Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006360.1 Hibiscus syriacus cultivar Beakdansim tig00015249_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: 48746
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:430 original size:21 final size:21
Alignment explanation
Indices: 399--459 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
389 AGTCTTATCT
399 AGCCG-TTGGGGATGTTTTAG
1 AGCCGTTTGGGGATGTTTTAG
419 AGCCGTTTGGGGATGTTTTAG
1 AGCCGTTTGGGGATGTTTTAG
*
440 AGCCTTTTGGGGATGATTTT
1 AGCCGTTTGGGGATG-TTTT
460 CTGCAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 5 0.13
21 29 0.76
22 4 0.11
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.39
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTAG
Found at i:945 original size:17 final size:19
Alignment explanation
Indices: 901--950 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
891 AAATTTAATG
*
901 AAAAGATACCATTGTTAAC
1 AAAAGATACCAATGTTAAC
*
920 AAAAGGATATCAATGTT-A-
1 AAAA-GATACCAATGTTAAC
938 AAAAGATACCAAT
1 AAAAGATACCAAT
951 TGTTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.30
18 4 0.15
19 5 0.19
20 10 0.37
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAAGATACCAATGTTAAC
Found at i:7571 original size:18 final size:17
Alignment explanation
Indices: 7548--7581 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7538 CAATGCGGAG
7548 AATAAACATTTCATTACT
1 AATAAACA-TTCATTACT
*
7566 AATAAATATTCATTAC
1 AATAAACATTCATTAC
7582 CTCTTGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAACATTCATTACT
Found at i:18355 original size:28 final size:27
Alignment explanation
Indices: 18302--18356 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
18292 GAGATTGAAT
* *
18302 AAAATGGGTTTTTGAGTGTTATGTTAG
1 AAAATGAGTTTTTAAGTGTTATGTTAG
18329 AAAATGAGTTTTTAATGATGTT-TGTTAG
1 AAAATGAGTTTTTAA-G-TGTTATGTTAG
18357 TATTTGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 7 0.29
29 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.45
Consensus pattern (27 bp):
AAAATGAGTTTTTAAGTGTTATGTTAG
Found at i:19240 original size:55 final size:55
Alignment explanation
Indices: 19198--19581 Score: 624
Period size: 55 Copynumber: 7.0 Consensus size: 55
19188 TAATTTGTTT
*
19198 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTTA
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
19253 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
* * *
19308 ATGAATTTCTGTATGGGCACTTTATGTGTAACCTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
** * *
19363 ATGAATTTTTGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGGGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
*
19418 ATGAATTTCCGTATGGGCACTTTATGTGTAAATTTAAGAAATTCATACTAAGTGA
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
* * *
19473 ATGAATTTCCATATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
* * * *
19528 ATGAATTTCTGTATGGGCACTTTATGTGCAAAATTAGGAAATTCATACTAAGTG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTG
19582 TAAAAATTTC
Statistics
Matches: 307, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 307 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
Found at i:20254 original size:15 final size:16
Alignment explanation
Indices: 20236--20265 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20226 TCCGAAAAAA
20236 TTTA-ATATCCAAATT
1 TTTAGATATCCAAATT
20251 TTTAGATATCCAAAT
1 TTTAGATATCCAAAT
20266 ATTTGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTAGATATCCAAATT
Found at i:22780 original size:262 final size:261
Alignment explanation
Indices: 22316--22849 Score: 921
Period size: 262 Copynumber: 2.0 Consensus size: 261
22306 CGATGAACTC
* *
22316 ATGTTTGAATTTAGTAGTAAATCAAGCTTAAAATATTTTATTCAATTAGGCCTAAGAGAAGGAGA
1 ATGTTTGAATTAAGTAGAAAATCAAGCTTAAAATATTTTATTCAATTAGGCCTAAGAGAAGGAGA
22381 CAAAGAAAAATAGTGGGAAAATTATACGTGTAGAAATGATGTATGGGTGATTCTACATGCTTAAA
66 C-AAGAAAAATAGTGGGAAAATTATACGTGTAGAAATGATGTATGGGTGATTCTACATGCTTAAA
*
22446 ATATGATTTGGACCAATCTGGGAAATTGTGATAGTATAGGAACCTATTTGTATAGTTTAAGAAAA
130 ATATGATTTGGACCAATCTGAGAAATTGTGATAGTATAGGAACCTATTTGTATAGTTTAAGAAAA
* *
22511 ATAAGGATTTATGTACAATTGTGTAATAGTTGATGTGTTATGTTAAAATTAAATGCTGGAA-TTT
195 ATAAGGATCTATATACAATTGTGTAATAGTTGATGTGTTATGTTAAAATTAAATGCTGGAATTTT
22575 AG
260 AG
*
22577 ATGTTTGAATTAAGTAGAAAATCAAGCTTAAAATATTTTATTCAATTAGGCCTAGGAGAAGGAGA
1 ATGTTTGAATTAAGTAGAAAATCAAGCTTAAAATATTTTATTCAATTAGGCCTAAGAGAAGGAGA
22642 C-AGAAAAATAGTGGGAAAATTATACAAGGTGTAGAAATGATGTATGGGTGATTCTACATGCTTA
66 CAAGAAAAATAGTGGGAAAATTATAC---GTGTAGAAATGATGTATGGGTGATTCTACATGCTTA
*
22706 AAATATGATTTGGACCAATTTGAGAAATTGTGATAGTATAAGG-ACCTATTTGTATAGTTTAAGA
128 AAATATGATTTGGACCAATCTGAGAAATTGTGATAGTAT-AGGAACCTATTTGTATAGTTTAAGA
*
22770 AAAATAAGGATCTATATGCAATTGTGTAATAGTTGATGTGTTATGTTAAAATTAAATGCTGGAAT
192 AAAATAAGGATCTATATACAATTGTGTAATAGTTGATGTGTTATGTTAAAATTAAATGCTGGAAT
22835 TTTAG
257 TTTAG
*
22840 ATGTTAGAAT
1 ATGTTTGAAT
22850 GTTGAATTTG
Statistics
Matches: 259, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
259 24 0.09
261 63 0.24
262 155 0.60
263 17 0.07
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (261 bp):
ATGTTTGAATTAAGTAGAAAATCAAGCTTAAAATATTTTATTCAATTAGGCCTAAGAGAAGGAGA
CAAGAAAAATAGTGGGAAAATTATACGTGTAGAAATGATGTATGGGTGATTCTACATGCTTAAAA
TATGATTTGGACCAATCTGAGAAATTGTGATAGTATAGGAACCTATTTGTATAGTTTAAGAAAAA
TAAGGATCTATATACAATTGTGTAATAGTTGATGTGTTATGTTAAAATTAAATGCTGGAATTTTA
G
Found at i:36012 original size:17 final size:18
Alignment explanation
Indices: 35985--36018 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
35975 AAAACAAAAA
35985 ATAACTAAAAATTTTACT
1 ATAACTAAAAATTTTACT
36003 ATAACT-AAAATTTTAC
1 ATAACTAAAAATTTTAC
36019 AAAAATATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTAAAAATTTTACT
Found at i:38833 original size:20 final size:20
Alignment explanation
Indices: 38808--38850 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
38798 TCCTAAGACT
*
38808 CATTTAGGTTCATATAGATG
1 CATTTAGGATCATATAGATG
*
38828 CATTTAGGATCATATAGTTG
1 CATTTAGGATCATATAGATG
38848 CAT
1 CAT
38851 GTGGTGGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.40
Consensus pattern (20 bp):
CATTTAGGATCATATAGATG
Found at i:43253 original size:41 final size:41
Alignment explanation
Indices: 43167--43304 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 41
43157 CGATTTTGGC
* * * *
43167 AGCATGTACTAATTCTCAATTTGATTCAATTCAATCAT-AA
1 AGCATGCAATAATTCACAATTTGATTCAATTCAATCATGGA
** * * *
43207 TAGCATGCAATGGTTTACCATTTGATTCAATTCAATCATGGC
1 -AGCATGCAATAATTCACAATTTGATTCAATTCAATCATGGA
** *
43249 AGCATGCAATAATTCACAATTCAATTCAATTCAATTATGGA
1 AGCATGCAATAATTCACAATTTGATTCAATTCAATCATGGA
*
43290 AGCATACAATAATTC
1 AGCATGCAATAATTC
43305 CCCATTCAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (41 bp):
AGCATGCAATAATTCACAATTTGATTCAATTCAATCATGGA
Found at i:43312 original size:41 final size:41
Alignment explanation
Indices: 43231--43372 Score: 126
Period size: 41 Copynumber: 3.5 Consensus size: 41
43221 TTACCATTTG
* *
43231 ATTCAATTCAATCATGGCAGCATGCAATAATTCACAATTCA
1 ATTCAATTCAATCATGGAAGCATACAATAATTCACAATTCA
* * *
43272 ATTCAATTCAATTATGGAAGCATACAATAATTCCCCATTCAA
1 ATTCAATTCAATCATGGAAGCATACAATAATTCACAATTC-A
* * * * * * *
43314 ATT-GATTCGATCAAGTTAA-TATGCAATAATTCATAATTCA
1 ATTCAATTCAATCATG-GAAGCATACAATAATTCACAATTCA
* *
43354 ATTCCATTCGATCATGGAA
1 ATTCAATTCAATCATGGAA
43373 ACATGTATTT
Statistics
Matches: 80, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
40 6 0.08
41 68 0.85
42 6 0.08
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (41 bp):
ATTCAATTCAATCATGGAAGCATACAATAATTCACAATTCA
Found at i:45141 original size:22 final size:22
Alignment explanation
Indices: 45111--45177 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
45101 ATTGGGTCCT
45111 TTTTCCAATTCAATTAATTTAAA
1 TTTT-CAATTCAATTAATTTAAA
*
45134 TTTTCAATTCAATTAGATATT-TA
1 TTTTCAATTCAATTA-AT-TTAAA
*
45157 -TTT-AATTCCATTAATTTAAA
1 TTTTCAATTCAATTAATTTAAA
45177 T
1 T
45178 ATCTATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 9 0.24
22 14 0.38
23 7 0.19
24 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (22 bp):
TTTTCAATTCAATTAATTTAAA
Done.