Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000307.1 Hibiscus syriacus cultivar Beakdansim tig00000577_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: 58485
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5834 original size:74 final size:75
Alignment explanation
Indices: 5537--5924 Score: 409
Period size: 75 Copynumber: 5.2 Consensus size: 75
5527 CTGCAACAGA
* * * * *
5537 AACTGTTGATCAAATTGGGATTGC-GACAATATAAAAAC-AGAATCATGAAGTTGTTGTTGCTGC
1 AACTGTTGATCAAATTGGGGTTGCTG-CAATAT-ATAACTAGAATCCTGAACTAGTTGTTG-T--
*
5600 TGTTGTCGCTGCTCCTGC
61 TG-T-T-GCTGCTGCTGC
** * ** * * *
5618 TGCTGTTGTTCAAATTGGAATTGCTGCAATATATAACCAGAATCCGGAACTA------GTTGCTG
1 AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACTAGAATCCTGAACTAGTTGTTGTTGTTG
*
5677 CTGCTGCTTC
66 CTGCTGCTGC
* * * * *
5687 AACTGTTGATCAAATTGGGGTTGCTGAAATATATAA-TCACAATCCGGAACAAGTTGTTGTTGCT
1 AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACT-AGAATCCTGAACTAGTTGTTGTTGTT
5751 GCTGCTGCTGC
65 GCTGCTGCTGC
* *
5762 AACTGTTGATCAAATTGAGGTTGCTGCAAT-TATAACTAGAATCCTGAACTAGTTGATGTTGTTG
1 AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACTAGAATCCTGAACTAGTTGTTGTTGTTG
*
5826 TTGCTGCTGC
66 CTGCTGCTGC
*
5836 AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACTAGAATCCTGAACTAGTTGTTCTTGTTG
1 AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACTAGAATCCTGAACTAGTTGTTGTTGTTG
5901 CTGCTGCTGC
66 CTGCTGCTGC
5911 AACTGTTGATCAAA
1 AACTGTTGATCAAA
5925 CTGTTGAACG
Statistics
Matches: 262, Mismatches: 34, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
69 51 0.19
70 1 0.00
72 2 0.01
74 66 0.25
75 101 0.39
80 4 0.02
81 36 0.14
82 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (75 bp):
AACTGTTGATCAAATTGGGGTTGCTGCAATATATAACTAGAATCCTGAACTAGTTGTTGTTGTTG
CTGCTGCTGC
Found at i:7996 original size:15 final size:15
Alignment explanation
Indices: 7976--8007 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7966 ATTGTTTTGT
7976 TGAATCAGTCAGCAC
1 TGAATCAGTCAGCAC
*
7991 TGAATCATTCAGCAC
1 TGAATCAGTCAGCAC
8006 TG
1 TG
8008 TTTTGTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (15 bp):
TGAATCAGTCAGCAC
Found at i:8010 original size:38 final size:38
Alignment explanation
Indices: 7953--8040 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
7943 ACTTATGTGT
* *
7953 TGAATCATTCAACATTGTTTTGTTGAATCAGTCAGCAC
1 TGAATCATTCAGCACTGTTTTGTTGAATCAGTCAGCAC
* *
7991 TGAATCATTCAGCACTGTTTTGTTGAATCAGTTAGTAC
1 TGAATCATTCAGCACTGTTTTGTTGAATCAGTCAGCAC
8029 TGAATCATTCAG
1 TGAATCATTCAG
8041 AGATGCGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (38 bp):
TGAATCATTCAGCACTGTTTTGTTGAATCAGTCAGCAC
Found at i:21934 original size:61 final size:60
Alignment explanation
Indices: 21890--22011 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
21880 TAGTTTGGAG
*
21890 ATGAAACTAAAAATATTAAAAAGTTTAAGGA-CTAATTTAAAATGATAATCATAGTTTAAGA
1 ATGAAA-TAAAAATATTAAAAAGTTTAAAGATC-AATTTAAAATGATAATCATAGTTTAAGA
** * * * *
21951 ATGAAATTGAAATATTTAAAAGTTTAAAGATCAATTTAAAATAAAAATCATAATTTAAGA
1 ATGAAATAAAAATATTAAAAAGTTTAAAGATCAATTTAAAATGATAATCATAGTTTAAGA
22011 A
1 A
22012 CATACAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 46 0.87
61 7 0.13
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (60 bp):
ATGAAATAAAAATATTAAAAAGTTTAAAGATCAATTTAAAATGATAATCATAGTTTAAGA
Found at i:25162 original size:19 final size:19
Alignment explanation
Indices: 25138--25187 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
25128 AAAACGTTTT
25138 TATGAATAGTACTATACGG
1 TATGAATAGTACTATACGG
**
25157 TATGAATAGTACTATATTG
1 TATGAATAGTACTATACGG
*
25176 TATGAACAGTAC
1 TATGAATAGTAC
25188 CGTAAACAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (19 bp):
TATGAATAGTACTATACGG
Found at i:25243 original size:21 final size:21
Alignment explanation
Indices: 25219--25260 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25209 CCATGAATAG
25219 TGCTACAGTGTACCGATGCAC
1 TGCTACAGTGTACCGATGCAC
* *
25240 TGCTATAGTGTATCGATGCAC
1 TGCTACAGTGTACCGATGCAC
25261 AAAAACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:27492 original size:12 final size:12
Alignment explanation
Indices: 27462--27494 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
27452 ACTAGTTTTA
*
27462 TGTGATCGTAGT
1 TGTGATTGTAGT
27474 TGTGATTGTAGT
1 TGTGATTGTAGT
27486 TGTGATTGT
1 TGTGATTGT
27495 TTCTAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.33, T:0.48
Consensus pattern (12 bp):
TGTGATTGTAGT
Found at i:29540 original size:33 final size:33
Alignment explanation
Indices: 29501--29575 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
29491 ACATCAGATG
*
29501 ATATGATATATTATCA-TT-TTAAGACGACGTGAC
1 ATATGATATA-TATCACTTCATAA-ACGACGTGAC
* *
29534 ATATGATATATATCACTTCATAAATGATGTGAC
1 ATATGATATATATCACTTCATAAACGACGTGAC
29567 ATATGATAT
1 ATATGATAT
29576 GTTAACCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.14
33 29 0.78
34 3 0.08
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (33 bp):
ATATGATATATATCACTTCATAAACGACGTGAC
Found at i:45161 original size:17 final size:18
Alignment explanation
Indices: 45139--45174 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
45129 TTTTATATGA
*
45139 AATTT-AGGGGTTAAAAT
1 AATTTAAGGGATTAAAAT
45156 AATTTAAGGGATTAAAAT
1 AATTTAAGGGATTAAAAT
45174 A
1 A
45175 CAATAACGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
AATTTAAGGGATTAAAAT
Found at i:51805 original size:18 final size:18
Alignment explanation
Indices: 51782--51834 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
51772 CGTAGAAATT
*
51782 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
51800 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
51818 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
51835 GATAATCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:55595 original size:8 final size:8
Alignment explanation
Indices: 55584--55614 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
55574 AATTAGTTAA
*
55584 TTAGTTTT
1 TTAGTTTG
55592 TTAGTTTG
1 TTAGTTTG
55600 TTAGTTTG
1 TTAGTTTG
55608 TTAGTTT
1 TTAGTTT
55615 AAGTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.19, T:0.68
Consensus pattern (8 bp):
TTAGTTTG
Found at i:58137 original size:15 final size:16
Alignment explanation
Indices: 58100--58138 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
58090 ATATATAAAG
*
58100 ATAAATTCTACTAGTT
1 ATAAATTCAACTAGTT
58116 ATAAATTCAACTA-TT
1 ATAAATTCAACTAGTT
*
58131 TTAAATTC
1 ATAAATTC
58139 GATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (16 bp):
ATAAATTCAACTAGTT
Found at i:58181 original size:11 final size:11
Alignment explanation
Indices: 58167--58362 Score: 69
Period size: 11 Copynumber: 16.5 Consensus size: 11
58157 TCTATTTAAA
*
58167 TATTTAATCAT
1 TATTAAATCAT
*
58178 TATTAAATAAT
1 TATTAAATCAT
58189 TATTAGTAATCAT
1 TATTA--AATCAT
*
58202 TATTAAATCGT
1 TATTAAATCAT
*
58213 TAGTATCAAATTAT
1 TA-T-T-AAATCAT
*
58227 TATTATAATTTAAT
1 TATTA-AA--TCAT
58241 TATTACTAATCAT
1 TATTA--AATCAT
*
58254 TACTAAATC-T
1 TATTAAATCAT
58264 TAGTATCAAATCAT
1 TA-T-T-AAATCAT
* * *
58278 TA--ATATTAA
1 TATTAAATCAT
58287 TA-TAAATCAT
1 TATTAAATCAT
58297 TATTAATAATCAT
1 TATT-A-AATCAT
*
58310 TACTAAAT-AT
1 TATTAAATCAT
58320 TATTACTAAAATCAT
1 TA-T--T-AAATCAT
*
58335 TAAATAAATCAT
1 T-ATTAAATCAT
*
58347 TATTAAAACAT
1 TATTAAATCAT
58358 TATTA
1 TATTA
58363 TATAATTATA
Statistics
Matches: 141, Mismatches: 21, Indels: 46
0.68 0.10 0.22
Matches are distributed among these distances:
9 6 0.04
10 13 0.09
11 43 0.30
12 15 0.11
13 35 0.25
14 22 0.16
15 6 0.04
16 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:58307 original size:13 final size:12
Alignment explanation
Indices: 58290--58362 Score: 69
Period size: 13 Copynumber: 6.0 Consensus size: 12
58280 ATATTAATAT
58290 AAATCATTATTA
1 AAATCATTATTA
*
58302 ATAATCATTACTA
1 A-AATCATTATTA
* *
58315 AATATTATTACTA
1 AA-ATCATTATTA
*
58328 AAATCATTA-AA
1 AAATCATTATTA
58339 TAAATCATTATTA
1 -AAATCATTATTA
58352 AAA-CATTATTA
1 AAATCATTATTA
58363 TATAATTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
11 9 0.17
12 20 0.38
13 23 0.44
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATCATTATTA
Found at i:58367 original size:26 final size:25
Alignment explanation
Indices: 58286--58367 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 25
58276 ATTAATATTA
*
58286 ATATAAATCATTATTAATAATCATT
1 ATATAAATCATTATTAAAAATCATT
*
58311 A-CTAAAT-ATTATTACTAAAATCATT
1 ATATAAATCATTATTA--AAAATCATT
* *
58336 AAATAAATCATTATTAAAACATTATT
1 ATATAAATCATTATTAAAA-ATCATT
58362 ATATAA
1 ATATAA
58368 TTATAAGACT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.15
24 5 0.11
25 13 0.28
26 15 0.32
27 7 0.15
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAAATCATTATTAAAAATCATT
Done.