Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002436.1 Hibiscus syriacus cultivar Beakdansim tig00004988_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: 64244
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2966 original size:12 final size:12
Alignment explanation
Indices: 2949--2973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2939 TGTGCACAAA
2949 ACACATGCCAAT
1 ACACATGCCAAT
2961 ACACATGCCAAT
1 ACACATGCCAAT
2973 A
1 A
2974 ACGAGCCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
ACACATGCCAAT
Found at i:14288 original size:29 final size:29
Alignment explanation
Indices: 14242--14315 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
14232 TTTCATATGT
14242 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
14270 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
14299 TTATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
14316 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:14348 original size:12 final size:12
Alignment explanation
Indices: 14331--14366 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
14321 TATCATGTTC
14331 TCATATCACATG
1 TCATATCACATG
*
14343 TCATATCACATA
1 TCATATCACATG
14355 TCATATCACATG
1 TCATATCACATG
14367 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:14432 original size:23 final size:25
Alignment explanation
Indices: 14382--14432 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
14372 ATATATGTCT
14382 TATGCATGTATCACAACAATTATCATA
1 TATGCATGTATCACAAC-A-TATCATA
*
14409 TATGCATGT-TCACAAC-TATTATA
1 TATGCATGTATCACAACATATCATA
14432 T
1 T
14433 TATAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
26 7 0.30
27 9 0.39
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (25 bp):
TATGCATGTATCACAACATATCATA
Found at i:14782 original size:64 final size:64
Alignment explanation
Indices: 14674--14815 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 64
14664 TAATGAAGGT
* * * **
14674 ATGCATCGATGCACTACTGATGCATTGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATTGATGCATAAAAGGCATTCGATGT-GTCACTATTAATGGG
* * * ** *
14738 ATGCATCGATGCACTCCTTATGCATTGATGCACT-GATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTGATGCATTGATGCA-TAAAAGGCATTCGATGTGTCACTATTAATGGG
14802 ATGCATCGATGCAC
1 ATGCATCGATGCAC
14816 GAATTACATT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 1 0.02
64 63 0.97
65 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATTGATGCATAAAAGGCATTCGATGTGTCACTATTAATGGG
Found at i:14936 original size:21 final size:21
Alignment explanation
Indices: 14910--14986 Score: 154
Period size: 21 Copynumber: 3.7 Consensus size: 21
14900 TTAACCTTGA
14910 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
14931 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
14952 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
14973 TGCATCGATGCACT
1 TGCATCGATGCACT
14987 CTGCCCAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Found at i:21340 original size:29 final size:29
Alignment explanation
Indices: 21294--21367 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
21284 TTTCATATGT
21294 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
21322 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
21351 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
21368 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:21400 original size:12 final size:12
Alignment explanation
Indices: 21383--21418 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
21373 TATCATGTTC
21383 TCATATCACATG
1 TCATATCACATG
21395 TCATATCACATG
1 TCATATCACATG
21407 TCATATCACATG
1 TCATATCACATG
21419 AACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:21834 original size:64 final size:64
Alignment explanation
Indices: 21726--21902 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
21716 TAATGAAGGT
* * ** ** * * **
21726 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* *
21790 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
21854 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
21903 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.03
64 94 0.97
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:21923 original size:64 final size:63
Alignment explanation
Indices: 21789--21950 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 63
21779 TTATTGCTGG
* * *
21789 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAAAGA
* *
21853 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATTAAAGA
** *
21916 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
21951 ATTCAAACAA
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 4 0.05
64 80 0.92
65 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:28795 original size:135 final size:135
Alignment explanation
Indices: 28553--28812 Score: 466
Period size: 135 Copynumber: 1.9 Consensus size: 135
28543 TTTATGAAAA
* * * *
28553 AAATAATAACTATACGGAGATGATCGATCTTTCTAATTAGGAAGTCTAAACGTGTTTTATCCGTA
1 AAATAATAACTATACGAAGATAATCGATATTTCTAATTAGGAAGTCTAAACGTGTCTTATCCGTA
*
28618 AAGAATACTTTAAAAATAGAAAATAGTGAAGAAATTTGTATAATATAAGCTTTAATTTGTATAAA
66 AAGAATACTTTAAAAATAGAAAATAGTGAAGAAATTTGTATAAAATAAGCTTTAATTTGTATAAA
28683 TAAAT
131 TAAAT
*
28688 AAATAATAACTATACGAAGATAATCGATATTTCTAATTAGGAAGTCTAAATGTGTCTTATCCGTA
1 AAATAATAACTATACGAAGATAATCGATATTTCTAATTAGGAAGTCTAAACGTGTCTTATCCGTA
28753 AAGAATACTTTAAAAATAGAAAATAGTGAAGAAATTTGTATAAAATAAGCTTTAATTTGT
66 AAGAATACTTTAAAAATAGAAAATAGTGAAGAAATTTGTATAAAATAAGCTTTAATTTGT
28813 GATACTACAA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
135 119 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (135 bp):
AAATAATAACTATACGAAGATAATCGATATTTCTAATTAGGAAGTCTAAACGTGTCTTATCCGTA
AAGAATACTTTAAAAATAGAAAATAGTGAAGAAATTTGTATAAAATAAGCTTTAATTTGTATAAA
TAAAT
Found at i:33768 original size:15 final size:15
Alignment explanation
Indices: 33720--33769 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
33710 CTTTTCGGGC
* *
33720 TCTTCCTCTTCCTCC
1 TCTTCCTCTTCTTCA
*
33735 TCTTCCTCTTTCTT-T
1 TCTTCCTC-TTCTTCA
33750 TCTTCCTCTTCTTCA
1 TCTTCCTCTTCTTCA
33765 TCTTC
1 TCTTC
33770 TTCAGGAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTTCCTCTTCTTCA
Found at i:35520 original size:17 final size:17
Alignment explanation
Indices: 35500--35546 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
35490 ATTCTATTGA
35500 AATAAA-AATTACATTTT
1 AATAAATAATTA-ATTTT
*
35517 AATAAATACTTAATTTT
1 AATAAATAATTAATTTT
*
35534 AATTAAATCATTA
1 AA-TAAATAATTA
35547 TACTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATAATTAATTTT
Found at i:49371 original size:7 final size:7
Alignment explanation
Indices: 49359--49391 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
49349 AATTTGATCG
49359 AATTTTT
1 AATTTTT
49366 AATTTTT
1 AATTTTT
49373 AATTTTT
1 AATTTTT
49380 -ATATTTT
1 AAT-TTTT
49387 AATTT
1 AATTT
49392 GAGAAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:49643 original size:17 final size:17
Alignment explanation
Indices: 49621--49654 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49611 CATAGTTTGA
49621 AACTTAACACGATATAT
1 AACTTAACACGATATAT
49638 AACTTAACACGATATAT
1 AACTTAACACGATATAT
49655 GAATCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
AACTTAACACGATATAT
Found at i:49788 original size:2 final size:2
Alignment explanation
Indices: 49781--49827 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
49771 TTGAAAATTA
49781 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
49823 AT AT A
1 AT AT A
49828 ATGAAGCTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52878 original size:23 final size:23
Alignment explanation
Indices: 52848--52893 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
52838 TAAAGAGAAA
*
52848 TTGATGGAATCACAAAAATGGGG
1 TTGATGGAAACACAAAAATGGGG
52871 TTGATGGAAACACAAAAATGGGG
1 TTGATGGAAACACAAAAATGGGG
52894 AAGAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.30, T:0.20
Consensus pattern (23 bp):
TTGATGGAAACACAAAAATGGGG
Found at i:52902 original size:22 final size:23
Alignment explanation
Indices: 52858--52902 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52848 TTGATGGAAT
** *
52858 CACAAAAATGGGGTTGATGGAAA
1 CACAAAAATGGGGAAGATAGAAA
52881 CACAAAAATGGGGAAGA-AGAAA
1 CACAAAAATGGGGAAGATAGAAA
52903 GATCACCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.51, C:0.09, G:0.29, T:0.11
Consensus pattern (23 bp):
CACAAAAATGGGGAAGATAGAAA
Found at i:55021 original size:25 final size:25
Alignment explanation
Indices: 54993--55051 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
54983 GTTCAAAAGC
54993 TTATTTAAATTTTTGAAA-AATAAAA
1 TTATTTAAATTTTT-AAATAATAAAA
55018 TTATTTTAAA-TTTTAAATAATAAAA
1 TTA-TTTAAATTTTTAAATAATAAAA
55043 -TATTTAAAT
1 TTATTTAAAT
55052 ATTCAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.19
24 5 0.16
25 14 0.45
26 6 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTATTTAAATTTTTAAATAATAAAA
Found at i:55050 original size:16 final size:16
Alignment explanation
Indices: 55025--55089 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
55015 AAATTATTTT
55025 AAAT-TTTAAATAATA
1 AAATATTTAAATAATA
*
55040 AAATATTTAAATATTCA
1 AAATATTTAAATAAT-A
55057 AAA-ATATT-AATAA-A
1 AAATAT-TTAAATAATA
55071 AAATA-TTAAA-AATTA
1 AAATATTTAAATAA-TA
55086 AAAT
1 AAAT
55090 TAAAATACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 10 0.24
16 15 0.37
17 6 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATTTAAATAATA
Done.