Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000991.1 Hibiscus syriacus cultivar Beakdansim tig00001985_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: 218077
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:185504 original size:21 final size:21
Alignment explanation
Indices: 185480--185545 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
185470 ACATAATTAA
185480 ATAAGCATAATATTATTATCC
1 ATAAGCATAATATTATTATCC
* * * **
185501 ATAATCAT-CTCTTTAATT-TAA
1 ATAAGCATAAT-ATT-ATTATCC
185522 ATAAGCATAATATTATTATCC
1 ATAAGCATAATATTATTATCC
185543 ATA
1 ATA
185546 CTCATCTCTT
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
20 4 0.13
21 23 0.74
22 4 0.13
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (21 bp):
ATAAGCATAATATTATTATCC
Found at i:185522 original size:42 final size:42
Alignment explanation
Indices: 185476--185563 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
185466 AATCACATAA
185476 TTAAATAAGCATAATATTATTATCCATAATCATCTCTTTAAT
1 TTAAATAAGCATAATATTATTATCCATAATCATCTCTTTAAT
*
185518 TTAAATAAGCATAATATTATTATCCATACTCATCTCTTTAAT
1 TTAAATAAGCATAATATTATTATCCATAATCATCTCTTTAAT
185560 TTAA
1 TTAA
185564 TAAAACGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (42 bp):
TTAAATAAGCATAATATTATTATCCATAATCATCTCTTTAAT
Found at i:185590 original size:41 final size:42
Alignment explanation
Indices: 185476--185590 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 42
185466 AATCACATAA
* * ** *
185476 TTAAATAAGCATAATATTATTATCCATAATCATCTCTTTAAT
1 TTAAAAAAGAATAATATTATTAAACATACTCATCTCTTTAAT
* * **
185518 TTAAATAAGCATAATATTATTATCCATACTCATCTCTTTAAT
1 TTAAAAAAGAATAATATTATTAAACATACTCATCTCTTTAAT
185560 TTAATAAAACGAATAATA-TA-TAAACA-ACTCA
1 TTAA-AAAA-GAATAATATTATTAAACATACTCA
185591 ATCAGAGATA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
41 5 0.08
42 49 0.74
43 5 0.08
44 7 0.11
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (42 bp):
TTAAAAAAGAATAATATTATTAAACATACTCATCTCTTTAAT
Found at i:186533 original size:29 final size:29
Alignment explanation
Indices: 186488--186651 Score: 213
Period size: 29 Copynumber: 5.6 Consensus size: 29
186478 GACCCGACCT
*
186488 GGGTGTTATTTTTGTAAATATTTTTAAAA
1 GGGTGATATTTTTGTAAATATTTTTAAAA
* *
186517 GGGTGCTATTTTAGTAAATATTTTTAAAA
1 GGGTGATATTTTTGTAAATATTTTTAAAA
186546 GGGTGATATTTTTGTAAATATTTTTAAAA
1 GGGTGATATTTTTGTAAATATTTTTAAAA
*
186575 GGGTGATATTTTAGTAAATATTTTTAAAA
1 GGGTGATATTTTTGTAAATATTTTTAAAA
* * * **
186604 GGGTGTTAGTTTTGTAATTAATTTCTT-TTA
1 GGGTGATATTTTTGTAAAT-ATTT-TTAAAA
*
186634 GGGTGCTATTTTTGTAAA
1 GGGTGATATTTTTGTAAA
186652 AGTTGACTGT
Statistics
Matches: 119, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
29 97 0.82
30 20 0.17
31 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (29 bp):
GGGTGATATTTTTGTAAATATTTTTAAAA
Found at i:186556 original size:17 final size:17
Alignment explanation
Indices: 186534--186586 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
186524 ATTTTAGTAA
186534 ATATTTTTAAAAGGGTG
1 ATATTTTTAAAAGGGTG
**
186551 ATATTTTTGTAA-----
1 ATATTTTTAAAAGGGTG
186563 ATATTTTTAAAAGGGTG
1 ATATTTTTAAAAGGGTG
186580 ATATTTT
1 ATATTTT
186587 AGTAAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 10 0.37
17 17 0.63
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (17 bp):
ATATTTTTAAAAGGGTG
Found at i:186578 original size:58 final size:58
Alignment explanation
Indices: 186488--186651 Score: 240
Period size: 58 Copynumber: 2.8 Consensus size: 58
186478 GACCCGACCT
186488 GGGTGTTATTTTTGTAAATATTTTTAAAAGGGTGCTATTTTAGTAAATATTTTTAAAA
1 GGGTGTTATTTTTGTAAATATTTTTAAAAGGGTGCTATTTTAGTAAATATTTTTAAAA
* *
186546 GGGTGATATTTTTGTAAATATTTTTAAAAGGGTGATATTTTAGTAAATATTTTTAAAA
1 GGGTGTTATTTTTGTAAATATTTTTAAAAGGGTGCTATTTTAGTAAATATTTTTAAAA
* * ** *
186604 GGGTGTTAGTTTTGTAATTAATTTCTT-TTAGGGTGCTATTTTTGTAAA
1 GGGTGTTATTTTTGTAAAT-ATTT-TTAAAAGGGTGCTATTTTAGTAAA
186652 AGTTGACTGT
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 72 0.76
59 21 0.22
60 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (58 bp):
GGGTGTTATTTTTGTAAATATTTTTAAAAGGGTGCTATTTTAGTAAATATTTTTAAAA
Found at i:187725 original size:25 final size:25
Alignment explanation
Indices: 187677--187726 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
187667 AGGGTAACTC
* *
187677 TTTTATGGGATTTACTGCAGTATGA
1 TTTTATGAGATTTACTGCACTATGA
* *
187702 TTTTATGAGATTTATTGGACTATGA
1 TTTTATGAGATTTACTGCACTATGA
187727 CTTGTATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATGA
Found at i:193947 original size:29 final size:29
Alignment explanation
Indices: 193905--194063 Score: 185
Period size: 29 Copynumber: 5.4 Consensus size: 29
193895 GATCCAGGTT
* *
193905 CTATTTTCGTAAATATTTTTAGAAGGGTG
1 CTATTTTTGTAAATATTTTTAAAAGGGTG
*
193934 CTATTTTTGTAAATATTTTTAAAATGGTG
1 CTATTTTTGTAAATATTTTTAAAAGGGTG
* * *
193963 CTACTTCTGTAAATATTTTTAAAATGGTG
1 CTATTTTTGTAAATATTTTTAAAAGGGTG
*
193992 CTATTTTAGTAAATATTTTTAAAAGGGTG
1 CTATTTTTGTAAATATTTTTAAAAGGGTG
* * * **
194021 TTAGTTTTGTAATTAATTTCTT-TTAGGGTG
1 CTATTTTTGTAAAT-ATTT-TTAAAAGGGTG
194051 CTATTTTTGTAAA
1 CTATTTTTGTAAA
194064 AGTTGACTGT
Statistics
Matches: 110, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
29 88 0.80
30 20 0.18
31 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (29 bp):
CTATTTTTGTAAATATTTTTAAAAGGGTG
Found at i:197784 original size:36 final size:36
Alignment explanation
Indices: 197744--197939 Score: 175
Period size: 36 Copynumber: 5.4 Consensus size: 36
197734 TTCATCTCGT
* *
197744 TTGAGATAGATTT-TCTTGAAATAAA-TTTGATCTCAC
1 TTGAGACA-ATTTCTCTTGAAACAAATTTTG-TCTCAC
*** * * *
197780 TTGAGATTGTTT-TCTTAAAAGTAAATTTTGTCTCGC
1 TTGAGACAATTTCTCTTGAAA-CAAATTTTGTCTCAC
* * *
197816 TTGAGACAATTTCTCTTTAAGCAAATTTTGTCTCCC
1 TTGAGACAATTTCTCTTGAAACAAATTTTGTCTCAC
* *
197852 TTGAGACATTTTCTCTTGAAACAAATTTTATCTCAC
1 TTGAGACAATTTCTCTTGAAACAAATTTTGTCTCAC
* * *
197888 TTGAGACAATTTAC-CTTGAACCAAATTTCGTCTCGC
1 TTGAGACAATTT-CTCTTGAAACAAATTTTGTCTCAC
*
197924 TTGAGACAGTTTCTCT
1 TTGAGACAATTTCTCT
197940 GTAAACATAA
Statistics
Matches: 133, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
35 11 0.08
36 111 0.83
37 11 0.08
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGAGACAATTTCTCTTGAAACAAATTTTGTCTCAC
Found at i:197946 original size:72 final size:72
Alignment explanation
Indices: 197802--197939 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 72
197792 TCTTAAAAGT
* * * * * *
197802 AAATTTTGTCTCGCTTGAGACAATTTCTCTTTAAGCAAATTTTGTCTCCCTTGAGACATTTTCTC
1 AAATTTTATCTCACTTGAGACAATTTCTCTTGAACCAAATTTCGTCTCCCTTGAGACAGTTTCTC
197867 TTGAAAC
66 TTGAAAC
*
197874 AAATTTTATCTCACTTGAGACAATTTAC-CTTGAACCAAATTTCGTCTCGCTTGAGACAGTTTCT
1 AAATTTTATCTCACTTGAGACAATTT-CTCTTGAACCAAATTTCGTCTCCCTTGAGACAGTTTCT
197938 CT
65 CT
197940 GTAAACATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 57 0.98
73 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (72 bp):
AAATTTTATCTCACTTGAGACAATTTCTCTTGAACCAAATTTCGTCTCCCTTGAGACAGTTTCTC
TTGAAAC
Found at i:198309 original size:68 final size:68
Alignment explanation
Indices: 198198--198352 Score: 217
Period size: 68 Copynumber: 2.3 Consensus size: 68
198188 TTGATCTCAC
* * *
198198 TTGAGATTGTTT-TC-CC-AAACAAAATTTCGTCTCGCTTGGGACATTTTCTCTCGAAACATAAA
1 TTGAGATTGTTTCTCTCCAAAACAAAATTTCGTATCACTTGAGACATTTTCTCTCGAAACATAAA
198260 CCT
66 CCT
* * * *
198263 TTGAGATTGTTTCTCTCCAAAACTAAATTTCGTATCACTTGAGACATTTTCTTTTGAAACATAAG
1 TTGAGATTGTTTCTCTCCAAAACAAAATTTCGTATCACTTGAGACATTTTCTCTCGAAACATAAA
198328 CCT
66 CCT
*
198331 TTGAGATTGTTTCTCTCAAAAA
1 TTGAGATTGTTTCTCTCCAAAA
198353 ATTAATCATC
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
65 12 0.15
66 2 0.03
67 2 0.03
68 63 0.80
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (68 bp):
TTGAGATTGTTTCTCTCCAAAACAAAATTTCGTATCACTTGAGACATTTTCTCTCGAAACATAAA
CCT
Found at i:198381 original size:68 final size:67
Alignment explanation
Indices: 198237--198390 Score: 175
Period size: 68 Copynumber: 2.3 Consensus size: 67
198227 TCTCGCTTGG
* * * *
198237 GACATTTTCTCTCGAAACATAAACCTTTGAGATTGTTTCTCTCCAAAACTAAATTTCGTATCACT
1 GACATTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAAAAATAAA-TTCATATCACT
*
198302 TGA
65 CGA
* * * * *
198305 GACATTTTCTTTTGAAACATAAGCCTTTGAGATTGTTTCTCTCAAAAAATTAA-TCATCTCGCTC
1 GACATTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAAAAATAAATTCATATCACTC
198369 GA
66 GA
*
198371 GACAGTTTTTCCCTTGAAAC
1 GACA--TTTTCTCTTGAAAC
198391 GCAAAATTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
66 13 0.18
68 59 0.82
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (67 bp):
GACATTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAAAAATAAATTCATATCACTC
GA
Found at i:198830 original size:137 final size:139
Alignment explanation
Indices: 198567--199067 Score: 560
Period size: 140 Copynumber: 3.6 Consensus size: 139
198557 CAACCAACCT
* * * ** * *
198567 GATCTCCTCAACGCGTAGGAGCTATGTCATCCTCGGATAATCATACTTCCTCATCACGTAGGAAC
1 GATCTCCTCAACACGTAGGAGCAACGTCATCCTCAAACAATCAGACTTCCTCATCACGTAGGAAC
* * * * * *
198632 TGTGTTGACTCCAAATTATCCCTAAAGATGATTAGACATCCTCATCATGTAGGAACAATGTCATC
66 AGTGTTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTC
198697 CACCGACCA
131 CACCGACCA
* ** * *
198706 TATCTCCTCAACACGTAGGAGCAACGTTTTCCTCATACAATC-GACTTTCTCATCACGTAGGAAT
1 GATCTCCTCAACACGTAGGAGCAACGTCATCCTCAAACAATCAGACTTCCTCATCACGTAGGAA-
* * * *
198770 C-GTGTTGTCTTCAAATTAT-CCTAAAGACGGCTAGGCGTCCTCATCACGTAGGAACAATGTCGT
65 CAGTGTTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGT
*
198833 CCACTGACCA
130 CCACCGACCA
* ** * * * * ** * *
198843 GATCTTCTCAATGCTTAGGAGAAACGTCATCCTCAAATAACCAGACTTCCTCATTGCATAAAGAA
1 GATCTCCTCAACACGTAGGAGCAACGTCATCCTCAAACAATCAGACTTCCTCATCACGT-AGGAA
** ** *
198908 TTGCATTG-CTTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAATAATGTCG
65 CAGTGTTGTC-TCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCG
198972 TCCACCGACCA
129 TCCACCGACCA
* * *
198983 GATATCCTCAACACGTAGGAGCAACCTCATCCTCAGACAATCAGACTTCCTCATCACGTAGGAAC
1 GATCTCCTCAACACGTAGGAGCAACGTCATCCTCAAACAATCAGACTTCCTCATCACGTAGGAAC
*
199048 AGTGTTGTCACCAAATTATC
66 AGTGTTGTCTCCAAATTATC
199068 TCTAGATTGA
Statistics
Matches: 290, Mismatches: 65, Indels: 14
0.79 0.18 0.04
Matches are distributed among these distances:
137 77 0.27
138 48 0.17
139 69 0.24
140 96 0.33
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (139 bp):
GATCTCCTCAACACGTAGGAGCAACGTCATCCTCAAACAATCAGACTTCCTCATCACGTAGGAAC
AGTGTTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTC
CACCGACCA
Found at i:200224 original size:29 final size:29
Alignment explanation
Indices: 200192--200247 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
200182 TTATTTCAAG
200192 TTAACAACTAACTTTTATTTTATTGCATA
1 TTAACAACTAACTTTTATTTTATTGCATA
*
200221 TTAACCACTAACTTTTATTTTATTGCA
1 TTAACAACTAACTTTTATTTTATTGCA
200248 CTCTAACTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (29 bp):
TTAACAACTAACTTTTATTTTATTGCATA
Found at i:200530 original size:16 final size:16
Alignment explanation
Indices: 200472--200530 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
200462 CTGATAACCA
*
200472 CTAACTGCTAACTTTT
1 CTAACCGCTAACTTTT
* *
200488 CTAACCGTTAATTTTT
1 CTAACCGCTAACTTTT
* ** *
200504 CTTACAACTAACATTT
1 CTAACCGCTAACTTTT
200520 CTAACCGCTAA
1 CTAACCGCTAA
200531 TTACTAACTG
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (16 bp):
CTAACCGCTAACTTTT
Found at i:200706 original size:16 final size:16
Alignment explanation
Indices: 200681--200716 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
200671 ATTTATATTA
*
200681 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
*
200697 TTTAAATTTATGCATT
1 TTTAAATTTATGCACT
200713 TTTA
1 TTTA
200717 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:207035 original size:3 final size:3
Alignment explanation
Indices: 207027--207081 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
207017 ATTTCAGAAC
* * *
207027 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
207075 TAT TAT T
1 TAT TAT T
207082 TGAGGACTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:212147 original size:14 final size:14
Alignment explanation
Indices: 212128--212175 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
212118 CGTTCGGTAA
212128 TATGTTCATTCATT
1 TATGTTCATTCATT
** *
212142 TATGTTTGTTCGTT
1 TATGTTCATTCATT
*
212156 TATGTGCATTCATT
1 TATGTTCATTCATT
212170 TATGTT
1 TATGTT
212176 TAGCCCAATC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (14 bp):
TATGTTCATTCATT
Found at i:212376 original size:13 final size:13
Alignment explanation
Indices: 212358--212383 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
212348 TTATGATCGT
212358 TTACGTTCGTTTA
1 TTACGTTCGTTTA
212371 TTACGTTCGTTTA
1 TTACGTTCGTTTA
212384 CGTTCATTTA
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:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
TTACGTTCGTTTA
Found at i:212381 original size:23 final size:23
Alignment explanation
Indices: 212354--212406 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
212344 TCATTTATGA
*
212354 TCGTTTACGTTCGTTTATTACGT
1 TCGTTTACGTTCATTTATTACGT
**
212377 TCGTTTACGTTCATTTATTGTGT
1 TCGTTTACGTTCATTTATTACGT
212400 TCGTTTA
1 TCGTTTA
212407 TCATTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.17, T:0.55
Consensus pattern (23 bp):
TCGTTTACGTTCATTTATTACGT
Done.