Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005983.1 Hibiscus syriacus cultivar Beakdansim tig00014064_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: 781742
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 5
Found at i:780793 original size:14 final size:14
Alignment explanation
Indices: 780685--780780 Score: 79
Period size: 14 Copynumber: 6.9 Consensus size: 14
780675 CAGTTTTCAA
*
780685 GTTTTGGGTTTTCAG
1 GTTTTGAGTTTT-AG
*
780700 GTTTCGA-TTTTAG
1 GTTTTGAGTTTTAG
** *
780713 GTTTCAAATTTTAG
1 GTTTTGAGTTTTAG
780727 GTTTT-AGGTTTTAG
1 GTTTTGA-GTTTTAG
* *
780741 GTTTTGATTTTTGG
1 GTTTTGAGTTTTAG
* *
780755 GTTTTGTGGTTTAG
1 GTTTTGAGTTTTAG
780769 GTTTTGAGTTTT
1 GTTTTGAGTTTT
780781 GGGGTTTAGG
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
13 9 0.14
14 50 0.77
15 6 0.09
ACGTcount: A:0.12, C:0.03, G:0.27, T:0.57
Consensus pattern (14 bp):
GTTTTGAGTTTTAG
Found at i:780809 original size:21 final size:21
Alignment explanation
Indices: 780785--780864 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
780775 AGTTTTGGGG
*
780785 TTTAGGTTT-GGGTTTCAAAGT
1 TTTAGGTTTCAGGTTTCAAA-T
** *
780806 TTTAAATTTCAGGTTTCAATT
1 TTTAGGTTTCAGGTTTCAAAT
* *
780827 TTTGGGTTTTAGGTTTCAAAT
1 TTTAGGTTTCAGGTTTCAAAT
* *
780848 TTCAGGTTTCGGGTTTC
1 TTTAGGTTTCAGGTTTC
780865 GGGTTTCAAA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
21 37 0.82
22 8 0.18
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTAGGTTTCAGGTTTCAAAT
Found at i:780850 original size:28 final size:28
Alignment explanation
Indices: 780819--780892 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
780809 AAATTTCAGG
* * *
780819 TTTCAATTTTTGGGTTTTAGGTTTCAAA
1 TTTCAAGTTTCGGGTTTCAGGTTTCAAA
* *
780847 TTTCAGGTTTCGGGTTTCGGGTTTCAAA
1 TTTCAAGTTTCGGGTTTCAGGTTTCAAA
* * *
780875 TTTTAGGTTTCAGGTTTC
1 TTTCAAGTTTCGGGTTTC
780893 TGTTTTCGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (28 bp):
TTTCAAGTTTCGGGTTTCAGGTTTCAAA
Found at i:780857 original size:7 final size:7
Alignment explanation
Indices: 780812--780921 Score: 58
Period size: 7 Copynumber: 15.7 Consensus size: 7
780802 AAGTTTTAAA
780812 TTTCAGG
1 TTTCAGG
**
780819 TTTCAAT
1 TTTCAGG
**
780826 TTTTGGG
1 TTTCAGG
*
780833 TTTTAGG
1 TTTCAGG
**
780840 TTTCAAA
1 TTTCAGG
780847 TTTCAGG
1 TTTCAGG
*
780854 TTTCGGG
1 TTTCAGG
*
780861 TTTCGGG
1 TTTCAGG
**
780868 TTTCAAA
1 TTTCAGG
*
780875 TTTTAGG
1 TTTCAGG
780882 TTTCAGG
1 TTTCAGG
* *
780889 TTTCTGT
1 TTTCAGG
*
780896 TTTCGGG
1 TTTCAGG
**
780903 TTTTGGG
1 TTTCAGG
*
780910 TTTCATG
1 TTTCAGG
780917 TTTCA
1 TTTCA
780922 AATTTTGGGT
Statistics
Matches: 75, Mismatches: 28, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 75 1.00
ACGTcount: A:0.14, C:0.11, G:0.25, T:0.51
Consensus pattern (7 bp):
TTTCAGG
Found at i:780870 original size:49 final size:49
Alignment explanation
Indices: 780812--781018 Score: 200
Period size: 49 Copynumber: 4.2 Consensus size: 49
780802 AAGTTTTAAA
* * * *
780812 TTTCAGGTTTCAATTTTTGGGTTTTAGGTTTCAAATTTCAGGTTTCGGG
1 TTTCAGGTTTCAAATTTTAGGTTTTAGGTTTCAATTTTCGGGTTTCGGG
* * ** *
780861 TTTCGGGTTTCAAATTTTAGGTTTCAGGTTTCTGTTTTCGGGTTTTGGG
1 TTTCAGGTTTCAAATTTTAGGTTTTAGGTTTCAATTTTCGGGTTTCGGG
* * * * * *
780910 TTTCATGTTTCAAATTTTGGGTTTTTGGTTTCGATTTTTGGGTTTCGTG
1 TTTCAGGTTTCAAATTTTAGGTTTTAGGTTTCAATTTTCGGGTTTCGGG
* * * * **
780959 TTTCAGGTTTAAAATTTTAGGTTTCATGTTTCGAGTTTT-GGGTTTCCAG
1 TTTCAGGTTTCAAATTTTAGGTTTTAGGTTTC-AATTTTCGGGTTTCGGG
*
781008 TTTTAGGTTTC
1 TTTCAGGTTTC
781019 GAGTTTTAAA
Statistics
Matches: 126, Mismatches: 31, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
49 122 0.97
50 4 0.03
ACGTcount: A:0.14, C:0.10, G:0.25, T:0.52
Consensus pattern (49 bp):
TTTCAGGTTTCAAATTTTAGGTTTTAGGTTTCAATTTTCGGGTTTCGGG
Found at i:780871 original size:21 final size:21
Alignment explanation
Indices: 780847--780920 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
780837 AGGTTTCAAA
780847 TTTCAGGTTTCGGGTTTCGGG
1 TTTCAGGTTTCGGGTTTCGGG
** ** *
780868 TTTCAAATTTTAGGTTTCAGG
1 TTTCAGGTTTCGGGTTTCGGG
* * *
780889 TTTCTGTTTTCGGGTTTTGGG
1 TTTCAGGTTTCGGGTTTCGGG
*
780910 TTTCATGTTTC
1 TTTCAGGTTTC
780921 AAATTTTGGG
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.09, C:0.12, G:0.27, T:0.51
Consensus pattern (21 bp):
TTTCAGGTTTCGGGTTTCGGG
Found at i:780899 original size:28 final size:28
Alignment explanation
Indices: 780838--780892 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
780828 TTGGGTTTTA
*
780838 GGTTTCAAATTTCAGGTTTCGGGTTTCG
1 GGTTTCAAATTTCAGGTTTCAGGTTTCG
*
780866 GGTTTCAAATTTTAGGTTTCAGGTTTC
1 GGTTTCAAATTTCAGGTTTCAGGTTTC
780893 TGTTTTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.16, C:0.13, G:0.25, T:0.45
Consensus pattern (28 bp):
GGTTTCAAATTTCAGGTTTCAGGTTTCG
Found at i:780927 original size:21 final size:21
Alignment explanation
Indices: 780903--780963 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
780893 TGTTTTCGGG
780903 TTTTGGGTTTCATGTTTCAAA
1 TTTTGGGTTTCATGTTTCAAA
* * *
780924 TTTTGGGTTT-TTGGTTTCGAT
1 TTTTGGGTTTCAT-GTTTCAAA
*
780945 TTTTGGGTTTCGTGTTTCA
1 TTTTGGGTTTCATGTTTCA
780964 GGTTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.10, C:0.08, G:0.25, T:0.57
Consensus pattern (21 bp):
TTTTGGGTTTCATGTTTCAAA
Found at i:780996 original size:14 final size:14
Alignment explanation
Indices: 780986--781026 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
780976 TAGGTTTCAT
*
780986 GTTTCGAGTTTTGG
1 GTTTCGAGTTTTAG
*
781000 GTTTCCAGTTTTAG
1 GTTTCGAGTTTTAG
781014 GTTTCGAGTTTTA
1 GTTTCGAGTTTTA
781027 AATTTAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.10, G:0.27, T:0.51
Consensus pattern (14 bp):
GTTTCGAGTTTTAG
Found at i:781122 original size:28 final size:29
Alignment explanation
Indices: 781091--781151 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
781081 GAGTTCCAGG
* *
781091 TTTCAAATTTTGGGTTTTGGGTTAT-AGT
1 TTTCAAATTTCGGGTTTCGGGTTATAAGT
* *
781119 TTTCAAGTTTCGGGTTTCGGGTTTTAAGT
1 TTTCAAATTTCGGGTTTCGGGTTATAAGT
781148 TTTC
1 TTTC
781152 GACTTTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.15, C:0.08, G:0.25, T:0.52
Consensus pattern (29 bp):
TTTCAAATTTCGGGTTTCGGGTTATAAGT
Found at i:781158 original size:29 final size:28
Alignment explanation
Indices: 781091--781158 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
781081 GAGTTCCAGG
* * *
781091 TTTCAAATTTTGGGTTTTGGGTTATAGT
1 TTTCAACTTTCGGGTTTCGGGTTATAGT
* *
781119 TTTCAAGTTTCGGGTTTCGGGTTTTAAGT
1 TTTCAACTTTCGGGTTTCGGGTTAT-AGT
*
781148 TTTCGACTTTC
1 TTTCAACTTTC
781159 TATTTCGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.15, C:0.10, G:0.24, T:0.51
Consensus pattern (28 bp):
TTTCAACTTTCGGGTTTCGGGTTATAGT
Found at i:781194 original size:13 final size:13
Alignment explanation
Indices: 781176--781215 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
781166 GGTTTCAAAT
781176 TTCGGGGTTCGGG
1 TTCGGGGTTCGGG
781189 TTCGGGGTTCGGGG
1 TTCGGGGTTC-GGG
* *
781203 CTCGGGGCTCGGG
1 TTCGGGGTTCGGG
781216 GCTCGGGCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (13 bp):
TTCGGGGTTCGGG
Found at i:781202 original size:7 final size:7
Alignment explanation
Indices: 781177--781402 Score: 297
Period size: 7 Copynumber: 34.7 Consensus size: 7
781167 GTTTCAAATT
*
781177 TCGGGGT
1 TCGGGGC
*
781184 TC-GGGT
1 TCGGGGC
*
781190 TCGGGGT
1 TCGGGGC
781197 TCGGGGC
1 TCGGGGC
781204 TCGGGGC
1 TCGGGGC
781211 TCGGGGC
1 TCGGGGC
781218 TC-GGGC
1 TCGGGGC
*
781224 GCGGGGC
1 TCGGGGC
781231 TC-GGGC
1 TCGGGGC
781237 TC-GGGC
1 TCGGGGC
781243 TCGGGGC
1 TCGGGGC
781250 TCGGGGC
1 TCGGGGC
781257 TCGGGGC
1 TCGGGGC
781264 TC-GGGC
1 TCGGGGC
781270 TC-GGGC
1 TCGGGGC
781276 TC-GGGC
1 TCGGGGC
781282 TCGGGGC
1 TCGGGGC
781289 TC---GC
1 TCGGGGC
781293 TCGGGGC
1 TCGGGGC
781300 TCGGGGC
1 TCGGGGC
781307 TCGGGGC
1 TCGGGGC
781314 TC-GGGC
1 TCGGGGC
781320 TC-GGGC
1 TCGGGGC
781326 TCGGGGC
1 TCGGGGC
781333 TC-GGGC
1 TCGGGGC
781339 TC-GGGC
1 TCGGGGC
781345 TC-GGGC
1 TCGGGGC
781351 TCGGGGC
1 TCGGGGC
781358 TC-GGGC
1 TCGGGGC
781364 TCGGGGC
1 TCGGGGC
781371 TCGGGGC
1 TCGGGGC
781378 TCGGGGC
1 TCGGGGC
781385 TCGGGGC
1 TCGGGGC
781392 TCGGGG-
1 TCGGGGC
781398 TCGGG
1 TCGGG
781403 TTTAGGGTTT
Statistics
Matches: 206, Mismatches: 3, Indels: 21
0.90 0.01 0.09
Matches are distributed among these distances:
4 4 0.02
6 82 0.40
7 120 0.58
ACGTcount: A:0.00, C:0.29, G:0.55, T:0.16
Consensus pattern (7 bp):
TCGGGGC
Found at i:781228 original size:13 final size:13
Alignment explanation
Indices: 781197--781402 Score: 268
Period size: 13 Copynumber: 15.9 Consensus size: 13
781187 GGTTCGGGGT
781197 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
781211 TCGGGGCTCGGGC
1 TCGGGGCTCGGGC
*
781224 GCGGGGCTCGGGC
1 TCGGGGCTCGGGC
781237 TC-GGGCTCGGGGC
1 TCGGGGCTC-GGGC
781250 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
781264 TC-GGGCTCGGGC
1 TCGGGGCTCGGGC
781276 TC-GGGCTCGGGGC
1 TCGGGGCTC-GGGC
781289 TC---GCTCGGGGC
1 TCGGGGCTC-GGGC
781300 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
781314 TC-GGGCTCGGGC
1 TCGGGGCTCGGGC
781326 TCGGGGCTCGGGC
1 TCGGGGCTCGGGC
781339 TC-GGGCTCGGGC
1 TCGGGGCTCGGGC
781351 TCGGGGCTCGGGC
1 TCGGGGCTCGGGC
781364 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
781378 TCGGGGCTCGGGGC
1 TCGGGGCTC-GGGC
781392 TCGGGG-TCGGG
1 TCGGGGCTCGGG
781403 TTTAGGGTTT
Statistics
Matches: 181, Mismatches: 2, Indels: 20
0.89 0.01 0.10
Matches are distributed among these distances:
11 11 0.06
12 39 0.22
13 74 0.41
14 57 0.31
ACGTcount: A:0.00, C:0.30, G:0.55, T:0.15
Consensus pattern (13 bp):
TCGGGGCTCGGGC
Found at i:781410 original size:7 final size:7
Alignment explanation
Indices: 781400--781740 Score: 400
Period size: 7 Copynumber: 50.4 Consensus size: 7
781390 GCTCGGGGTC
781400 GGGTTTA
1 GGGTTTA
781407 GGGTTTA
1 GGGTTTA
781414 GGGTTTA
1 GGGTTTA
781421 -GG-TTA
1 GGGTTTA
781426 -GGTTTA
1 GGGTTTA
781432 GGGTTTA
1 GGGTTTA
781439 GGGTTTA
1 GGGTTTA
781446 GGGTTTA
1 GGGTTTA
781453 GGGTTTA
1 GGGTTTA
781460 GGGTTTA
1 GGGTTTA
781467 GGGTTTA
1 GGGTTTA
781474 GGGTTTA
1 GGGTTTA
781481 GGGTTTA
1 GGGTTTA
781488 -GGTTTA
1 GGGTTTA
781494 -GGTTTA
1 GGGTTTA
781500 -GGTTTA
1 GGGTTTA
781506 GGGTTTA
1 GGGTTTA
781513 GGGTTTA
1 GGGTTTA
781520 GGGTTTA
1 GGGTTTA
781527 GGGTTTA
1 GGGTTTA
781534 GGGTTTA
1 GGGTTTA
781541 -GGTTTA
1 GGGTTTA
781547 GGGTTTA
1 GGGTTTA
781554 GGG-TTA
1 GGGTTTA
781560 -GGTTTA
1 GGGTTTA
781566 GGG-TTA
1 GGGTTTA
781572 GGGTTTA
1 GGGTTTA
781579 GGG-TTA
1 GGGTTTA
*
781585 GGCTTTA
1 GGGTTTA
*
781592 GGGCTTA
1 GGGTTTA
*
781599 GGGCTTA
1 GGGTTTA
*
781606 GGGCTTA
1 GGGTTTA
*
781613 GGGCTTA
1 GGGTTTA
*
781620 GGGCTTA
1 GGGTTTA
*
781627 GGGCTTA
1 GGGTTTA
*
781634 GGGCTTA
1 GGGTTTA
*
781641 GGGCTTA
1 GGGTTTA
*
781648 GGGCTTA
1 GGGTTTA
*
781655 GGGCTTA
1 GGGTTTA
*
781662 GGGCTTA
1 GGGTTTA
*
781669 GGGCTTA
1 GGGTTTA
*
781676 GGGCTTA
1 GGGTTTA
*
781683 -GGCTTA
1 GGGTTTA
*
781689 GGGCTTA
1 GGGTTTA
*
781696 GGGCTTA
1 GGGTTTA
*
781703 GGGCTTA
1 GGGTTTA
*
781710 GGGCTTA
1 GGGTTTA
*
781717 GGGCTTA
1 GGGTTTA
*
781724 GGGCTTA
1 GGGTTTA
*
781731 GGGCTTA
1 GGGTTTA
781738 GGG
1 GGG
781741 CT
Statistics
Matches: 322, Mismatches: 3, Indels: 18
0.94 0.01 0.05
Matches are distributed among these distances:
5 7 0.02
6 52 0.16
7 263 0.82
ACGTcount: A:0.15, C:0.06, G:0.42, T:0.37
Consensus pattern (7 bp):
GGGTTTA
Done.