Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 24
Found at i:350125 original size:85 final size:85
Alignment explanation
Indices: 350008--350211 Score: 272
Period size: 85 Copynumber: 2.4 Consensus size: 85
349998 GGTTTTTGAG
* * * *
350008 TGCATAGATGTATTGCATGG-TGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCATGG-T
1 TGCATAGATGCACTGCAGGGATGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCAGGGAT
*
350071 GCATCGATGCACTAGTGCA-GG-
66 GCATAGATGCAC---TGCAGGGA
* *
350092 TGCATGGATGCACTGCAGGGATGCATCGATGCACTAGTGCAGGTGCATGGATGCATTGCAGGGAT
1 TGCATAGATGCACTGCAGGGATGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCAGGGAT
350157 GCATAGATGCACTGCAGGGA
66 GCATAGATGCACTGCAGGGA
* *
350177 TGCATAGATGCACTGCAGGGGTGCATGGATGCACT
1 TGCATAGATGCACTGCAGGGATGCATCGATGCACT
350212 TTGACACCCT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
83 4 0.04
84 18 0.17
85 72 0.68
86 12 0.11
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.24
Consensus pattern (85 bp):
TGCATAGATGCACTGCAGGGATGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCAGGGAT
GCATAGATGCACTGCAGGGA
Found at i:350312 original size:29 final size:29
Alignment explanation
Indices: 350291--350348 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
350281 AAACTTTGAA
350291 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
350320 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
350349 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:350338 original size:30 final size:30
Alignment explanation
Indices: 350291--350350 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
350281 AAACTTTGAA
350291 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
350320 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
350351 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:350844 original size:27 final size:27
Alignment explanation
Indices: 350788--350844 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
350778 CTTGGATAAG
* * *
350788 AAATTACAAAAATAGCCCTATGGAGTA
1 AAATTACAAAAATAGCCATATGCAGCA
*
350815 AAATTACAAAAAT-GCCATAGTGCTGCA
1 AAATTACAAAAATAGCCATA-TGCAGCA
350842 AAA
1 AAA
350845 AGACCAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (27 bp):
AAATTACAAAAATAGCCATATGCAGCA
Found at i:355840 original size:32 final size:32
Alignment explanation
Indices: 355801--355919 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
355791 GTAACTGTTT
* * **
355801 TGCATTATCTAAATGCGACACTGACACTCCTA
1 TGCATTATCTGAATGCAACACTGACACTATTA
* * * * *
355833 TGCATTATTTGAATACAACATTGACTCTATTG
1 TGCATTATCTGAATGCAACACTGACACTATTA
* * *
355865 TGCATCATCTGAATGCAACACTTACACTGTTA
1 TGCATTATCTGAATGCAACACTGACACTATTA
* *
355897 TGCATTACCTGAATGCGACACTG
1 TGCATTATCTGAATGCAACACTG
355920 CTAGTATCTG
Statistics
Matches: 66, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTGACACTATTA
Found at i:356264 original size:32 final size:32
Alignment explanation
Indices: 356194--356311 Score: 119
Period size: 32 Copynumber: 3.7 Consensus size: 32
356184 GTAACTGCTT
** ** *
356194 TGCATTATCTAAATGTGACACTGACACTCATA
1 TGCATTATCTAAATGCAACACTGACACTGTTG
* * **
356226 TACATTATCTAAATGCAACAGTGACTTTGTTG
1 TGCATTATCTAAATGCAACACTGACACTGTTG
* * *
356258 TGCATTATCTGAATGTAACACTTACACTGTTG
1 TGCATTATCTAAATGCAACACTGACACTGTTG
*
356290 TGCATTACCTAAATGCAACACT
1 TGCATTATCTAAATGCAACACT
356312 ACTAGTATCT
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (32 bp):
TGCATTATCTAAATGCAACACTGACACTGTTG
Found at i:356382 original size:393 final size:392
Alignment explanation
Indices: 355653--356410 Score: 1239
Period size: 393 Copynumber: 1.9 Consensus size: 392
355643 CAGTAGGTAT
* *
355653 ATGCATGATCTTAATTAAGTGCTACCTACTTAAGGTTTTACTGTTCTATTGCTGAAGTATGAGTC
1 ATGCATGATCTTAATTAAGTGCTACCTACTTAAGGTTTTACTATTCTATTGCTGAAGTAGGAGTC
* * *
355718 TCATGCTTTCTTAATCCTTTGCTAAGAGCCTCTCCATGAGTACACCTCTATTGGGTCTCTACCCA
66 TCATGCTTCCTTAATCCTCTACTAAGAGCCTCTCCATGAGTACACCTCTATTGGGTCTCTACCCA
* * * * * *
355783 CACTGACTGTAACTGTTTTGCATTATCTAAATGCGACACTGACACTCCTATGCATTATTTGAATA
131 CACTAACTGTAACTGCTTTGCATTATCTAAATGCGACACTGACACTCATATACATTATCTAAATA
* *
355848 CAACATTGACTCTATTGTGCATCATCTGAATGCAACACTTACACTGTTATGCATTACCTGAATGC
196 CAACAGTGACTCTATTGTGCATCATCTGAATGCAACACTTACACTGTTATGCATTACCTAAATGC
* * *
355913 GACACTGCTAGTATCTGGCCTCACATAGCCATTATATACTAGTTAACTGAGGGAATTCAGTGTCA
261 AACACTACTAGTATCTGGCCTCACATAGCCATTATATACTAGTTAACTGAGGGAATTCAATGTCA
*
355978 CATAATATAGGTAAAATTCCCATTAAGTTGTTGAATGATCTATTGGCCTCACATAGTAATCAAGT
326 CATAATATAGGTAAAATTCCCACTAAGTTGTTGAATGATCTATTGGCCTCACATAGTAATCAAGT
356043 AC
391 AC
356045 ATGCATGATCTTAATTAAGTGCTACCTACTTAAGGTTTTACTATTCTATTGCTGAAGTAGGAGTC
1 ATGCATGATCTTAATTAAGTGCTACCTACTTAAGGTTTTACTATTCTATTGCTGAAGTAGGAGTC
356110 TCATGCTTCCCTTAATCCTCTACTAAGAGCCT-TGCCATGAGTACACCTCTATTGGGTCTCTACC
66 TCATGCTT-CCTTAATCCTCTACTAAGAGCCTCT-CCATGAGTACACCTCTATTGGGTCTCTACC
*
356174 CACACTAACTGTAACTGCTTTGCATTATCTAAATGTGACACTGACACTCATATACATTATCTAAA
129 CACACTAACTGTAACTGCTTTGCATTATCTAAATGCGACACTGACACTCATATACATTATCTAAA
* * * * * *
356239 TGCAACAGTGACTTTGTTGTGCATTATCTGAATGTAACACTTACACTGTTGTGCATTACCTAAAT
194 TACAACAGTGACTCTATTGTGCATCATCTGAATGCAACACTTACACTGTTATGCATTACCTAAAT
* *
356304 GCAACACTACTAGTATCTGGCCTCACATGGCCATTATATACTAGTTAATTGAGGGAATTCAATGT
259 GCAACACTACTAGTATCTGGCCTCACATAGCCATTATATACTAGTTAACTGAGGGAATTCAATGT
* *
356369 CACATAGTATAGGTAAAATTTCCACTAAGTTGTTGAATGATC
324 CACATAATATAGGTAAAATTCCCACTAAGTTGTTGAATGATC
356411 CCCTGGTCTG
Statistics
Matches: 336, Mismatches: 28, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
392 72 0.21
393 264 0.79
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (392 bp):
ATGCATGATCTTAATTAAGTGCTACCTACTTAAGGTTTTACTATTCTATTGCTGAAGTAGGAGTC
TCATGCTTCCTTAATCCTCTACTAAGAGCCTCTCCATGAGTACACCTCTATTGGGTCTCTACCCA
CACTAACTGTAACTGCTTTGCATTATCTAAATGCGACACTGACACTCATATACATTATCTAAATA
CAACAGTGACTCTATTGTGCATCATCTGAATGCAACACTTACACTGTTATGCATTACCTAAATGC
AACACTACTAGTATCTGGCCTCACATAGCCATTATATACTAGTTAACTGAGGGAATTCAATGTCA
CATAATATAGGTAAAATTCCCACTAAGTTGTTGAATGATCTATTGGCCTCACATAGTAATCAAGT
AC
Found at i:359366 original size:13 final size:14
Alignment explanation
Indices: 359345--359380 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
359335 TTTTAGGGTG
359345 TATAATTTAAAATT
1 TATAATTTAAAATT
*
359359 TA-AATTTAAGATT
1 TATAATTTAAAATT
359372 TATAATTTA
1 TATAATTTA
359381 GAATCTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATAATTTAAAATT
Found at i:359399 original size:21 final size:19
Alignment explanation
Indices: 359354--359402 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
359344 GTATAATTTA
* *
359354 AAATTTAAATTTAAGATTT
1 AAATTTAAATCTAAGATTG
359373 ATAATTTAGAATCTAAGAATTG
1 A-AATTTA-AATCTAAG-ATTG
359395 AAATTTAA
1 AAATTTAA
359403 GATTTTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 13 0.52
22 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATTTAAATCTAAGATTG
Found at i:359849 original size:2 final size:2
Alignment explanation
Indices: 359842--359881 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
359832 GAACCCTTAA
359842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
359882 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361211 original size:2 final size:2
Alignment explanation
Indices: 361192--361230 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
361182 TAATAATTAA
*
361192 AT AT A- AT AT TT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
361231 CTGATAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:361215 original size:20 final size:19
Alignment explanation
Indices: 361177--361230 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
361167 GTCAATTATC
*
361177 ATATTTAATA-ATTAAATAT
1 ATATTTAATATA-TATATAT
361196 AATATTTAATATATATATAT
1 -ATATTTAATATATATATAT
*
361216 ATATAT-ATATATATA
1 ATATTTAATATATATA
361231 CTGATAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.29
19 5 0.16
20 16 0.52
21 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTTAATATATATATAT
Found at i:361793 original size:23 final size:22
Alignment explanation
Indices: 361770--361847 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
361760 TTTAATATAT
361770 TTATATTTTTAAACTAAATTTA
1 TTATATTTTTAAACTAAATTTA
* ** *
361792 TTATTATTATTCTAC-ATATTTCA
1 TTA-TATTTTTAAACTAAATTT-A
361815 -TATATTTTTAAACTAAATTTA
1 TTATATTTTTAAACTAAATTTA
361836 TTAATATATTTT
1 TT-ATAT-TTTT
361848 CAAAATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
21 9 0.21
22 16 0.38
23 13 0.31
24 4 0.10
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATTTTTAAACTAAATTTA
Found at i:361798 original size:25 final size:24
Alignment explanation
Indices: 361767--361847 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 24
361757 GAGTTTAATA
361767 TATT-TATATTTTTAAACTAAATT
1 TATTATATATTTTTAAACTAAATT
* *
361790 TATTAT-TATTATT---CTACATAT
1 TATTATATATTTTTAAACTAAAT-T
*
361811 T-TCATATATTTTTAAACTAAATT
1 TATTATATATTTTTAAACTAAATT
361834 TATTAATATATTTT
1 TATT-ATATATTTT
361848 CAAAATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 8 0.18
21 8 0.18
23 12 0.27
24 7 0.16
25 9 0.20
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTATATATTTTTAAACTAAATT
Found at i:361834 original size:22 final size:21
Alignment explanation
Indices: 361771--361836 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 21
361761 TTAATATATT
361771 TATATTTTTAAACTAAATTTA
1 TATATTTTTAAACTAAATTTA
* **
361792 T-TATTATTATTCTACATATTTCA
1 TATATTTTTAAACTA-A-ATTT-A
361815 TATATTTTTAAACTAAATTTA
1 TATATTTTTAAACTAAATTTA
361836 T
1 T
361837 TAATATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
20 10 0.29
21 4 0.11
22 8 0.23
23 3 0.09
24 10 0.29
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTTTTAAACTAAATTTA
Found at i:363644 original size:77 final size:76
Alignment explanation
Indices: 363558--363779 Score: 302
Period size: 77 Copynumber: 2.9 Consensus size: 76
363548 CCTAACAATG
* *
363558 TCATGGTTCACTAAGAATTAGGTTATGATCTGTAATGTTAATATTTTTATTAATAAAATGGGTTG
1 TCATGGTTCACTAAGAAATAGGTTGTGATCTG-AATGTTAATATTTTTATTAATAAAATGGGTTG
**
363623 TGCCCAAGAATA
65 CACCCAAGAATA
* * * * *
363635 TCATGGTTCATTAAGAAATAAGTTGTGATATAGAATGTTAATATTTTTATTAACAAAATGGGTAG
1 TCATGGTTCACTAAGAAATAGGTTGTGATCT-GAATGTTAATATTTTTATTAATAAAATGGGTTG
363700 CACCCAAGAATA
65 CACCCAAGAATA
* * *
363712 TCATGCTTCACTAAGAAATAGGTTGGGATCTGGAATGTTAATATTTTT-TTAATAAAATGAGTTG
1 TCATGGTTCACTAAGAAATAGGTTGTGATCT-GAATGTTAATATTTTTATTAATAAAATGGGTTG
363776 CACC
65 CACC
363780 TAAAATGTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
76 17 0.13
77 108 0.86
78 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (76 bp):
TCATGGTTCACTAAGAAATAGGTTGTGATCTGAATGTTAATATTTTTATTAATAAAATGGGTTGC
ACCCAAGAATA
Found at i:364009 original size:184 final size:184
Alignment explanation
Indices: 363718--364329 Score: 906
Period size: 184 Copynumber: 3.3 Consensus size: 184
363708 AATATCATGC
* * * * *
363718 TTCACTAAGAAATAGGTTGGGATCTGGAATGTTAATATTTTT-TTAATAAAATGAGTTGCACCTA
1 TTCACTAAGAAATATGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCACCTA
* * * * *
363782 AAATGTTACCACA-ATTAAAACTGATGGAGCATTAGATTTTCCCACTATAAGAAAATAAATTAAA
66 AAATGTTA-CATAGTTTAAGA-TGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAATTAAA
363846 AACTAAAAATGTTATGAATATATATAAAATATGGTTGCGTCAAAAAATTGTCATTA
129 AACTAAAAATGTTATGAATATATATAAAATATGGTTGCGTCAAAAAATTGTCATTA
* *
363902 TTCACTGAGAAATTTGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCACCTA
1 TTCACTAAGAAATATGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCACCTA
363967 AAATGTTACATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAATTAAAAA
66 AAATGTTACATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAATTAAAAA
364032 CTAAAAATGTTATGAATATATATAAAATATGGTTGCGTCAAAAAATTGTCATTA
131 CTAAAAATGTTATGAATATATATAAAATATGGTTGCGTCAAAAAATTGTCATTA
* * *
364086 TTCACTGAGAAATTTGTTGCGATTTGAAATGTTAATATTTTTATTAATTAAATGGGTTGCACCTA
1 TTCACTAAGAAATATGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCACCTA
*
364151 AAATGTTACATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAGTTAAAAA
66 AAATGTTACATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAATTAAAAA
* * * * * * **
364216 CTGAAAATGTTAGGAATATATATAAGAAATACGGTTGCGCCTAAAAA-TATCATGG
131 CTAAAAATGTTATGAATATATAT-A-AAATATGGTTGCGTCAAAAAATTGTCATTA
* * * * *
364271 TTAACTAAGAAACATGTTGCAATATGAAATGTTGATATTTTTATTAATAAAATGGGTTG
1 TTCACTAAGAAATATGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTG
364330 GGCCCAAGAA
Statistics
Matches: 394, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
184 285 0.72
185 91 0.23
186 18 0.05
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (184 bp):
TTCACTAAGAAATATGTTGCGATTTGAAATGTTAATATTTTTATTAATAAAATGGGTTGCACCTA
AAATGTTACATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATAAATTAAAAA
CTAAAAATGTTATGAATATATATAAAATATGGTTGCGTCAAAAAATTGTCATTA
Found at i:364861 original size:260 final size:261
Alignment explanation
Indices: 364078--364920 Score: 932
Period size: 260 Copynumber: 3.2 Consensus size: 261
364068 GTCAAAAAAT
* * ** * * *
364078 TGTCATTATTCACTGAGAAATTTGTTGCGATTTGAAATGTTAATATTTTTATTAATTAAATGGGT
1 TGTCATGATTCACTAAGAAATAGGTTACAATTTGAAATGTTAATATTTTTATTAA-TAAATGGAT
* *
364143 TGCACCTAAAATGTTA-CATAGTTTAAGATGATGGAGCATTGGATTTTCCCACGATAAGAAAATA
65 TGCACCTAAAATGTTACCACAGTTTAAGCTGATGGAGCATT-GATTTTCCCACGATAAGAAAATA
* * *
364207 AGTTAAAAACTGAAAATGTTAGGAATATATATAAGAAATACGGTTGCGCCTAAAAATATCATGGT
129 AGTTAAAAACTGAAAATGTTATGAATATATATAAGAAATATGGTTGCGCCTAAAAATATCATGAT
* * *
364272 TAACTAAGAAACATGTTGCAATATGAAATGTTGATATTTTTATTAATAAAATGGGTTGGGCCCAA
194 TAACTAAGAAACATGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGCGCCCAA
364337 GAA
259 GAA
* * *
364340 TGTCATGATTCA-TGAAGAAATAGGTTACAATATGAAATATT-AT-TTTTT-TTAATAAAATGAA
1 TGTCATGATTCACT-AAGAAATAGGTTACAATTTGAAATGTTAATATTTTTATTAAT-AAATGGA
** * * * * * * *
364401 TTGCGTCTAAAATCTTACCACGGTTTAAACTGATGGAGCATAGGGTTTTCTCATGATAAGAAAAT
64 TTGCACCTAAAATGTTACCACAGTTTAAGCTGATGGAGCAT-TGATTTTCCCACGATAAGAAAAT
* * * *
364466 AAGTTAAAAACTGAAAATATTATGAATATATATAAAAAAATATGGTTGCGTCTAAAAATGTCAT-
128 AAGTTAAAAACTGAAAATGTTATGAATATATAT-AAGAAATATGGTTGCGCCTAAAAATATCATG
* * * * * *
364530 AGTTTACTAAGAAACATGTTGGGATCT-AGAATGTTAATATTTTTATTAATAAAATGAGTTACAC
192 A-TTAACTAAGAAACATGTTGCGATATGA-AATGTTAATATTTTTATTAATAAAATGGGTTGCGC
364594 CCAAGAA
255 CCAAGAA
* * * ** *
364601 TGTC-TCATTCACTAAGAAATAGGTTGCGACCTGGAATGTTAATATTTTT-TTAATAAATTGGAT
1 TGTCATGATTCACTAAGAAATAGGTTACAATTTGAAATGTTAATATTTTTATTAATAAA-TGGAT
* * * * *
364664 TGTACCTAAAATGTTACCACAATTTAAGCTAATTGAGCATTGAATTTCCCACGATAAGAAAATAA
65 TGCACCTAAAATGTTACCACAGTTTAAGCTGATGGAGCATTGATTTTCCCACGATAAGAAAATAA
* * * * *
364729 ATTGAAAATTGAAAATGTTATGAATATATATAAGAAATATGGTTGTGCCTAAAAATATCATGATA
130 GTTAAAAACTGAAAATGTTATGAATATATATAAGAAATATGGTTGCGCCTAAAAATATCATGATT
* * * ** * * * *
364794 AATTAAGAAATAGGTCACGATATGAAATTTTAATATTTTTATTAATAAAATGGGATGTGCTCAAG
195 AACTAAGAAACATGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGCGCCCAAG
364859 AA
260 AA
* **
364861 TGTCATGGTTCACTACTAAATAGGTTACAATATTTG-AATGTTAATATTTTTATTAATAAA
1 TGTCATGATTCACTAAGAAATAGGTTAC-A-ATTTGAAATGTTAATATTTTTATTAATAAA
364921 ATAGGTTGCA
Statistics
Matches: 473, Mismatches: 91, Indels: 33
0.79 0.15 0.06
Matches are distributed among these distances:
258 1 0.00
259 23 0.05
260 183 0.39
261 164 0.35
262 91 0.19
263 11 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (261 bp):
TGTCATGATTCACTAAGAAATAGGTTACAATTTGAAATGTTAATATTTTTATTAATAAATGGATT
GCACCTAAAATGTTACCACAGTTTAAGCTGATGGAGCATTGATTTTCCCACGATAAGAAAATAAG
TTAAAAACTGAAAATGTTATGAATATATATAAGAAATATGGTTGCGCCTAAAAATATCATGATTA
ACTAAGAAACATGTTGCGATATGAAATGTTAATATTTTTATTAATAAAATGGGTTGCGCCCAAGA
A
Found at i:365520 original size:75 final size:76
Alignment explanation
Indices: 365153--365541 Score: 411
Period size: 76 Copynumber: 5.1 Consensus size: 76
365143 TCTTGTGTAT
* * *
365153 AACCCA-TTTATTAATAAAAATATTAACA-TTCAAATCACACCTTATTTCTTAACT-AACCATGA
1 AACCCATTTTATTAATAAAAAT-TTAACATTTCAGATCACAACTTATTTCTT-AGTGAACCATGA
*
365215 CATTTTTTGG-CGC
64 CA-TTCTTGGACGC
* * * * * * *
365228 ATCCCATTTTATT--TAAAAAATAAAAATATTCCAAATCACAACCTATTTCTTAGTGAACCATAA
1 AACCCATTTTATTAATAAAAATTTAACAT-TT-CAGATCACAACTTATTTCTTAGTGAACCATGA
365291 CATTCTTGGACGC
64 CATTCTTGGACGC
* * * * ** *
365304 AACTCATTTTATTAATAAAAAATTAATATTAT-TGATCGTAACTTATTTCTTAGTAAACCATGAC
1 AACCCATTTTATTAATAAAAATTTAACATT-TCAGATCACAACTTATTTCTTAGTGAACCATGAC
365368 ATTCTT-GAGCGC
65 ATTCTTGGA-CGC
*
365380 AACCCATTTTATTAATAAAAATATTAACATTCCAGATCGTA-AACTTATTTCTTAGTGAACCATG
1 AACCCATTTTATTAATAAAAAT-TTAACATTTCAGATC--ACAACTTATTTCTTAGTGAACCATG
365444 ACATTCTTGGACGC
63 ACATTCTTGGACGC
* * *
365458 AACACATTTTATTAA-AAAAATTTAACATTTTAGATCACAACTTATTTCTTAGTGAACAATGACA
1 AACCCATTTTATTAATAAAAATTTAACATTTCAGATCACAACTTATTTCTTAGTGAACCATGACA
365522 TTCTTGGACGC
66 TTCTTGGACGC
*
365533 AACTCATTT
1 AACCCATTT
365542 GTAATATATT
Statistics
Matches: 266, Mismatches: 32, Indels: 32
0.81 0.10 0.10
Matches are distributed among these distances:
73 4 0.02
74 7 0.03
75 61 0.23
76 114 0.43
77 18 0.07
78 60 0.23
79 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (76 bp):
AACCCATTTTATTAATAAAAATTTAACATTTCAGATCACAACTTATTTCTTAGTGAACCATGACA
TTCTTGGACGC
Found at i:365536 original size:37 final size:37
Alignment explanation
Indices: 365421--365541 Score: 95
Period size: 37 Copynumber: 3.2 Consensus size: 37
365411 CCAGATCGTA
* *
365421 AACTTATTTCTTAGTGAACCATGACATTCTTGGACGC
1 AACTCATTTCTTAGTGAACAATGACATTCTTGGACGC
* * * * * * *
365458 AACACA-TT-TTATTAAAAAAATTTAACATT-TTAGATCAC
1 AACTCATTTCTTAGT-GAACAA--TGACATTCTTGGA-CGC
*
365496 AACTTATTTCTTAGTGAACAATGACATTCTTGGACGC
1 AACTCATTTCTTAGTGAACAATGACATTCTTGGACGC
365533 AACTCATTT
1 AACTCATTT
365542 GTAATATATT
Statistics
Matches: 59, Mismatches: 18, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
35 4 0.07
36 5 0.08
37 24 0.41
38 16 0.27
39 6 0.10
40 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (37 bp):
AACTCATTTCTTAGTGAACAATGACATTCTTGGACGC
Found at i:365541 original size:153 final size:151
Alignment explanation
Indices: 365159--365541 Score: 454
Period size: 153 Copynumber: 2.5 Consensus size: 151
365149 GTATAACCCA
* * * * *
365159 TTTATTAATAAAAATATTAACA-TTCAAATCACACCTTATTTCTTAACTAACCATGACATTTTTT
1 TTTATTAATAAAAAT-TTAACATTTTAGATCACAACTTATTTCTT-AGTAACCATGACA-TTCTT
* * *
365223 GG-CGCATCCCATTTTATTTAAAAAATAAAAATATTCCAAATCACAACCTATTTCTTAGTGAACC
63 GGACGCAACCCATTTTATTAAAAAAATAAAAACATTCCAAATCACAACCTATTTCTTAGTGAACC
*
365287 ATAACATTCTTGGACGCAACTCAT
128 ATAACATTCTTGGACGCAACACAT
* * **
365311 TTTATTAATAAAAAATTAATATTATT-GATCGTAACTTATTTCTTAGTAAACCATGACATTCTT-
1 TTTATTAATAAAAATTTAACATT-TTAGATCACAACTTATTTCTTAGT-AACCATGACATTCTTG
** * *
365374 GAGCGCAACCCATTTTATTAATAAAAATATTAACATTCCAGATCGTA-AACTTATTTCTTAGTGA
64 GA-CGCAACCCATTTTATTAA-AAAAATAAAAACATTCCAAATC--ACAACCTATTTCTTAGTGA
*
365438 ACCATGACATTCTTGGACGCAACACAT
125 ACCATAACATTCTTGGACGCAACACAT
*
365465 TTTATTAA-AAAAATTTAACATTTTAGATCACAACTTATTTCTTAGTGAACAATGACATTCTTGG
1 TTTATTAATAAAAATTTAACATTTTAGATCACAACTTATTTCTTAGT-AACCATGACATTCTTGG
*
365529 ACGCAACTCATTT
65 ACGCAACCCATTT
365542 GTAATATATT
Statistics
Matches: 196, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
150 1 0.01
151 11 0.06
152 57 0.29
153 75 0.38
154 51 0.26
155 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (151 bp):
TTTATTAATAAAAATTTAACATTTTAGATCACAACTTATTTCTTAGTAACCATGACATTCTTGGA
CGCAACCCATTTTATTAAAAAAATAAAAACATTCCAAATCACAACCTATTTCTTAGTGAACCATA
ACATTCTTGGACGCAACACAT
Found at i:365645 original size:125 final size:123
Alignment explanation
Indices: 365425--365666 Score: 335
Period size: 125 Copynumber: 2.0 Consensus size: 123
365415 ATCGTAAACT
**
365425 TATTTCTTAGTGAACCATGACATTCTTGGACGCAACACATTTTATTAAAAAAATTTAACATTTTA
1 TATTTCTTAGTGAACCATGACATTCTTGGACGCAACACATTTTATTAAAAAAATTTAACATTACA
365490 GATCACAACTTATTTCTTAGTGAACAATGACATTCTTGGACGCAACTCATTTGTAATA
66 GATCACAACTTATTTCTTAGTGAACAATGACATTCTTGGACGCAACTCATTTGTAATA
* * **
365548 TATTTCTTAGTGAATCATTACATT-TTGGGGTGCAAC-CTATTTTATTAATAAAAATATTAACAT
1 TATTTCTTAGTGAACCATGACATTCTT-GGACGCAACAC-ATTTTATTAA-AAAAAT-TTAACAT
** * * *
365611 TACAGATCGTAACTTATTTCTTAGTGAACCATGACATTCTTGGATGCAACTTATTT
62 TACAGATCACAACTTATTTCTTAGTGAACAATGACATTCTTGGACGCAACTCATTT
365667 TATTAATAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
122 3 0.03
123 39 0.38
124 6 0.06
125 56 0.54
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (123 bp):
TATTTCTTAGTGAACCATGACATTCTTGGACGCAACACATTTTATTAAAAAAATTTAACATTACA
GATCACAACTTATTTCTTAGTGAACAATGACATTCTTGGACGCAACTCATTTGTAATA
Found at i:365675 original size:77 final size:76
Alignment explanation
Indices: 365548--365744 Score: 270
Period size: 77 Copynumber: 2.5 Consensus size: 76
365538 ATTTGTAATA
* * * *
365548 TATTTCTTAGTGAATCATTACATTTTGGGGTGCAACCTATTTTATTAATAAAAATATTAACATTA
1 TATTTCTTAGTGAACCATGACATTTT-AGGTGCAACTTATTTTATTAATAAAAATATTAACATTA
* *
365613 CAGATCGTAACT
65 CAGATCGCAACC
365625 TATTTCTTAGTGAACCATGACATTCTT-GGATGCAACTTATTTTATTAATAAAAATATTAACATT
1 TATTTCTTAGTGAACCATGACATT-TTAGG-TGCAACTTATTTTATTAATAAAAATATTAACATT
*
365689 ACATATCGCAACC
64 ACAGATCGCAACC
*
365702 TGTTTCTTAGTGAACCATGACATTTTTAGGTGCAACTGTATTT
1 TATTTCTTAGTGAACCATGACA-TTTTAGGTGCAACT-TATTT
365745 CTTATATATA
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
76 2 0.02
77 95 0.88
78 11 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (76 bp):
TATTTCTTAGTGAACCATGACATTTTAGGTGCAACTTATTTTATTAATAAAAATATTAACATTAC
AGATCGCAACC
Found at i:365700 original size:40 final size:40
Alignment explanation
Indices: 365579--365700 Score: 101
Period size: 40 Copynumber: 3.1 Consensus size: 40
365569 ATTTTGGGGT
* *
365579 GCAACCTATTTTATTAATAAAAATATTAACATTACAGATC
1 GCAACTTATTTTATTAATAAAAATATTAACATTACATATC
* * * * ** * *
365619 GTAACTTA-TTTCTTAGT-GAACCA-TGACATT-CTTGGAT-
1 GCAACTTATTTTATTAATAAAAATATTAACATTACAT--ATC
365656 GCAACTTATTTTATTAATAAAAATATTAACATTACATATC
1 GCAACTTATTTTATTAATAAAAATATTAACATTACATATC
365696 GCAAC
1 GCAAC
365701 CTGTTTCTTA
Statistics
Matches: 57, Mismatches: 18, Indels: 14
0.64 0.20 0.16
Matches are distributed among these distances:
36 1 0.02
37 13 0.23
38 12 0.21
39 12 0.21
40 17 0.30
41 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (40 bp):
GCAACTTATTTTATTAATAAAAATATTAACATTACATATC
Found at i:367206 original size:19 final size:22
Alignment explanation
Indices: 367184--367225 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
367174 AAAGTTTGTT
367184 AATGATAAA-AA-A-AATTAGA
1 AATGATAAATAATAGAATTAGA
367203 AATGATAAATAATAGAATTAGA
1 AATGATAAATAATAGAATTAGA
367225 A
1 A
367226 CCTGCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 1 0.05
22 8 0.40
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (22 bp):
AATGATAAATAATAGAATTAGA
Found at i:368220 original size:35 final size:35
Alignment explanation
Indices: 368175--368502 Score: 264
Period size: 35 Copynumber: 9.3 Consensus size: 35
368165 CATAATAAAT
*
368175 AATATATAATATATAGTTTTGAAAACATTTTTGAA
1 AATATATAATATATAATTTTGAAAACATTTTTGAA
* * **
368210 AATATATAATATATTATTTTGAAAACGTTTGAGAA
1 AATATATAATATATAATTTTGAAAACATTTTTGAA
* ****
368245 AATATATAAT-TTTGAATTTTGAATTTTTTTTTG--
1 AATATATAATATAT-AATTTTGAAAACATTTTTGAA
* *
368278 ---A-AT--TATATAGTTTTGAAATCATTTTTGAA
1 AATATATAATATATAATTTTGAAAACATTTTTGAA
* *
368307 AATATATAATATATAATTTTGAAAATATTTTTAAAA
1 AATATATAATATATAATTTTGAAAACATTTTT-GAA
* *
368343 ACATATATAATGTATAGTTTTGAAAACA-TTTTGAA
1 A-ATATATAATATATAATTTTGAAAACATTTTTGAA
* *
368378 AATATATAATATATAATTTTGAAAACGTTTTGGAA
1 AATATATAATATATAATTTTGAAAACATTTTTGAA
368413 AATATATATATATTATATATTTTAGAAAACA-TTTTGAA
1 AATATATA-ATA-TATA-ATTTT-GAAAACATTTTTGAA
* * * **
368451 AATTTATATATAATATAATATTTTGAAAAAAAATTCCGAA
1 AATATATA-AT-ATAT-A-ATTTTG-AAAACATTTTTGAA
368491 AATATATAATAT
1 AATATATAATAT
368503 TATTTTTTAT
Statistics
Matches: 235, Mismatches: 37, Indels: 39
0.76 0.12 0.13
Matches are distributed among these distances:
27 16 0.07
28 2 0.01
29 2 0.01
30 1 0.00
32 1 0.00
33 2 0.01
34 25 0.11
35 89 0.38
36 10 0.04
37 27 0.11
38 27 0.11
39 21 0.09
40 12 0.05
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (35 bp):
AATATATAATATATAATTTTGAAAACATTTTTGAA
Found at i:368383 original size:97 final size:97
Alignment explanation
Indices: 368185--368383 Score: 233
Period size: 97 Copynumber: 2.1 Consensus size: 97
368175 AATATATAAT
* * *
368185 ATATAGTTTTGAAAACATTTTTGAAAATATATAATATATTATTTTGAAAACGTTTGAGAAAATAT
1 ATATAGTTTTGAAAACATTTTTGAAAATATATAATATATAATTTTGAAAAAGTTTGAAAAAATAT
* **** *
368250 ATAATTTTGAATTTTGAATTTTTTTTTGAATT
66 ATAATTATGAATTTTGAATAACATTTTGAATA
* * *
368282 ATATAGTTTTGAAATCATTTTTGAAAATATATAATATATAATTTTGAAAATATTTTTAAAAACAT
1 ATATAGTTTTGAAAACATTTTTGAAAATATATAATATATAATTTTGAAAA-AGTTTGAAAAA-AT
*
368347 ATATAATGTAT-AGTTTTGAA-AACATTTTGAA-A
64 ATATAAT-TATGAATTTTGAATAACATTTTGAATA
368379 ATATA
1 ATATA
368384 TAATATATAA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
97 53 0.62
98 14 0.16
99 17 0.20
100 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (97 bp):
ATATAGTTTTGAAAACATTTTTGAAAATATATAATATATAATTTTGAAAAAGTTTGAAAAAATAT
ATAATTATGAATTTTGAATAACATTTTGAATA
Found at i:368444 original size:73 final size:71
Alignment explanation
Indices: 368278--368479 Score: 244
Period size: 71 Copynumber: 2.7 Consensus size: 71
368268 TTTTTTTTTG
* * *
368278 AATTATATAGTTTTGAAATCATTTTTGAAAATATATAATATATAATTTTGAAAATATTTTTAAAA
1 AATTATATA-TTTTGAAAACA-TTTTGAAAATATATAATATATAATTTTGAAAACATTTTGAAAA
368343 ACATATAT
64 ACATATAT
* * *
368351 AATGTATA-GTTTTGAAAACATTTTGAAAATATATAATATATAATTTTGAAAACGTTTTGGAAAA
1 AAT-TATATATTTTGAAAACATTTTGAAAATATATAATATATAATTTTGAAAACATTTTGAAAAA
*
368415 TATATAT
65 CATATAT
*
368422 ATATTATATATTTTAGAAAACATTTTGAAAATTTATATATAATATAATATTTTGAAAA
1 A-ATTATATATTTT-GAAAACATTTTGAAAATATATA-AT-ATAT-A-ATTTTGAAAA
368480 AAAATTCCGA
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
71 51 0.46
72 16 0.14
73 24 0.21
74 6 0.05
75 4 0.04
76 1 0.01
77 10 0.09
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (71 bp):
AATTATATATTTTGAAAACATTTTGAAAATATATAATATATAATTTTGAAAACATTTTGAAAAAC
ATATAT
Found at i:368896 original size:18 final size:18
Alignment explanation
Indices: 368873--368908 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
368863 TGTTTTAGCC
*
368873 GGTCAACCAACAACCCTT
1 GGTCAAACAACAACCCTT
*
368891 GGTCAAACAATAACCCTT
1 GGTCAAACAACAACCCTT
368909 AACCTCGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.33, G:0.11, T:0.19
Consensus pattern (18 bp):
GGTCAAACAACAACCCTT
Found at i:372891 original size:25 final size:25
Alignment explanation
Indices: 372857--372908 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
372847 CCAAAGTAGC
*
372857 TGCCCTATGCCTCGTTTCATTGGCA
1 TGCCCCATGCCTCGTTTCATTGGCA
*
372882 TGCCCCATGCCTTGTTTCATTGGCA
1 TGCCCCATGCCTCGTTTCATTGGCA
372907 TG
1 TG
372909 AACCTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.21, T:0.37
Consensus pattern (25 bp):
TGCCCCATGCCTCGTTTCATTGGCA
Found at i:377960 original size:15 final size:17
Alignment explanation
Indices: 377930--377961 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
377920 CCGTCGTGTC
377930 CACATACCCGAATCCGA
1 CACATACCCGAATCCGA
377947 CACAT-CCC-AATCCGA
1 CACATACCCGAATCCGA
377962 GTAACATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.34, C:0.44, G:0.09, T:0.12
Consensus pattern (17 bp):
CACATACCCGAATCCGA
Found at i:382874 original size:14 final size:15
Alignment explanation
Indices: 382855--382887 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
382845 GCTCTCTCAA
*
382855 TTCTCTC-TATTTTT
1 TTCTCTCGTATATTT
382869 TTCTCTCGTATATTT
1 TTCTCTCGTATATTT
382884 TTCT
1 TTCT
382888 TTTGCTCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TTCTCTCGTATATTT
Found at i:388614 original size:15 final size:15
Alignment explanation
Indices: 388594--388623 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
388584 TGTAAGTCTC
388594 TGTTTTGATCATTCA
1 TGTTTTGATCATTCA
*
388609 TGTTTTGGTCATTCA
1 TGTTTTGATCATTCA
388624 ATTATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (15 bp):
TGTTTTGATCATTCA
Found at i:391933 original size:23 final size:24
Alignment explanation
Indices: 391886--391933 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
391876 GAATCGTGCT
391886 ATAAGAACAGAGAAAATACGTGTC
1 ATAAGAACAGAGAAAATACGTGTC
* *
391910 ATAAGAGCAGAGGAAA-ACGTGTC
1 ATAAGAACAGAGAAAATACGTGTC
391933 A
1 A
391934 CAAAAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (24 bp):
ATAAGAACAGAGAAAATACGTGTC
Found at i:393474 original size:31 final size:31
Alignment explanation
Indices: 393439--393497 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
393429 CTTCATATAA
393439 TTTCTAAATTTGACA-CCACAAAATAAATATT
1 TTTCTAAATTTGACATCC-CAAAATAAATATT
*
393470 TTTCTAAATTTGATATCCCAAAATAAAT
1 TTTCTAAATTTGACATCCCAAAATAAAT
393498 TTTAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (31 bp):
TTTCTAAATTTGACATCCCAAAATAAATATT
Found at i:405834 original size:31 final size:31
Alignment explanation
Indices: 405810--405982 Score: 265
Period size: 31 Copynumber: 5.6 Consensus size: 31
405800 CCATAGATTT
* *
405810 CGAAGAACCTAGCTAATCAGTCCATATGTCC
1 CGAAGAACATAGCTAAACAGTCCATATGTCC
*
405841 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGCTAAACAGTCCATATGTCC
* *
405872 CGAAGAACATAGGTAAACAGTCTATATGTCC
1 CGAAGAACATAGCTAAACAGTCCATATGTCC
* *
405903 CGAAAAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGCTAAACAGTCCATATGTCC
*
405934 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGCTAAACAGTCCATATGTCC
*
405965 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGCTAAAC
405983 CCTCGACCCT
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 135 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGCTAAACAGTCCATATGTCC
Found at i:405893 original size:62 final size:62
Alignment explanation
Indices: 405810--405982 Score: 301
Period size: 62 Copynumber: 2.8 Consensus size: 62
405800 CCATAGATTT
* * *
405810 CGAAGAACCTAGCTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCC
* *
405872 CGAAGAACATAGGTAAACAGTCTATATGTCCCGAAAAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCC
405934 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAAC
405983 CCTCGACCCT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 104 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (62 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:410065 original size:31 final size:31
Alignment explanation
Indices: 410027--410182 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
410017 CCCGAAGGAC
* * *
410027 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
410058 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
410089 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
410120 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
410151 CAGTCCATATGTCCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
410182 C
1 C
410183 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:420541 original size:15 final size:15
Alignment explanation
Indices: 420523--420552 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
420513 CCACGGTGCT
420523 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
420538 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
420553 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:441683 original size:37 final size:37
Alignment explanation
Indices: 441635--441926 Score: 252
Period size: 38 Copynumber: 7.6 Consensus size: 37
441625 CGGTAAACGA
*
441635 TTTTCAAAAATATATATTATATAGTTTTTTAAAA-AACG
1 TTTTTAAAAATATATATTATATAG-TTTTTAAAATAA-G
*
441673 TTTTTAAAATATATATATAATATATA-TTTTTGAAAA-CA-
1 TTTTTAAAA-ATATATAT--TATATAGTTTTT-AAAATAAG
* * * *
441711 TTTTGAAAACATTTATATATTATATAATTTTTTTAAA-AAC
1 TTTTTAAAA-A--TATATATTATAT-AGTTTTTAAAATAAG
*
441751 TTTTTGAAAACATATATATTATATAGTTTTTAAAATTAATTT
1 TTTTT-AAAA-ATATATATTATATAGTTTTTAAAA-TAA--G
* * * *
441793 TTTTTAAAAATATACATTATATAATTTTGAAAATTAG
1 TTTTTAAAAATATATATTATATAGTTTTTAAAATAAG
* *
441830 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
1 TTTTT-AAAAATATATATTATATAGTTTTTAAAATAAG
* * *
441868 TTTTTAAAAATATATATTATATAGTTTTGAAAATTAT
1 TTTTTAAAAATATATATTATATAGTTTTTAAAATAAG
*
441905 TTTTTAAACATATATATTATAT
1 TTTTTAAAAATATATATTATAT
441927 TATATAGTTT
Statistics
Matches: 220, Mismatches: 19, Indels: 31
0.81 0.07 0.11
Matches are distributed among these distances:
37 57 0.26
38 66 0.30
39 32 0.15
40 44 0.20
41 16 0.07
42 5 0.02
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTTAAAAATATATATTATATAGTTTTTAAAATAAG
Found at i:441714 original size:11 final size:11
Alignment explanation
Indices: 441700--441724 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
441690 TAATATATAT
441700 TTTTGAAAACA
1 TTTTGAAAACA
441711 TTTTGAAAACA
1 TTTTGAAAACA
441722 TTT
1 TTT
441725 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:441793 original size:79 final size:75
Alignment explanation
Indices: 441634--441941 Score: 268
Period size: 79 Copynumber: 4.0 Consensus size: 75
441624 TCGGTAAACG
* * *
441634 ATTTTCAAAAATATATATTATATAGTTTTTTAAAAAACGTTTTTAAAATATATATATAATATATA
1 ATTTTTAAAAATATATATTATATAATTTTTTAAAAAAC-TTTTTAAAA-A-ATATATATTATATA
*
441699 -TTTTTGAAAA--C
63 GTTTTT-AAAATTA
* * *
441710 ATTTTGAAAACATTTATATATTATATAATTTTTTTAAAAACTTTTTGAAAACATATATATTATAT
1 ATTTTTAAAA-A--TATATATTATATAATTTTTTAAAAAACTTTTT-AAAAAATATATATTATAT
441775 AGTTTTTAAAATTA
62 AGTTTTTAAAATTA
* * * *
441789 ATTTTTTTTAAAAATATACATTATATAA-TTTTGAAAATTAGTTTTTAAAAAATATATATTATAT
1 A---TTTTTAAAAATATATATTATATAATTTTTTAAAA-AACTTTTTAAAAAATATATATTATAT
*
441853 AGTTTTGAAAATTA
62 AGTTTTTAAAATTA
* * * * *
441867 GTTTTTAAAAATATATATTATAT-AGTTTTGAAAATTATTTTTTAAACATATATATTATATTATA
1 ATTTTTAAAAATATATATTATATAATTTTTTAAAA-AACTTTTTAAA-A-A-ATA-TATATTATA
441931 TAG-TTTTAAAA
61 TAGTTTTTAAAA
441942 CGTTTTTTAT
Statistics
Matches: 198, Mismatches: 18, Indels: 30
0.80 0.07 0.12
Matches are distributed among these distances:
74 1 0.01
75 41 0.21
76 10 0.05
77 19 0.10
78 57 0.29
79 61 0.31
81 1 0.01
82 8 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (75 bp):
ATTTTTAAAAATATATATTATATAATTTTTTAAAAAACTTTTTAAAAAATATATATTATATAGTT
TTTAAAATTA
Found at i:441806 original size:38 final size:37
Alignment explanation
Indices: 441635--441926 Score: 261
Period size: 37 Copynumber: 7.6 Consensus size: 37
441625 CGGTAAACGA
* * * *
441635 TTTTCAAAAATATATATTATATAGTTTTTTAAAA-AACG
1 TTTTTAAAAATATATATTATATAG-TTTTGAAAATTA-T
* *
441673 TTTTTAAAATATATATATAATATATATTTTTGAAAA-CA-
1 TTTTTAAAA-ATATATAT--TATATAGTTTTGAAAATTAT
* * *
441711 TTTTGAAAACATTTATATATTATATAATTTTTTTAAAA--ACT
1 TTTTTAAAA-A--TATATATTATAT-A-GTTTTGAAAATTA-T
* *
441752 TTTTGAAAACATATATATTATATAGTTTTTAAAATTAATTT
1 TTTTTAAAA-ATATATATTATATAGTTTTGAAAATT-A--T
* *
441793 TTTTTAAAAATATACATTATATAATTTTGAAAATTAGT
1 TTTTTAAAAATATATATTATATAGTTTTGAAAATTA-T
* *
441831 TTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
1 TTTTTAAAAATATATATTATATAGTTTTGAAAATTAT
441868 TTTTTAAAAATATATATTATATAGTTTTGAAAATTAT
1 TTTTTAAAAATATATATTATATAGTTTTGAAAATTAT
*
441905 TTTTTAAACATATATATTATAT
1 TTTTTAAAAATATATATTATAT
441927 TATATAGTTT
Statistics
Matches: 220, Mismatches: 21, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
37 65 0.30
38 57 0.26
39 23 0.10
40 49 0.22
41 26 0.12
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTTAAAAATATATATTATATAGTTTTGAAAATTAT
Found at i:441979 original size:3 final size:3
Alignment explanation
Indices: 441962--441996 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
441952 ATCTATTTAT
441962 TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
441997 TATCACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:446879 original size:33 final size:31
Alignment explanation
Indices: 446794--446879 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 31
446784 AATTCTAAAT
* * *
446794 AAATAATAAT-TATATAAATATATTTTAATAA
1 AAATAATAATATTTA-AAAAATATATTAATAA
* *
446825 AAAAAAT-ATATTTACATAAATATATTAATATA
1 AAATAATAATATTTA-AAAAATATATTAATA-A
446857 AAATAATAACTATTTAAAAAATA
1 AAATAATAA-TATTTAAAAAATA
446880 CTAACATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
30 2 0.05
31 21 0.49
32 7 0.16
33 7 0.16
34 6 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AAATAATAATATTTAAAAAATATATTAATAA
Found at i:448442 original size:65 final size:65
Alignment explanation
Indices: 448338--448492 Score: 283
Period size: 65 Copynumber: 2.4 Consensus size: 65
448328 CGACGCCTTC
* * *
448338 GTGTGAATTTATTCACCATGCGGGCCTAGCAAGTAGCCTTCGGTATTCTTATACCTTATGTCTTT
1 GTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCCTTCGGGATTCATATACCTTATGTCTTT
448403 GTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCCTTCGGGATTCATATACCTTATGTCTTT
1 GTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCCTTCGGGATTCATATACCTTATGTCTTT
448468 GTGTGAATTTATTCACCGTGCGGGC
1 GTGTGAATTTATTCACCGTGCGGGC
448493 ATAAGGGAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 87 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (65 bp):
GTGTGAATTTATTCACCGTGCGGGCCTAGCAAGTAGCCTTCGGGATTCATATACCTTATGTCTTT
Found at i:450764 original size:16 final size:16
Alignment explanation
Indices: 450745--450785 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
450735 CGAGCCGAGT
450745 CGAGCTCGAGTATTGC
1 CGAGCTCGAGTATTGC
450761 CGAGCTCGAGTATTGC
1 CGAGCTCGAGTATTGC
450777 CGAGCTCGA
1 CGAGCTCGA
450786 CTCGAACTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.22
Consensus pattern (16 bp):
CGAGCTCGAGTATTGC
Found at i:450790 original size:21 final size:20
Alignment explanation
Indices: 450738--450790 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 20
450728 GTGTAAACGA
450738 GCCGAGTCGAGCTCGAGTATT
1 GCCGAGTCGA-CTCGAGTATT
450759 GCCGA---G-CTCGAGTATT
1 GCCGAGTCGACTCGAGTATT
450775 GCCGAGCTCGACTCGA
1 GCCGAG-TCGACTCGA
450791 ACTCGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 15 0.56
18 1 0.04
20 1 0.04
21 10 0.37
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21
Consensus pattern (20 bp):
GCCGAGTCGACTCGAGTATT
Found at i:450891 original size:31 final size:31
Alignment explanation
Indices: 450854--450933 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
450844 AATTTTCAAG
*
450854 CTCGACTCAAACTCGAAAGATAATAATGAAA
1 CTCGACTCGAACTCGAAAGATAATAATGAAA
450885 CTCGACTCGAACTCGAAAGATAATAATGAAA
1 CTCGACTCGAACTCGAAAGATAATAATGAAA
450916 CTCGACTCGAACTCGAAA
1 CTCGACTCGAACTCGAAA
450934 AGGCTCAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.19
Consensus pattern (31 bp):
CTCGACTCGAACTCGAAAGATAATAATGAAA
Found at i:450977 original size:11 final size:11
Alignment explanation
Indices: 450957--451058 Score: 57
Period size: 11 Copynumber: 8.9 Consensus size: 11
450947 CAACTGAAGC
450957 TCAAGACTCGAT
1 TCAAG-CTCGAT
*
450969 TGAAGCTCGATT
1 TCAAGCTCGA-T
**
450981 TTGAGCTCGAT
1 TCAAGCTCGAT
* *
450992 TCAAACTCAATTT
1 TCAAGCTCGA--T
*
451005 TGAA-CTCGAT
1 TCAAGCTCGAT
*
451015 TCAAGCTTGAT
1 TCAAGCTCGAT
451026 T-ATGAGCTCGAT
1 TCA--AGCTCGAT
451038 TCAAGCTCGACT
1 TCAAGCTCGA-T
451050 T-AAGCTCGA
1 TCAAGCTCGA
451059 GAATGGGTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
10 5 0.07
11 33 0.47
12 27 0.39
13 5 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:451004 original size:23 final size:23
Alignment explanation
Indices: 450963--451047 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
450953 AAGCTCAAGA
*
450963 CTCGATTGAAGCTCGATTTTGAG
1 CTCGATTCAAGCTCGATTTTGAG
* * *
450986 CTCGATTCAAACTCAATTTTGAA
1 CTCGATTCAAGCTCGATTTTGAG
* *
451009 CTCGATTCAAGCTTGATTATGAG
1 CTCGATTCAAGCTCGATTTTGAG
451032 CTCGATTCAAGCTCGA
1 CTCGATTCAAGCTCGA
451048 CTTAAGCTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (23 bp):
CTCGATTCAAGCTCGATTTTGAG
Found at i:452739 original size:23 final size:23
Alignment explanation
Indices: 452681--452740 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
452671 GAATTTTATT
* * *
452681 AATC-AATAATGTATTTTTAATA
1 AATCTAATAATATAATTTTAAAA
*
452703 AATTTAATAATATAATTTTAAAA
1 AATCTAATAATATAATTTTAAAA
452726 AATCTAA-AATTATAA
1 AATCTAATAA-TATAA
452741 AATAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
AATCTAATAATATAATTTTAAAA
Found at i:455588 original size:249 final size:249
Alignment explanation
Indices: 455076--456404 Score: 1439
Period size: 249 Copynumber: 5.3 Consensus size: 249
455066 GTTGTCAGTC
* * * * *
455076 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCA-GGTACATCA-TT-C-ACATATACTCAAGGCT
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATA-ACTCAAGGCT
* * *
455136 AGAAGGGTT-TCTATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA-T
65 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
455199 TGCAGCA-CACTTAAGTCAAGAAGGGTTTTCTGCCAA-CATAAGACCTTTGAGTTCGACTACGCT
130 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA-AAGACCTTCGAGTTCGACTACGCT
* * *
455262 CAGCT-CAACG-ACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTGCCA
194 CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * *
455316 AAGACCCCCTAGTTCGATTACACTCAGCTTCGAGGGCATATCCATTTACAACATAACTCAAGGCT
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT-CATTTACAACATAACTCAAGGCT
* * * *
455381 AGAAGGG-T-TCTGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
65 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
455444 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
129 TTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
*
455509 CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCA
194 CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
*
455565 AAGACCCTCGAGTTCGATTACACTCA-CTTCGAGGGCACATCATTTAC-ATATAACTCAA-GCTA
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTA
* * *
455627 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCGCATCATTT
66 GAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * *
455692 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTTGATTACACTCA
131 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT--A--CG
* * * * * *
455753 CTCAGCTTCGAGGCACATCA-TTGCA--ACAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAG
192 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA--T-----------
*
455815 ACCGCCA
244 -CTGCCA
* * *
455822 AAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGGCACATCATTTGCAACATAGCTCAAG
1 AAGACCCTCGAGTTCGATT--A--CACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
* * * * * * * * ** *
455887 GCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGTTCAACTGTAAGGCATATC
62 GCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* ** * * *
455952 ATTTGCAGCATAACTTAAATCGAGAAAAGTTATCTACCAACCAAAGGCCTTCAAGTTCGACTACG
127 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * *
456017 CTCAGCTCCAAGGCGCATCATTTACAGCATAGCTTAAGTTGAGAAGGGCTATCTGCTA
192 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * *
456075 AAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTA
* * *
456140 TAAGGGTTATCCGTCACCAAAAGACCTTCGGGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
66 GAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
456205 ACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
131 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
456270 GCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGTTATATGCCAA
196 GCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A
* * * * * *
456325 TCGAAGACCTTCGAGTTCGATTACATTCAGC-T-GAGAGGCAAACCAATTTACAGCATAGCTCAA
1 ---AAGACCCTCGAGTTCGATTACACTCAGCTTCGAG-GGCACATC-ATTTACAACATAACTCAA
* * *
456388 AGCAAGAAGGGCTATCT
61 GGCTAGAAGGGTTATCT
456405 CAATAAATTG
Statistics
Matches: 906, Mismatches: 131, Indels: 91
0.80 0.12 0.08
Matches are distributed among these distances:
240 23 0.03
241 3 0.00
242 24 0.03
243 20 0.02
244 39 0.04
245 45 0.05
246 87 0.10
247 96 0.11
248 19 0.02
249 260 0.29
250 1 0.00
251 4 0.00
252 7 0.01
253 77 0.08
257 23 0.03
259 1 0.00
261 6 0.01
262 20 0.02
263 9 0.01
264 101 0.11
265 5 0.01
266 1 0.00
267 18 0.02
268 17 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (249 bp):
AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTA
GAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
Found at i:455657 original size:162 final size:163
Alignment explanation
Indices: 455076--456344 Score: 941
Period size: 165 Copynumber: 7.6 Consensus size: 163
455066 GTTGTCAGTC
* * * *
455076 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCA-GGTACATCA-TT-CA-CATATACTCAAGGCT
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATA-ACTCAA-GCT
* *
455136 AGAAGGGTT-TCTATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA-T
64 AGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
455199 TGCAGCACA-CTTAAGTCAAGAAGGGTTTTCTGCCAACA
128 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CA
* * * ** * * *
455237 TAAGACCTTTGAGTTCGACTACGCTCAGC-TC-AACG-ACATCATTTGCAGCATAGCTTAAGTCA
1 -AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAG-CT
** * * * * * *
455299 AGAAGGGTTATC--TG-CCAAAGACCCCCTAGTTCGATTACACTCAGCTTCGAGGGCATATCCAT
64 AGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT-CAT
* * * * * *
455361 TTACAACATAACTCAAGGCTAGAAGGG-T-TCTGTCACCAA
127 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-A
* *
455400 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAG-CTA
**
455465 GAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
65 GAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
455530 GCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCA
129 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * *
455565 AAGACCCTCGAGTTCGATTACACTCA-CTTCGAGGGCACATCATTTACA-TATAACTCAAGCTAG
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGCTAG
* *
455628 AAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCGCATCATTTG
66 AAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
455693 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
130 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * * *
455727 AAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGA-GGCACATCA-TTGCA--ACAGCTCAAG
1 AAGACCTTCGAGTTCGATT--A--CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAA-
* * * * * * * *
455788 GCAAGAAGGGCTATTTGCCAACAAAAGACCGCCAAAGACCCTCGAGTTTGATTACACTCACTCAG
61 GCTAGAAGGGTTATCTG--------TGA---CCAAAGACCTTCGAGTTCGACT--A--CGCTCAG
* * * * * * *
455853 CTTCGAGGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAA
111 C-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-A
* * ** * * * * * *
455911 AAGACCTTCGAGTTTGACTACGTTCAAC-T-GTAAGGCATATCATTTGCAGCATAACTTAAATCG
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCG-AGGGCACATCATTTGCAGCATAAC-TCAAGCT
** *** * * *
455974 AGAAAAGTTATCTACCAACCAAAGGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCGCATCATT
64 AGAAGGGTTATCT-GTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
456039 TACAGCATAGCTTAAGTTGAGAAGGGCTATCTGCTA
128 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * * *
456075 AAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAA-GCTA
* * * *
456140 TAAGGGTTATCCGTCACCAAAAGACCTTCGGGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
65 GAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* *
456205 ACAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCA
129 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCA
* * * * * * * *
456244 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAACATAGCTTAAGTCGA
1 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAG-CTA
* ** * *
456308 GAAGGGTTATATGCCAATCGAAGACCTTCGAGTTCGA
65 GAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGA
456345 TTACATTCAG
Statistics
Matches: 890, Mismatches: 151, Indels: 126
0.76 0.13 0.11
Matches are distributed among these distances:
160 24 0.03
161 22 0.02
162 178 0.20
163 36 0.04
164 81 0.09
165 186 0.21
166 18 0.02
167 31 0.03
168 101 0.11
169 65 0.07
171 1 0.00
173 19 0.02
175 18 0.02
176 3 0.00
177 1 0.00
178 1 0.00
179 9 0.01
180 54 0.06
181 6 0.01
182 1 0.00
183 14 0.02
184 21 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (163 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGCTAG
AAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
Found at i:455915 original size:99 final size:95
Alignment explanation
Indices: 455723--455916 Score: 352
Period size: 95 Copynumber: 2.0 Consensus size: 95
455713 AGGGCTATCT
455723 GCCAAAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGCACATCATTGCAACAGCTCAAG
1 GCCAAAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGCACATCATTGCAACAGCTCAAG
455788 GCAAGAAGGGCTATTTGCCAACAAAAGACC
66 GCAAGAAGGGCTATTTGCCAACAAAAGACC
455818 GCCAAAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGGCACATCATTTGCAACATAGCT
1 GCCAAAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGA-GGCACATCA-TTGCAAC--AGCT
455883 CAAGGCAAGAAGGGCTATTTGCCAACAAAAGACC
62 CAAGGCAAGAAGGGCTATTTGCCAACAAAAGACC
455917 TTCGAGTTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
95 41 0.43
96 9 0.09
97 7 0.07
99 38 0.40
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (95 bp):
GCCAAAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGCACATCATTGCAACAGCTCAAG
GCAAGAAGGGCTATTTGCCAACAAAAGACC
Found at i:456364 original size:84 final size:84
Alignment explanation
Indices: 455076--456344 Score: 886
Period size: 84 Copynumber: 15.2 Consensus size: 84
455066 GTTGTCAGTC
* * * *
455076 AAGACCTTCGAGTTCGACTACGCTCAGCTCC-AGGTACATCA-TT-CA-CATATACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATA-ACTTAAGTCGA
* ***
455137 GAAGGG-TTTCT-ATGACCAA
65 GAAGGGCTATCTGCCAACC-A
* * * *
455156 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA-TTGCAGCA-CACTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
* *
455219 AAGGGTTTTCTGCCAA-CA
66 AAGGGCTATCTGCCAACCA
* * * * *
455237 TAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACG-ACATCATTTGCAGCATAGCTTAAGTCAA
1 -AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGA
*
455300 GAAGGGTTATCTG----CCA
65 GAAGGGCTATCTGCCAACCA
** * * * * * * * * * *
455316 AAGACCCCCTAGTTCGATTACACTCAGCTTCGAGGGCATATCCATTTACAACATAACTCAAGGCT
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACAT-CATTTACAGCATAACTTAAGTCG
*
455381 AGAAGGG-T-TCTGTC-ACCAA
64 AGAAGGGCTATCTGCCAACC-A
* * * * *
455400 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGA
*
455465 GAAGGGTTATCTGCCAACCA
65 GAAGGGCTATCTGCCAACCA
* * *
455485 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAT
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
455550 AAGGGCTATCTG----CCA
66 AAGGGCTATCTGCCAACCA
* * * * * * * *
455565 AAGACCCTCGAGTTCGATTACACTCA-CTTCGAGGGCACATCATTTACA-TATAACTCAAG-CTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGA
* **
455627 GAAGGGTTATCTG-TGACCAA
65 GAAGGGCTATCTGCCAACC-A
* * * *
455647 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
455712 AAGGGCTATCTG----CCA
66 AAGGGCTATCTGCCAACCA
* * * * * * * * * * *
455727 AAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGCACATCA-TTGCA--ACAGCTCAAGG
1 AAGACCTTCGAGTTCGACT--A--CGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGT
* *
455789 CAAGAAGGGCTATTTGCCAACAAAAGACCGCCA
62 CGAGAAGGGCTATCTG-C--C---A-A---CCA
* * * * * * * * * *
455822 AAGACCCTCGAGTTTGATTACACTCACTCAGCTTCGAGGGCACATCATTTGCAACATAGCTCAAG
1 AAGACCTTCGAGTTCGACTACGCT----CAGC-TCCAAGGCACATCATTTACAGCATAACTTAAG
* * * *
455887 GCAAGAAGGGCTATTTGCCAACAA
61 TCGAGAAGGGCTATCTGCCAACCA
* * * ** * * *
455911 AAGACCTTCGAGTTTGACTACGTTCAACTGTAAGGCATATCATTTGCAGCATAACTTAAATCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
** * *
455976 AAAAGTTATCTACCAACCA
66 AAGGGCTATCTGCCAACCA
* * * * *
455995 AAGGCCTTCAAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTACAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
*
456060 AAGGGCTATCTG----CTA
66 AAGGGCTATCTGCCAACCA
* * * * * * * * * *
456075 AAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGTCGA
* * * *
456140 TAAGGGTTATCCGTC-ACCAA
65 GAAGGGCTATCTGCCAACC-A
*
456160 AAGACCTTCGGGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
456225 AAGGGCTATCTGCCAACCA
66 AAGGGCTATCTGCCAACCA
* * *
456244 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
* * * *
456309 AAGGGTTATATGCCAATCG
66 AAGGGCTATCTGCCAACCA
456328 AAGACCTTCGAGTTCGA
1 AAGACCTTCGAGTTCGA
456345 TTACATTCAG
Statistics
Matches: 958, Mismatches: 171, Indels: 116
0.77 0.14 0.09
Matches are distributed among these distances:
78 35 0.04
79 12 0.01
80 127 0.13
81 104 0.11
82 122 0.13
83 44 0.05
84 351 0.37
85 62 0.06
86 3 0.00
89 22 0.02
91 4 0.00
92 1 0.00
93 2 0.00
95 26 0.03
96 11 0.01
97 5 0.01
98 1 0.00
99 26 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCGAG
AAGGGCTATCTGCCAACCA
Found at i:457085 original size:11 final size:11
Alignment explanation
Indices: 457069--457093 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
457059 TATAATATAG
457069 TTTGAAAACAT
1 TTTGAAAACAT
457080 TTTGAAAACAT
1 TTTGAAAACAT
457091 TTT
1 TTT
457094 ATATTTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTGAAAACAT
Found at i:457243 original size:35 final size:35
Alignment explanation
Indices: 457125--457269 Score: 199
Period size: 34 Copynumber: 4.2 Consensus size: 35
457115 AATTGAAAAC
* **
457125 ATATTATATAGTTTT-TAAATTTTTTTTAAAATAT
1 ATATTATATAGTTTTGAAAATTAGTTTTAAAATAT
* *
457159 ACATTATATA-TTTTG-AAATTAGGTTTTAAAAAAT
1 ATATTATATAGTTTTGAAAATTA-GTTTTAAAATAT
457193 ATATTATATAG-TTTGAAAATTAGTTTTAAAATAT
1 ATATTATATAGTTTTGAAAATTAGTTTTAAAATAT
*
457227 ATATTATATAGTTTTGAAAATTATTTTTAAAATAT
1 ATATTATATAGTTTTGAAAATTAGTTTTAAAATAT
457262 ATATTATA
1 ATATTATA
457270 GTTTTAAAAC
Statistics
Matches: 99, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
33 9 0.09
34 54 0.55
35 36 0.36
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (35 bp):
ATATTATATAGTTTTGAAAATTAGTTTTAAAATAT
Found at i:457317 original size:22 final size:22
Alignment explanation
Indices: 457284--457325 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
457274 TAAAACGTTT
*
457284 TTTATATCTATTTTTTATTTTA
1 TTTATATCTATTATTTATTTTA
457306 TTTATTAT-TATTATTTATTT
1 TTTA-TATCTATTATTTATTT
457326 ATTATCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATATCTATTATTTATTTTA
Found at i:461574 original size:188 final size:186
Alignment explanation
Indices: 461158--461537 Score: 634
Period size: 188 Copynumber: 2.0 Consensus size: 186
461148 TTTTTTCTAC
**
461158 CGGAAATATTAATATCGGACACTATCTAAAATATTATTATTGGCAACAATCATCAATCATAAAAA
1 CGGAAATATTAATATAAGACACTATCTAAAATATTATTATTGGCAACAATCATCAATCATAAAAA
461223 ATAAATATTAATTCTTCTAACTGTTTAAATATATTACTTTTTCAATTTGAGGTAACATACATCTT
66 ATAAATATTAATTCTTCTAACTGTTTAAATATATTACTTTTTCAATTTGAGGTAACATACATCTT
461288 TCAACGTTTTAGTATCAGGAAAATCAATGAGTATCCTAGTAAGCATTTTTAAAACTA
131 TCAACGTTTTAGTATCAGGAAAATCAATGAGTATCCTAGTAAGCATTTTTAAAAC-A
**
461345 CCGGAAATATTAATATCGGACACTATCTAAAATATTATTATTGGCAACAATCATCAATCATATAA
1 -CGGAAATATTAATATAAGACACTATCTAAAATATTATTATTGGCAACAATCATCAATCATA-AA
461410 TAAATAAATATTAATTCTTCTAACTGTTTAAATATATTAACTTTTTCAATTTGAGGTAACAATAC
64 -AAATAAATATTAATTCTTCTAACTGTTTAAATATATT-ACTTTTTCAATTTGAGGTAAC-ATAC
461475 ATCTTTCAACGTGTTTAGTATCAGGAAAATCAAATGAGTATCCTATAGTAAGCATTTTTAAAA
126 ATCTTTCAACGT-TTTAGTATCAGGAAAATC-AATGAGTATCC--TAGTAAGCATTTTTAAAA
461538 GGATTATATA
Statistics
Matches: 184, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
188 61 0.33
189 2 0.01
190 37 0.20
191 21 0.11
192 16 0.09
193 18 0.10
194 11 0.06
196 18 0.10
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (186 bp):
CGGAAATATTAATATAAGACACTATCTAAAATATTATTATTGGCAACAATCATCAATCATAAAAA
ATAAATATTAATTCTTCTAACTGTTTAAATATATTACTTTTTCAATTTGAGGTAACATACATCTT
TCAACGTTTTAGTATCAGGAAAATCAATGAGTATCCTAGTAAGCATTTTTAAAACA
Found at i:462965 original size:28 final size:28
Alignment explanation
Indices: 462933--462993 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
462923 GGTCGACCCT
462933 GGGCCGGGGCAGGAGGGGCGCCCGCCCA
1 GGGCCGGGGCAGGAGGGGCGCCCGCCCA
462961 GGGCCGGGGCAGGAGGGGCGCCCGCCCA
1 GGGCCGGGGCAGGAGGGGCGCCCGCCCA
462989 GGGCC
1 GGGCC
462994 CATAATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.10, C:0.36, G:0.54, T:0.00
Consensus pattern (28 bp):
GGGCCGGGGCAGGAGGGGCGCCCGCCCA
Found at i:463574 original size:32 final size:32
Alignment explanation
Indices: 463513--463594 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
463503 TAATCTTAAT
* * * * *
463513 TACTTATTAAGTATGCAATCCCAATTTGTTAT
1 TACTTGTTAATTATGTAATCCCAACTTGTTAC
* *
463545 TACTTGTTCATTATGTAATCTCAACTTGTTAC
1 TACTTGTTAATTATGTAATCCCAACTTGTTAC
463577 TACTTGTTAATTATGTAA
1 TACTTGTTAATTATGTAA
463595 CTGGTAATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (32 bp):
TACTTGTTAATTATGTAATCCCAACTTGTTAC
Found at i:464984 original size:21 final size:21
Alignment explanation
Indices: 464960--465001 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
464950 ACCCGAGTTC
464960 TTAACGAGCCGAAACGAGCTA
1 TTAACGAGCCGAAACGAGCTA
**
464981 TTAACTTGCCGAAACGAGCTA
1 TTAACGAGCCGAAACGAGCTA
465002 CTTGATATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
TTAACGAGCCGAAACGAGCTA
Found at i:466054 original size:6 final size:6
Alignment explanation
Indices: 466045--466100 Score: 112
Period size: 6 Copynumber: 9.3 Consensus size: 6
466035 GAGTATTTAT
466045 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA
466093 AGAGGA AG
1 AGAGGA AG
466101 GTGGACGAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:466712 original size:17 final size:18
Alignment explanation
Indices: 466672--466706 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
466662 TTATGTCTGG
466672 AATTTAATATAGTGTTTTT
1 AATTTAATATA-TGTTTTT
466691 AATTTAATAT-TGTTTT
1 AATTTAATATATGTTTT
466707 ATATTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (18 bp):
AATTTAATATATGTTTTT
Found at i:469176 original size:22 final size:20
Alignment explanation
Indices: 469147--469215 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
469137 TTTTTTTATA
469147 AAAAAAAATCCTAAAATTCCT
1 AAAAAAAATCCT-AAATTCCT
* * *
469168 ATAAAAAAACCCCAAATTTCT
1 A-AAAAAAATCCTAAATTCCT
*
469189 AAATAAAAAATTCTAAATTCCT
1 -AA-AAAAAATCCTAAATTCCT
469211 AAAAA
1 AAAAA
469216 TCCCCCAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.08
21 11 0.29
22 24 0.63
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAAAATCCTAAATTCCT
Found at i:482407 original size:31 final size:33
Alignment explanation
Indices: 482356--482416 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 33
482346 AAGAAAATAG
*
482356 AGAAAATAAGTGTTTGGATTTTTGTTAGTTTAT
1 AGAAAATAAGTGTTTGGATTTTTGTAAGTTTAT
482389 AGAAAAT-AGTG-TTGGATTTTTGTAAGTT
1 AGAAAATAAGTGTTTGGATTTTTGTAAGTT
482417 CGCTTATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 16 0.59
32 4 0.15
33 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (33 bp):
AGAAAATAAGTGTTTGGATTTTTGTAAGTTTAT
Found at i:487859 original size:30 final size:29
Alignment explanation
Indices: 487821--487908 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
487811 CTTTTAATCT
487821 AAATACTTTAAGTACTTATTTTAATAAAA
1 AAATACTTTAAGTACTTATTTTAATAAAA
* * * *
487850 AAATAACTTTAAGTATTTACTTTGATCAAA
1 AAAT-ACTTTAAGTACTTATTTTAATAAAA
** *
487880 ATGTACTTTAACTACTTATTTTAATAAAA
1 AAATACTTTAAGTACTTATTTTAATAAAA
487909 GAGTAATTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
29 24 0.51
30 23 0.49
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATACTTTAAGTACTTATTTTAATAAAA
Found at i:487880 original size:29 final size:29
Alignment explanation
Indices: 487813--487938 Score: 89
Period size: 30 Copynumber: 4.3 Consensus size: 29
487803 TATTCAATCT
* *
487813 TTTAATC-TAAAT-ACTTTAAGTACTTAT
1 TTTAATCAAAAATAACTTTAAGTACTTAC
* *
487840 TTTAATAAAAAAATAACTTTAAGTATTTAC
1 TTTAAT-CAAAAATAACTTTAAGTACTTAC
* * * *
487870 TTTGATC-AAAATGTACTTTAACTACTTAT
1 TTTAATCAAAAAT-AACTTTAAGTACTTAC
* * *
487899 TTTAAT-AAAAGAGTAATTTTAAATATTTAC
1 TTTAATCAAAA-A-TAACTTTAAGTACTTAC
487929 TTTAATCAAA
1 TTTAATCAAA
487939 TTATACTTCA
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
27 6 0.08
28 5 0.07
29 24 0.32
30 36 0.48
31 4 0.05
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTAATCAAAAATAACTTTAAGTACTTAC
Found at i:487889 original size:59 final size:59
Alignment explanation
Indices: 487824--487938 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
487814 TTAATCTAAA
* * *
487824 TACTTTAAGTACTTATTTTAATAAAAAAATAACTTTAAGTATTTACTTTGATCAAAATG
1 TACTTTAACTACTTATTTTAATAAAAAAATAACTTTAAATATTTACTTTAATCAAAATG
* * *
487883 TACTTTAACTACTTATTTTAATAAAAGAGTAATTTTAAATATTTACTTTAATCAAA
1 TACTTTAACTACTTATTTTAATAAAAAAATAACTTTAAATATTTACTTTAATCAAA
487939 TTATACTTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (59 bp):
TACTTTAACTACTTATTTTAATAAAAAAATAACTTTAAATATTTACTTTAATCAAAATG
Found at i:487920 original size:30 final size:29
Alignment explanation
Indices: 487825--487934 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 29
487815 TAATCTAAAT
* *
487825 ACTTTAAGTACTTATTTTAATAAAAAAATA
1 ACTTTAAGTACTTACTTTAAT-AAAAAGTA
* * *
487855 ACTTTAAGTATTTACTTTGATCAAAATGT-
1 ACTTTAAGTACTTACTTTAAT-AAAAAGTA
* *
487884 ACTTTAACTACTTATTTTAATAAAAGAGTA
1 ACTTTAAGTACTTACTTTAATAAAA-AGTA
* * *
487914 ATTTTAAATATTTACTTTAAT
1 ACTTTAAGTACTTACTTTAAT
487935 CAAATTATAC
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 4 0.06
29 19 0.30
30 40 0.63
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (29 bp):
ACTTTAAGTACTTACTTTAATAAAAAGTA
Found at i:488138 original size:2 final size:2
Alignment explanation
Indices: 488131--488171 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
488121 GAAAGGAACA
488131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
488172 CATACAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:493662 original size:18 final size:18
Alignment explanation
Indices: 493639--493674 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
493629 TGTCCCATTT
493639 TTTTTATTATCATTATTA
1 TTTTTATTATCATTATTA
* *
493657 TTTTTATTTTTATTATTA
1 TTTTTATTATCATTATTA
493675 AATAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATTATCATTATTA
Found at i:494971 original size:14 final size:14
Alignment explanation
Indices: 494954--494993 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
494944 TCAACCATAA
494954 ATTTTATTATTTTT
1 ATTTTATTATTTTT
* *
494968 ATTTTATTATATGT
1 ATTTTATTATTTTT
494982 -TTTTATTATTTT
1 ATTTTATTATTTT
494994 AGTTACTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (14 bp):
ATTTTATTATTTTT
Found at i:495013 original size:2 final size:2
Alignment explanation
Indices: 495006--495035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
494996 TTACTAATTA
495006 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
495036 TAAAGGTAAA
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):
AT
Found at i:495319 original size:17 final size:17
Alignment explanation
Indices: 495279--495321 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
495269 TTTTAATTAT
*
495279 TATTTATTATAAATATA
1 TATTTATTAAAAATATA
495296 TATTTTATTAAAAGATA-A
1 TA-TTTATTAAAA-ATATA
495314 TATTTATT
1 TATTTATT
495322 CATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 12 0.52
19 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTTATTAAAAATATA
Found at i:497071 original size:105 final size:105
Alignment explanation
Indices: 496884--497101 Score: 420
Period size: 105 Copynumber: 2.1 Consensus size: 105
496874 ATGCTTATGC
496884 ACCAG-ATTTATCAGGTTATGCTCCAGTTTCTCTCAAAATGAATGATATTCAAGACATGCGAGGC
1 ACCAGTATTTATCAGGTTATGCTCCAGTTTCTCTCAAAATGAATGATATTCAAGACATGCGAGGC
496948 ATTTGGGAGAACTAGGATTCAAATAAAAAGCTACAGTTTT
66 ATTTGGGAGAACTAGGATTCAAATAAAAAGCTACAGTTTT
496988 ACCAGTATTTATCAGGTTATGCTCCAGTTTCTCTCAAAATGAATGATATTCAAGACATGCGAGGC
1 ACCAGTATTTATCAGGTTATGCTCCAGTTTCTCTCAAAATGAATGATATTCAAGACATGCGAGGC
497053 ATTTGGGAGAACTAGGATTCAAATAAAAAGCTACAGTTTT
66 ATTTGGGAGAACTAGGATTCAAATAAAAAGCTACAGTTTT
*
497093 ACTAGTATT
1 ACCAGTATT
497102 ACGGGGACAT
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
104 5 0.04
105 107 0.96
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (105 bp):
ACCAGTATTTATCAGGTTATGCTCCAGTTTCTCTCAAAATGAATGATATTCAAGACATGCGAGGC
ATTTGGGAGAACTAGGATTCAAATAAAAAGCTACAGTTTT
Found at i:499882 original size:16 final size:16
Alignment explanation
Indices: 499861--499899 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
499851 GACGTTTCTA
499861 CACACTTTAAAGACCC
1 CACACTTTAAAGACCC
499877 CACACTTTAAAGACCC
1 CACACTTTAAAGACCC
499893 CACACTT
1 CACACTT
499900 AGGCCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.38, G:0.05, T:0.21
Consensus pattern (16 bp):
CACACTTTAAAGACCC
Found at i:500303 original size:28 final size:29
Alignment explanation
Indices: 500271--500330 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
500261 ACTCCTATGC
500271 AAACCGTCGTT-CCTTACTGGTATGATGT
1 AAACCGTCGTTCCCTTACTGGTATGATGT
500299 AAACCGTCGTTCCCTTACTGGTATGATGT
1 AAACCGTCGTTCCCTTACTGGTATGATGT
500328 AAA
1 AAA
500331 AGCACATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (29 bp):
AAACCGTCGTTCCCTTACTGGTATGATGT
Found at i:505716 original size:56 final size:57
Alignment explanation
Indices: 505630--505743 Score: 221
Period size: 56 Copynumber: 2.0 Consensus size: 57
505620 GGATTGGAAT
505630 GAGAAGTTACCTTTTGCTTTATATACATATCGAACTACTGTGCGAACA-CTACTGGG
1 GAGAAGTTACCTTTTGCTTTATATACATATCGAACTACTGTGCGAACATCTACTGGG
505686 GAGAAGTTACCTTTTGCTTTATATACATATCGAACTACTGTGCGAACATCTACTGGG
1 GAGAAGTTACCTTTTGCTTTATATACATATCGAACTACTGTGCGAACATCTACTGGG
505743 G
1 G
505744 CAATACATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 48 0.84
57 9 0.16
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (57 bp):
GAGAAGTTACCTTTTGCTTTATATACATATCGAACTACTGTGCGAACATCTACTGGG
Found at i:507761 original size:123 final size:123
Alignment explanation
Indices: 507079--507776 Score: 1008
Period size: 124 Copynumber: 5.7 Consensus size: 123
507069 ATGGATTGTT
* * *
507079 ATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATTTAAAGAGGAAGAAGAAGTTCATAATCTGA
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
* * * *
507144 AGAACTTATTCAACCTTTTGCTTGATTCTATCGCAAAAGGAGAGAGAACAACATCAAC
66 AGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
*
507202 ATTTTCAGAAGGAGTTCGTAAT---AAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
* * * *
507264 AGAACTTATTCAACCTTTTGCTCGATTCTATCGCATAAGGAGATAGAGCATCATCAAC
66 AGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
* *
507322 ATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAACAAGTTCATAATCTGA
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
* * *
507387 AGAACATATTCAACCTTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCATCATCAAC
66 AGAACTTATTCAACC-TTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
* * *
507446 ATTTCCAAAAGAAGTTCGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAATCTGA
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
* * * **
507511 AGAACGTATTCAACCTTTTTGCTTGACTCTATCGCAGAATGAGATAGGGCAACATCGTC
66 AGAACTTATTCAACC-TTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
*
507570 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTAATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
* * * *
507635 AGAACGTATTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAAC
66 AGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
* ** * *
507693 TTTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCCAAAGAAGAAGAAGAAGTTCATAATAAT-
1 ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT-CTG
* *
507757 AAGAACTTGTTCAACATTTT
65 AAGAACTTATTCAACCTTTT
507777 CATTTTAATC
Statistics
Matches: 523, Mismatches: 47, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
120 111 0.21
123 182 0.35
124 230 0.44
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
ATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
AGAACTTATTCAACCTTTTGCTTGACTCTATCGCAGAAGGAGATAGAGCAACATCAAC
Found at i:507904 original size:3 final size:3
Alignment explanation
Indices: 507896--507952 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
507886 TTGTCCCATT
*
507896 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
507944 TTA TTA TTA
1 TTA TTA TTA
507953 AATAATAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:508805 original size:25 final size:27
Alignment explanation
Indices: 508754--508899 Score: 242
Period size: 27 Copynumber: 5.5 Consensus size: 27
508744 GGTGAGGGAA
*
508754 TCCTAGAGAGAGATTTTAGTTTCTCTC
1 TCCTAGAGAGAGATTTCAGTTTCTCTC
* *
508781 TTCTAGAGATAGATTTCAGTTTCTCTC
1 TCCTAGAGAGAGATTTCAGTTTCTCTC
508808 TCCTAGAGAGAGATTTCAGTTTCTCTC
1 TCCTAGAGAGAGATTTCAGTTTCTCTC
508835 TCCTAGAGAGAGATTTCAGTTTCTCTC
1 TCCTAGAGAGAGATTTCAGTTTCTCTC
508862 TCC--GAGAGAGATTTCAGTTTCTCTC
1 TCCTAGAGAGAGATTTCAGTTTCTCTC
*
508887 TCCGAGAGAGAGA
1 TCCTAGAGAGAGA
508900 AACATAAATG
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
25 25 0.22
27 87 0.78
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
TCCTAGAGAGAGATTTCAGTTTCTCTC
Found at i:509302 original size:26 final size:24
Alignment explanation
Indices: 509272--509346 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 24
509262 TTAAAGCCTT
*
509272 TAATTTTAATATTTTATTTACCCTAA
1 TAATTTTAATATTTTATTTAACC--A
*
509298 TAATTTAAATAATTTTTATTTTCAACCA
1 TAATTTTAAT-A-TTTTA-TTT-AACCA
*
509326 TAATTTTATTATTTTATTTAA
1 TAATTTTAATATTTTATTTAA
509347 TTATATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.05
25 3 0.07
26 14 0.34
27 2 0.05
28 14 0.34
29 3 0.07
30 3 0.07
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATTTTAATATTTTATTTAACCA
Found at i:509384 original size:2 final size:2
Alignment explanation
Indices: 509377--509435 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
509367 GTTACTATTA
509377 AT AT AT AT AT AT AT AT AT AT AT AT A- 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
509418 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
509436 TAAGGTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:510938 original size:76 final size:77
Alignment explanation
Indices: 510811--510960 Score: 252
Period size: 76 Copynumber: 1.9 Consensus size: 77
510801 TTCAAGAAGA
510811 TGATTGCCCACTGACTTTAGCAGATATATTTGAAATACATTGACCAAGAATTTCAAAGATT-GTG
1 TGATTGCCCACTGACTTTAGCAGA-ATATTTGAAATACATTGACCAAGAATTTCAAAGATTGGTG
510875 ACAAAGGTGATGG
65 ACAAAGGTGATGG
510888 TGATTGCCC-CTGACTTTAGCAG-ATATTTGAAATACATATTGACCAAGAATTTCAAAGATTGGT
1 TGATTGCCCACTGACTTTAGCAGAATATTTGAAATAC--ATTGACCAAGAATTTCAAAGATTGGT
510951 GACAAAGGTG
64 GACAAAGGTG
510961 TGGCTTTTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
74 13 0.19
76 36 0.51
77 21 0.30
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (77 bp):
TGATTGCCCACTGACTTTAGCAGAATATTTGAAATACATTGACCAAGAATTTCAAAGATTGGTGA
CAAAGGTGATGG
Found at i:512260 original size:26 final size:26
Alignment explanation
Indices: 512231--512281 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
512221 GAAAACAACC
512231 GGTCTTCTTACAGTGTTGGGAAGTTT
1 GGTCTTCTTACAGTGTTGGGAAGTTT
512257 GGTCTTCTTACAGTGTTGGGAAGTT
1 GGTCTTCTTACAGTGTTGGGAAGTT
512282 GTTCTATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.31, T:0.41
Consensus pattern (26 bp):
GGTCTTCTTACAGTGTTGGGAAGTTT
Found at i:513432 original size:11 final size:11
Alignment explanation
Indices: 513416--513442 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
513406 AAAATTACAT
513416 TATTAAAAATA
1 TATTAAAAATA
513427 TATTAAAAATA
1 TATTAAAAATA
513438 TATTA
1 TATTA
513443 TTGATGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:515806 original size:23 final size:23
Alignment explanation
Indices: 515777--515861 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
515767 CGAGCTTAAG
*
515777 TCGAGCTTGATTCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
515800 TCGAGCTCGAATCGAGCTTACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
515823 TCGAGTTTGAATCGAGCTCGA-AA
1 TCGAGCTTGAATCGAGCTC-ACAA
* *
515846 TCGAGCCTCAATCGAG
1 TCGAGCTTGAATCGAG
515862 TCTCGAGCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 51 0.98
24 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:515812 original size:11 final size:11
Alignment explanation
Indices: 515777--515867 Score: 69
Period size: 11 Copynumber: 7.9 Consensus size: 11
515767 CGAGCTTAAG
* *
515777 TCGAGCTTGAT
1 TCGAGCTCGAA
*
515788 TCGAGCTCACAA
1 TCGAGCTC-GAA
515800 TCGAGCTCGAA
1 TCGAGCTCGAA
515811 TCGAGCTTAC-AA
1 TCGAGC-T-CGAA
* *
515823 TCGAGTTTGAA
1 TCGAGCTCGAA
515834 TCGAGCTCGAAA
1 TCGAGCTCG-AA
515846 TCGAGCCTC-AA
1 TCGAG-CTCGAA
515857 TCGAGTCTCGA
1 TCGAG-CTCGA
515868 GCTTTAGTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
11 35 0.55
12 25 0.39
13 4 0.06
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (11 bp):
TCGAGCTCGAA
Found at i:515836 original size:34 final size:34
Alignment explanation
Indices: 515798--515862 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
515788 TCGAGCTCAC
*
515798 AATCGAGCTCG-AATCGAGCTTACAATCGAGTTTG
1 AATCGAGCTCGAAATCGAGCCT-CAATCGAGTTTG
515832 AATCGAGCTCGAAATCGAGCCTCAATCGAGT
1 AATCGAGCTCGAAATCGAGCCTCAATCGAGT
515863 CTCGAGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 20 0.69
35 9 0.31
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (34 bp):
AATCGAGCTCGAAATCGAGCCTCAATCGAGTTTG
Found at i:522217 original size:63 final size:63
Alignment explanation
Indices: 522118--522244 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
522108 AGGTAAGATT
522118 ATAGTAGTTCAAATTTATGTTGATGATATAATTTTGGTTCTACTAATGATGTTCTTTGCCAAG
1 ATAGTAGTTCAAATTTATGTTGATGATATAATTTTGGTTCTACTAATGATGTTCTTTGCCAAG
522181 ATAGTAGTTCAAATTTATGTTGATGATAT-ATATTTGGTTCTACTAATGATGTTCTTTGCCAAG
1 ATAGTAGTTCAAATTTATGTTGATGATATAAT-TTTGGTTCTACTAATGATGTTCTTTGCCAAG
522244 A
1 A
522245 ATTTTCTAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 2 0.03
63 61 0.97
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.44
Consensus pattern (63 bp):
ATAGTAGTTCAAATTTATGTTGATGATATAATTTTGGTTCTACTAATGATGTTCTTTGCCAAG
Found at i:523325 original size:21 final size:21
Alignment explanation
Indices: 523299--523338 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
523289 CCCCTTTTGA
*
523299 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
523320 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
523339 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:529549 original size:162 final size:163
Alignment explanation
Indices: 529360--529680 Score: 635
Period size: 162 Copynumber: 2.0 Consensus size: 163
529350 AATCATTCTA
529360 TCATCCCTTCTAGTAATAAGAGAGCTTTTATTGTATCTTAACGAGTATCAAGATGTCTTTACCCT
1 TCATCCCTTCTAGTAATAAGAGAGCTTTTATTGTATCTTAACGAGTATCAAGATGTCTTTACCCT
529425 AAAGAAAGAAGTGCAACTTCATTGCTTACAAAGATGCCCCAACTCAACTTAGGGATGAAATTATA
66 AAAGAAAGAAGTGCAACTTCATTGCTTACAAAGATGCCCCAACTCAACTTAGGGATGAAATTATA
529490 TAAAAAGTTAAATTTC-TCCTTATTAGTCTCTC
131 TAAAAAGTTAAATTTCATCCTTATTAGTCTCTC
529522 TCATCCCTTCTAGTAATAAGAGAGCTTTTATTGTATCTTAACGAGTATCAAGATGTCTTTACCCT
1 TCATCCCTTCTAGTAATAAGAGAGCTTTTATTGTATCTTAACGAGTATCAAGATGTCTTTACCCT
529587 AAAGAAAGAAGTGCAACTTCATTGCTTACAAAGATGCCCCAACTCAACTTAGGGATGAAATTATA
66 AAAGAAAGAAGTGCAACTTCATTGCTTACAAAGATGCCCCAACTCAACTTAGGGATGAAATTATA
529652 TAAAAAGTTAAATTTCATCCTTATTAGTC
131 TAAAAAGTTAAATTTCATCCTTATTAGTC
529681 GAATTCAATT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 146 0.92
163 12 0.08
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (163 bp):
TCATCCCTTCTAGTAATAAGAGAGCTTTTATTGTATCTTAACGAGTATCAAGATGTCTTTACCCT
AAAGAAAGAAGTGCAACTTCATTGCTTACAAAGATGCCCCAACTCAACTTAGGGATGAAATTATA
TAAAAAGTTAAATTTCATCCTTATTAGTCTCTC
Found at i:531516 original size:14 final size:14
Alignment explanation
Indices: 531497--531537 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
531487 ACACATTAAC
531497 AATGCATATTCTAG
1 AATGCATATTCTAG
531511 AATGCATATTCTAG
1 AATGCATATTCTAG
531525 AATGCATATTCTA
1 AATGCATATTCTA
531538 ATACATGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (14 bp):
AATGCATATTCTAG
Found at i:532108 original size:28 final size:28
Alignment explanation
Indices: 532068--532149 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
532058 GCAAGTTGGA
532068 AAGCTGGAAGATGCTCGAGAAAGAGTGC
1 AAGCTGGAAGATGCTCGAGAAAGAGTGC
532096 AAGCTGGAAGATGCTCGAGAAAGAGTGC
1 AAGCTGGAAGATGCTCGAGAAAGAGTGC
* *
532124 AAGCTGTAAGATGCTCTAGAAAGAGT
1 AAGCTGGAAGATGCTCGAGAAAGAGT
532150 ACAATATTCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.33, T:0.17
Consensus pattern (28 bp):
AAGCTGGAAGATGCTCGAGAAAGAGTGC
Found at i:532659 original size:32 final size:32
Alignment explanation
Indices: 532618--532679 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
532608 TGTTAAAAGC
532618 CAACAATTCACGACTAGTGAATTCGGTGGTTT
1 CAACAATTCACGACTAGTGAATTCGGTGGTTT
532650 CAACAATTCACGACTAGTGAATTCGGTGGT
1 CAACAATTCACGACTAGTGAATTCGGTGGT
532680 CCAAGTTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (32 bp):
CAACAATTCACGACTAGTGAATTCGGTGGTTT
Found at i:537030 original size:32 final size:32
Alignment explanation
Indices: 536989--537051 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
536979 TTGTTAAAAG
536989 TCAACAATTCACGGCTACTGAATTCGGTGGTT
1 TCAACAATTCACGGCTACTGAATTCGGTGGTT
537021 TCAACAATTCACGGCTACTGAATTCGGTGGT
1 TCAACAATTCACGGCTACTGAATTCGGTGGT
537052 CCAAGTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (32 bp):
TCAACAATTCACGGCTACTGAATTCGGTGGTT
Found at i:540692 original size:55 final size:54
Alignment explanation
Indices: 540492--540995 Score: 468
Period size: 53 Copynumber: 9.6 Consensus size: 54
540482 TGACGAGCCT
*
540492 GCTCCCTATTCC-TCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAA-TGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-AAAACT-TGTCC
* * * * *
540546 GCTCTCTATTCATTC--AGAGTATA-AGACTTGAATAATCTTCAATAAAAC-GGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-A-AAAACTTGTCC
* **
540599 GCTCTCTATTCCTTC--AGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACTTGTCC
* **
540652 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACTTGTCC
* *
540707 GCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCAAAAAC-GGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACTTGTCC
*
540760 GCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTC-AAAACTTGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACTTGTCC
* * *
540813 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACTTGTCC
* *
540864 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACTTGTCC
* * *
540915 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACTTGTCC
* *
540966 G-TCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
540996 ATCTCAACGA
Statistics
Matches: 415, Mismatches: 21, Indels: 31
0.89 0.04 0.07
Matches are distributed among these distances:
49 8 0.02
50 27 0.07
51 109 0.26
52 12 0.03
53 154 0.37
54 28 0.07
55 77 0.19
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACTTGTCC
Found at i:540874 original size:51 final size:51
Alignment explanation
Indices: 540631--541003 Score: 386
Period size: 51 Copynumber: 7.2 Consensus size: 51
540621 AGAACTCGAA
** * * *
540631 CAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 CAATCTTCA-ACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
** * * * *
540682 CGAACAATCTTCATA-AAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACT
1 ----CAATCTTCA-ACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
* * * * *
540737 CGAACAATCTTCAA-AAAC-GGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACT
1 ----CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
540790 CGAACAATCTTC-A-AAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 ----CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
*
540843 CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
* *
540894 CAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
540945 CAATCTTCAACAAACTTGTCCG-TCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
540995 C-ATC-TCAAC
1 CAATCTTCAAC
541004 GAACGAATTT
Statistics
Matches: 300, Mismatches: 15, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
48 5 0.02
49 11 0.04
50 28 0.09
51 109 0.36
52 5 0.02
53 77 0.26
54 5 0.02
55 60 0.20
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (51 bp):
CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
Found at i:542113 original size:9 final size:8
Alignment explanation
Indices: 542089--542207 Score: 51
Period size: 8 Copynumber: 13.4 Consensus size: 8
542079 TTGAACCCTC
542089 CTTTTATTT
1 CTTTT-TTT
542098 CTCTTTTTT
1 CT-TTTTTT
*
542107 CATTTTTT
1 CTTTTTTT
*
542115 CTTTTATT
1 CTTTTTTT
* *
542123 CCTTTTTC
1 CTTTTTTT
542131 CATTTTTTCT
1 C-TTTTTT-T
542141 CTTTTTTT
1 CTTTTTTT
*
542149 TTTCGTTTTT
1 CTT--TTTTT
542159 CCATCATTTTTT
1 -C-T--TTTTTT
542171 CTTTTTCTT
1 CTTTTT-TT
*
542180 -ATTTTTT
1 CTTTTTTT
*
542187 CTTCTTTCT
1 CTT-TTTTT
542196 CTTTTATTT
1 CTTTT-TTT
542205 CTT
1 CTT
542208 CTTCAAGCAA
Statistics
Matches: 83, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
7 2 0.02
8 32 0.39
9 31 0.37
10 10 0.12
11 1 0.01
12 6 0.07
14 1 0.01
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (8 bp):
CTTTTTTT
Found at i:542134 original size:24 final size:26
Alignment explanation
Indices: 542089--542140 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
542079 TTGAACCCTC
*
542089 CTTTTATTTCTCTTTTTTCATTTTTT
1 CTTTTATTTCTCTTTTTCCATTTTTT
542115 CTTTTA-TTC-CTTTTTCCATTTTTT
1 CTTTTATTTCTCTTTTTCCATTTTTT
542139 CT
1 CT
542141 CTTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.64
25 3 0.12
26 6 0.24
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (26 bp):
CTTTTATTTCTCTTTTTCCATTTTTT
Found at i:542208 original size:18 final size:19
Alignment explanation
Indices: 542164--542210 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
542154 TTTTTCCATC
* *
542164 ATTTTTTCTTTTTCTTATT
1 ATTTCTTCTTTCTCTTATT
*
542183 TTTTCTTCTTTCTCTT-TT
1 ATTTCTTCTTTCTCTTATT
542201 ATTTCTTCTT
1 ATTTCTTCTT
542211 CAAGCAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTCTTCTTTCTCTTATT
Found at i:549418 original size:18 final size:19
Alignment explanation
Indices: 549363--549418 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 19
549353 ATTATGAATG
*
549363 AATAAAATGC-GATGCAAA
1 AATAAAATGCATATGCAAA
* **
549381 AATTAAATGCAT-TTAAAA
1 AATAAAATGCATATGCAAA
*
549399 AAAAAAATGCATATGCAAA
1 AATAAAATGCATATGCAAA
549418 A
1 A
549419 TGCAGGGTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (19 bp):
AATAAAATGCATATGCAAA
Found at i:551904 original size:44 final size:46
Alignment explanation
Indices: 551840--551937 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 46
551830 TTGTTATCCA
551840 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATT
1 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATT
* *
551885 CAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATT
551931 CGAAAAA
1 C-AAAAA
551938 ACGAAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 28 0.58
45 9 0.19
46 6 0.12
47 5 0.10
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (46 bp):
CAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATT
Found at i:558574 original size:13 final size:14
Alignment explanation
Indices: 558549--558577 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
558539 TTTTAAAAAT
558549 AAAATATTATTTAA
1 AAAATATTATTTAA
558563 AAAATATT-TTTAA
1 AAAATATTATTTAA
558576 AA
1 AA
558578 TAATCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTATTTAA
Found at i:573383 original size:54 final size:54
Alignment explanation
Indices: 573317--573420 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
573307 TTGGTATATA
573317 AAAAAAGATCATTTTGATATAATTTAATGTTCATTTATAAATTTTATCTTTTAT
1 AAAAAAGATCATTTTGATATAATTTAATGTTCATTTATAAATTTTATCTTTTAT
* *
573371 AAAAAAGATCATTTTGATATAGTTTAATGTTTATTTATAAATTTTATCTT
1 AAAAAAGATCATTTTGATATAATTTAATGTTCATTTATAAATTTTATCTT
573421 ATCAAATTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (54 bp):
AAAAAAGATCATTTTGATATAATTTAATGTTCATTTATAAATTTTATCTTTTAT
Found at i:574598 original size:16 final size:16
Alignment explanation
Indices: 574551--574611 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
574541 TAATAAATAA
*
574551 ACGAACATATACGAAAC
1 ACGAACATAAACG-AAC
574568 ACGAACA-AAACGAAC
1 ACGAACATAAACGAAC
*
574583 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
**
574599 AAAAACATAAACG
1 ACGAACATAAACG
574612 TTGGAGACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
15 10 0.26
16 21 0.55
17 7 0.18
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:577204 original size:25 final size:25
Alignment explanation
Indices: 577170--577219 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
577160 TGTATCTGAA
577170 GAGTTCTATCCGATGAAACGAAAGC
1 GAGTTCTATCCGATGAAACGAAAGC
* **
577195 GAGTTTTATCCGATGAGCCGAAAGC
1 GAGTTCTATCCGATGAAACGAAAGC
577220 CGATGCATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (25 bp):
GAGTTCTATCCGATGAAACGAAAGC
Found at i:580725 original size:28 final size:30
Alignment explanation
Indices: 580690--580759 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
580680 TTAAAAATCA
580690 TAAGATATGATCAC-TTAATTTT-TTTAAT
1 TAAGATATGATCACATTAATTTTATTTAAT
* **
580718 TAAGATATAATCACATTTGTTTTTATTTAAT
1 TAAGATATGATCACA-TTAATTTTATTTAAT
*
580749 TAAGATGTGAT
1 TAAGATATGAT
580760 AATCATGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 13 0.38
30 6 0.18
31 15 0.44
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (30 bp):
TAAGATATGATCACATTAATTTTATTTAAT
Found at i:581807 original size:16 final size:18
Alignment explanation
Indices: 581782--581815 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
581772 AAATATTTTG
581782 TTATTAAGATTTA-AATT
1 TTATTAAGATTTACAATT
581799 TTATT-AGATTTACAATT
1 TTATTAAGATTTACAATT
581816 CTATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATTAAGATTTACAATT
Found at i:590191 original size:27 final size:27
Alignment explanation
Indices: 590159--590210 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
590149 ACAAAGGTGC
* *
590159 CAGTTTTTGGCTGATGCATAGAGGTTA
1 CAGTTTTAGGCTGATGCACAGAGGTTA
* *
590186 CAGTTTTAGGTTGATGTACAGAGGT
1 CAGTTTTAGGCTGATGCACAGAGGT
590211 GTTCAATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.37
Consensus pattern (27 bp):
CAGTTTTAGGCTGATGCACAGAGGTTA
Found at i:595778 original size:14 final size:15
Alignment explanation
Indices: 595759--595788 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
595749 CCGCATACTC
595759 TGATTTCTA-ATATT
1 TGATTTCTATATATT
595773 TGATTTCTATATATT
1 TGATTTCTATATATT
595788 T
1 T
595789 TTGATATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (15 bp):
TGATTTCTATATATT
Found at i:605004 original size:20 final size:20
Alignment explanation
Indices: 604979--605028 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
604969 CCAGAGCTAG
**
604979 AATATCGATACTCTTAGAGA
1 AATATCGATACTCCCAGAGA
604999 AATATCGATACTCCCAGAGA
1 AATATCGATACTCCCAGAGA
605019 AATATCGATA
1 AATATCGATA
605029 TTATCTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (20 bp):
AATATCGATACTCCCAGAGA
Found at i:613355 original size:21 final size:21
Alignment explanation
Indices: 613329--613401 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
613319 CACCAAAGTG
613329 CCACATAGTTGTCCTGAAGGA
1 CCACATAGTTGTCCTGAAGGA
613350 CCACATAGGTT-TGCAAC-GAAGTG-
1 CCACATA-GTTGT-C--CTGAAG-GA
* *
613373 CCACATAATTGTCCTGAGGGA
1 CCACATAGTTGTCCTGAAGGA
613394 CCACATAG
1 CCACATAG
613402 AACCCTCGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
20 2 0.05
21 18 0.44
22 7 0.17
23 12 0.29
24 2 0.05
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (21 bp):
CCACATAGTTGTCCTGAAGGA
Found at i:613364 original size:44 final size:44
Alignment explanation
Indices: 613315--613401 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
613305 CAGCTTGTAA
* *
613315 TTTGCACCAAAGTGCCACATAGTTGTCCTGAAGGACCACATAGG
1 TTTGCAACAAAGTGCCACATAATTGTCCTGAAGGACCACATAGG
* *
613359 TTTGCAACGAAGTGCCACATAATTGTCCTGAGGGACCACATAG
1 TTTGCAACAAAGTGCCACATAATTGTCCTGAAGGACCACATAG
613402 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (44 bp):
TTTGCAACAAAGTGCCACATAATTGTCCTGAAGGACCACATAGG
Found at i:613701 original size:14 final size:14
Alignment explanation
Indices: 613684--613711 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
613674 CATACATGTA
613684 ATCACATAACTTAT
1 ATCACATAACTTAT
613698 ATCACATAACTTAT
1 ATCACATAACTTAT
613712 TATTTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ATCACATAACTTAT
Found at i:617908 original size:15 final size:12
Alignment explanation
Indices: 617870--617898 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
617860 ACAAATGTGG
617870 GCTTGAATGAAA
1 GCTTGAATGAAA
617882 GCTTGAATGAAA
1 GCTTGAATGAAA
617894 GCTTG
1 GCTTG
617899 GAATATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (12 bp):
GCTTGAATGAAA
Found at i:627264 original size:30 final size:31
Alignment explanation
Indices: 627190--627264 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
627180 TTAAAAAACA
*
627190 TAAGATATGGTCCCTTTCGATTTTATTTAAT
1 TAAGATATGGTCACTTTCGATTTTATTTAAT
* *
627221 TAAGATATAGTCACTTTCGTTTTTA-TTAAT
1 TAAGATATGGTCACTTTCGATTTTATTTAAT
*
627251 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
627265 CCCGAGTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGATTTTATTTAAT
Found at i:633232 original size:35 final size:34
Alignment explanation
Indices: 633147--633233 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
633137 AATATAATTT
*
633147 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
633181 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
633219 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
633234 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Done.