Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005528.1 Hibiscus syriacus cultivar Beakdansim tig00012774_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: 61787
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1625 original size:29 final size:29
Alignment explanation
Indices: 1592--1652 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1582 GATTTAAAAA
1592 TCATAGTATGAAAGTCACAGTAGAACTTT
1 TCATAGTATGAAAGTCACAGTAGAACTTT
1621 TCATAGTATGAAAGTCACAGTAGAACTTT
1 TCATAGTATGAAAGTCACAGTAGAACTTT
1650 TCA
1 TCA
1653 ATGAAATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (29 bp):
TCATAGTATGAAAGTCACAGTAGAACTTT
Found at i:2319 original size:18 final size:17
Alignment explanation
Indices: 2296--2370 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 17
2286 CACATATGCC
2296 ATCATTATCGATGTCAAT
1 ATCATTATC-ATGTCAAT
**
2314 ATCATTATCATGATCTCT
1 ATCATTATCATG-TCAAT
* *
2332 ATCATTATCAATATGAAT
1 ATCATTATC-ATGTCAAT
*
2350 ATCGTTATCATGT-AAT
1 ATCATTATCATGTCAAT
2366 A-CATT
1 ATCATT
2371 TCACTCAGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.07
16 4 0.09
17 6 0.13
18 31 0.67
19 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (17 bp):
ATCATTATCATGTCAAT
Found at i:3408 original size:9 final size:9
Alignment explanation
Indices: 3394--3419 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3384 AATAGCCCTC
3394 AAATAAAAT
1 AAATAAAAT
3403 AAATAAAAT
1 AAATAAAAT
3412 AAATAAAA
1 AAATAAAA
3420 AAGTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:6635 original size:19 final size:20
Alignment explanation
Indices: 6611--6653 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6601 AGAGAAAAGT
*
6611 AAAGTTAA-AATGAAATAGA
1 AAAGTTAAGAATGAAAGAGA
*
6630 AAAGTTAAGGATGAAAGAGA
1 AAAGTTAAGAATGAAAGAGA
6650 AAAG
1 AAAG
6654 AAAAACTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (20 bp):
AAAGTTAAGAATGAAAGAGA
Found at i:13538 original size:23 final size:23
Alignment explanation
Indices: 13512--13560 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13502 ATAAAGAACC
*
13512 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
13535 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
13558 AAA
1 AAA
13561 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:16861 original size:30 final size:30
Alignment explanation
Indices: 16825--16899 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
16815 AAAATTACAT
*
16825 TTTGGTCCCTAAACTTTTCAAAGT-TTATAC
1 TTTGGTCCCTAAACTTTTCAAA-TCTTATAA
*
16855 TTTGGTCACC-AAACTTTTGAAATCTTATAA
1 TTTGGTC-CCTAAACTTTTCAAATCTTATAA
*
16885 TTTGGTCACTAAACT
1 TTTGGTCCCTAAACT
16900 AAATCCATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 35 0.90
31 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTGGTCCCTAAACTTTTCAAATCTTATAA
Found at i:18152 original size:10 final size:10
Alignment explanation
Indices: 18128--18173 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
18118 ATCTCTCATT
18128 TTTTTCTTTTCA
1 TTTTT-TTTT-A
18140 TTTTTTTTTA
1 TTTTTTTTTA
18150 --TTTTTTTA
1 TTTTTTTTTA
*
18158 TTTTTTTTCA
1 TTTTTTTTTA
18168 TTTTTT
1 TTTTTT
18174 CTATTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 8 0.26
10 14 0.45
11 4 0.13
12 5 0.16
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:18153 original size:9 final size:9
Alignment explanation
Indices: 18141--18212 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
18131 TTCTTTTCAT
18141 TTTTTTTTA
1 TTTTTTTTA
18150 -TTTTTTTA
1 TTTTTTTTA
18158 TTTTTTTTCA
1 TTTTTTTT-A
*
18168 TTTTTTCTA
1 TTTTTTTTA
*
18177 TTTTCTTCTTC
1 TTTT-TT-TTA
* * *
18188 TTCTTCTTC
1 TTTTTTTTA
*
18197 TTCTTTTTA
1 TTTTTTTTA
18206 TTTTTTT
1 TTTTTTT
18213 CCTTTTTCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 8 0.16
9 28 0.55
10 11 0.22
11 4 0.08
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:18187 original size:3 final size:3
Alignment explanation
Indices: 18179--18237 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
18169 TTTTTCTATT
* * * *
18179 TTC TTC TTC TTC TTC TTC TTC TTT TTA TT- TTT TTCC TTT TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
*
18224 TTC TTT TTC TTC TT
1 TTC TTC TTC TTC TT
18238 TTTAGTTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:18247 original size:10 final size:9
Alignment explanation
Indices: 18179--18240 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
18169 TTTTTCTATT
*
18179 TTCTTCTTC
1 TTCTTTTTC
*
18188 TTCTTCTTC
1 TTCTTTTTC
*
18197 TTCTTTTTA
1 TTCTTTTTC
18206 TT-TTTTTCC
1 TTCTTTTT-C
18215 TT-TTTCTTC
1 TTCTTT-TTC
18224 TTCTTTTTC
1 TTCTTTTTC
18233 TTCTTTTT
1 TTCTTTTT
18241 AGTTCTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.11
9 37 0.79
10 5 0.11
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.76
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:20798 original size:18 final size:18
Alignment explanation
Indices: 20735--20798 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
20725 CACATATGCC
*
20735 ATCATTATCCACATCAAT
1 ATCATTATCAACATCAAT
** **
20753 ATCATTATCATGATCTCT
1 ATCATTATCAACATCAAT
20771 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
*
20789 ATCGTTATCA
1 ATCATTATCA
20799 TGTAATACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:21056 original size:30 final size:30
Alignment explanation
Indices: 21022--21084 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
21012 CAAATACTTT
* *
21022 TGATATCTTTTATAATCTCATGTACAGTAC
1 TGATATCTTTTATAAGCCCATGTACAGTAC
*
21052 TGATATCTTTTATAAGCCCATGTACATTAC
1 TGATATCTTTTATAAGCCCATGTACAGTAC
21082 TGA
1 TGA
21085 GAACTCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (30 bp):
TGATATCTTTTATAAGCCCATGTACAGTAC
Found at i:21215 original size:21 final size:21
Alignment explanation
Indices: 21172--21223 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
21162 TATAAAATTA
*
21172 TCCCGAAGGATCTCGTATATG
1 TCCCGAAGGATCTCATATATG
* * *
21193 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATCTCATATATG
*
21214 TCCTGAAGGA
1 TCCCGAAGGA
21224 CCTGCAGAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
TCCCGAAGGATCTCATATATG
Found at i:23537 original size:29 final size:30
Alignment explanation
Indices: 23502--23561 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
23492 TCCTTGAAGT
* *
23502 TTTCAAAGT-TTATACTTTGGTCACCAAAC
1 TTTCAAAATCTTATAATTTGGTCACCAAAC
*
23531 TTTCAAAATCTTATAATTTGGTCACTAAAC
1 TTTCAAAATCTTATAATTTGGTCACCAAAC
23561 T
1 T
23562 AAAACCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (30 bp):
TTTCAAAATCTTATAATTTGGTCACCAAAC
Found at i:25338 original size:29 final size:29
Alignment explanation
Indices: 25306--25398 Score: 132
Period size: 29 Copynumber: 3.2 Consensus size: 29
25296 ATCGAACCAA
* * * * *
25306 AATTTATTTGGAAACTATTAATCGAAACG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
25335 AATTAATTTGAAAATTATTAACCGAACCA
1 AATTAATTTGAAAATTATTAACCGAACCG
25364 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
25393 AATTAA
1 AATTAA
25399 CCGATTTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:36612 original size:21 final size:19
Alignment explanation
Indices: 36574--36619 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
36564 AATTAATCCT
36574 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
36594 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
36615 A-TAAT
1 ACTAAT
36620 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:44575 original size:45 final size:45
Alignment explanation
Indices: 44546--44982 Score: 570
Period size: 45 Copynumber: 9.7 Consensus size: 45
44536 ACTCTAACAT
* *
44546 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * * *
44591 CTTTTATGTTGATAATGTACCCATATACATCTCAACTATATTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * *
44636 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
44681 CTTTTCTGTTGATAATGCACCCATATGCATTTCATCTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
44726 CTTTTCTGTTGATAATGCACCCATATGCATTTCAGCTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * *
44771 CTTTTATGTTGATAATGTACCCATATACATCTCAAC-CATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* * *
44816 TTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* *
44861 TTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * *
44906 CTTTTCTTTTGATAATGCACCCCATATGCATTTTAACTCTGGCATC
1 CTTTTCTGTTGATAATGCA-CCCATATGCATTTCAACTCTAGTATA
* ***
44952 CTTTTATGCCAATAATGCACCCATATGCATT
1 CTTTTCTGTTGATAATGCACCCATATGCATT
44983 ATTCTTTTAT
Statistics
Matches: 351, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 313 0.89
46 37 0.11
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:45442 original size:22 final size:20
Alignment explanation
Indices: 45396--45451 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
45386 TTGGCCCTTC
*
45396 AGTATCGATACCCCTATTAT
1 AGTATCGATACCCCTACTAT
*
45416 GGTATCGATACTACCCTACTAT
1 AGTATCGATAC--CCCTACTAT
45438 AGTATCGATACCCC
1 AGTATCGATACCCC
45452 CTACCATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 13 0.42
22 18 0.58
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTATCGATACCCCTACTAT
Found at i:51568 original size:45 final size:45
Alignment explanation
Indices: 51516--51933 Score: 511
Period size: 45 Copynumber: 9.3 Consensus size: 45
51506 AATACATCAT
* ** * * *
51516 TATGCATTTTAAACTCTAACAT-CTTTTCTATTCATAATGCACCCA
1 TATGCA-TTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
* * * * * *
51561 TATGCATTTCAATTATAGTATACTTTTATATTGATAATTTACTCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
* *
51606 TATACATCTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCA
1 TATGCATTTCAACTC-TAGTATACTTTTCTGTTGATAATGTACCCA
* *
51651 TATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
* *
51696 TATGCATTTTAACTCTAGTATACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
* *
51741 TATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
* * *
51786 TATACATCTCAAC-CATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTC-TAGTATACTTTTCTGTTGATAATGTACCCA
* * * * *
51831 TATACATTTCAACTCTAGCATACGTTTATGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
*
51876 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGCA-CCA
1 TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
*
51920 TATGCCTTTCAACT
1 TATGCATTTCAACT
51934 TTGGCATCCT
Statistics
Matches: 328, Mismatches: 40, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
44 26 0.08
45 300 0.91
46 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (45 bp):
TATGCATTTCAACTCTAGTATACTTTTCTGTTGATAATGTACCCA
Done.