Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005334.1 Hibiscus syriacus cultivar Beakdansim tig00012079_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: 253824
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 2
Found at i:222541 original size:2 final size:2
Alignment explanation
Indices: 222534--222558 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
222524 CATATCTACC
222534 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
222559 TCTCAAGATT
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:223423 original size:64 final size:63
Alignment explanation
Indices: 223325--223485 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
223315 TAATGAAGGT
* *
223325 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
223388 GG
62 GC
*
223390 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
223454 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
223486 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:229707 original size:26 final size:25
Alignment explanation
Indices: 229670--229727 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
229660 AATATTTCGA
229670 ATTTAAAAATAACATCTATAGTG-AT
1 ATTTAAAAATAACATCTATAG-GAAT
229695 ATTTAATAAATAACATCTATAGGAAT
1 ATTTAA-AAATAACATCTATAGGAAT
229721 ATTTAAA
1 ATTTAAA
229728 CATCATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (25 bp):
ATTTAAAAATAACATCTATAGGAAT
Found at i:229943 original size:77 final size:77
Alignment explanation
Indices: 229849--229999 Score: 230
Period size: 77 Copynumber: 2.0 Consensus size: 77
229839 CACATTCTTT
* *
229849 CAAAACTCGAAAATTAGAGACACTTGCACTTAAATACATTCGAATTCACAATTTTTAGCAAATGT
1 CAAAACTCGAAAATTAGAGACACTTGCACTTAAACACATTCGAATTCACAATTTTCAGCAAATGT
229914 CAATCAATCCTC
66 CAATCAATCCTC
* * * * *
229926 CAAAACTCGTAAATTAGAGACGCTTGCACTTGAACACATTTGAATTCACAATTTTCATCAAATGT
1 CAAAACTCGAAAATTAGAGACACTTGCACTTAAACACATTCGAATTCACAATTTTCAGCAAATGT
*
229991 TAATCAATC
66 CAATCAATC
230000 TAAACTCTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (77 bp):
CAAAACTCGAAAATTAGAGACACTTGCACTTAAACACATTCGAATTCACAATTTTCAGCAAATGT
CAATCAATCCTC
Found at i:232927 original size:16 final size:16
Alignment explanation
Indices: 232894--232935 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
232884 AAGGCGTTTC
232894 TATATAAATACGTCTT
1 TATATAAATACGTCTT
*
232910 TATA-AAATATGTCATT
1 TATATAAATACGTC-TT
*
232926 TAAATAAATA
1 TATATAAATA
232936 ATATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 9 0.41
17 5 0.23
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (16 bp):
TATATAAATACGTCTT
Found at i:233254 original size:2 final size:2
Alignment explanation
Indices: 233243--233347 Score: 86
Period size: 2 Copynumber: 57.5 Consensus size: 2
233233 GAATCCGAAA
* * *
233243 AT AT AT -T AT AT AT A- AA AT AT AT A- AA AT AT -T AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
233281 A- AT -T A- AT AT A- AA AA AT AT A- AA AT AT -T 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
233317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
233348 ATCGGGGCGG
Statistics
Matches: 88, Mismatches: 5, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
1 10 0.11
2 78 0.89
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:233255 original size:7 final size:7
Alignment explanation
Indices: 233242--233349 Score: 73
Period size: 7 Copynumber: 15.4 Consensus size: 7
233232 CGAATCCGAA
233242 AATATATT
1 AATATA-T
*
233250 ATATATAA
1 A-ATATAT
233258 AATATAT
1 AATATAT
*
233265 AAAATAT
1 AATATAT
*
233272 TATATAT
1 AATATAT
233279 ACA-AT-T
1 A-ATATAT
*
233285 AATATAA
1 AATATAT
*
233292 AAAATAT
1 AATATAT
*
233299 AAAATAT
1 AATATAT
*
233306 TATATAT
1 AATATAT
233313 -ATATAT
1 AATATAT
233319 -ATATAT
1 AATATAT
233325 -ATATAT
1 AATATAT
233331 ATATATAT
1 A-ATATAT
233339 ATATATAT
1 A-ATATAT
233347 AAT
1 AAT
233350 CGGGGCGGGG
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
5 1 0.01
6 22 0.27
7 37 0.45
8 18 0.22
9 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATAT
Found at i:233274 original size:23 final size:25
Alignment explanation
Indices: 233245--233293 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
233235 ATCCGAAAAT
233245 ATATTATATATA-AAAT-ATATAAA
1 ATATTATATATACAAATAATATAAA
*
233268 ATATTATATATACAATTAATATAAA
1 ATATTATATATACAAATAATATAAA
233293 A
1 A
233294 AATATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 3 0.13
25 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATTATATATACAAATAATATAAA
Found at i:233291 original size:34 final size:35
Alignment explanation
Indices: 233247--233327 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
233237 CCGAAAATAT
*
233247 ATTATATATAAAATATATAAAATATTATATATACA
1 ATTATATATAAAAAATATAAAATATTATATATACA
*
233282 ATTA-ATATAAAAAATATAAAATATTATATATATA
1 ATTATATATAAAAAATATAAAATATTATATATACA
233316 TATATATATATA
1 -AT-TATATATA
233328 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 28 0.68
35 6 0.15
36 2 0.05
37 5 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
ATTATATATAAAAAATATAAAATATTATATATACA
Found at i:234368 original size:29 final size:29
Alignment explanation
Indices: 234335--234403 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
234325 AATTTACGAA
234335 TATTAAAAATTATAAAATAATTATTTAAT
1 TATTAAAAATTATAAAATAATTATTTAAT
* * * * * **
234364 TATTATATATTTTAAATTACTTATTTTTT
1 TATTAAAAATTATAAAATAATTATTTAAT
234393 TATTAAAAATT
1 TATTAAAAATT
234404 GATGATAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTAAAAATTATAAAATAATTATTTAAT
Found at i:234554 original size:15 final size:16
Alignment explanation
Indices: 234525--234565 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
234515 TATCACTATT
234525 TATTAAAA-A-ATAAA
1 TATTAAAATATATAAA
234539 T-TTAAAATATATAAA
1 TATTAAAATATATAAA
234554 TAATTAAAATAT
1 T-ATTAAAATAT
234566 TATTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 2 0.09
15 6 0.26
17 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAAATATATAAA
Found at i:237052 original size:183 final size:183
Alignment explanation
Indices: 236741--237108 Score: 556
Period size: 183 Copynumber: 2.0 Consensus size: 183
236731 TTGCTTGCCC
* *
236741 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTGCACTTGCTTTCAAGGTAAATTTGAGTTTTCAT
1 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
* *
236806 ATGATACACACGAATTCGATCATCTGAGCTATGTTATTTAGACTCAAGTGTGAGCGTCAGATACA
66 ATGATACACACGAATTCGATCATCTAAGCTATGTTATTTAGACTCAAGTGTGAGCGCCAGATACA
* * * * *
236871 AGTTTTTGATGAATCAAATTGATTCGGAATGTCTTTTGTTTTGACAATGTGCA
131 AGTTTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
*
236924 TTGTTTCTGCTTCTGTTTTCTTGGTAGATCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
1 TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
* * ** * *
236989 ATGATACACACGAATTTGATCATTTAAGCTATGTTATTTAGACTCGGGTGTGAGTGCCAGATACG
66 ATGATACACACGAATTCGATCATCTAAGCTATGTTATTTAGACTCAAGTGTGAGCGCCAGATACA
* * * *
237054 AGTTTCTGACGATTTAAATCGGTTATGAATGTCTTTTGTTCTGACAATGTGCA
131 AGTTTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
237107 TT
1 TT
237109 ATTAAAAAGG
Statistics
Matches: 165, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (183 bp):
TTGTTTCTGCTTCTGTTTTCTTGGTAGACCCTACACTTGCTTTCAAGATAAATTTGAGTTTTCAT
ATGATACACACGAATTCGATCATCTAAGCTATGTTATTTAGACTCAAGTGTGAGCGCCAGATACA
AGTTTCTGACGAATCAAATCGATTAGGAATGTCTTTTGTTCTGACAATGTGCA
Found at i:240645 original size:22 final size:25
Alignment explanation
Indices: 240608--240654 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
240598 TAAATTAAGG
240608 TTTATATTAATTAAAA-ATTATTTT
1 TTTATATTAATTAAAATATTATTTT
240632 TTTATA-T-ATTAAAATATTATTTT
1 TTTATATTAATTAAAATATTATTTT
240655 AATTATGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 9 0.41
24 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATATTAATTAAAATATTATTTT
Found at i:242746 original size:200 final size:200
Alignment explanation
Indices: 242394--242764 Score: 514
Period size: 200 Copynumber: 1.9 Consensus size: 200
242384 ATGACTATTG
*
242394 TCTTGGTAGACCATGCACTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGATTTTG
1 TCTTGGTAGACCATGCACTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTTG
* * * * *
242459 ATAATCGAAACTATGTTATTTAGACTCGGGTGTGAGTCTCAGATACGAGTTTTCGACGAATCAAA
66 ATAATCGAAACTATGCTATTTAAACTCGGATGTGAGTCTCAAATACGAGTTTCCGACGAATCAAA
* * *
242524 TTGGTTATAATTTTTGTTTTGTTTTGACAATGTGCATTGTTTATGTTTGCCCTTGTTTCTGCTAC
131 TTGGCTATAATGTCTGTTTTGTTTTGACAATGTGCATTGTTTATGTTTGCCCTTGTTTCTGCTAC
242589 TGTTC
196 TGTTC
* *
242594 TCTTGGTAGATCC-TGCACTTGTTTTCAAGGTAAATTTTAGTTTTCATATGATACACACGAATTT
1 TCTTGGTAGA-CCATGCACTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTT
* * * * ** * *
242658 GATCATC-AAAGCTATGCTATTTAAATTTGGATGTGAGTGTCAAATACGAGTTTCCGGGGATTCG
65 GATAATCGAAA-CTATGCTATTTAAACTCGGATGTGAGTCTCAAATACGAGTTTCCGACGAATCA
*
242722 AATTGGCTATGAATGTCT-TTTTGTTTTGATAATGTGCATTGTT
129 AATTGGCTAT-AATGTCTGTTTTGTTTTGACAATGTGCATTGTT
242765 AAAAGGAGGA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
199 3 0.02
200 138 0.93
201 7 0.05
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.42
Consensus pattern (200 bp):
TCTTGGTAGACCATGCACTTGCTTTCAAGGTAAATTTGAGTTTTCATATGATACACACGAATTTG
ATAATCGAAACTATGCTATTTAAACTCGGATGTGAGTCTCAAATACGAGTTTCCGACGAATCAAA
TTGGCTATAATGTCTGTTTTGTTTTGACAATGTGCATTGTTTATGTTTGCCCTTGTTTCTGCTAC
TGTTC
Found at i:248106 original size:27 final size:28
Alignment explanation
Indices: 248045--248111 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
248035 CAGTGACAAT
*
248045 AGAATTAGATCGGTTTGCTTTTAAAAAA
1 AGAATTAGATCGATTTGCTTTTAAAAAA
248073 AGAATTAGATCGATTTGCTTTTAAAAAA
1 AGAATTAGATCGATTTGCTTTTAAAAAA
248101 A-AATTAGATCG
1 AGAATTAGATCG
248112 GTTGTAAGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (28 bp):
AGAATTAGATCGATTTGCTTTTAAAAAA
Found at i:248438 original size:19 final size:21
Alignment explanation
Indices: 248394--248441 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
248384 ATCTTTAAAC
*
248394 TTTAAAATATATACATTCATA
1 TTTAAATTATATACATTCATA
*
248415 CTTAAATTATA-ACATTCAT-
1 TTTAAATTATATACATTCATA
248434 TTTAAATT
1 TTTAAATT
248442 GTTCACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 9 0.38
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAATTATATACATTCATA
Found at i:249784 original size:2 final size:2
Alignment explanation
Indices: 249779--249808 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
249769 ACACACACAC
*
249779 AT AT AT GT 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
249809 TATTACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Done.