Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006409.1 Hibiscus syriacus cultivar Beakdansim tig00015454_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: 41099
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:765 original size:22 final size:23
Alignment explanation
Indices: 740--789 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
730 GGAATTGATA
740 CCCCCCTT-AAAGGGAACCGATT
1 CCCCCCTTGAAAGGGAACCGATT
* *
762 CCCCCTTTGAAGGGGAACCGATT
1 CCCCCCTTGAAAGGGAACCGATT
785 CCCCC
1 CCCCC
790 TGTAGGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (23 bp):
CCCCCCTTGAAAGGGAACCGATT
Found at i:777 original size:23 final size:22
Alignment explanation
Indices: 741--811 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 22
731 GAATTGATAC
*
741 CCCCCTT-AAAGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
762 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
* * *
785 CCCCC-TGTAGGGGAATCGATA
1 CCCCCTTGAAGGGGAACCGATT
806 CCCCCT
1 CCCCCT
812 AGGGGTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 23 0.53
22 2 0.05
23 18 0.42
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.20
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:816 original size:19 final size:20
Alignment explanation
Indices: 772--816 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
762 CCCCCTTTGA
*
772 AGGGGAACCGATTCCCCCTGT
1 AGGGGAACCGATACCCCC-GT
*
793 AGGGGAATCGATACCCCC-T
1 AGGGGAACCGATACCCCCGT
812 AGGGG
1 AGGGG
817 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
21 16 0.73
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCGT
Found at i:11403 original size:17 final size:18
Alignment explanation
Indices: 11367--11414 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
11357 AAGAAACTAC
11367 AATTATATTAAAATATTTA
1 AATTATA-TAAAATATTTA
11386 AATTATATAAAA-ATTTA
1 AATTATATAAAATATTTA
* *
11403 AAATATTTAAAA
1 AATTATATAAAA
11415 GCACGACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 5 0.19
19 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATATAAAATATTTA
Found at i:11410 original size:9 final size:9
Alignment explanation
Indices: 11374--11414 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
11364 TACAATTATA
11374 TTAAAATAT
1 TTAAAATAT
*
11383 TTAAATTAT
1 TTAAAATAT
*
11392 ATAAAA-AT
1 TTAAAATAT
11400 TTAAAATAT
1 TTAAAATAT
11409 TTAAAA
1 TTAAAA
11415 GCACGACCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAAATAT
Found at i:12226 original size:21 final size:21
Alignment explanation
Indices: 12200--12336 Score: 129
Period size: 21 Copynumber: 6.6 Consensus size: 21
12190 GACCAACAAA
*
12200 ATCGCAACGCGACTGTAAACT
1 ATCGCAACGCGAATGTAAACT
*
12221 ATCGCAACGCGAAATGGAAA--
1 ATCGCAACGCG-AATGTAAACT
* * *
12241 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATGTAAACT
*
12262 ATCGCAACGCGAAATGGAAA--
1 ATCGCAACGCG-AATGTAAACT
* *
12282 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCGAATGTAAACT
* * *
12303 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAATGTAAACT
12324 ATCGCAACGCGAA
1 ATCGCAACGCGAA
12337 ATGCAACACG
Statistics
Matches: 92, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.10
20 22 0.24
21 51 0.55
22 10 0.11
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAATGTAAACT
Found at i:12246 original size:20 final size:20
Alignment explanation
Indices: 12197--12293 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
12187 AATGACCAAC
* *
12197 AAAATCGCAACGCG-ACTGT
1 AAAATCGCAACGCGAAATGG
12216 AAACTATCGCAACGCGAAATGG
1 AAA--ATCGCAACGCGAAATGG
** **
12238 AAAATCGCAACGCGATTTTC
1 AAAATCGCAACGCGAAATGG
*
12258 AACTATCGCAACGCGAAATGG
1 AA-AATCGCAACGCGAAATGG
12279 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
12294 CTGTAGACTA
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
19 3 0.05
20 27 0.44
21 26 0.42
22 6 0.10
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAATGG
Found at i:12262 original size:41 final size:41
Alignment explanation
Indices: 12197--12481 Score: 267
Period size: 41 Copynumber: 7.0 Consensus size: 41
12187 AATGACCAAC
* * *
12197 AAAATCGCAACGCGACTGTAAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
12238 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
* * ** **
12279 AAAATCGCAACGCGACTGT-AGACTATCGCAACGCGATTTTC
1 AAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGG
* ** * * *
12320 AACTATCGCAACGCGAAATGCAAC-A-CG-AATTTGCGATGATGG
1 AA-AATCGCAACGCGATTTTCAACTATCGCAA--CGCGA-AATGG
* ****
12362 -AGATCGTGTTGCGA-TTTCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
* *
12401 AAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
* *
12442 AAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
12482 CAACGTGAAT
Statistics
Matches: 194, Mismatches: 39, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
39 11 0.06
40 25 0.13
41 140 0.72
42 17 0.09
43 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGG
Found at i:12395 original size:20 final size:20
Alignment explanation
Indices: 12372--12477 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
12362 AGATCGTGTT
*
12372 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
12392 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
12412 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
12433 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
12453 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
12474 GCGA
1 GCGA
12478 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:13877 original size:14 final size:14
Alignment explanation
Indices: 13859--13892 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
13849 CATACAGTGT
13859 ATAAAAATA-TACA
1 ATAAAAATATTACA
13872 ATTAAAAATATTACA
1 A-TAAAAATATTACA
13887 ATAAAA
1 ATAAAA
13893 TTTTTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAATATTACA
Found at i:15112 original size:25 final size:25
Alignment explanation
Indices: 15077--15133 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
15067 AAAATGACAT
15077 TTTTTTCAAAAATTACGAAAATAGCA
1 TTTTTTCAAAAATTAC-AAAATAGCA
*
15103 TTTTTT-AAAATTTACAAAATAGCA
1 TTTTTTCAAAAATTACAAAATAGCA
*
15127 TCTTTTC
1 TTTTTTC
15134 GAATTAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 14 0.50
25 8 0.29
26 6 0.21
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (25 bp):
TTTTTTCAAAAATTACAAAATAGCA
Found at i:19199 original size:14 final size:14
Alignment explanation
Indices: 19181--19213 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19171 CATACAGTGT
19181 ATAAAAATA-TACA
1 ATAAAAATATTACA
*
19194 ATTAAAATATTACA
1 ATAAAAATATTACA
19208 ATAAAA
1 ATAAAA
19214 TTTTTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAATATTACA
Found at i:35597 original size:2 final size:2
Alignment explanation
Indices: 35590--35664 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
35580 GAATTTTTAG
35590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35665 GAGAGCTAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.