Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005471.1 Hibiscus syriacus cultivar Beakdansim tig00012532_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: 70732
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2328 original size:13 final size:12
Alignment explanation
Indices: 2310--2348 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2300 ATATTATGAT
2310 TTTTCAAACATTG
1 TTTTCAAA-ATTG
*
2323 TTTTCAAAAATAG
1 TTTTC-AAAATTG
2336 TTTTCAAAATTG
1 TTTTCAAAATTG
2348 T
1 T
2349 CCATTAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 13 0.57
14 3 0.13
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTCAAAATTG
Found at i:3905 original size:13 final size:13
Alignment explanation
Indices: 3887--3911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3877 CCCAATTTAC
3887 ATATTGTTTATGA
1 ATATTGTTTATGA
3900 ATATTGTTTATG
1 ATATTGTTTATG
3912 GACTAATGGC
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
ATATTGTTTATGA
Found at i:4092 original size:13 final size:13
Alignment explanation
Indices: 4063--4095 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4053 AAGGAGTAAT
*
4063 TTTTCAAAATTGA
1 TTTTCAAAAATGA
4076 -TTTCAAAAATGA
1 TTTTCAAAAATGA
4088 TTTTCAAA
1 TTTTCAAA
4096 GAAAATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:6993 original size:24 final size:24
Alignment explanation
Indices: 6960--7006 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6950 GGATTAAACT
6960 TAAAATGCAAACATAAATTAGAATC
1 TAAAATGCAAACATAAA-TAGAATC
*
6985 TAAAA-GCAAACATACATAGAAT
1 TAAAATGCAAACATAAATAGAAT
7007 ACACACACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (24 bp):
TAAAATGCAAACATAAATAGAATC
Found at i:10089 original size:13 final size:14
Alignment explanation
Indices: 10071--10099 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10061 TTATCGAATT
10071 CGGATTTTTT-TAC
1 CGGATTTTTTCTAC
10084 CGGATTTTTTCTAC
1 CGGATTTTTTCTAC
10098 CG
1 CG
10100 TGTTTACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (14 bp):
CGGATTTTTTCTAC
Found at i:10308 original size:3 final size:3
Alignment explanation
Indices: 10300--10342 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
10290 AACCGTTTAC
10300 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAAA TAAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA T-AA TAA TA
10343 CAATATTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 25 0.66
4 11 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10324 original size:8 final size:8
Alignment explanation
Indices: 10302--10382 Score: 60
Period size: 8 Copynumber: 9.9 Consensus size: 8
10292 CCGTTTACTA
10302 ATAATAAT
1 ATAATAAT
10310 AATAATAAT
1 -ATAATAAT
10319 ATAATAAT
1 ATAATAAT
10327 A-AATAA-
1 ATAATAAT
10333 ATAAATAAT
1 AT-AATAAT
* *
10342 ACAATATT
1 ATAATAAT
*
10350 ATAATTTTAT
1 ATAA--TAAT
*
10360 ATGATAA-
1 ATAATAAT
10367 ATAATAAT
1 ATAATAAT
10375 GATAATAA
1 -ATAATAA
10383 ATCATAGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
6 1 0.02
7 11 0.19
8 24 0.42
9 16 0.28
10 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:10339 original size:23 final size:20
Alignment explanation
Indices: 10300--10347 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
10290 AACCGTTTAC
10300 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
10320 TAATAATAAATAAATAAATAATA
1 TAATAAT-AAT-AAT-AATAATA
*
10343 CAATA
1 TAATA
10348 TTATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 3 0.12
22 3 0.12
23 11 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:12502 original size:23 final size:23
Alignment explanation
Indices: 12450--12495 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
12440 CCAGAAAAAA
12450 CTAAG-GGAGAAAAATAATATTTT
1 CTAAGAGG-GAAAAATAATATTTT
*
12473 CTAAGAGGGAAATATAATATTTT
1 CTAAGAGGGAAAAATAATATTTT
12496 TCAAGAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (23 bp):
CTAAGAGGGAAAAATAATATTTT
Found at i:15669 original size:18 final size:18
Alignment explanation
Indices: 15646--15683 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
15636 TCATCTTCTA
15646 ATAATTTCTTTATAATTT
1 ATAATTTCTTTATAATTT
15664 ATAATTTCTTTATAATTT
1 ATAATTTCTTTATAATTT
15682 AT
1 AT
15684 GGTGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATAATTTCTTTATAATTT
Found at i:16118 original size:11 final size:11
Alignment explanation
Indices: 16102--16143 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
16092 CTTAAAATCT
*
16102 TTCGATGCTCA
1 TTCGATACTCA
16113 TTCGATACTCA
1 TTCGATACTCA
16124 TTCGATACTCA
1 TTCGATACTCA
16135 TTCGATACT
1 TTCGATACT
16144 AATTTCATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (11 bp):
TTCGATACTCA
Found at i:20387 original size:21 final size:21
Alignment explanation
Indices: 20361--20400 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20351 TAGAACCCTA
*
20361 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
20382 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
20401 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:20409 original size:23 final size:21
Alignment explanation
Indices: 20383--20440 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
20373 TTCCCCTGTG
20383 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
20406 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
20426 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
20441 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:25698 original size:21 final size:20
Alignment explanation
Indices: 25651--25705 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
25641 GTTTGGAGCG
*
25651 TGGGGGGAATCGGTACCCCG
1 TGGGGGGAATCGGTACCCCC
**
25671 TATGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCCC
25691 TGGGGGGGAATCGGT
1 T-GGGGGGAATCGGT
25706 TCCCTCCGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCCC
Found at i:33924 original size:19 final size:20
Alignment explanation
Indices: 33886--33924 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33876 TTTAAATATT
*
33886 AAATATTCAAAATTTATTCA
1 AAATATTCAAAATATATTCA
*
33906 AAATTTTCAAAA-ATATTCA
1 AAATATTCAAAATATATTCA
33925 CTAATTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTCAAAATATATTCA
Found at i:41652 original size:224 final size:225
Alignment explanation
Indices: 41236--41653 Score: 493
Period size: 224 Copynumber: 1.9 Consensus size: 225
41226 CTTTTCGGTT
* * * * * * ** *
41236 AATATTTTTGAAGTCAATTTCAACTCCACGATGGAGGATATTGGCTTCAAAAACCTATTCAGAAT
1 AATATTCTCGAAGTCAATTTCAACCCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAAT
* * * *
41301 CAATTGCAGTCTAGCTTAACTCAACGATGATGAGCTAGTTTCCAGTCGAAGTTTTCAGGCTAGGT
66 CAATTGCAGTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAAGT
* * ** * ** *
41366 TTCAACTTCACGACCAAGTATACTTGACTAGGAAATGCATCCAAAATTGACTGCATTTTGGCTTG
131 TTCAACTTCACGACCAAGAATACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGCTTG
41431 ACTCAGCAACGAGTATCCATCTTCTAGTCA
196 ACTCAGCAACGAGTATCCATCTTCTAGTCA
* * * *
41461 AATATTCTCGAAGTCAATTTCAACCCCACAACGGAGGACATTTAATTCGAGAACCAATTCGGAAT
1 AATATTCTCGAAGTCAATTTCAACCCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAAT
* *
41526 CAATTGCAGTCTAG-TTAACT-AA-GCACTGAGGAGCTAGTTTCCAGTTGAAATTTTTAGGCCAA
66 CAATTGCAGTCTAGCTTAACTCAACG-A-TGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAA
** * * *
41588 GTTTCAACTTCACGACGGAGAACT-CTTGACCATGAAGCACATCAAAAAAGGACTGTAATTTGGC
129 GTTTCAACTTCACGACCAAGAA-TACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGC
41652 TT
193 TT
41654 AACCCAGTAG
Statistics
Matches: 158, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
222 1 0.01
223 3 0.02
224 87 0.55
225 67 0.42
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (225 bp):
AATATTCTCGAAGTCAATTTCAACCCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAAT
CAATTGCAGTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAAGT
TTCAACTTCACGACCAAGAATACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGCTTG
ACTCAGCAACGAGTATCCATCTTCTAGTCA
Found at i:41686 original size:224 final size:224
Alignment explanation
Indices: 41236--41716 Score: 488
Period size: 224 Copynumber: 2.1 Consensus size: 224
41226 CTTTTCGGTT
* * * * ** *
41236 AATATTTTTGAAGTCAATTTCAACTCCACGATGGAGGATATTGGCTTCAAAAACCTATTCAGAAT
1 AATA-TTTCGAAGTCAATTTCAACTCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAAT
* * * *
41301 CAATTGCAGTCTAGCTTAACTCAACGATGATGAGCTAGTTTCCAGTCGAAGTTTTCAGGCTAGGT
65 CAATTGCAGTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAAGT
* * ** * ** * *
41366 TTCAACTTCACGACCAAGTATACTTGACTAGGAAATGCATCCAAAATTGACTGCATTTTGGCTTG
130 TTCAACTTCACGACCAAGAATACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGCTTA
* * *
41431 ACTCAGCAACGAGTATCCATCTTCTAGTCA
195 ACCCAGCAACGAGTAACCATCTTCCAGTCA
* * * * *
41461 AATATTCTCGAAGTCAATTTCAACCCCACAACGGAGGACATTTAATTCGAGAACCAATTCGGAAT
1 AATATT-TCGAAGTCAATTTCAACTCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAAT
* *
41526 CAATTGCAGTCTAG-TTAACT-AA-GCACTGAGGAGCTAGTTTCCAGTTGAAATTTTTAGGCCAA
65 CAATTGCAGTCTAGCTTAACTCAACG-A-TGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAA
** * * *
41588 GTTTCAACTTCACGACGGAGAACT-CTTGACCATGAAGCACATCAAAAAAGGACTGTAATTTGGC
128 GTTTCAACTTCACGACCAAGAA-TACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGC
* * *
41652 TTAACCCAGTAGCGA-TAAACCATTTTCCAGTCA
192 TTAACCCAGCAACGAGT-AACCATCTTCCAGTCA
*
41685 AACCTA-TTCGAAGTTAGATTTCAACTCCACAA
1 AA--TATTTCGAAGTCA-ATTTCAACTCCACAA
41717 AGAAGGATAT
Statistics
Matches: 208, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
222 1 0.00
223 4 0.02
224 121 0.58
225 80 0.38
226 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (224 bp):
AATATTTCGAAGTCAATTTCAACTCCACAACGGAGGACATTGAATTCAAAAACCAATTCAGAATC
AATTGCAGTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCCAGTCGAAATTTTCAGGCCAAGTT
TCAACTTCACGACCAAGAATACTTGACCAGGAAACACATCAAAAAAGGACTGCAATTTGGCTTAA
CCCAGCAACGAGTAACCATCTTCCAGTCA
Found at i:46898 original size:64 final size:65
Alignment explanation
Indices: 46719--46878 Score: 261
Period size: 65 Copynumber: 2.5 Consensus size: 65
46709 GATTTAGTTG
*
46719 AACATCGAATACATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAAGGTTTTATGAA
1 AACATCGAATACATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAAGGTTTTATCAA
*
46784 AACATCGAATACATTTGATGTATCGATGCACATACCATGCATCGATGCACTC-AGGCTTTT-TCA
1 AACATCGAATACATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAAGG-TTTTATCA
46847 A
65 A
* *
46848 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATACATTTGATGCATCGATGCAC
46879 TCTTAGTGCA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
64 34 0.38
65 55 0.62
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATACATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAAGGTTTTATCAA
Found at i:52680 original size:24 final size:24
Alignment explanation
Indices: 52651--52700 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
52641 TGGTGGTTGA
*
52651 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
52675 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
52699 TT
1 TT
52701 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:54057 original size:24 final size:24
Alignment explanation
Indices: 54028--54077 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
54018 TGGTGGTTGA
*
54028 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
54052 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
54076 TT
1 TT
54078 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:54583 original size:17 final size:16
Alignment explanation
Indices: 54552--54585 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54542 CACGTGAGGA
54552 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
54568 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
54585 T
1 T
54586 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:64816 original size:17 final size:16
Alignment explanation
Indices: 64785--64818 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
64775 CACGTGAGGA
64785 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
64801 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
64818 T
1 T
64819 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Done.