Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007218.1 Hibiscus syriacus cultivar Beakdansim tig00019088_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: 49361
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:3226 original size:2 final size:2
Alignment explanation
Indices: 3221--3269 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
3211 ACACACACAC
3221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3262 AT AT AT AT
1 AT AT AT AT
3270 TAAAATTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4468 original size:2 final size:2
Alignment explanation
Indices: 4398--4449 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
4388 AAACGAATTA
4398 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4439 AT AT AT AT AT A
1 AT AT AT AT AT A
4450 AGTATAAGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4778 original size:3 final size:3
Alignment explanation
Indices: 4770--4810 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
4760 GACTTAATTG
4770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4811 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:15938 original size:23 final size:23
Alignment explanation
Indices: 15894--15953 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
15884 GAACACCTAC
* *
15894 GCGAACATATAAAAGAATATATTT
1 GCGAACAT-TAAATGAACATATTT
*
15918 GCGTACATTAAATGAACATATTT
1 GCGAACATTAAATGAACATATTT
*
15941 GCGAACAATAAAT
1 GCGAACATTAAAT
15954 AAACGAACAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (23 bp):
GCGAACATTAAATGAACATATTT
Found at i:17436 original size:2 final size:2
Alignment explanation
Indices: 17429--17458 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17419 TTCAAGTGAC
17429 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
17459 TTGGCAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19425 original size:16 final size:16
Alignment explanation
Indices: 19404--19434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19394 TTTTGTATTT
19404 TTAAAGAAATAAAAAA
1 TTAAAGAAATAAAAAA
*
19420 TTAAAGTAATAAAAA
1 TTAAAGAAATAAAAA
19435 TATATATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TTAAAGAAATAAAAAA
Found at i:29945 original size:19 final size:19
Alignment explanation
Indices: 29921--29957 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29911 ATGACCAACA
*
29921 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
29940 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
29958 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:30048 original size:21 final size:21
Alignment explanation
Indices: 30002--30055 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
29992 GATTTTTACT
*
30002 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
30023 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
30044 ATCGCAATGCGA
1 ATCGCATTGCGA
30056 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:30771 original size:20 final size:20
Alignment explanation
Indices: 30683--30788 Score: 108
Period size: 20 Copynumber: 5.4 Consensus size: 20
30673 AAATCACAAC
*
30683 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
30702 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** **
30721 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
30741 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
**
30761 GCGATTTTCATTTTCGTATT
1 GCGATTTTCATTTTCGCGTT
30781 GCGATTTT
1 GCGATTTT
30789 AAGTTTCATA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
19 25 0.33
20 51 0.67
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:30795 original size:20 final size:20
Alignment explanation
Indices: 30752--30795 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30742 CGATAGTCAT
* * *
30752 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
30772 TTTCGTATTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
30792 TTTC
1 TTTC
30796 ATAAACTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:32670 original size:20 final size:20
Alignment explanation
Indices: 32647--32715 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
32637 GAAACTTAAA
32647 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
32667 ATCGCAACGTGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
32687 ATCGCAACACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
32707 ATCGCAACG
1 ATCGCAACG
32716 GGATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:32746 original size:33 final size:34
Alignment explanation
Indices: 32707--32782 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
32697 GAATTTGACT
*
32707 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
32740 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
32774 ATCGCAACG
1 ATCGCAACG
32783 CGAATTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:32772 original size:20 final size:20
Alignment explanation
Indices: 32749--32786 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32739 AATCGCAACG
*
32749 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
32769 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
32787 TTTAATTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:32804 original size:19 final size:19
Alignment explanation
Indices: 32782--32823 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
32772 AAATCGCAAC
*
32782 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
32801 GCGATTTTTATTTCGCATT
1 GCGAATTTAATTTCGCATT
32820 GCGA
1 GCGA
32824 TTATCCCGTA
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:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:32859 original size:20 final size:20
Alignment explanation
Indices: 32834--32897 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
32824 TTATCCCGTA
*
32834 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAATTTCGCGTT
32854 GCGATAGTC-ATTTCCGCGTT
1 GCGATAGTCAATTT-CGCGTT
* *
32874 GC-ATAGTCATTTTTGCGTT
1 GCGATAGTCAATTTCGCGTT
32893 GCGAT
1 GCGAT
32898 TTTTTCGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 16 0.42
20 22 0.58
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGATAGTCAATTTCGCGTT
Found at i:32881 original size:19 final size:20
Alignment explanation
Indices: 32834--32897 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
32824 TTATCCCGTA
*
32834 GCGATAGTCAAATT-CGCGTT
1 GCGATAGTC-ATTTCCGCGTT
32854 GCGATAGTCATTTCCGCGTT
1 GCGATAGTCATTTCCGCGTT
**
32874 GC-ATAGTCATTTTTGCGTT
1 GCGATAGTCATTTCCGCGTT
32893 GCGAT
1 GCGAT
32898 TTTTTCGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 20 0.51
20 19 0.49
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGATAGTCATTTCCGCGTT
Found at i:33474 original size:42 final size:42
Alignment explanation
Indices: 33410--33491 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
33400 CTGTCATCGT
* * *
33410 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * *
33452 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCTCCTGTCATC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATC
33492 GTTGAAAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:33494 original size:21 final size:21
Alignment explanation
Indices: 33399--33494 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
33389 GCCCGACTCA
33399 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
33420 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
33441 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** * *
33462 CCTCCCACCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGGCC
33483 CCTGTCATCGTT
1 CCTGTCATCGTT
33495 GAAAAGGTGC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.18, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:34274 original size:20 final size:20
Alignment explanation
Indices: 34249--34383 Score: 198
Period size: 20 Copynumber: 6.8 Consensus size: 20
34239 ATTGTCTGAT
34249 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
34269 TTGCGATAATCAAATTCGTG
1 TTGCGATAGTCAAATTCGCG
*
34289 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
34309 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
34329 TTGCGATAGTCAAATTCGTG
1 TTGCGATAGTCAAATTCGCG
* *
34349 TTGTGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
* *
34369 CTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
34384 GAATGTGTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:36857 original size:24 final size:24
Alignment explanation
Indices: 36823--36876 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36813 CTGAAACATC
*
36823 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
36847 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
36871 ATCAAA
1 ATCAAA
36877 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:37552 original size:17 final size:17
Alignment explanation
Indices: 37530--37567 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
37520 CGGATGGGGA
37530 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
37547 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
37564 AGGA
1 AGGA
37568 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:37576 original size:22 final size:20
Alignment explanation
Indices: 37527--37577 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
37517 TGCCGGATGG
37527 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
37547 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
37564 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
37578 CCGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Done.