Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004329.1 Hibiscus syriacus cultivar Beakdansim tig00009489_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: 38484
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:819 original size:20 final size:22
Alignment explanation
Indices: 780--824 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
770 GGGACTCATT
*
780 CTTTCAATTAAAGCATTATGTA
1 CTTTCAATTAAAGAATTATGTA
802 CTTTC-ATTAAA-AATTATGTA
1 CTTTCAATTAAAGAATTATGTA
822 CTT
1 CTT
825 GCCGAATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 6 0.27
22 5 0.23
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (22 bp):
CTTTCAATTAAAGAATTATGTA
Found at i:2420 original size:23 final size:23
Alignment explanation
Indices: 2394--2441 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2384 GGAATTATTA
2394 TAAAGTAATAATAATGTGCATAT
1 TAAAGTAATAATAATGTGCATAT
2417 TAAAGTAATAATAATGTGCATAT
1 TAAAGTAATAATAATGTGCATAT
2440 TA
1 TA
2442 TAAAGATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (23 bp):
TAAAGTAATAATAATGTGCATAT
Found at i:2957 original size:16 final size:17
Alignment explanation
Indices: 2922--2959 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
2912 AAAACAAAAG
2922 AGAAAAGCACAATAAGA
1 AGAAAAGCACAATAAGA
2939 AGAAAAGC-CAA-AAGAA
1 AGAAAAGCACAATAAG-A
2955 AGAAA
1 AGAAA
2960 TTTCCAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 8 0.40
ACGTcount: A:0.68, C:0.11, G:0.18, T:0.03
Consensus pattern (17 bp):
AGAAAAGCACAATAAGA
Found at i:10751 original size:35 final size:37
Alignment explanation
Indices: 10682--10765 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 37
10672 ATACTATTTC
* *
10682 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
10719 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
10754 CATCACCA-AATC
1 CATCACCATAATC
10766 TTCAAATATC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 3 0.07
35 21 0.49
36 3 0.07
37 16 0.37
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.27
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:10755 original size:11 final size:11
Alignment explanation
Indices: 10715--10761 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
10705 TATCACGCCT
10715 ATATCATCACC
1 ATATCATCACC
10726 ATAGTCCATCACC
1 ATA-T-CATCACC
10739 ATATCA-CACC
1 ATATCATCACC
10749 TATATCATCACC
1 -ATATCATCACC
10761 A
1 A
10762 AATCTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:10759 original size:22 final size:24
Alignment explanation
Indices: 10715--10761 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
10705 TATCACGCCT
10715 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
10739 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
10761 A
1 A
10762 AATCTTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:12073 original size:36 final size:35
Alignment explanation
Indices: 11999--12076 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
11989 ATGGAATTTA
* **
11999 GTGATGATATAGGTGTGATATGGTGATGGACTACG
1 GTGATGATATAGGCGTGATATGGTGATGGAAGACG
*
12034 GTGATGATATAGGCGTGATAATGGTGATGGAAGATG
1 GTGATGATATAGGCGTGAT-ATGGTGATGGAAGACG
12070 GTGATGA
1 GTGATGA
12077 ACAGATAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 18 0.47
36 20 0.53
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.29
Consensus pattern (35 bp):
GTGATGATATAGGCGTGATATGGTGATGGAAGACG
Found at i:16193 original size:35 final size:36
Alignment explanation
Indices: 16147--16226 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
16137 AAATAGAATT
* **
16147 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCCTGATAATGGTGATGGAAGA
16182 TGGTGATGATATAGGCCTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCCTGATAATGGTGATGGAAGA
16218 TGGTGATGA
1 TGGTGATGA
16227 ACAGATAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCCTGATAATGGTGATGGAAGA
Found at i:16613 original size:19 final size:20
Alignment explanation
Indices: 16566--16614 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
16556 GAAACCCCTT
**
16566 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
16586 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
16605 TGAAGATACA
1 TGAAAATACA
16615 AGTTCTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:21478 original size:24 final size:24
Alignment explanation
Indices: 21451--21510 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
21441 AAGAAAAATC
*
21451 AGAAAAAAAAGTGAAGCACTCAAA
1 AGAAAAAAAAGTCAAGCACTCAAA
* *
21475 AGAAAGAAAAAATCCAGCACTCAAA
1 AGAAA-AAAAAGTCAAGCACTCAAA
*
21500 AGAAGAAAAAG
1 AGAAAAAAAAG
21511 CAAAGAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 10 0.33
25 20 0.67
ACGTcount: A:0.63, C:0.13, G:0.17, T:0.07
Consensus pattern (24 bp):
AGAAAAAAAAGTCAAGCACTCAAA
Found at i:22856 original size:24 final size:25
Alignment explanation
Indices: 22810--22864 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
22800 ATAGTTATGC
*
22810 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
22834 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
22859 CA-TTGA
1 CACTTGA
22865 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:29180 original size:11 final size:11
Alignment explanation
Indices: 29166--29229 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
29156 TCTTTTTGAA
29166 TTCTTTTTCTT
1 TTCTTTTTCTT
29177 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
29190 TTCTTCTTT-TT
1 TTCTT-TTTCTT
*
29201 CTCTTCTTT-TT
1 TTCTT-TTTCTT
*
29212 GTCTTTTTC-T
1 TTCTTTTTCTT
29222 TTCTTTTT
1 TTCTTTTT
29230 GCACTCCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 11 0.24
11 19 0.41
12 7 0.15
13 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:29184 original size:27 final size:27
Alignment explanation
Indices: 29154--29210 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
29144 CTTGGCTTGC
*
29154 TTTCTT-TTTGAATTCTTTTTCTTTTCT
1 TTTCTTCTTT-AATTCTTTTTCTCTTCT
**
29181 TTTCTTCTTTTCTTCTTTTTCTCTTCT
1 TTTCTTCTTTAATTCTTTTTCTCTTCT
29208 TTT
1 TTT
29211 TGTCTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTCTTCTTTAATTCTTTTTCTCTTCT
Found at i:29216 original size:19 final size:19
Alignment explanation
Indices: 29183--29230 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
29173 TCTTTTCTTT
29183 TCTTCTTTTCT-TCTTTTTC
1 TCTTCTTTT-TGTCTTTTTC
29202 TCTTCTTTTTGTCTTTTTC
1 TCTTCTTTTTGTCTTTTTC
29221 T-TTCTTTTTG
1 TCTTCTTTTTG
29231 CACTCCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (19 bp):
TCTTCTTTTTGTCTTTTTC
Found at i:32287 original size:17 final size:19
Alignment explanation
Indices: 32250--32287 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32240 AACTATATAA
32250 TGCATATAATATAATGATG
1 TGCATATAATATAATGATG
*
32269 TGCATATTAT-TAA-GATG
1 TGCATATAATATAATGATG
32286 TG
1 TG
32288 AACTATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (19 bp):
TGCATATAATATAATGATG
Found at i:33880 original size:5 final size:5
Alignment explanation
Indices: 33860--33899 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
33850 TTTTTTGAAT
33860 TTTTC TTTTAC TTTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTT-C -TTTTC TTTTC TTTTC TTTTC TTTTC TTT
33900 GCAATGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 27 0.82
6 2 0.06
7 4 0.12
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Done.