Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004031.1 Hibiscus syriacus cultivar Beakdansim tig00008807_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: 62151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1478 original size:35 final size:35
Alignment explanation
Indices: 1417--1485 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1407 TAATTTAATA
*
1417 TAATTATATAATTTTAATATGTTTGAATAATTATTG
1 TAATTATATAATTTTAATATGATTGAAT-ATTATTG
*
1453 TAATT-TATATTTTTAAT-TGAATTGAATATTATT
1 TAATTATATAATTTTAATATG-ATTGAATATTATT
1486 TTTGTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.27
35 17 0.57
36 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (35 bp):
TAATTATATAATTTTAATATGATTGAATATTATTG
Found at i:2805 original size:2 final size:2
Alignment explanation
Indices: 2748--2797 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2738 TTATTTTTTA
2748 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
2790 AT AT AT AT
1 AT AT AT AT
2798 GCATATATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8061 original size:21 final size:22
Alignment explanation
Indices: 8020--8077 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
8010 ATATATCTAT
* *
8020 ATATTATTTTT-TTCAATTAAA
1 ATATTATTTTTATTAAATAAAA
*
8041 TTATTATTTTTATTAAATAAAA
1 ATATTATTTTTATTAAATAAAA
*
8063 ATAATATTTTTATTA
1 ATATTATTTTTATTA
8078 TTTCGGGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 10 0.32
22 21 0.68
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTATTTTTATTAAATAAAA
Found at i:9568 original size:2 final size:2
Alignment explanation
Indices: 9563--9587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9553 TTTATTTTTT
9563 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 T
9588 TTAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23512 original size:2 final size:2
Alignment explanation
Indices: 23505--23545 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
23495 GTTTTTCTTT
23505 TA TA TA TA 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 TA TA TA TA T
23546 TGTCATACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31782 original size:31 final size:31
Alignment explanation
Indices: 31744--31804 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
31734 TTATGTCCAT
31744 ATCTGAATCGGTGTACAAATGCCATAGTCTA
1 ATCTGAATCGGTGTACAAATGCCATAGTCTA
*
31775 ATCTGAATCGGTGTACATATGCCATAGTCT
1 ATCTGAATCGGTGTACAAATGCCATAGTCT
31805 TAACATGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (31 bp):
ATCTGAATCGGTGTACAAATGCCATAGTCTA
Found at i:33334 original size:3 final size:3
Alignment explanation
Indices: 33326--33351 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33316 ATTAATGATT
33326 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
33352 TTGGAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38254 original size:182 final size:186
Alignment explanation
Indices: 37910--38262 Score: 527
Period size: 190 Copynumber: 1.9 Consensus size: 186
37900 GTTGACAAAT
* * *
37910 CAACCGGCACCGGTATCCGACATATATACAGATTATAATCGAACATCTTCGAAAGAAAAATCAAA
1 CAACCGGAACCGGTATCCAACATATATACAGATTATAATCGAACATCTTAGAAAGAAAAATCAAA
** *
37975 GATTCCCATGTTAGATACCTAGCTATATCCATAACACAGTAGCACTCATCTCCCATTCTCCCTCG
66 GATTCCCATGTTAGATACAAAGCTATATCCATAACACAGTAG--C-CATCT-CCATTCTCCCTCA
*
38040 TGCAGCACATAAATCATAGTCCTGTATTATCATACAAACTAAGTTGACGGATCAACCGGG
127 TGCAGCACATAAATCATAGTCATGTATTATCATACAAACTAAGTTGACGGATCAACCGGG
*
38100 CAACCGGAACCTGTATCCAACATATATACAGATTATAATCGAACATCTTAGAAAGAAAAATCAAA
1 CAACCGGAACCGGTATCCAACATATATACAGATTATAATCGAACATCTTAGAAAGAAAAATCAAA
*
38165 GA-TCTCCATGTTAGATACAAAGCTATATCCATAACATAGTAG-C-TCT-CA-TCTCCCTCATGC
66 GATTC-CCATGTTAGATACAAAGCTATATCCATAACACAGTAGCCATCTCCATTCTCCCTCATGC
* *
38225 ATCACCTAAATCATAGTCATGTATTATCATACAAACTA
130 AGCACATAAATCATAGTCATGTATTATCATACAAACTA
38263 TAATTTTTTT
Statistics
Matches: 151, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
182 46 0.30
183 2 0.01
185 3 0.02
186 1 0.01
189 2 0.01
190 97 0.64
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (186 bp):
CAACCGGAACCGGTATCCAACATATATACAGATTATAATCGAACATCTTAGAAAGAAAAATCAAA
GATTCCCATGTTAGATACAAAGCTATATCCATAACACAGTAGCCATCTCCATTCTCCCTCATGCA
GCACATAAATCATAGTCATGTATTATCATACAAACTAAGTTGACGGATCAACCGGG
Found at i:40742 original size:24 final size:24
Alignment explanation
Indices: 40675--40742 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
40665 CATTCGGTAA
* *
40675 TATGTTCGTTCATTTATATTTATT
1 TATGTTCGTTCATTTATGTTCATT
*
40699 TATGTTCG-TCTATGTT-TGTTCGTT
1 TATGTTCGTTC-AT-TTATGTTCATT
*
40723 TATGTGCGTTCATTTATGTT
1 TATGTTCGTTCATTTATGTT
40743 TAGCCCAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 4 0.11
24 28 0.78
25 4 0.11
ACGTcount: A:0.15, C:0.10, G:0.16, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTTCATT
Found at i:40958 original size:13 final size:13
Alignment explanation
Indices: 40936--40996 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
40926 CGTTCGTTTA
*
40936 TGTTCATTTATTG
1 TGTTCGTTTATTG
40949 TGTTCGTTTA---
1 TGTTCGTTTATTG
*
40959 CGTTCGTTCGT-TTG
1 TGTTCGTT--TATTG
40973 TGTTCGTTTATTG
1 TGTTCGTTTATTG
40986 TGTTCGTTTAT
1 TGTTCGTTTAT
40997 GTTCATTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
10 7 0.18
12 2 0.05
13 23 0.59
14 7 0.18
ACGTcount: A:0.08, C:0.11, G:0.21, T:0.59
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:40977 original size:37 final size:37
Alignment explanation
Indices: 40926--41000 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
40916 TTTTCGTTTA
40926 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGTT
1 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGTT
* * *
40963 CGTTCGTTTGTGTTCGTTTATTGTGTTCGTTTATGTT
1 CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGTT
41000 C
1 C
41001 ATTTACATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.08, C:0.13, G:0.21, T:0.57
Consensus pattern (37 bp):
CGTTCGTTTATGTTCATTTATTGTGTTCGTTTACGTT
Found at i:40978 original size:24 final size:23
Alignment explanation
Indices: 40949--41027 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 23
40939 TCATTTATTG
*
40949 TGTTCGTTTACGTTCGTTCGTTTG
1 TGTTCGTTTAC-TTCGTTCGTTTA
*
40973 TGTTCGTTTA-TTGTGTTCGTTTA
1 TGTTCGTTTACTT-CGTTCGTTTA
* *
40996 TGTTCATTTACATCAGTTCGTTTA
1 TGTTCGTTTACTTC-GTTCGTTTA
41020 TGTTCGTT
1 TGTTCGTT
41028 CATTTGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.04
23 17 0.37
24 27 0.59
ACGTcount: A:0.10, C:0.14, G:0.20, T:0.56
Consensus pattern (23 bp):
TGTTCGTTTACTTCGTTCGTTTA
Found at i:41024 original size:10 final size:10
Alignment explanation
Indices: 40912--41027 Score: 61
Period size: 10 Copynumber: 10.2 Consensus size: 10
40902 ATTATTTTCA
*
40912 TTTATTTTCG
1 TTTATGTTCG
*
40922 TTTACGTTCG
1 TTTATGTTCG
*
40932 TTTATGTTCA
1 TTTATGTTCG
40942 TTTATTGTGTTCG
1 TTTA---TGTTCG
40955 TTTACGTTCGTTCG
1 TTTA---T-GTTCG
*
40969 TTTGTGTTCG
1 TTTATGTTCG
40979 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
40992 TTTATGTTCA
1 TTTATGTTCG
41002 TTTACATCAGTTCG
1 TTT--AT--GTTCG
41016 TTTATGTTCG
1 TTTATGTTCG
41026 TT
1 TT
41028 CATTTGTGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
10 43 0.52
11 1 0.01
12 4 0.05
13 20 0.24
14 15 0.18
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:41038 original size:24 final size:23
Alignment explanation
Indices: 40964--41044 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
40954 GTTTACGTTC
*
40964 GTTCGTTTGTGTTCGTTTATTGT
1 GTTCGTTTATGTTCGTTTATTGT
* * **
40987 GTTCGTTTATGTTCATTTACATCA
1 GTTCGTTTATGTTCGTTTA-TTGT
*
41011 GTTCGTTTATGTTCGTTCATTTGT
1 GTTCGTTTATGTTCGTTTA-TTGT
*
41035 GTTCGCTTAT
1 GTTCGTTTAT
41045 CATTTAAATG
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
23 17 0.38
24 28 0.62
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.56
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTTATTGT
Found at i:41645 original size:15 final size:16
Alignment explanation
Indices: 41625--41665 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41615 GTTTACTTCA
*
41625 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
41640 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
41656 GAATGATTCA
1 GAATGATTCA
41666 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:42859 original size:30 final size:31
Alignment explanation
Indices: 42818--42883 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
42808 AAGATTCACA
*
42818 TAAAATGGAGGACCACATTGAATTA-TTTTT
1 TAAAATAGAGGACCACATTGAATTATTTTTT
*
42848 TAAAATAGAGGACCACGTTGAATTATTTTTT
1 TAAAATAGAGGACCACATTGAATTATTTTTT
42879 TAAAA
1 TAAAA
42884 AATATTCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (31 bp):
TAAAATAGAGGACCACATTGAATTATTTTTT
Found at i:43550 original size:19 final size:20
Alignment explanation
Indices: 43528--43565 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43518 GTGTTGCAAA
43528 TTACA-ATTCGCGTTGCGAT
1 TTACATATTCGCGTTGCGAT
43547 TTACATATTCGCGTTGCGA
1 TTACATATTCGCGTTGCGA
43566 ATTTGTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTACATATTCGCGTTGCGAT
Found at i:48177 original size:24 final size:24
Alignment explanation
Indices: 48149--48206 Score: 62
Period size: 30 Copynumber: 2.2 Consensus size: 24
48139 GGAGATGATG
48149 GAGGTGGTTGTGTTGGTAGGGGTA
1 GAGGTGGTTGTGTTGGTAGGGGTA
48173 GAGGTGGCGGTGGTTGTGTTGGTAGGGGTA
1 GA------GGTGGTTGTGTTGGTAGGGGTA
48203 GAGG
1 GAGG
48207 AGGTGGAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
24 4 0.14
30 24 0.86
ACGTcount: A:0.12, C:0.02, G:0.57, T:0.29
Consensus pattern (24 bp):
GAGGTGGTTGTGTTGGTAGGGGTA
Found at i:48263 original size:21 final size:21
Alignment explanation
Indices: 48225--48264 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48215 GTGGTGGTGA
* *
48225 TGGAGATGATGGAGGTGGCGG
1 TGGAGATGATGAAAGTGGCGG
*
48246 TGGAGGTGATGAAAGTGGC
1 TGGAGATGATGAAAGTGGC
48265 AAAGGTGGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.53, T:0.20
Consensus pattern (21 bp):
TGGAGATGATGAAAGTGGCGG
Found at i:53712 original size:2 final size:2
Alignment explanation
Indices: 53707--53742 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
53697 AAGCCCCCCA
53707 TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53743 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:53747 original size:2 final size:2
Alignment explanation
Indices: 53742--53770 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53732 TCTCTCTCTC
53742 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53771 GTAAGTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:53763 original size:13 final size:13
Alignment explanation
Indices: 53745--53770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53735 CTCTCTCTAT
53745 ATATATATATATA
1 ATATATATATATA
53758 ATATATATATATA
1 ATATATATATATA
53771 GTAAGTTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:61637 original size:17 final size:16
Alignment explanation
Indices: 61589--61637 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
61579 TTTTTTTCAT
*
61589 TAAATTTTATATTATTAT
1 TAAA-TTTAT-TTATTAC
61607 TAAATTTA-TTATTAC
1 TAAATTTATTTATTAC
61622 TAAATATTATTTATTA
1 TAAAT-TTATTTATTA
61638 TTATTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 10 0.36
18 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TAAATTTATTTATTAC
Found at i:61651 original size:2 final size:2
Alignment explanation
Indices: 61644--61672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61634 ATTATTATTT
61644 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 T
61673 TACAAGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.