Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006508.1 Hibiscus syriacus cultivar Beakdansim tig00015839_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: 53208
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2067 original size:24 final size:24
Alignment explanation
Indices: 2031--2080 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2021 TAATTTGTTA
* *
2031 TTAAAATTTTAAAAATTTTAT-ATT
1 TTAAAATTATAAAAAGTTT-TAATT
2055 TTAAAATTATAAAAAGTTTTAATT
1 TTAAAATTATAAAAAGTTTTAATT
2079 TT
1 TT
2081 TATTATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAAAATTATAAAAAGTTTTAATT
Found at i:2640 original size:18 final size:17
Alignment explanation
Indices: 2601--2654 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2591 TTGAAAAGTA
2601 TAATAGTTTATTAAAAAT-
1 TAATA-TTTATT-AAAATC
2619 TAATCATTTATTAAAATC
1 TAAT-ATTTATTAAAATC
* *
2637 TAATTTTTATTATAATC
1 TAATATTTATTAAAATC
2654 T
1 T
2655 TCTTTTGGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 17 0.53
18 14 0.44
19 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATATTTATTAAAATC
Found at i:3263 original size:40 final size:40
Alignment explanation
Indices: 3219--3320 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
3209 CATACTTTCG
*
3219 TGACGTTTTTATATAAAT-CCGTTATAGAC-TAGTACGTCAT
1 TGACGTTTTTATATAAATGCCGCTATA-ACTTA-TACGTCAT
* *
3259 TGACGTTTTTATATAAATGCTGCTATAACTTATGCGTCAT
1 TGACGTTTTTATATAAATGCCGCTATAACTTATACGTCAT
* *
3299 TGACG-TTTTATACAAATACCGC
1 TGACGTTTTTATATAAATGCCGC
3321 AAATTTATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
39 14 0.26
40 32 0.59
41 8 0.15
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (40 bp):
TGACGTTTTTATATAAATGCCGCTATAACTTATACGTCAT
Found at i:5186 original size:49 final size:47
Alignment explanation
Indices: 5112--5205 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 47
5102 AGTTTTGACG
5112 TCTTTGTGACGTGGAGTACTATTAATGATGATTTAGCACGTCTGAAA
1 TCTTTGTGACGTGGAGTACTATTAATGATGATTTAGCACGTCTGAAA
* *
5159 TCTTTTTGACGGTGGTGCTACTATTAATGATGATTTAGCACGTCTGA
1 TCTTTGTGAC-GTGGAG-TACTATTAATGATGATTTAGCACGTCTGA
5206 CTTATGTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 9 0.21
48 5 0.12
49 29 0.67
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (47 bp):
TCTTTGTGACGTGGAGTACTATTAATGATGATTTAGCACGTCTGAAA
Found at i:6319 original size:21 final size:21
Alignment explanation
Indices: 6293--6332 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6283 TTTTTATCCT
6293 TACTATTCTTTAATTCTTGAA
1 TACTATTCTTTAATTCTTGAA
6314 TACTATTCTTTAATTCTTG
1 TACTATTCTTTAATTCTTG
6333 TATAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (21 bp):
TACTATTCTTTAATTCTTGAA
Found at i:7688 original size:40 final size:40
Alignment explanation
Indices: 7633--7712 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
7623 TAGTAGATAC
*
7633 CGAAATAAGTGTACACGAAGGAGGAACGAATACAAACCTT
1 CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
*
7673 CGAAATAAGTGTACACAAAGGAGGAACGAATATAAACCTT
1 CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
7713 TATACGTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (40 bp):
CGAAATAAGTGTACACAAAGGAGGAACGAATACAAACCTT
Found at i:9386 original size:17 final size:18
Alignment explanation
Indices: 9347--9388 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9337 AAGTAGTGTT
*
9347 CTTGAAAGAAAAATGAAT
1 CTTGAAAGAAAAATGAAG
* *
9365 ATTGAATGAAAAAT-AAG
1 CTTGAAAGAAAAATGAAG
9382 CTTGAAA
1 CTTGAAA
9389 TGCTCAAACT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
CTTGAAAGAAAAATGAAG
Found at i:9804 original size:57 final size:56
Alignment explanation
Indices: 9688--9806 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 56
9678 AGCGCATCGA
* *
9688 TGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGG
*
9744 TGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAGCAT-G
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGC-CAGAGTGCATCGATGCATAGC-TGG
9801 TGCATC
1 TGCATC
9807 GATGGATGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
56 20 0.36
57 32 0.57
58 4 0.07
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTGG
Found at i:12559 original size:23 final size:22
Alignment explanation
Indices: 12529--12610 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
12519 GCATGACCTT
12529 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
12551 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
12573 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
12596 GATGCATCGGTGCAC
1 G-TGCATCGATGCAC
12611 TATTAAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 19 0.40
24 11 0.23
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:12585 original size:21 final size:22
Alignment explanation
Indices: 12529--12591 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
12519 GCATGACCTT
12529 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * *
12552 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
12573 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
12592 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:12621 original size:44 final size:44
Alignment explanation
Indices: 12533--12629 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
12523 GACCTTGTGC
*
12533 ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATAGTGT
*
12577 ATCGATGCACATTCAAAGG-GATGCATCGGTGCA-CTATTA-AGTGT
1 ATCGATGCACATTC-AAGGAG-TGCATCGGTGCACCT-TCATAGTGT
12621 ATCGATGCA
1 ATCGATGCA
12630 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 30 0.62
45 18 0.38
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGGTGCACCTTCATAGTGT
Found at i:18501 original size:20 final size:20
Alignment explanation
Indices: 18476--18539 Score: 128
Period size: 20 Copynumber: 3.2 Consensus size: 20
18466 GTGCATCGAC
18476 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
18496 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
18516 GCATGGCTGGTGCATCAAAT
1 GCATGGCTGGTGCATCAAAT
18536 GCAT
1 GCAT
18540 TCGATGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
GCATGGCTGGTGCATCAAAT
Found at i:21944 original size:3 final size:3
Alignment explanation
Indices: 21938--21979 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
21928 TTTCTTCTTG
* *
21938 ATT ATT AAT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21980 GATATGTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:23413 original size:13 final size:12
Alignment explanation
Indices: 23397--23429 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
23387 TCCATATATT
23397 TTATTTATTTAAA
1 TTATTTATTT-AA
23410 TTATTTATTTAA
1 TTATTTATTTAA
23422 TT-TTTATT
1 TTATTTATT
23430 CCTTAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 4 0.20
13 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTATTTAA
Found at i:23526 original size:5 final size:5
Alignment explanation
Indices: 23516--23937 Score: 640
Period size: 5 Copynumber: 85.2 Consensus size: 5
23506 TTATTTTTCT
23516 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
23566 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-T- TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
23614 TATTA TTTATTA TATTA TATTATA TATTA TATTA TATTA TATTA TATTA
1 TATTA --TATTA TATTA TA-T-TA TATTA TATTA TATTA TATTA TATTA
23663 TATTA TATTA TATTA TATTA TATATA TATTA TATTA TA-T- TATTA TATTA
1 TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TATTA
23712 TATTA TATTA TATTA TATTA TATTA TATTATA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TA-T-TA TATTA TATTA TATTA TATTA
23764 T-TTA TATTA TATTA TATTA TA-TA TATTA TATTA TATTA TA-T- TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
23810 TATTA TATTA TATTA TATTA TATTA TA-T- TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
23858 TATTA TA-TA TATTA TTATTA TATTA T-TATA TATTA TA-TA TATTA TATTA
1 TATTA TATTA TATTA -TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA
23907 TATATA TATTTA TATTA TA-T- TATTA TATTA T
1 TAT-TA TA-TTA TATTA TATTA TATTA TATTA T
23938 GTATATATAT
Statistics
Matches: 391, Mismatches: 0, Indels: 52
0.88 0.00 0.12
Matches are distributed among these distances:
3 10 0.03
4 27 0.07
5 317 0.81
6 23 0.06
7 14 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:23985 original size:44 final size:38
Alignment explanation
Indices: 23518--23986 Score: 323
Period size: 35 Copynumber: 12.7 Consensus size: 38
23508 ATTTTTCTTA
*
23518 TTATATTATAT-TATATTATATTATAT-TATAT-TATA-
1 TTATATTATATATATA-TATATTGTATATATATATATAT
*
23553 TTATATTATAT-TATATTATATTATAT-TATAT-TATA-
1 TTATATTATATATATA-TATATTGTATATATATATATAT
* *
23588 TTATATTATAT-TATAT-TATTATAT-TATATTATTTA-
1 TTATATTATATATATATATATTGTATATATA-TATATAT
*
23623 TTATATTATATTATATATTATATTATAT-TATAT-TATA-
1 TTATATTATA-TATATA-TATATTGTATATATATATATAT
*
23660 TTATATTATAT-TATATTATATTATATATATAT-TATA-
1 TTATATTATATATATA-TATATTGTATATATATATATAT
*
23696 TTATATTAT-TATAT-TATATTATAT-TATAT-TATA-
1 TTATATTATATATATATATATTGTATATATATATATAT
* *
23729 TTATATTATATTATATATTATATTATAT-TATATTATTTAT
1 TTATATTATA-TATATA-TATATTGTATATATA-TATATAT
*
23769 ATTATATTATAT-TATATATATTATAT-TATAT-TATATT
1 -TTATATTATATATATATATATTGTATATATATATATA-T
23806 ATTATATTATAT-TATAT-TATAT-TATAT-TATAT-TA-
1 -TTATATTATATATATATATAT-TGTATATATATATATAT
*
23840 TTATATTATAT-TATATTATATTATATATAT-TAT-TAT
1 TTATATTATATATATA-TATATTGTATATATATATATAT
*
23876 TATATTATTATATATTATATATATTATAT-TATATATATAT
1 T-TA-TATTATATA-TATATATATTGTATATATATATATAT
*
23916 TTATATTATAT-TAT-TATATTATGTATATATATTTAATATT
1 TTATATTATATATATATATA-T-TGTATATATATAT-ATA-T
23956 TTATAACCCTTATATATATATATATTGTATA
1 TTAT-A---TTATATATATATATATTGTATA
23987 ATCAAAAGTT
Statistics
Matches: 386, Mismatches: 6, Indels: 75
0.83 0.01 0.16
Matches are distributed among these distances:
33 45 0.12
34 14 0.04
35 101 0.26
36 43 0.11
37 59 0.15
38 42 0.11
39 37 0.10
40 14 0.04
41 11 0.03
44 12 0.03
45 4 0.01
46 4 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (38 bp):
TTATATTATATATATATATATTGTATATATATATATAT
Found at i:26839 original size:21 final size:19
Alignment explanation
Indices: 26795--26833 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26785 TGCCAACACT
26795 ACAAACTTCAATTTTTTTA
1 ACAAACTTCAATTTTTTTA
26814 ACAAACTTCAATTTTTTTA
1 ACAAACTTCAATTTTTTTA
26833 A
1 A
26834 GACAAATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (19 bp):
ACAAACTTCAATTTTTTTA
Found at i:30441 original size:20 final size:20
Alignment explanation
Indices: 30416--30459 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30406 ATGTGGTGTT
* *
30416 TGATTAATTTTTCATGTATA
1 TGATTAACTTTTCATGCATA
*
30436 TGATTAACTTTTCCTGCATA
1 TGATTAACTTTTCATGCATA
30456 TGAT
1 TGAT
30460 ATATCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
TGATTAACTTTTCATGCATA
Found at i:35086 original size:19 final size:19
Alignment explanation
Indices: 35046--35110 Score: 51
Period size: 22 Copynumber: 3.2 Consensus size: 19
35036 ATCTAATTTT
* *
35046 GGTATCGATACCGGTAG-GG
1 GGTATCGATACC-ATAGTAG
35065 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTA-G
*
35085 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
35107 GGTA
1 GGTA
35111 CCATGGTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 5 0.13
22 17 0.45
23 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:35094 original size:22 final size:23
Alignment explanation
Indices: 35066--35110 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
35056 CCGGTAGGGG
35066 GTATCGATACCATAGT-AGGGTA
1 GTATCGATACCATAGTAAGGGTA
*
35088 GTATCGATACCATGGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
35111 CCATGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:35126 original size:14 final size:14
Alignment explanation
Indices: 35088--35126 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
35078 TAGTAGGGTA
35088 GTATCGATACCATG
1 GTATCGATACCATG
** *
35102 GTAAGGGTACCATG
1 GTATCGATACCATG
35116 GTATCGATACC
1 GTATCGATACC
35127 TGGCAACGTC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (14 bp):
GTATCGATACCATG
Found at i:35562 original size:2 final size:2
Alignment explanation
Indices: 35510--35548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35500 TTTTTAATAA
35510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
35549 GTGCATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35640 original size:55 final size:55
Alignment explanation
Indices: 35581--35872 Score: 386
Period size: 55 Copynumber: 5.3 Consensus size: 55
35571 TGTGTACTAT
* * * *
35581 AGGCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
35636 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
35691 AAGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * *
35746 AGGCACTATATGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* * * ** *
35801 ATGCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTAC
1 AGGCACTTTGTGTGCAT-ATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
* *
35857 AAGCACTATGTGTGCA
1 AGGCACTTTGTGTGCA
35873 GCCCACAAAA
Statistics
Matches: 208, Mismatches: 28, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
55 162 0.78
56 46 0.22
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (55 bp):
AGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC
Found at i:35909 original size:110 final size:110
Alignment explanation
Indices: 35583--35872 Score: 427
Period size: 110 Copynumber: 2.6 Consensus size: 110
35573 TGTACTATAG
* * * *
35583 GCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTACAGGCACTTTGTG
1 GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
* *
35648 TGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATACAA
66 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
* * * *
35693 GCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATACAGGCACTATATG
1 GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
*
35758 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAT
66 TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
* ** * *
35803 GCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTACAAGCACTATGT
1 GCACTTTGTGTGCAT-ATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGT
35868 GTGCA
65 GTGCA
35873 GCCCACAAAA
Statistics
Matches: 159, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
110 114 0.72
111 45 0.28
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (110 bp):
GCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATGTG
TGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTACAA
Found at i:35917 original size:110 final size:110
Alignment explanation
Indices: 35581--35917 Score: 426
Period size: 110 Copynumber: 3.1 Consensus size: 110
35571 TGTGTACTAT
* * * *
35581 AGGCACTTTGTGTGTATATTCACGAAATTCATCATAAGTTGATGAATTACCGTACAGGCACTTTG
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
* *
35646 TGTGCATATTCACGGAATTCATCATGAGTTGATAAATCATCATAC
66 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
* * * * *
35691 AAGCACTTTGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCATACAGGCACTATA
1 AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
35756 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
66 TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
* * ** * *
35801 ATGCACTTTGTGTGCATAATCCACGGAATTCATCATAAAATGAAGAATCACCGTACAAGCACTAT
1 AGGCACTTTGTGTGCAT-ATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTAT
*** ** * *
35866 GTGTGCA-GCCCACAAAATTCATCATGGGTTGATGAATTC-TCGTAT
65 GTGTGCATATTCACGGAATTCATCATGAGTTGATGAA-TCATCGTAC
35911 AGGCACT
1 AGGCACT
35918 AATAGTGCAC
Statistics
Matches: 196, Mismatches: 29, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
110 149 0.76
111 47 0.24
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (110 bp):
AGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTATG
TGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCGTAC
Found at i:42183 original size:22 final size:23
Alignment explanation
Indices: 42157--42201 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
42147 CTGATAGGGG
*
42157 GTATCGGTACCATAGT-AGGGTA
1 GTATCGATACCATAGTAAGGGTA
*
42179 GTATCGATACCATGGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
42202 TCGATATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:42204 original size:20 final size:20
Alignment explanation
Indices: 42155--42207 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
42145 TACTGATAGG
* *
42155 GGGTATCGGTACCATAGTAG
1 GGGTATCGATACCATAGTAA
*
42175 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
42197 GGGTATCGATA
1 GGGTATCGATA
42208 TCTGGCAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:42682 original size:55 final size:55
Alignment explanation
Indices: 42616--42882 Score: 376
Period size: 55 Copynumber: 4.9 Consensus size: 55
42606 CTATGTGTAC
* * * *
42616 TACAGGCACTTTGTGTGCATATTCACGAAATTCATTATAAGTTGATGAATTATCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
* *
42671 TACAGGCACTTTGTGTGCATATTTACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
* *
42726 TACAGACACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
42781 TACAGGCACTTTGTGTGCATATTCCACGGAATTCATCATAAGTTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATT-CACGGAATTCATCATAAGTTGATGAATCACCG
* * * * **
42837 TATAGACACTATGTGTGCAGCA--CACGGAATTCATCATGGGTTGATG
1 TACAGGCACTTTGTGTGCA-TATTCACGGAATTCATCATAAGTTGATG
42883 GATTCTCGTA
Statistics
Matches: 194, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
54 22 0.11
55 124 0.64
56 47 0.24
57 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (55 bp):
TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCG
Found at i:47885 original size:16 final size:17
Alignment explanation
Indices: 47835--47885 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
47825 AAAAAAATTA
47835 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
47852 GA-TT-AAA-TTAAGAGT
1 AATTTGAAAGTT-AGAGT
47867 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
47883 AAT
1 AAT
47886 CAAATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 10 0.36
17 5 0.18
18 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:50456 original size:2 final size:2
Alignment explanation
Indices: 50449--50483 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50439 GATAATAACA
50449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50484 GATTTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50809 original size:2 final size:2
Alignment explanation
Indices: 50804--50832 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50794 TTGTCCGATT
50804 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50833 GTTTGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50902 original size:36 final size:35
Alignment explanation
Indices: 50862--51183 Score: 217
Period size: 34 Copynumber: 9.1 Consensus size: 35
50852 ATCACATAAT
* **
50862 ATATATAGTTTTGAAAACGATTTTTTTAAATATATA
1 ATATATAGTTTTAAAAAC-ATTTTTGAAAATATATA
*
50898 ATATATAGTTTAAAAAACA-TTTTGAAAATATATA
1 ATATATAGTTTTAAAAACATTTTTGAAAATATATA
* *
50932 ATATATGGTTTTTAAAACA-TTTT-AAAA-ACT-TA
1 ATATATAGTTTTAAAAACATTTTTGAAAATA-TATA
*
50964 GATAATATAG-TTTAGAAATCA-TTTTG-AAATATAT-
1 -AT-ATATAGTTTTA-AAAACATTTTTGAAAATATATA
* *
50998 ATAATATAGTTTTTTAAAACA-TTCTGAAAACTTATATA
1 AT-ATATAG-TTTTAAAAACATTTTTGAAAA--TATATA
* * *
51036 ATATATAATTTTAAAAATATTTTTGAAAAATTATGTA
1 ATATATAGTTTTAAAAACATTTTTG-AAAA-TATATA
*
51073 ATATATAGTTTTAAAAAATATTTTTTGAAAACTTATATA
1 ATATATAGTTTT-AAAAACA-TTTTTGAAAA--TATATA
* *
51112 ATAT-T--TTTT-AAATCATTTTTGAAAACTATATG
1 ATATATAGTTTTAAAAACATTTTTGAAAA-TATATA
* *
51144 ATATATAGGTTTGAAAACTTATTTTT-AAAA-ATATA
1 ATATATAGTTTTAAAAAC--ATTTTTGAAAATATATA
51179 ATATA
1 ATATA
51184 GTTTAAAGAT
Statistics
Matches: 235, Mismatches: 27, Indels: 49
0.76 0.09 0.16
Matches are distributed among these distances:
32 12 0.05
33 30 0.13
34 64 0.27
35 21 0.09
36 33 0.14
37 35 0.15
38 24 0.10
39 16 0.07
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
ATATATAGTTTTAAAAACATTTTTGAAAATATATA
Found at i:51232 original size:13 final size:13
Alignment explanation
Indices: 51211--51252 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
51201 GAAATATATA
51211 TTATATTATTTTAT
1 TTAT-TTATTTTAT
51225 TTATTTATTTTAT
1 TTATTTATTTTAT
*
51238 TAATTCT-TTTTAT
1 TTATT-TATTTTAT
51251 TT
1 TT
51253 TCTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:52374 original size:24 final size:24
Alignment explanation
Indices: 52347--52392 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52337 ATTTAACCCT
* *
52347 TTTTTTTTCACTCTTTTTATTTGG
1 TTTTTTTTCACTATTATTATTTGG
52371 TTTTTTTTCACTATTATTATTT
1 TTTTTTTTCACTATTATTATTT
52393 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTTTTTCACTATTATTATTTGG
Found at i:52421 original size:4 final size:4
Alignment explanation
Indices: 52387--52464 Score: 53
Period size: 4 Copynumber: 20.5 Consensus size: 4
52377 TTCACTATTA
*
52387 TTAT TT-T TTAA TT-T TTAT TTAT CTCTA- TTAT TTAT TTAT TTAT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT -T-TAT TTAT TTAT TTAT TTAT TTAT
* *
52433 ATTA- TTAT TAAA TTAT TT-T TT-T TTAT TTAT TT
1 -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
52465 TCTTTTGACT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
3 17 0.29
4 39 0.66
5 1 0.02
6 2 0.03
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:52477 original size:15 final size:14
Alignment explanation
Indices: 52445--52494 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
52435 TATTATTAAA
* *
52445 TTATTTTTTTTTAT
1 TTATTTTTTTTGAC
52459 TTATTTTCTTTTGAC
1 TTATTTT-TTTTGAC
52474 TTA-TTTTTTT--C
1 TTATTTTTTTTGAC
52485 TTATTTTTTT
1 TTATTTTTTT
52495 CATTTTCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 4 0.12
12 6 0.19
13 4 0.12
14 10 0.31
15 8 0.25
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (14 bp):
TTATTTTTTTTGAC
Found at i:52489 original size:30 final size:29
Alignment explanation
Indices: 52414--52500 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
52404 TTTATCTCTA
* * *
52414 TTATTTATTTATTTATTTTATT-ATTATTAAA
1 TTATTT-TTT-TTTATTTTTTTCATT-TTGAC
52445 TTATTTTTTTTTATTTATTTTC-TTTTGAC
1 TTATTTTTTTTTATTT-TTTTCATTTTGAC
52474 TTATTTTTTTCTTATTTTTTTCATTTT
1 TTATTTTTTT-TTATTTTTTTCATTTT
52501 CCATCTCTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
29 25 0.51
30 18 0.37
31 6 0.12
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75
Consensus pattern (29 bp):
TTATTTTTTTTTATTTTTTTCATTTTGAC
Done.