Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015038.1 Kokia drynarioides strain JFW-HI SEQ_130082, 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: 531193
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 680 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:265723 original size:30 final size:26
Alignment explanation
Indices: 265663--265713 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
265653 TCTAGGCGTT
*
265663 TTTA-TATATGTTAATATATTTATTA
1 TTTATTATATATTAATATATTTATTA
265688 TTTATTATATATTAATATATTTATTA
1 TTTATTATATATTAATATATTTATTA
265714 ATTGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATTATATATTAATATATTTATTA
Found at i:266341 original size:37 final size:37
Alignment explanation
Indices: 266300--266380 Score: 162
Period size: 37 Copynumber: 2.2 Consensus size: 37
266290 CCAAAACGGT
266300 GCCGTTTTGGTATTGGCTTAAAAGCCCCAAAAACGAC
1 GCCGTTTTGGTATTGGCTTAAAAGCCCCAAAAACGAC
266337 GCCGTTTTGGTATTGGCTTAAAAGCCCCAAAAACGAC
1 GCCGTTTTGGTATTGGCTTAAAAGCCCCAAAAACGAC
266374 GCCGTTT
1 GCCGTTT
266381 CACCTCAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (37 bp):
GCCGTTTTGGTATTGGCTTAAAAGCCCCAAAAACGAC
Found at i:266870 original size:29 final size:29
Alignment explanation
Indices: 266819--266951 Score: 121
Period size: 29 Copynumber: 4.6 Consensus size: 29
266809 AAAAACCCTA
* *
266819 TTTTAGCCCCCGAGCTTCTCAAAAATTACAT
1 TTTTA-CCCCTGAACTTC-CAAAAATTACAT
*
266850 TTTTACCCCTGAATTTCCAAAAATTACA-
1 TTTTACCCCTGAACTTCCAAAAATTACAT
* * *
266878 TTTT-GCCATCGAACTTCTCAAAAAATACAT
1 TTTTACCCCT-GAACTTC-CAAAAATTACAT
*
266908 TTTTACCCTCT-AACTTCCAAAAATCACAT
1 TTTTACCC-CTGAACTTCCAAAAATTACAT
*
266937 TTTGACCCC-GAACTT
1 TTTTACCCCTGAACTT
266952 TCCCGAAGTC
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
27 3 0.04
28 16 0.19
29 38 0.45
30 19 0.23
31 7 0.08
32 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTTACCCCTGAACTTCCAAAAATTACAT
Found at i:266949 original size:58 final size:57
Alignment explanation
Indices: 266826--266951 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 57
266816 CTATTTTAGC
* * * *
266826 CCCCGAGCTTCTCAAAAATTACATTTTTACCCCTGAATTTCCAAAAATTACATTTTG
1 CCCCGAACTTCTCAAAAAATACATTTTTACCCCTGAACTTCCAAAAATCACATTTTG
*
266883 CCATCGAACTTCTCAAAAAATACATTTTTACCCTCT-AACTTCCAAAAATCACATTTTG
1 CC-CCGAACTTCTCAAAAAATACATTTTTACCC-CTGAACTTCCAAAAATCACATTTTG
266941 ACCCCGAACTT
1 -CCCCGAACTT
266952 TCCCGAAGTC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 2 0.03
58 54 0.90
59 4 0.07
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.33
Consensus pattern (57 bp):
CCCCGAACTTCTCAAAAAATACATTTTTACCCCTGAACTTCCAAAAATCACATTTTG
Found at i:268049 original size:15 final size:15
Alignment explanation
Indices: 268031--268069 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
268021 CAATTTAATA
*
268031 ATGATAAAACATAAC
1 ATGACAAAACATAAC
* *
268046 ATGACATAACATGAC
1 ATGACAAAACATAAC
268061 ATGACAAAA
1 ATGACAAAA
268070 AAAGGGACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.18
Consensus pattern (15 bp):
ATGACAAAACATAAC
Found at i:268295 original size:18 final size:18
Alignment explanation
Indices: 268250--268296 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
268240 ACTAAATACG
268250 TAAAACAAATATAATAATA
1 TAAAA-AAATATAATAATA
* *
268269 TTAATAAATA-AATATATA
1 TAAAAAAATATAATA-ATA
268287 TAAAAAAATA
1 TAAAAAAATA
268297 GAAAGGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAAATATAATAATA
Found at i:270659 original size:30 final size:30
Alignment explanation
Indices: 270623--270702 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
270613 GTGACCTTGA
** *
270623 TATAATGTCAACTTGTGTGAGCCATTC-TGT
1 TATAATGTCAACTTGTGTGAG-CAACCATGG
* * *
270653 TATAATGTCATCCTGTGTAAGCAACCATGG
1 TATAATGTCAACTTGTGTGAGCAACCATGG
270683 TAT-ATGTCAACTTGTGTGAG
1 TATAATGTCAACTTGTGTGAG
270703 AAAATTATTC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (30 bp):
TATAATGTCAACTTGTGTGAGCAACCATGG
Found at i:279114 original size:23 final size:23
Alignment explanation
Indices: 279088--279439 Score: 445
Period size: 23 Copynumber: 15.3 Consensus size: 23
279078 TTATATCTAC
*
279088 GCTTAAATGTTAATGTGATTTGT
1 GCTTAAATATTAATGTGATTTGT
* *
279111 GCTTAAATATTAATAT-ATTTTAT
1 GCTTAAATATTAATGTGA-TTTGT
* *
279134 GATTAAATATTAATGTGACTTGT
1 GCTTAAATATTAATGTGATTTGT
* *
279157 GCTTAAGTATTAATGTGATTTAT
1 GCTTAAATATTAATGTGATTTGT
* *
279180 ACTTAAATATTAATATGATTTGT
1 GCTTAAATATTAATGTGATTTGT
* * *
279203 GCTCAAATATTAAGGTGATTTGC
1 GCTTAAATATTAATGTGATTTGT
* *
279226 GCTCAAATATTAATGTGATTTAT
1 GCTTAAATATTAATGTGATTTGT
* *
279249 GCTCAAATATTAATGTGATTTAT
1 GCTTAAATATTAATGTGATTTGT
**
279272 GCTTAAATATTAATGTGGCTTGT
1 GCTTAAATATTAATGTGATTTGT
*
279295 GCATAAATATTAATGTGATTTGT
1 GCTTAAATATTAATGTGATTTGT
* *
279318 GCTTAAATATTAATATAATTTGT
1 GCTTAAATATTAATGTGATTTGT
* * *
279341 GCTCAAATATTAATATGATTTAT
1 GCTTAAATATTAATGTGATTTGT
279364 GCTTAAATATTAATGTGATTTGT
1 GCTTAAATATTAATGTGATTTGT
* *
279387 GCTTAAATATTAATATGATTTAT
1 GCTTAAATATTAATGTGATTTGT
*
279410 GATTAAATATTAATGTGATTTGT
1 GCTTAAATATTAATGTGATTTGT
279433 GCTTAAA
1 GCTTAAA
279440 GAATTAAGAT
Statistics
Matches: 282, Mismatches: 45, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
22 1 0.00
23 280 0.99
24 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.45
Consensus pattern (23 bp):
GCTTAAATATTAATGTGATTTGT
Found at i:281716 original size:19 final size:17
Alignment explanation
Indices: 281673--281721 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
281663 GTTTTGTATG
281673 AAATTGAA-GAGAAAGA
1 AAATTGAAGGAGAAAGA
281689 AAA--GAAGGAGAAAGA
1 AAATTGAAGGAGAAAGA
*
281704 CCAAATTGAAGGAAAAAG
1 --AAATTGAAGGAGAAAG
281722 GAAAGGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 8 0.30
16 3 0.11
17 3 0.11
19 10 0.37
ACGTcount: A:0.61, C:0.04, G:0.27, T:0.08
Consensus pattern (17 bp):
AAATTGAAGGAGAAAGA
Found at i:282696 original size:24 final size:26
Alignment explanation
Indices: 282669--282716 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
282659 AGAGAAATGT
282669 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
282693 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
282717 CCATGTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:283243 original size:19 final size:19
Alignment explanation
Indices: 283221--283265 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
283211 TTATATTAGG
283221 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
283240 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
283259 ATTTAAT
1 ATTTAAT
283266 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:284115 original size:21 final size:22
Alignment explanation
Indices: 284080--284126 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
284070 TTCCTATTTC
284080 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTATTTTCTTTTAT
*
284102 TTTTAATT-TTTTTTCTTTTAT
1 TTTTAATTCTATTTTCTTTTAT
284123 TTTT
1 TTTT
284127 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTAATTCTATTTTCTTTTAT
Found at i:286895 original size:13 final size:13
Alignment explanation
Indices: 286871--286927 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
286861 CCAATTATTA
286871 TTATTATTATTTTT
1 TTATT-TTATTTTT
286885 TTATTTTATTTTT
1 TTATTTTATTTTT
* *
286898 CTATCTTA---TT
1 TTATTTTATTTTT
*
286908 TTATTTTATTTAT
1 TTATTTTATTTTT
286921 TTATTTT
1 TTATTTT
286928 TGTCCAGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 8 0.23
13 22 0.63
14 5 0.14
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTATTTTT
Found at i:286908 original size:18 final size:18
Alignment explanation
Indices: 286865--286927 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
286855 GGCAACCCAA
* *
286865 TTATTATTATTATTATTTTT
1 TTATT-TTATT-TTATCTAT
286885 TTATTTTATTTT-TCTAT
1 TTATTTTATTTTATCTAT
*
286902 CTTATTTTATTTTATTTAT
1 -TTATTTTATTTTATCTAT
286921 TTATTTT
1 TTATTTT
286928 TGTCCAGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
17 3 0.08
18 21 0.55
19 9 0.24
20 5 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTATTTTATCTAT
Found at i:288464 original size:19 final size:20
Alignment explanation
Indices: 288409--288468 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
288399 TTTTTTAAAT
* * *
288409 ATATTTAATATTAGGATTTA
1 ATATTTAAGATTTGTATTTA
*
288429 ATATTTAAGATAT-TATTTA
1 ATATTTAAGATTTGTATTTA
*
288448 TTATTTAA-ATTTGTATTTA
1 ATATTTAAGATTTGTATTTA
288467 AT
1 AT
288469 TTATGTCTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 3 0.09
19 19 0.59
20 10 0.31
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
ATATTTAAGATTTGTATTTA
Found at i:289252 original size:21 final size:22
Alignment explanation
Indices: 289216--289262 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
289206 TTTTTATTTC
*
289216 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
289238 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
289259 TTTT
1 TTTT
289263 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:292039 original size:23 final size:23
Alignment explanation
Indices: 292010--292264 Score: 350
Period size: 23 Copynumber: 11.1 Consensus size: 23
292000 AATGTTTAAG
*
292010 AATATTAATGTGATTTGTGCTTA
1 AATATTAATGTGATTTATGCTTA
* *
292033 AACATTAATATGATTTATGAC-TA
1 AATATTAATGTGATTTATG-CTTA
*
292056 AATATTAATGTGACTTATGCTTA
1 AATATTAATGTGATTTATGCTTA
*
292079 AGTATTAATGTGATTTATGCTTA
1 AATATTAATGTGATTTATGCTTA
* *
292102 AATATTAATATGATTTATGCTGA
1 AATATTAATGTGATTTATGCTTA
*
292125 AATATTAATGTGATTTGTGCTTA
1 AATATTAATGTGATTTATGCTTA
* * *
292148 AATATTAATATGATTTGTGCTCA
1 AATATTAATGTGATTTATGCTTA
*
292171 AATATTAATGTGATTTATACTTA
1 AATATTAATGTGATTTATGCTTA
292194 AATATTAATGTGATTTATGCTTA
1 AATATTAATGTGATTTATGCTTA
* * *
292217 ATTATTAATGTGACTTGTGCTTA
1 AATATTAATGTGATTTATGCTTA
*
292240 AATATTAATGTGATTTGTGCTTA
1 AATATTAATGTGATTTATGCTTA
292263 AA
1 AA
292265 GAATTAAGAT
Statistics
Matches: 204, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
22 1 0.00
23 202 0.99
24 1 0.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (23 bp):
AATATTAATGTGATTTATGCTTA
Found at i:296394 original size:48 final size:48
Alignment explanation
Indices: 296336--296492 Score: 262
Period size: 48 Copynumber: 3.3 Consensus size: 48
296326 AATTATGTGC
*
296336 TAAATGCATCTTTGTTTAATAA-CATGCATCATTAAGTGTTTTGTTTGT
1 TAAATGCATCTTTGTTTAATAATC-TGCATCATTAAATGTTTTGTTTGT
* *
296384 TAAATTCATCTTTGTTTAATAATCTGCATCATTAAATATTTTGTTTGT
1 TAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTTTTGTTTGT
*
296432 TAAATGCATCTTTGTTTAATAATCTACATCATTAAATGTTTTGTTTGT
1 TAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTTTTGTTTGT
296480 TAAATGCATCTTT
1 TAAATGCATCTTT
296493 AAAGACTGCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 101 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (48 bp):
TAAATGCATCTTTGTTTAATAATCTGCATCATTAAATGTTTTGTTTGT
Found at i:297011 original size:78 final size:79
Alignment explanation
Indices: 296881--297034 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 79
296871 AATAAACACA
* * *
296881 TTAAGGATACACTAAGTCTTCATTAAGGAGAAATGTCATGCCTTTTTAACTACATTAGATCCTAA
1 TTAAGGATACAATAAGTCTTCATTAAGGAGAAATGTCATGCCTTTTCAACTACATCAGATCCTAA
296946 TGAAGAGACATAGG
66 TGAAGAGACATAGG
*
296960 TTAAGGATACAATAATTCTTCA-TAAGGAGAAATGTCATGCCTTTTCAACTACATCAGATCCTAA
1 TTAAGGATACAATAAGTCTTCATTAAGGAGAAATGTCATGCCTTTTCAACTACATCAGATCCTAA
297024 TGAAGAGACAT
66 TGAAGAGACAT
297035 GACTCATTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
78 51 0.72
79 20 0.28
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (79 bp):
TTAAGGATACAATAAGTCTTCATTAAGGAGAAATGTCATGCCTTTTCAACTACATCAGATCCTAA
TGAAGAGACATAGG
Found at i:297692 original size:343 final size:341
Alignment explanation
Indices: 297068--297747 Score: 1182
Period size: 343 Copynumber: 2.0 Consensus size: 341
297058 GTTAAAAACG
* ** * *
297068 AAATTAGTGCTTGTATTGACTTTGGTTAATGGCCGAATATGAAAGGTCTCACATAGGCATTTGAA
1 AAATTAGGGCTTGTATCAACTCTGGTTAATGGCAGAATATGAAAGGTCTCACATAGGCATTTGAA
* * *
297133 TGGTCACAAAAGTGTATAAATAACCTGTAAGTAGAACCTTGTTGGCTAATAAATATTTTTGAGTT
66 TAGTCACAAAAGTGTATAAATAACCTGTAAGTAGAACCTCGTTGGCTAATAAATATTTCTGAGTT
297198 TATGCGAGAATTCTATCTCTTTGTTATTGGTCTAACTTACTTGGACTTATCAAGGAATTCCTTAT
131 TATGCGAGAATTCTATCTCTTTGTTATTGGTCTAACTTACTTGGACTTATCAAGGAATTCCTTAT
297263 GGCATCAACCCCTTTTCGTTTGAACTTAAATCTTCCTTTCTTCTTTCTGAAGTATGGCGTCCTAA
196 GGCATCAACCCCTTTTCGTTTGAACTTAAATCTTCCTTTCTTCTTTCTGAAGTATGGCGTCCTAA
297328 TATATCGTTGGTTCCTATTTTGCTAAATAGTGGGTCACAATTTACCTTTTCTTTTCTTCTTGATT
261 TATATCGTTGGTTCCTATTTTGCTAAATAGTGGGTCACAATTTACCTTTTCTTTTCTTCTTGATT
297393 TGTTTGTTATTTTGCT
326 TGTTTGTTATTTTGCT
297409 AAATTAGGGCTTGTATCAACTCTGGTTAATGGCAGAATATGAAAGGTCTCACATAGGCATTTGAA
1 AAATTAGGGCTTGTATCAACTCTGGTTAATGGCAGAATATGAAAGGTCTCACATAGGCATTTGAA
*
297474 TAGTCACAAAAGTGTCTATAAATAACCTGTAAGTAGAACCTCGTTGGCTAATGAATATTTCTGAG
66 TAGTCACAAAAGTG--TATAAATAACCTGTAAGTAGAACCTCGTTGGCTAATAAATATTTCTGAG
* *
297539 TTTATGCGAGAATTCTATCTCTTTGTTCTTGGTCTAACTTACTTGGACTTATCAAGGACTTCCTT
129 TTTATGCGAGAATTCTATCTCTTTGTTATTGGTCTAACTTACTTGGACTTATCAAGGAATTCCTT
* * *
297604 GTGGCATCAACCCCTTTTCGTTTGAACTTATCA-CTTCCTTTCTTCTTTCTGAAGTGTGGCGTCC
194 ATGGCATCAACCCCTTTTCGTTTGAACTTA-AATCTTCCTTTCTTCTTTCTGAAGTATGGCGTCC
* *
297668 TAATATATCGTTGGTTCTTATTTTGCTAAATAGTGGGTCACAATTTACCTTTTCTTTTCTTGTTG
258 TAATATATCGTTGGTTCCTATTTTGCTAAATAGTGGGTCACAATTTACCTTTTCTTTTCTTCTTG
297733 ATTTGTTTGTTATTT
323 ATTTGTTTGTTATTT
297748 CGCTTAATAG
Statistics
Matches: 320, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
341 73 0.23
343 246 0.77
344 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (341 bp):
AAATTAGGGCTTGTATCAACTCTGGTTAATGGCAGAATATGAAAGGTCTCACATAGGCATTTGAA
TAGTCACAAAAGTGTATAAATAACCTGTAAGTAGAACCTCGTTGGCTAATAAATATTTCTGAGTT
TATGCGAGAATTCTATCTCTTTGTTATTGGTCTAACTTACTTGGACTTATCAAGGAATTCCTTAT
GGCATCAACCCCTTTTCGTTTGAACTTAAATCTTCCTTTCTTCTTTCTGAAGTATGGCGTCCTAA
TATATCGTTGGTTCCTATTTTGCTAAATAGTGGGTCACAATTTACCTTTTCTTTTCTTCTTGATT
TGTTTGTTATTTTGCT
Found at i:302160 original size:30 final size:30
Alignment explanation
Indices: 302124--302180 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
302114 CGCTATGGTG
302124 TCAACCAGTTTCCCTTTCCCTTTATCAGCA
1 TCAACCAGTTTCCCTTTCCCTTTATCAGCA
*
302154 TCAACCATTTTCCCTTTCCCTTTATCA
1 TCAACCAGTTTCCCTTTCCCTTTATCA
302181 TTCCTGCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.37, G:0.04, T:0.40
Consensus pattern (30 bp):
TCAACCAGTTTCCCTTTCCCTTTATCAGCA
Found at i:306160 original size:6 final size:6
Alignment explanation
Indices: 306149--306186 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
306139 GGTGGGATTA
* *
306149 GGGTTT GGGTTT GGGTTT GGGTTT GGATTT GGATTT GG
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GG
306187 ATTTTTGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.05, C:0.00, G:0.47, T:0.47
Consensus pattern (6 bp):
GGGTTT
Found at i:306172 original size:18 final size:18
Alignment explanation
Indices: 306143--306186 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
306133 GAGGGAGGTG
* *
306143 GGATTAGGGTTTGGGTTT
1 GGATTTGGGTTTGGATTT
*
306161 GGGTTTGGGTTTGGATTT
1 GGATTTGGGTTTGGATTT
306179 GGATTTGG
1 GGATTTGG
306187 ATTTTTGGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.45, T:0.45
Consensus pattern (18 bp):
GGATTTGGGTTTGGATTT
Found at i:306187 original size:6 final size:6
Alignment explanation
Indices: 306152--306190 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
306142 GGGATTAGGG
* * *
306152 TTTGGG TTTGGG TTTGGG TTTGGA TTTGGA TTTGGA TTT
1 TTTGGA TTTGGA TTTGGA TTTGGA TTTGGA TTTGGA TTT
306191 TTGGGGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (6 bp):
TTTGGA
Found at i:306187 original size:12 final size:12
Alignment explanation
Indices: 306152--306190 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
306142 GGGATTAGGG
*
306152 TTTGGGTTTGGG
1 TTTGGGTTTGGA
306164 TTTGGGTTTGGA
1 TTTGGGTTTGGA
*
306176 TTTGGATTTGGA
1 TTTGGGTTTGGA
306188 TTT
1 TTT
306191 TTGGGGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.00, G:0.38, T:0.54
Consensus pattern (12 bp):
TTTGGGTTTGGA
Found at i:315769 original size:40 final size:41
Alignment explanation
Indices: 315696--315775 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
315686 TTCTTATTGT
* * *
315696 ATTTTTAATTTTTTTGTTATTTTACGAATTGTTTTAATATC
1 ATTTTTAATTTGTTTGATATTTTAAGAATTGTTTTAATATC
* *
315737 ATTTTTAATTTGTTTGAT-TTTTAATATTTGTTTTAATAT
1 ATTTTTAATTTGTTTGATATTTTAAGAATTGTTTTAATAT
315776 TTTTAACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (41 bp):
ATTTTTAATTTGTTTGATATTTTAAGAATTGTTTTAATATC
Found at i:317461 original size:19 final size:19
Alignment explanation
Indices: 317437--317473 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
317427 TATAAAATTG
* *
317437 AAAATTATTAAAATTATTT
1 AAAATTATAAAAAATATTT
317456 AAAATTATAAAAAATATT
1 AAAATTATAAAAAATATT
317474 GTTATGTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTATAAAAAATATTT
Found at i:331171 original size:17 final size:18
Alignment explanation
Indices: 331140--331173 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
331130 TTATTTTCTT
331140 GAAATAAATTTAAAAAAC
1 GAAATAAATTTAAAAAAC
331158 GAAATAAA-TTAAAAAA
1 GAAATAAATTTAAAAAA
331174 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (18 bp):
GAAATAAATTTAAAAAAC
Found at i:331174 original size:18 final size:18
Alignment explanation
Indices: 331140--331174 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
331130 TTATTTTCTT
*
331140 GAAATAAATTTAAAAAAC
1 GAAATAAATTAAAAAAAC
331158 GAAATAAATTAAAAAAA
1 GAAATAAATTAAAAAAA
331175 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (18 bp):
GAAATAAATTAAAAAAAC
Found at i:332846 original size:2 final size:2
Alignment explanation
Indices: 332839--332871 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
332829 TCACAGTGCC
332839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
332872 CTAAATACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:351177 original size:51 final size:51
Alignment explanation
Indices: 351099--351235 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
351089 TAAACGAAAG
*** *
351099 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACCTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACCAAGACGAATTAAA
* * * *
351150 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCAAGATGAATTATA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACCAAGACGAATTAAA
* * *
351201 GGTCCGATGACTCAGTATCATCGTGAGTATATGAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA
351236 CTTTTATACG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAACCAAGACGAATTAAA
Found at i:356211 original size:19 final size:17
Alignment explanation
Indices: 356187--356233 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
356177 AAATTATAAG
356187 AAATATAGAACATTATTAA
1 AAATATAGAA-A-TATTAA
* *
356206 ATATATATAAATATTAA
1 AAATATAGAAATATTAA
356223 AAATATAGAAA
1 AAATATAGAAA
356234 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 15 0.62
18 1 0.04
19 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
AAATATAGAAATATTAA
Found at i:356304 original size:21 final size:19
Alignment explanation
Indices: 356278--356316 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
356268 ATGTAGAAAT
356278 ATATTTAAAATTTATAAAAAA
1 ATATTTAAAA--TATAAAAAA
356299 ATATTTAAAATATAAAAA
1 ATATTTAAAATATAAAAA
356317 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATTTAAAATATAAAAAA
Found at i:356843 original size:13 final size:14
Alignment explanation
Indices: 356815--356857 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
356805 AAACATAGAT
* *
356815 AATATCATAAACTA
1 AATAACATAAAATA
356829 AATAAC-TAAAATA
1 AATAACATAAAATA
*
356842 AATAACAAAAAATA
1 AATAACATAAAATA
356856 AA
1 AA
356858 ATAGAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAACATAAAATA
Found at i:359831 original size:21 final size:20
Alignment explanation
Indices: 359788--359831 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
359778 ACTCAATTAA
*
359788 AAATGATTCTCAAATGTTTT
1 AAATGATTCTCAAATATTTT
359808 AAATGACTTCT-AAATATTTAT
1 AAATGA-TTCTCAAATATTT-T
359829 AAA
1 AAA
359832 CCATGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (20 bp):
AAATGATTCTCAAATATTTT
Found at i:363751 original size:17 final size:17
Alignment explanation
Indices: 363726--363785 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
363716 CTCAACAAAT
363726 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
363743 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
* * *
363760 TTAAATTAATTATAAAT
1 TTAAATTTATTTTAAAA
363777 TTAAATTTA
1 TTAAATTTA
363786 AAATTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:363762 original size:23 final size:24
Alignment explanation
Indices: 363723--363799 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 24
363713 GGGCTCAACA
*
363723 AATT-TAAATTT-ATTTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
363745 AAGTT-T-ATTTTAAATTT-AAATT
1 AA-TTATAAATTTAAATTTAAAATT
363767 AATTATAAATTTAAATTTAAAATT
1 AATTATAAATTTAAATTTAAAATT
*
363791 CATT-TAAAT
1 AATTATAAAT
363800 AATGTCCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
23 22 0.48
24 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
AATTATAAATTTAAATTTAAAATT
Found at i:363790 original size:7 final size:6
Alignment explanation
Indices: 363722--363787 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
363712 TGGGCTCAAC
* * * *
363722 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAA-TT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
363767 -AATTAT AAATTT AAATTT AAA
1 AAATT-T AAATTT AAATTT AAA
363788 ATTCATTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.04
5 11 0.23
6 31 0.65
7 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:364517 original size:16 final size:16
Alignment explanation
Indices: 364478--364518 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
364468 TATTAATTTA
364478 ATAATAAT-AATGACC
1 ATAATAATAAATGACC
*
364493 ATAACAATAAATGA-C
1 ATAATAATAAATGACC
364508 ATTAATAATAA
1 A-TAATAATAA
364519 TAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (16 bp):
ATAATAATAAATGACC
Found at i:365612 original size:29 final size:30
Alignment explanation
Indices: 365568--365872 Score: 312
Period size: 29 Copynumber: 10.3 Consensus size: 30
365558 CCTTAAACAG
365568 TCCAAAAAT-TCAATTTTT-ACCCTCGAACT
1 TCCAAAAATCTC-ATTTTTGACCCTCGAACT
365597 TCCAAAAATCTCATTTTTGACCC-CGAAACT
1 TCCAAAAATCTCATTTTTGACCCTCG-AACT
* * *
365627 TCCAAAAAT-TCCATCTTT-ACCCCCTAACT
1 TCCAAAAATCT-CATTTTTGACCCTCGAACT
*
365656 TCCAAAAATCTCATTTTTGA-CCACGAAACT
1 TCCAAAAATCTCATTTTTGACCCTCG-AACT
*
365686 TCCAAAAATTTCATTTTT-ACCCTCGAACT
1 TCCAAAAATCTCATTTTTGACCCTCGAACT
* *
365715 TCCAAAAATCCCATTTTTGACCAT-GAAACT
1 TCCAAAAATCTCATTTTTGACCCTCG-AACT
*
365745 TCCAAAAAT-TCCATTTTT-ACCCTCAAACT
1 TCCAAAAATCT-CATTTTTGACCCTCGAACT
* * * *
365774 TTCAAAAATCCCATTTTTGACCCCCAAAACT
1 TCCAAAAATCTCATTTTTGACCCTC-GAACT
* *
365805 TCCAAAAAT-TCCGTTTTT-ACCCTCGAGCT
1 TCCAAAAATCT-CATTTTTGACCCTCGAACT
365834 TCCAAAAATCTCATTTTTGA-CCTCGAAACT
1 TCCAAAAATCTCATTTTTGACCCTCG-AACT
365864 TCCAAAAAT
1 TCCAAAAAT
365873 TACCATTTTA
Statistics
Matches: 232, Mismatches: 24, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
29 112 0.48
30 101 0.44
31 19 0.08
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (30 bp):
TCCAAAAATCTCATTTTTGACCCTCGAACT
Found at i:365660 original size:59 final size:59
Alignment explanation
Indices: 365568--365885 Score: 467
Period size: 59 Copynumber: 5.4 Consensus size: 59
365558 CCTTAAACAG
* *
365568 TCCAAAAATTCAATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAAACT
* * *
365627 TCCAAAAATTCCATCTTTACCCCCTAACTTCCAAAAATCTCATTTTTGACCACGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAAACT
* * *
365686 TCCAAAAATTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCATGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAAACT
* * * * *
365745 TCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGA-CCACGAAACT
* * *
365805 TCCAAAAATTCCGTTTTTACCCTCGAGCTTCCAAAAATCTCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAAACT
365864 TCCAAAAATTACCA-TTTTACCC
1 TCCAAAAATT-CCATTTTTACCC
365886 CCGGATATTC
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
59 179 0.77
60 53 0.23
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCACGAAACT
Found at i:366345 original size:51 final size:51
Alignment explanation
Indices: 366289--366441 Score: 135
Period size: 51 Copynumber: 3.1 Consensus size: 51
366279 TCTTCAAATC
366289 GAAATAATCGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCT
1 GAAATAATCGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCT
* ** * * * * * *
366340 GAAATATTGCGCCTTA-ACTCACTAG-GTGCAA---TT--TT-TCTTCAAATC-
1 GAAATAAT-CG-AATACCCTTAATCGAG-GCAATGTTTCCTTATCTTCGATTCT
366385 GAAATAATCGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCT
1 GAAATAATCGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCT
366436 GAAATA
1 GAAATA
366442 TTATGCCTTA
Statistics
Matches: 72, Mismatches: 18, Indels: 24
0.63 0.16 0.21
Matches are distributed among these distances:
43 2 0.03
44 11 0.15
45 8 0.11
46 8 0.11
47 4 0.06
49 4 0.06
50 8 0.11
51 14 0.19
52 11 0.15
53 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (51 bp):
GAAATAATCGAATACCCTTAATCGAGGCAATGTTTCCTTATCTTCGATTCT
Found at i:366376 original size:96 final size:96
Alignment explanation
Indices: 366246--366499 Score: 438
Period size: 96 Copynumber: 2.7 Consensus size: 96
366236 CGAGTTTCGA
366246 AAAT-TTGTGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1 AAATATTGTGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
366310 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
66 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
*
366341 AAATATTGCGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1 AAATATTGTGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
366406 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
66 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
* * ** * *
366437 AAATATTATGCCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAGATAATCGAATATCCTT
1 AAATATTGTGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTT
366500 TTGCAAAAAT
Statistics
Matches: 150, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 4 0.03
96 146 0.97
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (96 bp):
AAATATTGTGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
TCGAGGCAATGTTTCCTTATCTTCGATTCTG
Found at i:369907 original size:2 final size:2
Alignment explanation
Indices: 369900--369924 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
369890 TAAGCTTAAT
369900 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
369925 GAAAGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371696 original size:19 final size:19
Alignment explanation
Indices: 371660--371696 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
371650 ACTCAATAAG
*
371660 TTATTATCAGTTGAAAATT
1 TTATTATCACTTGAAAATT
*
371679 TTATTATCACTTGGAAAT
1 TTATTATCACTTGAAAAT
371697 GTTGCTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (19 bp):
TTATTATCACTTGAAAATT
Found at i:373239 original size:23 final size:22
Alignment explanation
Indices: 373197--373239 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
373187 TAGTTTTTTT
*
373197 ATTCCTTTTATTTTAGTTTTCC
1 ATTCCTTTTATTTTACTTTTCC
373219 ATTCGCTTTTAGTTTT-CTTTT
1 ATTC-CTTTTA-TTTTACTTTT
373240 ATGTTTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.12, C:0.16, G:0.07, T:0.65
Consensus pattern (22 bp):
ATTCCTTTTATTTTACTTTTCC
Found at i:374436 original size:74 final size:75
Alignment explanation
Indices: 374358--374511 Score: 204
Period size: 74 Copynumber: 2.1 Consensus size: 75
374348 ATCTGATCAT
* * * * **
374358 AAAAAAATTTAACACATGTGACTATTTATTATTGTCA-AATTTGTTTATAATTTTAGTG-TCAAA
1 AAAAAAATTGAACACATGTGACAATTTATTACTATCACAATTT-CCTATAATTTTAGTGTTCAAA
374421 AATTTGGTCAC
65 AATTTGGTCAC
* * *
374432 AAAAAAGTTGAATACATGTGACAATTTATTACTATCACAATTTCCTATAATTTTAGTGTTCAACA
1 AAAAAAATTGAACACATGTGACAATTTATTACTATCACAATTTCCTATAATTTTAGTGTTCAAAA
374497 ATTTGGTCAC
66 ATTTGGTCAC
374507 AAAAA
1 AAAAA
374512 TTTAAATGCT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
74 44 0.64
75 25 0.36
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (75 bp):
AAAAAAATTGAACACATGTGACAATTTATTACTATCACAATTTCCTATAATTTTAGTGTTCAAAA
ATTTGGTCAC
Found at i:379967 original size:13 final size:13
Alignment explanation
Indices: 379949--379974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379939 TTAATTATAA
379949 TTATTTTAATATT
1 TTATTTTAATATT
379962 TTATTTTAATATT
1 TTATTTTAATATT
379975 CCTATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTAATATT
Found at i:385353 original size:20 final size:21
Alignment explanation
Indices: 385310--385353 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
385300 AACTAAGCTT
*
385310 AATTTCTATCAAATTCACACC
1 AATTTCTATCAAATTCACAAC
*
385331 AATTTC-ATCAAATTCTCAAC
1 AATTTCTATCAAATTCACAAC
385351 AAT
1 AAT
385354 GAAATCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTTCTATCAAATTCACAAC
Found at i:387114 original size:11 final size:11
Alignment explanation
Indices: 387092--387126 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
387082 CGATCCGCCC
387092 ATATTGATTTTT
1 ATATT-ATTTTT
387104 ATATTATTTTT
1 ATATTATTTTT
*
387115 ATATAATTTTT
1 ATATTATTTTT
387126 A
1 A
387127 AATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:387281 original size:30 final size:30
Alignment explanation
Indices: 387245--387309 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
387235 CAACTTAACA
* *
387245 AACAAATGTCTCTAAAATAGTAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
387275 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
387305 AACAA
1 AACAA
387310 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:389554 original size:22 final size:22
Alignment explanation
Indices: 389526--389621 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 22
389516 TAAAATTTAT
389526 TTTAAATATATAATATTACATA
1 TTTAAATATATAATATTACATA
*
389548 TTTAAATATATAATATTACGTA
1 TTTAAATATATAATATTACATA
* * *
389570 ATT-AAT-T-TCATATTGAAATTTA
1 TTTAAATATATAATATT-ACA--TA
*
389592 TTTTAAATATATAATTTTACATA
1 -TTTAAATATATAATATTACATA
389615 TTTAAAT
1 TTTAAAT
389622 TTTTATCGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
19 6 0.10
20 2 0.03
21 3 0.05
22 32 0.55
23 4 0.07
24 3 0.05
25 3 0.05
26 5 0.09
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTAAATATATAATATTACATA
Found at i:394382 original size:49 final size:49
Alignment explanation
Indices: 394260--394391 Score: 117
Period size: 49 Copynumber: 2.7 Consensus size: 49
394250 AGTAAGTAGT
* **
394260 AAGTGGCCTTGCTCCTAAACGCATGGACGGAGGCTTACAAAATATATCA
1 AAGTGACCTTGCTCCTAGGCGCATGGACGGAGGCTTACAAAATATATCA
* * * * * * * *
394309 AAGTGACCTCGCT-CTCGGGTGCAT-GAGGGGAGGCTTATAGAATGTATTA
1 AAGTGACCTTGCTCCT-AGGCGCATGGA-CGGAGGCTTACAAAATATATCA
394358 AAGTGACCTTGCTCCTAGGCGCATGG-CGAGAGGC
1 AAGTGACCTTGCTCCTAGGCGCATGGACG-GAGGC
394392 CTAGTCCGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
48 5 0.08
49 55 0.87
50 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (49 bp):
AAGTGACCTTGCTCCTAGGCGCATGGACGGAGGCTTACAAAATATATCA
Found at i:395133 original size:21 final size:20
Alignment explanation
Indices: 395087--395140 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
395077 CCTGTACTAT
395087 TTCTACCGATACAAGTATAAG
1 TTCTACCGATACAAGTAT-AG
*
395108 TTCTACCGATACATGTCAT-G
1 TTCTACCGATACAAGT-ATAG
395128 TATCTACCGATAC
1 T-TCTACCGATAC
395141 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (20 bp):
TTCTACCGATACAAGTATAG
Found at i:395856 original size:61 final size:60
Alignment explanation
Indices: 395727--395905 Score: 245
Period size: 61 Copynumber: 3.0 Consensus size: 60
395717 GTTTCACTCG
* * * * *
395727 CATTTATTACTCACGATGACACAAAGTCATCGAACC-CTTGTT-CGCATTGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCG-ACCTCTTGTTCCGTATAGGAACTCATTT
395786 CATTTAATACTCACGATGACATATAGTCATCAGACCTCTTGTTCCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATC-GACCTCTTGTTCCGTATAGGAACTCATTT
* * *
395847 CATTTAATACTCACGATAACATATAGTCATCGGACCTCTTATTCCGTATAGGAATTCAT
1 CATTTAATACTCACGATGACATATAGTCATC-GACCTCTTGTTCCGTATAGGAACTCAT
395906 ATACTCACGA
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
59 31 0.29
60 7 0.06
61 70 0.65
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (60 bp):
CATTTAATACTCACGATGACATATAGTCATCGACCTCTTGTTCCGTATAGGAACTCATTT
Found at i:395928 original size:53 final size:51
Alignment explanation
Indices: 395853--396041 Score: 202
Period size: 51 Copynumber: 3.6 Consensus size: 51
395843 ATTTCATTTA
* *
395853 ATACTCACGATAACA-TATAGTCATCGGACCTCTTATTCCGTATAGGAATTCAT
1 ATACTCACAATAACACT-TAGTCATCGGACCT-TTAATCCGTATAGG-ATTCAT
* * **
395906 ATACTCACGATAACACTGAGTCATCGGACCTTTAATCCACCAT-GGATTCAT
1 ATACTCACAATAACACTTAGTCATCGGACCTTTAATCC-GTATAGGATTCAT
* * * *
395957 TTACTCACAATGACACTTAATCATCGGACCTTTAATCCGTAAAGGATTCAT
1 ATACTCACAATAACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCAT
* * *
396008 TTATTCACAATGACACTTAGTCATCGGATCCTTT
1 ATACTCACAATAACACTTAGTCATCGGA-CCTTT
396042 CGTTTATAGC
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
51 73 0.62
52 13 0.11
53 30 0.25
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (51 bp):
ATACTCACAATAACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCAT
Found at i:397515 original size:18 final size:18
Alignment explanation
Indices: 397489--397527 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
397479 GATGATAATA
397489 AAGACACAG-CTGAGGAAG
1 AAGACACAGTC-GAGGAAG
*
397507 AAGATACAGTCGAGGAAG
1 AAGACACAGTCGAGGAAG
397525 AAG
1 AAG
397528 GAGCAACGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.46, C:0.13, G:0.33, T:0.08
Consensus pattern (18 bp):
AAGACACAGTCGAGGAAG
Found at i:403500 original size:17 final size:17
Alignment explanation
Indices: 403468--403501 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
403458 CGAATGCCAT
403468 CAGTTGGTGGTGCCACA
1 CAGTTGGTGGTGCCACA
403485 CAGTATGGTGGT-CCACA
1 CAGT-TGGTGGTGCCACA
403502 TACATTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (17 bp):
CAGTTGGTGGTGCCACA
Found at i:416048 original size:52 final size:52
Alignment explanation
Indices: 415942--416054 Score: 156
Period size: 54 Copynumber: 2.2 Consensus size: 52
415932 AGATTTTGAA
*
415942 AGAAAAAAAATTTAGTGTTGGTCATGCATTGGCCGACACCAGTATTTTTTATC
1 AGAAAAAAAATTTAGTGTTGGTCATGCATTGGCCGACACCAG-ACTTTTTATC
* * *
415995 AGAAAAAAGAATTTGGTGTTGGTCATGCATTGGCTGACACCA-CCTTTTTATC
1 AGAAAAAA-AATTTAGTGTTGGTCATGCATTGGCCGACACCAGACTTTTTATC
*
416047 AGATAAAA
1 AGAAAAAA
416055 TTATTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 15 0.28
53 8 0.15
54 31 0.57
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (52 bp):
AGAAAAAAAATTTAGTGTTGGTCATGCATTGGCCGACACCAGACTTTTTATC
Found at i:416314 original size:62 final size:60
Alignment explanation
Indices: 416006--416489 Score: 266
Period size: 61 Copynumber: 8.0 Consensus size: 60
415996 GAAAAAAGAA
* * * *
416006 TTTGGTGTTGGTCATGCATTGGCTGACACCACCTTTTTATCAGAT--AAAATT--ATTTTT
1 TTTGGTGTTGGCCAT-CGTTGGCCGACACCACTTTTTTATCAGATAAAAAATTCAATTTTT
* * * * * * ** * *
416063 TTTGGTGGTAGTCATTGCTTGGTCGACACTACCTTTTTTATTTGACAAAAAATT-TATTTATT
1 TTTGGTGTTGGCCATCG-TTGGCCGACACCA-CTTTTTTATCAGATAAAAAATTCAATTT-TT
* ** * * *
416125 TTT-GTGTTGGCCATTGCTTGGTTGACACCATCTTTTTAATCTA-ACAAAAAATTCAAAATTTT
1 TTTGGTGTTGGCCATCG-TTGGCCGACACCA-CTTTTTTATC-AGATAAAAAATTC-AATTTTT
** ** *
416187 TTTACTGTTGGCCATATATTGGCCGACATCAGCATTTTTTATCAGAT----AATT---TTTTT
1 TTTGGTGTTGGCCAT-CGTTGGCCGACACCA-C-TTTTTTATCAGATAAAAAATTCAATTTTT
** * * * *
416243 TTTAATGTTGGTCATCGTTTGGCCGACACCACCTCTTTAATCTGATAAAAAATTCAATTTTT
1 TTTGGTGTTGGCCATCG-TTGGCCGACACCA-CTTTTTTATCAGATAAAAAATTCAATTTTT
* *
416305 TTTGGTGTTGGCCATGCGTTGGCCGACACCAGTATTTTTTTATCAAATAAAAAA-T--ATTTTT
1 TTTGGTGTTGGCCAT-CGTTGGCCGACACC---ACTTTTTTATCAGATAAAAAATTCAATTTTT
* * * * * ** *
416366 TTTGGTGTTGACCATTGCCTGACCGACACCATCTTTTTTATCTGATAAAAAATTCAAAATCT
1 TTTGGTGTTGGCCATCG-TTGGCCGACACCA-CTTTTTTATCAGATAAAAAATTCAATTTTT
* * *
416428 TTTGGTGTTGGCCATGCATTGGCCGACACCA-TTTTTTATCAGATAAAAAAATAAATTTTT
1 TTTGGTGTTGGCCAT-CGTTGGCCGACACCACTTTTTTATCAGATAAAAAATTCAATTTTT
416488 TT
1 TT
416490 GTATTGGTCA
Statistics
Matches: 327, Mismatches: 69, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
55 10 0.03
56 30 0.09
57 23 0.07
58 11 0.03
59 21 0.06
60 37 0.11
61 74 0.23
62 67 0.20
63 28 0.09
64 25 0.08
65 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (60 bp):
TTTGGTGTTGGCCATCGTTGGCCGACACCACTTTTTTATCAGATAAAAAATTCAATTTTT
Found at i:416416 original size:123 final size:120
Alignment explanation
Indices: 415956--416496 Score: 418
Period size: 123 Copynumber: 4.5 Consensus size: 120
415946 AAAAAATTTA
* *
415956 GTGTTGGTCATGCATTGGCCGACACCAGTATTTTTTATCAGA-AAAAAGA-A----TTTGGTGTT
1 GTGTTGGCCATGCATTGGCCGACACCAG-ATTTTTTATCAGATAAAAA-ATATTTTTTTTGTGTT
* * * * *
416015 GGTCA-TGCATTGGCTGACACCACCTTTTT-ATCAGAT--AAAATT--ATTTTTTTTG
64 GGCCATTGC-TTGGCCGACACCATCTTTTTAATCTGATAAAAAATTCAAATTTTTTTG
* * * * * ** ** *
416067 GTGGTAGTCATTGC-TTGGTCGACACTACCTTTTTTATTTGACAAAAAATTTATTTATTTTTGTG
1 GTGTTGGCCA-TGCATTGGCCGACACCAGATTTTTTATCAGATAAAAAA--TATTT-TTTTTGTG
** * * *
416131 TTGGCCATTGCTTGGTTGACACCATCTTTTTAATCTAACAAAAAATTCAAAATTTTTTTA
62 TTGGCCATTGCTTGGCCGACACCATCTTTTTAATCTGATAAAAAATTC-AAATTTTTTTG
* ** * * *
416191 CTGTTGGCCATATATTGGCCGACATCAGCATTTTTTATCAGAT----AATTTTTTTTTTAATGTT
1 GTGTTGGCCATGCATTGGCCGACACCAG-ATTTTTTATCAGATAAAAAATATTTTTTTT-GTGTT
* * * * * *
416252 GGTCATCGTTTGGCCGACACCACCTCTTTAATCTGATAAAAAATTCAATTTTTTTTG
64 GGCCATTGCTTGGCCGACACCATCTTTTTAATCTGATAAAAAATTCAAATTTTTTTG
* *
416309 GTGTTGGCCATGCGTTGGCCGACACCAGTATTTTTTTATCAAATAAAAAATATTTTTTTTGGTGT
1 GTGTTGGCCATGCATTGGCCGACACCAG-A-TTTTTTATCAGATAAAAAATATTTTTTTT-GTGT
* * * * * *
416374 TGACCATTGCCTGACCGACACCATCTTTTTTATCTGATAAAAAATTCAAAATCTTTTG
63 TGGCCATTGCTTGGCCGACACCATCTTTTTAATCTGATAAAAAATTCAAATTTTTTTG
* *
416432 GTGTTGGCCATGCATTGGCCGACACC--ATTTTTTATCAGATAAAAAAATAAATTTTTTTGTATT
1 GTGTTGGCCATGCATTGGCCGACACCAGATTTTTTATCAGAT-AAAAAAT-ATTTTTTTTGTGTT
416495 GG
64 GG
416497 TCATGCATTG
Statistics
Matches: 332, Mismatches: 71, Indels: 45
0.74 0.16 0.10
Matches are distributed among these distances:
110 11 0.03
111 24 0.07
112 3 0.01
113 1 0.00
118 68 0.20
119 76 0.23
120 13 0.04
121 16 0.05
123 86 0.26
124 24 0.07
125 10 0.03
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (120 bp):
GTGTTGGCCATGCATTGGCCGACACCAGATTTTTTATCAGATAAAAAATATTTTTTTTGTGTTGG
CCATTGCTTGGCCGACACCATCTTTTTAATCTGATAAAAAATTCAAATTTTTTTG
Found at i:416977 original size:57 final size:57
Alignment explanation
Indices: 416887--417002 Score: 157
Period size: 57 Copynumber: 2.0 Consensus size: 57
416877 AAAAAAAATA
* * *
416887 TTTTTTATCTGATAAATAAAAGGTGTCGACCAATGCATGG-CGAACA-CAAATTTTTT
1 TTTTTTATCAGATAAATAAAAGATGTCGACCAATGCA-GGACCAACACCAAATTTTTT
416943 TTTTTTATCAGATAAA-AAATATGATGTCGACCAATGCAGGACCAACACCAAATTTTTT
1 TTTTTTATCAGATAAATAAA-A-GATGTCGACCAATGCAGGACCAACACCAAATTTTTT
417001 TT
1 TT
417003 CCTGATAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
55 3 0.06
56 18 0.34
57 20 0.38
58 12 0.23
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (57 bp):
TTTTTTATCAGATAAATAAAAGATGTCGACCAATGCAGGACCAACACCAAATTTTTT
Found at i:418903 original size:71 final size:71
Alignment explanation
Indices: 418787--418932 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
418777 CAAGGGGTAC
*
418787 ATAGCTGCATCATGCACCCCTCACAACCCTCCTAATTATTGCATCCTGGGATGCAAAAATAGTGC
1 ATAGCTGCATCACGCACCCCTCACAACCCTCCTAATTATTGCATCCTGGGATGCAAAAATAGTGC
418852 TAAATG
66 TAAATG
418858 ATAGCTGCATCACGCACCCCTCACAACCCTCCTAATTATTGCATCCTGGGATGCAAAAATAGTGC
1 ATAGCTGCATCACGCACCCCTCACAACCCTCCTAATTATTGCATCCTGGGATGCAAAAATAGTGC
418923 TAAATG
66 TAAATG
418929 ATAG
1 ATAG
418933 TCTTTCCCCA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (71 bp):
ATAGCTGCATCACGCACCCCTCACAACCCTCCTAATTATTGCATCCTGGGATGCAAAAATAGTGC
TAAATG
Found at i:420909 original size:18 final size:20
Alignment explanation
Indices: 420869--420914 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
420859 TTGAACTTTT
* *
420869 TTTTTTATTTTAGTTAGATA
1 TTTTTAATTTTAGTAAGATA
420889 TTTTTAATTTT-GTAAGA-A
1 TTTTTAATTTTAGTAAGATA
*
420907 TTTATAAT
1 TTTTTAAT
420915 AGGTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTTAATTTTAGTAAGATA
Found at i:426712 original size:16 final size:16
Alignment explanation
Indices: 426688--426718 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
426678 TTTATGTTTA
*
426688 TTTAGGGTTTAAGGTT
1 TTTAAGGTTTAAGGTT
426704 TTTAAGGTTTAAGGT
1 TTTAAGGTTTAAGGT
426719 ATTATGGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (16 bp):
TTTAAGGTTTAAGGTT
Found at i:427845 original size:43 final size:43
Alignment explanation
Indices: 427780--427876 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
427770 AATTGCTCAA
* * *
427780 TTAATAACATGTCACGATATTAATA-AGAGTCAAGTAATATAAT
1 TTAATAACATGCCACCATATTAACACA-AGTCAAGTAATATAAT
* *
427823 TTAGTAACATGCCACCATATTAACACAAGTCAAGTAATGTAAT
1 TTAATAACATGCCACCATATTAACACAAGTCAAGTAATATAAT
427866 TTAATAACATG
1 TTAATAACATG
427877 TCAATGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (43 bp):
TTAATAACATGCCACCATATTAACACAAGTCAAGTAATATAAT
Found at i:429822 original size:24 final size:26
Alignment explanation
Indices: 429786--429837 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
429776 CTTAAAATAA
429786 TAATTACTAAATAAAATA-TAACATT
1 TAATTACTAAATAAAATATTAACATT
* *
429811 TAATTAC-CAATAAAATATTTACATT
1 TAATTACTAAATAAAATATTAACATT
429836 TA
1 TA
429838 CTTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATTACTAAATAAAATATTAACATT
Found at i:430028 original size:4 final size:4
Alignment explanation
Indices: 430012--430070 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
430002 GTATATTTAC
* * * *
430012 CTTT CTCT CTTT CTTT CTTT TTTT CTTT CCTCT CATTT TTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT C-TTT CTTT CTTT CTTT
430062 CTTTT CTTT
1 C-TTT CTTT
430071 GCTGTTTGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
4 35 0.80
5 9 0.20
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:436163 original size:25 final size:26
Alignment explanation
Indices: 436113--436172 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
436103 ACGCAGAAAG
**
436113 CCTTTGTGGCTAATCTTGTGGTAAAA
1 CCTTTGTGGCTAATCTTGTGAAAAAA
*
436139 CTTTTGTGGCTAATCTT-TGAAAAAA
1 CCTTTGTGGCTAATCTTGTGAAAAAA
436164 CCTTTGTGG
1 CCTTTGTGG
436173 TATGTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (26 bp):
CCTTTGTGGCTAATCTTGTGAAAAAA
Found at i:436695 original size:23 final size:22
Alignment explanation
Indices: 436660--436706 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
436650 ATAAATAAAT
* *
436660 AATAAACCTAAATTACAAGCTCA
1 AATAAACC-AAAATACAAACTCA
*
436683 AATATACCAAAATACAAACTCA
1 AATAAACCAAAATACAAACTCA
436705 AA
1 AA
436707 AACAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.19
Consensus pattern (22 bp):
AATAAACCAAAATACAAACTCA
Found at i:437780 original size:30 final size:30
Alignment explanation
Indices: 437745--437927 Score: 190
Period size: 30 Copynumber: 6.2 Consensus size: 30
437735 TTATGTTTTT
* * *
437745 ACCCTTAAATTTTCAAAAAATTCAAATTTG
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
* * * *
437775 GCCCTTCAACTTTCCAAAAATTCAAATTTG
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
* ** *
437805 A-CCTCAAACTTTC-AAAAATTTGAATTTT
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
* *
437833 ACCCTTAAATTTTCTAAAAATTCTAATTTA
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
*
437863 ACCCCTAAACTTTCTAAAAATTCAAATTTA
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
* ** *
437893 ACTCTTGCACTTTCTAAAAATTCAAATTTG
1 ACCCTTAAACTTTCTAAAAATTCAAATTTA
437923 ACCCT
1 ACCCT
437928 GTTTTAATGT
Statistics
Matches: 127, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.10
29 20 0.16
30 94 0.74
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.37
Consensus pattern (30 bp):
ACCCTTAAACTTTCTAAAAATTCAAATTTA
Found at i:442134 original size:31 final size:31
Alignment explanation
Indices: 442098--442157 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
442088 TACCAGATTT
442098 AAATGGTTAGATGAGAGGTTCAAAGCTTTAA
1 AAATGGTTAGATGAGAGGTTCAAAGCTTTAA
442129 AAATGGTTAGATGAGAGGTTCAAAGCTTT
1 AAATGGTTAGATGAGAGGTTCAAAGCTTT
442158 TGAAGGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (31 bp):
AAATGGTTAGATGAGAGGTTCAAAGCTTTAA
Found at i:442732 original size:14 final size:14
Alignment explanation
Indices: 442713--442740 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
442703 TGTTGGAGAA
442713 AGTACCAAAAGGTT
1 AGTACCAAAAGGTT
442727 AGTACCAAAAGGTT
1 AGTACCAAAAGGTT
442741 TGCTCCTAGA
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:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGTACCAAAAGGTT
Found at i:448658 original size:227 final size:227
Alignment explanation
Indices: 448262--448716 Score: 838
Period size: 227 Copynumber: 2.0 Consensus size: 227
448252 AAGGCTATCC
* *
448262 AACATGGCCAGGTGTACTAGAAATAGATGATGCAAGCCTATGATAAAAAGGTTCGCCCAATTCCA
1 AACATGGCCAGGTGTACCAGAAACAGATGATGCAAGCCTATGATAAAAAGGTTCGCCCAATTCCA
*
448327 CAAGGGATATCTAGTTTTGAAAAAAGATCCTTCCTATGCAAAAAGACTTTCGGGGCAACTGGATG
66 CAAGGGATATCTAGTTTTGAAAAAAGATCCTTCCTATGCAAAAAGACTTTCGGGGCAAATGGATG
* *
448392 CCAAATTGGGAAGGACCATATGTTGTAAAGAATGCCTTCTCTGGAGGAGTTTTTATTCTAAATGA
131 CCAAATTGGGAAGGACCATATGTTGTAAAGAAAGCCTTCTCTGGAGGAGCTTTTATTCTAAATGA
*
448457 GATGGACAACAAATATTTGTCAAACCCCGTGA
196 GATGGACAACAAAGATTTGTCAAACCCCGTGA
*
448489 AACATGGCCAGGTGTACCAGAAACAGATGATGCAAGCCTATGATAAAAAGGTTCGCCCTATTCCA
1 AACATGGCCAGGTGTACCAGAAACAGATGATGCAAGCCTATGATAAAAAGGTTCGCCCAATTCCA
448554 CAAGGGATATCTAGTTTTGAAAAAAGATCCTTCCTATGCAAAAAGACTTTCGGGGCAAATGGATG
66 CAAGGGATATCTAGTTTTGAAAAAAGATCCTTCCTATGCAAAAAGACTTTCGGGGCAAATGGATG
*
448619 CCAAATTGGGAAGGCCCATATGTTGTAAAGAAAGCCTTCTCTGGAGGAGCTTTTATTCTAAATGA
131 CCAAATTGGGAAGGACCATATGTTGTAAAGAAAGCCTTCTCTGGAGGAGCTTTTATTCTAAATGA
448684 GATGGACAACAAAGATTTGTCAAACCCCGTGA
196 GATGGACAACAAAGATTTGTCAAACCCCGTGA
448716 A
1 A
448717 CTCAGATTTA
Statistics
Matches: 220, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
227 220 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (227 bp):
AACATGGCCAGGTGTACCAGAAACAGATGATGCAAGCCTATGATAAAAAGGTTCGCCCAATTCCA
CAAGGGATATCTAGTTTTGAAAAAAGATCCTTCCTATGCAAAAAGACTTTCGGGGCAAATGGATG
CCAAATTGGGAAGGACCATATGTTGTAAAGAAAGCCTTCTCTGGAGGAGCTTTTATTCTAAATGA
GATGGACAACAAAGATTTGTCAAACCCCGTGA
Found at i:449758 original size:50 final size:50
Alignment explanation
Indices: 449639--449785 Score: 197
Period size: 50 Copynumber: 2.9 Consensus size: 50
449629 ATCAAATCCT
* * ** * *
449639 ATACCCCTAAAGCTGTAGAAGAACAAATTGAAGCCGCAATGGCAAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCGAATCTC
*
449689 ATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGCAATGGCGAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCGAATCTC
* *
449739 ATTCACCTAAAGCTGTAGAGGGGCAGATTGAAGCTGCAA-GAGCGAAT
1 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATG-GCGAAT
449786 GGAGTGAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 85 0.99
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (50 bp):
ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCGAATCTC
Found at i:450043 original size:40 final size:40
Alignment explanation
Indices: 449982--450306 Score: 340
Period size: 40 Copynumber: 8.2 Consensus size: 40
449972 ATCTAATTTC
* * *
449982 TTACCCCGACCATGAGGTAGATTGAAGACCATCCAATATT
1 TTACCCCAATCATGAGGTAGATTGAAGACCATCCAATCTT
* *
450022 TTACCCTAATCA-GAGAATAGATTGAAGACCATCCAATCTT
1 TTACCCCAATCATGAG-GTAGATTGAAGACCATCCAATCTT
* * * * *
450062 TTACCCCAACCATGGGGCAAATTGAAG-CAATCCAATCTT
1 TTACCCCAATCATGAGGTAGATTGAAGACCATCCAATCTT
* * *
450101 TTACCCTAATCATG-GGATAGATTGAAG-CAATCTAATCTTT
1 TTACCCCAATCATGAGG-TAGATTGAAGACCATCCAATC-TT
*
450141 TTACCCCGATCATGAGGTAGATTGAAGACCATCCAATCTT
1 TTACCCCAATCATGAGGTAGATTGAAGACCATCCAATCTT
* * *
450181 TTACCCCGATCATGAGGCAGATTGAAGTA--ATCCAGTCTT
1 TTACCCCAATCATGAGGTAGATTGAAG-ACCATCCAATCTT
* * *
450220 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTT
1 TTACCCCAATCATGAGGTAGATTGAAGACCATCCAATCTT
* * * *
450260 TTACCCTAATCA-GAGGGCAGATTAAAGACCATCAAATCTT
1 TTACCCCAATCATGA-GGTAGATTGAAGACCATCCAATCTT
450300 TTACCCC
1 TTACCCC
450307 TAAAGCTATA
Statistics
Matches: 244, Mismatches: 31, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
38 3 0.01
39 80 0.33
40 148 0.61
41 13 0.05
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (40 bp):
TTACCCCAATCATGAGGTAGATTGAAGACCATCCAATCTT
Found at i:450121 original size:79 final size:80
Alignment explanation
Indices: 449982--450306 Score: 401
Period size: 79 Copynumber: 4.1 Consensus size: 80
449972 ATCTAATTTC
* * * *
449982 TTACCCCGACCATGAGGTAGATTGAAGACCATCCAATATTTTACCCTAATCAGAGAATAGATTGA
1 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGACAGATTGA
450047 AGACCATCCAATCTT
66 AGACCATCCAATCTT
* * * * *
450062 TTACCCCAACCATGGGGCAAATTGAAG-CAATCCAATCTTTTACCCTAATCATG-GGATAGATTG
1 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCA-GAGGACAGATTG
* *
450125 AAG-CAATCTAATCTTT
65 AAGACCATCCAATC-TT
* * **
450141 TTACCCCGATCATGAGGTAGATTGAAGACCATCCAATCTTTTACCCCGATCATGAGG-CAGATTG
1 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCA-GAGGACAGATTG
*
450205 AAGTA--ATCCAGTCTT
65 AAG-ACCATCCAATCTT
* *
450220 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTAA
1 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGACAGATTGA
*
450285 AGACCATCAAATCTT
66 AGACCATCCAATCTT
450300 TTACCCC
1 TTACCCC
450307 TAAAGCTATA
Statistics
Matches: 209, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
78 13 0.06
79 117 0.56
80 77 0.37
81 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (80 bp):
TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGACAGATTGA
AGACCATCCAATCTT
Found at i:450205 original size:119 final size:119
Alignment explanation
Indices: 449982--450306 Score: 386
Period size: 119 Copynumber: 2.7 Consensus size: 119
449972 ATCTAATTTC
* * * * * **
449982 TTACCCCGACCATGAGGTAGATTGAAGACCATCCAATATTTTACCCTAATCAGAGAATAGATTGA
1 TTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTTTTACCCCAATCAGAGGGTAGATTGA
*
450047 AGACCATCCAATCTTTTACCCCAACCATGGGGCAAATTGAAGCAATCCAATCTT
66 AGACCATCCAATCTTTTACCCCAACCATGAGGCAAATTGAAGCAATCCAATCTT
* * * * *
450101 TTACCCTAATCATG-GGATAGATTGAAG-CAATCTAATCTTTTTACCCCGATCATGA-GGTAGAT
1 TTACCCCAACCATGAGG-CAGATTGAAGACAATCCAATC-TTTTACCCCAATCA-GAGGGTAGAT
* * * * *
450163 TGAAGACCATCCAATCTTTTACCCCGATCATGAGGCAGATTGAAGTAATCCAGTCTT
63 TGAAGACCATCCAATCTTTTACCCCAACCATGAGGCAAATTGAAGCAATCCAATCTT
* * * * *
450220 TTACCCCGACCATGAGGCAGATTGAAGACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTAA
1 TTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTTTTACCCCAATCAGAGGGTAGATTGA
*
450285 AGACCATCAAATCTTTTACCCC
66 AGACCATCCAATCTTTTACCCC
450307 TAAAGCTATA
Statistics
Matches: 173, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
118 11 0.06
119 150 0.87
120 12 0.07
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (119 bp):
TTACCCCAACCATGAGGCAGATTGAAGACAATCCAATCTTTTACCCCAATCAGAGGGTAGATTGA
AGACCATCCAATCTTTTACCCCAACCATGAGGCAAATTGAAGCAATCCAATCTT
Found at i:450962 original size:63 final size:63
Alignment explanation
Indices: 450866--451050 Score: 282
Period size: 63 Copynumber: 2.9 Consensus size: 63
450856 TTTTCTTATT
*
450866 TTTTATTTTATTTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTTA
1 TTTTATTTTA--TTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAA
* *
450931 TTTTATTTTATTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAA
1 TTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAA
* * *
450994 TTTTGTTTTATTATTTATTTATTATTTTATAAATATAGATAAATAAATA-AATAATAA
1 TTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAA-AATAA
451051 ACCCAAATTA
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
62 2 0.02
63 99 0.89
65 10 0.09
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (63 bp):
TTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAA
Found at i:452171 original size:29 final size:30
Alignment explanation
Indices: 452138--452340 Score: 144
Period size: 30 Copynumber: 6.8 Consensus size: 30
452128 CCCTCAAATA
* *
452138 TTCCAAATATTCAAATTTGGCCC-CGAACT
1 TTCCAAAAATTCAAATTTGACCCTCGAACT
* *
452167 TTCCAAAAATTCGAATTTGACCCTCGAATT
1 TTCCAAAAATTCAAATTTGACCCTCGAACT
* ** *
452197 TTCTAAAAATTTGAATTTGACCCT--AATTTT
1 TTCCAAAAATTCAAATTTGACCCTCGAA--CT
* * *
452227 TTTCAAAAA-TCTAAATTTAACCCTTGAACT
1 TTCCAAAAATTC-AAATTTGACCCTCGAACT
* * * *
452257 TTTCAAAAATTTAAATTTAACCCTCAAACT
1 TTCCAAAAATTCAAATTTGACCCTCGAACT
* * ** *
452287 TTCTAAAATTTTGAATTTGACCCCCCGAACT
1 TTCCAAAAATTCAAATTTGA-CCCTCGAACT
* *
452318 TTCTAAAAATTCAAATTTAACCC
1 TTCCAAAAATTCAAATTTGACCC
452341 GATTTTTAAT
Statistics
Matches: 140, Mismatches: 26, Indels: 15
0.77 0.14 0.08
Matches are distributed among these distances:
28 2 0.01
29 21 0.15
30 90 0.64
31 25 0.18
32 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (30 bp):
TTCCAAAAATTCAAATTTGACCCTCGAACT
Found at i:452304 original size:60 final size:60
Alignment explanation
Indices: 452163--452340 Score: 173
Period size: 60 Copynumber: 3.0 Consensus size: 60
452153 TTTGGCCCCG
* * * * *
452163 AACTTTCCAAAAATTCGAATTTGACCCTCGAA-TTTTCTAAAAATTTGAATTTGACCCTA
1 AACTTTCTAAAAATTTGAATTTAACCCTCGAACTTTTCTAAAAATTTAAATTTAACCCTA
** * * * *
452222 ATTTTTTTCAAAAATCTAAATTTAACCCTTGAACTTTTC-AAAAATTTAAATTTAACCCTCA
1 AACTTTCT-AAAAATTTGAATTTAACCCTCGAACTTTTCTAAAAATTTAAATTTAACCCT-A
* * * *
452283 AACTTTCTAAAATTTTGAATTTGACCCCCCGAAC-TTTCTAAAAATTCAAATTTAACCC
1 AACTTTCTAAAAATTTGAATTT-AACCCTCGAACTTTTCTAAAAATTTAAATTTAACCC
452341 GATTTTTAAT
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
59 4 0.04
60 52 0.56
61 37 0.40
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (60 bp):
AACTTTCTAAAAATTTGAATTTAACCCTCGAACTTTTCTAAAAATTTAAATTTAACCCTA
Found at i:454417 original size:25 final size:25
Alignment explanation
Indices: 454368--454423 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
454358 GGTCAAAAAA
* * *
454368 AGTCAACGGGTCAGTCAATAGGTCT
1 AGTCAACGAGTCAGTCAACAAGTCT
* *
454393 GGTCAACGAGTTAGTCAACAAGTCT
1 AGTCAACGAGTCAGTCAACAAGTCT
454418 AGTCAA
1 AGTCAA
454424 ATCGAATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
AGTCAACGAGTCAGTCAACAAGTCT
Found at i:456455 original size:3 final size:3
Alignment explanation
Indices: 456447--456516 Score: 113
Period size: 3 Copynumber: 23.3 Consensus size: 3
456437 CCCACAAGTT
* * *
456447 TTA TTA TTA TTA TTG TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
456495 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
456517 ATTTTTTCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:469391 original size:26 final size:26
Alignment explanation
Indices: 469361--469418 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
469351 TCTCATCTCA
*
469361 ATTTTACCCCCA-ATAAAATTTTGATG
1 ATTTTA-CCCCATATAAAATTTTGACG
* *
469387 ATTTTACCCTATGTAAAATTTTGACG
1 ATTTTACCCCATATAAAATTTTGACG
469413 ATTTTA
1 ATTTTA
469419 ATTAGGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (26 bp):
ATTTTACCCCATATAAAATTTTGACG
Found at i:470914 original size:7 final size:7
Alignment explanation
Indices: 470902--470926 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
470892 GTGTAACAAT
470902 GAAAGAA
1 GAAAGAA
470909 GAAAGAA
1 GAAAGAA
470916 GAAAGAA
1 GAAAGAA
470923 GAAA
1 GAAA
470927 ACTCTCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:481477 original size:21 final size:24
Alignment explanation
Indices: 481428--481485 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 24
481418 CCTAAGTTTC
*
481428 AACTATCGATACATCTATACATAT
1 AACTATCGATACATCTACACATAT
*
481452 AACTATCGATAC-TC-ACA-ATTT
1 AACTATCGATACATCTACACATAT
*
481473 AACTACCGATACA
1 AACTATCGATACA
481486 ACTCAGGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 14 0.47
22 2 0.07
23 2 0.07
24 12 0.40
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (24 bp):
AACTATCGATACATCTACACATAT
Found at i:486399 original size:52 final size:51
Alignment explanation
Indices: 486313--486557 Score: 249
Period size: 52 Copynumber: 4.7 Consensus size: 51
486303 ATTTTACTTC
* * * ** *
486313 ATTCATATACTCACGATGACACATAGCCACCGGACCTTATAATCCACGAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTT-TAATCCATAAAGG
* ** * * * *
486365 ATTCATATACTCACGATAACACAAAGTTATCGGACCTCTTAATTCGTAAATG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCATAAAGG
* *
486417 ATTCATATACTCATGATGACACTTAGTCATCGGACCTTTAAATCAATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTT-AATCCATAAAGG
* * *
486469 ATTTCATATACTCATGATGACACTTAGTCATCGGACCTCATAAT-CAGTAAGGG
1 A-TTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCA-TAAAGG
* *
486522 ATTCATTTACTCACGATAACACTTAGTCATCGGACC
1 ATTCATATACTCACGATGACACTTAGTCATCGGACC
486558 CTATTTCATT
Statistics
Matches: 162, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
51 2 0.01
52 113 0.70
53 46 0.28
54 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGG
Found at i:486533 original size:105 final size:104
Alignment explanation
Indices: 486313--486557 Score: 287
Period size: 105 Copynumber: 2.3 Consensus size: 104
486303 ATTTTACTTC
* * * * * *
486313 ATTCATATACTCACGATGACACATAGCCACCGGACCTTATAATCCACGAGGGATTCATATACTCA
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTATAATCAACAAAGGATTCATATACTCA
* * *
486378 CGATAACACAAAGTTATCGGACCTCTTAATTCGTAAATG
66 CGATAACACAAAGTCATCGGACCTCATAATTCGTAAAGG
* *
486417 ATTCATATACTCATGATGACACTTAGTCATCGGACCTT-TAAATCAATAAAGGATTTCATATACT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTAT-AATCAACAAAGGA-TTCATATACT
* * ** *
486481 CATGATGACACTTAGTCATCGGACCTCATAA-TCAGTAAGGG
64 CACGATAACACAAAGTCATCGGACCTCATAATTC-GTAAAGG
* *
486522 ATTCATTTACTCACGATAACACTTAGTCATCGGACC
1 ATTCATATACTCACGATGACACTTAGTCATCGGACC
486558 CTATTTCATT
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
103 1 0.01
104 45 0.38
105 73 0.61
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (104 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTATAATCAACAAAGGATTCATATACTCA
CGATAACACAAAGTCATCGGACCTCATAATTCGTAAAGG
Found at i:487861 original size:36 final size:36
Alignment explanation
Indices: 487821--487940 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
487811 TTAGCACAAT
* * * *
487821 ATATTCACTGTCACATGACATGACTAACATATCCAC
1 ATATTTACTGTCACATGGCATGAATAACATAACCAC
* *
487857 ATATTTATTGTCACATGGCATGAATAACATAACTAC
1 ATATTTACTGTCACATGGCATGAATAACATAACCAC
* * * *
487893 ATATTTACTATCACATGGCATAAATAACGTACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATAACCAC
*
487929 ATATTTATTGTC
1 ATATTTACTGTC
487941 TCAATAGTCA
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.33
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATAACCAC
Found at i:491441 original size:22 final size:24
Alignment explanation
Indices: 491416--491467 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
491406 TAATTATGTA
*
491416 AATTTAAAATAATTA-TT-AAAAT
1 AATTTAAAATAAATACTTCAAAAT
491438 AA-TT-AAATAAATACTTCAAAAT
1 AATTTAAAATAAATACTTCAAAAT
491460 AATTTAAA
1 AATTTAAA
491468 GGCCAGGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 9 0.36
23 2 0.08
24 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTTAAAATAAATACTTCAAAAT
Found at i:494348 original size:71 final size:71
Alignment explanation
Indices: 494227--494360 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 71
494217 TTAGTTTTTT
* *
494227 TTTTATTAAAATTTACATATATTTTTACTATAAAAAATTGATGTGATTGATAAAATAACCAAACA
1 TTTTATTAAAATTTACATACATTTTTACTATAAAAAATTGATATGATTGATAAAATAACCAAACA
494292 GATACA
66 GATACA
* * * * * * * *
494298 TTTTATTAAACTTTACATCCATTTTTACTATTAAAAGTTGGTATGGTTGATAGAATAATCAAA
1 TTTTATTAAAATTTACATACATTTTTACTATAAAAAATTGATATGATTGATAAAATAACCAAA
494361 TAGTTACACG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (71 bp):
TTTTATTAAAATTTACATACATTTTTACTATAAAAAATTGATATGATTGATAAAATAACCAAACA
GATACA
Found at i:495243 original size:30 final size:31
Alignment explanation
Indices: 495207--495268 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
495197 TTTACATTTT
* *
495207 AGTCCCTCAAC-TTTGAAAATGTGATAAAAC
1 AGTCCCTCAACTTTTGAAAATATGACAAAAC
495237 AGTCCCTCAACTTTTGAAAATATGACAAAAC
1 AGTCCCTCAACTTTTGAAAATATGACAAAAC
495268 A
1 A
495269 ATCCTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (31 bp):
AGTCCCTCAACTTTTGAAAATATGACAAAAC
Found at i:496774 original size:30 final size:31
Alignment explanation
Indices: 496706--496777 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
496696 ATAACAAGAG
* *
496706 GACTATTTTGTCACTTTTCAATAACTTTAGT
1 GACTGTTTTGTCACTTTTCAATAACTTGAGT
* *
496737 GATTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCAATAACTTGAGT
496767 GACTGTTTTGT
1 GACTGTTTTGT
496778 TACACGTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCAATAACTTGAGT
Found at i:499092 original size:21 final size:21
Alignment explanation
Indices: 499068--499111 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
499058 TTTTTTTTTG
499068 TATTTTTACACAA-TTTTTAAA
1 TATTTTTA-ACAATTTTTTAAA
*
499089 TATTTTTAATAATTTTTTAAA
1 TATTTTTAACAATTTTTTAAA
499110 TA
1 TA
499112 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTAACAATTTTTTAAA
Found at i:500583 original size:2 final size:2
Alignment explanation
Indices: 500576--500611 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
500566 TTTATTTTAT
500576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
500612 AAAGTACGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:501038 original size:21 final size:21
Alignment explanation
Indices: 501012--501055 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
501002 TTAAATATGT
501012 TAAAAATATTT-TAATTATAATA
1 TAAAAA-ATTTAT-ATTATAATA
501034 TAAAAAATTTATATTATAATA
1 TAAAAAATTTATATTATAATA
501055 T
1 T
501056 TTGAATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAAATTTATATTATAATA
Found at i:503797 original size:6 final size:6
Alignment explanation
Indices: 503786--503830 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
503776 TTCACAAGTC
503786 TCCATT TCCATT TCCATT TCCATT TCCATT TCCA-- TCCATT TCCAT
1 TCCATT TCCATT TCCATT TCCATT TCCATT TCCATT TCCATT TCCAT
503831 CAATTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
6 33 0.89
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.47
Consensus pattern (6 bp):
TCCATT
Found at i:504390 original size:29 final size:30
Alignment explanation
Indices: 504340--504399 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
504330 TAAAAGAGGG
*
504340 ATTAAGTCTAATATAAAACAAAT-AATAGAA
1 ATTAAATCTAATATAAAACAAATGAAT-GAA
504370 ATTAAATCTAA-ATAAAACAAATGAATGAA
1 ATTAAATCTAATATAAAACAAATGAATGAA
504399 A
1 A
504400 ACTCTAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.25
Consensus pattern (30 bp):
ATTAAATCTAATATAAAACAAATGAATGAA
Found at i:507844 original size:30 final size:29
Alignment explanation
Indices: 507805--507899 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 29
507795 TAAATTTTTT
*
507805 AAAATTTTGAATTTGACCCCAAACTTCCC
1 AAAAATTTGAATTTGACCCCAAACTTCCC
* * * **
507834 ACCAAATTTGAATTTGACCCTCGAGCTTTTC
1 A-AAAATTTGAATTTGACCC-CAAACTTCCC
*
507865 AAAAATTTGAATTTGACCCCTAAACTTTCC
1 AAAAATTTGAATTTGACCCC-AAACTTCCC
507895 AAAAA
1 AAAAA
507900 AAATTTAACC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 44 0.83
31 7 0.13
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAAATTTGAATTTGACCCCAAACTTCCC
Found at i:508485 original size:104 final size:108
Alignment explanation
Indices: 508351--508585 Score: 273
Period size: 109 Copynumber: 2.2 Consensus size: 108
508341 TGGTTACAAT
* *
508351 TTTTTCTTCGAACCTAAATAATTGAATATCCTATTC-AAA-AATTGA-G-GCAATATTCTT-TTA
1 TTTTTCTTTGAACCTAAATAATTGAATATCCTATTCGAAACAATTAATGCGCAATATT-TTGTTA
* * *** *
508411 TTTTAGGGAAGTCGAGGGATTGTGTCCTAACGTATTGGGTATGA
65 TTTTAGGGAACTCAAAAAATTGTGCCCTAACGTATTGGGTATGA
* *
508455 TTTTTCTTTGAACCTAAATAATTGGATATCCTATTCGAAACCAATTAATGCTCAATATTTTGTTA
1 TTTTTCTTTGAACCTAAATAATTGAATATCCTATTCGAAA-CAATTAATGCGCAATATTTTGTTA
* * *
508520 TTTTAGGGGACTCAAAAAATTGTGCCCTAACTTGTTGGGTATGA
65 TTTTAGGGAACTCAAAAAATTGTGCCCTAACGTATTGGGTATGA
* * *
508564 TTTTGCCTTGAACCTAAGTAAT
1 TTTTTCTTTGAACCTAAATAAT
508586 CAAATATTTC
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
104 34 0.31
105 3 0.03
107 5 0.05
108 3 0.03
109 64 0.59
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (108 bp):
TTTTTCTTTGAACCTAAATAATTGAATATCCTATTCGAAACAATTAATGCGCAATATTTTGTTAT
TTTAGGGAACTCAAAAAATTGTGCCCTAACGTATTGGGTATGA
Found at i:513591 original size:21 final size:19
Alignment explanation
Indices: 513546--513596 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
513536 TCATTAAATG
*
513546 TGATGTTTATTTATTTTCA
1 TGATGTTTATTTATATTCA
* *
513565 TCATGTTTGTATTATATTCAA
1 TGATGTTTAT-TTATATTC-A
513586 TGATG-TTATTT
1 TGATGTTTATTT
513597 TTTTTGTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (19 bp):
TGATGTTTATTTATATTCA
Found at i:517054 original size:13 final size:13
Alignment explanation
Indices: 517036--517060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517026 AATAGAGAGA
517036 AGAGAAAAGCTAG
1 AGAGAAAAGCTAG
517049 AGAGAAAAGCTA
1 AGAGAAAAGCTA
517061 AATGTTTTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (13 bp):
AGAGAAAAGCTAG
Found at i:524172 original size:29 final size:29
Alignment explanation
Indices: 524116--524172 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
524106 TATGAAAAAA
*
524116 TTTATTCAATTTAAAATCAATTAGAATAG
1 TTTATTCAATTTAAAATCAATCAGAATAG
* *
524145 TTTATTCAATTTAAAATCACTCATAATA
1 TTTATTCAATTTAAAATCAATCAGAATA
524173 ATTTTAGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTATTCAATTTAAAATCAATCAGAATAG
Found at i:528111 original size:132 final size:131
Alignment explanation
Indices: 527875--528234 Score: 636
Period size: 132 Copynumber: 2.8 Consensus size: 131
527865 TTTTATTTAT
*
527875 AAACATATATTTTT-AAAAATAAGGTACGATTTAAATAAAAAGGGTTTCAAAAGAGAATAAGAAA
1 AAACATATATTTTTAAAAAATAAGGTACGATTTAAATAAAAAGGGTTTCGAAAGAGAATAAGAAA
527939 TCATTTTGAAATTTCACAAGAATAAAACAAAAAAATCAAAAAACCATTAAAAAA-AGAAAGATTT
66 TCATTTTGAAATTTCACAAGAATAAAACAAAAAAATCAAAAAACCATTAAAAAAGAG-AA-ATTT
528003 TCG
129 TCG
*
528006 AAACATATATTTTTAAAAAATAAAGTACGATTTAAATAAAAAGGGTTTCGAAAGAGAATAAGAAA
1 AAACATATATTTTTAAAAAATAAGGTACGATTTAAATAAAAAGGGTTTCGAAAGAGAATAAGAAA
528071 TCATTTTGAAATTTCACAAGAATAAAACAAAAAAATCAAAAAACCATTAAAAAAGAGAAATTTTC
66 TCATTTTGAAATTTCACAAGAATAAAACAAAAAAATCAAAAAACCATTAAAAAAGAGAAATTTTC
528136 G
131 G
* *
528137 AAACATATA-TTTTAAAAAATAAGGTACGATTTAAATAAAAAGGGTTTCGAAAGAAAATAAAAAA
1 AAACATATATTTTTAAAAAATAAGGTACGATTTAAATAAAAAGGGTTTCGAAAGAGAATAAGAAA
*
528201 TTATTTTGAAATTTCACAAGAATAAAACAAAAAA
66 TCATTTTGAAATTTCACAAGAATAAAACAAAAAA
528235 GAAAAAAAAA
Statistics
Matches: 221, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
130 85 0.38
131 30 0.14
132 104 0.47
133 2 0.01
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.26
Consensus pattern (131 bp):
AAACATATATTTTTAAAAAATAAGGTACGATTTAAATAAAAAGGGTTTCGAAAGAGAATAAGAAA
TCATTTTGAAATTTCACAAGAATAAAACAAAAAAATCAAAAAACCATTAAAAAAGAGAAATTTTC
G
Done.