Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009097.1 Hibiscus syriacus cultivar Beakdansim tig00112551_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: 56281
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1960 original size:2 final size:2
Alignment explanation
Indices: 1955--1992 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1945 TTTTCAATCA
1955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1993 CATGTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6795 original size:23 final size:24
Alignment explanation
Indices: 6754--6814 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
6744 ATAATAATTT
* * *
6754 TATTAATTTTTTTAAAAAATATTAG
1 TATTAATTTTTTTAAAAAGT-TAAA
6779 TATTAATTTTTTT-AAAAGTTAAA
1 TATTAATTTTTTTAAAAAGTTAAA
6802 TATTAATTTTTTT
1 TATTAATTTTTTT
6815 CAATATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 15 0.45
24 5 0.15
25 13 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TATTAATTTTTTTAAAAAGTTAAA
Found at i:7437 original size:27 final size:27
Alignment explanation
Indices: 7398--7449 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
7388 AAATATCCAA
* *
7398 TGTGATACTTGTACTTTGAGAAAATGT
1 TGTGATACATGTACTTTGACAAAATGT
* *
7425 TGTGGTACATGTATTTTGACAAAAT
1 TGTGATACATGTACTTTGACAAAAT
7450 ATCCAATTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
TGTGATACATGTACTTTGACAAAATGT
Found at i:7766 original size:28 final size:28
Alignment explanation
Indices: 7697--7766 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
7687 AGTAATGTAC
* *
7697 CATATTAATATTTTAAAAGTATGAGTAT
1 CATATTAATATTTTAAAAGTATAACTAT
* *
7725 CA-CTTACAT-TTTTTAAAGTATAACTAT
1 CATATTA-ATATTTTAAAAGTATAACTAT
7752 CATATTAGATATTTT
1 CATATTA-ATATTTT
7767 TCAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 20 0.61
28 9 0.27
29 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (28 bp):
CATATTAATATTTTAAAAGTATAACTAT
Found at i:7816 original size:2 final size:2
Alignment explanation
Indices: 7809--7861 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
7799 AAAATTTCAA
7809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7850 AT AT AT AT AT AT
1 AT AT AT AT AT AT
7862 GAATATTCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17340 original size:23 final size:23
Alignment explanation
Indices: 17307--17351 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17297 TTTAATATTA
17307 TTAAATAAATAA-AAATAGATAAT
1 TTAAATAAATAATAAATA-ATAAT
*
17330 TTAAATTAATAATAAATAATAA
1 TTAAATAAATAATAAATAATAA
17352 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAATAAATAATAAATAATAAT
Found at i:21131 original size:20 final size:20
Alignment explanation
Indices: 21095--21132 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21085 ATCCTATTCC
**
21095 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
21115 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
21133 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:24391 original size:59 final size:60
Alignment explanation
Indices: 24321--24460 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 60
24311 ACTCATATTT
* ** * *
24321 TAAATTGGTCCTTAAACTTTTAAATATTTTGA-TTCATCCCTAAACTATGA-TTGTAATTC
1 TAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCACTAAACTATGACCT-TAATTC
* * * * *
24380 TAAATTAGTCCTCAATCTTTTGAATATTTCAATTTCTTCACTAAACTATGACCTTCATTC
1 TAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCACTAAACTATGACCTTAATTC
* *
24440 TGAATTAGTCCCTAAACTTTT
1 TAAATTAGTCCTTAAACTTTT
24461 GAACATTCCC
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 26 0.40
60 38 0.58
61 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCACTAAACTATGACCTTAATTC
Found at i:44032 original size:29 final size:29
Alignment explanation
Indices: 43974--44032 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
43964 AACGAGTCTT
* *
43974 AAGGTTTCAATCCCCCTTTAATGAGCTGA
1 AAGGTTTCAATCCCCCTTCAACGAGCTGA
* *
44003 AAGGTTTCAATCTCCCTTCAACGAGTTGA
1 AAGGTTTCAATCCCCCTTCAACGAGCTGA
44032 A
1 A
44033 TTGTCAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (29 bp):
AAGGTTTCAATCCCCCTTCAACGAGCTGA
Found at i:45128 original size:212 final size:209
Alignment explanation
Indices: 44424--45256 Score: 1107
Period size: 212 Copynumber: 4.0 Consensus size: 209
44414 ATTTCATTTT
*
44424 AATAA-TT-TGTTCTTGATCAAGCAGGCATTCAAGCTCAATTTCATCTCTGGAAATTTAATTTCA
1 AATAATTTATGTTCTTGATCAAGCA-GCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTTCA
* * *
44487 ACTTAAAGCAATATAGTTTGTACCTCACTGTTGTATCCCCACTATCACGAAA-AAGCTTGTACAA
65 ACTT-AAGCCATATAGTTTGTAACTCACTGCTGTATCCCCACTATCACGAAATAAGCTTGTACAA
* * * * *
44551 TCTCCAGC-AAGAAAAATAACATTTGTCTCTCCAGAAAGAATAAGCTATCAACTCACAACCTAAG
129 TCTCCAGCAAAAAAAAATTACA-TAGTCTCTCTAGAAAGAAAAAGCTATCAACTCACAACCTAAG
44615 AGCAA-TTTAAGAAC-A
193 AGCAATTTTAAGAACAA
* * *
44630 AATAATTTATGTTCTCGCTCAATCAGCAGCATTCGAGCTCAATTTCATCTCTGGAAATTTTATTT
1 AATAATTTATGTTCTTGATC-A--AGCAGCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTT
* * *
44695 CAACATAAAGCCATATAGTTTGTAACTCACTGCTGTATTCCCACTATCATG-AATAAGCTTGTAC
63 CAAC-TTAAGCCATATAGTTTGTAACTCACTGCTGTATCCCCACTATCACGAAATAAGCTTGTAC
* * * *
44759 AGTCTCCAGGAAAAAAACATT---TA-TCTCTCTAGAAAGAATAAGCTATCAACTCACAACCTAA
127 AATCTCCAGCAAAAAAAAATTACATAGTCTCTCTAGAAAGAAAAAGCTATCAACTCACAACCTAA
* *
44820 GAGCAGTTTTATGAACAA
192 GAGCAATTTTAAGAACAA
* * * *
44838 AATAATTTATGTTC-TGATCAAGAAGCGTTCAAGATCAATTTCATCTCTGGAAAATTTATTTCAA
1 AATAATTTATGTTCTTGATCAAGCAGCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTTCAA
* * *
44902 CTTAAAGCCATATAGTTTGTAACTCATTGCTGTATCCCCACTATCATGAAATAAGCTTCTACAAT
66 CTT-AAGCCATATAGTTTGTAACTCACTGCTGTATCCCCACTATCACGAAATAAGCTTGTACAAT
44967 CTCCAGCAAGAAAAATAATTACATAGGTCTCTCTAGAAAGAAAAAGCTATCAACTCACAACCTAA
130 CTCCAGCAA-AAAAA-AATTACATA-GTCTCTCTAGAAAGAAAAAGCTATCAACTCACAACCTAA
45032 GAGCAATTTTAAGAACAA
192 GAGCAATTTTAAGAACAA
*
45050 AATAATTTATGTTCTTGCTCAAGCAGCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTTCAA
1 AATAATTTATGTTCTTGATCAAGCAGCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTTCAA
* * * *
45115 CTTAAGGCATATAGTTTGTGACTCACTGATGTAGCCCCACTATCACGAAATAAGCTTGTACAATC
66 CTTAAGCCATATAGTTTGTAACTCACTGCTGTATCCCCACTATCACGAAATAAGCTTGTACAATC
* * *
45180 TCCATCAAAAAAAAATACTACATTCGTCTCTCTGGAAAGAATAAA-CTATCAACTCACAACCTAA
131 TCCAGCAAAAAAAAAT--TACA-TAGTCTCTCTAGAAAGAA-AAAGCTATCAACTCACAACCTAA
*
45244 GAGCAAATTTAAG
192 GAGCAATTTTAAG
45257 CTAAATCTAT
Statistics
Matches: 551, Mismatches: 52, Indels: 42
0.85 0.08 0.07
Matches are distributed among these distances:
203 1 0.00
204 82 0.15
205 22 0.04
206 53 0.10
207 17 0.03
208 24 0.04
209 3 0.01
210 101 0.18
211 17 0.03
212 179 0.32
213 52 0.09
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (209 bp):
AATAATTTATGTTCTTGATCAAGCAGCATTCAAGCTCAATTTCATCTCTGGAAATTTTATTTCAA
CTTAAGCCATATAGTTTGTAACTCACTGCTGTATCCCCACTATCACGAAATAAGCTTGTACAATC
TCCAGCAAAAAAAAATTACATAGTCTCTCTAGAAAGAAAAAGCTATCAACTCACAACCTAAGAGC
AATTTTAAGAACAA
Found at i:46606 original size:12 final size:12
Alignment explanation
Indices: 46589--46614 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46579 AAGCACCTTC
46589 CCCTTTCAACAA
1 CCCTTTCAACAA
46601 CCCTTTCAACAA
1 CCCTTTCAACAA
46613 CC
1 CC
46615 AAGCGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (12 bp):
CCCTTTCAACAA
Found at i:47311 original size:25 final size:24
Alignment explanation
Indices: 47262--47312 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
47252 AAAATTTATA
* *
47262 AAATAAAATAATTATTATTGATAT
1 AAATAAAATAATCATTATAGATAT
47286 AAATAAAATAATCACTTA-AGAGTAT
1 AAATAAAATAATCA-TTATAGA-TAT
47311 AA
1 AA
47313 CAAACGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAAATAATCATTATAGATAT
Found at i:48122 original size:21 final size:21
Alignment explanation
Indices: 48096--48149 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
48086 TTGGGCCGGG
48096 TATATATATATTTAAATTAAA
1 TATATATATATTTAAATTAAA
*
48117 TATATATATATTTAATTTAAA
1 TATATATATATTTAAATTAAA
*
48138 TATATAAATATT
1 TATATATATATT
48150 ATATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATATTTAAATTAAA
Found at i:48166 original size:32 final size:29
Alignment explanation
Indices: 48113--48208 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 29
48103 ATATTTAAAT
48113 TAAATATATATATATTTAATTTAAATATA
1 TAAATATATATATATTTAATTTAAATATA
48142 TAAATAT-TATATATTT--TTTAAAT-T-
1 TAAATATATATATATTTAATTTAAATATA
* * *
48166 TAAAT-TAAATTTA-TTAATATTATATATA
1 TAAATATATATATATTTAAT-TTAAATATA
*
48194 TATATATATATATAT
1 TAAATATATATATAT
48209 ATATATAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
23 3 0.06
24 9 0.17
25 2 0.04
26 12 0.23
27 1 0.02
28 13 0.25
29 13 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAAATATATATATATTTAATTTAAATATA
Found at i:48193 original size:2 final size:2
Alignment explanation
Indices: 48182--48215 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
48172 AAATTTATTA
48182 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48216 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53280 original size:16 final size:17
Alignment explanation
Indices: 53249--53281 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53239 TGGAGATATT
*
53249 TTTATTATACTTTTTTA
1 TTTAATATACTTTTTTA
53266 TTTAATATA-TTTTTTA
1 TTTAATATACTTTTTTA
53282 AAGAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATATACTTTTTTA
Found at i:53612 original size:45 final size:47
Alignment explanation
Indices: 53541--53651 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 47
53531 GTAAATATTG
53541 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC-
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
* *
53588 TTGTTCAAAAAATAAAT-CTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
53634 TTTATTCGAAAAAATAAA
1 -TTATTC-AAAAAATAAA
53652 AATAAATGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 27 0.47
46 10 0.17
47 11 0.19
48 10 0.17
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA
Done.