Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008308.1 Hibiscus syriacus cultivar Beakdansim tig00110998_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: 1044366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:240342 original size:74 final size:72
Alignment explanation
Indices: 240116--240360 Score: 224
Period size: 74 Copynumber: 3.3 Consensus size: 72
240106 TCAGACTTGT
* * * *
240116 AAAGGGGAGTCATCCAAACAATCAAGACTTCTTGAACCAT--GAAGGGGAATTATCTCATTTAAC
1 AAAGGGGAGTCATCCAAACAATCAAGACTGCTT-AA-AATGCGAAGGGGAGTTATCTCATTTGAC
*
240179 CTAAGCCCAC
64 TTAA-CCCAC
* * * * ** * * *
240189 AAAGGGAAGTCATCCAAATAATTAAGAATAGCTTAAACCGCGAAGGAGAGTTGTCTCACTTGACT
1 AAAGGGGAGTCATCCAAACAATCAAGACT-GCTTAAAATGCGAAGGGGAGTTATCTCATTTGACT
*
240254 TAGACCCAT
65 TA-ACCCAC
* ** *
240263 GAAGGGGAGTCATCCAAACAATCAAGACTGGCTTAAAATGCGAAGGGGAGTTATCTTGTTTGGAT
1 AAAGGGGAGTCATCCAAACAATCAAGACT-GCTTAAAATGCGAAGGGGAGTTATCTCATTT-GAC
*
240328 TTAACCCGC
64 TTAACCCAC
*
240337 AAAGGGGAGTCATCCAAAGAATCA
1 AAAGGGGAGTCATCCAAACAATCA
240361 TTCATTTGGA
Statistics
Matches: 134, Mismatches: 33, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
73 27 0.20
74 101 0.75
75 6 0.04
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (72 bp):
AAAGGGGAGTCATCCAAACAATCAAGACTGCTTAAAATGCGAAGGGGAGTTATCTCATTTGACTT
AACCCAC
Found at i:243235 original size:37 final size:38
Alignment explanation
Indices: 243170--243279 Score: 113
Period size: 37 Copynumber: 2.9 Consensus size: 38
243160 GCATGTCACA
* *
243170 TGACTTAAACCCGCAAAGGGAAAATCATCTGAAGAA-CT
1 TGACTTAAACCCGCGAA-GGAAAGTCATCTGAAGAACCT
* *
243208 TGACTTAAACTCGCGAAGGAAAGTCATC-CAATGAACCT
1 TGACTTAAACCCGCGAAGGAAAGTCATCTGAA-GAACCT
243246 T-ACTTAAACCCGCGAAAGG-AAGTCA-CATGAAGAA
1 TGACTTAAACCCGCG-AAGGAAAGTCATC-TGAAGAA
243280 TCATGTTGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
36 3 0.05
37 34 0.56
38 24 0.39
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (38 bp):
TGACTTAAACCCGCGAAGGAAAGTCATCTGAAGAACCT
Found at i:243404 original size:73 final size:74
Alignment explanation
Indices: 243297--243575 Score: 312
Period size: 74 Copynumber: 3.8 Consensus size: 74
243287 GCATGACTCA
* * *
243297 AAACCGTGAAGGGAAGTCATCTCGCTTGACTTAGACCTGCGAAGGGGAGTCATCCAAATAATCAA
1 AAACCGTGAAGGGGAGTCATCTCACTTAACTTAGACCTGCGAAGGGGAGTCATCCAAATAATCAA
243362 GACT-GATT
66 GACTGGATT
** * *
243370 AAACCGTGAAGGGGAGTTGTCTCATTTAACTTAGACCCT-TGAAGGGGAGTCATCCAAATAATCA
1 AAACCGTGAAGGGGAGTCATCTCACTTAACTTAGA-CCTGCGAAGGGGAGTCATCCAAATAATCA
*
243434 AGATTGGATT
65 AGACTGGATT
* ** *
243444 AAACCGTGAAGGGGAGTCGTCTCACTTAACTTAGACCTGC-ATAGAAGAGTCATCCAAAGAATCA
1 AAACCGTGAAGGGGAGTCATCTCACTTAACTTAGACCTGCGA-AGGGGAGTCATCCAAATAATCA
*
243508 AGACTGGCTT
65 AGACTGGATT
** * *** ** * *
243518 AAACTATAAAGGGGAGTCATCTTGTTTGGCTTAAACCCGCGAAGGGGAGTCATCCAAA
1 AAACCGTGAAGGGGAGTCATCTCACTTAACTTAGACCTGCGAAGGGGAGTCATCCAAA
243576 GATGCCTTCA
Statistics
Matches: 172, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
73 61 0.35
74 110 0.64
75 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (74 bp):
AAACCGTGAAGGGGAGTCATCTCACTTAACTTAGACCTGCGAAGGGGAGTCATCCAAATAATCAA
GACTGGATT
Found at i:243980 original size:200 final size:199
Alignment explanation
Indices: 243634--244254 Score: 640
Period size: 200 Copynumber: 3.1 Consensus size: 199
243624 GAATTATATT
* * * * * * * * *
243634 TCAACCAAATATTTCAAGTTCGATTCCATTCAACTCGAA-AGCACATTAATCGCATGGTAGCAGT
1 TCAACCAAATCTTTCAAGTTTGATTACACTCAAATC-AAGAGCACATTGACCACATGGTAGCAGC
* * **
243698 GAGTAACTACCTTCCAGTTAAAATTCAAACAGAGGTCTTTAAGCAAACAAGAAGACCCAATTTGG
65 GAGGAACTACCTTCCAGTTAAAATTCAAACAGAGGTCTTTAAGCAAAGAAGAAGACCCAGGTT-G
* * * *
243763 ATGTGACTTGGCAACAAAGAACCATTTCTCATCCATATTTCAACATAGCTTAAATAAAGAAGAGC
129 ATGTGATTTGGCAACAAAGAACCATTTCTCACCCAGATTTCAACATAGCTTAAATCAAGAAGAGC
243828 TATTTG
194 TATTTG
* * * ** *
243834 TCGACCAAATCTTTCAAGTTTGATTTCACTCAACTCAAGTTCACGTTGACCACATGGTAGCAGCG
1 TCAACCAAATCTTTCAAGTTTGATTACACTCAAATCAAGAGCACATTGACCACATGGTAGCAGCG
* * * * *
243899 AGGGACTACCTTCCAGTCAAAATTCAAACTGAGGTCTTTAAGCCAAGAA-AACGACTCAGGTTGA
66 AGGAACTACCTTCCAGTTAAAATTCAAACAGAGGTCTTTAAGCAAAGAAGAA-GACCCAGGTTG-
* * * * * ** * *
243963 ATGCGATTTGGCAACAAAAAACCACTTCCCAGCCAGATTTTGACATAGATTAAATCGAGAAGAGC
129 ATGTGATTTGGCAACAAAGAACCATTTCTCACCCAGATTTCAACATAGCTTAAATCAAGAAGAGC
244028 TATCTT-
194 TAT-TTG
* ** *
244034 TCAACCAAAGCTTTCAAGTTTGATTACACTCAAATCAAGAGCACATTGACTGCATGGTAGCAACG
1 TCAACCAAATCTTTCAAGTTTGATTACACTCAAATCAAGAGCACATTGACCACATGGTAGCAGCG
* * *
244099 AGGAACTACTTTTCAGTTAAAATTCAAACCA-AGGTCTTTAAGCTAAGAAGAAGACCCAGGTTTG
66 AGGAACTACCTTCCAGTTAAAATTCAAA-CAGAGGTCTTTAAGCAAAGAAGAAGACCCAGG-TTG
* * * * * * *
244163 TTGTGATTTGGAAACAATGAACCACTTT-TTAGCCCAGATTTCAACATAACTTAAGTCAAGAAAA
129 ATGTGATTTGGCAACAAAGAACCA-TTTCTCA-CCCAGATTTCAACATAGCTTAAATCAAGAAGA
*
244227 GCTATATG
192 GCTATTTG
* *
244235 TCAACCAAATATTTAAAGTT
1 TCAACCAAATCTTTCAAGTT
244255 CAACTCTACG
Statistics
Matches: 341, Mismatches: 70, Indels: 19
0.79 0.16 0.04
Matches are distributed among these distances:
199 5 0.01
200 280 0.82
201 56 0.16
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (199 bp):
TCAACCAAATCTTTCAAGTTTGATTACACTCAAATCAAGAGCACATTGACCACATGGTAGCAGCG
AGGAACTACCTTCCAGTTAAAATTCAAACAGAGGTCTTTAAGCAAAGAAGAAGACCCAGGTTGAT
GTGATTTGGCAACAAAGAACCATTTCTCACCCAGATTTCAACATAGCTTAAATCAAGAAGAGCTA
TTTG
Found at i:245249 original size:10 final size:10
Alignment explanation
Indices: 245234--245258 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
245224 TTTTTTGTTC
245234 TTCTTCTTCT
1 TTCTTCTTCT
245244 TTCTTCTTCT
1 TTCTTCTTCT
245254 TTCTT
1 TTCTT
245259 TTTCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:245249 original size:13 final size:14
Alignment explanation
Indices: 245231--245259 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
245221 CGATTTTTTG
245231 TTCTTCTTC-TTCT
1 TTCTTCTTCTTTCT
245244 TTCTTCTTCTTTCT
1 TTCTTCTTCTTTCT
245258 TT
1 TT
245260 TTCCTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:245391 original size:19 final size:18
Alignment explanation
Indices: 245364--245407 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
245354 AAATCGATAA
* *
245364 TTTTTTTTTTATTTTTCT
1 TTTTTTTTTTATCTTTAT
245382 TTTATTTTTTTATCTTTAT
1 TTT-TTTTTTTATCTTTAT
245401 TTTTTTT
1 TTTTTTT
245408 GTCAATCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTTATCTTTAT
Found at i:245397 original size:15 final size:15
Alignment explanation
Indices: 245365--245406 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
245355 AATCGATAAT
* *
245365 TTTTTTTTTATTTTTC
1 TTTTATTTT-TTTATC
245381 TTTTATTTTTTTATC
1 TTTTATTTTTTTATC
245396 -TTTATTTTTTT
1 TTTTATTTTTTT
245407 TGTCAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTATTTTTTTATC
Found at i:246218 original size:89 final size:93
Alignment explanation
Indices: 246113--246295 Score: 304
Period size: 92 Copynumber: 2.0 Consensus size: 93
246103 TATTTTTTAT
*
246113 TTATCTTGCAGTATCTTTAAGT-TTTTTT-ATTTCAAA-TTTAGTGT-AAATTTATTTTCATGCA
1 TTATCTTGCAGCATCTTTAAGTGTTTTTTAATTTCAAATTTTAGTGTAAAATTT-TTTTCATGCA
246174 TGTATTTGAATTT-TTTTTTGTGTTCTTG
65 TGTATTTGAATTTGTTTTTTGTGTTCTTG
*
246202 TTATCTTGCAGCATCTTTAAGTGTTTTTTAATTTCAAATTTTAGTGTAAAATTTTTTTCATGTAT
1 TTATCTTGCAGCATCTTTAAGTGTTTTTTAATTTCAAATTTTAGTGTAAAATTTTTTTCATGCAT
246267 GTATTTGAATTTGTTTTTTGTGTTCTTG
66 GTATTTGAATTTGTTTTTTGTGTTCTTG
246295 T
1 T
246296 GACCCTTTTA
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
89 21 0.24
90 6 0.07
91 8 0.09
92 30 0.34
93 22 0.25
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (93 bp):
TTATCTTGCAGCATCTTTAAGTGTTTTTTAATTTCAAATTTTAGTGTAAAATTTTTTTCATGCAT
GTATTTGAATTTGTTTTTTGTGTTCTTG
Found at i:246829 original size:3 final size:3
Alignment explanation
Indices: 246821--246874 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
246811 TTATTTTGAT
* *
246821 TTA TTA TTA TAA TTA TT- TTA TTA -TA TTA TTA -TA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
246866 TTA TTA TTA
1 TTA TTA TTA
246875 AATAATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:246836 original size:22 final size:22
Alignment explanation
Indices: 246811--246874 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
246801 TTTTTGTTTT
246811 TTATTTTGATT-TATTATTATAA
1 TTATTTT-ATTATATTATTATAA
246833 TTATTTTATTATATTATTAT-A
1 TTATTTTATTATATTATTATAA
*
246854 TTAATATTATTATTATTATTA
1 TT-ATTTTATTA-TATTATTA
246875 AATAATAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 6 0.16
22 24 0.63
23 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTTTATTATATTATTATAA
Found at i:246842 original size:17 final size:17
Alignment explanation
Indices: 246820--246870 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
246810 TTTATTTTGA
*
246820 TTTATTATTATAATTAT
1 TTTATTATTATTATTAT
246837 TTTATTA-TATTATTAT
1 TTTATTATTATTATTAT
* *
246853 ATTAATATTATTATTAT
1 TTTATTATTATTATTAT
246870 T
1 T
246871 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTATTATTATTAT
Found at i:246843 original size:14 final size:14
Alignment explanation
Indices: 246824--246872 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
246814 TTTTGATTTA
246824 TTATTATAATTATT
1 TTATTATAATTATT
246838 TTATTAT-ATTATT
1 TTATTATAATTATT
*
246851 ATATTA-ATATTATT
1 TTATTATA-ATTATT
246865 ATTATTAT
1 -TTATTAT
246873 TAAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 11 0.38
14 13 0.45
15 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATAATTATT
Found at i:246880 original size:22 final size:23
Alignment explanation
Indices: 246821--246881 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
246811 TTATTTTGAT
* *
246821 TTATTATTATAATTATTTTATTA
1 TTATTATTATAATAATATTATTA
*
246844 -TATTATTATATTAATATTATTA
1 TTATTATTATAATAATATTATTA
246866 TTATTATTA-AATAATA
1 TTATTATTATAATAATA
246882 AATAATTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATTATTATAATAATATTATTA
Found at i:248353 original size:25 final size:27
Alignment explanation
Indices: 248310--248371 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
248300 TTTTCTGATA
248310 TTTTTAGATAAATAAATAT-TT-T-TAT
1 TTTTTA-ATAAATAAATATATTATCTAT
*
248335 TTTTTAATAAATTATATATATTAATCTAT
1 TTTTTAATAAA-TAAATATATT-ATCTAT
248364 TTTTTAAT
1 TTTTTAAT
248372 TATTTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 5 0.16
25 12 0.39
26 2 0.06
28 1 0.03
29 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTAATAAATAAATATATTATCTAT
Found at i:249051 original size:15 final size:15
Alignment explanation
Indices: 249027--249059 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
249017 TTATATATAC
249027 TTATTATTATTTTTA
1 TTATTATTATTTTTA
*
249042 TTATTTTTATTTTTA
1 TTATTATTATTTTTA
249057 TTA
1 TTA
249060 AATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTATTTTTA
Found at i:252334 original size:15 final size:15
Alignment explanation
Indices: 252314--252345 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
252304 GATCAATACC
252314 TTTTACATACATTCA
1 TTTTACATACATTCA
252329 TTTTACATACATTCA
1 TTTTACATACATTCA
252344 TT
1 TT
252346 ATTCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTACATACATTCA
Found at i:261496 original size:113 final size:113
Alignment explanation
Indices: 261298--261882 Score: 541
Period size: 113 Copynumber: 5.0 Consensus size: 113
261288 GAAAATATTC
261298 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
261363 AAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTTTGCCT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCAT
261411 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
261476 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTTGCAT
* *** * * * * *
261525 GAATTCATCGTTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
261590 -AGGAAGAATAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTGCAT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCAT
* *** * *
261636 GACTATATCACA-GAAGGAGATAGATCATTATCAACTTTTCCAGAGGAAGAGTTCATAATGAGAA
1 G---A-ATC-CATTACTCA-ATGGATCA--A-C-A--TTACCAGAGG-A-AGTTCATAATGAGAA
* *
261700 GAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAGCTTGTTCAACCGTTTGTTTG-A
52 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC---T-TTTGCA
261764 T
113 T
* ** * * ** * * ** *
261765 TATATCCCAGAAAGAGATAAATCAACATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTT
1 GA-AT-CC---ATTA-CTCAAT--GGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTC
**
261830 ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAAACCTTTTG
58 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTTG
261883 TTAGATCATC
Statistics
Matches: 406, Mismatches: 36, Indels: 53
0.82 0.07 0.11
Matches are distributed among these distances:
111 7 0.02
113 140 0.34
114 64 0.16
115 2 0.00
116 9 0.02
118 1 0.00
119 1 0.00
120 4 0.01
121 1 0.00
122 9 0.02
123 34 0.08
124 60 0.15
125 40 0.10
126 13 0.03
127 1 0.00
129 4 0.01
130 9 0.02
131 2 0.00
132 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (113 bp):
GAATCCATTACTCAATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCAT
Found at i:261703 original size:124 final size:122
Alignment explanation
Indices: 261543--261880 Score: 523
Period size: 124 Copynumber: 2.7 Consensus size: 122
261533 CGTTCGATGG
261543 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAAGTTCATA
* * **
261608 ATGAGAAGAGCTTGTTCAACCTTTGCATGACTATATCACAGAAGGAGATAGATCATT
66 ATGAGAAGAGCTTGTTCAACCTTTGCATGACTATATCACAGAAAGAGATAAATCAAC
*
261665 ATCAACTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTC
1 ATCAACTTTTCCAGA-GAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAATAAGTTC
** * *
261730 ATAATGAGAAGAGCTTGTTCAACCGTTTGTTTGATTATATCCCAGAAAGAGATAAATCAAC
63 ATAATGAGAAGAGCTTGTTCAACC-TTTGCATGACTATATCACAGAAAGAGATAAATCAAC
* *
261791 ATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAAGTTCATA
*
261856 ATGAGAAGAGTTTGTTCAAACCTTT
66 ATGAGAAGAGCTTGTTC-AACCTTT
261881 TGTTAGATCA
Statistics
Matches: 198, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
122 15 0.08
123 39 0.20
124 60 0.30
125 41 0.21
126 43 0.22
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAATAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTGCATGACTATATCACAGAAAGAGATAAATCAAC
Found at i:262111 original size:3 final size:3
Alignment explanation
Indices: 262103--262143 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
262093 TTATTTTGAT
* *
262103 TTA TTA TTA TAA TTA TTT TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
262144 AATAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:262130 original size:23 final size:22
Alignment explanation
Indices: 262093--262142 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
262083 CATTCGTTTT
262093 TTATTTTGATTTATTATTATAA
1 TTATTTTGATTTATTATTATAA
* *
262115 TTATTTTTATTATATTATTATTA
1 TTATTTTGATT-TATTATTATAA
262138 TTATT
1 TTATT
262143 AAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATTTTGATTTATTATTATAA
Found at i:263050 original size:8 final size:8
Alignment explanation
Indices: 263037--263137 Score: 91
Period size: 8 Copynumber: 14.1 Consensus size: 8
263027 TTGCAGCCTT
263037 GATGCATG
1 GATGCATG
263045 GATGCATG
1 GATGCATG
263053 G-T--A-G
1 GATGCATG
*
263057 GATGCATC
1 GATGCATG
263065 GATGCATG
1 GATGCATG
263073 GATGCAT-
1 GATGCATG
263080 G--GCA-G
1 GATGCATG
*
263085 GATGCATC
1 GATGCATG
263093 GATGCATG
1 GATGCATG
263101 GATGCAT-
1 GATGCATG
263108 G--GCA-G
1 GATGCATG
*
263113 GATGCATC
1 GATGCATG
263121 GATGCATG
1 GATGCATG
263129 GATGCATG
1 GATGCATG
263137 G
1 G
263138 TAGGATGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
4 2 0.03
5 10 0.13
7 10 0.13
8 53 0.71
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.23
Consensus pattern (8 bp):
GATGCATG
Found at i:263077 original size:28 final size:28
Alignment explanation
Indices: 263037--263154 Score: 218
Period size: 28 Copynumber: 4.2 Consensus size: 28
263027 TTGCAGCCTT
*
263037 GATGCATGGATGCATGGTAGGATGCATC
1 GATGCATGGATGCATGGCAGGATGCATC
263065 GATGCATGGATGCATGGCAGGATGCATC
1 GATGCATGGATGCATGGCAGGATGCATC
263093 GATGCATGGATGCATGGCAGGATGCATC
1 GATGCATGGATGCATGGCAGGATGCATC
*
263121 GATGCATGGATGCATGGTAGGATGCATC
1 GATGCATGGATGCATGGCAGGATGCATC
263149 GATGCA
1 GATGCA
263155 CTAAGTGCAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 88 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (28 bp):
GATGCATGGATGCATGGCAGGATGCATC
Found at i:263147 original size:20 final size:20
Alignment explanation
Indices: 263037--263129 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
263027 TTGCAGCCTT
263037 GATGCATGGATGCATGGTAG
1 GATGCATGGATGCATGGTAG
*
263057 GATGCATCGATGCATGG-ATG
1 GATGCATGGATGCATGGTA-G
* *
263077 CATGGCA-GGATGCA---T-C
1 GAT-GCATGGATGCATGGTAG
*
263093 GATGCATGGATGCATGGCAG
1 GATGCATGGATGCATGGTAG
*
263113 GATGCATCGATGCATGG
1 GATGCATGGATGCATGG
263130 ATGCATGGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
15 3 0.05
16 9 0.16
19 1 0.02
20 41 0.72
21 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.23
Consensus pattern (20 bp):
GATGCATGGATGCATGGTAG
Found at i:263152 original size:20 final size:20
Alignment explanation
Indices: 263065--263154 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
263055 AGGATGCATC
*
263065 GATGCATGGATGCATGGCAG
1 GATGCATGGATGCATGGTAG
*
263085 GATGCATCGATGCATGG-ATG
1 GATGCATGGATGCATGGTA-G
* *
263105 CATGGCA-GGATGCA---T-C
1 GAT-GCATGGATGCATGGTAG
263121 GATGCATGGATGCATGGTAG
1 GATGCATGGATGCATGGTAG
*
263141 GATGCATCGATGCA
1 GATGCATGGATGCA
263155 CTAAGTGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
15 3 0.05
16 9 0.16
19 2 0.04
20 38 0.69
21 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.22
Consensus pattern (20 bp):
GATGCATGGATGCATGGTAG
Found at i:263210 original size:20 final size:20
Alignment explanation
Indices: 263059--263210 Score: 51
Period size: 20 Copynumber: 8.1 Consensus size: 20
263049 CATGGTAGGA
*
263059 TGCATCGATGCATGGATGCAT
1 TGCAT-GATGCATCGATGCAT
* *
263080 GGCAGGATGCATCGATGCA-
1 TGCATGATGCATCGATGCAT
* *
263099 TG---GATGCATGGCA-GGA-
1 TGCATGATGCATCG-ATGCAT
*
263115 TGCATCGATGCATGGATGCAT
1 TGCAT-GATGCATCGATGCAT
* * * *
263136 GGTAGGATGCATCGATGCAC
1 TGCATGATGCATCGATGCAT
* *
263156 T--AAG-TGCATTCGATG-TT
1 TGCATGATGCA-TCGATGCAT
* *
263173 TG-A-G-TGCATGGATACAT
1 TGCATGATGCATCGATGCAT
263190 TGCATGATGCATCGATGCAT
1 TGCATGATGCATCGATGCAT
263210 T
1 T
263211 AGTGCAGGTG
Statistics
Matches: 97, Mismatches: 21, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
16 16 0.16
17 14 0.14
18 10 0.10
19 3 0.03
20 49 0.51
21 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (20 bp):
TGCATGATGCATCGATGCAT
Found at i:263354 original size:29 final size:29
Alignment explanation
Indices: 263322--263384 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
263312 GAAACCTTTT
263322 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
263352 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
263382 AAA
1 AAA
263385 CATTTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:263380 original size:30 final size:29
Alignment explanation
Indices: 263333--263391 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
263323 AAACTTTGAA
*
263333 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
263362 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
263392 CCTTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:265190 original size:13 final size:14
Alignment explanation
Indices: 265172--265200 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
265162 TCTTCTTGTT
265172 TTTCTTCA-CTTCC
1 TTTCTTCATCTTCC
265185 TTTCTTCATCTTCC
1 TTTCTTCATCTTCC
265199 TT
1 TT
265201 CACCATCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCTTCATCTTCC
Found at i:266689 original size:20 final size:19
Alignment explanation
Indices: 266603--266693 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
266593 GTTACAGCCT
* *
266603 TGATGCATGGATGCATGGCA
1 TGATGCATCGATGCATTG-A
* *
266623 GGATGCATCGATGCACT-A
1 TGATGCATCGATGCATTGA
* *
266641 AG-TGCATTCGATG-TTTGA
1 TGATGCA-TCGATGCATTGA
*
266659 -G-TGCATGGATGCATTGCA
1 TGATGCATCGATGCATTG-A
266677 TGATGCATCGATGCATT
1 TGATGCATCGATGCATT
266694 AGTGCAGGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 10 0.18
19 1 0.02
20 26 0.47
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
TGATGCATCGATGCATTGA
Found at i:266837 original size:29 final size:29
Alignment explanation
Indices: 266805--266867 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
266795 GAAACCTTTT
266805 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
266835 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
266865 AAA
1 AAA
266868 CATTTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:266863 original size:30 final size:29
Alignment explanation
Indices: 266816--266874 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
266806 AAACTTTGAA
*
266816 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
266845 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
266875 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:268206 original size:17 final size:17
Alignment explanation
Indices: 268184--268217 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
268174 GACTTTTAAG
268184 AAAAATA-ATTATATTTT
1 AAAAATATATT-TATTTT
268201 AAAAATATATTTATTTT
1 AAAAATATATTTATTTT
268218 TCAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATATATTTATTTT
Found at i:272180 original size:21 final size:22
Alignment explanation
Indices: 272145--272191 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
272135 AAAAGTGTTT
* *
272145 ATATAAAATAATATATTTACAA
1 ATATAAAATAATATAATTAAAA
*
272167 ATATAATA-AATATAATTAAAA
1 ATATAAAATAATATAATTAAAA
272188 ATAT
1 ATAT
272192 TTTAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAAATAATATAATTAAAA
Found at i:272693 original size:24 final size:21
Alignment explanation
Indices: 272664--272714 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 21
272654 ATAAAAACTC
272664 AAATAATTTGACTTAAACTTTATA
1 AAATAATTTGAC-TAAA--TTATA
*
272688 AAATAAATTTTACTAAATTATA
1 AAAT-AATTTGACTAAATTATA
272710 AAATA
1 AAATA
272715 TCTATCCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
24 8 0.32
25 7 0.28
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATAATTTGACTAAATTATA
Found at i:275070 original size:15 final size:15
Alignment explanation
Indices: 275046--275080 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
275036 CGGTGACGCA
*
275046 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
275061 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
275076 GAGGA
1 GAGGA
275081 TGATGAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:280150 original size:2 final size:2
Alignment explanation
Indices: 280138--280180 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
280128 TGGTTTTTCA
280138 AT AT A- 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
280179 AT
1 AT
280181 CTGACAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:284944 original size:15 final size:15
Alignment explanation
Indices: 284924--284955 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
284914 TCTGACCCGA
284924 TCAGGTCGAGTCGGG
1 TCAGGTCGAGTCGGG
*
284939 TCAGGTCGGGTCGGG
1 TCAGGTCGAGTCGGG
284954 TC
1 TC
284956 GAAACCCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.22, G:0.47, T:0.22
Consensus pattern (15 bp):
TCAGGTCGAGTCGGG
Found at i:285147 original size:20 final size:20
Alignment explanation
Indices: 285076--285148 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 20
285066 ATACCCCTAT
285076 ATATATTA-TTTTTTAATTAA
1 ATATATTATTTTTTTAA-TAA
*
285096 ATCCATATT-TTTTATTGAATATA
1 AT--ATATTATTTT-TTTAATA-A
285119 AGTA-A-TATTTTTTTAATAA
1 A-TATATTATTTTTTTAATAA
285138 ATATATTATTT
1 ATATATTATTT
285149 CAGGTCGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 14 0.33
21 5 0.12
22 11 0.26
23 6 0.14
24 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
ATATATTATTTTTTTAATAA
Found at i:300056 original size:19 final size:21
Alignment explanation
Indices: 300021--300076 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
300011 AGCTAAAAAT
*
300021 GGTATTAATAC-CAA-GGGTC
1 GGTATTGATACTCAAGGGGTC
300040 GGTATTGATACTC-AGGGGTC
1 GGTATTGATACTCAAGGGGTC
* * *
300060 AGTACTGATACTGAAGG
1 GGTATTGATACTCAAGG
300077 CTTAGAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 11 0.37
20 16 0.53
21 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (21 bp):
GGTATTGATACTCAAGGGGTC
Found at i:302047 original size:16 final size:16
Alignment explanation
Indices: 302026--302070 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
302016 TTTGTGTTAT
302026 ATTTGGTTATTTTTGG
1 ATTTGGTTATTTTTGG
302042 ATTTGGTTATTTTTGG
1 ATTTGGTTATTTTTGG
*
302058 ATTTGGGTATTTT
1 ATTTGGTTATTTT
302071 ATGCACATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.62
Consensus pattern (16 bp):
ATTTGGTTATTTTTGG
Found at i:304547 original size:31 final size:31
Alignment explanation
Indices: 304472--304550 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
304462 ATAATGACAG
304472 AGTGACCATTTTGTTACAAATCGATAATGTT
1 AGTGACCATTTTGTTACAAATCGATAATGTT
* **
304503 -GATGGCCATTTTGTTACAAATTTATAACT-TT
1 AG-TGACCATTTTGTTACAAATCGATAA-TGTT
*
304534 AGTGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
304551 TTTGAAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.03
31 37 0.93
32 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAATGTT
Found at i:307483 original size:19 final size:20
Alignment explanation
Indices: 307446--307497 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
307436 TCAAGTTATT
307446 TTTTAATTTTT-TAGTTTAG
1 TTTTAATTTTTATAGTTTAG
*
307465 TTTTAATTTTTATTG-TTAG
1 TTTTAATTTTTATAGTTTAG
*
307484 TTTCATATTTTTAT
1 TTTTA-ATTTTTAT
307498 CAAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTAATTTTTATAGTTTAG
Found at i:312085 original size:64 final size:63
Alignment explanation
Indices: 311999--312119 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
311989 ATGGTTCAAG
* * * * *
311999 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATACACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACAACGAATGTCATCA
* *
312063 GTGTATCGATACACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACAACGAATG
1 GTGTATCGATACACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACAACGAATG
312120 GGATTTATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 16 0.32
64 34 0.68
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (63 bp):
GTGTATCGATACACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACAACGAATGTCATCA
Found at i:320110 original size:19 final size:18
Alignment explanation
Indices: 320077--320113 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
320067 TCATTAGAAT
320077 TCTATTTTATTGTCTTAA
1 TCTATTTTATTGTCTTAA
*
320095 TCTATTCTTCTTGTCTTAA
1 TCTATT-TTATTGTCTTAA
320114 CTTCAGCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.59
Consensus pattern (18 bp):
TCTATTTTATTGTCTTAA
Found at i:322408 original size:2 final size:2
Alignment explanation
Indices: 322401--322428 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
322391 TCTATTTTAA
322401 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
322429 TGTATTAATC
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:324193 original size:2 final size:2
Alignment explanation
Indices: 324188--324217 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
324178 TCTATAAAAT
324188 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
324218 AAGTGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:324539 original size:34 final size:34
Alignment explanation
Indices: 324499--324565 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
324489 TTTAAACTCC
*
324499 CATTTTTGAATTCCTGAGTTTGTCACTGTGTATT
1 CATTTTTGAATTCCTGAGTTTGTCACTGCGTATT
324533 CATTTTTGAATTCCTGAGTTTGTCACTGCGTAT
1 CATTTTTGAATTCCTGAGTTTGTCACTGCGTAT
324566 GACAACCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (34 bp):
CATTTTTGAATTCCTGAGTTTGTCACTGCGTATT
Found at i:325003 original size:111 final size:111
Alignment explanation
Indices: 324804--325022 Score: 350
Period size: 111 Copynumber: 2.0 Consensus size: 111
324794 TTTTCTGTCA
* *
324804 TAATCTTTTCCAATCCTAAATTAGACTAAATTTCTTAGACTCTCCCGTAGGACTTGTCAGCAGAA
1 TAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCAGAA
* *
324869 AGACGTCGCAAAGGGTAGGCGCCTGGAGGCAGCCCCACAGGTCTCG
66 AGACGTCGCAAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTCTCG
* * **
324915 TAATTTTTTCCAATCCTAAGTTAGACGACCTTTCTTAGACTCTCCCCTAGGACTTGTCAGCAGAA
1 TAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCAGAA
324980 AGACGTCGCGAAA-GGAAGGCGCCTGGAGCCAGCCCCACAGGTC
66 AGACGTCGC-AAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTC
325023 CTAAACACGA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
111 96 0.97
112 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (111 bp):
TAATCTTTTCCAATCCTAAATTAGACGAAATTTCTTAGACTCTCCCCTAGGACTTGTCAGCAGAA
AGACGTCGCAAAGGGAAGGCGCCTGGAGCCAGCCCCACAGGTCTCG
Found at i:340308 original size:21 final size:21
Alignment explanation
Indices: 340266--340308 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
340256 TTTCTGGGCT
*
340266 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
340287 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
340308 A
1 A
340309 ATGAACCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:341867 original size:103 final size:103
Alignment explanation
Indices: 341642--341856 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
341632 GTCGGGGGTC
341642 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
341707 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
* *
341745 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
* *
341810 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
341848 TATGTGGTC
1 TATGTGGTC
341857 CTTATGGACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
Found at i:341912 original size:24 final size:23
Alignment explanation
Indices: 341876--341944 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
341866 ATTATTATAT
* *
341876 GGCACTACGGTGCAATTTTACGC
1 GGCACTCCGGTGCAATTATACGC
* *
341899 GGCACTCCCGGTGCAATTCTACGT
1 GGCACT-CCGGTGCAATTATACGC
* *
341923 GGTACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTATACG
341945 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGC
Found at i:341937 original size:23 final size:24
Alignment explanation
Indices: 341883--341944 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
341873 TATGGCACTA
*
341883 CGGTGCAATTTTACGCGGCACTCC
1 CGGTGCAATTATACGCGGCACTCC
* * * *
341907 CGGTGCAATTCTACGTGGTACT-T
1 CGGTGCAATTATACGCGGCACTCC
341930 CGGTGCAATTATACG
1 CGGTGCAATTATACG
341945 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (24 bp):
CGGTGCAATTATACGCGGCACTCC
Found at i:345497 original size:21 final size:21
Alignment explanation
Indices: 345455--345497 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
345445 TTTCTGGGCT
* *
345455 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
345476 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
345497 A
1 A
345498 ACTAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:345570 original size:23 final size:22
Alignment explanation
Indices: 345526--345570 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
345516 AATCTCATAG
*
345526 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
345548 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
345571 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:348723 original size:17 final size:17
Alignment explanation
Indices: 348701--348734 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
348691 TCGAAATGAA
348701 GCTCCTTACTTAGCCAC
1 GCTCCTTACTTAGCCAC
348718 GCTCCTTACTTAGCCAC
1 GCTCCTTACTTAGCCAC
348735 ACTCTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.12, T:0.29
Consensus pattern (17 bp):
GCTCCTTACTTAGCCAC
Found at i:349801 original size:17 final size:17
Alignment explanation
Indices: 349770--349820 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
349760 CTTGAAGAGG
349770 AAAATGAG-A-GAAGGA
1 AAAATGAGAAGGAAGGA
349785 AAAATGAGAAGGAAGGA
1 AAAATGAGAAGGAAGGA
349802 AAAATGAGAAGGAAGGA
1 AAAATGAGAAGGAAGGA
349819 AA
1 AA
349821 TGAAGAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.24
16 1 0.03
17 25 0.74
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (17 bp):
AAAATGAGAAGGAAGGA
Found at i:354385 original size:3 final size:3
Alignment explanation
Indices: 354377--354406 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
354367 AATTAGAATA
354377 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
354407 TTTTTGTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:355155 original size:28 final size:27
Alignment explanation
Indices: 355107--355164 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
355097 TCGAGGGAGA
*
355107 CAAAATTTGTTTCAATGGAAAC-GATCT
1 CAAAATTGGTTTCAATGGAAACTG-TCT
355134 CAAAGATTGGTTTCAA-GAGAAACTGTCT
1 CAAA-ATTGGTTTCAATG-GAAACTGTCT
355162 CAA
1 CAA
355165 GGGAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.19
28 21 0.78
29 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (27 bp):
CAAAATTGGTTTCAATGGAAACTGTCT
Found at i:355176 original size:64 final size:63
Alignment explanation
Indices: 355045--355238 Score: 203
Period size: 64 Copynumber: 3.0 Consensus size: 63
355035 CAAAGATGGT
* * ** *
355045 TTTGTTTCAAACGAAAC-ATACTCAAAGATTTTGTGTTTCCAGAGAAACTACCTCGAGGGAGACA
1 TTTGTTTC-AAGGAAACGAT-CTCAAAGA--TTG-GTTTCAAGAGAAACTGTCTCAAGGGAGACA
355109 AAA
61 AAA
*
355112 TTTGTTTCAATGGAAACGATCTCAAAGATTGGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA
1 TTTGTTTCAA-GGAAACGATCTCAAAGATTGGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
** * * *
355176 TTTGTTTCAAGGAAAACGA-CTCAAAGATGTTTTTTCAAAAGAAAATGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGG-AAACGATCTCAAAGAT-TGGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
355239 TTTTTTTTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
63 11 0.10
64 72 0.65
65 3 0.03
66 2 0.02
67 21 0.19
68 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (63 bp):
TTTGTTTCAAGGAAACGATCTCAAAGATTGGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
Found at i:356621 original size:8 final size:7
Alignment explanation
Indices: 356591--356691 Score: 57
Period size: 7 Copynumber: 14.1 Consensus size: 7
356581 TATGTGCCTC
356591 TTTTCTT
1 TTTTCTT
*
356598 TTTTATT
1 TTTTCTT
356605 TCTTTCTT
1 T-TTTCTT
356613 TTGTTCTT
1 TT-TTCTT
356621 TTTTC--
1 TTTTCTT
**
356626 TTTGATT
1 TTTTCTT
356633 TTTTCTT
1 TTTTCTT
356640 TGTTTCTT
1 T-TTTCTT
* *
356648 TTCTATT
1 TTTTCTT
*
356655 TTCTCTT
1 TTTTCTT
356662 TTTT-TT
1 TTTTCTT
356668 TCTCTTCTCT
1 T-T-TTCT-T
*
356678 TTGT-TT
1 TTTTCTT
356684 TTTTCTT
1 TTTTCTT
356691 T
1 T
356692 GCTTTTTACT
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
5 3 0.04
6 7 0.10
7 35 0.49
8 23 0.32
9 2 0.03
10 2 0.03
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:356646 original size:27 final size:28
Alignment explanation
Indices: 356589--356656 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
356579 TGTATGTGCC
*
356589 TCTTTTCTTTTTTATTTCTTTCTTTTGT
1 TCTTTTCTTTTTGATTTCTTTCTTTTGT
356617 TCTTTT-TTCTTTGATTT-TTTC-TTTGTT
1 TCTTTTCTT-TTTGATTTCTTTCTTTTG-T
356644 TCTTTTCTATTTT
1 TCTTTTCT-TTTT
356657 CTCTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.11
27 13 0.37
28 17 0.49
29 1 0.03
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (28 bp):
TCTTTTCTTTTTGATTTCTTTCTTTTGT
Found at i:356675 original size:17 final size:17
Alignment explanation
Indices: 356624--356690 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
356614 TGTTCTTTTT
*
356624 TCTTTGATTTTTTCTT-
1 TCTTTGTTTTTTTCTTC
* *
356640 TGTTTCTTTTCTATT-TTC
1 TCTTTGTTTT-T-TTCTTC
356658 TCTTT-TTTTTTCTCTTC
1 TCTTTGTTTTTT-TCTTC
356675 TCTTTGTTTTTTTCTT
1 TCTTTGTTTTTTTCTT
356691 TGCTTTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.02
16 9 0.22
17 19 0.46
18 12 0.29
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.76
Consensus pattern (17 bp):
TCTTTGTTTTTTTCTTC
Found at i:356684 original size:19 final size:19
Alignment explanation
Indices: 356636--356689 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
356626 TTTGATTTTT
*
356636 TCTTTGTTTCTTTTCTATTT
1 TCTTTGTTT-TTTTCTATTC
*
356656 TCTCTT-TTTTTTTCTCTTC
1 TCT-TTGTTTTTTTCTATTC
356675 TCTTTGTTTTTTTCT
1 TCTTTGTTTTTTTCT
356690 TTGCTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.07
19 20 0.67
20 6 0.20
21 2 0.07
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (19 bp):
TCTTTGTTTTTTTCTATTC
Found at i:356686 original size:51 final size:50
Alignment explanation
Indices: 356592--356692 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
356582 ATGTGCCTCT
* * *
356592 TTTCTTTTTTATTTCTTTCTTTTGTTCTTTTTTCTTTGATTTTTTCTTTG
1 TTTCTTTTCTATTTCTTTCTTTTGTTCTCTTCTCTTTGATTTTTTCTTTG
* *
356642 TTTCTTTTCTATTTTCTCTT-TTTTTTTCTCTTCTCTTTGTTTTTTTCTTTG
1 TTTCTTTTCTA-TTTCT-TTCTTTTGTTCTCTTCTCTTTGATTTTTTCTTTG
356693 CTTTTTACTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
50 10 0.23
51 32 0.73
52 2 0.05
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (50 bp):
TTTCTTTTCTATTTCTTTCTTTTGTTCTCTTCTCTTTGATTTTTTCTTTG
Found at i:356690 original size:12 final size:12
Alignment explanation
Indices: 356619--356698 Score: 58
Period size: 12 Copynumber: 6.3 Consensus size: 12
356609 TCTTTTGTTC
*
356619 TTTTTTCTTTGA
1 TTTTTTCTTTGT
356631 TTTTTTCTTTGT
1 TTTTTTCTTTGT
356643 TTCTTTTCTATT-T
1 TT-TTTTCT-TTGT
356656 TCTCTTTT-TTT-T
1 T-T-TTTTCTTTGT
*
356668 TCTCTTCTCTTTGT
1 T-T-TTTTCTTTGT
356682 TTTTTTCTTTGCT
1 TTTTTTCTTTG-T
356695 TTTT
1 TTTT
356699 ACTCTTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
12 31 0.53
13 18 0.31
14 10 0.17
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:361472 original size:13 final size:13
Alignment explanation
Indices: 361454--361479 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
361444 TATTGTTTTC
361454 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
361467 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
361480 GTTCTTCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTCTTCT
Found at i:362076 original size:3 final size:3
Alignment explanation
Indices: 362068--362144 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
362058 AAATAGAGTA
362068 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
362116 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
362145 AGTAATATTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:371761 original size:17 final size:17
Alignment explanation
Indices: 371724--371770 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
371714 AATAATTTTT
* **
371724 AAGAAAAAATAATTTTT
1 AAGAAAAAATAAATTAA
371741 AAGAAAAAATAAATTAA
1 AAGAAAAAATAAATTAA
371758 AAGATAAAAATAA
1 AAGA-AAAAATAA
371771 CATGCGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (17 bp):
AAGAAAAAATAAATTAA
Found at i:371770 original size:18 final size:17
Alignment explanation
Indices: 371711--371752 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
371701 AATACCATTT
371711 AAAAATAATTTTTAAGA
1 AAAAATAATTTTTAAGA
371728 AAAAATAATTTTTAAGA
1 AAAAATAATTTTTAAGA
371745 AAAAATAA
1 AAAAATAA
371753 ATTAAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAAATAATTTTTAAGA
Found at i:372853 original size:21 final size:21
Alignment explanation
Indices: 372829--372877 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
372819 CACCGAAGTG
* *
372829 CCACATATTTGTCCCGGAGGA
1 CCACATATTTGTCCCGAAAGA
*
372850 CCACATATTTGTCCTGAAAGA
1 CCACATATTTGTCCCGAAAGA
372871 CCACATA
1 CCACATA
372878 AGACCCTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
CCACATATTTGTCCCGAAAGA
Found at i:373021 original size:21 final size:21
Alignment explanation
Indices: 372997--373047 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
372987 CATAGAGTTT
*
372997 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
*
373018 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTGATTCAAA
*
373039 GATCACATT
1 GTTCACATT
373048 TCCCTAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:373625 original size:41 final size:41
Alignment explanation
Indices: 373547--373628 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
373537 ATGTTTTAAG
*
373547 GTATCGATACCATCATTCAGGTACCGATACTACCCCTTACA
1 GTATCGATACCATCATACAGGTACCGATACTACCCCTTACA
*
373588 GTATCGATACC-TCATCAACAGGTATCGATACTA-CCCTTACA
1 GTATCGATACCATCAT--ACAGGTACCGATACTACCCCTTACA
373629 AAATACTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.11
41 19 0.51
42 14 0.38
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (41 bp):
GTATCGATACCATCATACAGGTACCGATACTACCCCTTACA
Found at i:379646 original size:21 final size:22
Alignment explanation
Indices: 379621--379722 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 22
379611 GTAATTTGCA
379621 CCGAAGTG-CCACATAATTGTC
1 CCGAAGTGACCACATAATTGTC
*
379642 CCGAA-TGACCATATAAGTT-TGC
1 CCGAAGTGACCACATAA-TTGT-C
*
379664 ACCGAAGTG-CCACATATTTGTC
1 -CCGAAGTGACCACATAATTGTC
* * *
379686 TCGGAG-GACCACATATTTGTC
1 CCGAAGTGACCACATAATTGTC
*
379707 CTGAAG-GACCACATAA
1 CCGAAGTGACCACATAA
379723 GACCCTCGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
20 3 0.05
21 42 0.65
22 6 0.09
23 12 0.18
24 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (22 bp):
CCGAAGTGACCACATAATTGTC
Found at i:379865 original size:21 final size:21
Alignment explanation
Indices: 379841--379891 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
379831 AATAGAGTTT
*
379841 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
*
379862 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTGATTCAAA
*
379883 GATCACATT
1 GTTCACATT
379892 TCCATAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:380247 original size:22 final size:22
Alignment explanation
Indices: 380196--380269 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
380186 ATGTTTAGAA
* *
380196 GTATCAGTACTACCCT--AATG
1 GTATCAATACTACCCTACAAGG
* *
380216 GTACCGATACTACCCTACAAGG
1 GTATCAATACTACCCTACAAGG
380238 GTATCAATACTACCCTACAAGG
1 GTATCAATACTACCCTACAAGG
380260 GTATCAATAC
1 GTATCAATAC
380270 CTCCTCATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.28
22 33 0.72
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (22 bp):
GTATCAATACTACCCTACAAGG
Found at i:380342 original size:54 final size:54
Alignment explanation
Indices: 380255--380396 Score: 164
Period size: 54 Copynumber: 2.6 Consensus size: 54
380245 TACTACCCTA
* *
380255 CAAGGGTATCAATACCTCCTCATGCTATCGATACCAAAATAACATTCGATGTTT
1 CAAGGGTATCGATACCTCCTCAAGCTATCGATACCAAAATAACATTCGATGTTT
* ** **
380309 CAAGGGTATCGATACCTCCTCAAGGTA-CTGATACCAATCTGGCATTCGATGTTT
1 CAAGGGTATCGATACCTCCTCAAGCTATC-GATACCAAAATAACATTCGATGTTT
*
380363 CAA-GGTATCGATACCATCCTTC-AGGTATCGATAC
1 CAAGGGTATCGATACC-TCC-TCAAGCTATCGATAC
380397 TACCCCTTAC
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
53 13 0.17
54 61 0.79
55 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (54 bp):
CAAGGGTATCGATACCTCCTCAAGCTATCGATACCAAAATAACATTCGATGTTT
Found at i:380404 original size:21 final size:21
Alignment explanation
Indices: 380365--380466 Score: 61
Period size: 20 Copynumber: 5.0 Consensus size: 21
380355 CGATGTTTCA
*
380365 AGGTATCGATACCATCCTT-C
1 AGGTATCGATACCACCCTTAC
*
380385 AGGTATCGATACTACCCCTTAC
1 AGGTATCGATACCA-CCCTTAC
* * * *
380407 A-GTATGGATACC-TCATCAAC
1 AGGTATCGATACCACCCT-TAC
* *
380427 AGGTATCGATACTCA-TC-AAC
1 AGGTATCGATAC-CACCCTTAC
*
380447 AGGTATCGATACTACCCTTA
1 AGGTATCGATACCACCCTTA
380467 GAAAAAAAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 15
0.69 0.15 0.17
Matches are distributed among these distances:
19 3 0.05
20 32 0.52
21 23 0.38
22 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
AGGTATCGATACCACCCTTAC
Found at i:380441 original size:20 final size:20
Alignment explanation
Indices: 380408--380459 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
380398 ACCCCTTACA
*
380408 GTATGGATACCTCATCAACAG
1 GTATCGATA-CTCATCAACAG
380429 GTATCGATACTCATCAACAG
1 GTATCGATACTCATCAACAG
380449 GTATCGATACT
1 GTATCGATACT
380460 ACCCTTAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCATCAACAG
Found at i:381405 original size:29 final size:29
Alignment explanation
Indices: 381359--381416 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
381349 AACCAAAAAA
*
381359 GTAAATGTTGAAATTTAAAGGAA-TGAAAT
1 GTAAATGTGGAAATTTAAA-GAACTGAAAT
381388 GTAAATGCTGGAAA-TTAAAGAACTGAAAT
1 GTAAATG-TGGAAATTTAAAGAACTGAAAT
381417 TGAATTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.28
Consensus pattern (29 bp):
GTAAATGTGGAAATTTAAAGAACTGAAAT
Found at i:385859 original size:21 final size:21
Alignment explanation
Indices: 385830--385870 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
385820 AAAGGAGAAG
*
385830 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
385851 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
385871 GTGAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:393558 original size:20 final size:20
Alignment explanation
Indices: 393521--393563 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
393511 AATCCACCAC
393521 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
393541 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
393561 ATG
1 ATG
393564 GGACTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:396906 original size:14 final size:14
Alignment explanation
Indices: 396887--396921 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
396877 ATATTTACTC
*
396887 TATTATTTTTTCAT
1 TATTATTTTGTCAT
*
396901 TATTATTTTGTCTT
1 TATTATTTTGTCAT
396915 TATTATT
1 TATTATT
396922 ATTATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (14 bp):
TATTATTTTGTCAT
Found at i:407517 original size:18 final size:18
Alignment explanation
Indices: 407494--407536 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
407484 TAAGTCGAAG
407494 AAGAAAAATAA-AAAAGAA
1 AAGAAAAATAACAAAA-AA
407512 AAG-AAAATAACAAAAAA
1 AAGAAAAATAACAAAAAA
407529 AAGAAAAA
1 AAGAAAAA
407537 ATGTTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (18 bp):
AAGAAAAATAACAAAAAA
Found at i:407587 original size:6 final size:6
Alignment explanation
Indices: 407576--407605 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
407566 CCTAAATTGA
407576 AAAAAG AAAAAG AGAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA
407606 TAAGGTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:407595 original size:13 final size:12
Alignment explanation
Indices: 407576--407605 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
407566 CCTAAATTGA
407576 AAAAAGAAAAAG
1 AAAAAGAAAAAG
407588 AGAAAAGAAAAAG
1 A-AAAAGAAAAAG
407601 AAAAA
1 AAAAA
407606 TAAGGTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:408598 original size:118 final size:118
Alignment explanation
Indices: 408437--408667 Score: 347
Period size: 118 Copynumber: 2.0 Consensus size: 118
408427 TTTACACAAT
* * * *
408437 ATTGGATTTCAACTTCATGACGAATGATATCCAAATCAAGGCTCAACTTCACAATAAAGGGGCCA
1 ATTGGATTTCAACTTCACGAAGAATGATATCCAAATCAAGGCTCAACTTCACAACAAAGAGGCCA
* *
408502 TCCACGATTTCAACTTCACGACGAAGGATATCGTG-CACACCAGCAACATTCAG
66 TCCAAGATTTCAACTTCACGACGAAGGATATCGTGTC-CACCAACAACATTCAG
* * *
408555 ATTGGATTTCAATTTCACGAAGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCA
1 ATTGGATTTCAACTTCACGAAGAATGATATCCAAATCAAGGCTCAACTTCACAACAAAGAGGCCA
* *
408620 TCCAAGATTTTAACTTCACGACGAAGGATATTGTGTCCACCAACAACA
66 TCCAAGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAACAACA
408668 CCCATCCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
118 100 0.99
119 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (118 bp):
ATTGGATTTCAACTTCACGAAGAATGATATCCAAATCAAGGCTCAACTTCACAACAAAGAGGCCA
TCCAAGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAACAACATTCAG
Found at i:408699 original size:58 final size:58
Alignment explanation
Indices: 408625--408767 Score: 223
Period size: 58 Copynumber: 2.5 Consensus size: 58
408615 GGCCATCCAA
* *
408625 GATTTTAACTTCACGACGAAGGATATTGTGTCCACCAACAACACCCATCCTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTCCACCAACAACACCCATCCTTAGATTG
* * *
408683 GATTTCAACTTAACGACGAAGGATATCGTGTCCACCAACAATACCTATCCTTAGATTG
1 GATTTCAACTTCACGACGAAGGATATCGTGTCCACCAACAACACCCATCCTTAGATTG
* *
408741 GATTTCAACTTCACGAAGAAGAATATC
1 GATTTCAACTTCACGACGAAGGATATC
408768 CAATTGAAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 77 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (58 bp):
GATTTCAACTTCACGACGAAGGATATCGTGTCCACCAACAACACCCATCCTTAGATTG
Found at i:408819 original size:182 final size:173
Alignment explanation
Indices: 408507--408888 Score: 475
Period size: 182 Copynumber: 2.2 Consensus size: 173
408497 GGCCATCCAC
* *
408507 GATTTCAACTTCACGACGAAGGATATCGTGCACACCAGCAACATTCAGATTGGATTTCAATTTCA
1 GATTTCAACTTCACGACGAAGGATATCGTGCACACCAACAACATTCAGATTGGATTTCAACTTCA
*
408572 CGAAGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCATCCAAGATTTTAACTTC
66 CGAAGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCATCCAAGATTTCAACTTC
* * ** *
408637 ACGACGAAGGATATTGTGTCCACCAA-CAACACCCATCCTTAGATTG
131 ACGACGAAGGATATCGTGCCCA-CAACCAACATAC-T-C-AAGATTG
* *
408683 GATTTCAACTTAACGACGAAGGATATCGTGTC-CACCAACAATACCTATCCTTAGATTGGATTTC
1 GATTTCAACTTCACGACGAAGGATATCGTG-CACACCAAC-A-A-C-AT--TCAGATTGGATTTC
* * *
408747 AACTTCACGAAGAA-GAATATCCAATTGAAGGCTCAACTTCACAACGAAGGGGTCATCCACA-AT
59 AACTTCACGAAGAATG-ATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCATCCA-AGAT
* *
408810 TTCAACTTCACGATGAAGGATATCGTGCCCACAACCAACTTACTCAAGATTG
122 TTCAACTTCACGACGAAGGATATCGTGCCCACAACCAACATACTCAAGATTG
*
408862 GATTTCAACTTCACGAAGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
408889 TAATTCAAAG
Statistics
Matches: 179, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
176 35 0.20
177 2 0.01
178 1 0.01
179 32 0.18
180 3 0.02
181 5 0.03
182 100 0.56
183 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (173 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCACACCAACAACATTCAGATTGGATTTCAACTTCA
CGAAGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGAGGCCATCCAAGATTTCAACTTC
ACGACGAAGGATATCGTGCCCACAACCAACATACTCAAGATTG
Found at i:408902 original size:121 final size:124
Alignment explanation
Indices: 408684--408915 Score: 337
Period size: 121 Copynumber: 1.9 Consensus size: 124
408674 CTTAGATTGG
* *
408684 ATTTCAACTTAACGACGAAGGATATCGTGTCCACCAACAATACCTATCCTTAGATTGGATTTCAA
1 ATTTCAACTTAACGACGAAGGATATCGTGCCCACCAACAATACCTATCCTAAGATTGGATTTCAA
* *
408749 CTTCACGAAGAAGAATATCCAATTGAAGGCTCAACTTCACAACGAAGGGGTCATCCACA
66 CTTCACGAAGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGTCATCCACA
* * * *
408808 ATTTCAACTTCACGATGAAGGATATCGTGCCCA-CAACCA-A-CT-TACTCAAGATTGGATTTCA
1 ATTTCAACTTAACGACGAAGGATATCGTGCCCACCAACAATACCTATCCT-AAGATTGGATTTCA
* *
408869 ACTTCACGAAGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAA
65 ACTTCACGAAGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAA
408916 TGAGCTTTCC
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
120 3 0.03
121 58 0.60
122 1 0.01
123 5 0.05
124 30 0.31
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (124 bp):
ATTTCAACTTAACGACGAAGGATATCGTGCCCACCAACAATACCTATCCTAAGATTGGATTTCAA
CTTCACGAAGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGTCATCCACA
Found at i:410921 original size:12 final size:12
Alignment explanation
Indices: 410893--410950 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 12
410883 TATTGTTGTA
*
410893 TATATATTTTA-
1 TATATTTTTTAT
*
410904 TATATTTATTAT
1 TATATTTTTTAT
410916 TATA-TTTTT-T
1 TATATTTTTTAT
410926 TATATATTTTTAT
1 TATAT-TTTTTAT
410939 T-TATTTTTTAT
1 TATATTTTTTAT
410950 T
1 T
410951 TTTTTACATC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 5 0.12
11 21 0.52
12 12 0.30
13 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATATTTTTTAT
Found at i:410930 original size:10 final size:10
Alignment explanation
Indices: 410893--410956 Score: 60
Period size: 10 Copynumber: 6.2 Consensus size: 10
410883 TATTGTTGTA
*
410893 TATATATTTTA
1 TATAT-TTTTT
410904 TATATTTATTAT
1 TATATTT-TT-T
410916 TATATTTTTT
1 TATATTTTTT
*
410926 TATATATTTT
1 TATATTTTTT
410936 TAT-TTATTTT
1 TATATT-TTTT
410946 T-TATTTTTT
1 TATATTTTTT
410955 TA
1 TA
410957 CATCTTCGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.16
10 22 0.49
11 9 0.20
12 7 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATATTTTTT
Found at i:410931 original size:24 final size:22
Alignment explanation
Indices: 410899--410947 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
410889 TGTATATATA
410899 TTTTATATATTTATTATTATATTT
1 TTTTATATATTT-TTATT-TATTT
410923 TTTTATATATTTTTATTTATTT
1 TTTTATATATTTTTATTTATTT
410945 TTT
1 TTT
410948 ATTTTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 8 0.32
23 5 0.20
24 12 0.48
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATATATTTTTATTTATTT
Found at i:413102 original size:19 final size:20
Alignment explanation
Indices: 413067--413114 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
413057 CTCACAATAA
413067 GAAAATATTTTTAAAAAACT
1 GAAAATATTTTTAAAAAACT
*
413087 GAAAATATTTTT-AAAAATT
1 GAAAATATTTTTAAAAAACT
413106 GAAAATATT
1 GAAAATATT
413115 ATGAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (20 bp):
GAAAATATTTTTAAAAAACT
Found at i:414349 original size:186 final size:187
Alignment explanation
Indices: 414012--414370 Score: 424
Period size: 186 Copynumber: 1.9 Consensus size: 187
414002 CTTTTTTATG
* * ** * **
414012 ATAAATATATTAACATTTCATATCACAACTTATTTTCATAGAGAATTATAATATTTTTTGGTGTA
1 ATAAAAATATTAACATTTCAGATCACAACTTATTTTCATAGAGAACCATAACATTTTTTGGACTA
* * * * * *
414077 ACTCATTTTATTAATAAAAGTATTAACATTCTAGATCACAATTTATTTCTTAGTAAATCATGACA
66 ACCCATTTTATTAATAAAAATATTAACATTCTAGATCACAACTTATTTCTTAATAAAGCATAACA
414142 TTCTTAGGTGAAACCGTATTTCTTATACATAATT-ATAACATTTCAGGAGTAATGTTA
131 TTCTTAGGTGAAACCGTATTTCTTATACAT-ATTCATAACATTTCAGGAGTAATGTTA
* * *
414199 ATAAAAATATTAA-ATTTCAGATCACAACTTA-TTTCTTAGTGAACCATGACA-TTTTTGGACTC
1 ATAAAAATATTAACATTTCAGATCACAACTTATTTTCATAGAGAACCATAACATTTTTTGGACT-
* *** *
414261 AACCCATTTTATTAATAAAAATATTAACATTCTATATTGTAACTTATTTTTTTAATAAAGCATAA
65 AACCCATTTTATTAATAAAAATATTAACATTCTAGATCACAACTTA-TTTCTTAATAAAGCATAA
* *
414326 CATTCTT-GAGT-ACAACTGTATTTCTTATATATATTCATAACATTT
129 CATTCTTAG-GTGA-AACCGTATTTCTTATACATATTCATAACATTT
414371 TCAGTTTCTA
Statistics
Matches: 144, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
184 8 0.06
185 58 0.40
186 66 0.46
187 12 0.08
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (187 bp):
ATAAAAATATTAACATTTCAGATCACAACTTATTTTCATAGAGAACCATAACATTTTTTGGACTA
ACCCATTTTATTAATAAAAATATTAACATTCTAGATCACAACTTATTTCTTAATAAAGCATAACA
TTCTTAGGTGAAACCGTATTTCTTATACATATTCATAACATTTCAGGAGTAATGTTA
Found at i:415910 original size:21 final size:22
Alignment explanation
Indices: 415879--415935 Score: 80
Period size: 21 Copynumber: 2.5 Consensus size: 22
415869 TTATTTTATG
415879 TTAAGAGATAAAATTATAAAATT
1 TTAA-AGATAAAATTATAAAATT
*
415902 TT-AAGATAAATTTATAAAATT
1 TTAAAGATAAAATTATAAAATT
415923 TTAAAAGATAAAA
1 TT-AAAGATAAAA
415936 ATAAATTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.63
22 1 0.03
23 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
TTAAAGATAAAATTATAAAATT
Found at i:417409 original size:21 final size:21
Alignment explanation
Indices: 417383--417451 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
417373 AATCAATTTG
417383 CCTCCGCTTGTCCCTAAACTC
1 CCTCCGCTTGTCCCTAAACTC
* *
417404 CCTCCGCTTGTCCCTGAACTT
1 CCTCCGCTTGTCCCTAAACTC
417425 CCTCCGCTTGTCCCTAAACTC
1 CCTCCGCTTGTCCCTAAACTC
417446 CCTCCG
1 CCTCCG
417452 GTTACAGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.12, C:0.48, G:0.12, T:0.29
Consensus pattern (21 bp):
CCTCCGCTTGTCCCTAAACTC
Found at i:422819 original size:26 final size:26
Alignment explanation
Indices: 422790--422858 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
422780 TTTGAAGCGT
* * *
422790 ACTCATACGTTTCATTAGAAACATTA
1 ACTCATACATTACATTAGAAACACTA
* *
422816 ACTCCTACATTACATTAGAAGCACTA
1 ACTCATACATTACATTAGAAACACTA
*
422842 ACTCATATATTACATTA
1 ACTCATACATTACATTA
422859 CTATACAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (26 bp):
ACTCATACATTACATTAGAAACACTA
Found at i:424904 original size:29 final size:30
Alignment explanation
Indices: 424858--424914 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
424848 CAAATTTTGG
*
424858 TTAGTGACCAAAACATAAA-TTTTGAAAGT
1 TTAGTGACCAAAACATAAAGTTTAGAAAGT
* **
424887 TTAGTGGCCAAAGTATAAAGTTTAGAAA
1 TTAGTGACCAAAACATAAAGTTTAGAAA
424915 AGATAAGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.30
Consensus pattern (30 bp):
TTAGTGACCAAAACATAAAGTTTAGAAAGT
Found at i:438918 original size:23 final size:23
Alignment explanation
Indices: 438859--438960 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
438849 GAGTTGAGGG
* *
438859 TTCTACGCT-GTCCTTTGGGACAA
1 TTCTACG-TGGTCCTTCGGGACAT
*
438882 TT-TATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
438904 TTCTACGCT-GTCCTTCTGGACAT
1 TTCTACG-TGGTCCTTCGGGACAT
* * * *
438927 ATCTATGTGGTCATTCGGGATAAT
1 TTCTACGTGGTCCTTCGGGA-CAT
438951 TTCTACGTGG
1 TTCTACGTGG
438961 CATTTCGGTG
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.02
22 18 0.29
23 32 0.52
24 11 0.18
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:438925 original size:45 final size:47
Alignment explanation
Indices: 438859--438957 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 47
438849 GAGTTGAGGG
* * *
438859 TTCTACGCTGTCCTTTGGGACA-ATTTATGTGGTCCTTCGGGA-CAT
1 TTCTACGCTGTCCTTTGGGACATATCTATGTGGTCATTCGGGATAAT
438904 TTCTACGCTGTCCTTCT-GGACATATCTATGTGGTCATTCGGGATAAT
1 TTCTACGCTGTCCTT-TGGGACATATCTATGTGGTCATTCGGGATAAT
438951 TTCTACG
1 TTCTACG
438958 TGGCATTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
45 20 0.42
46 19 0.40
47 9 0.19
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (47 bp):
TTCTACGCTGTCCTTTGGGACATATCTATGTGGTCATTCGGGATAAT
Found at i:440062 original size:13 final size:13
Alignment explanation
Indices: 440044--440074 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
440034 TTGGTCTAAG
440044 TGGAGAAGTTAGA
1 TGGAGAAGTTAGA
440057 TGGAGAAGTTAGA
1 TGGAGAAGTTAGA
440070 TGGAG
1 TGGAG
440075 CAATCTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.42, T:0.23
Consensus pattern (13 bp):
TGGAGAAGTTAGA
Found at i:445665 original size:15 final size:15
Alignment explanation
Indices: 445645--445697 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
445635 ACGTTTTATA
445645 CTATGTGATATTGAG
1 CTATGTGATATTGAG
445660 CTATGTGATTATATGA-
1 CTATGTGA-TAT-TGAG
* *
445676 ATATGTGATA-TAAG
1 CTATGTGATATTGAG
445690 CTATGTGA
1 CTATGTGA
445698 AATGTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.06
14 7 0.22
15 10 0.31
16 10 0.31
17 3 0.09
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (15 bp):
CTATGTGATATTGAG
Found at i:445820 original size:22 final size:23
Alignment explanation
Indices: 445802--445846 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
445792 ATAATTTTAT
445802 GAGGTCTTTCAGGACATTTCTAC
1 GAGGTCTTTCAGGACATTTCTAC
* * *
445825 GTGGTCTTTCGGGACATATCTA
1 GAGGTCTTTCAGGACATTTCTA
445847 TATTCTTCTT
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:0.20, G:0.24, T:0.36
Consensus pattern (23 bp):
GAGGTCTTTCAGGACATTTCTAC
Found at i:445893 original size:24 final size:24
Alignment explanation
Indices: 445866--445911 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
445856 TTGGGGCAAT
*
445866 TTCTACGTGGCACTTCGGTGCATA
1 TTCTACGCGGCACTTCGGTGCATA
445890 TTCTACGCGGCACTTCGGTGCA
1 TTCTACGCGGCACTTCGGTGCA
445912 ATTTATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGCACTTCGGTGCATA
Found at i:446495 original size:18 final size:16
Alignment explanation
Indices: 446477--446507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
446467 CCTACTAATT
446477 TTTAAAAAGTCAATGA
1 TTTAAAAAGTCAATGA
*
446493 TTTGAAAAGTCAATG
1 TTTAAAAAGTCAATG
446508 TGACACCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.32
Consensus pattern (16 bp):
TTTAAAAAGTCAATGA
Found at i:448735 original size:2 final size:2
Alignment explanation
Indices: 448728--448753 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
448718 TGCTTCCTTC
448728 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
448754 AATAAAATCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:452358 original size:24 final size:23
Alignment explanation
Indices: 452324--452459 Score: 68
Period size: 24 Copynumber: 5.9 Consensus size: 23
452314 TCTTATCTTT
*
452324 GTTTTAGGTATTTTAGTTTAAATA
1 GTTTTAAGTATTTTA-TTTAAATA
*
452348 GTTTTAAGTATTTTAATT--A-A
1 GTTTTAAGTATTTTATTTAAATA
* * *
452368 GATTT-AGGATATTATTTTAAATA
1 GTTTTAAGTATTTTA-TTTAAATA
* ** *
452391 -TTATATTA-TATTTTATCTTATCTTT
1 GTT-T-TAAGTATTTTAT-TTA-AATA
*
452416 GTTTTAGGTATTTTAGTTTAAATA
1 GTTTTAAGTATTTTA-TTTAAATA
*
452440 GTTTTAAGTATTTTAATTAA
1 GTTTTAAGTATTTTATTTAA
452460 GATTTATTTT
Statistics
Matches: 81, Mismatches: 19, Indels: 25
0.65 0.15 0.20
Matches are distributed among these distances:
19 7 0.09
20 7 0.09
21 1 0.01
22 2 0.02
23 9 0.11
24 39 0.48
25 13 0.16
26 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (23 bp):
GTTTTAAGTATTTTATTTAAATA
Found at i:452486 original size:92 final size:92
Alignment explanation
Indices: 452278--452465 Score: 376
Period size: 92 Copynumber: 2.0 Consensus size: 92
452268 AAACTCATGT
452278 TTTAGGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTT
1 TTTAGGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTT
452343 AAATAGTTTTAAGTATTTTAATTAAGA
66 AAATAGTTTTAAGTATTTTAATTAAGA
452370 TTTAGGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTT
1 TTTAGGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTT
452435 AAATAGTTTTAAGTATTTTAATTAAGA
66 AAATAGTTTTAAGTATTTTAATTAAGA
452462 TTTA
1 TTTA
452466 TTTTCTTTAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (92 bp):
TTTAGGATATTATTTTAAATATTATATTATATTTTATCTTATCTTTGTTTTAGGTATTTTAGTTT
AAATAGTTTTAAGTATTTTAATTAAGA
Found at i:452986 original size:17 final size:17
Alignment explanation
Indices: 452961--452994 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
452951 ATTTATCTCA
*
452961 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
452978 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
452995 TTATCTCATT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:458269 original size:30 final size:29
Alignment explanation
Indices: 458192--458276 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
458182 TAAAAAATGT
*
458192 TATATAAAAATGTTAAAAGAAAAAATTAAA
1 TATA-AAAAATGTTAAAAGAAAAAATAAAA
* ** ***
458222 TATTAAATTTCAGAAAAGAAAATAATAAAA
1 TATAAAAAATGTTAAAAGAAAA-AATAAAA
458252 TATAAAAAATGTTAAAAGAGAAAAA
1 TATAAAAAATGTTAAAAGA-AAAAA
458277 ATTAAAAACA
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
29 13 0.32
30 24 0.60
31 3 0.08
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (29 bp):
TATAAAAAATGTTAAAAGAAAAAATAAAA
Found at i:458333 original size:16 final size:16
Alignment explanation
Indices: 458303--458332 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
458293 AAAAAATGGG
458303 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
458319 AAAAT-AAGATAAAA
1 AAAATAAAGATAAAA
458333 AGGGAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:458341 original size:33 final size:32
Alignment explanation
Indices: 458281--458349 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
458271 GAAAAAATTA
*
458281 AAAACAAAATTAAAAAAATGGGAAAATAAAGAT
1 AAAACAAAATTAAAAAAAAGGGAAAAT-AAGAT
*
458314 AAAACAAAA-TAAGATAAAAAGGG-AAATATGAT
1 AAAACAAAATTAA-A-AAAAAGGGAAAATAAGAT
458346 AAAA
1 AAAA
458350 TAATAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 11 0.34
33 14 0.44
34 7 0.22
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.14
Consensus pattern (32 bp):
AAAACAAAATTAAAAAAAAGGGAAAATAAGAT
Found at i:458422 original size:18 final size:18
Alignment explanation
Indices: 458401--458443 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
458391 GTTGTTTTTA
* *
458401 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
458419 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
458437 AAATAAA
1 AAATAAA
458444 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:458976 original size:24 final size:24
Alignment explanation
Indices: 458949--459011 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
458939 TTATCCTAAT
*
458949 TAAAATACTTAAAACTATTTAAAC
1 TAAAATACCTAAAACTATTTAAAC
458973 TAAAATACCTAAAACTATTTAAAC
1 TAAAATACCTAAAACTATTTAAAC
458997 TAAAATACCTAAAAC
1 TAAAATACCTAAAAC
459012 AAAGATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAAATACCTAAAACTATTTAAAC
Found at i:459654 original size:202 final size:202
Alignment explanation
Indices: 459308--459693 Score: 549
Period size: 202 Copynumber: 1.9 Consensus size: 202
459298 AAGGTGGCTT
* * **
459308 CTTGTTGCCAAATCGTAGTCAACCTTGGTCTTCTTCTCGGTTTAAAGACCTCGGTTTGAAAATTC
1 CTTGTTGCCAAATCGTAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTGAAAATTC
* * * *
459373 AACCAAAAAGTAGTTCCTCATTGATACCATATGGTTGATATGCCCTCGAGCTGAATGGAATCGAA
66 AACCAAAAAGTAGTTCATCATTGATACCATATGGTTGATATGCCCTAGAACTGAATGGAATCAAA
* * *
459438 CTCCAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGATGTAAATTCGACTGGGAG
131 CTCAAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGATGTAAATTCGACTGGGAG
459503 ATAGTTC
196 ATAGTTC
*
459510 CTTGTTGCTAAATCGTAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTGAAAATTC
1 CTTGTTGCCAAATCGTAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTGAAAATTC
* ** * * *
459575 CACTGAAAATTAGTTCATCGA-TGCTACCATATGGTTGATATGCCCTAGAACTGAATGTAATCAA
66 AACCAAAAAGTAGTTCATC-ATTGATACCATATGGTTGATATGCCCTAGAACTGAATGGAATCAA
* * * * *
459639 ACTCAAAGTTTTTTGTTGATAGATATCCATTCTTGCCTTGAGCTATGTTGTAAAT
130 ACTCAAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGATGTAAAT
459694 AGGCTATGAG
Statistics
Matches: 160, Mismatches: 23, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
202 159 0.99
203 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (202 bp):
CTTGTTGCCAAATCGTAGCCAACCTAGGTCTTCTTCTCGACTTAAAGACCTCGGTTTGAAAATTC
AACCAAAAAGTAGTTCATCATTGATACCATATGGTTGATATGCCCTAGAACTGAATGGAATCAAA
CTCAAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGATGTAAATTCGACTGGGAG
ATAGTTC
Found at i:460510 original size:32 final size:32
Alignment explanation
Indices: 460437--460512 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
460427 TTCATATCAG
* * *
460437 GATGTTGAATCCCCAAAGATACACCAATATTC
1 GATGTTGAATCTCCAAAAATACACCAACATTC
* * *
460469 GATGTTGAATCTCCAAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAAATACACCAACATTC
*
460501 GATGATGAATCT
1 GATGTTGAATCT
460513 TCAATACCCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAAATACACCAACATTC
Found at i:461694 original size:2 final size:2
Alignment explanation
Indices: 461687--461728 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
461677 AGATACATAC
* * *
461687 AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT GT 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
461729 GGATTAATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:461700 original size:16 final size:16
Alignment explanation
Indices: 461679--461728 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
461669 ACAACAAGAG
461679 ATACATACATATATAT
1 ATACATACATATATAT
461695 ATACATACATATATAT
1 ATACATACATATATAT
* **
461711 ATATATGTATATATAT
1 ATACATACATATATAT
461727 AT
1 AT
461729 GGATTAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:461704 original size:20 final size:20
Alignment explanation
Indices: 461679--461716 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
461669 ACAACAAGAG
461679 ATACATACATATATATATAC
1 ATACATACATATATATATAC
*
461699 ATACATATATATATATAT
1 ATACATACATATATATAT
461717 GTATATATAT
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:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
ATACATACATATATATATAC
Done.