Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009470.1 Hibiscus syriacus cultivar Beakdansim tig00114143_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: 52800
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Found at i:1688 original size:31 final size:31
Alignment explanation
Indices: 1652--1718 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1642 AAAATCAAAA
* *
1652 TATTATTAA-AATAAA-AGTATAATATTATATT
1 TATTA-TAATAATAAAGAATATAATATCATA-T
*
1683 TATTATAATATTAAAGAATATAATATCATAT
1 TATTATAATAATAAAGAATATAATATCATAT
1714 TATTA
1 TATTA
1719 GAATTATGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 3 0.10
31 16 0.52
32 12 0.39
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (31 bp):
TATTATAATAATAAAGAATATAATATCATAT
Found at i:1692 original size:28 final size:29
Alignment explanation
Indices: 1651--1718 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
1641 AAAAATCAAA
*
1651 ATATTATTAAAATA-AAAG-TATAATATT
1 ATATTATTAAAATATAAAGATATAATATC
*
1678 ATATTTATTATAATATTAAAGAATATAATATC
1 ATA-TTATTAAAATA-TAAAG-ATATAATATC
1710 ATATTATTA
1 ATATTATTA
1719 GAATTATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 3 0.09
28 10 0.29
30 4 0.12
31 6 0.18
32 11 0.32
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
ATATTATTAAAATATAAAGATATAATATC
Found at i:3260 original size:2 final size:2
Alignment explanation
Indices: 3255--3284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3245 ATTATAAAAA
3255 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
3285 CCAAGAAATA
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:9237 original size:38 final size:38
Alignment explanation
Indices: 9195--9269 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
9185 TTATTGAAAA
9195 ATCATTAT-ATATTATAA-AATAAAAGTATAATATTATAT
1 ATCATTATAATATTA-AAGAATAAAA-TATAATATTATAT
* *
9233 ATCATTATAATATTAAAGAATATAATATCATATTATA
1 ATCATTATAATATTAAAGAATAAAATATAATATTATA
9270 GAATTATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 21 0.64
39 12 0.36
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (38 bp):
ATCATTATAATATTAAAGAATAAAATATAATATTATAT
Found at i:15056 original size:21 final size:22
Alignment explanation
Indices: 15018--15059 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15008 TTAAGATTAT
*
15018 TAAATTTTATTGAATTTTTTAA
1 TAAATTATATTGAATTTTTTAA
15040 TAAATTATATT-AATTTTTTA
1 TAAATTATATTGAATTTTTTA
15060 TTATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TAAATTATATTGAATTTTTTAA
Found at i:15071 original size:22 final size:22
Alignment explanation
Indices: 15025--15071 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
15015 TATTAAATTT
*
15025 TATTGAATTTTTTAATAAATTA
1 TATTGAATTTTTTAATAAATAA
*
15047 TATT-AATTTTTTATTATAATAA
1 TATTGAATTTTTTAATA-AATAA
15069 TAT
1 TAT
15072 ATTCTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTGAATTTTTTAATAAATAA
Found at i:21658 original size:18 final size:19
Alignment explanation
Indices: 21632--21673 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
21622 ATATATATAT
21632 ATATATATTTTTATGAAA-A
1 ATATATATTTTTAT-AAATA
21651 ATAT-TATTTTTATAAATA
1 ATATATATTTTTATAAATA
21669 ATATA
1 ATATA
21674 AAAGTCCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 14 0.67
19 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATTTTTATAAATA
Found at i:24013 original size:9 final size:9
Alignment explanation
Indices: 23994--24022 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
23984 TTTCATAGAT
23994 TATTA-AAA
1 TATTATAAA
24002 TATTATAAA
1 TATTATAAA
24011 TATTATAAA
1 TATTATAAA
24020 TAT
1 TAT
24023 AGTTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATTATAAA
Found at i:24271 original size:31 final size:29
Alignment explanation
Indices: 24233--24296 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
24223 ATTTAATAAT
*
24233 AATAAAAGGAAAAATCATTATATATTATTAA
1 AATAAAA-GAAAAAT-ATTATATATCATTAA
* * *
24264 AATAAAAGTATAATATTATATATCATTAT
1 AATAAAAGAAAAATATTATATATCATTAA
24293 AATA
1 AATA
24297 TTAAAGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.59
30 5 0.17
31 7 0.24
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAAAAGAAAAATATTATATATCATTAA
Found at i:32750 original size:2 final size:2
Alignment explanation
Indices: 32743--32772 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32733 TTAATTCTTG
32743 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
32773 TTTATTTTTT
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:37352 original size:2 final size:2
Alignment explanation
Indices: 37340--37376 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
37330 ATTCTCAGCA
37340 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37377 AAATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:38684 original size:22 final size:21
Alignment explanation
Indices: 38655--38698 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
38645 TATTAAAATA
*
38655 AAAGTATATTAT-ATATATATT
1 AAAGTATAATATCATAT-TATT
38676 AAAGATATAATATCATATTATT
1 AAAG-TATAATATCATATTATT
38698 A
1 A
38699 GAATTATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
AAAGTATAATATCATATTATT
Found at i:44654 original size:140 final size:141
Alignment explanation
Indices: 44398--44679 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 141
44388 CTCTAACAAT
*
44398 TCAAAAAAATTATATTTTTAGTCTCTAAACCATTTTTGCTCACAATTTAGCCCTTAAATAAAATA
1 TCAAAAAAA-TATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATA
*
44463 TAATTATCATGTACCATTGCTCGATACTTGCAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAA
65 TAATTATCATGTACCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAA
44528 GTGTTAATGTAG
130 GTGTTAATGTAG
44540 TCAAAAAAA-ATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
1 TCAAAAAAATATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
* *
44604 AATTATCATGTCCCATTGCTCGATACTTACAAGGTGATTCTAAATGTGGAGATGGAAGTTCAAAG
66 AATTATCATGTACCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAAG
44669 TGTTAATGTAG
131 TGTTAATGTAG
44680 CTATCATAGG
Statistics
Matches: 136, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
140 127 0.93
142 9 0.07
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (141 bp):
TCAAAAAAATATATTTTTAGTCTCTAAACCATTTTTACTCACAATTTAGCCCTTAAATAAAATAT
AATTATCATGTACCATTGCTCGATACTTACAAGGTGATCCTAAATGTGGAGATGGAAGTTCAAAG
TGTTAATGTAG
Found at i:44898 original size:17 final size:20
Alignment explanation
Indices: 44876--44917 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 20
44866 CTTTTAATAA
44876 ATTATAATAAT-T-TTTTT-
1 ATTATAATAATATATTTTTG
44893 ATTATAATAATATATTTTTG
1 ATTATAATAATATATTTTTG
44913 ATTAT
1 ATTAT
44918 TTTAATTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 5 0.23
20 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTATAATAATATATTTTTG
Found at i:49975 original size:2 final size:2
Alignment explanation
Indices: 49970--49994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49960 AAAAATATCT
49970 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49995 TTCCAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51322 original size:26 final size:26
Alignment explanation
Indices: 51275--51339 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
51265 TTGAAAAATC
51275 ATTATAT-ATTATTAAATAAAAGTAA-
1 ATTATATCATTATTAAATAAAAG-AAT
*
51300 ATTATATCATTA-TAATATTAAAGAAT
1 ATTATATCATTATTAA-ATAAAAGAAT
*
51326 ATAATATCA-TATTA
1 ATTATATCATTATTA
51340 TAGAATTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (26 bp):
ATTATATCATTATTAAATAAAAGAAT
Done.