Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007589.1 Hibiscus syriacus cultivar Beakdansim tig00021849_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: 223780
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:211218 original size:269 final size:268
Alignment explanation
Indices: 210709--211338 Score: 904
Period size: 269 Copynumber: 2.3 Consensus size: 268
210699 AGTTCGGGTC
* * * * * *
210709 ATCTAAGGGTGACATGCCTCCTATGTGATGAGGAGGTCT-AGTTGGGGGATGACACTGCTCATAC
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGA-TCGGGGGATGACACGGCTCATAC
* * ** * * *
210773 ATGATGAAGAGTTCTTGGCCATCTTTAGGGAGGGTGATAACTCGGTTCCTACGCGATGAGGATGA
65 GTGATGAAGAGTTC-TGGCCATCTTTAGGAAAAGTGATAACTCGATTCCTACACGATGAGGACGA
* * * *
210838 CTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGAAGGTTTGGTAAGGGGATGACACGGTT
129 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGAAGATCTGGTAAGGGGATGACACGGCT
* * *
210903 CCTACGTGATGAAGAGTTCTGGCCATCTTTAAGAAGAGTGATAACTCAGTTCCTATGCGATGAGG
194 CATACGTGATGAAGAGTTCTGGCCATCTTTAAGAAGAGTAATAACTCAGTTCCTACGCGATGAGG
*
210968 ATGACTAGTT
259 ACGACTAGTT
*
210978 TTCT-AGGAGTGACACGACTCCTACGTGATGAGGAGATCTGATCGGGGGGATGACACGGCTCATA
1 ATCTAAGG-GTGACACGACTCCTACGTGATGAGGAGATCTGATC-GGGGGATGACACGGCTCATA
* *
211042 CGTGATGAAAAGTTCTGGCCATCTTTAGGAAAAGTGATAACTCGATTCCTACACGATGAGGACGG
64 CGTGATGAAGAGTTCTGGCCATCTTTAGGAAAAGTGATAACTCGATTCCTACACGATGAGGACGA
* **
211107 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCT
129 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGAAGATCTGGTAAGGGGATGACACGGCT
* * *
211172 CATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTAATAACTCGGTTCCTACGCGATGAGG
194 CATACGTGATGAAGAGTTCTGGCCATCTTTAAGAAGAGTAATAACTCAGTTCCTACGCGATGAGG
211237 ACGACTAGTT
259 ACGACTAGTT
* * *
211247 ATCTAAGGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGACTCATACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGATCGGGGGATGACACGGCTCATACG
*
211312 TGATGAAGAGTTCTGGCCATATTTAGG
66 TGATGAAGAGTTCTGGCCATCTTTAGG
211339 GATAATAATT
Statistics
Matches: 321, Mismatches: 36, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
268 49 0.15
269 236 0.74
270 36 0.11
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (268 bp):
ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGATCGGGGGATGACACGGCTCATACG
TGATGAAGAGTTCTGGCCATCTTTAGGAAAAGTGATAACTCGATTCCTACACGATGAGGACGACT
GGTTATCTAGGGGTGACACGACTCCTACGTGATGAGAAGATCTGGTAAGGGGATGACACGGCTCA
TACGTGATGAAGAGTTCTGGCCATCTTTAAGAAGAGTAATAACTCAGTTCCTACGCGATGAGGAC
GACTAGTT
Found at i:211428 original size:29 final size:29
Alignment explanation
Indices: 211346--211432 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
211336 AGGGATAATA
* *
211346 ATTTCAAAAGAAACCGACTCAAAGATGAT
1 ATTTCAAAAGAAACAGAATCAAAGATGAT
* * * *
211375 GTTTCAAAAGGAATAGACA-CTAAGATGAT
1 ATTTCAAAAGAAACAGA-ATCAAAGATGAT
211404 ATTTCAAAAGAAACAGAATCAAAGATGAT
1 ATTTCAAAAGAAACAGAATCAAAGATGAT
211433 TTTGTTAAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (29 bp):
ATTTCAAAAGAAACAGAATCAAAGATGAT
Found at i:211550 original size:29 final size:29
Alignment explanation
Indices: 211467--211613 Score: 152
Period size: 29 Copynumber: 5.0 Consensus size: 29
211457 AGAGCCAAAA
*
211467 TTTTGTTTCAAAGGAAATGACTCAAAGATT
1 TTTTGTTTCAAAAGAAATGACTCAAAGA-T
* * **
211497 GTTTTGTTTTAATAGAAACAACTCAAAGAT
1 -TTTTGTTTCAAAAGAAATGACTCAAAGAT
* * * *
211527 TTTTATTTCAAAATAAATGACTCACAGAC
1 TTTTGTTTCAAAAGAAATGACTCAAAGAT
*
211556 TTTTGTTTCAAGAGAAATAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAAT-GACTCAAAGAT
* *
211586 TTTT-TTTCAAGAGAAACGACTCAAAGAT
1 TTTTGTTTCAAAAGAAATGACTCAAAGAT
211614 GATTGTTTGT
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
28 11 0.11
29 48 0.50
30 14 0.15
31 23 0.24
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (29 bp):
TTTTGTTTCAAAAGAAATGACTCAAAGAT
Found at i:212275 original size:36 final size:35
Alignment explanation
Indices: 212158--212275 Score: 83
Period size: 36 Copynumber: 3.4 Consensus size: 35
212148 AAGATGATTT
*
212158 TTTGTTTTATGAGAAA-AGGTCTCAAGGAAAATAAGA
1 TTTG-TTTAAGAGAAATA-GTCTCAAGGAAAATAAGA
*
212194 TTTGCTTTAAGTGAAAT-GATCTC----AAAA-AAG-
1 TTTG-TTTAAGAGAAATAG-TCTCAAGGAAAATAAGA
*
212224 GTTGTTTGATA-AGAAATAGTCTCAAGGAAAATAAGA
1 TTTGTTT-A-AGAGAAATAGTCTCAAGGAAAATAAGA
212260 TTTGTTTCAAGAGAAA
1 TTTGTTT-AAGAGAAA
212276 CATACTGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
29 3 0.05
30 13 0.21
31 5 0.08
32 4 0.06
34 4 0.06
35 5 0.08
36 29 0.46
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (35 bp):
TTTGTTTAAGAGAAATAGTCTCAAGGAAAATAAGA
Found at i:212497 original size:101 final size:103
Alignment explanation
Indices: 212374--212566 Score: 239
Period size: 103 Copynumber: 1.9 Consensus size: 103
212364 AATTTTGAAA
* * * * * * * *
212374 ATCTCAAGTGAGATTAATTTTGTTTCAA-AT-CAACAAATT-TAAATTTTTATTTCATAGAAAAA
1 ATCTCAAATGAGATCAACTTTGTTT-AATATGAAACAAATTCGAAATTTCTATCTCAAAGAAAAA
*
212436 ATGTCTCAAGCGAGACGAAGTTTATTTTTTGAGAAAGCG
65 ATGTCTCAAGCGAGACGAAATTTATTTTTTGAGAAAGCG
* *
212475 ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTCTATCTCAAAGGAAAAA
1 ATCTCAAATGAGATCAACTTTGTTTAATATGAAACAAATTCGAAATTTCTATCTCAAAGAAAAAA
* *
212540 TGTCTCAAGTGAGACGAAATTTGTTTT
66 TGTCTCAAGCGAGACGAAATTTATTTT
212567 GAAAGAAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
100 2 0.03
101 23 0.30
102 8 0.11
103 43 0.57
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (103 bp):
ATCTCAAATGAGATCAACTTTGTTTAATATGAAACAAATTCGAAATTTCTATCTCAAAGAAAAAA
TGTCTCAAGCGAGACGAAATTTATTTTTTGAGAAAGCG
Found at i:212583 original size:36 final size:35
Alignment explanation
Indices: 212535--212678 Score: 177
Period size: 36 Copynumber: 4.1 Consensus size: 35
212525 ATCTCAAAGG
* *
212535 AAAAA-TGTCTCAAGTGAGACGAAATTTGTTTTGA
1 AAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
*
212569 AAGAAATTGTCTCAAGTGAGACAAAATTTGATTTT-A
1 AA-AAATTGTCTCAAGCGAGACAAAATTTG-TTTTGA
* *
212605 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGA
1 AAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
*
212640 GAAAAATTATCTCAAGCGAGACAAAAATTTGTTTT-A
1 -AAAAATTGTCTCAAGCGAGAC-AAAATTTGTTTTGA
212676 AAA
1 AAA
212679 TTCTCAAAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
34 6 0.06
35 32 0.33
36 43 0.44
37 16 0.16
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (35 bp):
AAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGA
Found at i:212617 original size:71 final size:71
Alignment explanation
Indices: 212534--212675 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
212524 TATCTCAAAG
* * * *
212534 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTGA-AAGAAATTGTCTCAAGTGAGAC-AAAATT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGAA-AAATTATCTCAAGCGAGACAAAAATT
212597 TGATTTTA
65 TG-TTTTA
*
212605 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAATTATCTCAAGCGAGACAAAAATTT
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAATTATCTCAAGCGAGACAAAAATTT
212670 GTTTTA
66 GTTTTA
212676 AAATTCTCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 54 0.84
72 10 0.16
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (71 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAAATTATCTCAAGCGAGACAAAAATTT
GTTTTA
Found at i:214393 original size:12 final size:11
Alignment explanation
Indices: 214361--214447 Score: 50
Period size: 12 Copynumber: 7.1 Consensus size: 11
214351 TGTTTTTTGC
*
214361 TCTTTTCTTTT
1 TCTTTTTTTTT
*
214372 T-TTCTTTTTT
1 TCTTTTTTTTT
*
214382 TGTTTGTTTTTT
1 TCTTT-TTTTTT
214394 TCTTTTTTTTCT
1 TCTTTTTTTT-T
214406 TGCTCTTTGTTTTT
1 T-CT-TTT-TTTTT
214420 TCTTTACTTCTTTT
1 TCTTT--TT-TTTT
214434 CTCTTTGTTTTTT
1 -TCTTT-TTTTTT
214447 T
1 T
214448 GTTCTCTTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
10 8 0.13
11 8 0.13
12 15 0.25
13 9 0.15
14 12 0.20
15 9 0.15
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:214413 original size:35 final size:34
Alignment explanation
Indices: 214345--214420 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
214335 CTCTTTGTCA
214345 TTTTTTTGTTTTTTGCTCTTTTCTTTTTTTCTTT-
1 TTTTTTTGTTTTTT-CTCTTTTCTTTTTTTCTTTG
214379 TTTTGTTTGTTTTTT-TCTTTT-TTTTCTTGCTCTTTG
1 TTTT-TTTGTTTTTTCTCTTTTCTTTT-TT--TCTTTG
214415 TTTTTT
1 TTTTTT
214421 CTTTACTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
32 4 0.11
33 8 0.22
34 4 0.11
35 17 0.46
36 4 0.11
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (34 bp):
TTTTTTTGTTTTTTCTCTTTTCTTTTTTTCTTTG
Found at i:214414 original size:27 final size:26
Alignment explanation
Indices: 214384--214447 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
214374 TCTTTTTTTG
*
214384 TTTGTTTTTTTCTTT-TTTTTCTTGCTC
1 TTTGTTTTTTTCTTTATTCTT-TT-CTC
214411 TTTG-TTTTTTCTTTACTTCTTTTCTC
1 TTTGTTTTTTTCTTTA-TTCTTTTCTC
214437 TTTGTTTTTTT
1 TTTGTTTTTTT
214448 GTTCTCTTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 17 0.52
27 12 0.36
28 4 0.12
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTGTTTTTTTCTTTATTCTTTTCTC
Found at i:214418 original size:25 final size:24
Alignment explanation
Indices: 214333--214447 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 24
214323 TCATTGTCTG
*
214333 TGCTCTTTGTCATTTTTTT-GTTTTT
1 TGCTCTTTGT--TTTTTTTCTTTTTT
214358 TGCTCTTT-TCTTTTTTTCTTTTTT
1 TGCTCTTTGT-TTTTTTTCTTTTTT
*
214382 TG---TTTGTTTTTTTCTTTTTTTTCT
1 TGCTCTTTG-TTTTTT-TTCTTTTT-T
*
214406 TGCTCTTTGTTTTTTCTTTACTTCTTT
1 TGCTCTTTG-TTTTT-TTT-CTTTTTT
214433 T-CTCTTTGTTTTTTT
1 TGCTCTTTGTTTTTTT
214448 GTTCTCTTCG
Statistics
Matches: 75, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
21 3 0.04
22 5 0.07
23 15 0.20
24 13 0.17
25 13 0.17
26 7 0.09
27 14 0.19
28 5 0.07
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.77
Consensus pattern (24 bp):
TGCTCTTTGTTTTTTTTCTTTTTT
Found at i:214897 original size:23 final size:23
Alignment explanation
Indices: 214867--214931 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
214857 GGAAGTTGAG
214867 TCGAGATGCCCCTCATTGTCTTC
1 TCGAGATGCCCCTCATTGTCTTC
214890 TCGAGATGCCCCTCATTGTCTTC
1 TCGAGATGCCCCTCATTGTCTTC
*
214913 TCGAGATGCCCCACATTGT
1 TCGAGATGCCCCTCATTGT
214932 GTCTTATTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.32
Consensus pattern (23 bp):
TCGAGATGCCCCTCATTGTCTTC
Found at i:218495 original size:2 final size:2
Alignment explanation
Indices: 218396--218486 Score: 159
Period size: 2 Copynumber: 46.5 Consensus size: 2
218386 TTACATGATT
218396 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
218437 TT TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
218478 TA TA TA TA T
1 TA TA TA TA T
218487 GCATATATAC
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 83 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:220060 original size:3 final size:3
Alignment explanation
Indices: 220043--220122 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
220033 ATGTAAACTG
* * *
220043 TAA TAT TAA -AA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
220090 TAA TAA T-A TAAA TAA TAT TAA TAA TAG TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
220123 AATTAAATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.06
3 58 0.91
4 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:221429 original size:2 final size:2
Alignment explanation
Indices: 221422--221454 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
221412 TAATAAATAA
221422 AT AT AT AT 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 AT AT AT AT A
221455 AATACCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.