Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005306.1 Hibiscus syriacus cultivar Beakdansim tig00012009_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: 45291
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2748 original size:20 final size:21
Alignment explanation
Indices: 2719--2761 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2709 TGTTGTTCAA
* *
2719 TTCGATTTGACTCGTTG-TCG
1 TTCGACTTGACTCATTGTTCG
2739 TTCGACTTGACTCATTGTTCG
1 TTCGACTTGACTCATTGTTCG
2760 TT
1 TT
2762 GAACTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (21 bp):
TTCGACTTGACTCATTGTTCG
Found at i:5759 original size:38 final size:38
Alignment explanation
Indices: 5675--5759 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 38
5665 AAAAAACGCG
*
5675 ACCTAAAATATTATAAATATCATAACATTTTCGATTTA
1 ACCTAAAATATTATAAATATCATAACATTTTCGATTGA
* * * * *
5713 ACCGAAAATATTATGAAATA-GATAATATTTTCGGTTGC
1 ACCTAAAATATTAT-AAATATCATAACATTTTCGATTGA
5751 ACCTAAAAT
1 ACCTAAAAT
5760 GTTAGAAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (38 bp):
ACCTAAAATATTATAAATATCATAACATTTTCGATTGA
Found at i:7866 original size:2 final size:2
Alignment explanation
Indices: 7853--7884 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7843 TTAAATTCTA
*
7853 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7885 GTTTAGAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13192 original size:41 final size:41
Alignment explanation
Indices: 13129--13222 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
13119 ATTTATGTAG
13129 CTTTCAAGGTGCGCATCGTTATTTATCAGCTTTGAATTCCC
1 CTTTCAAGGTGCGCATCGTTATTTATCAGCTTTGAATTCCC
* *
13170 CTTTCAAGGTGCGTATCTTTATTTATCAGCTTTGAATTCCC
1 CTTTCAAGGTGCGCATCGTTATTTATCAGCTTTGAATTCCC
13211 CTTTCAAGGTGC
1 CTTTCAAGGTGC
13223 CCTAAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (41 bp):
CTTTCAAGGTGCGCATCGTTATTTATCAGCTTTGAATTCCC
Found at i:18693 original size:22 final size:22
Alignment explanation
Indices: 18660--18785 Score: 93
Period size: 22 Copynumber: 5.9 Consensus size: 22
18650 TTTCAAAAAA
*
18660 AAAATA-AT-ATATGGTTTTTG
1 AAAATATATAATATAGTTTTTG
*
18680 AAAATATATAATATAATTTTT-
1 AAAATATATAATATAGTTTTTG
***
18701 AAAATCATATGGCATAGTTTTTG
1 AAAAT-ATATAATATAGTTTTTG
* *
18724 AAAACATAT--TATAG-TTTTA
1 AAAATATATAATATAGTTTTTG
* *
18743 AAACAAACATATATATAGTTTTTG
1 AAA-ATATATA-ATATAGTTTTTG
*
18767 AAAATATATAGTATAGTTT
1 AAAATATATAATATAGTTT
18786 CAAAAACATA
Statistics
Matches: 82, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
19 7 0.09
20 14 0.17
21 7 0.09
22 33 0.40
23 14 0.17
24 7 0.09
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (22 bp):
AAAATATATAATATAGTTTTTG
Found at i:18721 original size:44 final size:43
Alignment explanation
Indices: 18673--18798 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 43
18663 ATAATATATG
* *
18673 GTTTTTGAAAATATATAATATAATTTTTAAAATCATATGGCATA
1 GTTTTTGAAAATATAT-ATATAATTTTAAAAAACATATGGCATA
* * **
18717 GTTTTTGAAAACATAT-TATAGTTTTAAAACAAACATAT-ATATA
1 GTTTTTGAAAATATATATATAATTTT-AAA-AAACATATGGCATA
* *
18760 GTTTTTGAAAATATATAGTAT-AGTTTCAAAAACATATGG
1 GTTTTTGAAAATATATA-TATAATTTTAAAAAACATATGG
18799 TTTTGAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
42 16 0.24
43 22 0.33
44 25 0.38
45 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (43 bp):
GTTTTTGAAAATATATATATAATTTTAAAAAACATATGGCATA
Found at i:18775 original size:17 final size:17
Alignment explanation
Indices: 18753--18814 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
18743 AAACAAACAT
18753 ATATATAGTTTTTGAAA
1 ATATATAGTTTTTGAAA
*
18770 ATATATAGTATAGTTTCAAA
1 ATATATAGT-T--TTTGAAA
* *
18790 A-ACATATGGTTTTGAAA
1 ATATATA-GTTTTTGAAA
18807 ATATATAG
1 ATATATAG
18815 CATAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 17 0.49
18 5 0.14
19 5 0.14
20 8 0.23
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.40
Consensus pattern (17 bp):
ATATATAGTTTTTGAAA
Found at i:18915 original size:21 final size:20
Alignment explanation
Indices: 18827--18925 Score: 58
Period size: 21 Copynumber: 4.8 Consensus size: 20
18817 TAATTTAAAA
*
18827 AAAAACATATTATTATATTTT
1 AAAAACATAATA-TATATTTT
**
18848 AAAAACAT-ATA-ATTATTGAA
1 AAAAACATAATATA-TATT-TT
* *
18868 AAAATACGTAATATATATACTT
1 AAAA-ACATAATATATAT-TTT
* *
18890 GAAAACATATTATATGATTTT
1 AAAAACATAATATAT-ATTTT
*
18911 AAAAATATAATATAT
1 AAAAACATAATATAT
18926 TATATAATTT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 6 0.11
21 34 0.60
22 11 0.19
23 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAACATAATATATATTTT
Found at i:18925 original size:26 final size:29
Alignment explanation
Indices: 18896--18961 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 29
18886 ACTTGAAAAC
*
18896 ATATTATATGA-TTTTA-AAAATATA-AT
1 ATATTATATAATTTTTAGAAAATATATAT
18922 ATATTATATAATTTTTAGAAAATATATAT
1 ATATTATATAATTTTTAGAAAATATATAT
18951 ATATATATATA
1 ATAT-TATATA
18962 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 10 0.29
27 5 0.14
28 8 0.23
29 6 0.17
30 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
ATATTATATAATTTTTAGAAAATATATAT
Found at i:18948 original size:2 final size:2
Alignment explanation
Indices: 18943--18974 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18933 TTTTTAGAAA
18943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18975 TAAGCTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20252 original size:12 final size:12
Alignment explanation
Indices: 20235--20265 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
20225 GGTAAGATGT
20235 GAGGGAACTAAG
1 GAGGGAACTAAG
20247 GAGGGAACTAAG
1 GAGGGAACTAAG
20259 GAGGGAA
1 GAGGGAA
20266 AAGAAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.45, T:0.06
Consensus pattern (12 bp):
GAGGGAACTAAG
Found at i:24619 original size:44 final size:44
Alignment explanation
Indices: 24568--24885 Score: 426
Period size: 44 Copynumber: 7.2 Consensus size: 44
24558 TATGCATTTA
* * *
24568 ATTTTCA-TTAGTGGCACCTTTATGCCAATAATGCACCGTTATGC
1 ATTTTCATTTA-TGACACATTTCTGCCAATAATGCACCGTTATGC
**
24612 ATTTTCATTTATGACACATTTCTG-CAATTAATGCATAGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAA-TAATGCACCGTTATGC
*
24656 ATTTTCATTTATGACACCTTTCTGCCAATAATGCACCGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
24700 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
* * *
24744 ATTTTCATTTATGACTCATTTCTGTCAATAATGCACTGTTATGC
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
* * *
24788 AGTTTCATTTATGACACCTTTC-GTCCAATAATGCACCATTATGC
1 ATTTTCATTTATGACACATTTCTG-CCAATAATGCACCGTTATGC
* * * ** *
24832 ATTTTCATTTATGACACTTTTCTTCCAATAAAGCAATGTTATGT
1 ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
24876 ATTTTCATTT
1 ATTTTCATTT
24886 TTTTTTATTT
Statistics
Matches: 243, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
43 4 0.02
44 233 0.96
45 6 0.02
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (44 bp):
ATTTTCATTTATGACACATTTCTGCCAATAATGCACCGTTATGC
Found at i:31549 original size:45 final size:45
Alignment explanation
Indices: 31483--31600 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
31473 TGAAACTAAT
* *
31483 CTTACAAGCTTATGGAGTAAATGGTAAGTATATTGGTAAAATAAG
1 CTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAG
* *
31528 CTTACGAGCTTATGGAATAAATGGAAAGTATATTGGTAGAATAAG
1 CTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAG
* *
31573 CTTACGAGCTTCTAGG-ATAAATGATAAG
1 CTTACGAGCTTAT-GGAATAAATGGTAAG
31601 AAATTTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 63 0.97
46 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
CTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAG
Found at i:37902 original size:23 final size:21
Alignment explanation
Indices: 37850--37911 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
37840 TTTTGGTGCA
*
37850 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
37870 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
37891 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
37912 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:39578 original size:12 final size:12
Alignment explanation
Indices: 39561--39591 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39551 AGATGAGCCT
*
39561 GAGCAGCCCGAG
1 GAGCAGCCCGAA
39573 GAGCAGCCCGAA
1 GAGCAGCCCGAA
39585 GAGCAGC
1 GAGCAGC
39592 ACAACAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.39, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAA
Found at i:43168 original size:44 final size:44
Alignment explanation
Indices: 43123--43468 Score: 425
Period size: 44 Copynumber: 8.0 Consensus size: 44
43113 TCATTAGTGG
* *
43123 CACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
**
43167 CACCTTTCTG-CAATTAATGCACAATTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAA-TAATGCACCGTTATGCATTTTCATTTATGA
*
43211 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCA-TTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
*
43254 CACCTTTCTGCCAATAATGCACTGTTATGCA-TTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* ** * * *
43297 AACCTTT-TGCCAATGTTGTAACATTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * * * *
43340 CATCTTTCTTCCAATAATGCATCGTTATG-AATTTCATTTTTGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
*
43383 C-CCTTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGG
1 CACC-TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
** * *
43427 CACCTTTCTGCCAATAATGCAATGTTATGCCTTTTTATTTAT
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
43469 TCATTCATTT
Statistics
Matches: 258, Mismatches: 36, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
42 23 0.09
43 102 0.40
44 128 0.50
45 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (44 bp):
CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
Found at i:43231 original size:34 final size:39
Alignment explanation
Indices: 43205--43456 Score: 148
Period size: 43 Copynumber: 5.9 Consensus size: 39
43195 GCATTTTCAT
43205 TTATGACACCTTTCTGCCAATAATGCATCGTTATGCATTTTCA
1 TTATGACACCTTTCTGCCAATAATGCATC-TTATGCA--TT-A
*
43248 TTATGACACCTTTCTGCCAATAATGCACTGTTATGCATTTCA
1 TTATGACACCTTTCTGCCAATAATGCA-TCTTATGCA-TT-A
* ** * *
43290 TTTATGAAACCTTT-TGCCAATGTTGTAACATTATGCATTTTCA
1 -TTATGACACCTTTCTGCCAATAATGCATC-TTATGCA--TT-A
* * *
43333 TTTATGACATCTTTCTTCCAATAATGCATCGTTATGAATTTCA
1 -TTATGACACCTTTCTGCCAATAATGCATC-TTATGCA-TT-A
* * *
43376 TTTTTGGC-CCTTTTCTGCCAATAATGCACCGTTATGCATTTTCA
1 -TTATGACACC-TTTCTGCCAATAATGCATC-TTATGCA--TT-A
* *
43420 TTTATGGCACCTTTCTGCCAATAATGCAATGTTATGC
1 -TTATGACACCTTTCTGCCAATAATGC-ATCTTATGC
43457 CTTTTTATTT
Statistics
Matches: 175, Mismatches: 25, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
42 23 0.13
43 98 0.56
44 51 0.29
45 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (39 bp):
TTATGACACCTTTCTGCCAATAATGCATCTTATGCATTA
Found at i:43354 original size:129 final size:130
Alignment explanation
Indices: 43108--43441 Score: 464
Period size: 129 Copynumber: 2.6 Consensus size: 130
43098 TTATGCATTT
*
43108 AATTGTCATTAGTGGCACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTT
1 AATT-TCATTA-TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTT
*
43173 TCTG-CAATTAATGCACAATTATGCATTTTCATTTATGACACCTTTCTGCCAATAATGCATCGTT
64 TCTGCCAATT-ATGAACAATTATGCATTTTCATTTATGACACCTTTCTGCCAATAATGCATCGTT
43237 ATG
128 ATG
* * * **
43240 CATTTTCATTATGACACCTTTCTGCCAATAATGCACTGTTATGCA-TTTCATTTATGAAACCTTT
1 -AATTTCATTATGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTT
* *
43304 -TGCCAATGT-TGTAAC-ATTATGCATTTTCATTTATGACATCTTTCTTCCAATAATGCATCGTT
65 CTGCCAAT-TATG-AACAATTATGCATTTTCATTTATGACACCTTTCTGCCAATAATGCATCGTT
43366 ATG
128 ATG
*
43369 AATTTCATTTTTGGC-CCTTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTT
1 AATTTCA-TTATGGCACC-TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTT
43433 TCTGCCAAT
64 TCTGCCAAT
43442 AATGCAATGT
Statistics
Matches: 179, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
128 8 0.04
129 83 0.46
130 40 0.22
131 39 0.22
132 6 0.03
133 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (130 bp):
AATTTCATTATGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACCTTTC
TGCCAATTATGAACAATTATGCATTTTCATTTATGACACCTTTCTGCCAATAATGCATCGTTATG
Done.