Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009420.1 Hibiscus syriacus cultivar Beakdansim tig00113393_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: 47088
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7477 original size:2 final size:2
Alignment explanation
Indices: 7470--7499 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7460 GTTATTGATA
7470 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7500 GATTCAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8611 original size:2 final size:2
Alignment explanation
Indices: 8604--8628 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8594 CTCGAGGTAC
8604 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8629 CACATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9301 original size:57 final size:57
Alignment explanation
Indices: 9208--9333 Score: 189
Period size: 57 Copynumber: 2.2 Consensus size: 57
9198 TTCGATTTGC
* * ** * *
9208 GAAATTCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTATCATTGCGAATTT
1 GAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAATTT
9265 GAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAATTT
1 GAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAATTT
*
9322 GAAAATTGCGTT
1 GAAAATCGCGTT
9334 CGGTAATTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (57 bp):
GAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAATTT
Found at i:9342 original size:34 final size:34
Alignment explanation
Indices: 9299--9367 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
9289 TTTACCTATA
9299 TCGGTAATTAGCATTGCGAATTTGAAAATTGCGT
1 TCGGTAATTAGCATTGCGAATTTGAAAATTGCGT
*
9333 TCGGTAATTAGTATTGCGAATTTGAAAATTGCGT
1 TCGGTAATTAGCATTGCGAATTTGAAAATTGCGT
9367 T
1 T
9368 GCGATAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (34 bp):
TCGGTAATTAGCATTGCGAATTTGAAAATTGCGT
Found at i:9397 original size:91 final size:91
Alignment explanation
Indices: 9242--9418 Score: 266
Period size: 91 Copynumber: 1.9 Consensus size: 91
9232 TTTACCTATA
*
9242 TCGGTAATTATCATTGCGAATTTGAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAAT
1 TCGGTAATTATCATTGCGAATTTGAAAATCGCGTTGCCATAATACTATTTACCTATATCGGTAAT
* *
9307 TAGCATTGCGAATTTGAAAATTGCGT
66 TAGCATTACGAATATGAAAATTGCGT
* * * *
9333 TCGGTAATTAGT-ATTGCGAATTTGAAAATTGCGTTGCGATAATACTGTTTAGCTATATCGGTAA
1 TCGGTAATTA-TCATTGCGAATTTGAAAATCGCGTTGCCATAATACTATTTACCTATATCGGTAA
*
9397 TTAGCGTTACGAATATGAAAAT
65 TTAGCATTACGAATATGAAAAT
9419 CTCGTTGCGA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 76 0.99
92 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (91 bp):
TCGGTAATTATCATTGCGAATTTGAAAATCGCGTTGCCATAATACTATTTACCTATATCGGTAAT
TAGCATTACGAATATGAAAATTGCGT
Found at i:9429 original size:20 final size:20
Alignment explanation
Indices: 9400--9445 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
9390 TCGGTAATTA
*
9400 GCGTTACGAATATGAAAATC
1 GCGTTGCGAATATGAAAATC
* *
9420 TCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATATGAAAATC
9440 GCGTTG
1 GCGTTG
9446 TGATAGTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (20 bp):
GCGTTGCGAATATGAAAATC
Found at i:9475 original size:77 final size:77
Alignment explanation
Indices: 9346--9505 Score: 221
Period size: 77 Copynumber: 2.1 Consensus size: 77
9336 GTAATTAGTA
* *
9346 TTGCGAATTTGAAAATTGCGTTGCGATAATACTGTTTAGCTATATCGGTAATTAGCGTTACGAAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTAGCTATATCGGTAATTAGCGTTACGAAT
* *
9411 ATGAAAATCTCG
66 ATAAAAATCGCG
* * * ** *
9423 TTGCGAATTTGAAAATCGCGTTGTGATAGTACTATTTATCTATATCTTTAATTAGCGTTGCGAAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTAGCTATATCGGTAATTAGCGTTACGAAT
*
9488 TTAAAAATCGCG
66 ATAAAAATCGCG
9500 TTGCGA
1 TTGCGA
9506 TAGTATTGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (77 bp):
TTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTAGCTATATCGGTAATTAGCGTTACGAAT
ATAAAAATCGCG
Found at i:9482 original size:57 final size:56
Alignment explanation
Indices: 9421--9620 Score: 292
Period size: 57 Copynumber: 3.5 Consensus size: 56
9411 ATGAAAATCT
* * **
9421 CGTTGCGAATTTGAAAATCGCGTTGTGATAGTACTATTTATCTATATCTTTAATTAG
1 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTA-CTATATCGGTAATTAG
* * *
9478 CGTTGCGAATTTAAAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAA
1 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTA-CTATATCGGTAATTAG
*
9535 CGTTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAG
1 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTAC-TATATCGGTAATTAG
*
9592 CGTTGCGAATTTGAAAATCACGTTGCGAT
1 CGTTGCGAATTTGAAAATCGCGTTGCGAT
9621 TTTGGAACCT
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
56 1 0.01
57 127 0.99
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (56 bp):
CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACTATATCGGTAATTAG
Found at i:11002 original size:35 final size:35
Alignment explanation
Indices: 10954--11023 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
10944 TACACAATTT
10954 GCTAATATATTTGAATTAATCA-TTGTTATCCGATC
1 GCTAATATATTTGAATTAATCATTTG-TATCCGATC
*
10989 GCTAATATCTTTGAATTAATCATTTGTATCCGATC
1 GCTAATATATTTGAATTAATCATTTGTATCCGATC
11024 TATTGATCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 30 0.91
36 3 0.09
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (35 bp):
GCTAATATATTTGAATTAATCATTTGTATCCGATC
Found at i:16393 original size:19 final size:19
Alignment explanation
Indices: 16369--16410 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
16359 TTGCAATTAT
16369 AGGTGACGCTACTGTTTTG
1 AGGTGACGCTACTGTTTTG
16388 AGGTGACGCTACTGTTTTG
1 AGGTGACGCTACTGTTTTG
16407 AGGT
1 AGGT
16411 TCATCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (19 bp):
AGGTGACGCTACTGTTTTG
Found at i:22363 original size:2 final size:2
Alignment explanation
Indices: 22356--22399 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
22346 ACTATTCACA
22356 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
22398 AT
1 AT
22400 TAATCTATAC
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:24277 original size:29 final size:29
Alignment explanation
Indices: 24244--24344 Score: 148
Period size: 29 Copynumber: 3.4 Consensus size: 29
24234 TTTGAATAGT
*
24244 TTAAATACTTATTTTGATTAAAAATAATC
1 TTAAATATTTATTTTGATTAAAAATAATC
24273 TTAAATATTTATTTTGATTAAAAATAATC
1 TTAAATATTTATTTTGATTAAAAATAATC
* *
24302 TTAAATATTTATTTTTGATAAAAATAATAATT
1 TTAAATATTTA-TTTTGAT-TAAA-AATAATC
24334 TTAAATATTTA
1 TTAAATATTTA
24345 AATAAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
29 39 0.59
30 7 0.11
31 3 0.05
32 17 0.26
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TTAAATATTTATTTTGATTAAAAATAATC
Found at i:25115 original size:28 final size:28
Alignment explanation
Indices: 25078--25131 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
25068 ACCATCAATG
*
25078 GAAGGGAAGAAAGAAAATACAGAAACAA
1 GAAGGAAAGAAAGAAAATACAGAAACAA
* * *
25106 GAAGGAAAGAAATAAGATAGAGAAAC
1 GAAGGAAAGAAAGAAAATACAGAAAC
25132 GAGATTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.26, T:0.06
Consensus pattern (28 bp):
GAAGGAAAGAAAGAAAATACAGAAACAA
Found at i:41356 original size:27 final size:26
Alignment explanation
Indices: 41314--41365 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
41304 GCTACAAAAG
*
41314 AAAAACATAAAATTAAGGGATTAAAT
1 AAAAACATAAAATTAAAGGATTAAAT
*
41340 AAAAA-ATAGAAATTTAAAGTATTAAA
1 AAAAACATA-AAA-TTAAAGGATTAAA
41366 ATAGCGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 3 0.14
26 8 0.36
27 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (26 bp):
AAAAACATAAAATTAAAGGATTAAAT
Found at i:43213 original size:152 final size:152
Alignment explanation
Indices: 42933--43236 Score: 590
Period size: 152 Copynumber: 2.0 Consensus size: 152
42923 TCCTTCGTCG
42933 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
42998 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
43063 TGAAATCCAATGTTGTTTGTGA
131 TGAAATCCAATGTTGTTTGTGA
43085 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
* *
43150 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
43215 TGAAATCCAATGTTGTTTGTGA
131 TGAAATCCAATGTTGTTTGTGA
43237 GCACGATATC
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (152 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCATTCGCTATAAAGT
TGAAATCCAATGTTGTTTGTGA
Found at i:43367 original size:170 final size:170
Alignment explanation
Indices: 43085--43395 Score: 604
Period size: 170 Copynumber: 1.8 Consensus size: 170
43075 TTGTTTGTGA
43085 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
43150 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
43215 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
131 TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
*
43255 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGA
1 TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
*
43320 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTGAAGT
66 ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
43385 TGAAATCCAAT
131 TGAAATCCAAT
43396 CTTCAGTAAA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 139 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (170 bp):
TGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGAAATTGGCTCTGA
ATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGATATCCTTCGCTGTAAAGT
TGAAATCCAATGTTGTTTGTGAGCACGATATCCTTCGTCG
Done.