Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004885.1 Hibiscus syriacus cultivar Beakdansim tig00011003_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: 45118
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:178 original size:14 final size:14
Alignment explanation
Indices: 158--192 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
148 AGTGTGAAAT
*
158 ATGTTTGTTCTTTA
1 ATGTTTGTTCTCTA
*
172 CTGTTTGTTCTCTA
1 ATGTTTGTTCTCTA
186 ATGTTTG
1 ATGTTTG
193 GAATGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (14 bp):
ATGTTTGTTCTCTA
Found at i:1523 original size:18 final size:19
Alignment explanation
Indices: 1478--1524 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1468 ACCCCTTTGA
1478 AAATACATGATTTTTAAATG
1 AAATACATGATTTTT-AATG
1498 AAATACATGA-TTTT-ATG
1 AAATACATGATTTTTAATG
1515 AAGATACATG
1 AA-ATACATG
1525 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 7 0.27
19 4 0.15
20 10 0.38
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (19 bp):
AAATACATGATTTTTAATG
Found at i:2464 original size:28 final size:29
Alignment explanation
Indices: 2427--2484 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
2417 ACATGCTGCC
**
2427 ATGATATCTAAATGATATGCAAACATAAT
1 ATGATATCTAAAACATATGCAAACATAAT
* *
2456 ATGA-ATCTAAAACATATGTAAGCATAAT
1 ATGATATCTAAAACATATGCAAACATAAT
2484 A
1 A
2485 AAGCTAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (29 bp):
ATGATATCTAAAACATATGCAAACATAAT
Found at i:2874 original size:39 final size:39
Alignment explanation
Indices: 2799--2874 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
2789 ATGTTAGTTA
* **
2799 TCATATCATTCATACCATCCTATGTTTAGTTCATCATGT
1 TCATATCATTCATACCATCCTATGATTACATCATCATGT
* *
2838 TCATATCATTCATATCTATGCTATGATTACAT-ATCAT
1 TCATATCATTCATA-CCATCCTATGATTACATCATCAT
2875 TTCTTGGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 19 0.61
40 12 0.39
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (39 bp):
TCATATCATTCATACCATCCTATGATTACATCATCATGT
Found at i:9243 original size:15 final size:15
Alignment explanation
Indices: 9208--9236 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9198 GTGCTTCAAC
9208 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
9222 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
9237 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:24493 original size:10 final size:10
Alignment explanation
Indices: 24480--24541 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 10
24470 CTTTTTGAAA
24480 TTCTTTTTTT
1 TTCTTTTTTT
24490 TTCTTTTTTT
1 TTCTTTTTTT
24500 CTT-TTTTGATTT
1 -TTCTTTT--TTT
24512 TTCTCTTCTTTT
1 TTCT-TT-TTTT
* *
24524 GTCTTTTTCT
1 TTCTTTTTTT
24534 TTCTTTTT
1 TTCTTTTT
24542 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 24 0.56
11 6 0.14
12 10 0.23
13 2 0.05
14 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.81
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:24498 original size:8 final size:8
Alignment explanation
Indices: 24485--24541 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
24475 TGAAATTCTT
24485 TTTTTTTC
1 TTTTTTTC
24493 TTTTTTTC
1 TTTTTTTC
**
24501 TTTTTTGA
1 TTTTTTTC
*
24509 TTTTTCTC
1 TTTTTTTC
24517 TTCTTTTGTC
1 TT-TTTT-TC
24527 TTTTTCTTTC
1 -TTTT-TTTC
24537 TTTTT
1 TTTTT
24542 GTACTCCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 22 0.56
9 7 0.18
10 6 0.15
11 4 0.10
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:24523 original size:18 final size:18
Alignment explanation
Indices: 24493--24544 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
24483 TTTTTTTTTC
24493 TTTT-TTTCTTTTT-TGAT
1 TTTTCTTTCTTTTTGT-AT
*
24510 TTTTCTCTTC-TTTTGTCT
1 TTTTCT-TTCTTTTTGTAT
24528 TTTTCTTTCTTTTTGTA
1 TTTTCTTTCTTTTTGTA
24545 CTCCAATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 7 0.24
18 18 0.62
19 4 0.14
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTCTTTCTTTTTGTAT
Found at i:27307 original size:19 final size:19
Alignment explanation
Indices: 27283--27332 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
27273 CGGCCAAGAG
* **
27283 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATCAAAAT
27302 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
27321 CATGTATTTTCA
1 CATGTATTTTCA
27333 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:28155 original size:17 final size:16
Alignment explanation
Indices: 28124--28158 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28114 AACAAAAAGC
28124 AACAAAAAAAAAAGAA
1 AACAAAAAAAAAAGAA
*
28140 AACAAAAGAGAAAAGAA
1 AACAAAA-AAAAAAGAA
28157 AA
1 AA
28159 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAAGAA
Found at i:35072 original size:19 final size:18
Alignment explanation
Indices: 35048--35092 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
35038 TTTTTTCTTT
35048 TCTTCTTTTCGGATTTTTC
1 TCTTCTTTT-GGATTTTTC
**
35067 TCTTCTTTTGTCTTTTTC
1 TCTTCTTTTGGATTTTTC
35085 T-TTCTTTT
1 TCTTCTTTT
35093 TGCAGTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (18 bp):
TCTTCTTTTGGATTTTTC
Found at i:35093 original size:18 final size:18
Alignment explanation
Indices: 35032--35094 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
35022 CTTTTTGAAA
35032 TTCTTT-TTTTT-TC-TT
1 TTCTTTCTTTTTGTCTTT
* **
35047 TTC-TTCTTTTCGGATTT
1 TTCTTTCTTTTTGTCTTT
35064 TTCTCTTC-TTTTGTCTTT
1 TTCT-TTCTTTTTGTCTTT
35082 TTCTTTCTTTTTG
1 TTCTTTCTTTTTG
35095 CAGTCCAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
14 2 0.06
15 7 0.19
17 8 0.22
18 16 0.44
19 3 0.08
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (18 bp):
TTCTTTCTTTTTGTCTTT
Found at i:35397 original size:19 final size:20
Alignment explanation
Indices: 35360--35399 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
35350 GAATAATAAT
35360 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
35380 ATAAG-AAT-AAAATGAAATA
1 ATAAGTAATGAAAAT-AAATA
35399 A
1 A
35400 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:41050 original size:656 final size:656
Alignment explanation
Indices: 39797--41107 Score: 2478
Period size: 656 Copynumber: 2.0 Consensus size: 656
39787 ACACGCTTTG
* *
39797 ATGGAAGAGAGTAGAGAGGCTTATTGTGTCTCGAACTAGGATTGACAAGTACTGATGTCCTTGAA
1 ATGGAAGAGAGTAGAGAGGCTTATTGTGTCCCGAACTAGGATTAACAAGTACTGATGTCCTTGAA
39862 TTTATAAGTTTGGGCTACAAAATAAGATAAGAAAAGAATGACTAATAATGGAATTAATAAAGGGA
66 TTTATAAGTTTGGGCTACAAAATAAGATAAGAAAAGAATGACTAATAATGGAATTAATAAAGGGA
39927 ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATGAAATAAAGAAAGGATAGAGGTGG
131 ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATGAAATAAAGAAAGGATAGAGGTGG
*
39992 CCGCGAAATTGATGGAATTGATGGATGATGTTGATGATGAAAGGCAATGGTGGTGATGTTGTATC
196 CCGCGAAATTGATGGAATTGATGGATGATGTTGATGATGAAAGGAAATGGTGGTGATGTTGTATC
* * *
40057 TCAAACACGCCAAAGAGGAAACTATGCTATTAAGCACAATCCCGGTCTTCACAAACTTGCTTGAG
261 TCAAACACGCCAAAGAGGAAACTATACTATGAAGAACAATCCCGGTCTTCACAAACTTGCTTGAG
*
40122 GGGTGGTGATAGTGTCTTTAACCCACTAGATATTAATCTAAGAATTTTGGAATCAAAATGGAAGG
326 GGGTGGTGATAGTGTCTTCAACCCACTAGATATTAATCTAAGAATTTTGGAATCAAAATGGAAGG
40187 AATGACGCCACAAGTATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGA
391 AATGACGCCACAAGTATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGA
40252 GAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATCCTTACAAATGAAGGCAAGACACT
456 GAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATCCTTACAAATGAAGGCAAGACACT
*
40317 CTATTTATAGAAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTTT
521 CTATTTATAGAAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCT
* *
40382 TTAGGAAAATACATAATGCTTGGGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCGGCTAA
586 TTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAA
40447 CTCTTC
651 CTCTTC
*
40453 ATGGAAGAGAGTAGATAGGCTTATTGTGTCCCGAACTAGGATTAACAAGTACTGATGTCCTTGAA
1 ATGGAAGAGAGTAGAGAGGCTTATTGTGTCCCGAACTAGGATTAACAAGTACTGATGTCCTTGAA
*
40518 TTTATAAGTTTGGGCTACAAAATAAGATAAGAAAAGAATGATTAATAATGGAATTAATAAAGGGA
66 TTTATAAGTTTGGGCTACAAAATAAGATAAGAAAAGAATGACTAATAATGGAATTAATAAAGGGA
40583 ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATGAAATAAAGAAAGGATAGAGGTGG
131 ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATGAAATAAAGAAAGGATAGAGGTGG
* *
40648 CCTCGGAATTGATGGAATTGATGGATGATGTTGATGATGAAAGGAAATGGTGGTGATGTTGTATC
196 CCGCGAAATTGATGGAATTGATGGATGATGTTGATGATGAAAGGAAATGGTGGTGATGTTGTATC
*
40713 TCAAACACGCCAAAGAGGAAACTATACTATGAAGAACAATCCCGGTCTTCAGAAACTTGCTTGAG
261 TCAAACACGCCAAAGAGGAAACTATACTATGAAGAACAATCCCGGTCTTCACAAACTTGCTTGAG
*
40778 GGGTGGTGATAGTGTCTTCAACCCACTAGATATTAATCTAGGAATTTTGGAATCAAAATGGAAGG
326 GGGTGGTGATAGTGTCTTCAACCCACTAGATATTAATCTAAGAATTTTGGAATCAAAATGGAAGG
40843 AATGACGCCACAAGTATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGA
391 AATGACGCCACAAGTATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGA
40908 GAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATCCTTACAAATGAAGGCAAGACACT
456 GAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATCCTTACAAATGAAGGCAAGACACT
40973 CTATTTATAGAAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCT
521 CTATTTATAGAAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCT
41038 TTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAA
586 TTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAA
41103 CTCTT
651 CTCTT
41108 TATGAAAGGC
Statistics
Matches: 639, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
656 639 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (656 bp):
ATGGAAGAGAGTAGAGAGGCTTATTGTGTCCCGAACTAGGATTAACAAGTACTGATGTCCTTGAA
TTTATAAGTTTGGGCTACAAAATAAGATAAGAAAAGAATGACTAATAATGGAATTAATAAAGGGA
ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATGAAATAAAGAAAGGATAGAGGTGG
CCGCGAAATTGATGGAATTGATGGATGATGTTGATGATGAAAGGAAATGGTGGTGATGTTGTATC
TCAAACACGCCAAAGAGGAAACTATACTATGAAGAACAATCCCGGTCTTCACAAACTTGCTTGAG
GGGTGGTGATAGTGTCTTCAACCCACTAGATATTAATCTAAGAATTTTGGAATCAAAATGGAAGG
AATGACGCCACAAGTATAGGAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGA
GAAATAACTCACAAGAGTATATTTTATATAAGAGATGAGATCCTTACAAATGAAGGCAAGACACT
CTATTTATAGAAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGCTAGATACATGTCT
TTAGGAAAATACATAATGCTTGAGATGAATGAATAAGTCCTTTGGGCTTGTGATGGTTCAGCTAA
CTCTTC
Found at i:45099 original size:15 final size:17
Alignment explanation
Indices: 45068--45100 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
45058 TAAAGGGAAT
45068 AATATATAAGTAATGAA
1 AATATATAAGTAATGAA
45085 AATA-ATAAG-AATGAA
1 AATATATAAGTAATGAA
45100 A
1 A
45101 TGAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (17 bp):
AATATATAAGTAATGAA
Done.