Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001250.1 Hibiscus syriacus cultivar Beakdansim tig00002452_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: 46965
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:985 original size:22 final size:21
Alignment explanation
Indices: 943--982 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
933 GAGTTTATTT
*
943 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
964 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
983 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2847 original size:19 final size:19
Alignment explanation
Indices: 2823--2859 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2813 TGGAGCGTGG
2823 GGGGAATCGGTACCCTAAT
1 GGGGAATCGGTACCCTAAT
*
2842 GGGGAATCGGTTCCCTAA
1 GGGGAATCGGTACCCTAA
2860 GTGTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (19 bp):
GGGGAATCGGTACCCTAAT
Found at i:4921 original size:21 final size:21
Alignment explanation
Indices: 4886--4938 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
4876 ATTTAGCTTC
4886 CATTCAAGC-TTCTAACAACAT
1 CATTCAAGCATTCTAACAAC-T
*
4907 -ATTCAATCATTCTAACAACT
1 CATTCAAGCATTCTAACAACT
4927 CATTCAAGCATT
1 CATTCAAGCATT
4939 ACAGATCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (21 bp):
CATTCAAGCATTCTAACAACT
Found at i:8376 original size:21 final size:21
Alignment explanation
Indices: 8339--8391 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8329 ATTTAACTTC
*
8339 CATTCAATC-TCCTAACAACAT
1 CATTCAATCATTCTAACAAC-T
8360 -ATTCAATCATTCTAACAACT
1 CATTCAATCATTCTAACAACT
*
8380 CATTCAAGCATT
1 CATTCAATCATT
8392 ACACATCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (21 bp):
CATTCAATCATTCTAACAACT
Found at i:10039 original size:11 final size:11
Alignment explanation
Indices: 10022--10051 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10012 AAATATTTTT
10022 TAAGATAAATA
1 TAAGATAAATA
*
10033 TAGGATAAATA
1 TAAGATAAATA
10044 TAAGATAA
1 TAAGATAA
10052 TATCTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (11 bp):
TAAGATAAATA
Found at i:13371 original size:32 final size:34
Alignment explanation
Indices: 13335--13410 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 34
13325 TTTTTGTTCA
*
13335 GGTCGGGTC-GT-GTTTTTTAAGTGTGATATTCG
1 GGTCGGGTCAGTGGGTTTTTAAGTGTGATATTCG
13367 GGTCGGGTCGAGTCGGGGTTTTTAAGTGTGATATTCG
1 GGTCGGGTC-AGT--GGGTTTTTAAGTGTGATATTCG
13404 GGTCGGG
1 GGTCGGG
13411 CCAGGTCGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
32 9 0.24
34 2 0.05
37 27 0.71
ACGTcount: A:0.12, C:0.11, G:0.41, T:0.37
Consensus pattern (34 bp):
GGTCGGGTCAGTGGGTTTTTAAGTGTGATATTCG
Found at i:13419 original size:37 final size:37
Alignment explanation
Indices: 13348--13420 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
13338 CGGGTCGTGT
*
13348 TTTTTAAGTGTGATATTCGGGTCGGGTCGAGTCGGGG
1 TTTTTAAGTGTGATATTCGGGTCGGGCCGAGTCGGGG
13385 TTTTTAAGTGTGATATTCGGGTCGGGCC-AGGTCGGG
1 TTTTTAAGTGTGATATTCGGGTCGGGCCGA-GTCGGG
13421 TCGGGTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 1 0.03
37 33 0.97
ACGTcount: A:0.14, C:0.12, G:0.40, T:0.34
Consensus pattern (37 bp):
TTTTTAAGTGTGATATTCGGGTCGGGCCGAGTCGGGG
Found at i:13823 original size:8 final size:8
Alignment explanation
Indices: 13810--13834 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
13800 AAAATTTAAT
13810 ATTTTTTA
1 ATTTTTTA
13818 ATTTTTTA
1 ATTTTTTA
13826 ATTTTTTA
1 ATTTTTTA
13834 A
1 A
13835 AATATATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTTA
Found at i:13968 original size:17 final size:18
Alignment explanation
Indices: 13942--13988 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
13932 TATGGAATTG
*
13942 GATTCCAATTCC-TAACA
1 GATTCTAATTCCTTAACA
*
13959 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTAACA
*
13977 AATTCTAATTCC
1 GATTCTAATTCC
13989 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (18 bp):
GATTCTAATTCCTTAACA
Found at i:16719 original size:12 final size:12
Alignment explanation
Indices: 16704--16745 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
16694 TTTTCGGTAT
16704 ATATTATTTATA
1 ATATTATTTATA
16716 ATA-TATTTATA
1 ATATTATTTATA
16727 AT-TTCATTTATA
1 ATATT-ATTTATA
*
16739 ATTTTAT
1 ATATTAT
16746 AATTTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.41
12 14 0.52
13 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTATTTATA
Found at i:20534 original size:21 final size:21
Alignment explanation
Indices: 20510--20564 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20500 GTTATATGAA
*
20510 GTCCTTCGGGATATATACGAG
1 GTCCTTCGGGATATACACGAG
* *
20531 GTCCTTCGGGACATACATGAG
1 GTCCTTCGGGATATACACGAG
**
20552 GTGATTCGGGATA
1 GTCCTTCGGGATA
20565 AATTTTATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (21 bp):
GTCCTTCGGGATATACACGAG
Found at i:22203 original size:57 final size:56
Alignment explanation
Indices: 22086--22193 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 56
22076 GTGCATCGAA
* * *
22086 GCATCAAGTGCATTTGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
1 GCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGT
* * *
22142 GCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 GCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
22194 TATGTGCATC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 17 0.39
57 24 0.55
58 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (56 bp):
GCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGGT
Found at i:28711 original size:21 final size:21
Alignment explanation
Indices: 28619--28723 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
28609 AGTTGAGGGT
* *
28619 TATATGAAGTCCTTCGGAACA
1 TATATGAGGTCCTTCGGGACA
* **
28640 TATACGAGGTCCTTCGATACA
1 TATATGAGGTCCTTCGGGACA
* * *
28661 TATATGAGGTCTTTTGGGTCA
1 TATATGAGGTCCTTCGGGACA
*
28682 TATACGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
* * *
28703 TACATGAGGCCCTTCAGGACA
1 TATATGAGGTCCTTCGGGACA
28724 AATTTTATAT
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
TATATGAGGTCCTTCGGGACA
Found at i:29671 original size:12 final size:12
Alignment explanation
Indices: 29654--29678 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29644 TAATAAGCCA
29654 ATATTTAGAAGT
1 ATATTTAGAAGT
29666 ATATTTAGAAGT
1 ATATTTAGAAGT
29678 A
1 A
29679 CCAGGTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATATTTAGAAGT
Found at i:30775 original size:77 final size:77
Alignment explanation
Indices: 30687--30847 Score: 223
Period size: 77 Copynumber: 2.1 Consensus size: 77
30677 AAATAAAACC
* ** * *
30687 ACAACAACATGACCTAGTTGCTTTTTCAATTAACATAAAATGACAAAAACCACAATAATAGTTCA
1 ACAATAACATGACCTAAATGCATGTTCAATTAACATAAAATGACAAAAACCACAATAATAGTTCA
30752 ATATATGCTTAA
66 ATATATGCTTAA
* * * *
30764 ACAATAACATGACCTAAATGGATGTTCAATTAACATAACATGACAGAAACCACAATTATAGTTCA
1 ACAATAACATGACCTAAATGCATGTTCAATTAACATAAAATGACAAAAACCACAATAATAGTTCA
* *
30829 ATATATTCTTGA
66 ATATATGCTTAA
30841 ACAATAA
1 ACAATAA
30848 ATAACTTGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (77 bp):
ACAATAACATGACCTAAATGCATGTTCAATTAACATAAAATGACAAAAACCACAATAATAGTTCA
ATATATGCTTAA
Found at i:33574 original size:18 final size:19
Alignment explanation
Indices: 33551--33603 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
33541 GAATCTAAAT
*
33551 TAAGTATCGATACTTA-GG
1 TAAGTATCGATACTCAGGG
*
33569 TAAGTATCGATACACAGGG
1 TAAGTATCGATACTCAGGG
33588 TAGAGTATCGATACTC
1 TA-AGTATCGATACTC
33604 CCCATAGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (19 bp):
TAAGTATCGATACTCAGGG
Found at i:33835 original size:34 final size:34
Alignment explanation
Indices: 33792--33856 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
33782 AAGTATTCAA
33792 TACAAGTGAAAACAAATAAGTTAACTGGATTTAT
1 TACAAGTGAAAACAAATAAGTTAACTGGATTTAT
* *
33826 TACAAGTGAAAATAAATAAGTTAACTTGATT
1 TACAAGTGAAAACAAATAAGTTAACTGGATT
33857 CTCACTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.31
Consensus pattern (34 bp):
TACAAGTGAAAACAAATAAGTTAACTGGATTTAT
Found at i:34830 original size:15 final size:15
Alignment explanation
Indices: 34810--34927 Score: 87
Period size: 15 Copynumber: 7.9 Consensus size: 15
34800 GATCTTCCAC
34810 CACTACCCATTTCAA
1 CACTACCCATTTCAA
*
34825 CACTACCCATTTCAC
1 CACTACCCATTTCAA
* *
34840 CACTGCCCATTTCCTTA
1 CACTACCCATTT-C-AA
**
34857 TTCT-CCC-TTTCAA
1 CACTACCCATTTCAA
* *
34870 CACTACCCATTCCAG
1 CACTACCCATTTCAA
* *
34885 CACTATCCATTTCAC
1 CACTACCCATTTCAA
* *
34900 CACTACCTATTTCAG
1 CACTACCCATTTCAA
* *
34915 CATTGCCCATTTC
1 CACTACCCATTTC
34928 TGTATCATCC
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
13 3 0.04
14 4 0.05
15 66 0.84
16 4 0.05
17 2 0.03
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.32
Consensus pattern (15 bp):
CACTACCCATTTCAA
Found at i:34843 original size:30 final size:30
Alignment explanation
Indices: 34807--34927 Score: 102
Period size: 30 Copynumber: 4.0 Consensus size: 30
34797 TTGGATCTTC
34807 CACCACTACCCATTTCAACACTACCCATTT
1 CACCACTACCCATTTCAACACTACCCATTT
* * **
34837 CACCACTGCCCATTTCCTTATTCT-CCC-TTT
1 CACCACTACCCATTT-C-AACACTACCCATTT
* * * *
34867 CAACACTACCCATTCCAGCACTATCCATTT
1 CACCACTACCCATTTCAACACTACCCATTT
* * * *
34897 CACCACTACCTATTTCAGCATTGCCCATTT
1 CACCACTACCCATTTCAACACTACCCATTT
34927 C
1 C
34928 TGTATCATCC
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
28 2 0.03
29 3 0.04
30 57 0.83
31 4 0.06
32 3 0.04
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.31
Consensus pattern (30 bp):
CACCACTACCCATTTCAACACTACCCATTT
Found at i:35927 original size:18 final size:18
Alignment explanation
Indices: 35893--35927 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35883 AGAAAACCAA
* *
35893 CAACATATTTATGAAAAT
1 CAACATATATATCAAAAT
35911 CAACATATATATCAAAA
1 CAACATATATATCAAAA
35928 ACCCTAAGCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (18 bp):
CAACATATATATCAAAAT
Found at i:38060 original size:22 final size:22
Alignment explanation
Indices: 37972--38059 Score: 122
Period size: 22 Copynumber: 4.0 Consensus size: 22
37962 TCGAGGGTTA
* *
37972 CATAGGTCCTTCGGGACATATA
1 CATAGGTCCTTCGGGACAAATT
*
37994 CAGAGGTCCTTCGGGACAAATT
1 CATAGGTCCTTCGGGACAAATT
*
38016 CATAGGTCCTTTGGGACAAATT
1 CATAGGTCCTTCGGGACAAATT
* *
38038 TATAGGTCCTTCGAGACAAATT
1 CATAGGTCCTTCGGGACAAATT
38060 TTAAATGCCC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACAAATT
Found at i:39143 original size:29 final size:29
Alignment explanation
Indices: 39054--39258 Score: 172
Period size: 29 Copynumber: 7.2 Consensus size: 29
39044 CCGTTGATCG
*
39054 GGTGATATTGTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
**
39083 GGCAATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
*
39112 GGTGATATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
39141 GGTGCTATTTTCA-TAATTTTTTTTAAAA-
1 GGTGATATTTT-AGTAATTATTTTGAAAAT
* * * * *
39169 AGTGATAATTTCGTAA--A-TTTAAAAAA
1 GGTGATATTTTAGTAATTATTTTGAAAAT
** * *
39195 AATGATA-TTTAGTAATAATTTTGAAAAG
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * *
39223 GGTGATATTTTTGTAAATT-TTTTAAAAAG
1 GGTGATATTTTAGT-AATTATTTTGAAAAT
39252 GGTGATA
1 GGTGATA
39259 AATGTGTAAA
Statistics
Matches: 143, Mismatches: 25, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
25 14 0.10
26 6 0.04
27 1 0.01
28 23 0.16
29 96 0.67
30 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTTTGAAAAT
Found at i:39266 original size:29 final size:29
Alignment explanation
Indices: 39213--39268 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
39203 TTAGTAATAA
* ** *
39213 TTTTGAAAAGGGTGATATTTTTGTAAATT
1 TTTTAAAAAGGGTGATAAATGTGTAAATT
39242 TTTTAAAAAGGGTGATAAATGTGTAAA
1 TTTTAAAAAGGGTGATAAATGTGTAAA
39269 ATGGTTGATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (29 bp):
TTTTAAAAAGGGTGATAAATGTGTAAATT
Found at i:46566 original size:28 final size:28
Alignment explanation
Indices: 46373--46573 Score: 187
Period size: 29 Copynumber: 7.2 Consensus size: 28
46363 CGTTGACCGT
46373 TGATATTTTAGTAATTATTTTGAAAATGG
1 TGATATTTTAGTAATTATTTT-AAAATGG
46402 TGATATTTTAGTAATTATTTTGAAAATGG
1 TGATATTTTAGTAATTATTTT-AAAATGG
* * *
46431 TGATATTTTGGTAATTATTTTTAAATTG
1 TGATATTTTAGTAATTATTTTAAAATGG
** * *
46459 TGATATTTTCTTAATTTTTTTAAAA-AG
1 TGATATTTTAGTAATTATTTTAAAATGG
* * * ***
46486 TGATAATTTCGTAA--ATTTAAAAAAAA
1 TGATATTTTAGTAATTATTTTAAAATGG
*
46512 TGATATTTTAGTAATTATTTTGAAAAGGG
1 TGATATTTTAGTAATTATTTT-AAAATGG
*
46541 TGATATTTT-GTAAATTCTTTTAAAA-GG
1 TGATATTTTAGT-AATTATTTTAAAATGG
46568 TTGATA
1 -TGATA
46574 AATGTGTAAA
Statistics
Matches: 146, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.05
26 13 0.09
27 15 0.10
28 41 0.28
29 70 0.48
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.48
Consensus pattern (28 bp):
TGATATTTTAGTAATTATTTTAAAATGG
Done.