Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002594.1 Hibiscus syriacus cultivar Beakdansim tig00005250_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: 65239
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:6659 original size:25 final size:26
Alignment explanation
Indices: 6608--6659 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
6598 AAGCTTCAGG
* *
6608 TTCTACATCTTATTTTCTTCTTTTTT
1 TTCTACATCTTATTTCCTTCTTGTTT
6634 TTCTA-ATCTT-TTTCCTTCATTGTTT
1 TTCTACATCTTATTTCCTTC-TTGTTT
6659 T
1 T
6660 GGGATCCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (26 bp):
TTCTACATCTTATTTCCTTCTTGTTT
Found at i:14406 original size:18 final size:19
Alignment explanation
Indices: 14366--14410 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
14356 TTTGGTTCAC
*
14366 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
*
14386 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTACCAGG
14404 GGAATAA
1 GGAATAA
14411 GATTACCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.22
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:14620 original size:36 final size:36
Alignment explanation
Indices: 14549--14621 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
14539 GTTGGAAAAT
* *
14549 ATTTATATATTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTCTTTAAAAAATTAAAAATCATAAA
* *
14585 ATTTATATACTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATA-TTTCTTTAAAAAATTAAAAATCATAAA
14621 A
1 A
14622 AAGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTCTTTAAAAAATTAAAAATCATAAA
Found at i:15548 original size:22 final size:22
Alignment explanation
Indices: 15523--15571 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
15513 TCAGATCGAA
*
15523 TCTCGGGTGGAGGATTCCTAAT
1 TCTCGGATGGAGGATTCCTAAT
*
15545 TCTCGGATGGATGATTCCTAAT
1 TCTCGGATGGAGGATTCCTAAT
15567 TCTCG
1 TCTCG
15572 AATTGGGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (22 bp):
TCTCGGATGGAGGATTCCTAAT
Found at i:16406 original size:200 final size:197
Alignment explanation
Indices: 15960--16474 Score: 676
Period size: 200 Copynumber: 2.6 Consensus size: 197
15950 TATATTTACT
* *
15960 TATTTTCTAACTAAACCGGTATATTTATACCGGTAACATTGAAAATTTACCTATTACATTATAAT
1 TATTTTCTAA-TAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
* * *
16025 TATTGGTTTCGATGTTTTTGGGATCGATACAATTT-TAAATGTATCAACACTTTATGTGTGCACC
65 TATTGGTTTCGATGTTTTTGGGATCGATA-ATTTTATAAATGTATCGACACTTTATGCGTGCACC
* * *
16089 TCGTTGTGCATTCATTCTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACATTATGTA
129 ACGTTGGGCATTAATTCTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACATTATGTA
16154 GACC
194 GACC
* * * * *
16158 TATTTTCTCATAAAAAC-ATATATTTCTACCGGGTACATTGTAAATTTACCTATTACATTATAAT
1 TATTTTCTAAT-AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAAT
* *
16222 TATCGGTTTCGATGTTTTTGGGATCGATATTTTTTATAAATGTATCGACACTTTATGCGTGCACC
65 TATTGGTTTCGATGTTTTTGGGATCGATA-ATTTTATAAATGTATCGACACTTTATGCGTGCACC
* * *
16287 ACGTTTGGGCATTAATTCTGGACAAAAAGTATCGACACAAA-TTCCATAAGTGTCGATACATTAT
129 ACG-TTGGGCATTAATTCTGGA-AAAAAATATCGACACAAACTT-AAAAAGTGTCGATACATTAT
*
16351 GTTGACC
191 GTAGACC
* * * *
16358 TGTTTTCTAATTAACCGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATT
1 TATTTTCTAATAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATT
* * * * * *
16423 ATTGGTTTCAATATTTTTGGGGTCAATACTTTTAGGAAATGTATCGACACTT
66 ATTGGTTTCGATGTTTTTGGGATCGATAATTTTA-TAAATGTATCGACACTT
16475 ATGTTTACCT
Statistics
Matches: 274, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
197 74 0.27
198 42 0.15
199 26 0.09
200 132 0.48
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (197 bp):
TATTTTCTAATAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATT
ATTGGTTTCGATGTTTTTGGGATCGATAATTTTATAAATGTATCGACACTTTATGCGTGCACCAC
GTTGGGCATTAATTCTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACATTATGTAGA
CC
Found at i:16943 original size:19 final size:19
Alignment explanation
Indices: 16916--16965 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
16906 ATTACATTTA
16916 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
* *
16935 TATAGAAAATTATAAATCT
1 TATACAAAATTATAAATCG
16954 TATACAAAATTA
1 TATACAAAATTA
16966 ACATTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:18538 original size:18 final size:18
Alignment explanation
Indices: 18515--18552 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
18505 TCCTCCTCAT
18515 TTCCTCCATATTTTCTTC
1 TTCCTCCATATTTTCTTC
*
18533 TTCCTCCATCTTTTCTTC
1 TTCCTCCATATTTTCTTC
18551 TT
1 TT
18553 AATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.34, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCCTCCATATTTTCTTC
Found at i:21748 original size:181 final size:182
Alignment explanation
Indices: 21286--22008 Score: 1092
Period size: 182 Copynumber: 4.0 Consensus size: 182
21276 GTGGTGCTTT
* * * *
21286 ACCAGTTTTATCATATTTTTACATGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATAGA
1 ACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* * *
21351 CACTTTATAAGCACCATTACTGATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATT
66 CACTTTATAGGCGCCATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATT
* * * *
21416 ATCGACACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATATCGAG
131 ATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAG
* *
21468 ACC-GATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAACACATTTTTATAAAGTATCG
1 ACCAG-TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
*
21532 ACACTTTATAGGCGCCATTACTGCTTCTTTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAT
65 ACACTTTATAGGCGCCATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAT
21597 TATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTT-TCATTTCGAG
130 TATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAG
* *
21649 ACCAGTTTTGTCATATTTTTACCTGTTATATGGTTATGGATCGATACATTTTTATCAAGTATCGA
1 ACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
* * * * * *
21714 CACTTTATAGGTGCTATTACTTCTTTTATTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGT
66 CACTTTATAGGCGCCATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATT
*
21779 ATCGACACTTTCAACATATCTGGTGGCGCTTTACCGATTTTGTCATTTCGAG
131 ATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAG
* *
21831 ACCGGTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTATAAAGTATCG
1 ACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTATAAAGTATCG
* * * *
21896 ACATTTTATAGGCGCTATTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTAT-TTAAAT
65 ACACTTTATAGGCGCCATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAT
* * * *
21960 CTAATCGATACTTTCAACATATCTGGTAGCACTTTACTGGTTTTGTCAT
130 -T-ATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCAT
22009 ATTTTTACCT
Statistics
Matches: 495, Mismatches: 40, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
181 168 0.34
182 217 0.44
183 69 0.14
184 41 0.08
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
ACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTATAGGCGCCATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATT
ATCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAG
Found at i:22105 original size:163 final size:164
Alignment explanation
Indices: 21831--22171 Score: 558
Period size: 163 Copynumber: 2.1 Consensus size: 164
21821 TCATTTCGAG
* * *
21831 ACCGGTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTATAAAGTATCG
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTTACAAAGTATCG
* *
21896 ACATTTTATAGGCGCTATTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATC
66 ACACTTTATAGACGCTATTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATC
21961 TAATCGATACTTTCAACATATCTGGTAGCACTTT
131 TAATCGATACTTTCAACATATCTGGTAGCACTTT
*
21995 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACA-TTTTTACAAAGTATCG
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTTACAAAGTATCG
* * *
22059 ACACTTTATAGACGCTATTACTTCTTCTGTTTTAAATTCCAAAAGTGTCGATATTTATTTAAATC
66 ACACTTTATAGACGCTATTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATC
* * **
22124 TAATCGATACTTTCAATATATTTGGTAGCGTTTT
131 TAATCGATACTTTCAACATATCTGGTAGCACTTT
22158 ACCGGTTTTGTCAT
1 ACCGGTTTTGTCAT
22172 TTTGAGACCG
Statistics
Matches: 163, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
163 118 0.72
164 45 0.28
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (164 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTTACAAAGTATCG
ACACTTTATAGACGCTATTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATC
TAATCGATACTTTCAACATATCTGGTAGCACTTT
Found at i:22133 original size:184 final size:184
Alignment explanation
Indices: 21943--22320 Score: 473
Period size: 183 Copynumber: 2.1 Consensus size: 184
21933 TCCAAAAGTG
* * *
21943 TCGATACTTATTTAAATCTAATCGATA-C-TTTCAAC-ATATCTGGTAGCACTTT-ACTGGTTTT
1 TCGATACTT-TTTAAATATAATCGATAGCGTTTCAACGAT-T-TGGT--CACTTTGACCGATTTT
*
22004 GTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTACAAAGTATCGACACTTTATA
61 GTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTACAAAATATCGACACTTTATA
* *
22069 GACGCTATTACTTCTTCTGTTTTAAA-TTCCAAAAGTGTCGATATTTATTTAAATCTAA
126 GACGCTATTACTTCTTCTATTTTAAATTTCCAAAAGTGTCGATACTTATTTAAATCTAA
* * * * * * * * *
22127 TCGATAC--TTTCAATATATTTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTC
1 TCGATACTTTTTAAATATAATCGATAGCGTTTCAACGATTTGGTCACTTT--GACCGATTTTGTC
* * *
22190 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTTATAGGC
64 ATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTACAAAATATCGACACTTTATAGAC
*
22255 GCTATTACTTCTTCTATTTTAAATTTCTAAAAGTGTCGATACTTATTTAAATCTAA
129 GCTATTACTTCTTCTATTTTAAATTTCCAAAAGTGTCGATACTTATTTAAATCTAA
22311 TCGATACTTT
1 TCGATACTTT
22321 CAACATATCC
Statistics
Matches: 166, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
180 5 0.03
181 12 0.07
182 4 0.02
183 99 0.60
184 45 0.27
186 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (184 bp):
TCGATACTTTTTAAATATAATCGATAGCGTTTCAACGATTTGGTCACTTTGACCGATTTTGTCAT
ATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTACAAAATATCGACACTTTATAGACGC
TATTACTTCTTCTATTTTAAATTTCCAAAAGTGTCGATACTTATTTAAATCTAA
Found at i:22365 original size:347 final size:346
Alignment explanation
Indices: 21653--22394 Score: 1184
Period size: 347 Copynumber: 2.1 Consensus size: 346
21643 TTCGAGACCA
*
21653 GTTTTGTCATATTTTTACCTGTTATATGGTTATGGATCGATACATTTTTATCAAGTATCGACACT
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATCAAGTATCGACACT
** * *
21718 TTATAGGTGCTATTACTTCTTTTATTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCG
66 TTATAGACGCTATTACTTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTATATTAAACTATCG
* *
21783 ACACTTTCAACATATCTGGTGGCGCTTTACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATT
131 ACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCGATTTTGTCATATT
* * *
21848 TTTACTTGTTATATTGTTATGGATCGATACATTTTTTATAAAGTATCGACATTTTATAGGCGCTA
196 TTTACCTGTTATATTGTTATGGATCGATACATTTTTTATAAAATATCGACACTTTATAGGCGCTA
*
21913 TTAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATCTAATCGATACTTTCAAC
261 TTAATTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTATTTAAATCTAATCGATACTTTCAAC
* *
21978 ATATCTGGTAGCACTTTACTG
326 ATATCCGGTAGCACTTTACCG
*
21999 GTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTA-CAAAGTATCGACAC
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATC-AAGTATCGACAC
* *
22063 TTTATAGACGCTATTACTTCTTCTGTTTTAAATTCCAAAAGTGTCGATATTTAT-TTAAATCTAA
65 TTTATAGACGCTATTACTTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTATATTAAA-CT-A
* * * * * *
22127 TCGATACTTTCAATATATTTGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCAT
128 TCGACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCGATTTTGTCAT
22192 ATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTATAAAATATCGACACTTTATAGGCG
193 ATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTATAAAATATCGACACTTTATAGGCG
* *
22256 CTATTACTTCTTCTATTTTAAATTTCTAAAAGTGTCGATACTTATTTAAATCTAATCGATACTTT
258 CTATTAATTCTTCTATTTTAAA-TTCCAAAAGTGTCGATACTTATTTAAATCTAATCGATACTTT
*
22321 CAACATATCCGGTAGCGCTTTACCG
322 CAACATATCCGGTAGCACTTTACCG
* *
22346 GTTTTGTCATATTTTTACCTGTTATATTGCTATGGATCAATACATTTTT
1 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
22395 TATTTGTATA
Statistics
Matches: 364, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
345 6 0.02
346 158 0.43
347 200 0.55
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (346 bp):
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATCAAGTATCGACACT
TTATAGACGCTATTACTTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTATATTAAACTATCG
ACACTTTCAACATATCTGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCGATTTTGTCATATT
TTTACCTGTTATATTGTTATGGATCGATACATTTTTTATAAAATATCGACACTTTATAGGCGCTA
TTAATTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTATTTAAATCTAATCGATACTTTCAAC
ATATCCGGTAGCACTTTACCG
Found at i:25799 original size:31 final size:30
Alignment explanation
Indices: 25734--25808 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
25724 ACCCCTAGAT
* * * *
25734 TTTAGACATAATATTAAATTCATCATAAAT
1 TTTAGATAAAATATTAAATTAATCATAAAC
* *
25764 TTTAGATGAAATATTAATTTAATCTATAAAC
1 TTTAGATAAAATATTAAATTAATC-ATAAAC
25795 TTTAGATAAAATAT
1 TTTAGATAAAATAT
25809 CAACATGATC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTAGATAAAATATTAAATTAATCATAAAC
Found at i:27932 original size:2 final size:2
Alignment explanation
Indices: 27925--27949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27915 TCATAAAATT
27925 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
27950 TACAAAATTG
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:28934 original size:19 final size:19
Alignment explanation
Indices: 28904--28959 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
28894 CGAAAAAATG
28904 AATAATAAATAATAATAAAA
1 AATAA-AAATAATAATAAAA
*
28924 AATAAAAATAATAATAACA
1 AATAAAAATAATAATAAAA
*
28943 TATAAAAATAAATAATA
1 AATAAAAAT-AATAATA
28960 TTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
AATAAAAATAATAATAAAA
Found at i:28940 original size:29 final size:30
Alignment explanation
Indices: 28897--28957 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
28887 CCTAAAACGA
28897 AAAAATGAATAATAA-ATAATAATAAA-AAAT
1 AAAAATGAATAATAACAT-ATAA-AAATAAAT
28927 AAAAAT-AATAATAACATATAAAAATAAAT
1 AAAAATGAATAATAACATATAAAAATAAAT
28956 AA
1 AA
28958 TATTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
30 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (30 bp):
AAAAATGAATAATAACATATAAAAATAAAT
Found at i:29061 original size:68 final size:68
Alignment explanation
Indices: 28987--29248 Score: 275
Period size: 67 Copynumber: 3.8 Consensus size: 68
28977 AATCATTTTT
** * *
28987 AAAACTATATATTATATACCTTTTCAAAAATATTTTCAAAAACTATAT-TAT-TTTTTGAAAA-G
1 AAAACTATATA-TATATATGTTTTC-AAAATGTTTT-AAAAACTATATATATATTTTTAAAAATG
29049 TTTTCA
63 TTTTCA
* *
29055 AAAACTATATATATATATGTTTTCCAAAATGTTTTTAAAACTATATATATAAGTTTTCAAAAATG
1 AAAACTATATATATATATGTTTT-CAAAATGTTTTAAAAACTATATATAT-A-TTTTTAAAAATG
29120 TTTTC-
63 TTTTCA
* * *
29125 AAAACTATATATATA-A-GTTTTCAAAATGTTTTTAAAACTATATAATATAAGTTTTCAAAATGT
1 AAAACTATATATATATATGTTTTCAAAATGTTTTAAAAACTATAT-ATAT-ATTTTTAAAAATGT
29188 TTTCA
64 TTTCA
*
29193 AAAACTATATTATATATATATATATTCAAAATGTTTTTAAAAACTATATATTATAT
1 AAAACTATA-TATATATATGT-T-TTCAAAATG-TTTTAAAAACTATATA-TATAT
29249 ATATTTTTTC
Statistics
Matches: 167, Mismatches: 12, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
66 10 0.06
67 58 0.35
68 32 0.19
69 7 0.04
70 24 0.14
71 7 0.04
72 1 0.01
73 11 0.07
74 17 0.10
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (68 bp):
AAAACTATATATATATATGTTTTCAAAATGTTTTAAAAACTATATATATATTTTTAAAAATGTTT
TCA
Found at i:29100 original size:34 final size:33
Alignment explanation
Indices: 28982--29248 Score: 236
Period size: 34 Copynumber: 7.6 Consensus size: 33
28972 TAAAAAATCA
* *
28982 TTTTTAAAACTATATATTATATACCTTTTCAAAAATA
1 TTTTTAAAACTATATA-TATAT--GTTTTC-AAAATG
* *
29019 TTTTCAAAAACTATAT-TAT-T-TTTTGAAAA-G
1 TTTT-TAAAACTATATATATATGTTTTCAAAATG
*
29049 TTTTCAAAAACTATATATATATATGTTTTCCAAAATG
1 TTTT-TAAAAC--TATATATATATGTTTT-CAAAATG
*
29086 TTTTTAAAACTATATATATAAGTTTTCAAAAATG
1 TTTTTAAAACTATATATATATGTTTTC-AAAATG
* *
29120 TTTTCAAAACTATATATATAAGTTTTCAAAATG
1 TTTTTAAAACTATATATATATGTTTTCAAAATG
*
29153 TTTTTAAAACTATATAATATAAGTTTTCAAAATG
1 TTTTTAAAACTATAT-ATATATGTTTTCAAAATG
* *
29187 TTTTCAAAAACTATATTATATATATATATATTCAAAATG
1 TTTT-TAAAAC--TA-TATATATATGT-T-TTCAAAATG
29226 TTTTTAAAAACTATATATTATAT
1 TTTTT-AAAACTATATA-TATAT
29249 ATATTTTTTC
Statistics
Matches: 200, Mismatches: 12, Indels: 36
0.81 0.05 0.15
Matches are distributed among these distances:
30 11 0.05
31 4 0.02
32 9 0.05
33 24 0.12
34 70 0.35
35 10 0.05
36 16 0.08
37 24 0.12
38 14 0.07
39 18 0.09
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (33 bp):
TTTTTAAAACTATATATATATGTTTTCAAAATG
Found at i:29276 original size:41 final size:39
Alignment explanation
Indices: 29178--29276 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
29168 AATATAAGTT
* * *
29178 TTCAAAATGTTTTCAAAAACTATATTATATATATATATA
1 TTCAAAACGATTTAAAAAACTATATTATATATATATATA
* * * * *
29217 TTCAAAATGTTTTTAAAAACTATA-TATTATATATATTTT
1 TTCAAAACGATTTAAAAAACTATATTA-TATATATATATA
29256 TTCAAGAACCGATTTAAAAAA
1 TTCAA-AA-CGATTTAAAAAA
29277 TAAAAAAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
38 2 0.04
39 38 0.75
40 2 0.04
41 9 0.18
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.42
Consensus pattern (39 bp):
TTCAAAACGATTTAAAAAACTATATTATATATATATATA
Found at i:29498 original size:23 final size:23
Alignment explanation
Indices: 29472--29516 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29462 AATTTAAATT
*
29472 ATTATGA-TTATAATATAGATTTG
1 ATTATGATTTAAAAT-TAGATTTG
29495 ATTATGATTTAAAATTAGATTT
1 ATTATGATTTAAAATTAGATTT
29517 TTGGTGTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (23 bp):
ATTATGATTTAAAATTAGATTTG
Found at i:30284 original size:20 final size:20
Alignment explanation
Indices: 30259--30296 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30249 ATAAAAGGTT
*
30259 GTTAGGGATGTTAGAAATCA
1 GTTAGGGAAGTTAGAAATCA
30279 GTTAGGGAAGTTAGAAAT
1 GTTAGGGAAGTTAGAAAT
30297 TGTTAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.32, T:0.29
Consensus pattern (20 bp):
GTTAGGGAAGTTAGAAATCA
Found at i:30476 original size:15 final size:16
Alignment explanation
Indices: 30450--30480 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
30440 TGGCTCCTAC
30450 TTTTGCCTCTTTTTCG
1 TTTTGCCTCTTTTTCG
30466 TTTTG-CTCTTTTTCG
1 TTTTGCCTCTTTTTCG
30481 CCTGATTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.00, C:0.23, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTTGCCTCTTTTTCG
Found at i:33363 original size:63 final size:63
Alignment explanation
Indices: 33268--33409 Score: 203
Period size: 63 Copynumber: 2.2 Consensus size: 63
33258 ACATTCAATA
** *
33268 TGCATCGATGCACTCTGATAAAATAAAAACATCGAATGCCATTAGTGCATCGATGCATAAGGAG
1 TGCATCGATGCAC-CCCATAAAATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAG
* ** * *
33332 TGCATCGATGCACCCCATTAAATAAAAACATCGAATGTGATTCGTGCACCGATGCATAAGTAG
1 TGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAG
33395 TGCATCGATGCACCC
1 TGCATCGATGCACCC
33410 GTTAAGGAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 57 0.81
64 13 0.19
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (63 bp):
TGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTAGTGCACCGATGCATAAGGAG
Found at i:33976 original size:18 final size:18
Alignment explanation
Indices: 33953--34025 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
33943 AGGGATAATC
33953 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
33971 AGTGGTTCTTTGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
33990 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
34009 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
34026 AATACTGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:37046 original size:20 final size:20
Alignment explanation
Indices: 36997--37046 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
36987 GAATAAAAGG
* *
36997 TTGTTAG-GGATGTTAGAAA
1 TTGTTAGAGGAAGTTAAAAA
*
37016 TCAGTTA-AGGAAGTTAAAAA
1 T-TGTTAGAGGAAGTTAAAAA
37036 TTGTTAGAGGA
1 TTGTTAGAGGA
37047 TTAGTTAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGTTAGAGGAAGTTAAAAA
Found at i:38323 original size:18 final size:18
Alignment explanation
Indices: 38297--38352 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
38287 TAAAAAATCC
38297 AAAATTAATATTTTATTA
1 AAAATTAATATTTTATTA
* ** *
38315 AAAAATAATGATTAAAATA
1 AAAATTAAT-ATTTTATTA
*
38334 AAAATTAATTTTTTATTA
1 AAAATTAATATTTTATTA
38352 A
1 A
38353 TATATCACAT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATTAATATTTTATTA
Found at i:54111 original size:2 final size:2
Alignment explanation
Indices: 54104--54159 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
54094 CATGTAACAA
54104 AT AT AT AT AT 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
* *
54146 AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT
54160 GTCCTTATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:54501 original size:23 final size:23
Alignment explanation
Indices: 54475--54535 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
54465 CTCGTATAAA
*
54475 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
54498 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
54521 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
54536 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:64785 original size:23 final size:23
Alignment explanation
Indices: 64719--64803 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
64709 TCGTATAAAT
64719 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
** **
64742 TTGTC-GTGAAG-GACCGTGTAGAA
1 TTG-CACCGAAGTG-CCACGTAGAA
*
64765 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
64788 TTGCATCGTAGTGCCA
1 TTGCACCGAAGTGCCA
64804 TATAATATGT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
22 2 0.04
23 42 0.91
24 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Done.