Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006201.1 Hibiscus syriacus cultivar Beakdansim tig00014767_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: 61086
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8763 original size:19 final size:19
Alignment explanation
Indices: 8739--8778 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8729 GTTAGTACAA
8739 TACTAACATATGTAATCGT
1 TACTAACATATGTAATCGT
8758 TACTAACATATGTAATCGT
1 TACTAACATATGTAATCGT
8777 TA
1 TA
8779 TGAATTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TACTAACATATGTAATCGT
Found at i:9361 original size:33 final size:33
Alignment explanation
Indices: 9319--9385 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
9309 CCTAGTACAG
9319 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
9352 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACGGATT
9385 A
1 A
9386 GCACTACGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACGGATT
Found at i:9473 original size:20 final size:20
Alignment explanation
Indices: 9445--9487 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9435 TATATTGGGC
* *
9445 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
9465 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
9485 TAT
1 TAT
9488 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:9554 original size:46 final size:45
Alignment explanation
Indices: 9493--9591 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 45
9483 GTTATGGAAT
* *
9493 AATGGCAAGTGTATTGGTAAAATAAGCTTA-CGAGCTTAT-GGTATTA
1 AATGGTAAGTATATTGGTAAAATAAGCTTATC-AGCTTATAGG-A-TA
9539 AATGGTAAGTATATTGGTAAAATAAGCTTATCAGCTTATAGGATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTATCAGCTTATAGGATA
9584 AATGGTAA
1 AATGGTAA
9592 AAGATTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
45 10 0.20
46 36 0.73
47 3 0.06
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTATCAGCTTATAGGATA
Found at i:25963 original size:21 final size:21
Alignment explanation
Indices: 25937--25998 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
25927 AGTAAAAAAT
*
25937 AATAATAATAATTTAGGTAAA
1 AATAATAATATTTTAGGTAAA
*
25958 AATAATAATATTTTAGATAAA
1 AATAATAATATTTTAGGTAAA
*
25979 AATAATAATATTTTAAGTAA
1 AATAATAATATTTTAGGTAA
25999 TTTAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (21 bp):
AATAATAATATTTTAGGTAAA
Found at i:27632 original size:2 final size:2
Alignment explanation
Indices: 27593--27617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27583 ACTAATAAAT
27593 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
27618 TAAGAAAATA
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:35283 original size:18 final size:21
Alignment explanation
Indices: 35238--35283 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
35228 CTCTTATGGG
*
35238 GAGTATCGATACTCTACCCTT
1 GAGTATCGATACTCTACCCAT
35259 G-GTATCGATA-T-T-CCCAT
1 GAGTATCGATACTCTACCCAT
35276 GAGTATCG
1 GAGTATCG
35284 GTACCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 1 0.04
20 9 0.39
21 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
GAGTATCGATACTCTACCCAT
Found at i:36344 original size:14 final size:15
Alignment explanation
Indices: 36319--36347 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
36309 GTCCATTCGA
36319 ATAAACCCAAAACTC
1 ATAAACCCAAAACTC
36334 ATAAA-CCAAAACTC
1 ATAAACCCAAAACTC
36348 GAGGCGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (15 bp):
ATAAACCCAAAACTC
Found at i:42927 original size:23 final size:23
Alignment explanation
Indices: 42857--42931 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
42847 ACTTAACTAA
* *
42857 AAAATAAAATAACGATAATAAAAAAT
1 AAAATAAAA-AATGA-AA-AAAACAT
* *
42883 AAAAATAAAAAGTGACAAAAACAT
1 AAA-ATAAAAAATGAAAAAAACAT
42907 AAAATAAAAAAT-AAAATAAACAT
1 AAAATAAAAAATGAAAA-AAACAT
42930 AA
1 AA
42932 GTACAAGGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.07
23 16 0.39
24 9 0.22
25 1 0.02
26 6 0.15
27 6 0.15
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATAAAAAATGAAAAAAACAT
Found at i:43059 original size:51 final size:52
Alignment explanation
Indices: 42972--43095 Score: 139
Period size: 51 Copynumber: 2.4 Consensus size: 52
42962 AACAGTAGCT
* * *
42972 AAAATGCAAAAAT-AAAAT-TTAGTAGTTAAATAAGAAA-TAAATAGTGACC
1 AAAATGCAAAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
* * *
43021 AAAATGCAAAAATGAAAATAATAGTAGCTAAATCAGAAATTAAAAAGTTACT
1 AAAATGCAAAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
43073 AAAATG-AATAAATTGCAAAATAA
1 AAAATGCAA-AAA-TG-AAAATAA
43096 CATCCAAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
49 13 0.21
50 5 0.08
51 18 0.29
52 18 0.29
53 2 0.03
54 7 0.11
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.23
Consensus pattern (52 bp):
AAAATGCAAAAATGAAAATAATAGTAGCTAAATAAGAAATTAAAAAGTGACC
Found at i:44670 original size:58 final size:58
Alignment explanation
Indices: 44540--44739 Score: 222
Period size: 58 Copynumber: 3.4 Consensus size: 58
44530 GTAAGACGTG
* * *
44540 GCTGATTCGAAGTGTTGTGAATCGAGCACATGAAATGTAATCCCCTCTAGTGGGGCATT
1 GCTGATTCGAAGTGTTGTGAATCGAGCA-AAGAAATGTAAACCCCTCTGGTGGGGCATT
* ** * **
44599 GCTAATTCGAAGTGTCATGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGTGTGTT
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
* * * * *
44657 GTTGATTCAAAGTGTTGTGAATCGAGTAAAGAAATGTTAACCCCTCTGGTGGGGCATC
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
* * **
44715 ACTGATTC-AAATGACGTGAATCGAG
1 GCTGATTCGAAGTGTTGTGAATCGAG
44740 TGAAGGAAAT
Statistics
Matches: 116, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
57 14 0.12
58 77 0.66
59 25 0.22
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (58 bp):
GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAATGTAAACCCCTCTGGTGGGGCATT
Found at i:44837 original size:20 final size:20
Alignment explanation
Indices: 44809--44876 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
44799 ATCTTGCTCA
44809 AAAGACTTATAGATGGCCCG
1 AAAGACTTATAGATGGCCCG
* * * **
44829 AATGACTTACACAT-GCTTG
1 AAAGACTTATAGATGGCCCG
44848 AAAGACTTACT-GATGGCCCG
1 AAAGACTTA-TAGATGGCCCG
*
44868 AAGGACTTA
1 AAAGACTTA
44877 AGCTGATTCG
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (20 bp):
AAAGACTTATAGATGGCCCG
Found at i:47163 original size:4 final size:4
Alignment explanation
Indices: 47154--47227 Score: 77
Period size: 4 Copynumber: 19.8 Consensus size: 4
47144 CGGTTTTCTT
* *
47154 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTT TTTC TTT- TTTG TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
47200 TTTC CTTC -TTC TTT- TTT- ATTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
47228 TCTATCTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
3 14 0.23
4 47 0.77
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:47228 original size:12 final size:11
Alignment explanation
Indices: 47154--47243 Score: 69
Period size: 12 Copynumber: 7.9 Consensus size: 11
47144 CGGTTTTCTT
47154 TTTCTTTCTTTC
1 TTTCTTT-TTTC
47166 TTTCTTTCTTTC
1 TTTCTTT-TTTC
47178 TTTCTTTTTTTC
1 TTTC-TTTTTTC
47190 TTT-TTTGTTT-
1 TTTCTTT-TTTC
* *
47200 TTTCCTTCTTC
1 TTTCTTTTTTC
*
47211 TTT-TTTATTC
1 TTTCTTTTTTC
47221 TTTCTTTTCTATC
1 TTTCTTTT-T-TC
*
47234 TTTATTTTTT
1 TTTCTTTTTT
47244 TTTTTGATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
10 16 0.25
11 12 0.18
12 25 0.38
13 12 0.18
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:47264 original size:56 final size:53
Alignment explanation
Indices: 47147--47267 Score: 138
Period size: 53 Copynumber: 2.2 Consensus size: 53
47137 ATTTTATCGG
* * *
47147 TTTTCTTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTCTTTTTTGTTT
1 TTTTCTTCTTCTTTCTTTCATTCTTTCTTTCTATCTTTTTTTCTTTTTTGTTT
* *
47200 TTTCCTTCTTCTTT-TTT-ATTCTTTCTTTTCTATCTTTATTTTTTTTTTTGATATAT
1 TTTTCTTCTTCTTTCTTTCATTCTTTC-TTTCTATCTTT-TTTTCTTTTTTG-T-T-T
47256 TTTTCTTCTTCT
1 TTTTCTTCTTCT
47268 CTCAGTGTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
51 7 0.12
52 13 0.23
53 23 0.40
54 1 0.02
55 1 0.02
56 12 0.21
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (53 bp):
TTTTCTTCTTCTTTCTTTCATTCTTTCTTTCTATCTTTTTTTCTTTTTTGTTT
Found at i:51193 original size:51 final size:50
Alignment explanation
Indices: 51096--51200 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 50
51086 GCATAAAATA
* * *
51096 AAATAATAGTGACTAAAATACAAGAAAATAAAATTTAGTAGTTAAATAAG
1 AAATAATAGTGACCAAAATACAAGAAAATAAAATATAGTAGCTAAATAAG
* * * *
51146 AAATAAATATTGACCAAAATGCAA-AAATTAAAATAATAGTAGCTAAATCAG
1 AAAT-AATAGTGACCAAAATACAAGAAAATAAAAT-ATAGTAGCTAAATAAG
51197 AAAT
1 AAAT
51201 TAAAAAGTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
50 13 0.28
51 33 0.72
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (50 bp):
AAATAATAGTGACCAAAATACAAGAAAATAAAATATAGTAGCTAAATAAG
Found at i:51217 original size:51 final size:50
Alignment explanation
Indices: 51103--51225 Score: 115
Period size: 51 Copynumber: 2.4 Consensus size: 50
51093 ATAAAATAAT
* * * * *
51103 AGTGACTAAAATACAAGAAAATAAAATTTAGTAGTTAAATAAGAAATAAAT
1 AGTGACT-AAATGCAAGAAATTAAAATATAGTAGCTAAATAAGAAATAAAA
* * *
51154 ATTGACCAAAATGCAA-AAATTAAAATAATAGTAGCTAAATCAGAAATTAAAA
1 AGTGA-CTAAATGCAAGAAATTAAAAT-ATAGTAGCTAAATAAGAAA-TAAAA
*
51206 AGTGACTAAATG-AATAAATT
1 AGTGACTAAATGCAAGAAATT
51226 GCAAATATCA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
50 11 0.19
51 38 0.66
52 9 0.16
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.25
Consensus pattern (50 bp):
AGTGACTAAATGCAAGAAATTAAAATATAGTAGCTAAATAAGAAATAAAA
Found at i:58954 original size:13 final size:13
Alignment explanation
Indices: 58936--58960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58926 AGAAGAGAGA
58936 GAGATGGAGATGG
1 GAGATGGAGATGG
58949 GAGATGGAGATG
1 GAGATGGAGATG
58961 AATTTTGGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (13 bp):
GAGATGGAGATGG
Found at i:61053 original size:22 final size:22
Alignment explanation
Indices: 61028--61080 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
61018 AAGTGCCTCG
61028 GCACTGATACGAAAGTGCATTA
1 GCACTGATACGAAAGTGCATTA
* *
61050 GCACTAATACGGAAGTGCATTA
1 GCACTGATACGAAAGTGCATTA
61072 GCACTGATA
1 GCACTGATA
61081 TACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (22 bp):
GCACTGATACGAAAGTGCATTA
Done.