Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005098.1 Hibiscus syriacus cultivar Beakdansim tig00011464_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: 91274
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:6915 original size:35 final size:35
Alignment explanation
Indices: 6867--6937 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
6857 AAGAAATAAG
*
6867 TTTATAAGCCCTGCTTCTAATTTAGTTTATTAATA
1 TTTATAAGCCCTGCTTCTAATTTAGTATATTAATA
* * *
6902 TTTATAGGTCCTGCTTTTAATTTAGTATATTAATA
1 TTTATAAGCCCTGCTTCTAATTTAGTATATTAATA
6937 T
1 T
6938 ATTTTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (35 bp):
TTTATAAGCCCTGCTTCTAATTTAGTATATTAATA
Found at i:16512 original size:16 final size:16
Alignment explanation
Indices: 16491--16534 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
16481 CGACAAAATT
16491 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
16507 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
16523 TTTACTATTCAC
1 TTTACTATTCAC
16535 ATAAATAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:22805 original size:31 final size:31
Alignment explanation
Indices: 22767--22861 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
22757 GAACCTCGGC
* *
22767 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
22798 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
22829 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
22860 AA
1 AA
22862 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:23566 original size:21 final size:21
Alignment explanation
Indices: 23542--23586 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23532 TTTTGTTCGT
* *
23542 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23563 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23584 TTG
1 TTG
23587 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:29596 original size:21 final size:20
Alignment explanation
Indices: 29567--29632 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
29557 GGCAACCAAC
*
29567 TTTGAAAATGGTTTTCAAAG
1 TTTGTAAATGGTTTTCAAAG
29587 TTTGGTAAAT-G-TTT---A-
1 TTT-GTAAATGGTTTTCAAAG
*
29602 TTTGAAAATGGTTTTCAAAG
1 TTTGTAAATGGTTTTCAAAG
29622 TTTAGTAAATG
1 TTT-GTAAATG
29633 TTTCTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 15
0.66 0.06 0.28
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 7 0.20
21 11 0.31
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTGTAAATGGTTTTCAAAG
Found at i:29653 original size:36 final size:35
Alignment explanation
Indices: 29566--29670 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
29556 TGGCAACCAA
29566 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
29601 ATTTGAAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
29636 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
29671 GGTAGATGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:34213 original size:21 final size:20
Alignment explanation
Indices: 34184--34249 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
34174 GGCAACCAAC
*
34184 TTTGAAAATGGTTTTCAAAG
1 TTTGTAAATGGTTTTCAAAG
34204 TTTGGTAAAT-G-TTTC----
1 TTT-GTAAATGGTTTTCAAAG
*
34219 TTTGAAAATGGTTTTCAAAG
1 TTTGTAAATGGTTTTCAAAG
34239 TTTAGTAAATG
1 TTT-GTAAATG
34250 TTTCTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 15
0.66 0.06 0.28
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 7 0.20
21 11 0.31
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
TTTGTAAATGGTTTTCAAAG
Found at i:34270 original size:36 final size:35
Alignment explanation
Indices: 34183--34287 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
34173 TGGCAACCAA
34183 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
34218 CTTTGAAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
34253 CTTTGAAAAATGTTTTTCAAATTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
34288 GGTAGATGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 43 0.66
36 22 0.34
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:39620 original size:27 final size:27
Alignment explanation
Indices: 39589--39705 Score: 234
Period size: 27 Copynumber: 4.3 Consensus size: 27
39579 ATAATGTCTT
39589 TGAATCATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAATGTACTTCTGTGC
39616 TGAATCATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAATGTACTTCTGTGC
39643 TGAATCATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAATGTACTTCTGTGC
39670 TGAATCATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAATGTACTTCTGTGC
39697 TGAATCATT
1 TGAATCATT
39706 TAGGGGTGAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTCTGTGC
Found at i:88727 original size:23 final size:23
Alignment explanation
Indices: 88692--88748 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
88682 ATCAAGCACA
*
88692 ATAATATATTAGGTAGCGCTTAG
1 ATAATATAATAGGTAGCGCTTAG
* *
88715 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAG
*
88738 ATAATAAAATA
1 ATAATATAATA
88749 TGCATTTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAG
Found at i:88810 original size:87 final size:86
Alignment explanation
Indices: 88660--88826 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
88650 CGGTTATGTT
* * * *
88660 ATATCATTTAACCGGAAATATTATCAAGCACAATAATATATTAGGTAGCGCTTAGATAATGTAAT
1 ATATCATTTAACCAGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAAT
88725 AGGTAGCGCTTATATAATAAA
66 AGGTAGCGCTTATATAATAAA
* * *
88746 ATATGCATTTAACCAGAAATATTATAAAGTAGAATAACAAATTAGGTAGCGCTTATATAATGTAA
1 ATAT-CATTTAACCAGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAA
*
88811 TAGGTAGCGTTTATAT
65 TAGGTAGCGCTTATAT
88827 TAACCTATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 4 0.06
87 68 0.94
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (86 bp):
ATATCATTTAACCAGAAATATTATAAAGCACAATAACAAATTAGGTAGCGCTTAGATAATGTAAT
AGGTAGCGCTTATATAATAAA
Done.