Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000974.1 Hibiscus syriacus cultivar Beakdansim tig00001950_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: 51005
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1467 original size:18 final size:17
Alignment explanation
Indices: 1435--1469 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1425 TTCGAATATT
1435 AATCTAAATTAAAACTA
1 AATCTAAATTAAAACTA
*
1452 AATCTAAAATTGAAACTA
1 AATCT-AAATTAAAACTA
1470 TGAAGCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (17 bp):
AATCTAAATTAAAACTA
Found at i:3400 original size:18 final size:19
Alignment explanation
Indices: 3369--3417 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
3359 AATTTATAAT
3369 CAAAATTATAAACATAACA
1 CAAAATTATAAACATAACA
*
3388 CAAACTTAT-AACAT-A-A
1 CAAAATTATAAACATAACA
*
3404 CAATATTATAAACA
1 CAAAATTATAAACA
3418 AAAAGTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 5 0.19
19 8 0.31
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (19 bp):
CAAAATTATAAACATAACA
Found at i:4638 original size:88 final size:88
Alignment explanation
Indices: 4503--4779 Score: 328
Period size: 88 Copynumber: 3.1 Consensus size: 88
4493 CCAAAACTAA
* * * *
4503 ATCCGTAGGGCTTACCCTCAGCACACAGCAAAAAAGG-AGCCAACCTAAGGATA-GTCCTTGGAG
1 ATCCGTAGGG-TTACCTTAAG-ACAAAGC-AAAAAGGAAACCAACCTAAGGATATG-CCTTGG-G
* *
4566 CCTATGGCCTACCCAAGGGTATCCTTAG
61 CCTATGGCCTACCTAAGGATATCCTTAG
* *
4594 ATCCGTAGGGTTACCTTAA-ACACA-CAACAAAGGAAACTAACCTAAGGATATGCCTTAGGGCCT
1 ATCCGTAGGGTTACCTTAAGACAAAGCAA-AAAGGAAACCAACCTAAGGATATGCCTT-GGGCCT
*
4657 ATGGCCTACCTAAGGATATCATTAG
64 ATGGCCTACCTAAGGATATCCTTAG
* * *
4682 ATCCGTAGGTTTACCTTAAGTACAAAGCAAAAAGTAAACCAACCTAAGAATATGCCTTGGGGCCT
1 ATCCGTAGGGTTACCTTAAG-ACAAAGCAAAAAGGAAACCAACCTAAGGATATGCCTT-GGGCCT
4747 ATGGGCCTACCTAAGGATATCCTTAG
64 AT-GGCCTACCTAAGGATATCCTTAG
4773 ATCCGTA
1 ATCCGTA
4780 TGGTCTTACC
Statistics
Matches: 164, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
86 2 0.01
87 6 0.04
88 67 0.41
89 3 0.02
90 44 0.27
91 42 0.26
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (88 bp):
ATCCGTAGGGTTACCTTAAGACAAAGCAAAAAGGAAACCAACCTAAGGATATGCCTTGGGCCTAT
GGCCTACCTAAGGATATCCTTAG
Found at i:9513 original size:88 final size:89
Alignment explanation
Indices: 9333--9575 Score: 357
Period size: 88 Copynumber: 2.7 Consensus size: 89
9323 CTAAAACTAC
* * *
9333 ATCCGTAGAGCTTACGC-TAAGCACACAGCAAAAAGGGAGCCAACCTAAGGATATTCCTTGGGGC
1 ATCCGTAG-GGTTAC-CTTAAGCACACA-CAAAAAGGAAACCAACCTAAGGATATTCCTTGGGGC
*
9397 CTATGGCCTACCCAAGGGTATCCTTAG
63 CTATGGCCTACCCAAGGATATCCTTAG
* *
9424 ATCCGTAGGGTTACCTTAAGTACACA-ACAAAGGAAACCAACCTAAGGATATTCC-TGGGGCCTA
1 ATCCGTAGGGTTACCTTAAGCACACACAAAAAGGAAACCAACCTAAGGATATTCCTTGGGGCCTA
9487 TGGGCCTACCCAAGGATATCCTTAG
66 T-GGCCTACCCAAGGATATCCTTAG
*
9512 ATCCGTAGGGTTACCTTAAGCACACAGCAAAAAGGAAACCAACCTAAGAATATTCCTTGGGGCC
1 ATCCGTAGGGTTACCTTAAGCACACA-CAAAAAGGAAACCAACCTAAGGATATTCCTTGGGGCC
9576 ATATCCTTAG
Statistics
Matches: 138, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
87 10 0.07
88 72 0.52
89 1 0.01
90 40 0.29
91 15 0.11
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (89 bp):
ATCCGTAGGGTTACCTTAAGCACACACAAAAAGGAAACCAACCTAAGGATATTCCTTGGGGCCTA
TGGCCTACCCAAGGATATCCTTAG
Found at i:13209 original size:15 final size:15
Alignment explanation
Indices: 13177--13271 Score: 52
Period size: 15 Copynumber: 6.0 Consensus size: 15
13167 TAAAATTTAA
*
13177 AAAAATATTTAAATT
1 AAAAATATTAAAATT
13192 AAAAATA-TAAAATAT
1 AAAAATATTAAAAT-T
13207 AAACAATTATTAAGATATT
1 AAA-AA-TATTAA-A-ATT
* * *
13226 CAATACATT-AAATAT
1 AAAAATATTAAAAT-T
13241 AAAAATACTATAAAATT
1 AAAAATA-T-TAAAATT
*
13258 -AAACTATTAAAATT
1 AAAAATATTAAAATT
13272 TTTCAACTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
14 14 0.23
15 18 0.29
16 9 0.15
17 7 0.11
18 8 0.13
19 4 0.06
20 2 0.03
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (15 bp):
AAAAATATTAAAATT
Found at i:13756 original size:31 final size:31
Alignment explanation
Indices: 13718--13809 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
13708 TCGAATTCAA
13718 GGGTCAAATTGATATTTTATCTAAAGTTTAG
1 GGGTCAAATTGATATTTTATCTAAAGTTTAG
* * *
13749 GGGTCAAAATGTTATTTTA-CATAAAGTTCAG
1 GGGTCAAATTGATATTTTATC-TAAAGTTTAG
* * *
13780 GGGTTAAATT-AGTATTCTATATAAAGTTTA
1 GGGTCAAATTGA-TATTTTATCTAAAGTTTA
13810 ATGGTTATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (31 bp):
GGGTCAAATTGATATTTTATCTAAAGTTTAG
Found at i:15462 original size:17 final size:16
Alignment explanation
Indices: 15424--15462 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15414 CTTCAGCTAT
*
15424 TAAAATACTTGGAAAA
1 TAAAATACTTGCAAAA
*
15440 TCAAATACTTGCCAAAA
1 TAAAATACTTG-CAAAA
15457 TAAAAT
1 TAAAAT
15463 TTCCAGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (16 bp):
TAAAATACTTGCAAAA
Found at i:17740 original size:24 final size:24
Alignment explanation
Indices: 17713--17758 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17703 GCATGACATG
17713 GTACATAGATGTTTTACACATCGT
1 GTACATAGATGTTTTACACATCGT
*
17737 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTACACATC
17759 ATATGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (24 bp):
GTACATAGATGTTTTACACATCGT
Found at i:29604 original size:26 final size:26
Alignment explanation
Indices: 29568--29618 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
29558 ACCAAAGTGC
29568 TAATACACATAAGATCATGCCCACCA
1 TAATACACATAAGATCATGCCCACCA
* *
29594 TAATACACATAAGGTCGTGCCCACC
1 TAATACACATAAGATCATGCCCACC
29619 GTATGCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (26 bp):
TAATACACATAAGATCATGCCCACCA
Found at i:35947 original size:26 final size:26
Alignment explanation
Indices: 35911--35960 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
35901 ACCGAAATGC
* *
35911 TAATACACATAATGTCGTGCCCACTA
1 TAATACACATAAGGTCATGCCCACTA
35937 TAATACACATAAGGTCATGCCCAC
1 TAATACACATAAGGTCATGCCCAC
35961 CATATGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACTA
Found at i:39960 original size:63 final size:63
Alignment explanation
Indices: 39861--39980 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
39851 GAGTTGCAAC
*
39861 ACAGCTTGTATGAGAACAAAAGAATGAACATTCTTAGGCTCCTAGCCCTTGCAAAATGTTGGA
1 ACAGCTTGTATGAGAACAAAAGAATGAACATTCTTAGGATCCTAGCCCTTGCAAAATGTTGGA
* *
39924 ACAGCTTGTATGAGAACAAAAGAATGGACATTCTTAGTATCCTAGCCCTTGCAAAAT
1 ACAGCTTGTATGAGAACAAAAGAATGAACATTCTTAGGATCCTAGCCCTTGCAAAAT
39981 ATACATGGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (63 bp):
ACAGCTTGTATGAGAACAAAAGAATGAACATTCTTAGGATCCTAGCCCTTGCAAAATGTTGGA
Found at i:42530 original size:44 final size:43
Alignment explanation
Indices: 42482--42599 Score: 157
Period size: 42 Copynumber: 2.7 Consensus size: 43
42472 AATCTCATTA
* *
42482 TTTTACCTTTATAATAGAGACCCTTAATTTTTTTCAATCACACT
1 TTTTACATTTATAATTGAGACCC-TAATTTTTTTCAATCACACT
* * *
42526 TTTTACATTTAGAATTGAGGCCCTAA-TTTTTTCAATCCCACT
1 TTTTACATTTATAATTGAGACCCTAATTTTTTTCAATCACACT
* *
42568 TTTTATATTTATAATTGAGACTCTAATTTTTT
1 TTTTACATTTATAATTGAGACCCTAATTTTTT
42600 AATGCACCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 37 0.58
43 8 0.12
44 19 0.30
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (43 bp):
TTTTACATTTATAATTGAGACCCTAATTTTTTTCAATCACACT
Done.