Alignment explanation
Indices: 52317--52380 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
52307 AATAATTACT
**
52317 AAAATAGCACCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCCATTTCGAATTAAATTCCC
* *
52347 ACAATAGCACCCATTTCGAATT-AATTCCT
1 AAAATAGCACCCATTTCGAATTAAATTCCC
52376 AAAAT
1 AAAAT
52381 GTCACCCGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAATAGCACCCATTTCGAATTAAATTCCC
Found at i:52421 original size:13 final size:13
Alignment explanation
Indices: 52403--52427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52393 ACGGTCAACG
52403 GTCAACGGGTCGA
1 GTCAACGGGTCGA
52416 GTCAACGGGTCG
1 GTCAACGGGTCG
52428 GGTCGGGTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:52447 original size:22 final size:23
Alignment explanation
Indices: 52408--52454 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
52398 CAACGGTCAA
52408 CGGGTCGAGTCAACGGGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
*
52431 CGGGTCG-GTCAATGGGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
52453 CG
1 CG
52455 TAACCGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (23 bp):
CGGGTCGAGTCAACGGGTCGGGT
Found at i:57381 original size:31 final size:31
Alignment explanation
Indices: 57345--57442 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
57335 TTAAAAAATA
*
57345 AAAATAAGTATTAAATTTATTAATTGATTAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
* * * *
57376 AAAATAATTATCATACTTATTAAATT-ACTAT
1 AAAATAATTATTAAATTTATT-AATTGATTAT
* *
57407 AAAATAATTATTAAATTTATTCATTG-TCAT
1 AAAATAATTATTAAATTTATTAATTGATTAT
57437 AAAATA
1 AAAATA
57443 GTCATAATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
30 11 0.20
31 39 0.72
32 4 0.07
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAAATAATTATTAAATTTATTAATTGATTAT
Found at i:57498 original size:76 final size:77
Alignment explanation
Indices: 57408--57554 Score: 251
Period size: 76 Copynumber: 1.9 Consensus size: 77
57398 AATTACTATA
*
57408 AAATAATTATTAAATTTATTCATTGTCATAAAATAGTCATAATAATTATATTTTTCACG-AAGCT
1 AAATAATTATTAAATTTATTCATTGTAATAAAATAGTCATAATAATTATATTTTTCACGAAAGCT
57472 TTTTTTATTGAG
66 TTTTTTATTGAG
* * *
57484 AAATATTTATTAAATTTATTCATTGTAATAAAATAGTCATAATATTTATATTTTTCACGAAAGTT
1 AAATAATTATTAAATTTATTCATTGTAATAAAATAGTCATAATAATTATATTTTTCACGAAAGCT
57549 TTTTTT
66 TTTTTT
57555 TTTTTTTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 56 0.85
77 10 0.15
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (77 bp):
AAATAATTATTAAATTTATTCATTGTAATAAAATAGTCATAATAATTATATTTTTCACGAAAGCT
TTTTTTATTGAG
Found at i:63193 original size:19 final size:19
Alignment explanation
Indices: 63146--63196 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
63136 ATATAATTAA
**
63146 TGTACCGATATACCCCTAG
1 TGTACCGATGCACCCCTAG
63165 TGTACCGATGCACCCCTAG
1 TGTACCGATGCACCCCTAG
*
63184 TGTACTGATGCAC
1 TGTACCGATGCAC
63197 TAAGTCTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (19 bp):
TGTACCGATGCACCCCTAG
Found at i:66612 original size:20 final size:20
Alignment explanation
Indices: 66574--66612 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
66564 AAAGCTTTAA
* * *
66574 GATCATTATTTTCTTTTGAT
1 GATCATCATTTACTCTTGAT
66594 GATCATCATTTACTCTTGA
1 GATCATCATTTACTCTTGA
66613 AAGTAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.51
Consensus pattern (20 bp):
GATCATCATTTACTCTTGAT
Found at i:67580 original size:128 final size:128
Alignment explanation
Indices: 67350--67606 Score: 435
Period size: 128 Copynumber: 2.0 Consensus size: 128
67340 GATGATCGTC
*
67350 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGG
1 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
* **
67415 AATGATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATCTATCCGTCATAGCTTT
66 AATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
* *
67478 GTCTTCTTTGATTGCCAAGATTTTGGAAGA-AAGTAAACTAACTTCCTCACAAGCTTCTCGTTTG
1 GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAA-TAAACTAACTTCCTCACAAGCTTCCCATTTG
*
67542 AAATAATCTCTCCATATGATTTGAGACCATTGATAATCGTGGAAAATAAATCCGTCATAGCTTT
65 AAATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
67606 G
1 G
67607 ATATCTTCAT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
127 2 0.02
128 119 0.98
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (128 bp):
GTCTTCTTTGATTGCCAAGATTTTGGAAGAGAATAAACTAACTTCCTCACAAGCTTCCCATTTGA
AATAATCTCTCCATATGATTTGAGACCATTGACAATCGTGGAAAATAAATCCGTCATAGCTTT
Done.