Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000724.1 Hibiscus syriacus cultivar Beakdansim tig00001404_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: 50175
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:908 original size:42 final size:43
Alignment explanation
Indices: 825--920 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
815 GACGAAAATA
* **
825 TTTTGTCACTAGTCTTAGTTGGTGGTTTTATAATGACAATTAT
1 TTTTGTCACTAGTCTTAGTTGGTGGTTTTACAACAACAATTAT
* * * *
868 TTTTGTTATTAGTCTTAGTTGGTGG-TTTGCAACAATAATTAT
1 TTTTGTCACTAGTCTTAGTTGGTGGTTTTACAACAACAATTAT
910 TTTTGTCACTA
1 TTTTGTCACTA
921 TTTAAGTGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 21 0.48
43 23 0.52
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (43 bp):
TTTTGTCACTAGTCTTAGTTGGTGGTTTTACAACAACAATTAT
Found at i:6881 original size:2 final size:2
Alignment explanation
Indices: 6864--6901 Score: 58
Period size: 2 Copynumber: 18.0 Consensus size: 2
6854 GCTACAAAGG
6864 AT AT CAT AT GAT 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
6902 GTCTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 30 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7985 original size:23 final size:23
Alignment explanation
Indices: 7896--7977 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
7886 ACCTTATATA
* * * *
7896 GCACTTCGGTGTATTTCTACGCG
1 GCACTACGGTGCAATTCTACGTG
*
7919 GCACTACGGTACAATTCTACGTG
1 GCACTACGGTGCAATTCTACGTG
*
7942 GTACTACGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGTG
*
7965 GCACTTCGGTGCA
1 GCACTACGGTGCA
7978 TTTATACGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGTG
Found at i:12221 original size:2 final size:2
Alignment explanation
Indices: 12214--12243 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12204 TGAATCATTG
12214 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
12244 GTGCGTGTGT
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:13671 original size:8 final size:8
Alignment explanation
Indices: 13645--13677 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
13635 TGAACAAGAA
13645 ATAAGAGAT
1 ATAAGAG-T
13654 ATAA-AGT
1 ATAAGAGT
13661 ATAAGAGT
1 ATAAGAGT
13669 ATAAGAGT
1 ATAAGAGT
13677 A
1 A
13678 ATAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.22
8 14 0.61
9 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (8 bp):
ATAAGAGT
Found at i:16290 original size:41 final size:41
Alignment explanation
Indices: 16233--16356 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
16223 CTACAATTCA
*
16233 TTACCTAGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
1 TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
16274 TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
1 TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
16315 TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
1 TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
16356 T
1 T
16357 GTGGAGATAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
TTACCTGGAGGATTCCAAAACCAGATAAACTCCTTGGAGTC
Found at i:22375 original size:23 final size:23
Alignment explanation
Indices: 22345--22396 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
22335 GAGTCGAGGG
22345 ATTCTACGCGGTCCTTCGGAACA
1 ATTCTACGCGGTCCTTCGGAACA
* *
22368 ATTCTACGTGGTCCTTCGGGACA
1 ATTCTACGCGGTCCTTCGGAACA
*
22391 AATCTA
1 ATTCTA
22397 TTTGACACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (23 bp):
ATTCTACGCGGTCCTTCGGAACA
Found at i:40707 original size:32 final size:32
Alignment explanation
Indices: 40665--40730 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
40655 ATTTTTTAAT
*
40665 AAATTTAATGATCATTTTATAACAATTTGATA
1 AAATATAATGATCATTTTATAACAATTTGATA
* * *
40697 AAATATAATGATCATTTTGTAATATTTTGATA
1 AAATATAATGATCATTTTATAACAATTTGATA
40729 AA
1 AA
40731 TTTAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (32 bp):
AAATATAATGATCATTTTATAACAATTTGATA
Found at i:42582 original size:3 final size:3
Alignment explanation
Indices: 42574--42619 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
42564 GGCTTGTAAT
*
42574 TAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
42620 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 33 0.87
4 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42625 original size:12 final size:13
Alignment explanation
Indices: 42574--42622 Score: 75
Period size: 12 Copynumber: 3.9 Consensus size: 13
42564 GGCTTGTAAT
42574 TAATAATAAATAA
1 TAATAATAAATAA
*
42587 TAAT-ATTAATAA
1 TAATAATAAATAA
42599 TAATAATAAAT-A
1 TAATAATAAATAA
42611 TAATAATAAATA
1 TAATAATAAATA
42623 TAAAAAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:42894 original size:20 final size:19
Alignment explanation
Indices: 42869--42911 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
42859 TGATTGGAGA
42869 TTTTTTAACGAAAAAATTTCT
1 TTTTTTAA--AAAAAATTTCT
*
42890 TTTTTTTAAAAAAATTTCT
1 TTTTTTAAAAAAAATTTCT
42909 TTT
1 TTT
42912 CAATCGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
21 7 0.33
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTTAAAAAAAATTTCT
Found at i:45449 original size:7 final size:7
Alignment explanation
Indices: 45437--45464 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
45427 ATATACATAC
45437 TATATAT
1 TATATAT
45444 TATATAT
1 TATATAT
45451 TATATAT
1 TATATAT
45458 TATATAT
1 TATATAT
45465 GTCCACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Done.