Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000927.1 Hibiscus syriacus cultivar Beakdansim tig00001851_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: 106268
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6122 original size:35 final size:36
Alignment explanation
Indices: 6058--6128 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
6048 AGCATCTATG
*
6058 ATACCATCTATTGTATGCCTCATGGAAGAAAAATAC
1 ATACCATCTACTGTATGCCTCATGGAAGAAAAATAC
*
6094 ATACCTTCTACTGTATG-CTCATGGAAGAAAAATAC
1 ATACCATCTACTGTATGCCTCATGGAAGAAAAATAC
6129 TATGTAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 18 0.55
36 15 0.45
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (36 bp):
ATACCATCTACTGTATGCCTCATGGAAGAAAAATAC
Found at i:12163 original size:29 final size:29
Alignment explanation
Indices: 12121--12180 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12111 TTCCAAAAAA
12121 TTACCAAATTTTGGGCGAGTTTAATATTC
1 TTACCAAATTTTGGGCGAGTTTAATATTC
12150 TTACCAAATTTTGGGCGAGTTTAATATTC
1 TTACCAAATTTTGGGCGAGTTTAATATTC
12179 TT
1 TT
12181 TGTATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (29 bp):
TTACCAAATTTTGGGCGAGTTTAATATTC
Found at i:15124 original size:20 final size:20
Alignment explanation
Indices: 15084--15124 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
15074 TTTGATCATG
*
15084 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
15104 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
15124 A
1 A
15125 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:19521 original size:14 final size:15
Alignment explanation
Indices: 19502--19532 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19492 AACTCTTGCA
19502 ATTCTTT-TGGAGCC
1 ATTCTTTATGGAGCC
19516 ATTCTTTATGGAGCC
1 ATTCTTTATGGAGCC
19531 AT
1 AT
19533 GGCAATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (15 bp):
ATTCTTTATGGAGCC
Found at i:22274 original size:76 final size:76
Alignment explanation
Indices: 22148--22313 Score: 278
Period size: 76 Copynumber: 2.2 Consensus size: 76
22138 AAGCCAAAAA
* **
22148 TTCCAGATTGCTAAGAGGAAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCTAAATGGTTT
1 TTCCAGAATGCTCGGAGGAAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCTAAATGGTTT
22213 GGCTCCGAGAT
66 GGCTCCGAGAT
* *
22224 TTCCAGAATGCTCGGAGGGAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCTGAATGGTTT
1 TTCCAGAATGCTCGGAGGAAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCTAAATGGTTT
*
22289 GGCTCCGATAT
66 GGCTCCGAGAT
22300 TTCCAGAATGCTCG
1 TTCCAGAATGCTCG
22314 AAATATTTGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 84 1.00
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.23
Consensus pattern (76 bp):
TTCCAGAATGCTCGGAGGAAACCGATTCCCCCCCAAGGGGGTACCGATTCCCCCCTAAATGGTTT
GGCTCCGAGAT
Found at i:28105 original size:23 final size:21
Alignment explanation
Indices: 28053--28114 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
28043 TTTTGGTGCA
*
28053 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
28073 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
28094 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
28115 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:28122 original size:21 final size:21
Alignment explanation
Indices: 28096--28135 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28086 CCCCCTTTGA
*
28096 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
28117 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
28136 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:38461 original size:29 final size:29
Alignment explanation
Indices: 38427--38485 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38417 CCTAAATTAA
38427 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
38456 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
38485 T
1 T
38486 AGGTGAAAAT
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:43149 original size:29 final size:29
Alignment explanation
Indices: 43115--43173 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
43105 CCTAAATTAA
43115 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
43144 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
43173 T
1 T
43174 AGGTGAAAAT
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:49024 original size:29 final size:29
Alignment explanation
Indices: 48991--49077 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
48981 TTTCACATAC
48991 CTAAATTGATGTAAGCGATGACATCAAAA
1 CTAAATTGATGTAAGCGATGACATCAAAA
49020 CTAAATTGATGTAAGCGATGACATCAAAAA
1 CTAAATTGATGTAAGCGATGACATC-AAAA
*
49050 CTAAATTGATGTAAGCAATGACATCAAA
1 CTAAATTGATGTAAGCGATGACATCAAA
49078 TTAATTTAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 28 0.50
30 28 0.50
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (29 bp):
CTAAATTGATGTAAGCGATGACATCAAAA
Found at i:49052 original size:30 final size:30
Alignment explanation
Indices: 48991--49077 Score: 158
Period size: 30 Copynumber: 2.9 Consensus size: 30
48981 TTTCACATAC
48991 CTAAATTGATGTAAGCGATGACATC-AAAA
1 CTAAATTGATGTAAGCGATGACATCAAAAA
49020 CTAAATTGATGTAAGCGATGACATCAAAAA
1 CTAAATTGATGTAAGCGATGACATCAAAAA
*
49050 CTAAATTGATGTAAGCAATGACATCAAA
1 CTAAATTGATGTAAGCGATGACATCAAA
49078 TTAATTTAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
29 25 0.45
30 31 0.55
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (30 bp):
CTAAATTGATGTAAGCGATGACATCAAAAA
Found at i:57972 original size:21 final size:21
Alignment explanation
Indices: 57946--57990 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57936 GATTTCTGGG
* *
57946 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
57967 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
57988 CAA
1 CAA
57991 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:58593 original size:18 final size:18
Alignment explanation
Indices: 58570--58604 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58560 CTAGGAGATT
58570 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
58588 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
58605 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:58690 original size:21 final size:22
Alignment explanation
Indices: 58661--58704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58651 GTTGTATGAT
58661 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
58682 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
58704 A
1 A
58705 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:59691 original size:149 final size:149
Alignment explanation
Indices: 59421--59871 Score: 834
Period size: 149 Copynumber: 3.0 Consensus size: 149
59411 GAGTCGAGGG
59421 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
59486 ACTTGATCCCTAGCATATGTATATAATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
59551 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
59570 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
59635 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
59700 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
59719 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
59784 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCA-T-
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
59847 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
59866 TCTACG
1 TCTACG
59872 GGGCACTTCG
Statistics
Matches: 295, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
147 24 0.08
148 1 0.00
149 270 0.92
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:59894 original size:23 final size:23
Alignment explanation
Indices: 59850--59894 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59840 ACATCATTAT
*
59850 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
59873 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
59895 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:67909 original size:21 final size:21
Alignment explanation
Indices: 67883--67927 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
67873 GATTTCTGGG
* *
67883 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
67904 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
67925 CAA
1 CAA
67928 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:68530 original size:18 final size:18
Alignment explanation
Indices: 68507--68541 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
68497 CTAGGAGATT
68507 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
68525 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
68542 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:68627 original size:21 final size:22
Alignment explanation
Indices: 68598--68641 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
68588 GTTGTATGAT
68598 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
68619 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
68641 A
1 A
68642 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:69816 original size:149 final size:149
Alignment explanation
Indices: 69353--69805 Score: 861
Period size: 149 Copynumber: 3.0 Consensus size: 149
69343 GAGTCGAGGG
69353 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
69418 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
69483 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
69502 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
69567 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
69632 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
69651 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
69716 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
69781 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
69800 TCTACG
1 TCTACG
69806 GGGCACTTCG
Statistics
Matches: 298, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 298 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:69828 original size:23 final size:23
Alignment explanation
Indices: 69784--69828 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
69774 ATCATTATAT
*
69784 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
69807 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
69829 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:75458 original size:11 final size:10
Alignment explanation
Indices: 75444--75480 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 10
75434 ATTCTCTTCA
75444 TTTCTTCTTTT
1 TTTC-TCTTTT
75455 TTTCTCATTTT
1 TTTCTC-TTTT
75466 TTTCTCTTTT
1 TTTCTCTTTT
75476 TTTCT
1 TTTCT
75481 ACAAGCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 11 0.44
11 14 0.56
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTCTTTT
Found at i:81272 original size:12 final size:12
Alignment explanation
Indices: 81255--81281 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
81245 ACACATAGGA
81255 TTAGCTCTCGTC
1 TTAGCTCTCGTC
81267 TTAGCTCTCGTC
1 TTAGCTCTCGTC
81279 TTA
1 TTA
81282 AAAAGTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.30, G:0.15, T:0.44
Consensus pattern (12 bp):
TTAGCTCTCGTC
Found at i:85660 original size:10 final size:10
Alignment explanation
Indices: 85645--85673 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
85635 TTTAGCTATC
85645 TAAACATGTA
1 TAAACATGTA
85655 TAAACATGTA
1 TAAACATGTA
85665 TAAACATGT
1 TAAACATGT
85674 CATTTCACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (10 bp):
TAAACATGTA
Found at i:86313 original size:2 final size:2
Alignment explanation
Indices: 86306--86330 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86296 ATTTCATACT
86306 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
86331 CACTTATATT
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:91203 original size:20 final size:20
Alignment explanation
Indices: 91178--91216 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
91168 TTTTCAAGGG
91178 CATGCACCGATACACCAATC
1 CATGCACCGATACACCAATC
* *
91198 CATGCATCGATACATCAAT
1 CATGCACCGATACACCAAT
91217 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
CATGCACCGATACACCAATC
Found at i:91268 original size:19 final size:20
Alignment explanation
Indices: 91244--91296 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
91234 AATGTATTTT
*
91244 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
* *
91263 ATGCATCGTTGCACAAGACT
1 ATGCATCGATGCACAAGACC
91283 ATGCATCGATGCAC
1 ATGCATCGATGCAC
91297 TCAGGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:99888 original size:45 final size:46
Alignment explanation
Indices: 99837--99927 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
99827 TTGAACATAA
* * *
99837 TGCATTTTATATATCGATGTAC-ATACCAAGCATCGATGCACTCAG
1 TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
* * * *
99882 TGCATTTGATGCATCGATGTACAAGACTATGCATTGATGCACTCAG
1 TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
99928 GCTTTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 19 0.50
46 19 0.50
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATACATCGATGTACAAGACCAAGCATCGATGCACTCAG
Found at i:105268 original size:23 final size:22
Alignment explanation
Indices: 105238--105281 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
105228 ATTTTTTGGT
105238 AAAAAATT-CATTAATATTTTAC
1 AAAAAATTACATTAAT-TTTTAC
*
105260 AAAATAATTACTTTAATTTTTA
1 AAAA-AATTACATTAATTTTTA
105282 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 9 0.47
24 6 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAAATTACATTAATTTTTAC
Done.