Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009114.1 Hibiscus syriacus cultivar Beakdansim tig00112597_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: 101017
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:20747 original size:32 final size:32
Alignment explanation
Indices: 20711--20798 Score: 167
Period size: 32 Copynumber: 2.8 Consensus size: 32
20701 GGAGGTCAAT
20711 AAATGTAATTGTATGAAATGGAAAGTATTAGC
1 AAATGTAATTGTATGAAATGGAAAGTATTAGC
20743 AAATGTAATTGTATGAAATGGAAAGTATTAGC
1 AAATGTAATTGTATGAAATGGAAAGTATTAGC
*
20775 AAATGTAATTGTATGAAACGGAAA
1 AAATGTAATTGTATGAAATGGAAA
20799 CCACGTGGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (32 bp):
AAATGTAATTGTATGAAATGGAAAGTATTAGC
Found at i:23601 original size:30 final size:30
Alignment explanation
Indices: 23565--23624 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
23555 GCTATGTTTC
*
23565 TCTTTGGATTTTCCATCGGCTTTTCATCGA
1 TCTTTGGATTTTCCATCAGCTTTTCATCGA
*
23595 TCTTTGGATTTTGCATCAGCTTTTCATCGA
1 TCTTTGGATTTTCCATCAGCTTTTCATCGA
23625 AGCATGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (30 bp):
TCTTTGGATTTTCCATCAGCTTTTCATCGA
Found at i:23960 original size:26 final size:26
Alignment explanation
Indices: 23906--23995 Score: 155
Period size: 26 Copynumber: 3.5 Consensus size: 26
23896 GAACAACGTA
23906 TATTGAAATTAACTATTAAAAAAAGTT
1 TATTGAAATTAACTATT-AAAAAAGTT
23933 TATTGAAATTAACTATTAAAAAAGTT
1 TATTGAAATTAACTATTAAAAAAGTT
*
23959 TATTGAAATTAACTATT-AAAAAGTA
1 TATTGAAATTAACTATTAAAAAAGTT
23984 TATTGAAATTAA
1 TATTGAAATTAA
23996 AGAGGCATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
25 19 0.31
26 26 0.42
27 17 0.27
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (26 bp):
TATTGAAATTAACTATTAAAAAAGTT
Found at i:27069 original size:21 final size:21
Alignment explanation
Indices: 27037--27084 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
27027 TAATTTTCAA
*
27037 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
27058 ATATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
27079 ACATTG
1 ACATTG
27085 CAATATTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:31727 original size:21 final size:21
Alignment explanation
Indices: 31697--31744 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
31687 TAATTTTCAA
*
31697 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
31718 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
31739 ACATTG
1 ACATTG
31745 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:50283 original size:3 final size:3
Alignment explanation
Indices: 50275--50315 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
50265 TACTGATTTT
50275 TTA TTA TTA TT- TTA TTA TTA TTA TTA TT- TATA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
50316 CTTATTACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50295 original size:17 final size:18
Alignment explanation
Indices: 50275--50315 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
50265 TACTGATTTT
50275 TTATTATTATTT-TATTA
1 TTATTATTATTTATATTA
50292 TTATTATTATTTATATTA
1 TTATTATTATTTATATTA
50310 -TATTAT
1 TTATTAT
50316 CTTATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTATTTATATTA
Found at i:54693 original size:420 final size:419
Alignment explanation
Indices: 53917--55160 Score: 2048
Period size: 420 Copynumber: 3.0 Consensus size: 419
53907 TATCATTGAG
* * * * * *
53917 TTTGTGATTGGCTTTTCTATTAAGTGATTTGAAACTGGTGACAGTTGTGGAAAACGTGATTGTGA
1 TTTGTGATTGGTTTTTCTATTAAGTGATTTGAAACAGGTGACGGTCGTGGCAAAGGTGATTGTGA
* ** * * *
53982 TGGCGGTAAAGCTCCAGGGGGAAGGGGCAATGGATACACATTTACTTGCCGATTGTTTTGAAGC-
66 TGGCTGTAAAGCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
** *
54046 -CACTCAGAATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTTCGGGCTAA--CAGGACT
131 GCAC-CAG-ATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTGGGGGCTAAGGAAGGACT
* * *
54108 AGAAAAAGCCGTTGTTGGAGCACTCCTGGGATGAACATTCAGCCTCAAGTTGTGGTAAACACTCC
194 AGATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCC
* * ** *
54173 CATAATTCTCAAGAGAGAAGCCCCTGCGATGACTTAATAAAGATTTGGCTGAATCTGCAACATCA
259 CATAATTCTCAGGAGAGAAGCCCCTGCGACGACTTAAGGAAGATTTGGCTGAATCTGCATCATCA
54238 TAAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTGGCAGGGGTTGAGAAAAAACTTGT
324 TAAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTGGCAGGGGTTGAGAAAAAACTTGT
*
54303 TACACCCCTACTCGTTGTGGCGACTATTGGC
389 TACACCCCTACTCGTTGTGGCGACTATTAGC
54334 TTTGTGATTGGTTTTTCTATTAAGTGATTTGAAACAGGTGACGGTCGTGGCAAAGGTGATTGTGA
1 TTTGTGATTGGTTTTTCTATTAAGTGATTTGAAACAGGTGACGGTCGTGGCAAAGGTGATTGTGA
54399 TGGCTGTAAAGCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
66 TGGCTGTAAAGCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
54464 GCACCAGATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTGGGGGCTAATGGAAGGACTA
131 GCACCAGATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTGGGGGCTAA-GGAAGGACTA
*
54529 GATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCCA
195 GATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCCC
*
54594 ATAATTCTCAGGAGAGAAGCCCCTGCGACGACTTAAGG-AGAATTTGGCTGAATCTGCGTCATCA
260 ATAATTCTCAGGAGAGAAGCCCCTGCGACGACTTAAGGAAG-ATTTGGCTGAATCTGCATCATCA
* *
54658 TAAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTAGCAGGGGTTGAGAAAACACTTGT
324 TAAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTGGCAGGGGTTGAGAAAAAACTTGT
* *
54723 TACACCCCTACTTGTTGTGTCGACTATTAGC
389 TACACCCCTACTCGTTGTGGCGACTATTAGC
* *
54754 TTTGTGATTGGTTTTTCTATTATGTGATTTGAAACAGGTGACGATCGTGGCAAAGGTGATTGTGA
1 TTTGTGATTGGTTTTTCTATTAAGTGATTTGAAACAGGTGACGGTCGTGGCAAAGGTGATTGTGA
* *
54819 CGGCTGTAAACCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
66 TGGCTGTAAAGCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
* *
54884 GCACCAGGTGGTCTGAATGAAAAGGACCTACTGTTTTTGATCTTTGGGGGCTAACGGAAGGACTA
131 GCACCAGATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTGGGGGCTAA-GGAAGGACTA
54949 GATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCCC
195 GATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCCC
* *
55014 ATAATTCTTAGGAGAGAAGCCCCTGTGACGACTTAAGGAAGATTTGGCTGAATCTGCATCATCAT
260 ATAATTCTCAGGAGAGAAGCCCCTGCGACGACTTAAGGAAGATTTGGCTGAATCTGCATCATCAT
* *
55079 AAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGACGACTGGCAGGGGTTGAGAAAAAACTTTTT
325 AAGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTGGCAGGGGTTGAGAAAAAACTTGTT
55144 ACACCCCTACTCGTTGT
390 ACACCCCTACTCGTTGT
55161 CGCAACACTT
Statistics
Matches: 774, Mismatches: 46, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
417 162 0.21
418 3 0.00
419 5 0.01
420 602 0.78
421 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (419 bp):
TTTGTGATTGGTTTTTCTATTAAGTGATTTGAAACAGGTGACGGTCGTGGCAAAGGTGATTGTGA
TGGCTGTAAAGCTCCAGGGGGAAGGGGCAATGGATATGCATTTTCCTGCAGATTGTTTTGAAGCA
GCACCAGATGGTCTGAATGAAAAGGACCTACTGTTCTTGATCTTTGGGGGCTAAGGAAGGACTAG
ATAAAGCCGTTGTTGGAGCACTCCTGGGATGCACATTCAGCCTCAAGTTGTGGTCAACACTCCCA
TAATTCTCAGGAGAGAAGCCCCTGCGACGACTTAAGGAAGATTTGGCTGAATCTGCATCATCATA
AGAGTAAAAATGATCTTGGTTGTTCGATCTTTGAGGACTGGCAGGGGTTGAGAAAAAACTTGTTA
CACCCCTACTCGTTGTGGCGACTATTAGC
Found at i:57118 original size:25 final size:22
Alignment explanation
Indices: 57085--57134 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
57075 AATAGAAATG
*
57085 TTTATCGTTAAATGATTAAGAGTTT
1 TTTAACGTTAAATG-TTAA-A-TTT
57110 TTTAACGTTAAATGTTAAATTT
1 TTTAACGTTAAATGTTAAATTT
57132 TTT
1 TTT
57135 CAATGACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 4 0.17
25 13 0.54
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (22 bp):
TTTAACGTTAAATGTTAAATTT
Found at i:70684 original size:2 final size:2
Alignment explanation
Indices: 70677--70707 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
70667 AAAGGAGAAT
70677 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 T
70708 TAATAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:75855 original size:20 final size:20
Alignment explanation
Indices: 75830--75869 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
75820 AACCTTGCAG
75830 GTTAAATCCTATAGAAACTT
1 GTTAAATCCTATAGAAACTT
* *
75850 GTTAAATGCTGTAGAAACTT
1 GTTAAATCCTATAGAAACTT
75870 TCATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
GTTAAATCCTATAGAAACTT
Found at i:78216 original size:59 final size:58
Alignment explanation
Indices: 78075--78226 Score: 146
Period size: 60 Copynumber: 2.6 Consensus size: 58
78065 TAAACTGTGC
* * *
78075 TCTTTTTTGCTTTAAGCCCCTAAATTATTTTTTGGTCAAAATAAGTCCTTAAACTATTA
1 TCTTTTTT-CTTTAATCCCCTAAACTATTTTTTGGTCAAAATAAGTCCCTAAACTATTA
* **** *
78134 TATGTGACCACTTTAAGT-ACCTAAACTATTTTTTGGTCAAAATAAG-CCCTAAACTAATTA
1 TCT-T-TTTTCTTTAA-TCCCCTAAACTATTTTTTGGTCAAAATAAGTCCCTAAACT-ATTA
*
78194 TCCTTTTTTCTTTAATCCCCTAAACTGTTTTTT
1 T-CTTTTTTCTTTAATCCCCTAAACTATTTTTT
78227 TTGTCACAAC
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
58 1 0.01
59 30 0.42
60 39 0.55
61 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (58 bp):
TCTTTTTTCTTTAATCCCCTAAACTATTTTTTGGTCAAAATAAGTCCCTAAACTATTA
Found at i:80758 original size:9 final size:9
Alignment explanation
Indices: 80744--80769 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
80734 AAATTCGGTT
80744 TTAATCGAA
1 TTAATCGAA
80753 TTAATCGAA
1 TTAATCGAA
80762 TTAATCGA
1 TTAATCGA
80770 CCGAACCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (9 bp):
TTAATCGAA
Found at i:81043 original size:17 final size:17
Alignment explanation
Indices: 81021--81059 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
81011 TGAATCAAAT
*
81021 TAATTAGATATTTTTTA
1 TAATTAGATATTATTTA
81038 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
81055 -AATTA
1 TAATTA
81060 ATTGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:91007 original size:57 final size:57
Alignment explanation
Indices: 90919--91029 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
90909 TTTTGCTTTC
* *
90919 GTCCTTGGCAATAGTTGTAAATGAGATGGTTAGTGACAGTTTCCGACCATCACGTGT
1 GTCCTTGGCAATAGTTATAAATGAGATGGTTAGTGACAGTTTCCAACCATCACGTGT
*
90976 GTCCTTGGCGATAGTTATAAATGAGATGGTTAGTGACAGTTTCCAACCATCACG
1 GTCCTTGGCAATAGTTATAAATGAGATGGTTAGTGACAGTTTCCAACCATCACG
91030 AGCGTTGAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (57 bp):
GTCCTTGGCAATAGTTATAAATGAGATGGTTAGTGACAGTTTCCAACCATCACGTGT
Done.