Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001979.1 Hibiscus syriacus cultivar Beakdansim tig00004021_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: 51071
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:741 original size:32 final size:32
Alignment explanation
Indices: 705--771 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
695 GTTGATGAAT
705 GAAGGATGAT-TTAATG-GTGATGAATGGTAATG
1 GAAGGATGATGTTAATGCGTGAT--ATGGTAATG
* *
737 GAAGGATGATGTTATTGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGCGTGATATGGTAATG
769 GAA
1 GAA
772 TATGGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 21 0.68
33 5 0.16
34 5 0.16
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.31
Consensus pattern (32 bp):
GAAGGATGATGTTAATGCGTGATATGGTAATG
Found at i:4095 original size:23 final size:24
Alignment explanation
Indices: 4067--4114 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4057 TAGAAAAGGT
* * *
4067 TAAGAAAGGAT-AAAGTAATGAAA
1 TAAGAAAAGATGAAAGAAAGGAAA
4090 TAAGAAAAGATGAAAGAAAGGAAA
1 TAAGAAAAGATGAAAGAAAGGAAA
4114 T
1 T
4115 GAAATAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (24 bp):
TAAGAAAAGATGAAAGAAAGGAAA
Found at i:4748 original size:33 final size:33
Alignment explanation
Indices: 4710--4808 Score: 78
Period size: 33 Copynumber: 2.9 Consensus size: 33
4700 GTTGATGAAT
*
4710 GATGAT-TTAATGGTGATGAAATGGTAATGGAAG
1 GATGATGTTAATGGCG-TGAAATGGTAATGGAAG
* * *
4743 GATGATGTTATTGGCGTGATATGGTGATGGAATTG
1 GATGATGTTAATGGCGTGAAATGGTAATGGAA--G
* *
4778 G-TGATGAT-ATAGGCGTGATAATGGTGATGGA
1 GATGATGTTAAT-GGCGTGA-AATGGTAATGGA
4809 CAGATTGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
33 21 0.39
34 20 0.37
35 13 0.24
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (33 bp):
GATGATGTTAATGGCGTGAAATGGTAATGGAAG
Found at i:18489 original size:32 final size:33
Alignment explanation
Indices: 18428--18494 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
18418 ACAACATTAA
* *
18428 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
18460 AAGAAAGTAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAAG-AAATGATTAA-AATAGAAAATGGATAG
18493 AA
1 AA
18495 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:19024 original size:19 final size:19
Alignment explanation
Indices: 18984--19025 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18974 GAAACCCCTT
* **
18984 TGAAAATACATGATTTTGA
1 TGAAAACACATGATTTAAA
19003 TGAAAACACATGATTTAAA
1 TGAAAACACATGATTTAAA
19022 TGAA
1 TGAA
19026 GATACGTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (19 bp):
TGAAAACACATGATTTAAA
Found at i:27363 original size:28 final size:26
Alignment explanation
Indices: 27332--27389 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
27322 TTTGAATGTA
27332 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTC-TTTT
* *
27360 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
27386 CTTT
1 CTTT
27390 CTTAGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 12 0.44
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (26 bp):
CTTTGAATCTTTCTTCCTTTTCTTTT
Found at i:27443 original size:15 final size:16
Alignment explanation
Indices: 27423--27453 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
27413 AGAAGTATTC
27423 TTTTTTCTT-TTTCTT
1 TTTTTTCTTCTTTCTT
27438 TTTTTTCTTCTTTCTT
1 TTTTTTCTTCTTTCTT
27454 GTTGCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTCTTTCTT
Found at i:28260 original size:19 final size:20
Alignment explanation
Indices: 28213--28263 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
28203 GAAACCCCTT
**
28213 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
28233 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
28252 TGAAGATACATG
1 TGAAAATACATG
28264 CTCTTGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:31429 original size:28 final size:28
Alignment explanation
Indices: 31374--31429 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
31364 TCGTGGGGTT
*
31374 CATAACACCATGTTCATCATTTGTTTTG
1 CATAACACCATATTCATCATTTGTTTTG
* *
31402 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACACCATATTCATCATTTGTTTTG
31430 TTAAATTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (28 bp):
CATAACACCATATTCATCATTTGTTTTG
Found at i:31494 original size:28 final size:28
Alignment explanation
Indices: 31454--31508 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
31444 ACTCACATTC
*
31454 ACATAACATCATGTTCATCATTTGTTTT
1 ACATAACAGCATGTTCATCATTTGTTTT
31482 ACATAACAGCATGTTCATCATTTGTTT
1 ACATAACAGCATGTTCATCATTTGTTT
31509 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (28 bp):
ACATAACAGCATGTTCATCATTTGTTTT
Found at i:31514 original size:81 final size:80
Alignment explanation
Indices: 31374--31535 Score: 261
Period size: 81 Copynumber: 2.0 Consensus size: 80
31364 TCGTGGGGTT
* * *
31374 CATAACACCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTTAAATTCA
1 CATAACACCATGTTCATCATTTGTTTTACATAACAGCATATTCATCATTTGTTTAGTT-AATTCA
*
31439 CGTGCACTCACATTCA
65 CGTGCACCCACATTCA
* *
31455 CATAACATCATGTTCATCATTTGTTTTACATAACAGCATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACACCATGTTCATCATTTGTTTTACATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
31520 GTGCACCCACATTCA
66 GTGCACCCACATTCA
31535 C
1 C
31536 TTTACAACAT
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
80 22 0.29
81 53 0.71
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (80 bp):
CATAACACCATGTTCATCATTTGTTTTACATAACAGCATATTCATCATTTGTTTAGTTAATTCAC
GTGCACCCACATTCA
Found at i:32495 original size:26 final size:26
Alignment explanation
Indices: 32456--32513 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
32446 TGAACGTCTA
*
32456 AGGTTCGGGTTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
*
32482 AGGTTTGGGCTTATACTCTTTAGTAT
1 AGGTTCGGGCTTATACTCTTTAGTAT
32508 AGGTTC
1 AGGTTC
32514 TTCCTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (26 bp):
AGGTTCGGGCTTATACTCTTTAGTAT
Found at i:32806 original size:28 final size:27
Alignment explanation
Indices: 32775--32839 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
32765 ATTCATCTTG
32775 AAAAAAAAAATTCCGAAAATTAAAAAA
1 AAAAAAAAAATTCCGAAAATTAAAAAA
*
32802 AAAAAACAAATTCCGAAAATTAAAAAA
1 AAAAAAAAAATTCCGAAAATTAAAAAA
*
32829 AGAAAAGAAAA
1 A-AAAAAAAAA
32840 GAAAAGTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.74, C:0.08, G:0.06, T:0.12
Consensus pattern (27 bp):
AAAAAAAAAATTCCGAAAATTAAAAAA
Found at i:45144 original size:28 final size:28
Alignment explanation
Indices: 45111--45244 Score: 109
Period size: 28 Copynumber: 4.9 Consensus size: 28
45101 TCGTGGGGTT
*
45111 CATAACAGCATGTTCATCATTTTTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
45139 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * ** **
45167 --TAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
45191 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
45219 CATAACAACATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
45245 AGTTAATTCA
Statistics
Matches: 78, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.21
27 4 0.05
28 52 0.67
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.42
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:45211 original size:80 final size:80
Alignment explanation
Indices: 45111--45271 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
45101 TCGTGGGGTT
* * * *
45111 CATAACAGCATGTTCATCATTTTTTTTGCATAACAGCATATTTATCATTTGTTTTGTAAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
*
45176 GTGCACTCACATTCA
66 GTGCACCCACATTCA
* *
45191 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
45256 GTGCACCCACATTCA
66 GTGCACCCACATTCA
45271 C
1 C
45272 TTTACAACAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (80 bp):
CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
GTGCACCCACATTCA
Found at i:46996 original size:19 final size:20
Alignment explanation
Indices: 46972--47023 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
46962 CGGCCAAGAG
*
46972 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
46991 CATGTATTTTCATTAAAAAAT
1 CATGTATTTTCATT-AAAAAT
47012 CATGTATTTTCA
1 CATGTATTTTCA
47024 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:47588 original size:11 final size:11
Alignment explanation
Indices: 47564--47608 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
47554 TTGGTGCTGG
47564 AAACAAGATAA
1 AAACAAGATAA
* *
47575 AAATAAGATTA
1 AAACAAGATAA
47586 AAACAAGATAA
1 AAACAAGATAA
47597 AGAA-AAGATAA
1 A-AACAAGATAA
47608 A
1 A
47609 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:47592 original size:22 final size:22
Alignment explanation
Indices: 47564--47605 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
47554 TTGGTGCTGG
47564 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
47586 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
47606 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Done.