Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001264.1 Hibiscus syriacus cultivar Beakdansim tig00002482_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: 88041
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:9700 original size:143 final size:142
Alignment explanation
Indices: 9378--9760 Score: 509
Period size: 142 Copynumber: 2.7 Consensus size: 142
9368 TTCAACAATG
*
9378 TTGTAACCTAAAATGTTAAATGCGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
1 TTGTAACCTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
* * * * * *
9443 AAGTATTGATACTTAGTTACAACCTAAAGTGTTATCCACTCCAACTTAAAATTTTATATCTTAGG
66 AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAACTTAAAATGTTATATATTAGG
9508 TAACATTTTCGA
131 TAACATTTTCGA
* * * * *
9520 TTGTAACGTAAAATGTTAAATGTAGTTCAATAGTTATTTCATGACAAGTATCAATACTTGTTACT
1 TTGTAACCTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
* * * *
9585 AAATATCGATACTTAGTTACAACCTAAAATATTATACAGTCTAATCTTAAAATGTTATATATTTG
66 AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAA-CTTAAAATGTTATATATTAG
*
9650 GTAATATTTTCGA
130 GTAACATTTTCGA
* ** * *
9663 TTGTAACTTAAAATGTTAAATGTGGTTTGATACTTATTTTACGA-AATGTATCAATACTTGAAAC
1 TTGTAACCTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAA-GTATCAATACTTGTAAC
* * *
9727 TGAGT-TCGATACTTAGTTATAATCTAAAATATTA
65 TAAGTATCGATACTTAGTTACAACCTAAAATATTA
9761 CTCCCTCCAT
Statistics
Matches: 209, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
142 125 0.60
143 84 0.40
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (142 bp):
TTGTAACCTAAAATGTTAAATGTGGTTCAATACTTATTTTATGACAAGTATCAATACTTGTAACT
AAGTATCGATACTTAGTTACAACCTAAAATATTATACACTCCAACTTAAAATGTTATATATTAGG
TAACATTTTCGA
Found at i:11171 original size:6 final size:6
Alignment explanation
Indices: 11146--11188 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
11136 GTATGTGTTG
*
11146 TTAATAA TTAAAA -AAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
1 TTAA-AA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
11189 GATCATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 25 0.76
7 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:11427 original size:24 final size:21
Alignment explanation
Indices: 11400--11450 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 21
11390 AGATAAAATA
11400 TTAATTTAAAGATAAAATATCAAT
1 TTAATTT-AA-ATAAAATATC-AT
11424 TTAAAATTTAAATAAAATATCAT
1 TT--AATTTAAATAAAATATCAT
11447 TTAA
1 TTAA
11451 CCTGTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 2 0.08
23 4 0.16
24 12 0.48
25 2 0.08
26 5 0.20
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAATTTAAATAAAATATCAT
Found at i:11437 original size:19 final size:19
Alignment explanation
Indices: 11390--11428 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11380 TATAAGTTTT
*
11390 AGATAAAATATTAATTTAA
1 AGATAAAATATCAATTTAA
11409 AGATAAAATATCAATTTAA
1 AGATAAAATATCAATTTAA
11428 A
1 A
11429 ATTTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
AGATAAAATATCAATTTAA
Found at i:13705 original size:15 final size:15
Alignment explanation
Indices: 13668--13708 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13658 ATATTCAAAT
13668 AAAA-AATTTAA-TC
1 AAAATAATTTAATTC
*
13681 -AAATACTTTAATTC
1 AAAATAATTTAATTC
13695 AAAATAATTTAATT
1 AAAATAATTTAATT
13709 GTTTTATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 3 0.13
13 6 0.26
14 2 0.09
15 12 0.52
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATAATTTAATTC
Found at i:29407 original size:31 final size:31
Alignment explanation
Indices: 29369--29491 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
29359 CCCGAAGGAC
* *
29369 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
29400 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29431 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
29462 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
29492 CCCTCGACCC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:29986 original size:16 final size:18
Alignment explanation
Indices: 29965--30005 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29955 GCATGTTAAC
29965 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
29981 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
29999 TCATATA
1 ACATATA
30006 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:30388 original size:21 final size:21
Alignment explanation
Indices: 30358--30402 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30348 ATTCTGTCGT
* *
30358 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
30379 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
30400 TTG
1 TTG
30403 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31649 original size:65 final size:63
Alignment explanation
Indices: 31516--31725 Score: 228
Period size: 65 Copynumber: 3.3 Consensus size: 63
31506 TGCACTAAGA
* ** * *
31516 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATTC-TAGTGCATCGATGCATGATTG
31580 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTCTCAGTGCATCGATGCATGATAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATTCT-AGTGCATCGATGCATGAT-T
31645 -
63 G
* * ** *
31645 GTGCATCGATGCATGAAATTCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATTC-TAGTGCATCGATGCAT-GATT
31709 G
63 G
*
31710 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
31726 CTTTGATAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
63 3 0.02
64 50 0.40
65 69 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATTCTAGTGCATCGATGCATGATTG
Found at i:34264 original size:30 final size:30
Alignment explanation
Indices: 34228--34298 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
34218 AACATTTCTC
*
34228 AAATTAAATGTTCAATATAATTTTTTTTAA
1 AAATTAAATGTTCAATATAATTTTTTTAAA
*
34258 AAATTAAACGTTCAATATAATTTTTTTAAA
1 AAATTAAATGTTCAATATAATTTTTTTAAA
34288 AAATTAAATGT
1 AAATTAAATGT
34299 CTGAGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTAAATGTTCAATATAATTTTTTTAAA
Found at i:40353 original size:19 final size:20
Alignment explanation
Indices: 40329--40376 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
40319 AATAGTGATT
*
40329 TTAATATTATAT-TATTATA
1 TTAATATTATATAAATTATA
40348 TTAATATTGA-ATAAATTATA
1 TTAATATT-ATATAAATTATA
40368 -TAATATTAT
1 TTAATATTAT
40377 TCATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAATATTATATAAATTATA
Found at i:42490 original size:2 final size:2
Alignment explanation
Indices: 42483--42534 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
42473 CTCAAATAGC
42483 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42525 CT CT C- CT CT C
1 CT CT CT CT CT C
42535 CTTTTTACAG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:44597 original size:20 final size:20
Alignment explanation
Indices: 44572--44622 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
44562 ATATATTATT
*
44572 TTTTCGAGTTAATCACGAGC
1 TTTTCGAGTCAATCACGAGC
*
44592 TTTTCGAGTCGATCACGAGC
1 TTTTCGAGTCAATCACGAGC
44612 TTTTCGAGTCA
1 TTTTCGAGTCA
44623 GACATCAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
TTTTCGAGTCAATCACGAGC
Found at i:47722 original size:30 final size:30
Alignment explanation
Indices: 47662--47722 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
47652 TTTGATATTC
* *
47662 AACGTTTTATTTTAGGGTAAAAATGCTCAT
1 AACGTTTCATTTTAGGGTAAAAATACTCAT
* *
47692 AACGTTTCATTTTAGGTTAAAAATATTCAT
1 AACGTTTCATTTTAGGGTAAAAATACTCAT
47722 A
1 A
47723 TTTTTTAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (30 bp):
AACGTTTCATTTTAGGGTAAAAATACTCAT
Found at i:51466 original size:15 final size:15
Alignment explanation
Indices: 51446--51475 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51436 AAACTTTGAA
*
51446 AAACATTTTTCAAAG
1 AAACATTTTCCAAAG
51461 AAACATTTTCCAAAG
1 AAACATTTTCCAAAG
51476 TTGGTTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
AAACATTTTCCAAAG
Found at i:55547 original size:16 final size:16
Alignment explanation
Indices: 55523--55556 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
55513 TATCACCGAT
*
55523 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
55539 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
55555 CG
1 CG
55557 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:56025 original size:15 final size:15
Alignment explanation
Indices: 56005--56034 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55995 AAACTTTGAA
*
56005 AAACATTTTTCAAAG
1 AAACATTTTCCAAAG
56020 AAACATTTTCCAAAG
1 AAACATTTTCCAAAG
56035 TTGGTTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
AAACATTTTCCAAAG
Found at i:60313 original size:3 final size:3
Alignment explanation
Indices: 60305--60333 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
60295 GTTGTTACCC
60305 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
60334 TAGCATTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:62350 original size:13 final size:13
Alignment explanation
Indices: 62332--62356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62322 ACAAAATATC
62332 GTATAAAACCATA
1 GTATAAAACCATA
62345 GTATAAAACCAT
1 GTATAAAACCAT
62357 TTAATCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
GTATAAAACCATA
Found at i:64266 original size:56 final size:57
Alignment explanation
Indices: 64201--64308 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 57
64191 ATGTAAAATC
* **
64201 TAATAAATTAATAATTTAAT-ATCTTTCTTATTATTTGTTAGAATATTAATAAAATAT
1 TAATAAATTAATAATTT-ATCATATTTCTTATTATTTACTAGAATATTAATAAAATAT
* *
64258 TAAT-AATTATTAATTTATCATATTTCTTATTATTTACTAGCATATTAATAA
1 TAATAAATTAATAATTTATCATATTTCTTATTATTTACTAGAATATTAATAA
64309 TTATTAACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 2 0.04
56 39 0.87
57 4 0.09
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (57 bp):
TAATAAATTAATAATTTATCATATTTCTTATTATTTACTAGAATATTAATAAAATAT
Found at i:69172 original size:29 final size:29
Alignment explanation
Indices: 69130--69188 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
69120 ATAATATGTA
** *
69130 TTATCACTGCATTAAAGTACTTGTTGGTT
1 TTATCACTGCATTAAAACACTAGTTGGTT
69159 TTATCACTGCATTAAAACACTAGTTGGTT
1 TTATCACTGCATTAAAACACTAGTTGGTT
69188 T
1 T
69189 GAGGTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (29 bp):
TTATCACTGCATTAAAACACTAGTTGGTT
Found at i:77933 original size:24 final size:24
Alignment explanation
Indices: 77888--77934 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
77878 CATGATGAGT
* **
77888 AAAGTACACGAGAGGTTGTTAAAA
1 AAAGTACACAAGAGGTCATTAAAA
77912 AAAGTACACAAGAGGTCATTAAA
1 AAAGTACACAAGAGGTCATTAAA
77935 TTATGCTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (24 bp):
AAAGTACACAAGAGGTCATTAAAA
Found at i:79836 original size:14 final size:14
Alignment explanation
Indices: 79819--79846 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
79809 ACATGGTAAC
79819 TATATAATGGACCT
1 TATATAATGGACCT
79833 TATATAATGGACCT
1 TATATAATGGACCT
79847 AAAGTGTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TATATAATGGACCT
Done.