Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006335.1 Hibiscus syriacus cultivar Beakdansim tig00015142_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: 76761
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:765 original size:27 final size:27
Alignment explanation
Indices: 734--791 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
724 GCGGCGGAGA
*
734 CATCTGGTAATGGAAAGGCGATGGCGG
1 CATCTGATAATGGAAAGGCGATGGCGG
761 CATCTGATAATGGAAAGGCGATGGCGG
1 CATCTGATAATGGAAAGGCGATGGCGG
788 CATC
1 CATC
792 ATATATGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (27 bp):
CATCTGATAATGGAAAGGCGATGGCGG
Found at i:2469 original size:17 final size:17
Alignment explanation
Indices: 2447--2497 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
2437 AAATTATATT
2447 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
*
2464 AGTAAAATACCTAAATAA
1 AGTAAAATA-TTAAATAA
*
2482 ATTAAATAATATTAAA
1 AGT-AA-AATATTAAA
2498 AATATTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.32
18 9 0.32
19 6 0.21
20 4 0.14
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:2480 original size:18 final size:17
Alignment explanation
Indices: 2447--2487 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2437 AAATTATATT
*
2447 AGTAAAATATTAAATAA
1 AGTAAAATACTAAATAA
2464 AGTAAAATACCTAAATAA
1 AGTAAAATA-CTAAATAA
*
2482 ATTAAA
1 AGTAAA
2488 TAATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (17 bp):
AGTAAAATACTAAATAA
Found at i:2862 original size:29 final size:29
Alignment explanation
Indices: 2804--2862 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2794 TACTGCTACG
* *
2804 GGTGTTAGATCGAGAAATATAATATGACT
1 GGTGTTAGATCGAGAAATATAAGATCACT
*
2833 GGTGTTAGATCGA-AAATATACCGATCACT
1 GGTGTTAGATCGAGAAATATA-AGATCACT
2862 G
1 G
2863 ATGAATTACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAAGATCACT
Found at i:13320 original size:56 final size:56
Alignment explanation
Indices: 13250--13407 Score: 280
Period size: 56 Copynumber: 2.8 Consensus size: 56
13240 AGGGGCACCG
* *
13250 AATCGAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAGGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
*
13306 AATCAAATATATCTATCAGTTGTTGTCATTAATAAGTATAAAAATAAAGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
*
13362 AATCAAATATATCTATCAGTTGTTCCCATTAATAAGTATAAAAATA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATA
13408 GAGCCCCGAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 97 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (56 bp):
AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
Found at i:15606 original size:2 final size:2
Alignment explanation
Indices: 15599--15627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15589 TTATGCTTCC
15599 TA 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 TA T
15628 TAATTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19013 original size:182 final size:181
Alignment explanation
Indices: 18704--19356 Score: 853
Period size: 182 Copynumber: 3.6 Consensus size: 181
18694 CGATACAAAT
* * * * *
18704 TAAAAATGTATCGATCTATAGCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGA
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGA-AATGA
* ** * *
18768 TAAAACCGATAAATCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAATGTCGACACT
65 TAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACT
* *
18833 TTTGTAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAGGTATCGATATTTTA
130 TTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTATCGATACTTTA
* * *
18886 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAATAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
18951 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
*
19016 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCTTGAAAAGTATCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTATCGATACTTTA
* * * * * * *
19068 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGATGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
* * * *
19133 AAAACCGGTAAAAAGATATCGGATATATTGAAAATGTCGGTAAATTAATATAAGTATCGACACTT
66 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* * *
19198 TCGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTA
131 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTATCGATACTTTA
* * * * * * *
19250 -AGAAAATATATCGATCCATAACAATATAATAGGTAAAAACATGATAAAACCGGTATCGAAATGA
1 TA-AAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGA
* * ** *
19314 CAACACCGGTAAAGCGCTACC-GATTATGTTGAAAGTGTCGATA
65 TAAAACCGGTAAAAAGCTACCGGA-TATATTGAAAGTGTCGATA
19357 CTTTAATAAG
Statistics
Matches: 412, Mismatches: 55, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
181 3 0.01
182 404 0.98
183 5 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (181 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGAT
AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTATCGATACTTTA
Found at i:21348 original size:204 final size:205
Alignment explanation
Indices: 20822--21353 Score: 677
Period size: 201 Copynumber: 2.6 Consensus size: 205
20812 GCAAAAGTGC
20822 CCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAAGTGTC
1 CCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAAGTGTC
*
20887 GATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTA
66 GATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTCTA
* ** * * * ** **
20952 AATTTACCGGTTTTATGAGAAAATCGGTCTACAATATGTGCCGACACTTTATTCATTTGTGTCGA
131 AATATACCGGTTTTATGAGAAAAGAGGTATACAATAAGTACCGACACTTTATAAATTTGTACCGA
21017 TATATGTTGT
196 TATATGTTGT
* * * * * ** *
21027 CCAGAATGT-ATTT-C---CAAATCAAGTGCACGAACA-AAGTGTCGATACATTTATAAAAAGTA
1 CCATAATGTGTTTTCCAAACAAAACAAGTTCAC-AA-ATAAGTGTCGACACATTTATATCAAGTG
* * * * ** *
21086 TCGATCCTAAAAACATCGAAATCCGTAATTATAATGTAATAGGTAAAATAACAATGTAACCGGTC
64 TCGATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTC
* *
21151 TAAATATACC-GTTTTATGAGAAAAGAGGTATTC-ATAAAGTATCGACACTTTATAAATTTGTAC
129 TAAATATACCGGTTTTATGAGAAAAGAGGTATACAAT-AAGTACCGACACTTTATAAATTTGTAC
*
21214 CGATACTTTG-TGT
193 CGATA-TATGTTGT
*
21227 CCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCAACACATTTATATCAAGTGTC
1 CCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAAGTGTC
* *
21292 GATCCCAAAAAAATCGAAACCCGTAACTATAATGTAATAGGTCACTTTATAATGTAACCGGT
66 GATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGT
21354 TTTATGAGAA
Statistics
Matches: 270, Mismatches: 47, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
199 2 0.01
200 67 0.25
201 96 0.36
202 2 0.01
203 2 0.01
204 81 0.30
205 20 0.07
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (205 bp):
CCATAATGTGTTTTCCAAACAAAACAAGTTCACAAATAAGTGTCGACACATTTATATCAAGTGTC
GATCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTACAATGTAACCGGTCTA
AATATACCGGTTTTATGAGAAAAGAGGTATACAATAAGTACCGACACTTTATAAATTTGTACCGA
TATATGTTGT
Found at i:21481 original size:187 final size:189
Alignment explanation
Indices: 20993--21740 Score: 618
Period size: 198 Copynumber: 3.8 Consensus size: 189
20983 CAATATGTGC
* * * **
20993 CGACACTTTATTCATTTGTGTCGATA-TATGTTGTCCAGAATGTA-TTTCCAAATCAAGTGCACG
1 CGACACTTTATACATTTGTGTCGACACT-T-TAGTCCAGAATAAATTTTCCAAA-CAAGTGCACG
* * *
21056 AACAAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAATCCGTAATTATAAT
63 AA-AAAGTGTCGACACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAAT
* ** * * ** * *
21121 GTAATAGGTAAAATAACAATGTAACCGGTCTAAATATACCGTTTTATGAGAAAAGAGGTATTCAT
127 GTAATAGGTCACTTTATAATGTAACCGGT-T---T-TA-C-TGGTAT-A-AAAAAAGGTATACAT
*
21186 AAAGTAT
183 AATGTAT
* ** * * * *** *
21193 CGACACTTTATAAATTTGTACCGATACTTTGTGTCCATAATGTGTTTTCCAAACAAAACAAGTTC
1 CGACACTTTATACATTTGTGTCGACACTTT-AGTCCAGAATAAATTTT-C---C-AAACAAGTGC
* ** * * *
21258 AC-AAATAAGTGTCAACACATTTATATCAAGTGTCGATCCCAAAAAAATCGAAACCCGTAACTAT
60 ACGAAA-AAGTGTCGACACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTAT
* * *
21322 AATGTAATAGGTCACTTTATAATGTAACCGGTTTTA-T-G-A-GAAAATAGGTCTACA-ATATG-
124 AATGTAATAGGTCACTTTATAATGTAACCGGTTTTACTGGTATAAAAAAAGGTATACATA-ATGT
21381 AGT
188 A-T
* * **
21384 CGACACTTTATTCATTTGTGTCGATACATGTTA-TCCAGAATGTA-TTTCCAAACCAAGTGCACG
1 CGACACTTTATACATTTGTGTCGACAC-T-TTAGTCCAGAATAAATTTTCCAAA-CAAGTGCACG
* * * *
21447 AACAAAGTGTCGATACATTTATAAAAAGTGTCGATCCTACAAACATCGAAACACATAATTATAAT
63 AA-AAAGTGTCGACACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAAT
* * * * *
21512 GTAATCGGTAACATAACAATGTAACCGGTCTAAATTTACTGGTTATTTAAAAAAAGGTATACATA
127 GTAATAGGTCACTTTATAATGTAACCGG--T---TTTACTGG-TA--TAAAAAAAGGTATACATA
21577 ATGTAT
184 ATGTAT
* * *
21583 CGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAA
1 CGACACTTTATACATTTGTGTCGACACTTTA-GTCCAGAATAAATTTTCCAAACAAGTGCACGAA
*
21648 AAAGTGTCGACACATTTAGAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAATGTA
65 AAAGTGTCGACACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAATGTA
21713 ATAGGTCACTTTATAATGTAACCGGTTT
130 ATAGGTCACTTTATAATGTAACCGGTTT
21741 AAATTTACCG
Statistics
Matches: 445, Mismatches: 70, Indels: 73
0.76 0.12 0.12
Matches are distributed among these distances:
185 3 0.01
186 9 0.02
187 76 0.17
188 1 0.00
189 2 0.00
190 5 0.01
191 46 0.10
192 5 0.01
193 5 0.01
194 2 0.00
196 3 0.01
197 3 0.01
198 81 0.18
199 62 0.14
200 45 0.10
201 4 0.01
202 1 0.00
203 2 0.00
204 78 0.18
205 9 0.02
206 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (189 bp):
CGACACTTTATACATTTGTGTCGACACTTTAGTCCAGAATAAATTTTCCAAACAAGTGCACGAAA
AAGTGTCGACACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAATGTAA
TAGGTCACTTTATAATGTAACCGGTTTTACTGGTATAAAAAAAGGTATACATAATGTAT
Found at i:21597 original size:22 final size:21
Alignment explanation
Indices: 21569--21614 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21559 TAAAAAAAGG
*
21569 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
21591 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
21612 TAT
1 TAT
21615 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:21733 original size:198 final size:202
Alignment explanation
Indices: 21428--21812 Score: 537
Period size: 198 Copynumber: 1.9 Consensus size: 202
21418 CCAGAATGTA
* * *
21428 TTTCCAAACCAAGTGCACGAACAAAGTGTCGATACATTTATAAAAAGTGTCGATCCTACAAACAT
1 TTTCCAAACCAAGTGCACGAACAAAGTGTCGACACATTTAGAAAAAGTGTCGATCCTAAAAACAT
* * *
21493 CGAAACACATAATTATAATGTAATCGGTAACATAACAATGTAACCGGTCTAAATTTACTGGTTAT
66 CGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATTTACCGATT-T
* * *
21558 T-T-A-AAAAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCA
130 TATGAGAAAAAAGGTATACATAATGTATCGACACTTTATAAATTAGTGTCGACACTTTATGTCCA
21620 TAATAAAT
195 TAATAAAT
*
21628 TTTCCAAA-CAAGTTCACGAA-AAAGTGTCGACACATTTAGAAAAAGTGTCGATCCTAAAAACAT
1 TTTCCAAACCAAGTGCACGAACAAAGTGTCGACACATTTAGAAAAAGTGTCGATCCTAAAAACAT
* * * * * * *
21691 CGAAACCCGTAATTATAATGTAATAGGTCACTTTATAATGTAACCGGTTTAAATTTACCGATTTT
66 CGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATTTACCGATTTT
* * * *
21756 ATGAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTAGTGTCGATACTTT
131 ATGAGAAAAAAGGTATACATAATGTATCGACACTTTATAAATTAGTGTCGACACTTT
21813 TGAAAATTAC
Statistics
Matches: 161, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
197 2 0.01
198 94 0.58
199 12 0.07
200 53 0.33
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (202 bp):
TTTCCAAACCAAGTGCACGAACAAAGTGTCGACACATTTAGAAAAAGTGTCGATCCTAAAAACAT
CGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATTTACCGATTTT
ATGAGAAAAAAGGTATACATAATGTATCGACACTTTATAAATTAGTGTCGACACTTTATGTCCAT
AATAAAT
Found at i:25080 original size:21 final size:21
Alignment explanation
Indices: 25056--25108 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
25046 GTGTACGCAT
25056 AAAGTGTCGATACATTTTTAA
1 AAAGTGTCGATACATTTTTAA
*
25077 AAAGTGTCAATACATTTTTAA
1 AAAGTGTCGATACATTTTTAA
*
25098 AAAGTATCGAT
1 AAAGTGTCGAT
25109 CCTCGAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (21 bp):
AAAGTGTCGATACATTTTTAA
Found at i:25505 original size:87 final size:87
Alignment explanation
Indices: 25398--25560 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
25388 AAATAGGTCA
*
25398 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
*
25463 CCGGTTAAATGCCTATTTTATT
66 CCAGTTAAATGCCTATTTTATT
* * * *
25485 ATATAAACGTTACCTATTACATTATCTAAGCTCTACCTAATTTGTTATTGTGCTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
*
25550 CTAGTTAAATG
66 CCAGTTAAATG
25561 ATATAACATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
CCAGTTAAATGCCTATTTTATT
Found at i:34398 original size:2 final size:2
Alignment explanation
Indices: 34381--34422 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
34371 TATAATACTA
* *
34381 AT AT AC AT AC AT 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 AT AT AT AT AT AT
34423 TAATAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38024 original size:2 final size:2
Alignment explanation
Indices: 38017--38042 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38007 GCTTACACTT
38017 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
38043 AGAGCATATA
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):
TA
Found at i:40049 original size:28 final size:28
Alignment explanation
Indices: 40009--40065 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39999 TTTAAAATAC
40009 GTATCAATGAACGTAAGAAATGTGACAT
1 GTATCAATGAACGTAAGAAATGTGACAT
40037 GTATCAATGAACGTAAGAAATGTGACAT
1 GTATCAATGAACGTAAGAAATGTGACAT
40065 G
1 G
40066 ATAATCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (28 bp):
GTATCAATGAACGTAAGAAATGTGACAT
Found at i:40972 original size:75 final size:75
Alignment explanation
Indices: 40849--40998 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
40839 ATTGTTAAGG
*
40849 TTAGATCATAAGTGGACGTCTTCGTTGCAACGTTCATGTACTTCTCAAATGTGGGTACATAATCA
1 TTAGATCATAAGTGGACGTCTTCGTTGCAACGCTCATGTACTTCTCAAATGTGGGTACATAATCA
40914 TCATGGCACC
66 TCATGGCACC
40924 TTAGATCATAAGTGGACGTCTTCGTTGCAACGCTCATGTACTTCTCAAATGTGGGTACATAATCA
1 TTAGATCATAAGTGGACGTCTTCGTTGCAACGCTCATGTACTTCTCAAATGTGGGTACATAATCA
40989 TCATGGCACC
66 TCATGGCACC
40999 ACATCGTCTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (75 bp):
TTAGATCATAAGTGGACGTCTTCGTTGCAACGCTCATGTACTTCTCAAATGTGGGTACATAATCA
TCATGGCACC
Found at i:44824 original size:20 final size:20
Alignment explanation
Indices: 44799--44846 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
44789 GACACCAGTT
44799 TTGGTATTGATAGCTAATTG
1 TTGGTATTGATAGCTAATTG
44819 TTGGTATTGATAGCTAATTG
1 TTGGTATTGATAGCTAATTG
44839 TTGGTATT
1 TTGGTATT
44847 TATTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (20 bp):
TTGGTATTGATAGCTAATTG
Found at i:46425 original size:37 final size:37
Alignment explanation
Indices: 46349--46425 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
46339 TTTTTATATT
*
46349 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
46386 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
46423 TTT
1 TTT
46426 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:49032 original size:2 final size:2
Alignment explanation
Indices: 49020--49073 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
49010 CTCGGGGCGT
*
49020 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49062 TC TC TC TC TC TC
1 TC TC TC TC TC TC
49074 AATCCCCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:51180 original size:28 final size:28
Alignment explanation
Indices: 51148--51201 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
51138 TTTGTTTATT
*
51148 TTATGTCGTCGAATCAATGTTTGAAACA
1 TTATGTCGTCGAATCAATGCTTGAAACA
* *
51176 TTATGTCGTCGAGTCAGTGCTTGAAA
1 TTATGTCGTCGAATCAATGCTTGAAA
51202 GCAACGATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (28 bp):
TTATGTCGTCGAATCAATGCTTGAAACA
Found at i:55203 original size:18 final size:18
Alignment explanation
Indices: 55180--55218 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55170 GTTCTGAAGT
* *
55180 ACCAACTTCTGGTCAAAC
1 ACCAACATCTGATCAAAC
55198 ACCAACATCTGATCAAAC
1 ACCAACATCTGATCAAAC
55216 ACC
1 ACC
55219 CGGGAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.36, G:0.08, T:0.18
Consensus pattern (18 bp):
ACCAACATCTGATCAAAC
Found at i:67414 original size:18 final size:17
Alignment explanation
Indices: 67383--67416 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
67373 AGTCCATCCT
67383 TAAAATTTAAATTAGTG
1 TAAAATTTAAATTAGTG
*
67400 TAAAGATTTAGATTAGT
1 TAAA-ATTTAAATTAGT
67417 ATAAGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TAAAATTTAAATTAGTG
Found at i:70402 original size:26 final size:26
Alignment explanation
Indices: 70371--70466 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 26
70361 AAATCAACAG
70371 ATATTAAAAACAAGGGTTAAATGCAA
1 ATATTAAAAACAAGGGTTAAATGCAA
*
70397 ATATTAAAAACAA--ATTCAAA-GCACA
1 ATATTAAAAACAAGGGTT-AAATGCA-A
*
70422 GATATTAAAAACAAGAAAGGGTTAAATGCAG
1 -ATATTAAAAAC----AAGGGTTAAATGCAA
70453 ATATTAAAAACAAG
1 ATATTAAAAACAAG
70467 TTCAAAGCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
24 5 0.09
25 4 0.07
26 27 0.47
30 13 0.23
31 3 0.05
32 5 0.09
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (26 bp):
ATATTAAAAACAAGGGTTAAATGCAA
Found at i:70496 original size:56 final size:56
Alignment explanation
Indices: 70367--70475 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
70357 CATTAAATCA
70367 ACAGATATTAAAAAC----AAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
1 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
* *
70419 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAGATATTAAAAACAAGTTCAAAGC
1 ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
70475 A
1 A
70476 TAGTTCATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
52 15 0.29
56 36 0.71
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (56 bp):
ACAGATATTAAAAACAAGAAAGGGTTAAATGCAAATATTAAAAACAAATTCAAAGC
Found at i:75478 original size:14 final size:15
Alignment explanation
Indices: 75459--75494 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
75449 TTAAATTGAT
75459 TTATAAA-TATTAAA
1 TTATAAATTATTAAA
75473 TTATAAATTATTAAA
1 TTATAAATTATTAAA
75488 TGTATAA
1 T-TATAA
75495 TTAGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 8 0.40
16 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TTATAAATTATTAAA
Found at i:75487 original size:22 final size:22
Alignment explanation
Indices: 75462--75533 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
75452 AATTGATTTA
75462 TAAATATTAAATTATAAATTAT
1 TAAATATTAAATTATAAATTAT
* *
75484 TAAAT-GTATAATTAGAAATTAGT
1 TAAATATTA-AATTATAAATTA-T
* *
75507 TAAAAATTTAAA-TATAATTTAAT
1 TAAATA-TTAAATTATAAATT-AT
75530 TAAA
1 TAAA
75534 ATATAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 2 0.05
22 16 0.41
23 16 0.41
24 3 0.08
25 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAATATTAAATTATAAATTAT
Done.