Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007982.1 Hibiscus syriacus cultivar Beakdansim tig00110423_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: 74398
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1425 original size:19 final size:19
Alignment explanation
Indices: 1401--1443 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1391 ATCGTAGTCG
1401 TCACCACCGGTATCATCTT
1 TCACCACCGGTATCATCTT
1420 TCACCACCGGTATCATCTT
1 TCACCACCGGTATCATCTT
1439 TCACC
1 TCACC
1444 GCCGACGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.40, G:0.09, T:0.30
Consensus pattern (19 bp):
TCACCACCGGTATCATCTT
Found at i:5911 original size:20 final size:20
Alignment explanation
Indices: 5852--5911 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
5842 CATATGAAAT
* *
5852 TGTCCCGAAAGACCTATGAA
1 TGTCCCGAAGGACCTATGTA
* * *
5872 TATCCCGAAGGATCTCTGTA
1 TGTCCCGAAGGACCTATGTA
*
5892 TGTCCAGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
5912 ACTTTCCATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:11092 original size:28 final size:29
Alignment explanation
Indices: 11039--11117 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
11029 TCGAACTAAC
*
11039 TTACTAAC-TTTTATTTATTCACTTTATTATTA
1 TTACTAACATTTTATTT-TT---TTTACTATTA
* *
11071 -TACTAACTTTTTATTTTTTTTACTGTTA
1 TTACTAACATTTTATTTTTTTTACTATTA
11099 TTACTAACATTTTATTTTT
1 TTACTAACATTTTATTTTT
11118 ACTGTACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.19
29 17 0.40
31 9 0.21
32 8 0.19
ACGTcount: A:0.25, C:0.11, G:0.01, T:0.62
Consensus pattern (29 bp):
TTACTAACATTTTATTTTTTTTACTATTA
Found at i:23381 original size:21 final size:22
Alignment explanation
Indices: 23334--23382 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
23324 TACCCCATAA
* * *
23334 GGGAACCGATTCTCCCTTTGAAT
1 GGGAACCAATTCCCCCTTT-AAG
23357 GGGAACCAATTCCCCCTTT-AG
1 GGGAACCAATTCCCCCTTTAAG
23378 GGGAA
1 GGGAA
23383 TCGATACCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
23 17 0.74
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
GGGAACCAATTCCCCCTTTAAG
Found at i:36537 original size:198 final size:197
Alignment explanation
Indices: 36200--36586 Score: 551
Period size: 198 Copynumber: 2.0 Consensus size: 197
36190 TGTTGTCTCC
* * * * * * *
36200 AAGTCATCTTCTGATCGACCTGGTTTCTTCAAAATGAAGGAGCAACGTCATCTTTTTACCTGAAA
1 AAGTCATCTCCTGATCGACCCGATTTCTTCAAAACGAAGGAACAACATCATCTTTTTACATGAAA
* * * * * *
36265 ACGACCAGATCTCTTCAACATGGATGAACATTGTCGTCTTCAACATCAAATTGTGTCCAGGTCGA
66 ACGACCAGATCTCTTCAACATGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATCGA
* *
36330 CCTGATCTCCTCAACACGAAGGAGCAGTGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGG
131 CCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGG
36395 AA
196 AA
*
36397 AAGTCATCTCCTGATTGACCCGATTTCTTCAAAAACGAAGGAACAACATCATCTTTTTACATGAA
1 AAGTCATCTCCTGATCGACCCGATTTCTTC-AAAACGAAGGAACAACATCATCTTTTTACATGAA
* * * *
36462 AATGACTAGATCTCTTCAACACT-GATGAACAGTGTCATCTTTAACATCAAACTATCTCCAGATT
65 AACGACCAGATCTCTTCAACA-TGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATC
* *
36526 GACCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCTCATACAATCAGACTTCCTCAACG
129 GACCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACG
36587 CGAAAGAACC
Statistics
Matches: 166, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
197 26 0.16
198 139 0.84
199 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (197 bp):
AAGTCATCTCCTGATCGACCCGATTTCTTCAAAACGAAGGAACAACATCATCTTTTTACATGAAA
ACGACCAGATCTCTTCAACATGGATGAACAGTGTCATCTTCAACATCAAACTATCTCCAGATCGA
CCCGATCTCCTCAACACGAAGGAGCAGCGTCATCCGCAGACAATCAGACTTCCTCAACGTGAAGG
AA
Found at i:47777 original size:28 final size:29
Alignment explanation
Indices: 47724--47802 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
47714 TCGAACTAAC
*
47724 TTACTAAC-TTTTATTTATTCGCTTTATTATTA
1 TTACTAACATTTTATTT-TT---TTTACTATTA
* *
47756 -TACTAACTTTTTATTTTTTTTACTGTTA
1 TTACTAACATTTTATTTTTTTTACTATTA
47784 TTACTAACATTTTATTTTT
1 TTACTAACATTTTATTTTT
47803 ACTGTACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.19
29 17 0.40
31 9 0.21
32 8 0.19
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.62
Consensus pattern (29 bp):
TTACTAACATTTTATTTTTTTTACTATTA
Found at i:56450 original size:85 final size:86
Alignment explanation
Indices: 56305--56508 Score: 295
Period size: 86 Copynumber: 2.4 Consensus size: 86
56295 TTGCCCTAAA
* * * *
56305 ATCTAAAATGAAACGTTGGGGACCAAAATGCTCCAAAAAAGAATAAGGGTTAAAGTGACTATTTA
1 ATCTAAAATGAGACGTTGGGG-CCAAAATGCTCAAAAAAAGAATAAAGGTTAAAGCGACTA-TTA
*
56370 GTCAAACTTTA-GGACC-TTTTG
64 ATCAAACTTTAGGGACCTTTTTG
* * *
56391 ATCTAAAATTAGACGTTGGGGTCAAAGTGCTCAAAAAAAGAATAAAGGTTAAAGCGACTATTAAT
1 ATCTAAAATGAGACGTTGGGGCCAAAATGCTCAAAAAAAGAATAAAGGTTAAAGCGACTATTAAT
56456 CAAACTTTAGGGACCTTTTTG
66 CAAACTTTAGGGACCTTTTTG
*
56477 ACCTAAAATGAGACGTTGGGGCCAAAATGCTC
1 ATCTAAAATGAGACGTTGGGGCCAAAATGCTC
56509 CGAAAGTGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
84 13 0.12
85 39 0.38
86 52 0.50
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (86 bp):
ATCTAAAATGAGACGTTGGGGCCAAAATGCTCAAAAAAAGAATAAAGGTTAAAGCGACTATTAAT
CAAACTTTAGGGACCTTTTTG
Found at i:59195 original size:18 final size:16
Alignment explanation
Indices: 59165--59208 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
59155 AAAAAAAATT
59165 TTTAAAAAAATAAAAA
1 TTTAAAAAAATAAAAA
*
59181 TTTAAAAATACATAAAAC
1 TTTAAAAA-A-ATAAAAA
59199 TTCTAAAAAA
1 TT-TAAAAAA
59209 TTTAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 9 0.38
19 6 0.25
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
TTTAAAAAAATAAAAA
Found at i:59962 original size:21 final size:22
Alignment explanation
Indices: 59936--59983 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
59926 AGACATAAAG
*
59936 AAGAAAATATAT-ATAAAAATA
1 AAGAAAATATATAATAAAAAAA
*
59957 AAGAAAATTTATGAATAAAAAAA
1 AAGAAAATATAT-AATAAAAAAA
59980 AAGA
1 AAGA
59984 CAAAAACTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (22 bp):
AAGAAAATATATAATAAAAAAA
Found at i:62059 original size:65 final size:66
Alignment explanation
Indices: 61985--62125 Score: 212
Period size: 66 Copynumber: 2.2 Consensus size: 66
61975 AACTATCTCG
*
61985 AGAGACAAAATTTGTTTAAAGGAAAACAGATTAAAAGA-TTTTGTTTCAAGGGAAACTGTCTCAA
1 AGAGACAAAATCTGTTTAAAGGAAAACAGATTAAAAGATTTTTGTTTCAAGGGAAACTGTCTCAA
62049 A
66 A
* * * *
62050 AGAGACAAAATCTGTTTCAAGGGAAATAGATTTAAAGATTTTTGTTTCAAGGGAAACTGTCTCAA
1 AGAGACAAAATCTGTTTAAAGGAAAACAGATTAAAAGATTTTTGTTTCAAGGGAAACTGTCTCAA
*
62115 G
66 A
*
62116 AGAGATAAAA
1 AGAGACAAAA
62126 AAATTTAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
65 33 0.49
66 35 0.51
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (66 bp):
AGAGACAAAATCTGTTTAAAGGAAAACAGATTAAAAGATTTTTGTTTCAAGGGAAACTGTCTCAA
A
Found at i:62169 original size:36 final size:36
Alignment explanation
Indices: 62090--62339 Score: 184
Period size: 36 Copynumber: 7.2 Consensus size: 36
62080 TTTAAAGATT
* * * *
62090 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
***
62126 --AAATTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
* * **
62160 TTTGTTTTAA-AAAAAACTGTCTCAAGGGAGATGAAA
1 TTTGTTTTAAGAGAAAA-TGTCTCAAGAGAGACAAAA
* **
62196 TTTGTTTCAAGA-AAAA-----C---AGATTCAAAGA
1 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA-A
* * *
62224 TATTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 T-TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
*** *
62261 -AAATTTTAAGAGAAAATGTCTCAAGAGAAACAAAA
1 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
*
62296 TTTGTTTTAATAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
62332 TTTGTTTT
1 TTTGTTTT
62340 GAGATAAACC
Statistics
Matches: 162, Mismatches: 36, Indels: 32
0.70 0.16 0.14
Matches are distributed among these distances:
27 4 0.02
28 2 0.01
29 10 0.06
30 4 0.02
34 27 0.17
35 34 0.21
36 72 0.44
37 2 0.01
38 7 0.04
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
Found at i:62182 original size:136 final size:137
Alignment explanation
Indices: 62037--62338 Score: 457
Period size: 136 Copynumber: 2.2 Consensus size: 137
62027 GTTTCAAGGG
* * ** * * *
62037 AAACTGTCTCAAAAGAGACAAAATCTGTTTCAAGGGAAATAGATTTAAAGATTTTTGTTTCAAGG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGATTCAAAGA-TATTGTTTCAAGG
* *
62102 GAAACTGTCTCAAGAGAGATAAAAAAA-TTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTT
65 GAAACTGTCTCAAGAGAGACAAAAAAATTTTAAGAGAAAATGTCTCAAGAGAAACAAAATTTGTT
62166 TTAA-AAA
130 TTAATAAA
* **
62173 AAACTGTCTCAAGGGAGATGAAATTTGTTTCAAGAAAAACAGATTCAAAGATATTGTTTCAAGGG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGATTCAAAGATATTGTTTCAAGGG
62238 AAACTGTCTCAAGAGAGACAAAAAAATTTTAAGAGAAAATGTCTCAAGAGAAACAAAATTTGTTT
66 AAACTGTCTCAAGAGAGACAAAAAAATTTTAAGAGAAAATGTCTCAAGAGAAACAAAATTTGTTT
*
62303 TAATAGA
131 TAATAAA
62310 AAA-TGTCTCAAGAGAGACAAAATTTGTTT
1 AAACTGTCTCAAGAGAGACAAAATTTGTTT
62339 TGAGATAAAC
Statistics
Matches: 148, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
135 38 0.26
136 105 0.71
137 5 0.03
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (137 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGATTCAAAGATATTGTTTCAAGGG
AAACTGTCTCAAGAGAGACAAAAAAATTTTAAGAGAAAATGTCTCAAGAGAAACAAAATTTGTTT
TAATAAA
Found at i:62355 original size:36 final size:36
Alignment explanation
Indices: 62264--62356 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
62254 GACAAAAAAA
**
62264 TTTTAAGAGAAAATGTCTCAAGAGAAACAAAATTTG
1 TTTTAAGAGAAAACATCTCAAGAGAAACAAAATTTG
* ** *
62300 TTTTAATAGAAAATGTCTCAAGAGAGACAAAATTTG
1 TTTTAAGAGAAAACATCTCAAGAGAAACAAAATTTG
* * *
62336 TTTTGAGATAAACCATCTCAA
1 TTTTAAGAGAAAACATCTCAA
62357 AGGTGATAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (36 bp):
TTTTAAGAGAAAACATCTCAAGAGAAACAAAATTTG
Found at i:63821 original size:95 final size:96
Alignment explanation
Indices: 63665--63841 Score: 295
Period size: 95 Copynumber: 1.9 Consensus size: 96
63655 ATTATCAGGT
* * *
63665 TAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGTGACAGCTCAAGCTT
1 TAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTT
63730 TATTGTATA-GTATAATCACCTTCATCAGAC
66 TATTGTATATGTATAATCACCTTCATCAGAC
*
63760 TAGCTTAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGAGGGACAACTCAAGCT
1 TAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGGGACAACTCAAGCT
63824 TTATTGTATATGTATAAT
65 TTATTGTATATGTATAAT
63842 ATTATAATCT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
94 2 0.03
95 67 0.88
96 7 0.09
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (96 bp):
TAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGGACAACTCAAGCTT
TATTGTATATGTATAATCACCTTCATCAGAC
Found at i:68094 original size:3 final size:3
Alignment explanation
Indices: 68077--68169 Score: 63
Period size: 3 Copynumber: 31.0 Consensus size: 3
68067 ATATACACGT
*
68077 TAA TAG TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T-A TGAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* *
68120 -AA TATA TAA TAA CTTA TAAA TAA GGTAA AAA TAA TAA -AA -AA TAA
1 TAA TA-A TAA TAA -TAA T-AA TAA --TAA TAA TAA TAA TAA TAA TAA
68164 TAA TAA
1 TAA TAA
68170 CAAGGATCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
2 12 0.16
3 51 0.69
4 8 0.11
5 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:74388 original size:19 final size:19
Alignment explanation
Indices: 74361--74397 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
74351 AAATGACCAA
*
74361 ATAAATCGCAATGCGATCG
1 ATAAATCGCAACGCGATCG
*
74380 ATAATTCGCAACGCGATC
1 ATAAATCGCAACGCGATC
74398 T
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (19 bp):
ATAAATCGCAACGCGATCG
Done.