Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002513.1 Hibiscus syriacus cultivar Beakdansim tig00005113_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: 74787
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7505 original size:60 final size:60
Alignment explanation
Indices: 7407--7535 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
7397 AAGGGTAAAG
* *** * *
7407 TACACAAATGATCCCTCAACTATAGGGTGTTATATTGTTGAGTCCCTCTACTATTAAAAAT
1 TACA-AAATGATCCCACAACTATAGGACATTATATTGTTGAGTCCCCCGACTATTAAAAAT
* * *
7468 TACAAAATGATCCCACAACTATAGGACATTGTTTTGTTGAGTCCCCCGACTATTAAAAGT
1 TACAAAATGATCCCACAACTATAGGACATTATATTGTTGAGTCCCCCGACTATTAAAAAT
7528 TACAAAAT
1 TACAAAAT
7536 TGTCACCCGA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 55 0.93
61 4 0.07
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (60 bp):
TACAAAATGATCCCACAACTATAGGACATTATATTGTTGAGTCCCCCGACTATTAAAAAT
Found at i:10496 original size:20 final size:19
Alignment explanation
Indices: 10452--10500 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
10442 ACATTTATTA
10452 TTTT-TTATTTTTTATAAT
1 TTTTGTTATTTTTTATAAT
* * *
10470 ATGTGTTATTTGTTTTTAAT
1 TTTTGTTATTT-TTTATAAT
10490 TTTTGTTATTT
1 TTTTGTTATTT
10501 AAAAATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 16 0.67
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.73
Consensus pattern (19 bp):
TTTTGTTATTTTTTATAAT
Found at i:25171 original size:12 final size:12
Alignment explanation
Indices: 25154--25179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25144 AAGTTTTGCT
25154 AAAAAAAAGGAA
1 AAAAAAAAGGAA
25166 AAAAAAAAGGAA
1 AAAAAAAAGGAA
25178 AA
1 AA
25180 TTGACGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:25477 original size:2 final size:2
Alignment explanation
Indices: 25470--25496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25460 TTGGTTAATG
25470 TA 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 TA T
25497 TATTTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25527 original size:16 final size:16
Alignment explanation
Indices: 25506--25548 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
25496 TTATTTTTAG
25506 TAATTTAATTTA-ATTT
1 TAATTT-ATTTATATTT
*
25522 TAATTTTTTTATATTT
1 TAATTTATTTATATTT
*
25538 TAATTTTTTTA
1 TAATTTATTTA
25549 AATGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TAATTTATTTATATTT
Found at i:26069 original size:2 final size:2
Alignment explanation
Indices: 26064--26090 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26054 AACAAGGGGG
26064 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
26091 TCAATGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32392 original size:13 final size:13
Alignment explanation
Indices: 32356--32393 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
32346 TATGTAAAAT
*
32356 AATAATAAAA-AA
1 AATAAGAAAATAA
32368 AATAATGAAAATAA
1 AATAA-GAAAATAA
32382 AATAAGAAAATA
1 AATAAGAAAATA
32394 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 5 0.22
13 11 0.48
14 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAGAAAATAA
Found at i:32548 original size:22 final size:22
Alignment explanation
Indices: 32523--32584 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 22
32513 AAGAGGGAGG
32523 AAAAAATATAATAATAATAGAA
1 AAAAAATATAATAATAATAGAA
* *
32545 AAAAAAAAT-A-AATAAT-GTA
1 AAAAAATATAATAATAATAGAA
*
32564 AATAAATATAATAATAA-AGAA
1 AAAAAATATAATAATAATAGAA
32585 GTAAAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 9 0.28
20 7 0.22
21 8 0.25
22 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAAAAATATAATAATAATAGAA
Found at i:32917 original size:201 final size:199
Alignment explanation
Indices: 32557--32961 Score: 688
Period size: 201 Copynumber: 2.0 Consensus size: 199
32547 AAAAAATAAA
32557 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACATAT
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACA-AT
32622 ATACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAATGTATACG
65 ATACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAA-GTATACG
* * *
32687 AATGTATAAAAAACTAATAATAGTATAAAATATATATAAATATTATAATGTAATATAAAAAGGTA
129 AATGTAAAAAAAACTAATAATAATAT-AAA-ATATATAAATATTATAATGTAATATAAAAAGATA
32752 ATTAAAAC
192 ATTAAAAC
*
32760 TAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTAC-ATA
1 TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACAATA
* *
32824 TACATATATATATATAATATAACATATAAGTGAAATAATACTATACTAATAATAAA-TATACGAA
66 TACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAAGTATACGAA
32888 TGTGTAAAAAAAACTAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAAGATAAT
131 --TGTAAAAAAAACTAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAAGATAAT
32953 TAAAAC
194 TAAAAC
32959 TAA
1 TAA
32962 AATCCCGAGA
Statistics
Matches: 194, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
199 52 0.27
200 3 0.02
201 79 0.41
203 60 0.31
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.30
Consensus pattern (199 bp):
TAATGTAAATAAATATAATAATAAAGAAGTAAAAAAATAGGGTAAAATACAAAATGTGTACAATA
TACATATATATATATAATATAACACATAAATGAAATAATACTATACTAATAATAAAGTATACGAA
TGTAAAAAAAACTAATAATAATATAAAATATATAAATATTATAATGTAATATAAAAAGATAATTA
AAAC
Found at i:40668 original size:27 final size:27
Alignment explanation
Indices: 40638--40702 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
40628 CATAAAATAA
* *
40638 TTCACCCGAAAATGGCCCAACTTGAAG
1 TTCACTCGAAAATGACCCAACTTGAAG
*
40665 TTCACTCGAAAATGACCCGACTTGAAG
1 TTCACTCGAAAATGACCCAACTTGAAG
*
40692 TGCACTCGAAA
1 TTCACTCGAAA
40703 CTAATATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (27 bp):
TTCACTCGAAAATGACCCAACTTGAAG
Found at i:45022 original size:18 final size:18
Alignment explanation
Indices: 44981--45031 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
44971 TATGGAATTG
*
44981 GATTCCAATTT-TTGACA
1 GATTCCAATTTCTTCACA
44998 GATTCCAATTTCTTCACA
1 GATTCCAATTTCTTCACA
* *
45016 TATTCCAATTCCTTCA
1 GATTCCAATTTCTTCA
45032 AAAACATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.41
Consensus pattern (18 bp):
GATTCCAATTTCTTCACA
Found at i:49530 original size:10 final size:10
Alignment explanation
Indices: 49501--49533 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
49491 AGTTTTTTAA
49501 ATAAATTTTT
1 ATAAATTTTT
49511 -TAAA-TTTT
1 ATAAATTTTT
49519 ATAAATTTTT
1 ATAAATTTTT
49529 ATAAA
1 ATAAA
49534 ATTGACACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.19
9 8 0.38
10 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATAAATTTTT
Found at i:50747 original size:61 final size:61
Alignment explanation
Indices: 50629--50750 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 61
50619 TATAGTTTGA
* * * * ** *
50629 GATGAAATTGGAATGTTAAAAAATTTTGAGGACTAATTTAGAATGAATGTGATATTTTGGG
1 GATGAAATTGAAATGTTAAAAAATTTAGAGGACCAATTTAGAAAGAAAATCATATTTTGGG
* *
50690 GATGAAATTGAAATTTTCAAAAATTTAG-GGACCAATTTAGAAAGAAAATCATAATTTTGGG
1 GATGAAATTGAAATGTTAAAAAATTTAGAGGACCAATTTAGAAAGAAAATCAT-ATTTTGGG
50751 ACGAAACTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 19 0.37
61 32 0.63
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (61 bp):
GATGAAATTGAAATGTTAAAAAATTTAGAGGACCAATTTAGAAAGAAAATCATATTTTGGG
Found at i:51226 original size:3 final size:3
Alignment explanation
Indices: 51218--51242 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
51208 GTATTTATTG
51218 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
51243 TCTGTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:51487 original size:29 final size:29
Alignment explanation
Indices: 51411--51487 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
51401 CTTCCCAGCA
*
51411 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
51440 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
51469 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
51488 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:51565 original size:14 final size:14
Alignment explanation
Indices: 51548--51587 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
51538 CTCGAATGGC
51548 CTCGGTCGGATGCA
1 CTCGGTCGGATGCA
*
51562 CTCGGTCGGATGCC
1 CTCGGTCGGATGCA
51576 CTCGGTCGGATG
1 CTCGGTCGGATG
51588 GCTTCGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.10, C:0.30, G:0.38, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGCA
Found at i:51594 original size:14 final size:14
Alignment explanation
Indices: 51543--51594 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
51533 GCTCGCTCGA
51543 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
51557 AT-GCACTCGGTCGG
1 ATGGC-CTCGGTCGG
*
51571 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
51585 ATGGCTTCGG
1 ATGGCCTCGG
51595 ATGCCCAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 2 0.06
14 30 0.91
15 1 0.03
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.23
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:52425 original size:30 final size:30
Alignment explanation
Indices: 52380--52439 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52370 ATTTTATAAA
*
52380 ATTTAAAAATCAAACAAGTTAAAA-ATTATT
1 ATTTAAAAATCAAACAA-ATAAAATATTATT
* *
52410 ATTTTAAAATTAAACAAATAAAATATTATT
1 ATTTAAAAATCAAACAAATAAAATATTATT
52440 TGATCTCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (30 bp):
ATTTAAAAATCAAACAAATAAAATATTATT
Found at i:58494 original size:2 final size:2
Alignment explanation
Indices: 58487--58512 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58477 GACATGCATA
58487 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
58513 TAAATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63046 original size:82 final size:73
Alignment explanation
Indices: 62891--63048 Score: 226
Period size: 82 Copynumber: 2.0 Consensus size: 73
62881 TATATTCCAC
62891 TTCATATTCTCTGTAACAGGATATGGTTTTGGTTGATTCTGTAACGGCCTTCCCATTTATATTTC
1 TTCATATTCTCTGTAACAGGATATGGTTTTGGTTGATTCTGTAACGGCCTTCCCATTTATATTTC
62956 GAAGATGG
66 GAAGATGG
*
62964 TTCATATTCTCTGTAACAGGATATGGAATGGTTTTGGTTGATTCTGTAACCCCGGCTTTCCCCAT
1 TTCATATTCTCTGTAACAGG--AT---ATGGTTTTGGTTGATTCTGTAA---CGGCCTT-CCCAT
63029 TTATATTTCGAAGATGG
57 TTATATTTCGAAGATGG
63046 TTC
1 TTC
63049 TTCTACAATA
Statistics
Matches: 75, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
73 20 0.27
75 2 0.03
78 22 0.29
81 6 0.08
82 25 0.33
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (73 bp):
TTCATATTCTCTGTAACAGGATATGGTTTTGGTTGATTCTGTAACGGCCTTCCCATTTATATTTC
GAAGATGG
Found at i:64053 original size:26 final size:26
Alignment explanation
Indices: 64016--64079 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
64006 TTTTGATAAC
*
64016 GTATTTTTTTAGTCTTATATTAGGTT
1 GTATTTTCTTAGTCTTATATTAGGTT
64042 GTATTTTCTTAGTCTTATATTAGGTT
1 GTATTTTCTTAGTCTTATATTAGGTT
* *
64068 GTCTTTCCTTAG
1 GTATTTTCTTAG
64080 ACTTCCTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.58
Consensus pattern (26 bp):
GTATTTTCTTAGTCTTATATTAGGTT
Found at i:71284 original size:20 final size:18
Alignment explanation
Indices: 71259--71303 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
71249 TCTTACCTAT
71259 TTTCTCTCTTGACCTTTTTC
1 TTTCTCTC-T-ACCTTTTTC
*
71279 TTTCTCTCTATCTTTTTC
1 TTTCTCTCTACCTTTTTC
71297 TTTCTCT
1 TTTCTCT
71304 ATATACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 15 0.62
19 1 0.04
20 8 0.33
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTCTCTCTACCTTTTTC
Done.