Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004753.1 Hibiscus syriacus cultivar Beakdansim tig00010728_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: 100961
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:5676 original size:66 final size:66
Alignment explanation
Indices: 5599--5723 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
5589 GTCCATTTTT
* * * *
5599 TTCTTCTGGTTGGTGGGTGCAGCTTCTCTCCCACGTTCCTCAGTAACAGTCGACTCGTTGGTGCT
1 TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTTGGTGCT
5664 C
66 C
* * * *
5665 TTCTTCGGGTTGGTGGGTGCAATTTCTTTCCCACGTCCCTCGGTAGCAGTCAACTCGTT
1 TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTT
5724 CGAGTTTTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (66 bp):
TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTTGGTGCT
C
Found at i:13533 original size:23 final size:23
Alignment explanation
Indices: 13483--13537 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
13473 AAACATGTTT
**
13483 GTTTAACGTTCACGAATATGTTC
1 GTTTAACGTTCACGAATATGAGC
* * *
13506 ATTTAATGTTCATGAATATGAGC
1 GTTTAACGTTCACGAATATGAGC
13529 GTTTAACGT
1 GTTTAACGT
13538 CGTTTAATGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
GTTTAACGTTCACGAATATGAGC
Found at i:14385 original size:35 final size:35
Alignment explanation
Indices: 14343--14418 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
14333 TGAAATACTT
* *
14343 TTATTATAAAGGATACTTAAACTTATTTATGTTTA
1 TTATTATAAAAGATACTTAAAATTATTTATGTTTA
* *
14378 TTATTATAAAATATGCTTAAAATTATTTATGTTTA
1 TTATTATAAAAGATACTTAAAATTATTTATGTTTA
14413 TT-TTAT
1 TTATTAT
14419 TTATTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 4 0.11
35 33 0.89
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.53
Consensus pattern (35 bp):
TTATTATAAAAGATACTTAAAATTATTTATGTTTA
Found at i:14911 original size:43 final size:41
Alignment explanation
Indices: 14863--15016 Score: 166
Period size: 41 Copynumber: 3.7 Consensus size: 41
14853 TTGCATTTCG
*
14863 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTT-AAAAT-TCGTTGCGATAGTCTACAGTTGT
** * *
14906 CGTTGCGATTTTTCAAATTCTTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTAAAATTCGTTGCGATAGTCTACAGTTGT
* * *
14947 TGTTGCGATAGATTACAAATTTGTTGCGATAGTCTACCGTTGT
1 CGTTGCGATAG-TTA-AAATTCGTTGCGATAGTCTACAGTTGT
* *
14990 CGTTGCGAT-TTTCCAAATTCGTTGCGA
1 CGTTGCGATAGTT-AAAATTCGTTGCGA
15017 AAATTTGTTG
Statistics
Matches: 92, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 43 0.47
42 6 0.07
43 43 0.47
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTTAAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:14935 original size:41 final size:41
Alignment explanation
Indices: 14886--15016 Score: 174
Period size: 41 Copynumber: 3.1 Consensus size: 41
14876 GAAAATCGCG
*
14886 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATTCT
1 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCT
* *
14927 TTGCGATAGTCTACAGTTGTTGTTGCGATAGATTACAAATT-T
1 TTGCGATAGTCTACAGTTGTCGTTGCGAT--TTTACAAATTCT
* * *
14969 GTTGCGATAGTCTACCGTTGTCGTTGCGATTTTCCAAATTCG
1 -TTGCGATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCT
15011 TTGCGA
1 TTGCGA
15017 AAATTTGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
41 42 0.54
42 1 0.01
43 35 0.45
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TTGCGATAGTCTACAGTTGTCGTTGCGATTTTACAAATTCT
Found at i:16014 original size:41 final size:41
Alignment explanation
Indices: 15957--16139 Score: 235
Period size: 41 Copynumber: 4.5 Consensus size: 41
15947 CATTTTTAAA
* **
15957 ACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
* *
15998 ACTATCGCAACGCGAAATGGAAAACCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
*
16039 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
* * * * *
16080 ACTATCGCAACGCGAAATGAAAAACCGCAACG-CGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCACAACGAC-ACTGT-AG
16121 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
16140 CAGCGTGAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 124 0.98
42 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
Found at i:16094 original size:82 final size:82
Alignment explanation
Indices: 15957--16111 Score: 283
Period size: 82 Copynumber: 1.9 Consensus size: 82
15947 CATTTTTAAA
** *
15957 ACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
16022 CCGCAACGACACTGTAG
66 CCGCAACGACACTGTAG
16039 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
1 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
16104 CCGCAACG
66 CCGCAACG
16112 CGATTTTCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.15
Consensus pattern (82 bp):
ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
CCGCAACGACACTGTAG
Found at i:16125 original size:82 final size:81
Alignment explanation
Indices: 15956--16139 Score: 280
Period size: 82 Copynumber: 2.2 Consensus size: 81
15946 CCATTTTTAA
** *
15956 AACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 AACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
16021 ACCGCAACGACACTGT
66 ACCGCAACGACACTGT
16037 AGACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAA
1 A-ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAA
* *
16102 AACCGCAACG-CGATTTT
65 AACCGCAACGAC-ACTGT
*
16119 CAACTATCGCAACGCGAAATG
1 -AACTATTGCAACGCGAAATG
16140 CAGCGTGAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
81 2 0.02
82 91 0.97
83 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (81 bp):
AACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
ACCGCAACGACACTGT
Found at i:17780 original size:14 final size:14
Alignment explanation
Indices: 17761--17787 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17751 AATTAATTTC
17761 AATAATAAATTTTT
1 AATAATAAATTTTT
17775 AATAATAAATTTT
1 AATAATAAATTTT
17788 ATTAAACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATAAATTTTT
Found at i:17787 original size:13 final size:13
Alignment explanation
Indices: 17755--17788 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17745 AAATAAAATT
*
17755 AATTTCAATAATA
1 AATTTTAATAATA
17768 AATTTTTAATAATA
1 AA-TTTTAATAATA
17782 AATTTTA
1 AATTTTA
17789 TTAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTAATAATA
Found at i:27423 original size:18 final size:19
Alignment explanation
Indices: 27384--27425 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27374 GTTTATCTAT
*
27384 TTTAAGTAAATATTTAAAA
1 TTTAAATAAATATTTAAAA
* *
27403 TTTAAATAATTATTTAAAT
1 TTTAAATAAATATTTAAAA
27422 TTTA
1 TTTA
27426 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAAATAAATATTTAAAA
Found at i:27431 original size:21 final size:21
Alignment explanation
Indices: 27403--27454 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
27393 ATATTTAAAA
*
27403 TTTAAAT-AATTATTTAA-ATT
1 TTTAAATAAAATA-TTAATATT
27423 TTATAAATAAAATATTAATATT
1 TT-TAAATAAAATATTAATATT
27445 TTTAAATAAA
1 TTTAAATAAA
27455 TGAATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAAATAAAATATTAATATT
Found at i:27433 original size:25 final size:23
Alignment explanation
Indices: 27405--27470 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 23
27395 ATTTAAAATT
27405 TAAATAATTATTTAA-ATTTTATAAA
1 TAAATAA-TA-TTAATATTTT-TAAA
27430 T-AA-AATATTAATATTTTTAAA
1 TAAATAATATTAATATTTTTAAA
*
27451 TAAATGAATAATTAACATTT
1 TAAAT-AAT-ATTAATATTT
27471 CAAAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
21 9 0.26
22 9 0.26
23 2 0.06
24 5 0.14
25 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATAATATTAATATTTTTAAA
Found at i:27462 original size:21 final size:22
Alignment explanation
Indices: 27420--27462 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
27410 AATTATTTAA
*
27420 ATTTTATAAATAAAATATTAAT
1 ATTTTATAAATAAAATAATAAT
27442 ATTTT-TAAAT-AAATGAATAAT
1 ATTTTATAAATAAAAT-AATAAT
27463 TAACATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTTATAAATAAAATAATAAT
Found at i:28144 original size:25 final size:25
Alignment explanation
Indices: 28116--28203 Score: 65
Period size: 25 Copynumber: 3.5 Consensus size: 25
28106 ATTTAAATTT
*
28116 ATAAATAAAATATTAATATTTTTAA
1 ATAAATAAAATATTAAAATTTTTAA
* * **
28141 ATAAAT-GAATAATTAACATTTCAAAA
1 ATAAATAAAAT-ATTAAAATTT-TTAA
*
28167 ATAAA-AACACTATTAAAATTTTTAGA
1 ATAAATAA-AATATTAAAATTTTTA-A
28193 A-AAATAAAATA
1 ATAAATAAAATA
28204 AATTTAAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
24 3 0.06
25 22 0.47
26 20 0.43
27 2 0.04
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAAATAAAATATTAAAATTTTTAA
Found at i:28146 original size:20 final size:20
Alignment explanation
Indices: 28074--28146 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 20
28064 GTTTATCTAT
*
28074 TTTTTAAGTAAATATTTAAA
1 TTTTTAAATAAATATTTAAA
* *
28094 -ATTTAAATAATTATTTAAA
1 TTTTTAAATAAATATTTAAA
*
28113 TTTATAAATAAA-ATATTAATA
1 TTTTTAAATAAATAT-TTAA-A
28134 TTTTTAAATAAAT
1 TTTTTAAATAAAT
28147 GAATAATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 18 0.43
20 12 0.29
21 12 0.29
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
TTTTTAAATAAATATTTAAA
Found at i:28153 original size:21 final size:21
Alignment explanation
Indices: 28112--28153 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28102 AATTATTTAA
*
28112 ATTTATAAATAAAATATTAAT
1 ATTTATAAATAAAATAATAAT
*
28133 ATTTTTAAAT-AAATGAATAAT
1 ATTTATAAATAAAAT-AATAAT
28154 TAACATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTATAAATAAAATAATAAT
Found at i:33530 original size:55 final size:55
Alignment explanation
Indices: 33371--34064 Score: 948
Period size: 55 Copynumber: 12.7 Consensus size: 55
33361 CTCCATAGTC
* *
33371 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGTCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
33426 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCACGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
33479 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTATGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
33534 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * * *
33587 CTTCAGAGAGTATAAGACCCAAAAAATCTTTAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
33642 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * ** *
33697 CTTCAGAGAGTATAAGACCCGAACAATCTTCAGCAATCGTGTCCACCCCTTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
33752 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCTCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
33807 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * *
33862 ATTCAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
33917 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * *
33971 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCACGTCAGCCCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
34026 CTTCAGAGAGTATGAGACTTGAACAATCTTCAACGATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
34065 TGGGGAACCT
Statistics
Matches: 564, Mismatches: 70, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
53 95 0.17
54 51 0.09
55 418 0.74
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:41472 original size:17 final size:17
Alignment explanation
Indices: 41446--41478 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
41436 TTTTGTTTTT
41446 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
41464 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
41479 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:41480 original size:17 final size:19
Alignment explanation
Indices: 41441--41480 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
41431 TAATATTTTG
*
41441 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
41460 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
41476 TTTTA
1 TTTTA
41481 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:43268 original size:33 final size:33
Alignment explanation
Indices: 43231--43297 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
43221 TACCCGATGT
* *
43231 CGCCGCCGCCACTATCACCTG-GTTTTATGACCC
1 CGCCGCCGCCACCATCA-CAGAGTTTTATGACCC
43264 CGCCGCCGCCACCATCACAGAGTTTTATGACCC
1 CGCCGCCGCCACCATCACAGAGTTTTATGACCC
43297 C
1 C
43298 TCCTAAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.21
Consensus pattern (33 bp):
CGCCGCCGCCACCATCACAGAGTTTTATGACCC
Found at i:43803 original size:33 final size:34
Alignment explanation
Indices: 43766--43839 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
43756 TAATACTTAC
43766 TTTATTTCATT-AATTTGGTTGGA-TTTATT-TTAA
1 TTTATTTCATTAAATTT-GTTGGACTTT-TTGTTAA
**
43799 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
*
43833 TGTATTT
1 TTTATTT
43840 TGGTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 17 0.49
34 18 0.51
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (34 bp):
TTTATTTCATTAAATTTGTTGGACTTTTTGTTAA
Found at i:43833 original size:34 final size:34
Alignment explanation
Indices: 43777--43853 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
43767 TTATTTCATT
*
43777 AATTTGGTTGGATTTATTTTAATTTATTTT-GTTA
1 AATTT-GTTGGATTTATTTTAATGTATTTTGGTTA
43811 AATTTGTTGGACTTT-TTGTTAATGTATTTTGGTTA
1 AATTTGTTGGA-TTTATT-TTAATGTATTTTGGTTA
*
43846 ATTTTGTT
1 AATTTGTT
43854 TATTACCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 8 0.21
34 19 0.50
35 11 0.29
ACGTcount: A:0.21, C:0.01, G:0.17, T:0.61
Consensus pattern (34 bp):
AATTTGTTGGATTTATTTTAATGTATTTTGGTTA
Found at i:45055 original size:21 final size:21
Alignment explanation
Indices: 45006--45069 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
44996 CATATGAAAT
*
45006 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
45027 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
* *
45049 TTGTCCCAAAGGATCTATGAA
1 TTGTCCCGAAGGACCTATGAA
45070 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:49743 original size:13 final size:14
Alignment explanation
Indices: 49720--49748 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49710 ATAATCATAT
49720 ATAATTATAAAAAA
1 ATAATTATAAAAAA
49734 ATAA-TATAAAAAA
1 ATAATTATAAAAAA
49747 AT
1 AT
49749 TACCTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAATTATAAAAAA
Found at i:50267 original size:16 final size:16
Alignment explanation
Indices: 50232--50281 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
50222 TGTTTATGAG
50232 GGAATTGGAATCTGTGAA
1 GGAATTGGAATC--TGAA
50250 GGAATTGGAATCTGAA
1 GGAATTGGAATCTGAA
*
50266 GGAATTGTAATCTGAA
1 GGAATTGGAATCTGAA
50282 TTTGAAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 19 0.61
18 12 0.39
ACGTcount: A:0.36, C:0.06, G:0.30, T:0.28
Consensus pattern (16 bp):
GGAATTGGAATCTGAA
Found at i:52194 original size:17 final size:17
Alignment explanation
Indices: 52172--52205 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52162 TTTATATAAA
*
52172 TTATTATTATTATTATT
1 TTATTAATATTATTATT
*
52189 TTATTAATATTTTTATT
1 TTATTAATATTATTATT
52206 GCACCCCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTAATATTATTATT
Found at i:55454 original size:15 final size:15
Alignment explanation
Indices: 55434--55462 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55424 AATAATTTTG
55434 ATAGCCGCCCATGTC
1 ATAGCCGCCCATGTC
55449 ATAGCCGCCCATGT
1 ATAGCCGCCCATGT
55463 TTTGTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
ATAGCCGCCCATGTC
Found at i:62740 original size:31 final size:30
Alignment explanation
Indices: 62699--62778 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
62689 CATGACTGAG
*
62699 GGACTAAAATCGAACGGACCGATAACATTA
1 GGACTAAAATCGGACGGACCGATAACATTA
* *
62729 TGGACTGAAATCGGATGGACCGATAACATTA
1 -GGACTAAAATCGGACGGACCGATAACATTA
*
62760 GAGACTTAAATCGGACGGA
1 G-GACTAAAATCGGACGGA
62779 GTGATGGCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (30 bp):
GGACTAAAATCGGACGGACCGATAACATTA
Found at i:64330 original size:2 final size:2
Alignment explanation
Indices: 64323--64350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64313 TTACAACTCA
64323 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
64351 CATAAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66391 original size:17 final size:17
Alignment explanation
Indices: 66359--66393 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66349 ACCAGATTTG
66359 ATATTAACTCGAATCTA
1 ATATTAACTCGAATCTA
66376 ATATCTAACTCG-ATCTA
1 ATAT-TAACTCGAATCTA
66393 A
1 A
66394 CTGACCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATTAACTCGAATCTA
Found at i:66444 original size:21 final size:21
Alignment explanation
Indices: 66418--66468 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
66408 AAACTAAATT
66418 TGAATCAAATCTAACCCGACC
1 TGAATCAAATCTAACCCGACC
*
66439 TGAATCAAATCTAACCTGACC
1 TGAATCAAATCTAACCCGACC
*
66460 TAAATCAAA
1 TGAATCAAA
66469 ACAAAGCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (21 bp):
TGAATCAAATCTAACCCGACC
Found at i:67151 original size:29 final size:29
Alignment explanation
Indices: 67117--67175 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
67107 CCTAAATTAA
67117 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
67146 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
67175 T
1 T
67176 ATGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:76206 original size:23 final size:24
Alignment explanation
Indices: 76169--76235 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
76159 TAATTATGCA
*
76169 TGTGTTGCACTTTTATCTCTG-AT
1 TGTGTTGCACGTTTATCTCTGTAT
*
76192 TGTGTTACACGTTTATCTCTGTAT
1 TGTGTTGCACGTTTATCTCTGTAT
*
76216 T-TGTGGCACGTTTATCTCTG
1 TGTGTTGCACGTTTATCTCTG
76236 CTTTTGTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 36 0.92
24 3 0.08
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.49
Consensus pattern (24 bp):
TGTGTTGCACGTTTATCTCTGTAT
Found at i:76241 original size:23 final size:22
Alignment explanation
Indices: 76175--76251 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
76165 TGCATGTGTT
* * *
76175 GCACTTTTATCTCTGATTGTGTT
1 GCACGTTTATCTCTG-TTTTGTG
*
76198 ACACGTTTATCTCTGTATTTGTG
1 GCACGTTTATCTCTGT-TTTGTG
76221 GCACGTTTATCTCTGCTTTTGTG
1 GCACGTTTATCTCTG-TTTTGTG
*
76244 GTACGTTT
1 GCACGTTT
76252 TTTAGTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.49
Consensus pattern (22 bp):
GCACGTTTATCTCTGTTTTGTG
Found at i:76841 original size:16 final size:17
Alignment explanation
Indices: 76820--76856 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
76810 GCGTTCAAAT
*
76820 TTTTTAATACTTT-TTA
1 TTTTTAATAATTTATTA
76836 TTTTTAATAATTTATTA
1 TTTTTAATAATTTATTA
76853 TTTT
1 TTTT
76857 ATAGCTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAATAATTTATTA
Found at i:85054 original size:23 final size:23
Alignment explanation
Indices: 85028--85074 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
85018 AAAAAAATGA
85028 AAAGACATATAAAAA-CATGTCAT
1 AAAGACATA-AAAAATCATGTCAT
* *
85051 AAAGATATAAAAAATCGTGTCAT
1 AAAGACATAAAAAATCATGTCAT
85074 A
1 A
85075 GGATAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (23 bp):
AAAGACATAAAAAATCATGTCAT
Found at i:85292 original size:2 final size:2
Alignment explanation
Indices: 85285--85353 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
85275 GATCGAATAC
85285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85327 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
85354 TGAATACAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85481 original size:33 final size:34
Alignment explanation
Indices: 85438--85502 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
85428 TCAGAAGGAC
*
85438 AAGTTTATTTAT-TTTTAAATATTATAATAGTGT
1 AAGTTCATTTATATTTTAAATATTATAATAGTGT
85471 AAGTTCATTTATATTTTAAATATTATAATAGT
1 AAGTTCATTTATATTTTAAATATTATAATAGT
85503 TACCAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.37
34 19 0.63
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (34 bp):
AAGTTCATTTATATTTTAAATATTATAATAGTGT
Found at i:91573 original size:20 final size:21
Alignment explanation
Indices: 91534--91579 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
91524 TATTCTTTTT
*
91534 TTTTTGTAATTTGATTTTTA-
1 TTTTTGTAATTTGATATTTAC
* *
91554 TTTTTGTATTTTTATATTTAC
1 TTTTTGTAATTTGATATTTAC
91575 TTTTT
1 TTTTT
91580 TTGGATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTTTGTAATTTGATATTTAC
Found at i:92043 original size:17 final size:18
Alignment explanation
Indices: 92021--92060 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
92011 GAAAATGGAT
92021 TCCTTTAA-AACGCTTGG
1 TCCTTTAAGAACGCTTGG
*
92038 TCCTTTAAGTACGCTTGG
1 TCCTTTAAGAACGCTTGG
92056 TCCTT
1 TCCTT
92061 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (18 bp):
TCCTTTAAGAACGCTTGG
Found at i:92384 original size:18 final size:18
Alignment explanation
Indices: 92361--92400 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
92351 TAAATATATA
92361 TAATATGTATTTAATTAT
1 TAATATGTATTTAATTAT
* *
92379 TAATATTTATTTAATTGT
1 TAATATGTATTTAATTAT
92397 TAAT
1 TAAT
92401 TAATAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TAATATGTATTTAATTAT
Found at i:93630 original size:98 final size:95
Alignment explanation
Indices: 93523--93700 Score: 311
Period size: 98 Copynumber: 1.8 Consensus size: 95
93513 TAAATCATAG
93523 AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATTT
1 AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAA-T-TAAATTTAATTT
93588 CATAACGGTTAACCAACAATTAACCGTTCATC
64 CATAACGGTTAACCAACAATTAACCGTTCATC
*
93620 AAAACTTATATTAGGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTAAATTTAATTTC
1 AAAA-TTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTAAATTTAATTTC
*
93685 TTAACGGTTAACCAAC
65 ATAACGGTTAACCAAC
93701 GACGTTCATC
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
96 28 0.36
97 5 0.06
98 45 0.58
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (95 bp):
AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTAAATTTAATTTCA
TAACGGTTAACCAACAATTAACCGTTCATC
Found at i:94709 original size:51 final size:51
Alignment explanation
Indices: 94649--94752 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
94639 TCGTGCAAAG
* * * *
94649 AAAGCTTTAGGATGTTTCTCTTTTCCCATTTTCCATCTGTTGGCCTTTTGT
1 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
94700 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
1 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
94751 AA
1 AA
94753 GAAGTTTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.45
Consensus pattern (51 bp):
AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
Found at i:99902 original size:15 final size:15
Alignment explanation
Indices: 99882--99911 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
99872 CGACGATCGG
99882 CGATGAGTACCATAA
1 CGATGAGTACCATAA
99897 CGATGAGTACCATAA
1 CGATGAGTACCATAA
99912 TTTAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (15 bp):
CGATGAGTACCATAA
Done.