Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007322.1 Hibiscus syriacus cultivar Beakdansim tig00019542_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: 31018
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:930 original size:15 final size:16
Alignment explanation
Indices: 910--981 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 16
900 CATTTATTTC
910 CATTTCCTTTCTT-AT
1 CATTTCCTTTCTTAAT
**
925 CATTTCCTTTCTTCTT
1 CATTTCCTTTCTTAAT
*
941 CTATTT-CTTT-TTTAT
1 C-ATTTCCTTTCTTAAT
*
956 -ATTTCC-ATCTTAAT
1 CATTTCCTTTCTTAAT
970 CATTT-CTTTCTT
1 CATTTCCTTTCTT
982 TTAATTTTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 24 0.53
16 6 0.13
17 4 0.09
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
CATTTCCTTTCTTAAT
Found at i:6128 original size:21 final size:21
Alignment explanation
Indices: 6076--6121 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
6066 ACTATCATTC
*
6076 CATCACCATTCACGTCTATAT
1 CATCACCATTCACGCCTATAT
6097 CATCACCATTCACGCCTATAT
1 CATCACCATTCACGCCTATAT
6118 CATC
1 CATC
6122 GTCATTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.37, G:0.04, T:0.30
Consensus pattern (21 bp):
CATCACCATTCACGCCTATAT
Found at i:6474 original size:13 final size:13
Alignment explanation
Indices: 6456--6482 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6446 ACATCACACA
6456 TTGCTTAATTTGT
1 TTGCTTAATTTGT
6469 TTGCTTAATTTGT
1 TTGCTTAATTTGT
6482 T
1 T
6483 CGAACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (13 bp):
TTGCTTAATTTGT
Found at i:9018 original size:12 final size:12
Alignment explanation
Indices: 9003--9036 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
8993 CACACCAACA
9003 CCATTACCATTT
1 CCATTACCATTT
9015 CCATTACCATTT
1 CCATTACCATTT
*
9027 -CATCACCATT
1 CCATTACCATT
9037 GAATCACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (12 bp):
CCATTACCATTT
Found at i:10484 original size:19 final size:20
Alignment explanation
Indices: 10437--10487 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
10427 GAAACCCCTT
**
10437 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
10457 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
10476 TGTAAATACATG
1 TGAAAATACATG
10488 CTCTTGGCCG
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:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:12181 original size:22 final size:21
Alignment explanation
Indices: 12155--12195 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12145 GTTGTGGAAC
*
12155 TGATGGTCTTGATGGATGAAGT
1 TGATGATCTTGAT-GATGAAGT
*
12177 TGATGATGTTGATGATGAA
1 TGATGATCTTGATGATGAA
12196 ATGGAGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGATCTTGATGATGAAGT
Found at i:14018 original size:26 final size:26
Alignment explanation
Indices: 13979--14046 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
13969 CCCTAGAACA
* * *
13979 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGACCAACC
14005 CCCATGTGCCTTGCATATGACCAACC
1 CCCATGTGCCTTGCATATGACCAACC
*
14031 CCTATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
14047 GTGGGTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.19, C:0.34, G:0.18, T:0.29
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAACC
Found at i:15259 original size:15 final size:16
Alignment explanation
Indices: 15239--15281 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
15229 AGTTATCATC
15239 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
15254 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
15270 AAAATAACTATA
1 ATAATAACTATA
15282 TTAAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:21675 original size:16 final size:17
Alignment explanation
Indices: 21651--21685 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21641 ATGATATGGT
21651 AATGAAATAAAAAAATG
1 AATGAAATAAAAAAATG
*
21668 AATG-AATAAAGAAATG
1 AATGAAATAAAAAAATG
21684 AA
1 AA
21686 ATAGTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (17 bp):
AATGAAATAAAAAAATG
Found at i:21901 original size:7 final size:7
Alignment explanation
Indices: 21879--21920 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
21869 GTTGTAGGAG
21879 TCTTTTCT
1 TCTTTT-T
21887 TCTTTTT
1 TCTTTTT
*
21894 TGTTTTT
1 TCTTTTT
21901 T-TTTCTT
1 TCTTT-TT
21908 TCTTTTT
1 TCTTTTT
21915 TCTTTT
1 TCTTTT
21921 ATTGCAGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
6 3 0.10
7 19 0.61
8 9 0.29
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (7 bp):
TCTTTTT
Found at i:21906 original size:20 final size:21
Alignment explanation
Indices: 21881--21920 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21871 TGTAGGAGTC
*
21881 TTTTC-TTCTTTTTTGTTTTT
1 TTTTCTTTCTTTTTTCTTTTT
21901 TTTTCTTTCTTTTTTCTTTT
1 TTTTCTTTCTTTTTTCTTTT
21921 ATTGCAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (21 bp):
TTTTCTTTCTTTTTTCTTTTT
Found at i:21913 original size:11 final size:11
Alignment explanation
Indices: 21881--21919 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
21871 TGTAGGAGTC
21881 TTTTC-TTCTT
1 TTTTCTTTCTT
*
21891 TTTTGTTT-TT
1 TTTTCTTTCTT
21901 TTTTCTTTCTT
1 TTTTCTTTCTT
21912 TTTTCTTT
1 TTTTCTTT
21920 TATTGCAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 13 0.52
11 12 0.48
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:22328 original size:13 final size:14
Alignment explanation
Indices: 22310--22345 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
22300 ATAGGCGTGA
22310 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
22323 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
22337 ATGGTGATG
1 ATGGTGATG
22346 AAACGATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:22348 original size:13 final size:13
Alignment explanation
Indices: 22310--22348 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
22300 ATAGGCGTGA
*
22310 ATGGTGATGGAAG
1 ATGGTGATGAAAG
22323 ATGGTGATGGAAAG
1 ATGGTGAT-GAAAG
22337 ATGGTGATGAAA
1 ATGGTGATGAAA
22349 CGATAGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:24351 original size:221 final size:221
Alignment explanation
Indices: 23964--24375 Score: 619
Period size: 221 Copynumber: 1.9 Consensus size: 221
23954 TAGAAGTGTT
* * *
23964 AGGTGATCCACCTAATGAAGTACCATCAAAAATAGGAAAATAACACCAAACTAATCTAATTCAAG
1 AGGTGATCCACCTAATCAAGTACCATCAAAAAGAGGAAAATAACACCAAACCAATCTAATTCAAG
* * *
24029 GTTCTATTATACATCGTCAAACATATAATCTCGAAGAAACCAAAGAGCTAGATTTGTTACAAAAA
66 GTTCCATCATACATCGTCAAACATACAATCTCGAAGAAACCAAAGAGCTAGATTTGTTACAAAAA
* * * * *
24094 GGCTACATCCAGGACATCCTTGGTCGTGAAGCCATCTTAATGATGAAACATGATTTGAACACTCA
131 GGATACATCCAGGAAAGCCTTAGTCGTGAAGCCATCTTAACGATGAAACATGATTTGAACACTCA
24159 TTTTGATGTAAGGCTATTCTGATGTA
196 TTTTGATGTAAGGCTATTCTGATGTA
* * *
24185 AGGTGATCCACCTAA-CATATTACCATTAGAAAGAGGAAAATAACACCAAACCAATCTAATTCAA
1 AGGTGATCCACCTAATCA-AGTACCATCAAAAAGAGGAAAATAACACCAAACCAATCTAATTCAA
** *
24249 GGTTCCATCATACATCGTCAAACATACAATCTCGAAGAAACCAAAGATTTAGATTTGTTGCAAAA
65 GGTTCCATCATACATCGTCAAACATACAATCTCGAAGAAACCAAAGAGCTAGATTTGTTACAAAA
* * * *
24314 ATGATACATCCAGTAAAGCCTTAGTCGTGACGCCATCTTAACGATGACACATGATTTGAACA
130 AGGATACATCCAGGAAAGCCTTAGTCGTGAAGCCATCTTAACGATGAAACATGATTTGAACA
24376 ACTCCACAGG
Statistics
Matches: 169, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
220 1 0.01
221 168 0.99
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (221 bp):
AGGTGATCCACCTAATCAAGTACCATCAAAAAGAGGAAAATAACACCAAACCAATCTAATTCAAG
GTTCCATCATACATCGTCAAACATACAATCTCGAAGAAACCAAAGAGCTAGATTTGTTACAAAAA
GGATACATCCAGGAAAGCCTTAGTCGTGAAGCCATCTTAACGATGAAACATGATTTGAACACTCA
TTTTGATGTAAGGCTATTCTGATGTA
Found at i:27466 original size:14 final size:14
Alignment explanation
Indices: 27438--27489 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
27428 TAGGCGTGAC
*
27438 TGGTGATAG-AAGA
1 TGGTGATGGAAAGA
27451 TGGTGATGGAAAGA
1 TGGTGATGGAAAGA
27465 TGGTGATGGAAAGA
1 TGGTGATGGAAAGA
* *
27479 TAGTGCTGGAA
1 TGGTGATGGAA
27490 CGATAGTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
13 8 0.23
14 27 0.77
ACGTcount: A:0.35, C:0.02, G:0.40, T:0.23
Consensus pattern (14 bp):
TGGTGATGGAAAGA
Found at i:27494 original size:14 final size:14
Alignment explanation
Indices: 27447--27496 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
27437 CTGGTGATAG
*
27447 AAGATGGTGATGGA
1 AAGATAGTGATGGA
*
27461 AAGATGGTGATGGA
1 AAGATAGTGATGGA
*
27475 AAGATAGTGCTGGA
1 AAGATAGTGATGGA
*
27489 ACGATAGT
1 AAGATAGT
27497 ATCTTATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.22
Consensus pattern (14 bp):
AAGATAGTGATGGA
Done.