Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005478.1 Hibiscus syriacus cultivar Beakdansim tig00012563_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: 63370
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3930 original size:22 final size:22
Alignment explanation
Indices: 3896--3972 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
3886 TTAGTGATCC
* *
3896 TTCGGGACATATCCAATGGTCA
1 TTCGGGACGTATCCAGTGGTCA
* *
3918 TTCGGAACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCA
*
3940 TTCGGGATGTATCCAGTGGTCA
1 TTCGGGACGTATCCAGTGGTCA
3962 TTCGGGACGTA
1 TTCGGGACGTA
3973 ATGGTCCTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCA
Found at i:3960 original size:44 final size:44
Alignment explanation
Indices: 3888--3972 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
3878 GAGGGTTTTT
3888 AGTGATCCTTCGGGACATATCCAATGGTCATTCGGAACGTATCC
1 AGTGATCCTTCGGGACATATCCAATGGTCATTCGGAACGTATCC
* ** * *
3932 AGTGGTCCTTCGGGATGTATCCAGTGGTCATTCGGGACGTA
1 AGTGATCCTTCGGGACATATCCAATGGTCATTCGGAACGTA
3973 ATGGTCCTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (44 bp):
AGTGATCCTTCGGGACATATCCAATGGTCATTCGGAACGTATCC
Found at i:7486 original size:40 final size:40
Alignment explanation
Indices: 7431--7552 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
7421 TGCAGGTTTA
*
7431 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
7471 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
7511 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
7551 TA
1 TA
7553 GCACTATGGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:7790 original size:47 final size:45
Alignment explanation
Indices: 7657--7775 Score: 157
Period size: 47 Copynumber: 2.6 Consensus size: 45
7647 GTAACCATGC
* * *
7657 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGTAAGTATTTTGAAAA
* **
7702 AAATAAGCTTACGAGCTTATGGAATTTAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAATGGTAAGTATTTTGAAAA
*
7749 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
7776 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 25 0.39
47 39 0.61
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGTAAGTATTTTGAAAA
Found at i:9372 original size:21 final size:21
Alignment explanation
Indices: 9348--9393 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
9338 GAGAAAAAGT
9348 AAAAGTTAAAAAATGAAAGAGA
1 AAAAGTT-AAAAATGAAAGAGA
* *
9370 AAAAATTAATAATGAAAGAGA
1 AAAAGTTAAAAATGAAAGAGA
9391 AAA
1 AAA
9394 GAAAAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAGTTAAAAATGAAAGAGA
Found at i:9706 original size:23 final size:23
Alignment explanation
Indices: 9664--9730 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
9654 ACTATGGTCC
9664 TTAC-AAATCAAATCAA-AAAATAT
1 TTACAAAAT-AAAT-AAGAAAATAT
* *
9687 TTACAAAATAAATAAGAAAAAAA
1 TTACAAAATAAATAAGAAAATAT
*
9710 TT--AAAATAAA-AGGAAAATAT
1 TTACAAAATAAATAAGAAAATAT
9730 T
1 T
9731 AAATATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 2 0.05
23 15 0.41
24 4 0.11
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (23 bp):
TTACAAAATAAATAAGAAAATAT
Found at i:33949 original size:13 final size:13
Alignment explanation
Indices: 33931--33959 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
33921 AATAAATTGA
33931 TTTTTTTTTTAAT
1 TTTTTTTTTTAAT
33944 TTTTTTTTTTAAT
1 TTTTTTTTTTAAT
33957 TTT
1 TTT
33960 ACCCGGTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTTAAT
Found at i:50102 original size:17 final size:18
Alignment explanation
Indices: 50082--50118 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
50072 ATTCATAATT
50082 AACACT-TATTACAT-ACC
1 AACACTCTA-TACATAACC
50099 AACACTCTATACATAACC
1 AACACTCTATACATAACC
50117 AA
1 AA
50119 GTACATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (18 bp):
AACACTCTATACATAACC
Found at i:50756 original size:12 final size:12
Alignment explanation
Indices: 50722--50756 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
50712 TATCATGTTC
**
50722 TCATATCACAGG
1 TCATATCACATA
50734 TCATATCACATA
1 TCATATCACATA
50746 TCATATCACAT
1 TCATATCACAT
50757 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:51352 original size:18 final size:19
Alignment explanation
Indices: 51317--51352 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
51307 TTTGAACCCG
*
51317 TAAATCCATTCATTTTTAT
1 TAAATCCATTCATGTTTAT
51336 TAAATCC-TTCATGTTTA
1 TAAATCCATTCATGTTTA
51353 ATCCCCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.50
Consensus pattern (19 bp):
TAAATCCATTCATGTTTAT
Found at i:53606 original size:2 final size:2
Alignment explanation
Indices: 53599--53686 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
53589 TAGCATATGC
53599 AT AT 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 AT AT
53641 AT AT 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 AT AT
53683 AT AT
1 AT AT
53687 TAAATAAATT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55297 original size:17 final size:17
Alignment explanation
Indices: 55275--55310 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55265 GTTAAATAAC
*
55275 TACCCTTAATCTATGAG
1 TACCCTTAATCGATGAG
55292 TACCCTTAATCGATGAG
1 TACCCTTAATCGATGAG
55309 TA
1 TA
55311 ATTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (17 bp):
TACCCTTAATCGATGAG
Found at i:57709 original size:21 final size:21
Alignment explanation
Indices: 57685--57725 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57675 TTTATAGACC
57685 TTTTC-TTCTTCTCTCTTTATT
1 TTTTCTTTCTT-TCTCTTTATT
*
57706 TTTTCTTTCTTTCTTTTTAT
1 TTTTCTTTCTTTCTCTTTAT
57726 AATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTCTTTCTCTTTATT
Found at i:57871 original size:18 final size:18
Alignment explanation
Indices: 57848--57902 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
57838 CGAAAAAGAA
57848 AATGTTGTCTCTATATAT
1 AATGTTGTCTCTATATAT
57866 AATGTTGTCTCTATATAT
1 AATGTTGTCTCTATATAT
57884 AATGTTGTCTCTATATAT
1 AATGTTGTCTCTATATAT
57902 A
1 A
57903 GAGGGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
AATGTTGTCTCTATATAT
Found at i:60331 original size:30 final size:30
Alignment explanation
Indices: 60297--60364 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
60287 TCGGGGACCA
* *
60297 TATTGCAAACGGACTAAATGTTGGGGACTG
1 TATTGCAAACGAACTAAATGTTAGGGACTG
* *
60327 TATTGCAAACGAACTAAATGTTAGGGATTT
1 TATTGCAAACGAACTAAATGTTAGGGACTG
60357 TATTGCAA
1 TATTGCAA
60365 GTTTTAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (30 bp):
TATTGCAAACGAACTAAATGTTAGGGACTG
Done.