Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006417.1 Hibiscus syriacus cultivar Beakdansim tig00015482_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: 67829
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1364 original size:30 final size:27
Alignment explanation
Indices: 1324--1403 Score: 70
Period size: 30 Copynumber: 2.8 Consensus size: 27
1314 AATTTTCTTA
*
1324 ATATTATTTATCTGATATCTGATTTACTGT
1 ATATTTTTTATCTGATATCTGA-TTAC--T
* * *
1354 ATATTTTTTATATGATCTATGATTACT
1 ATATTTTTTATCTGATATCTGATTACT
* *
1381 ATATTTCTGTATCTGATTTCTGA
1 ATATTT-TTTATCTGATATCTGA
1404 GTATGAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 7 0.17
28 12 0.29
29 4 0.10
30 18 0.44
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (27 bp):
ATATTTTTTATCTGATATCTGATTACT
Found at i:5378 original size:63 final size:63
Alignment explanation
Indices: 5277--5406 Score: 206
Period size: 63 Copynumber: 2.1 Consensus size: 63
5267 TTCCATAGAC
* * * *
5277 CAAAATCTTCAAACCTTAATAACAATTAATACCCAGAAACTAAAAGAGGGAAAACCCAAAGAT
1 CAAAATCTTCAAACCTTAATAACAAATAATACCAAGAAACTAAAAAAAGGAAAACCCAAAGAT
* *
5340 CAAAATCTTCAAACTTTAATAACAAATAATACCAAGAAACTAAAAAAAGGAAACCCCAAAGAT
1 CAAAATCTTCAAACCTTAATAACAAATAATACCAAGAAACTAAAAAAAGGAAAACCCAAAGAT
5403 CAAA
1 CAAA
5407 CAGCCAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.55, C:0.20, G:0.08, T:0.17
Consensus pattern (63 bp):
CAAAATCTTCAAACCTTAATAACAAATAATACCAAGAAACTAAAAAAAGGAAAACCCAAAGAT
Found at i:8395 original size:20 final size:19
Alignment explanation
Indices: 8354--8406 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
8344 AATGCATTTT
* *
8354 ATGCATCAATGCACATACC
1 ATGCATCGATGCACAGACC
8373 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCAC-AGACC
8393 ATGCATCGATGCAC
1 ATGCATCGATGCAC
8407 TCAGGCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAGACC
Found at i:10418 original size:21 final size:20
Alignment explanation
Indices: 10388--10426 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10378 TATGAGAAAT
10388 TGTTTAAAATAT-AAAAATGA
1 TGTTTAAAAT-TGAAAAATGA
10408 TGTTTCAAAATTGAAAAAT
1 TGTTT-AAAATTGAAAAAT
10427 AAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (20 bp):
TGTTTAAAATTGAAAAATGA
Found at i:17082 original size:45 final size:46
Alignment explanation
Indices: 17033--17120 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
17023 GAAAATCGAA
* * *
17033 TGCATTTTATGCATCGATGCA-TATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
17078 TGCATTTGATGCATCGATGCACAAGACCATGTATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
17121 CAGGCTACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:17969 original size:21 final size:21
Alignment explanation
Indices: 17943--18005 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
17933 AGTCGAGGGT
*
17943 TATAGTGGTTATTCGGGACAA
1 TATAGTGGTTCTTCGGGACAA
17964 TATAGTGGTTCTTCGGGACAA
1 TATAGTGGTTCTTCGGGACAA
* *
17985 TACAGTGGTCCTTCGGGACAA
1 TATAGTGGTTCTTCGGGACAA
18006 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (21 bp):
TATAGTGGTTCTTCGGGACAA
Found at i:19051 original size:38 final size:37
Alignment explanation
Indices: 18980--19082 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 37
18970 CACTGAATAT
*
18980 TTGTCCCGAAGGACCACTATATCCCGAAGGACCATTGA
1 TTGTCCCGAA-GACCACTATATCCCGAAGGACCACTGA
* * * * * *
19018 TTGTTCCGAAGAACCACTATGTTCTGAATGACCACTGT
1 TTGTCCCGAAG-ACCACTATATCCCGAAGGACCACTGA
19056 TTGTCCCGAATGACCACTGATAATCCC
1 TTGTCCCGAA-GACCACT-AT-ATCCC
19083 TCGACTCTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
37 1 0.02
38 44 0.88
39 3 0.06
40 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (37 bp):
TTGTCCCGAAGACCACTATATCCCGAAGGACCACTGA
Found at i:19082 original size:20 final size:20
Alignment explanation
Indices: 19043--19082 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19033 ACTATGTTCT
* **
19043 GAATGACCACTGTTTGTCCC
1 GAATGACCACTGATAATCCC
19063 GAATGACCACTGATAATCCC
1 GAATGACCACTGATAATCCC
19083 TCGACTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (20 bp):
GAATGACCACTGATAATCCC
Found at i:22069 original size:21 final size:21
Alignment explanation
Indices: 22045--22087 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22035 TGTAGCAGTA
*
22045 CTGTAGCAGGGTATCGGTTCC
1 CTGTAGCAGGGAATCGGTTCC
22066 CTGTAGCAGGGAATCGGTTCC
1 CTGTAGCAGGGAATCGGTTCC
22087 C
1 C
22088 CTATGACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.26
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGGTTCC
Found at i:22557 original size:2 final size:2
Alignment explanation
Indices: 22550--22593 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
22540 GGATATCGGA
22550 AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
22592 AT
1 AT
22594 GCACGAACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25424 original size:39 final size:40
Alignment explanation
Indices: 25335--25424 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
25325 GTTTTGATAA
* *
25335 AATAATATTTTATATTAAAACTGAAAATATTATTTTTTTT
1 AATAATATTTTAGATTAAAACTGAAAATATTATTATTTTT
** * * *
25375 CGTAATATTTTCGATTACAACTGAAAATGTTA-TATTTTT
1 AATAATATTTTAGATTAAAACTGAAAATATTATTATTTTT
25414 AATAATATTTT
1 AATAATATTTT
25425 TAGTTATAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
39 15 0.37
40 26 0.63
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (40 bp):
AATAATATTTTAGATTAAAACTGAAAATATTATTATTTTT
Found at i:30823 original size:35 final size:35
Alignment explanation
Indices: 30784--30863 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
30774 TTATTCCTTG
*
30784 AACCAAACACGATAATCTTAAATTCCTACTAAATC
1 AACCAAACACGATAATCTTAAATTCCTACTAAACC
*
30819 AACCAAACACGATAATCTTAAATTTCTACTAAACC
1 AACCAAACACGATAATCTTAAATTCCTACTAAACC
30854 AACCAAACAC
1 AACCAAACAC
30864 AAAATACAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.23
Consensus pattern (35 bp):
AACCAAACACGATAATCTTAAATTCCTACTAAACC
Found at i:40153 original size:25 final size:25
Alignment explanation
Indices: 40124--40182 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
40114 TGAATATTAT
40124 TATAATTATCTTTAAATATATAAGG
1 TATAATTATCTTTAAATATATAAGG
40149 TATAATTATCTTTAAATATATAAGG
1 TATAATTATCTTTAAATATATAAGG
40174 TATAATTAT
1 TATAATTAT
40183 ATTATTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (25 bp):
TATAATTATCTTTAAATATATAAGG
Found at i:47517 original size:18 final size:17
Alignment explanation
Indices: 47490--47523 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47480 TAAAAATAAG
*
47490 AAAAATAATTCCTAAAA
1 AAAAATAATTCATAAAA
47507 AAAAGATAATTCATAAA
1 AAAA-ATAATTCATAAA
47524 GATAATTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATAATTCATAAAA
Found at i:48423 original size:8 final size:9
Alignment explanation
Indices: 48402--48435 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
48392 AAATCACCCT
48402 TTTTTTCAA
1 TTTTTTCAA
48411 TTTTTTCAA
1 TTTTTTCAA
* *
48420 TTTTTTTAT
1 TTTTTTCAA
48429 TTTTTTC
1 TTTTTTC
48436 TTTTATGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTCAA
Found at i:51733 original size:15 final size:15
Alignment explanation
Indices: 51713--51780 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
51703 TGTTTAAAGA
*
51713 AAAATAAAATAGAAT
1 AAAATAAAATTGAAT
*
51728 AAAATAAGCATTTG-AT
1 AAAATAA--AATTGAAT
51744 AAAATAAAATTGAAT
1 AAAATAAAATTGAAT
* *
51759 AAAATAAATTTAAAT
1 AAAATAAAATTGAAT
*
51774 GAAATAA
1 AAAATAA
51781 GGTGTGCTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.09
15 28 0.64
16 9 0.20
17 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (15 bp):
AAAATAAAATTGAAT
Found at i:60214 original size:6 final size:6
Alignment explanation
Indices: 60203--60230 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
60193 TTAGCATCTT
60203 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
60231 GAAAACTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Done.