Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005926.1 Hibiscus syriacus cultivar Beakdansim tig00013913_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: 215791
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:174727 original size:22 final size:22
Alignment explanation
Indices: 174673--174744 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
174663 AGTCGAGGGT
174673 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
174694 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
174716 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
174738 TTTCATA
1 -TTCATA
174745 TGCCACACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:177996 original size:64 final size:64
Alignment explanation
Indices: 177891--178051 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
177881 TTGTTTAAGG
* * * * ** * *
177891 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTTAAATATAAACATCGAATATGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
**
177955 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
*
178019 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
178052 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
63 1 0.01
64 68 0.81
65 15 0.18
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
Found at i:179454 original size:21 final size:21
Alignment explanation
Indices: 179425--179465 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
179415 GTTGAGGGTT
179425 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
179446 TCATTGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
179466 ATTTCATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:187040 original size:22 final size:22
Alignment explanation
Indices: 187012--187053 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
187002 TTTTCCGCCG
*
187012 TTTGTAACTCATGTAATTACAC
1 TTTGTAACTCATATAATTACAC
*
187034 TTTGTAACTCTTATAATTAC
1 TTTGTAACTCATATAATTAC
187054 TCTGTAACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTGTAACTCATATAATTACAC
Found at i:200872 original size:18 final size:20
Alignment explanation
Indices: 200849--200885 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
200839 CTATATCACA
200849 ATATTAT-TTTTA-ATAATC
1 ATATTATATTTTATATAATC
200867 ATATTATATTTTATATAAT
1 ATATTATATTTTATATAAT
200886 TAAATATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATATTTTATATAATC
Found at i:201571 original size:27 final size:29
Alignment explanation
Indices: 201522--201580 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
201512 TAGATATAGG
*
201522 ATGATGCAATTAAATAACTTA-GGACTAAA
1 ATGATGCAA-TAAATAACTTAGGGACAAAA
**
201551 ATGATGCAA-AAATATTTTAGGGACAAAA
1 ATGATGCAATAAATAACTTAGGGACAAAA
201579 AT
1 AT
201581 AATAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 9 0.35
29 9 0.35
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.27
Consensus pattern (29 bp):
ATGATGCAATAAATAACTTAGGGACAAAA
Found at i:202465 original size:35 final size:36
Alignment explanation
Indices: 202414--202484 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
202404 TTAATATTAT
202414 TTACTTCTTATCGTTTAGTGTTAATAA-AAATCAAA
1 TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
* *
202449 TTACTTTTTATGGTTTAGTGTTAATAATAAATCAAA
1 TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
202485 ATTAAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (36 bp):
TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
Found at i:209322 original size:37 final size:31
Alignment explanation
Indices: 209281--209367 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 31
209271 CGTATATAGA
209281 ATGGATGAAATATTAATAAAATAAAATTAAACTAAAC
1 ATGGAT-AAATA--AAT-AAATAAAA-T-AACTAAAC
*
209318 ATGGATAAATAAATAAATAAAATAACTAAATG
1 ATGGATAAATAAATAAATAAAATAACTAAA-C
*
209350 AAGG-TAAATAAATAAATA
1 ATGGATAAATAAATAAATA
209368 CAAGAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 21 0.45
32 4 0.09
33 8 0.17
34 3 0.06
36 5 0.11
37 6 0.13
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.25
Consensus pattern (31 bp):
ATGGATAAATAAATAAATAAAATAACTAAAC
Found at i:209331 original size:4 final size:4
Alignment explanation
Indices: 209322--209381 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
209312 CTAAACATGG
* *
209322 ATAA ATAA ATAA ATAAA ATAA CTAA ATGAA GGTAA ATAA ATAA ATACA
1 ATAA ATAA ATAA AT-AA ATAA ATAA AT-AA -ATAA ATAA ATAA ATA-A
*
209370 AGAA ATAA ATAA
1 ATAA ATAA ATAA
209382 CAATGAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 34 0.74
5 11 0.24
6 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:212083 original size:197 final size:194
Alignment explanation
Indices: 211712--212287 Score: 657
Period size: 197 Copynumber: 2.9 Consensus size: 194
211702 GTTCCTTCGG
*
211712 GTTGAGGAAGTT-TAGTCAGTGGACGACATTGTTCCTACTTGATGAAGACATCTAGTCGTATTGA
1 GTTGAGG-AGTTCTAGTCAGTGGACGACATTGTT-CTACTTGATGAGGACATCTAGTCGTATTGA
* * * *
211776 AAGATTGTATCTGAAGACAACAT-TGTTCCTTCTTGTTGAGGAAATCTGATT-TCTTAGTGTAAC
64 AAGATTGTATCTAAAGAC-ACATAT-TT-CTTCTTGTTGAGG-AATCTGATTGCCTGAG-ATAAC
* * * *
211839 TTGATTTTGGGAAAAGACACGGCTCCTACGTGATAAGGATATCTGGTCACTTCTGATGATATTGC
124 TTGATTTT-GGAAAAGACAC-GCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGC
211904 TCCTTCAT
187 TCCTTCAT
* *
211912 GTTGATGAGTTCTAGTCAGTGGACGACATTGTTCTACTTGATTAGGACATCTAGTCGTA-TGAAA
1 GTTGAGGAGTTCTAGTCAGTGGACGACATTGTTCTACTTGATGAGGACATCTAGTCGTATTGAAA
*
211976 GATTGTATCTAAAGACGACACTATTTCTTCTTGTTGAGGAATCTGATTGCCTGGAGATAACTAGA
66 GATTGTATCTAAAGAC-ACA-TATTTCTTCTTGTTGAGGAATCTGATTGCCT-GAGATAACTTGA
* * *
212041 TTTTAGAAACGACACAGCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGTTCCTT
128 TTTTGGAAAAGACAC-GCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTT
212106 CAT
192 CAT
* * * * *
212109 GTTGAGGA-TGACTAGTTAGTGGATGACATTATTCTTGCTTGATGAGGA-AGTCTAGTCGTATTG
1 GTTGAGGAGT-TCTAGTCAGTGGACGACATTGTTC-TACTTGATGAGGACA-TCTAGTCGTATTG
* * * *
212172 AAAGA--ATATCTTAAGACA-ATATTGTTCTTTCTTGTTGAGGAATCTGATTGCCTAATATAACT
63 AAAGATTGTATCTAAAGACACATA-T-TTC-TTCTTGTTGAGGAATCTGATTGCCTGAGATAACT
* * * *
212234 TGATTTTGGAAATGACACGACTCTTACGTGATGAGAAGATCTGATCACTTCTGA
125 TGATTTTGGAAAAGACACG-CTCCTACGTGATGAGGAGATCTGGTCACTTCTGA
212288 CATTGCTCAT
Statistics
Matches: 329, Mismatches: 34, Indels: 30
0.84 0.09 0.08
Matches are distributed among these distances:
194 2 0.01
195 3 0.01
196 58 0.18
197 128 0.39
198 70 0.21
199 40 0.12
200 28 0.09
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (194 bp):
GTTGAGGAGTTCTAGTCAGTGGACGACATTGTTCTACTTGATGAGGACATCTAGTCGTATTGAAA
GATTGTATCTAAAGACACATATTTCTTCTTGTTGAGGAATCTGATTGCCTGAGATAACTTGATTT
TGGAAAAGACACGCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTTCAT
Found at i:213204 original size:43 final size:44
Alignment explanation
Indices: 213120--213206 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
213110 GAGGTATCAT
213120 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
1 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
*
213164 CGTGAGAGTGAAGTCTAAG-TTCTTATGTTGTATGTGATTATGA
1 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
213207 ATTTCTGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 23 0.55
44 19 0.45
ACGTcount: A:0.26, C:0.06, G:0.28, T:0.40
Consensus pattern (44 bp):
CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
Found at i:213808 original size:23 final size:24
Alignment explanation
Indices: 213760--213826 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
213750 AGAATATGAA
*
213760 TAATGAAAGATTTTTAAAAAATGTT
1 TAATG-AAGATTTTTGAAAAATGTT
*
213785 TAATGAAGAATTTTGAAAAA-GTT
1 TAATGAAGATTTTTGAAAAATGTT
*
213808 TGATGAAG-TTTTTGAAAAA
1 TAATGAAGATTTTTGAAAAA
213827 CGGTCTCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 10 0.26
23 10 0.26
24 13 0.34
25 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.37
Consensus pattern (24 bp):
TAATGAAGATTTTTGAAAAATGTT
Done.