Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007215.1 Hibiscus syriacus cultivar Beakdansim tig00019079_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: 49116
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8504 original size:3 final size:3
Alignment explanation
Indices: 8490--8539 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
8480 GGAAAGATAC
*
8490 GAA GAC GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A
8535 GAA GA
1 GAA GA
8540 GTTTTTGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11572 original size:36 final size:36
Alignment explanation
Indices: 11532--11602 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
11522 TTCAAACACC
* * * *
11532 ATGAATAATAAGGGTATGAGCATTCGATATCAAATG
1 ATGAACAATAAGGATATGAACATTCAATATCAAATG
*
11568 ATGAACAATAAGGATATGAACATTCAATGTCAAAT
1 ATGAACAATAAGGATATGAACATTCAATATCAAAT
11603 AATTGAGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (36 bp):
ATGAACAATAAGGATATGAACATTCAATATCAAATG
Found at i:12125 original size:17 final size:17
Alignment explanation
Indices: 12103--12138 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
12093 AATGAATATC
12103 ATTAAACCATTTGAAAG
1 ATTAAACCATTTGAAAG
*
12120 ATTAAACCATTTGAGAG
1 ATTAAACCATTTGAAAG
12137 AT
1 AT
12139 GTGGCACGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
ATTAAACCATTTGAAAG
Found at i:29887 original size:3 final size:3
Alignment explanation
Indices: 29879--29937 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
29869 TACATTACTT
*
29879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29927 TTA TTA TTA TT
1 TTA TTA TTA TT
29938 TATACATGAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30695 original size:138 final size:138
Alignment explanation
Indices: 30334--30803 Score: 538
Period size: 138 Copynumber: 3.4 Consensus size: 138
30324 AAGTGTAGTA
* *
30334 TCTAATATTAAAACCTAATCAATTTTAACAACTTATTGAAACGAATAATTAACTTGGAACCTCGA
1 TCTAATATTAAAACCTAATCAATTTTAACAAATTATTGAATCGAATAATTAACTTGGAACCTC-A
* * * ** *
30399 GAAAAAAGGCA-ACGACTAAATTAAAAAATTCACCTAAATTGAAGGACTAATATGAAATTAAAAT
65 GGAAAAAGG-AGACGACCAAATT-AAAAATTCACCTAAATTAAAGGACTAAGGTGAAATTAAAAC
*
30463 TAAGGTAAATGC
128 TAAGGTGAA-GC
* * *
30475 TCTAATACTAAAACCTAATCAATTTTAACAAATTATTGAATCTAATAATTAAATTGGAACCTC-G
1 TCTAATATTAAAACCTAATCAATTTTAACAAATTATTGAATCGAATAATTAACTTGGAACCTCAG
* * * ** ** *
30539 AGTAAAAGGCGATGACCAAATTTCAAATTCACCTAAATTAAATTACTAAGGTGAAACTAAAACTA
66 -GAAAAAGGAGACGACCAAATTAAAAATTCACCTAAATTAAAGGACTAAGGTGAAATTAAAACTA
30604 AGGTGAAGAC
130 AGGTGAAG-C
*
30614 TCTAATATTAAAACTTAAT-AATTTTAACAAATTATTGAATCGAATAATTAACTTGGAACAC-CA
1 TCTAATATTAAAACCTAATCAATTTTAACAAATTATTGAATCGAATAATTAACTTGGAAC-CTCA
* * * ** *
30677 GGCAAAAGGAGAGGACCAAATTAAAAATGCACCTAAATTAAAGGGTTAAGGTGAAATTAGAACTA
65 GGAAAAAGGAGACGACCAAATTAAAAATTCACCTAAATTAAAGGACTAAGGTGAAATTAAAACTA
*
30742 AAGTGAAGGC
130 AGGTGAA-GC
* *
30752 TCTAATATTGAAACCTAA-CGAATTTTAA-AAATTTATTGAATCAAATAATTAA
1 TCTAATATTAAAACCTAATC-AATTTTAACAAA-TTATTGAATCGAATAATTAA
30804 AATAAAACTT
Statistics
Matches: 280, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
138 118 0.42
139 89 0.32
140 15 0.05
141 58 0.21
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (138 bp):
TCTAATATTAAAACCTAATCAATTTTAACAAATTATTGAATCGAATAATTAACTTGGAACCTCAG
GAAAAAGGAGACGACCAAATTAAAAATTCACCTAAATTAAAGGACTAAGGTGAAATTAAAACTAA
GGTGAAGC
Found at i:31156 original size:2 final size:2
Alignment explanation
Indices: 31149--31247 Score: 137
Period size: 2 Copynumber: 48.5 Consensus size: 2
31139 TGTACATGTA
31149 AT AT AT AT AT 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 AT AT AT AT AT
* * *
31191 AGT -T AT GT AT GAT AT CAG GT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
31233 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
31248 ATAATGCAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
1 1 0.01
2 82 0.94
3 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32909 original size:22 final size:21
Alignment explanation
Indices: 32883--32948 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
32873 TCATTACGAA
32883 CTTCTTTCTTTTCGACTGAGTT
1 CTTCTTTCTTTT-GACTGAGTT
* *
32905 CTTC-TTATTATGA--G-GTT
1 CTTCTTTCTTTTGACTGAGTT
32922 CTTCTTTCTTTTTGACTGAGTT
1 CTTCTTTC-TTTTGACTGAGTT
32944 CTTCT
1 CTTCT
32949 CATTATGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 7 0.20
18 3 0.09
19 5 0.14
20 2 0.06
21 6 0.17
22 12 0.34
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.56
Consensus pattern (21 bp):
CTTCTTTCTTTTGACTGAGTT
Found at i:32926 original size:39 final size:39
Alignment explanation
Indices: 32865--32998 Score: 168
Period size: 39 Copynumber: 3.5 Consensus size: 39
32855 AGATTGAACA
* *
32865 AGTTCTTCTCATTACGAA---CTTCTTTCTTTTCGACTG
1 AGTTCTTCTCATTATGAACTTCTTCTTTCTTTTTGACTG
* **
32901 AGTTCTTCTTATTATGAGGTTCTTCTTTCTTTTTGACTG
1 AGTTCTTCTCATTATGAACTTCTTCTTTCTTTTTGACTG
* *
32940 AGTTCTTCTCATTATGAACTTCTT-TCTTCTTTTTGAATA
1 AGTTCTTCTCATTATGAACTTCTTCT-TTCTTTTTGACTG
32979 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
32999 CTTTTTGAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
36 15 0.18
38 1 0.01
39 69 0.81
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.51
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTTTCTTTTTGACTG
Found at i:32968 original size:21 final size:21
Alignment explanation
Indices: 32942--33002 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 21
32932 TTTGACTGAG
32942 TTCTTCTCATTATGAACTTCT
1 TTCTTCTCATTATGAACTTCT
* ***
32963 TTCTTCT--TTTTGAA-TAAG
1 TTCTTCTCATTATGAACTTCT
32981 TTCTTCTCATTATGAAC-TCT
1 TTCTTCTCATTATGAACTTCT
33001 TT
1 TT
33003 TTGAAAAGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 7
0.66 0.18 0.16
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 8 0.28
21 7 0.24
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (21 bp):
TTCTTCTCATTATGAACTTCT
Found at i:33260 original size:25 final size:25
Alignment explanation
Indices: 33232--33289 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
33222 AATGTCTTGC
*
33232 AAATCTTCACTTCATTTTCTAACTT
1 AAATCTTCACTTCATTTTCTAACTA
*
33257 AAATCTTCACTTCATTTTCTAGCTA
1 AAATCTTCACTTCATTTTCTAACTA
33282 AAATCTTC
1 AAATCTTC
33290 TTTTCTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (25 bp):
AAATCTTCACTTCATTTTCTAACTA
Found at i:35072 original size:20 final size:23
Alignment explanation
Indices: 35043--35100 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
35033 TTCACGATGA
35043 TATCAATAC-TCCCC-C-TTGGG
1 TATCAATACTTCCCCTCTTTGGG
*
35063 TATCAGTACTTCCCCTCTTTGGG
1 TATCAATACTTCCCCTCTTTGGG
* *
35086 TATCGATATTTCCCC
1 TATCAATACTTCCCC
35101 GAGTATCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
22 1 0.03
23 17 0.55
ACGTcount: A:0.17, C:0.33, G:0.14, T:0.36
Consensus pattern (23 bp):
TATCAATACTTCCCCTCTTTGGG
Found at i:36550 original size:6 final size:6
Alignment explanation
Indices: 36508--36581 Score: 75
Period size: 6 Copynumber: 12.7 Consensus size: 6
36498 TGAACTCTCA
* * *
36508 TTTTTC TTTTAT- TTTTTC TTTTTA TTTTTC -TTCTC TTTTTC TTTGTC
1 TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
36555 TTTTT- TTTTAT- TTTTTC TTTTTC TTTT
1 TTTTTC TTTT-TC TTTTTC TTTTTC TTTT
36582 GGTTTTTCTC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 10 0.18
6 46 0.81
7 1 0.02
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:44331 original size:33 final size:33
Alignment explanation
Indices: 44294--44360 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
44284 CTAATACATA
*
44294 AGCAATAGCATAACATTTCAAAGAATGAAATTG
1 AGCAATAACATAACATTTCAAAGAATGAAATTG
44327 AGCAATAACATAACATTTCAAAGAATGAAATTG
1 AGCAATAACATAACATTTCAAAGAATGAAATTG
44360 A
1 A
44361 ACCTTTATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (33 bp):
AGCAATAACATAACATTTCAAAGAATGAAATTG
Found at i:47431 original size:21 final size:21
Alignment explanation
Indices: 47407--47446 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47397 ATGTTTAACC
*
47407 ATTCTTGTTGTAGTCGTTAAT
1 ATTCTTGTTATAGTCGTTAAT
*
47428 ATTCTTGTTATAGTTGTTA
1 ATTCTTGTTATAGTCGTTA
47447 GCGTTTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.55
Consensus pattern (21 bp):
ATTCTTGTTATAGTCGTTAAT
Done.