Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004907.1 Hibiscus syriacus cultivar Beakdansim tig00011039_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: 273424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:246295 original size:98 final size:98
Alignment explanation
Indices: 246189--246382 Score: 352
Period size: 98 Copynumber: 2.0 Consensus size: 98
246179 TAAAATTATA
*
246189 TATAAACTATATGTATATTATAAACTATATAATTATTATAAATTATATATATAAATTATATTTAT
1 TATAAACTATATGTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
246254 GTGAACTATATATATAAACTATGTATATAAAAT
66 GTGAACTATATATATAAACTATGTATATAAAAT
* * *
246287 TATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATGTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
246352 GTGAACTATATATATAAACTATGTATATAAA
66 GTGAACTATATATATAAACTATGTATATAAA
246383 CTATATATGT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (98 bp):
TATAAACTATATGTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTGAACTATATATATAAACTATGTATATAAAAT
Found at i:246402 original size:15 final size:13
Alignment explanation
Indices: 246170--246402 Score: 104
Period size: 13 Copynumber: 17.3 Consensus size: 13
246160 ATATAATATA
*
246170 TATATAATATAAAA
1 TATAT-ATATAAAC
246184 T-TATATATAAAC
1 TATATATATAAAC
* *
246196 TATATGTAT--AT
1 TATATATATAAAC
*
246207 TATAAACTATATAA-
1 TATATA-TATA-AAC
*
246221 T-TAT-TATAAAT
1 TATATATATAAAC
*
246232 TATATATATAAAT
1 TATATATATAAAC
* *
246245 TATATTTATGTGAAC
1 TATA--TATATAAAC
246260 TATATATATAAAC
1 TATATATATAAAC
* *
246273 TATGTATATAAAA
1 TATATATATAAAC
* *
246286 T-TATAAACTATA-
1 TATATATA-TAAAC
*
246298 TTTATATTATAAAC
1 TATATA-TATAAAC
246312 TATATAATTATTATAAGC
1 TATAT-A-TA-TA-AA-C
*
246330 TATATATATAAAT
1 TATATATATAAAC
* * *
246343 TATGTTTATGTGAAC
1 TA--TATATATAAAC
246358 TATATATATAAAC
1 TATATATATAAAC
*
246371 TATGTATATAAAC
1 TATATATATAAAC
246384 TATATATGTATAAAC
1 TATATA--TATAAAC
246399 TATA
1 TATA
246403 AAAAGTGTAT
Statistics
Matches: 168, Mismatches: 29, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
10 2 0.01
11 10 0.06
12 19 0.11
13 78 0.46
14 9 0.05
15 37 0.22
16 4 0.02
17 3 0.02
18 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:246413 original size:18 final size:18
Alignment explanation
Indices: 246390--246432 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
246380 AAACTATATA
246390 TGTATAAACTATAAAAAG
1 TGTATAAACTATAAAAAG
246408 TGTATAAACTATAAAAAG
1 TGTATAAACTATAAAAAG
*
246426 TATATAA
1 TGTATAA
246433 TTTATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (18 bp):
TGTATAAACTATAAAAAG
Found at i:246509 original size:79 final size:81
Alignment explanation
Indices: 246384--246549 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 81
246374 GTATATAAAC
* *
246384 TATATATGTATAAACTATAAAAAGTGTATAAACTATAAAAAGTATATAATTTATAAAATATTATT
1 TATATATATATAAACTAT-AAAAGTGTATAAACTATAAAAAGTATATAATTTATAAAATATAATT
246449 TATATTAATATAGTATA
65 TATATTAATATAGTATA
* * ***
246466 TATATATATATAAACTAT-ATA-TGTATAAACTATATAAAA-TATATAGTTTATATGTTATAATT
1 TATATATATATAAACTATAAAAGTGTATAAACTATA-AAAAGTATATAATTTATAAAATATAATT
*
246528 TATTTTAATATAGTATA
65 TATATTAATATAGTATA
246545 TATAT
1 TATAT
246550 GTATGCATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 52 0.69
80 6 0.08
82 17 0.23
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (81 bp):
TATATATATATAAACTATAAAAGTGTATAAACTATAAAAAGTATATAATTTATAAAATATAATTT
ATATTAATATAGTATA
Found at i:246661 original size:2 final size:2
Alignment explanation
Indices: 246656--246700 Score: 54
Period size: 2 Copynumber: 21.0 Consensus size: 2
246646 TAATTTACTT
*
246656 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA CTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
246699 TA
1 TA
246701 CATAGTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 33 0.87
3 5 0.13
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:246682 original size:23 final size:24
Alignment explanation
Indices: 246656--246700 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
246646 TAATTTACTT
246656 TATATAGTATATATATA-TATATA
1 TATATAGTATATATATACTATATA
*
246679 TATATAGTTTATATATACTATA
1 TATATAGTATATATATACTATA
246701 CATAGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TATATAGTATATATATACTATATA
Found at i:246705 original size:20 final size:20
Alignment explanation
Indices: 246669--246716 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
246659 ATAGTATATA
*
246669 TATATATA-TATATATAGTT
1 TATATATACTATACATAGTT
246688 TATATATACTATACATAGTT
1 TATATATACTATACATAGTT
*
246708 TATACATAC
1 TATATATAC
246717 ATTAGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATATACTATACATAGTT
Found at i:246811 original size:7 final size:7
Alignment explanation
Indices: 246718--246818 Score: 67
Period size: 7 Copynumber: 14.4 Consensus size: 7
246708 TATACATACA
246718 TTAGGGT
1 TTAGGGT
* *
246725 TTATGAT
1 TTAGGGT
*
246732 TTATGGT
1 TTAGGGT
*
246739 TTAGGAT
1 TTAGGGT
*
246746 TTAGTGT
1 TTAGGGT
246753 TTAGGGT
1 TTAGGGT
*
246760 TTAGAGT
1 TTAGGGT
***
246767 TTATTAT
1 TTAGGGT
246774 TTAGGGT
1 TTAGGGT
**
246781 TTAAAGT
1 TTAGGGT
*
246788 TTAGGAT
1 TTAGGGT
* *
246795 TTATGAT
1 TTAGGGT
246802 TTAGGGT
1 TTAGGGT
*
246809 TTAAGGT
1 TTAGGGT
246816 TTA
1 TTA
246819 TATAAATTAT
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 70 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:247061 original size:19 final size:20
Alignment explanation
Indices: 247048--247092 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
247038 AATTTTTCTA
247048 TTCCCTCTAAATTTCTCAAT
1 TTCCCTCTAAATTTCTCAAT
* *
247068 TTCCCTTTAAA-TTCCCAAT
1 TTCCCTCTAAATTTCTCAAT
247087 TTCCCT
1 TTCCCT
247093 ATATTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (20 bp):
TTCCCTCTAAATTTCTCAAT
Found at i:247767 original size:20 final size:20
Alignment explanation
Indices: 247742--247794 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
247732 TTTATTTGAG
247742 AATTTAGAGGGAAATTAAGA
1 AATTTAGAGGGAAATTAAGA
* **
247762 AATTTAGAAGGAAATTGGGA
1 AATTTAGAGGGAAATTAAGA
247782 AATTTAGAGGGAA
1 AATTTAGAGGGAA
247795 TATAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (20 bp):
AATTTAGAGGGAAATTAAGA
Found at i:247861 original size:32 final size:31
Alignment explanation
Indices: 247821--247882 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
247811 GTTGGTGCCA
*
247821 AATTTATAAAATT-AAAGTAAAAGTGACAATTG
1 AATTTATAAAATTGAAA-TAAAAATGA-AATTG
247853 AATTTATAAAATTGAAATAAAAATGAAATT
1 AATTTATAAAATTGAAATAAAAATGAAATT
247883 TTCACGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 21 0.75
33 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (31 bp):
AATTTATAAAATTGAAATAAAAATGAAATTG
Found at i:252903 original size:14 final size:14
Alignment explanation
Indices: 252884--252928 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
252874 AAAAAAATGT
252884 AATTTATTTTATAA
1 AATTTATTTTATAA
* *
252898 AATTTATCTTCTAA
1 AATTTATTTTATAA
*
252912 AATCTATTTTAATAA
1 AATTTATTTT-ATAA
252927 AA
1 AA
252929 CAAACATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTATTTTATAA
Found at i:263113 original size:23 final size:23
Alignment explanation
Indices: 263087--263134 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
263077 ATAAAATACA
* *
263087 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
**
263110 ATAATGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
263133 AT
1 AT
263135 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:263584 original size:23 final size:23
Alignment explanation
Indices: 263549--263621 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
263539 ATACTTTACA
*
263549 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
263572 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
263595 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
263618 ATAT
1 ATAT
263622 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:263654 original size:20 final size:20
Alignment explanation
Indices: 263605--263656 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
263595 ATATAAGCGC
*
263605 TACCTATTACATCATATTTT
1 TACCTATTATATCATATTTT
263625 TACCTATTATATCATATTTT
1 TACCTATTATATCATATTTT
*
263645 TACTTATTATAT
1 TACCTATTATAT
263657 TGAAAGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (20 bp):
TACCTATTATATCATATTTT
Found at i:264098 original size:23 final size:23
Alignment explanation
Indices: 264069--264131 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
264059 ATATAAGCAT
264069 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGC
* *
264092 TATCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGC
*
264115 TACCTATTACATCATAT
1 TACCTATTACATTATAT
264132 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGC
Found at i:264504 original size:25 final size:25
Alignment explanation
Indices: 264476--264540 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
264466 CACTCAAAGA
* *
264476 TGTATATACTTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
264501 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
264526 TGTACATACCTAAAT
1 TGTACATACCTAAAT
264541 TTAATGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:268319 original size:3 final size:3
Alignment explanation
Indices: 268311--268385 Score: 87
Period size: 3 Copynumber: 25.0 Consensus size: 3
268301 ACTTGTTTGG
* * *
268311 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
268359 ATC GTC GTC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
268386 GTCAGCTTCA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.25, C:0.33, G:0.07, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:268386 original size:12 final size:12
Alignment explanation
Indices: 268315--268389 Score: 96
Period size: 12 Copynumber: 6.2 Consensus size: 12
268305 GTTTGGATCA
*
268315 TCATCATCATCA
1 TCATCATCATCG
*
268327 TCATCATCATCA
1 TCATCATCATCG
268339 TCATCATCATCG
1 TCATCATCATCG
* *
268351 TCAGCTTCATCG
1 TCATCATCATCG
*
268363 TCGTCATCATCG
1 TCATCATCATCG
*
268375 TCATCTTCATCG
1 TCATCATCATCG
268387 TCA
1 TCA
268390 GCTTCATCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:268394 original size:12 final size:12
Alignment explanation
Indices: 268345--268397 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
268335 ATCATCATCA
268345 TCATCGTCAGCT
1 TCATCGTCAGCT
*
268357 TCATCGTC-GTCA
1 TCATCGTCAG-CT
*
268369 TCATCGTCATCT
1 TCATCGTCAGCT
268381 TCATCGTCAGCT
1 TCATCGTCAGCT
268393 TCATC
1 TCATC
268398 TTCATTGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 1 0.03
12 34 0.97
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (12 bp):
TCATCGTCAGCT
Found at i:270866 original size:397 final size:400
Alignment explanation
Indices: 269853--272007 Score: 3866
Period size: 397 Copynumber: 5.4 Consensus size: 400
269843 TTTAAATTAG
269853 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
269918 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
269983 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
* * * *
270048 AAAACTATCGATACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAATCG
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
270113 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
*
270178 TGGGATCGACACTTTTTATATAT-GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCT
326 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
*
270242 GGACCAAAAC
391 GGACCAAAAA
270252 TATCGACAC-AACT-AAAAAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
270313 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
270378 TCGACACATTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
270443 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCA
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
270508 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGA-GTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
* * *
270572 TGGGATCGAAACTTTGTATATATGGATCGACACTTTATGGTTGCACCCT-GTTTCCATTCATTCT
326 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
*
270636 GGACC-AAAC
391 GGACCAAAAA
270645 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
270710 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTCTACTTTTGGTTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
270775 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTAGACC
131 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
270840 AAAAATATCGACACAAACTAAAAAAGTGTCAACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
270905 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
270970 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
326 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
271035 GGACCAAAAA
391 GGACCAAAAA
* *
271045 TATCGACACAAACTAAAAAAGTGTTGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271110 CTTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
271174 TCGACAC-TTTT-TATATGGATCGATACTTTATGGTTGCATCCTGTTTT-CATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
271236 AAAAATATCAACACAAACT-AAAAAGTGTCGACAC-TTA-TTAGACATATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
*
271298 GTATACTTGTATCGGTT--ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
271361 T-GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
326 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
271425 GGACCAAAAA
391 GGACCAAAAA
* *
271435 TATCGACACAAACTAAAAAAGTGTTGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271500 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
271565 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCATCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
271630 AAAAATATCG--ACAAACTAAAAAAG-GTCGACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
*
271692 GTATACTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
261 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
271757 TGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTC
326 TGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTC
271822 TGGACCAAAAA
390 TGGACCAAAAA
* * *
271833 TATCGATACAAACTAAAAAAGTGTAGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271898 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
271963 TCGACACTTTTTTATATATGGTTCGACACTTTATGGTTGCACCCT
131 TCGACAC-TTTTTATATATGGATCGATACTTTATGGTTGCACCCT
272008 TAATGTGTAT
Statistics
Matches: 1699, Mismatches: 37, Indels: 40
0.96 0.02 0.02
Matches are distributed among these distances:
390 153 0.09
391 103 0.06
392 19 0.01
393 99 0.06
394 118 0.07
395 333 0.20
396 81 0.05
397 340 0.20
398 256 0.15
399 116 0.07
400 81 0.05
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (400 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAATATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCT
GGACCAAAAA
Found at i:270903 original size:200 final size:200
Alignment explanation
Indices: 269853--272007 Score: 3839
Period size: 200 Copynumber: 10.9 Consensus size: 200
269843 TTTAAATTAG
269853 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
269918 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
269983 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
270048 AAAAC
196 AAAAA
* * *
270053 TATCGATACAAACTAAAAAAGTGTCGACATATTATTTAGACATATTCTCTCATAAAATCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
270118 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
270183 TCGACACTTTTTATATAT-GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
270247 AAAAC
196 AAAAA
270252 TATCGACAC-AACT-AAAAAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
270313 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
270378 TCGACACATTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
270443 AAAAA
196 AAAAA
*
270448 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
270513 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGA-GTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
270577 TCGAAACTTTGTATATATGGATCGACACTTTATGGTTGCACCCTG-TTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
*
270641 -AAAC
196 AAAAA
270645 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
270710 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTCTACTTTTGGTTTTCGATGTTTATGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
270775 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCACCCTGTTTTCCATTCATTCTAGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
270840 AAAAA
196 AAAAA
*
270845 TATCGACACAAACTAAAAAAGTGTCAACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
270910 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
270975 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
271040 AAAAA
196 AAAAA
* *
271045 TATCGACACAAACTAAAAAAGTGTTGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271110 CTTGTACCGGTTAGA-TGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
271174 TCGACAC-TTTT-TATATGGATCGATACTTTATGGTTGCATCCTGTTTT-CATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
271236 AAAAA
196 AAAAA
*
271241 TATCAACACAAACT-AAAAAGTGTCGACAC-TTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
271303 CTTGTATCGGTT--ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT-GGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
271365 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
271430 AAAAA
196 AAAAA
* *
271435 TATCGACACAAACTAAAAAAGTGTTGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271500 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
271565 TCGACACTTTTTATATATGGATCGATACTTTATGGTTGCATCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
271630 AAAAA
196 AAAAA
271635 TATCG--ACAAACTAAAAAAG-GTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
271697 CTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
271762 TCGACACTTTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGAC
131 TCGACAC-TTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
271827 CAAAAA
195 CAAAAA
* * *
271833 TATCGATACAAACTAAAAAAGTGTAGACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
271898 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
271963 TCGACACTTTTTTATATATGGTTCGACACTTTATGGTTGCACCCT
131 TCGACAC-TTTTTATATATGGATCGACACTTTATGGTTGCACCCT
272008 TAATGTGTAT
Statistics
Matches: 1874, Mismatches: 59, Indels: 43
0.95 0.03 0.02
Matches are distributed among these distances:
191 11 0.01
192 49 0.03
193 74 0.04
194 36 0.02
195 125 0.07
196 95 0.05
197 338 0.18
198 186 0.10
199 232 0.12
200 579 0.31
201 149 0.08
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:272089 original size:18 final size:18
Alignment explanation
Indices: 272066--272126 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
272056 TCTCATTCAT
*
272066 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
272084 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
272103 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
272122 AATTA
1 AATTA
272127 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:272102 original size:19 final size:19
Alignment explanation
Indices: 272078--272126 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
272068 TTATATTCAC
272078 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
272097 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
272116 ATACAAAATTA
1 ATACAAAATTA
272127 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:272714 original size:4 final size:4
Alignment explanation
Indices: 272705--272733 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
272695 AATGTCCTTT
272705 CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA C
272734 CAATCTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Done.