Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000600.1 Hibiscus syriacus cultivar Beakdansim tig00001167_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: 85379
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3176 original size:60 final size:59
Alignment explanation
Indices: 3067--3178 Score: 143
Period size: 60 Copynumber: 1.9 Consensus size: 59
3057 TGGACCATAC
* ** * *
3067 CACACGTTGGGATAGTTTGGGGAGCATTTTGAAGACATATACAGGTCACAAACAGATGA
1 CACACGTTGGGACAACTTGGGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
* **
3126 CACACGTTGGGACAACTTGGTGGAGCATTTGGGAGACATATATTGCTCACAAA
1 CACACGTTGGGACAACTTGG-GGAGCATTTGGAAGACATATACAGCTCACAAA
3179 TAGCTCACAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 17 0.39
60 27 0.61
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (59 bp):
CACACGTTGGGACAACTTGGGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
Found at i:11245 original size:8 final size:8
Alignment explanation
Indices: 11232--11262 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
11222 CTTTGAATGT
11232 ACTTTGCA
1 ACTTTGCA
11240 ACTTTGCA
1 ACTTTGCA
11248 ACTTTGCA
1 ACTTTGCA
11256 ACTTTGC
1 ACTTTGC
11263 TTCACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (8 bp):
ACTTTGCA
Found at i:11356 original size:13 final size:12
Alignment explanation
Indices: 11333--11367 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
11323 TGTAGGAGTC
11333 TTTCTCTTTTCTT
1 TTTCTC-TTTCTT
11346 TTTCTTCTTTCTT
1 TTTC-TCTTTCTT
11359 TTTCTCTTT
1 TTTCTCTTT
11368 TGTTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 14 0.67
14 2 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:15260 original size:22 final size:22
Alignment explanation
Indices: 15204--15261 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
15194 TGCAAAAGTG
15204 AAAGAAAAA-AAAGCACTCAAA
1 AAAGAAAAAGAAAGCACTCAAA
** **
15225 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAAAGAAAGCACTCAAA
15248 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
15262 AAAGATTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 11 0.38
ACGTcount: A:0.66, C:0.09, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAGAAAAAGAAAGCACTCAAA
Found at i:26597 original size:23 final size:24
Alignment explanation
Indices: 26564--26617 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
26554 TTATCTTTTC
*
26564 TTTTTTTAA-TTTTCAAAATT-TG
1 TTTTTTTAATTTTTCAAAATTCTA
*
26586 TTTTTTTAAATTTTTCAGAATTCTA
1 TTTTTTT-AATTTTTCAAAATTCTA
26611 TTTTTTT
1 TTTTTTT
26618 CAAGATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 10 0.37
25 8 0.30
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTTTTAATTTTTCAAAATTCTA
Found at i:27910 original size:28 final size:28
Alignment explanation
Indices: 27878--28012 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
27868 TGAATTAACT
*
27878 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
27906 AAACAAATGATGAACATGCTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
27932 TGAC-TTTGAGTGTACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
27959 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
27987 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
28013 AACCCCACGA
Statistics
Matches: 79, Mismatches: 21, Indels: 14
0.69 0.18 0.12
Matches are distributed among these distances:
25 3 0.04
26 12 0.15
27 10 0.13
28 54 0.68
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:29467 original size:28 final size:28
Alignment explanation
Indices: 29436--29507 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
29426 AAGAAAAATC
29436 AGAAAACAAAGTGAAGCACTC-AAAAGAA
1 AGAAAACAAAGTGAAGCACTCAAAAAG-A
* * *
29464 AGAAAAAAAAAT-CAGCACTCAAAAAGA
1 AGAAAACAAAGTGAAGCACTCAAAAAGA
*
29491 AGAAAAGCAAAGAGAAG
1 AGAAAA-CAAAGTGAAG
29508 AAAATAAAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 14 0.41
28 18 0.53
29 2 0.06
ACGTcount: A:0.64, C:0.12, G:0.18, T:0.06
Consensus pattern (28 bp):
AGAAAACAAAGTGAAGCACTCAAAAAGA
Found at i:32166 original size:11 final size:13
Alignment explanation
Indices: 32134--32163 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
32124 TGGCCAAAGA
32134 TGAAAAGGTATGT
1 TGAAAAGGTATGT
32147 TGAAAAGGTATG-
1 TGAAAAGGTATGT
32159 TGAAA
1 TGAAA
32164 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:35581 original size:21 final size:21
Alignment explanation
Indices: 35557--35609 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
35547 CATCCTTATT
35557 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
35578 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
35599 TCATTTCATTT
1 TCATTTCATTT
35610 AATCTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATTTCATTTCTTATCTTTA
Found at i:35903 original size:18 final size:17
Alignment explanation
Indices: 35864--35919 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
35854 ATTGGAGTGC
*
35864 AAAAAGAAAAGAAAATAT
1 AAAAAG-AAAGAAAATAG
35882 AAAAAGAAAGAAAATCAG
1 AAAAAGAAAGAAAAT-AG
*
35900 AAAACA-AAAGAAAAGAG
1 AAAA-AGAAAGAAAATAG
35917 AAA
1 AAA
35920 GCAAACCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 14 0.41
18 19 0.56
19 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAGAAAATAG
Found at i:35918 original size:17 final size:17
Alignment explanation
Indices: 35865--35924 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
35855 TTGGAGTGCA
* * *
35865 AAAAGAAAAGAAAATAT
1 AAAACAAAAGAAAACAG
35882 AAAA-AGAAAGAAAATCAG
1 AAAACA-AAAGAAAA-CAG
*
35900 AAAACAAAAGAAAAGAG
1 AAAACAAAAGAAAACAG
*
35917 AAAGCAAA
1 AAAACAAA
35925 CCAAGGAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 1 0.03
17 21 0.58
18 13 0.36
19 1 0.03
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAACAAAAGAAAACAG
Found at i:36635 original size:19 final size:21
Alignment explanation
Indices: 36592--36643 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
36582 ATGGATCCTT
36592 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
36613 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
36632 TGAAGATACATG
1 TGAAAATACATG
36644 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:46406 original size:19 final size:21
Alignment explanation
Indices: 46356--46407 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
46346 GAAACCCCTT
46356 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
46377 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
46396 TGAAGATACATG
1 TGAAAATACATG
46408 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:47401 original size:19 final size:20
Alignment explanation
Indices: 47360--47410 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
47350 GAAACCCCTT
*
47360 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
47380 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
47399 TGAAGATACATG
1 TGAAAATACATG
47411 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:52928 original size:30 final size:31
Alignment explanation
Indices: 52893--52952 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52883 CTTAGCTTTA
**
52893 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
52923 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
52953 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:53519 original size:16 final size:17
Alignment explanation
Indices: 53486--53520 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53476 ACCTATAGTT
*
53486 CACATCTTTATAATATG
1 CACATCATTATAATATG
53503 CACATCATTAT-ATATG
1 CACATCATTATAATATG
53519 CA
1 CA
53521 TTATATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:54351 original size:19 final size:21
Alignment explanation
Indices: 54327--54378 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
54317 CGGCCAAGAG
*
54327 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
54346 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
54367 CATGTATTTTCA
1 CATGTATTTTCA
54379 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:54807 original size:15 final size:15
Alignment explanation
Indices: 54789--54819 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54779 CAGCCATCTC
*
54789 TTTCATTTCTTTTTA
1 TTTCATTTCCTTTTA
54804 TTTCATTTCCTTTTA
1 TTTCATTTCCTTTTA
54819 T
1 T
54820 ATATATTCAT
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:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCATTTCCTTTTA
Found at i:58477 original size:19 final size:21
Alignment explanation
Indices: 58453--58504 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
58443 CGGCCAAGAG
*
58453 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
58472 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
*
58493 CACGTATTTTCA
1 CATGTATTTTCA
58505 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:59649 original size:19 final size:20
Alignment explanation
Indices: 59625--59675 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
59615 CGGCCAAGAG
* *
59625 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
59644 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
59664 CATGTATTTTCA
1 CATGTATTTTCA
59676 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:60426 original size:12 final size:12
Alignment explanation
Indices: 60407--60443 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
60397 AGAAAAGACT
60407 AAAG-AAGAAAA
1 AAAGAAAGAAAA
60418 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
60431 AAAGAAAGAAAA
1 AAAGAAAGAAAA
60443 A
1 A
60444 GACAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:60435 original size:21 final size:22
Alignment explanation
Indices: 60394--60466 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 22
60384 GTGCAAAAAG
* *
60394 AAAAGAAAAGAC-TAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
60415 AAAAAAGAAAGA-AAAAA-AAG-
1 AAAAAA-AAAGACAAAAAGAAGA
*
60435 AAAGAAAAAGACAAAAAGAAGA
1 AAAAAAAAAGACAAAAAGAAGA
60457 ATAAAAAAAA
1 A-AAAAAAAA
60467 ATCAAAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.12
20 10 0.24
21 11 0.26
22 9 0.21
23 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGACAAAAAGAAGA
Found at i:60479 original size:42 final size:40
Alignment explanation
Indices: 60388--60480 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
60378 ACTGGAGTGC
*
60388 AAAAAGA-AAAGAAAAGACTAAAGAAGAAAAAAAGAAAGA
1 AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
*
60427 AAAAAAAGAAAGAAAAAGACAAAAAGAAGAATAAAAA-AAA-A
1 AAAAAGAGAAAG-AAAAGAC-AAAAGAAGAA-AAAAAGAAAGA
*
60468 TCAAAAGAGAAAG
1 -AAAAAGAGAAAG
60481 CAAGCCAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
39 6 0.13
40 4 0.09
41 8 0.18
42 22 0.49
43 5 0.11
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (40 bp):
AAAAAGAGAAAGAAAAGACAAAAGAAGAAAAAAAGAAAGA
Found at i:62976 original size:30 final size:31
Alignment explanation
Indices: 62940--62999 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
62930 CTTAGCTTTA
**
62940 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
62970 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
63000 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:63919 original size:19 final size:20
Alignment explanation
Indices: 63895--63945 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
63885 CGGCCAAGAG
* *
63895 CATGTATATTCATTAAAA-T
1 CATGTATTTTCATCAAAAGT
63914 CATGTATTTTCATCAAAAGT
1 CATGTATTTTCATCAAAAGT
63934 CATGTATTTTCA
1 CATGTATTTTCA
63946 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAGT
Found at i:68884 original size:33 final size:35
Alignment explanation
Indices: 68840--68920 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
68830 ATGGTGATGA
* * *
68840 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
68874 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
68909 AATGGTGATGGA
1 AATGGTGATGGA
68921 CAGATTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 9 0.22
34 1 0.03
35 18 0.45
36 12 0.30
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:72846 original size:33 final size:33
Alignment explanation
Indices: 72804--72872 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
72794 GTTGATGAAT
*
72804 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
72837 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
72870 GAA
1 GAA
72873 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Done.