Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007828.1 Hibiscus syriacus cultivar Beakdansim tig00110167_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: 51322
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3333 original size:60 final size:59
Alignment explanation
Indices: 3224--3335 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 59
3214 TGGACCATAC
* * * *
3224 CACACGTTGGGATAGTTGGTGGAGCATTTTGAAGACATATACAGGTCACAAACAGATGA
1 CACACGTTGGGAAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
* **
3283 CACACGTTGGGACAACTTGGTGGAGCATTTGGGAGACATATATTGCTCACAAA
1 CACACGTTGGGA-AACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAA
3336 TAGCTCACAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 12 0.27
60 33 0.73
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (59 bp):
CACACGTTGGGAAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
Found at i:11363 original size:8 final size:8
Alignment explanation
Indices: 11350--11377 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
11340 TTGAATGTAC
11350 TTGCAACT
1 TTGCAACT
11358 TTGCAACT
1 TTGCAACT
11366 TTGCAACT
1 TTGCAACT
11374 TTGC
1 TTGC
11378 TTCACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (8 bp):
TTGCAACT
Found at i:11461 original size:6 final size:6
Alignment explanation
Indices: 11446--11484 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
11436 GATGTAGGAG
*
11446 TCTTTC TCTTTT TCTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
11485 GTTGCTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:11467 original size:12 final size:12
Alignment explanation
Indices: 11446--11484 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
11436 GATGTAGGAG
*
11446 TCTTTCTCTTTT
1 TCTTTTTCTTTT
11458 TCTTTTTCTTCTT
1 TCTTTTTCTT-TT
11471 TCTTTTTCTCTTT
1 TCTTTTTCT-TTT
11484 T
1 T
11485 GTTGCTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 9 0.38
13 14 0.58
14 1 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:15350 original size:22 final size:22
Alignment explanation
Indices: 15294--15351 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
15284 TGCAAAAGTG
15294 AAAGAAAAA-AAAGCACTCAAA
1 AAAGAAAAAGAAAGCACTCAAA
** **
15315 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAAAGAAAGCACTCAAA
15338 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
15352 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:19092 original size:19 final size:21
Alignment explanation
Indices: 19068--19119 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
19058 CGGCCAAGAG
* *
19068 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
19087 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
19108 CATGTATTTTCA
1 CATGTATTTTCA
19120 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 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:28474 original size:23 final size:24
Alignment explanation
Indices: 28441--28494 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
28431 TTATCTTTTC
*
28441 TTTTTTTAA-TTTTCAAAATT-TG
1 TTTTTTTAATTTTTCAAAATTCTA
*
28463 TTTTTTTAAATTTTTCAGAATTCTA
1 TTTTTTT-AATTTTTCAAAATTCTA
28488 TTTTTTT
1 TTTTTTT
28495 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:29787 original size:28 final size:28
Alignment explanation
Indices: 29755--29889 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
29745 TGAATTAACT
*
29755 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
29783 AAACAAATGATGAACATGCTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
29809 TGAC-TGTGAGTGTACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
29836 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
29864 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
29890 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:0.29
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:31344 original size:28 final size:28
Alignment explanation
Indices: 31313--31384 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
31303 AAGAAAAATC
31313 AGAAAACAAAGTGAAGCACTC-AAAAGAA
1 AGAAAACAAAGTGAAGCACTCAAAAAG-A
* * *
31341 AGAAAAAAAAAT-CAGCACTCAAAAAGA
1 AGAAAACAAAGTGAAGCACTCAAAAAGA
*
31368 AGAAAAGCAAAGAGAAG
1 AGAAAA-CAAAGTGAAG
31385 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:34046 original size:11 final size:13
Alignment explanation
Indices: 34014--34043 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34004 TGGCCAAAGA
34014 TGAAAAGGTATGT
1 TGAAAAGGTATGT
34027 TGAAAAGGTATG-
1 TGAAAAGGTATGT
34039 TGAAA
1 TGAAA
34044 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:37440 original size:5 final size:5
Alignment explanation
Indices: 37432--37499 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 5
37422 TCCCATCCTT
* *
37432 ATTTC ATTTC ATTTC -TTATC TTTATC ATTTC ATTTC -TTATC TTTATC
1 ATTTC ATTTC ATTTC ATT-TC ATT-TC ATTTC ATTTC ATT-TC ATT-TC
37479 ATTTC ATTTATC ATTTC ATTT
1 ATTTC A-TT-TC ATTTC ATTT
37500 AATCTTTGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.07
5 30 0.55
6 18 0.33
7 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTC
Found at i:37459 original size:21 final size:21
Alignment explanation
Indices: 37435--37487 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
37425 CATCCTTATT
37435 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
37456 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
37477 TCATTTCATTT
1 TCATTTCATTT
37488 ATCATTTCAT
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:37462 original size:26 final size:26
Alignment explanation
Indices: 37433--37499 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
37423 CCCATCCTTA
*
37433 TTTCATTTCATTTC-TTATCTTTATCA
1 TTTCATTTCATTTCTTTATCATT-TCA
37459 TTTCATTTC-TTATCTTTATCATTTCA
1 TTTCATTTCATT-TCTTTATCATTTCA
37485 TTTATCATTTCATTT
1 -TT-TCATTTCATTT
37500 AATCTTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 2 0.06
26 14 0.40
27 9 0.26
28 8 0.23
29 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTCATTTCATTTCTTTATCATTTCA
Found at i:37490 original size:12 final size:12
Alignment explanation
Indices: 37452--37500 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
37442 ATTTCTTATC
37452 TTTATCATTTCA
1 TTTATCATTTCA
37464 -TT-TC-TTATC-
1 TTTATCATT-TCA
37473 TTTATCATTTCA
1 TTTATCATTTCA
37485 TTTATCATTTCA
1 TTTATCATTTCA
37497 TTTA
1 TTTA
37501 ATCTTTGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 6 0.19
12 18 0.56
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTATCATTTCA
Found at i:37790 original size:18 final size:17
Alignment explanation
Indices: 37751--37806 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
37741 ATTGGAGTGC
*
37751 AAAAAGAAAAGAAAATAT
1 AAAAAG-AAAGAAAATAG
37769 AAAAAGAAAGAAAATCAG
1 AAAAAGAAAGAAAAT-AG
*
37787 AAAACA-AAAGAAAAGAG
1 AAAA-AGAAAGAAAATAG
37804 AAA
1 AAA
37807 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:37805 original size:17 final size:17
Alignment explanation
Indices: 37752--37811 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
37742 TTGGAGTGCA
* * *
37752 AAAAGAAAAGAAAATAT
1 AAAACAAAAGAAAACAG
37769 AAAA-AGAAAGAAAATCAG
1 AAAACA-AAAGAAAA-CAG
*
37787 AAAACAAAAGAAAAGAG
1 AAAACAAAAGAAAACAG
*
37804 AAAGCAAA
1 AAAACAAA
37812 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:38522 original size:19 final size:21
Alignment explanation
Indices: 38479--38530 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
38469 ATGGATCCTT
38479 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
38500 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
38519 TGAAGATACATG
1 TGAAAATACATG
38531 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:48296 original size:19 final size:21
Alignment explanation
Indices: 48246--48297 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
48236 GAAACCCCTT
48246 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
48267 TTAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
48286 TGAAGATACATG
1 TGAAAATACATG
48298 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
Done.