Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015382.1 Kokia drynarioides strain JFW-HI SEQ_130429, 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: 764726
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 399 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:302702 original size:205 final size:206
Alignment explanation
Indices: 302350--302771 Score: 616
Period size: 205 Copynumber: 2.1 Consensus size: 206
302340 TTATAATCGT
*
302350 CTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCAGATGAGATACAGAGAAACAGAT
1 CTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCAGATGAGATACAGAGAAACAGAA
* * *
302415 TGGAACAAACAACACGGTCATCTTTCTGATGAGATAATGAGAAGAAGACCAAATCAAACTCACGC
66 TCGAACAAACAACACGGTCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACACACGC
* * *
302480 TTGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCATGTCGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCAAGAAGCAGGTCGAAGCAAT
302545 AAAA-GGTTAG
196 AAAATGGTTAG
* * ** *
302555 CTTCCTGATGAGATACTGAGAAGTGGACCAAGTTCGTCTTCTTGATGAGGTACAGA-AAAGC-GA
1 CTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCAGATGAGATACAGAGAAA-CAGA
* * * *
302618 ATCGAAGCAAACGACGCTGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACACAC
65 ATCGAA-CAAACAACACGGTCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACACAC
* * * *
302683 GCTCGATTTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTA
129 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCAAGAAGCAGGTCGAAGCA
*
302748 ATAAAATTGTTAG
194 ATAAAATGGTTAG
302761 CTTCCTGATGA
1 CTTCCTGATGA
302772 AATAGGAGGA
Statistics
Matches: 193, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
204 9 0.05
205 168 0.87
206 16 0.08
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (206 bp):
CTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCAGATGAGATACAGAGAAACAGAA
TCGAACAAACAACACGGTCATCTTCCTGATGAGATAATGAGAAGAAGACCAAATCAAACACACGC
TCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCAAGAAGCAGGTCGAAGCAAT
AAAATGGTTAG
Found at i:303221 original size:17 final size:17
Alignment explanation
Indices: 303198--303255 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
303188 GCCCAACAGG
303198 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* * *
303215 GTTTAAATTTACTTAAA
1 ATTTAAATTTATTTTAA
*
303232 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
303249 ATTTAAA
1 ATTTAAA
303256 AAGTTTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:303967 original size:21 final size:20
Alignment explanation
Indices: 303923--303972 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
303913 TAAGTCATAT
* *
303923 TTAATATAATATTAAATGCA
1 TTAATATAATAGTAAATACA
303943 -TAATATATATAGTAAATACA
1 TTAATATA-ATAGTAAATACA
303963 TTAATA-AATA
1 TTAATATAATA
303973 AAGGAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TTAATATAATAGTAAATACA
Found at i:305205 original size:29 final size:29
Alignment explanation
Indices: 305159--305476 Score: 329
Period size: 29 Copynumber: 10.7 Consensus size: 29
305149 AAGGTCCCTA
305159 AACTATCCAAAAATTCCATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCCCG
* **
305189 AACATCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* *
305219 AATTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
305248 AACTTCCAAAAATTCCATTTTTAACCCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
*
305278 AAACTTCCAAAAAATTCCATTTTTACCCCCA
1 -AACTTCC-AAAAATTCCATTTTTACCCCCG
*
305309 AACTTCCAAAAATTCCATTTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* **
305338 AACTTCCAAAAATTCCATTTTTAACCTTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* *
305367 AAACTACAAAAAATTCCATTTTTACCCCC-
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* * **
305396 AAATCTCCAAAATTTCCATTTTTGA-CTTCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCCCG
* *
305426 AAACTTTCAAAAATTACCA-TTTTGCCCCCG
1 -AACTTCCAAAAATT-CCATTTTTACCCCCG
*
305456 AA-TGTCCAAAAACTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
305477 CGAGCTCAAA
Statistics
Matches: 241, Mismatches: 34, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.03
29 122 0.51
30 79 0.33
31 18 0.07
32 15 0.06
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:305227 original size:30 final size:29
Alignment explanation
Indices: 305158--305565 Score: 326
Period size: 29 Copynumber: 13.8 Consensus size: 29
305148 AAAGGTCCCT
*
305158 AAACTATCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* *
305188 GAACATCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
305218 AAATTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
*
305247 AAACTTCCAAAAATTCCATTTTTAACCCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCC-CA
*
305278 AAACTTCCAAAAAATTCCATTTTTACCCCC
1 AAACTTCC-AAAAATTCCATTTTTACCCCA
*
305308 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* ***
305337 GAACTTCCAAAAATTCCATTTTTAACCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * *
305367 AAACTACAAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* ** *
305396 AAA-TCTCCAAAATTTCCATTTTTGACTTCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCA
* * *
305426 AAACTTTCAAAAATTACCA-TTTTGCCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCA
* * * * *
305455 GAA-TGTCCAAAAACTCCATTTTCGAGCTCA
1 AAACT-TCCAAAAATTCCATTTT-TACCCCA
*
305485 AAAC--CCTTAAAATTACC-TTTTTACCCCA
1 AAACTTCC-AAAAATT-CCATTTTTACCCCA
* *
305513 AAA-TATCTAAAAATTCCATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCA
** *
305543 AATTTTCCTAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
305566 GTCCTCGAAA
Statistics
Matches: 303, Mismatches: 53, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
28 16 0.05
29 143 0.47
30 104 0.34
31 25 0.08
32 15 0.05
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:305256 original size:59 final size:58
Alignment explanation
Indices: 305164--305565 Score: 353
Period size: 59 Copynumber: 6.8 Consensus size: 58
305154 CCCTAAACTA
* *
305164 TCCAAAAATTCCATTTTTACCCCCGAACATCCAAAAATTCCATTTTTGACCCCAAAATT
1 TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCCAAAATT
* *
305223 TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCC-CAAAATT
** *
305283 TCCAAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCTGAACT
1 TCC-AAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAATT
*** * * * *
305342 TCCAAAAATTCCATTTTTAACCTTGAAACTACAAAAAATTCCATTTTTACCCCCAAATC
1 TCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAATT
* ** * * * ** *
305401 TCCAAAATTTCCATTTTTGACTTCGAAACTTTCAAAAATTACCA-TTTTGCCCCCGAATG
1 TCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATT-CCATTTTTACCCCAAAATT
* * * * * * *
305460 TCCAAAAACTCCATTTTCGAGCTCAAAAC--CCTTAAAATTACC-TTTTTACCCCAAAATA
1 TCCAAAAATTCCATTTT-TACCCCCAAACTTCC-AAAAATT-CCATTTTTACCCCAAAATT
* * * * *
305518 TCTAAAAATTCCATTTTTAACCCTAAATTTTCCTAAAATTACCATTTT
1 TCCAAAAATTCCATTTTTACCCCCAAA-CTTCCAAAAATT-CCATTTT
305566 GTCCTCGAAA
Statistics
Matches: 287, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
57 7 0.02
58 50 0.17
59 165 0.57
60 21 0.07
61 44 0.15
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCAAAATT
Found at i:305593 original size:117 final size:117
Alignment explanation
Indices: 305162--305583 Score: 288
Period size: 117 Copynumber: 3.6 Consensus size: 117
305152 GTCCCTAAAC
* * * * *
305162 TATCCAAAAATTCCATTTTTACCCCCG-AACATCCAAAAATT-CCATTTTTGACCCC-AAAATTT
1 TATCCAAAAATTCCATTTTTAACTCCGAAACTTTCAAAAATTACCA-TTTTGCCCCCGAAAA--T
* * * * * * *
305224 CCAAAAATTCCATTTT-TACCCCCAAACTTCC-AAAAATTCCATTTTTAACCCTCGAAAC
63 CCAAAAACTCCATTTTCGAGCTCAAAAC--CCTTAAAATTCCATTTTT-ACCC-C-AAAA
* * * * * **
305282 T-TCCAAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATT-CCATTTTTACCCCTGAACTTC
1 TATCC-AAAAATTCCATTTTTAACTCCGAAACTTTCAAAAATTACCA-TTTTGCCCCCGAAAATC
* ** * ** * ** *
305344 CAAAAATTCCATTTTTAACCTTGAAACTACAAAAAATTCCATTTTTACCCCCAAA
64 CAAAAACTCCATTTTCGAGCTCAAAAC-CCTTAAAATTCCATTTTTACCCCAAAA
* * * * **
305399 TCTCCAAAATTTCCATTTTTGACTTCGAAACTTTCAAAAATTACCATTTTGCCCCCGAATGTCCA
1 TATCCAAAAATTCCATTTTTAACTCCGAAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCCA
305464 AAAACTCCATTTTCGAGCTCAAAACCCTTAAAATTACC-TTTTTACCCCAAAA
66 AAAACTCCATTTTCGAGCTCAAAACCCTTAAAATT-CCATTTTTACCCCAAAA
* * * * * *
305516 TATCTAAAAATTCCATTTTTAAC-CCTAAATTTTCCTAAAATTACCATTTTGTCCTCGAAAATCC
1 TATCCAAAAATTCCATTTTTAACTCCGAAACTTT-CAAAAATTACCATTTTGCCCCCGAAAATCC
305580 AAAA
65 AAAA
305584 TTACCATTTT
Statistics
Matches: 246, Mismatches: 46, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
116 7 0.03
117 85 0.35
118 57 0.23
119 33 0.13
120 62 0.25
121 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (117 bp):
TATCCAAAAATTCCATTTTTAACTCCGAAACTTTCAAAAATTACCATTTTGCCCCCGAAAATCCA
AAAACTCCATTTTCGAGCTCAAAACCCTTAAAATTCCATTTTTACCCCAAAA
Found at i:307177 original size:84 final size:84
Alignment explanation
Indices: 307088--307257 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 84
307078 AGTATAATAT
*
307088 TCGAACAAAAAAATTTCTAAACCTGAAAGCACTTGAATTTTAAAAAGTCAAAATTCAAAAAACTT
1 TCGAACAAAAAAAATTCTAAACCTGAAAGCACTTGAATTTTAAAAAGTCAAAATTCAAAAAACTT
*
307153 CATACAAAAAAAGTGATAA
66 CACACAAAAAAAGTGATAA
307172 TCGAACAAAAAAAATTCTAAACCTGAAAGCACTTGAATTTTAAAAAGTCAAAATTCAAAAAACTT
1 TCGAACAAAAAAAATTCTAAACCTGAAAGCACTTGAATTTTAAAAAGTCAAAATTCAAAAAACTT
* *
307237 CGCATAAAAAAAGTGATAA
66 CACACAAAAAAAGTGATAA
307256 TC
1 TC
307258 TAAACCAGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (84 bp):
TCGAACAAAAAAAATTCTAAACCTGAAAGCACTTGAATTTTAAAAAGTCAAAATTCAAAAAACTT
CACACAAAAAAAGTGATAA
Found at i:307501 original size:114 final size:113
Alignment explanation
Indices: 307242--307507 Score: 292
Period size: 114 Copynumber: 2.3 Consensus size: 113
307232 AACTTCGCAT
307242 AAAAAAAGTGATAATCTAAACCAGAACCAATCTAGATAAAAAGAAAATTCAAACCTAAAAATTCT
1 AAAAAAAGTGATAATCTAAACCAGAACCAATCTAGAT-AAAAGAAAATTCAAACCTAAAAATTCT
* * * *
307307 AAAAAGGAAATTCAAAGCTTGAGTAAGTTCAAATCCGAAAACTTCAAATA
65 AAAAAGGAAATGC-AACCTTGAGTAAGTTCAAATCAGAAAACTTCAAAAA
* * * * *
307357 AAAAAAA-TGATAATCTAAACTACAACCAATCTCGAT-GAAG-AAATTCAAATCTAAAAATTCTA
1 AAAAAAAGTGATAATCTAAACCAGAACCAATCTAGATAAAAGAAAATTCAAACCTAAAAATTCTA
* * *
307419 TATATGAAA-GC-ACCTTGAGTAAG-TCAAAATTCAGAAAACTTCATATAAAAA
66 AAAAGGAAATGCAACCTTGAGTAAGTTC-AAA-TCAGAAAACTTC----AAAAA
* *
307470 AAAAAAAGTGATAATCTAAACCAGAATCAATCTGGATA
1 AAAAAAAGTGATAATCTAAACCAGAACCAATCTAGATA
307508 TGATAAACAA
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
107 2 0.02
108 14 0.11
109 11 0.09
110 1 0.01
111 27 0.21
112 3 0.02
113 11 0.09
114 51 0.40
115 7 0.06
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23
Consensus pattern (113 bp):
AAAAAAAGTGATAATCTAAACCAGAACCAATCTAGATAAAAGAAAATTCAAACCTAAAAATTCTA
AAAAGGAAATGCAACCTTGAGTAAGTTCAAATCAGAAAACTTCAAAAA
Found at i:308750 original size:23 final size:26
Alignment explanation
Indices: 308719--308768 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 26
308709 TATCTTTCAT
*
308719 TTTTCTTTTTCTT-TATATTTTT-TC
1 TTTTCTTTTTCTTCAATATTTTTATC
308743 -TTT-TTTTTCTTCAATATTTTTATC
1 TTTTCTTTTTCTTCAATATTTTTATC
308767 TT
1 TT
308769 ATTCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 2 0.09
25 1 0.05
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTCTTTTTCTTCAATATTTTTATC
Found at i:308752 original size:22 final size:24
Alignment explanation
Indices: 308724--308768 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
308714 TTCATTTTTC
*
308724 TTTTTCTT-TATATTTTT-TCTTT
1 TTTTTCTTCAATATTTTTATCTTT
308746 TTTTTCTTCAATATTTTTATCTT
1 TTTTTCTTCAATATTTTTATCTT
308769 ATTCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCTTCAATATTTTTATCTTT
Found at i:313449 original size:18 final size:18
Alignment explanation
Indices: 313426--313462 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
313416 AAAAAAAACT
* *
313426 TGTATAATAATATTGAAA
1 TGTATAAAAATATTAAAA
313444 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
313462 T
1 T
313463 AAAATTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:315646 original size:3 final size:3
Alignment explanation
Indices: 315638--315672 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
315628 TAAAGTTGTT
*
315638 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
315673 GTAACATCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:318555 original size:25 final size:24
Alignment explanation
Indices: 318522--318569 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
318512 ATAAATATTT
* *
318522 TATTTTTTCAAAATTATTTTTTAG
1 TATTTTTTCAAAAATAGTTTTTAG
318546 TATTCTTTTCAAAAATAGTTTTTA
1 TATT-TTTTCAAAAATAGTTTTTA
318570 AACGTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (24 bp):
TATTTTTTCAAAAATAGTTTTTAG
Found at i:319216 original size:2 final size:2
Alignment explanation
Indices: 319209--319240 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
319199 CAACCAAGCC
*
319209 CT CT CT CT AT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
319241 GTCGCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:323074 original size:22 final size:22
Alignment explanation
Indices: 323048--323096 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
323038 ATATTAACTT
* *
323048 TATTTAAATTTAATTATAAAAG
1 TATTTAAAATTAATTATAAAAA
* *
323070 TATTTAAAATTATTTTTAAAAA
1 TATTTAAAATTAATTATAAAAA
323092 TATTT
1 TATTT
323097 TCTTAAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTAAAATTAATTATAAAAA
Found at i:331752 original size:44 final size:44
Alignment explanation
Indices: 331689--331785 Score: 194
Period size: 44 Copynumber: 2.2 Consensus size: 44
331679 ATCATTTTTT
331689 TTGCACCGGATGGATGGTTAGACCGGTCAGGTCAAGCTTCTACG
1 TTGCACCGGATGGATGGTTAGACCGGTCAGGTCAAGCTTCTACG
331733 TTGCACCGGATGGATGGTTAGACCGGTCAGGTCAAGCTTCTACG
1 TTGCACCGGATGGATGGTTAGACCGGTCAGGTCAAGCTTCTACG
331777 TTGCACCGG
1 TTGCACCGG
331786 TTGATTCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.25
Consensus pattern (44 bp):
TTGCACCGGATGGATGGTTAGACCGGTCAGGTCAAGCTTCTACG
Found at i:336844 original size:79 final size:79
Alignment explanation
Indices: 336734--336952 Score: 273
Period size: 78 Copynumber: 2.8 Consensus size: 79
336724 GGTTGTATGA
* * *
336734 TGTCGGTTTAACTGACTAGAGCTGGGATCACATTTGCGGTTTATCCGCTAGGCATTGGGTG-TCA
1 TGTCAGTTTAACTAACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCATTGGGTGCT-A
*
336798 AGATTTGACGGACGT
65 AGATTTGACGGACAT
* *
336813 TGTCAGTTTAACTAACTTGAGCTGGGCTCACATTTGCGGTTTATCCGCTA-GCACTGGGTGCTAA
1 TGTCAGTTTAACTAACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCATTGGGTGCTAA
*
336877 GATTTGACGGATAT
66 GATTTGACGGACAT
* * * * * * *
336891 TGT-TGGTTAATCCAACTAGTGTTGGGCTCACAATTACGGTTTATCCGCTAGGCATTGGGTGC
1 TGTCAGTTTAA-CTAACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCATTGGGTGC
336953 CATAACTGTC
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
77 5 0.04
78 59 0.49
79 57 0.47
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (79 bp):
TGTCAGTTTAACTAACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCATTGGGTGCTAA
GATTTGACGGACAT
Found at i:338111 original size:17 final size:17
Alignment explanation
Indices: 338091--338123 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
338081 GTTGGGTTTA
338091 TATGGGTATTGGGCTTG
1 TATGGGTATTGGGCTTG
*
338108 TATGGTTATTGGGCTT
1 TATGGGTATTGGGCTT
338124 TAGATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.45
Consensus pattern (17 bp):
TATGGGTATTGGGCTTG
Found at i:338830 original size:39 final size:39
Alignment explanation
Indices: 338761--338854 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
338751 AGTCATGCGA
* ** *
338761 TGTTTACAGTGTCACTATCAGTTCGGAATAGC-ATCGCAG
1 TGTTTACAGTGTCACTACCAGTTCAAAATAGCTA-CACAG
338800 TGTTTACAGTGTCACTACCCA-TTCAAAATAGCTACACAG
1 TGTTTACAGTGTCACTA-CCAGTTCAAAATAGCTACACAG
* *
338839 TATTTACAATGTCACT
1 TGTTTACAGTGTCACT
338855 GCCAACTCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 44 0.94
40 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (39 bp):
TGTTTACAGTGTCACTACCAGTTCAAAATAGCTACACAG
Found at i:338979 original size:78 final size:78
Alignment explanation
Indices: 338835--338990 Score: 208
Period size: 78 Copynumber: 2.0 Consensus size: 78
338825 AAATAGCTAC
**
338835 ACAGTATTTACAATGTCACTGCCAACTCTGTACAGTATTACGGTGTTTACAGTGTCACCGTTAGT
1 ACAGTATTTACAATGTCACTGCCAACTCTGTACAGTATTACGGTGTTTACAGTGTCACCGCCAGT
*
338900 TCAATGTTGTATT
66 TCAATGTTATATT
* * * *
338913 ACAGTGTTTACAATGTCACTGTCAATTC-GATACAGT-TATATGGTGTTTACAGTGTCACCGCCA
1 ACAGTATTTACAATGTCACTGCCAACTCTG-TACAGTAT-TACGGTGTTTACAGTGTCACCGCCA
*
338976 GTTCAGTGTTATATT
64 GTTCAATGTTATATT
338991 TCAAATTACG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 2 0.03
78 66 0.97
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (78 bp):
ACAGTATTTACAATGTCACTGCCAACTCTGTACAGTATTACGGTGTTTACAGTGTCACCGCCAGT
TCAATGTTATATT
Found at i:343059 original size:30 final size:30
Alignment explanation
Indices: 343025--343105 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
343015 ATTTAACTTT
343025 AATAAAAAT-GTTAATTTTAATAGTAATAAA
1 AATAAAAATAGTTAATTTT-ATAGTAATAAA
* * **
343055 AATAAAAATATTTTATTTTATTTTAATAAA
1 AATAAAAATAGTTAATTTTATAGTAATAAA
* * *
343085 AATAACAATAATTTATTTTAT
1 AATAAAAATAGTTAATTTTAT
343106 TAATTTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 37 0.84
31 7 0.16
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (30 bp):
AATAAAAATAGTTAATTTTATAGTAATAAA
Found at i:343106 original size:30 final size:30
Alignment explanation
Indices: 343048--343106 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
343038 ATTTTAATAG
*
343048 TAATAAAAATAAAAATATTTTATTTTATTT
1 TAATAAAAATAAAAATAATTTATTTTATTT
*
343078 TAATAAAAATAACAATAATTTATTTTATT
1 TAATAAAAATAAAAATAATTTATTTTATT
343107 AATTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATAAAAATAAAAATAATTTATTTTATTT
Found at i:346927 original size:2 final size:2
Alignment explanation
Indices: 346920--346944 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
346910 AACATGAATG
346920 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
346945 TAGTGTTTGG
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:347287 original size:18 final size:18
Alignment explanation
Indices: 347246--347288 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
347236 TTCTATAATT
* *
347246 TAAAAATATTAAATTACA
1 TAAAAATATTAAAATAAA
*
347264 TTAAAATATTAAAATAAA
1 TAAAAATATTAAAATAAA
347282 TAAAAAT
1 TAAAAAT
347289 TATAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATATTAAAATAAA
Found at i:347400 original size:21 final size:20
Alignment explanation
Indices: 347376--347419 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
347366 TTTTTATAAC
347376 ATATTTAT-TATAATAGTAAAA
1 ATATTTATATA-AATA-TAAAA
347397 ATATTTATATAAATATAAAA
1 ATATTTATATAAATATAAAA
347417 ATA
1 ATA
347420 ACAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 12 0.55
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATTTATATAAATATAAAA
Found at i:347415 original size:20 final size:21
Alignment explanation
Indices: 347376--347419 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
347366 TTTTTATAAC
347376 ATATTTATTATAATAGTAAAA
1 ATATTTATTATAATAGTAAAA
347397 ATATTTA-TATAAATA-TAAAA
1 ATATTTATTAT-AATAGTAAAA
347417 ATA
1 ATA
347420 ACAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATTTATTATAATAGTAAAA
Found at i:348096 original size:8 final size:8
Alignment explanation
Indices: 348080--348122 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
348070 AACAAAATTA
*
348080 AAATGTAT
1 AAATATAT
348088 AAATATAT
1 AAATATAT
*
348096 ATATATAT
1 AAATATAT
*
348104 ATATATAT
1 AAATATAT
*
348112 ATATATAT
1 AAATATAT
348120 AAA
1 AAA
348123 AGGGTTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (8 bp):
AAATATAT
Found at i:348097 original size:2 final size:2
Alignment explanation
Indices: 348085--348120 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
348075 AATTAAAATG
*
348085 TA TA AA 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
348121 AAAGGGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:350695 original size:33 final size:31
Alignment explanation
Indices: 350594--350696 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 31
350584 AAGATTTTGG
* *
350594 TTTAGGTTTAAAAAATGTGGGGTTTTTCGGG-T
1 TTTAGGTTT-AAAAATTTGGGATTTTT-GGGAT
* * * *
350626 TTTAGATTTCAAAATTTTTGGGAATTTGGGGA-
1 TTTAGGTTT-AAAA-ATTTGGGATTTTTGGGAT
*
350658 TTTAGGTTTTAAAGATTTAGGGATTTTTGGGAT
1 TTTAGG-TTTAAAAATTT-GGGATTTTTGGGAT
350691 TTTAGG
1 TTTAGG
350697 GTTGTTGGGT
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
31 3 0.06
32 34 0.63
33 17 0.31
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (31 bp):
TTTAGGTTTAAAAATTTGGGATTTTTGGGAT
Found at i:350767 original size:45 final size:45
Alignment explanation
Indices: 350703--350794 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
350693 TAGGGTTGTT
* * *
350703 GGGTTTGGATAATTTGGTTTATGTTTAGGAAATTTGAGGA-TTTCG
1 GGGTTTGGAGAATTTGGTTTAAGTTTA-AAAATTTGAGGATTTTCG
* *
350748 GGGTTTGGAGATTTTGGTTTAAGTTTAAAAATTTGGGGATTTTCG
1 GGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTGAGGATTTTCG
350793 GG
1 GG
350795 ACTTAGGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 10 0.24
45 31 0.76
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (45 bp):
GGGTTTGGAGAATTTGGTTTAAGTTTAAAAATTTGAGGATTTTCG
Found at i:351068 original size:15 final size:15
Alignment explanation
Indices: 351048--351076 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
351038 TGATAATTTG
351048 TTTTGGTTTGTATAT
1 TTTTGGTTTGTATAT
351063 TTTTGGTTTGTATA
1 TTTTGGTTTGTATA
351077 CAAGAAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.66
Consensus pattern (15 bp):
TTTTGGTTTGTATAT
Found at i:351707 original size:19 final size:19
Alignment explanation
Indices: 351685--351733 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
351675 ATTATAAAAT
*
351685 AATTCAAAATAATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
*
351704 AATTAAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
351723 AATTTCAAAAT
1 AA-TTCAAAAT
351734 TTGTATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:351717 original size:18 final size:19
Alignment explanation
Indices: 351685--351723 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
351675 ATTATAAAAT
* *
351685 AATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
351704 AATTAAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
351722 AA
1 AA
351724 ATTTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:368297 original size:8 final size:8
Alignment explanation
Indices: 368280--368313 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
368270 AGTCTTAATG
368280 TTTTTT-T
1 TTTTTTCT
368287 TTTTTTCT
1 TTTTTTCT
368295 TTTTTTCT
1 TTTTTTCT
368303 TTTTTTCT
1 TTTTTTCT
368311 TTT
1 TTT
368314 GGAGATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTCT
Found at i:368558 original size:7 final size:7
Alignment explanation
Indices: 368546--368579 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
368536 ATTAAAAAAA
368546 TTAATTT
1 TTAATTT
368553 TTAATTT
1 TTAATTT
368560 TTAATTT
1 TTAATTT
*
368567 TTAATTA
1 TTAATTT
368574 TTAATT
1 TTAATT
368580 AGTCACATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTAATTT
Found at i:373963 original size:49 final size:50
Alignment explanation
Indices: 373890--373988 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
373880 CATCTATTTA
* * *
373890 AAGGTTGAAAAAACATTATTCTAATAAAAGTTAAATAGATGAAGTGTAGT
1 AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAATGTAGT
* *
373940 AAGGTTG-AAAAACATTATTCTAATTAATGTCAAATAGAAGAAATGTAGT
1 AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAATGTAGT
373989 TCTATATGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 37 0.84
50 7 0.16
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (50 bp):
AAGGTTGAAAAAACATTATTCTAATAAAAGTCAAATAGAAGAAATGTAGT
Found at i:375234 original size:22 final size:22
Alignment explanation
Indices: 375209--375259 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
375199 TTTTTTTCTA
*
375209 TTTTTTGAAT-TTTTTATTCAT
1 TTTTTTGAATATTTGTATTCAT
*
375230 TTTTTTGAATATTTGTATTTAT
1 TTTTTTGAATATTTGTATTCAT
375252 TATTTTTG
1 T-TTTTTG
375260 GAAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTTTGAATATTTGTATTCAT
Found at i:378197 original size:63 final size:65
Alignment explanation
Indices: 378123--378249 Score: 222
Period size: 63 Copynumber: 2.0 Consensus size: 65
378113 ATAAGAGAAA
378123 TCAATATTTCTTAAAATTTATTTAATTAAATTTATA-TTATATTATATA-TTTTTATTTTTAAAG
1 TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTTATATTATATATTTTTTATTTTTAAAG
* *
378186 TCAATTTTTCTTAAAATTTATTTAATTAAATTTATATTTGTATTATATATTTTTTATTTTTAAA
1 TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTTATATTATATATTTTTTATTTTTAAA
378250 TTTAATGGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 35 0.58
64 11 0.18
65 14 0.23
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (65 bp):
TCAATATTTCTTAAAATTTATTTAATTAAATTTATATTTATATTATATATTTTTTATTTTTAAAG
Found at i:380034 original size:72 final size:72
Alignment explanation
Indices: 379915--380061 Score: 267
Period size: 72 Copynumber: 2.0 Consensus size: 72
379905 ATTTGTCAAG
* *
379915 ACCTAATGCTTAAGCAACTTGCTGCTACCACCTCCATCTCTTTCACTCAGGAGCTGCCACGTCAG
1 ACCTAATGCTTAAGCAACTTGCTGCTACCACCTCCATCTCTTCCACTCAGGAGCTGCCACATCAG
379980 CACCGCC
66 CACCGCC
*
379987 ACCTAATGCTTAAGCAACTTGCTGCTACCGCCTCCATCTCTTCCACTCAGGAGCTGCCACATCAG
1 ACCTAATGCTTAAGCAACTTGCTGCTACCACCTCCATCTCTTCCACTCAGGAGCTGCCACATCAG
380052 CACCGCC
66 CACCGCC
380059 ACC
1 ACC
380062 AACAGCTCAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.22
Consensus pattern (72 bp):
ACCTAATGCTTAAGCAACTTGCTGCTACCACCTCCATCTCTTCCACTCAGGAGCTGCCACATCAG
CACCGCC
Found at i:381578 original size:29 final size:29
Alignment explanation
Indices: 381546--381679 Score: 142
Period size: 29 Copynumber: 4.5 Consensus size: 29
381536 TCTCAACTTC
* *
381546 CTAAAATCACATTTTTACCCCAAACTTTT
1 CTAAAATTACATTTTGACCCCAAACTTTT
* * *
381575 CTAAAATTACATTTTAACCCCCTTAAACCTTC
1 CTAAAATTACATTTTGA-CCCC--AAACTTTT
* ** *
381607 CTAAAATCACATTTTGACCTTAAACTTCT
1 CTAAAATTACATTTTGACCCCAAACTTTT
* *
381636 CTAAAATTACATTTTGACCCTAAAATTTT
1 CTAAAATTACATTTTGACCCCAAACTTTT
381665 CTAAAATTACATTTT
1 CTAAAATTACATTTT
381680 TACCATTTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
29 60 0.69
30 4 0.05
31 2 0.02
32 21 0.24
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (29 bp):
CTAAAATTACATTTTGACCCCAAACTTTT
Found at i:381794 original size:35 final size:35
Alignment explanation
Indices: 381746--381814 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
381736 TTTCGACCTC
*
381746 TTTTTTTTTATTTTGGTTCGCGATTCAATCATATA
1 TTTTTTTTAATTTTGGTTCGCGATTCAATCATATA
* * *
381781 TTTTTTTTAATTTTGGTTTGTGATTCTATCATAT
1 TTTTTTTTAATTTTGGTTCGCGATTCAATCATAT
381815 TTCGTACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.61
Consensus pattern (35 bp):
TTTTTTTTAATTTTGGTTCGCGATTCAATCATATA
Found at i:383298 original size:48 final size:48
Alignment explanation
Indices: 383212--383304 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
383202 ACTAAATCTG
** *
383212 TCTTCCTGATGAGATACAAAGAAGTAGATTGAAACAATGAGGCGGTCA
1 TCTTCCTGATGAGATACAAAGAAGTAGATCCAAACAATGAAGCGGTCA
* *
383260 TCTTTCTGATGAGATACAGAGAAGTAGA-CCAAATCAATGAAGCGG
1 TCTTCCTGATGAGATACAAAGAAGTAGATCCAAA-CAATGAAGCGG
383305 AGCTCAATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 3 0.08
48 36 0.92
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAAAGAAGTAGATCCAAACAATGAAGCGGTCA
Found at i:383417 original size:209 final size:208
Alignment explanation
Indices: 383003--383622 Score: 755
Period size: 209 Copynumber: 3.0 Consensus size: 208
382993 TAAAGCGGTC
* * * * * * *
383003 GTCTTCTTGATGAGATATAGAGAAGTGGATTAAAATAAGTGATGCGATCATCTTTTTAATTAGGT
1 GTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGAGGCGATCATCTTTCTGATGAGAT
* * * *
383068 ACAGAGAAGTAGACCAATTCAACGAAGCGAAGCTCAATGTA-AGAGAAACTTCAAA-CCTATCTT
66 ACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATG-AGAGTGAAACTTCAAACCCCATCTT
* * * * *
383131 CCTGATGAGATATAGAGAAGTGCGTCAAAGCAATAGAACGGTCATCTTCCTGATGAGATACAAAG
130 CCTGATGAGATACAGAGAAGTGAGTCGAAGCAATAAAAC-GTCATCTTCCTGATGAGATACAGAG
383196 AAGT-GAACTAAATCT
194 AAGTAG-ACTAAATCT
* * * * *
383211 GTCTTCCTGATGAGATACAAAGAAGTAGATTGAAACAA-TGAGGCGGTCATCTTTCTGATGAGAT
1 GTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGAGGCGATCATCTTTCTGATGAGAT
*
383275 ACAGAGAAGTAGACCAAATCAATGAAGCGGAGCTCAATGAGAGTGAAACTTTCCAAACCCCATCT
66 ACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGAGAGTGAAAC-TT-CAAACCCCATCT
* *
383340 TCCTGATGAGATA-AGAGAAGTAAGTCGAAGCAATAAAACGTTCATCTTCCTGATGAGATATAGA
129 TCCTGATGAGATACAGAGAAGTGAGTCGAAGCAATAAAACG-TCATCTTCCTGATGAGATACAGA
383404 GAAGTAGACTAAATCT
193 GAAGTAGACTAAATCT
* * * * * *
383420 ATCTTCTTGATAAGATACAGAGAAGTGGATTAAAACAAGTAAGGCGATCATATTCCTGATGAAAT
1 GTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGAGGCGATCATCTTTCTGATGAGAT
* ** * * *
383485 ACAGAGAAGTAAACCAAATCAATGAAGTAAAGCTCAAAGTGAGTGAAGCTTCAAACCCCATCTTC
66 ACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGAGAGTGAAACTTCAAACCCCATCTTC
* * * * * * *
383550 CTGATGAGATACAGAGAAGTGGGTTGAAGAAATGAAGCAGTCATCTTCTTGATGAAATACAGAGA
131 CTGATGAGATACAGAGAAGTGAGTCGAAGCAATAAAAC-GTCATCTTCCTGATGAGATACAGAGA
383615 AGTAGACT
195 AGTAGACT
383623 GAGAGATGAA
Statistics
Matches: 353, Mismatches: 50, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
206 1 0.00
207 63 0.18
208 60 0.17
209 145 0.41
210 84 0.24
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (208 bp):
GTCTTCTTGATGAGATACAGAGAAGTGGATTAAAACAAGTGAGGCGATCATCTTTCTGATGAGAT
ACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGAGAGTGAAACTTCAAACCCCATCTTC
CTGATGAGATACAGAGAAGTGAGTCGAAGCAATAAAACGTCATCTTCCTGATGAGATACAGAGAA
GTAGACTAAATCT
Found at i:384053 original size:27 final size:28
Alignment explanation
Indices: 383991--384058 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
383981 ACCAAAATGG
*
383991 AGCCCAAATA-AATTTTAAATTTAAAAT
1 AGCCCAAATACATTTTTAAATTTAAAAT
* *
384018 ATCCAAAATACATTTTTAAATTTAAAA-
1 AGCCCAAATACATTTTTAAATTTAAAAT
*
384045 GGCCCAAATTACAT
1 AGCCCAAA-TACAT
384059 GTCCTTAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.39
28 20 0.61
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (28 bp):
AGCCCAAATACATTTTTAAATTTAAAAT
Found at i:385691 original size:29 final size:29
Alignment explanation
Indices: 385593--385759 Score: 119
Period size: 29 Copynumber: 5.7 Consensus size: 29
385583 TTGAAAATTT
* * *
385593 CATTTTAACCCTCGAACTT-TCTCAAAATAA
1 CATTTTGA-CCTCAAACTTCTCT-AAAATCA
* * *
385623 CATTTT--CCCCAAACTTTTCTAAAATTA
1 CATTTTGACCTCAAACTTCTCTAAAATCA
* * *
385650 CAATTTAGCCCTCAAAATTCTCTAAAAGT-A
1 C-ATTTTGACCTCAAACTTCTCTAAAA-TCA
*
385680 CATTTTGACCTCGTTAAACCTTC-CCAAAATCA
1 CATTTTGACCTC---AAA-CTTCTCTAAAATCA
*
385712 CATTTTGACCTCAAACTTCTTTAAAATCA
1 CATTTTGACCTCAAACTTCTCTAAAATCA
*
385741 CATTTTGAACTCAAACTTC
1 CATTTTGACCTCAAACTTC
385760 CCAAAATTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
27 15 0.13
28 11 0.10
29 37 0.33
30 23 0.21
31 2 0.02
32 21 0.19
33 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CATTTTGACCTCAAACTTCTCTAAAATCA
Found at i:385775 original size:29 final size:28
Alignment explanation
Indices: 385699--385766 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
385689 CTCGTTAAAC
*
385699 CTTCCCAAAATCACATTTTGACCTCAAA
1 CTTCCCAAAATCACATTTTGAACTCAAA
**
385727 CTTCTTTAAAATCACATTTTGAACTCAAA
1 CTTC-CCAAAATCACATTTTGAACTCAAA
385756 CTTCCCAAAAT
1 CTTCCCAAAAT
385767 TACTTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (28 bp):
CTTCCCAAAATCACATTTTGAACTCAAA
Found at i:387862 original size:29 final size:29
Alignment explanation
Indices: 387800--387871 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
387790 ATTTTCAAAA
*
387800 TAATTTTAATAATTTTATATTATTTTCTT
1 TAATTTTAATAATTTTATAGTATTTTCTT
* *
387829 GAATTTTAAATAGTTTT-TAGTACTTTT-TT
1 TAATTTT-AATAATTTTATAGTA-TTTTCTT
387858 TAATTTT--TAATTTT
1 TAATTTTAATAATTTT
387872 TAAAAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.17
29 18 0.50
30 12 0.33
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (29 bp):
TAATTTTAATAATTTTATAGTATTTTCTT
Found at i:391554 original size:2 final size:2
Alignment explanation
Indices: 391547--391574 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
391537 ATATCTGCTT
391547 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
391575 ACAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:409071 original size:69 final size:68
Alignment explanation
Indices: 408935--409072 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 68
408925 AACCGGCAAC
*
408935 ATTAGGATTCATTTCGTAGTCTTGCAATTAATTTTCTTCTGCTGTTAAAATGAAAATGTAGCCTG
1 ATTAGGATTCATTTCGTAGTCTTGCAATGAATTTTCTTCTGCTGTTAAAATGAAAATGTAGCCTG
409000 TAA
66 TAA
* *
409003 ATTAGGATTCATTTCGTAGTCTTGCAGTGAATTTTTTTTCTGCTGTTAAAATGAAAATGTAGCCT
1 ATTAGGATTCATTTCGTAGTCTTGCAATGAA-TTTTCTTCTGCTGTTAAAATGAAAATGTAGCCT
409068 GTAA
65 GTAA
409072 A
1 A
409073 CCTAGGTTCT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 29 0.44
69 37 0.56
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (68 bp):
ATTAGGATTCATTTCGTAGTCTTGCAATGAATTTTCTTCTGCTGTTAAAATGAAAATGTAGCCTG
TAA
Found at i:410519 original size:22 final size:23
Alignment explanation
Indices: 410493--410554 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
410483 TAAAAATGAT
* *
410493 AAAATTTTAATTTAATTAT-TTA
1 AAAATTATAATTTAATTATCGTA
* * *
410515 AAAATTATATTTTTACTATCGTA
1 AAAATTATAATTTAATTATCGTA
410538 AAAATTATAATTTAATT
1 AAAATTATAATTTAATT
410555 TTGATCTCCC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAATTATAATTTAATTATCGTA
Found at i:415800 original size:21 final size:21
Alignment explanation
Indices: 415761--415800 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
415751 GACGGCACGA
*
415761 AAGGCAGTTGAAAGCAAAGTC
1 AAGGCAGCTGAAAGCAAAGTC
415782 AAGGCAGCTGACAAG-AAAG
1 AAGGCAGCTGA-AAGCAAAG
415801 CCAATTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.45, C:0.15, G:0.30, T:0.10
Consensus pattern (21 bp):
AAGGCAGCTGAAAGCAAAGTC
Found at i:417123 original size:21 final size:20
Alignment explanation
Indices: 417035--417129 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
417025 AAAATTTGGA
*
417035 AATTAAAATTTTATTTAAATT
1 AATTTAAATTTT-TTTAAATT
** * * *
417056 CTTTTATATTTGTATAAGATT
1 AATTTAAATTTTTTTAA-ATT
* * *
417077 AATTCAAGTTTTTTTATATT
1 AATTTAAATTTTTTTAAATT
*
417097 ATTTTAAATTTTTTTAAATTT
1 AATTTAAATTTTTTTAAA-TT
417118 AATTTAATATTT
1 AATTTAA-ATTT
417130 AATTAGTTGG
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
20 21 0.40
21 27 0.52
22 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTTAAATTTTTTTAAATT
Found at i:419843 original size:84 final size:84
Alignment explanation
Indices: 419702--419870 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
419692 TGTTATATTG
419702 CAACTAGGAATTCAAAGGACTCACCCATTCACCTGCTGCTCTGTATAGGCAAAGAGTCAAATAAA
1 CAACTAGGAATTCAAAGGACTCACCCATTCACCTGCTGCTCTGTATAGGCAAAGAGTCAAATAAA
419767 ACAAGCAAATTTTCTCTAA
66 ACAAGCAAATTTTCTCTAA
419786 CAACTAGGAATTCAAAGGACTCACCCATTCACCTGCTGCTCTGTATAGGCAAAGAGTCAAATAAA
1 CAACTAGGAATTCAAAGGACTCACCCATTCACCTGCTGCTCTGTATAGGCAAAGAGTCAAATAAA
419851 ACAAGCAAATTTTCTCTAA
66 ACAAGCAAATTTTCTCTAA
419870 C
1 C
419871 CCTAATTTTT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (84 bp):
CAACTAGGAATTCAAAGGACTCACCCATTCACCTGCTGCTCTGTATAGGCAAAGAGTCAAATAAA
ACAAGCAAATTTTCTCTAA
Found at i:422681 original size:42 final size:42
Alignment explanation
Indices: 422574--422685 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 42
422564 GTTTTTTAGT
* * ** *
422574 ATTTTTTTTTTCAGTCAAGGAAAAAAGCTCCTACGTGGAGGC
1 ATTTTTTTTCTCATTCAAGGAAAAGTGCTCCTACATGGAGGC
* * *
422616 -GTTTTTATCTCATTCAAGGAAAAGTGATTCC-ACATGGAGGC
1 ATTTTTTTTCTCATTCAAGGAAAAGTG-CTCCTACATGGAGGC
422657 ATTTTTTTTCTCATTCAAGGAAAAGTGCT
1 ATTTTTTTTCTCATTCAAGGAAAAGTGCT
422686 TACAATCGGA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 30 0.53
42 27 0.47
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (42 bp):
ATTTTTTTTCTCATTCAAGGAAAAGTGCTCCTACATGGAGGC
Found at i:425580 original size:42 final size:43
Alignment explanation
Indices: 425484--425642 Score: 223
Period size: 43 Copynumber: 3.7 Consensus size: 43
425474 GTTTATGAGG
425484 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTT-CTCCC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTAC-CCC
* **
425527 ACAAATGCCGCTAAAGAACATGGTCTTTAG-GGCGCTTACCCC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
* ** *
425569 AAAAATACCGCTAAAGAACATGGTCTTTAGCGGTACTTACCCA
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
*
425612 AAAAACACCGCTAAAGAACATGATCTTTAGC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGC
425643 AGCGTTTTTC
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
42 38 0.37
43 66 0.63
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
Found at i:425627 original size:85 final size:85
Alignment explanation
Indices: 425484--425641 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 85
425474 GTTTATGAGG
* * * **
425484 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTCCCACAAATGCCGCTAAAGAACATG
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCACTTCTCCAAAAAACACCGCTAAAGAACATG
*
425549 GTCTTTAGGGCGCTTACCCC
66 ATCTTTAGGGCGCTTACCCC
* *
425569 AAAAATACCGCTAAAGAACATGGTCTTTAGCGGTACTTAC-CCAAAAAACACCGCTAAAGAACAT
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCACTT-CTCCAAAAAACACCGCTAAAGAACAT
425633 GATCTTTAG
65 GATCTTTAG
425642 CAGCGTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 63 0.98
86 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (85 bp):
AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCACTTCTCCAAAAAACACCGCTAAAGAACATG
ATCTTTAGGGCGCTTACCCC
Found at i:425666 original size:43 final size:43
Alignment explanation
Indices: 425484--425669 Score: 205
Period size: 43 Copynumber: 4.3 Consensus size: 43
425474 GTTTATGAGG
*
425484 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTCCC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC
* ** **
425527 ACAAATGCCGCTAAAGAACATGGTCTTTAG-GGCGCTTACCCC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC
* ** *
425569 AAAAATACCGCTAAAGAACATGGTCTTTAGCGGTAC-TTACCC
1 AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC
* * * *
425611 AAAAAACACCGCTAAAGAACATGATCTTTAGCAGCGTTTTTCTC
1 -AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC
* *
425655 ACAAACGCCGCTAAA
1 AAAAACACCGCTAAA
425670 ATTAACAGAT
Statistics
Matches: 119, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 42 0.35
43 73 0.61
44 4 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
AAAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC
Found at i:426001 original size:24 final size:24
Alignment explanation
Indices: 425974--426025 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
425964 CTTGTTGCCT
425974 CTGCTTCATTCACTTTTCTCACTA
1 CTGCTTCATTCACTTTTCTCACTA
425998 CTGCTTCATTCACTTTTCTCACTA
1 CTGCTTCATTCACTTTTCTCACTA
426022 CTGC
1 CTGC
426026 CTCTGCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.35, G:0.06, T:0.44
Consensus pattern (24 bp):
CTGCTTCATTCACTTTTCTCACTA
Found at i:427336 original size:40 final size:40
Alignment explanation
Indices: 427292--427370 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
427282 AAAAGTCGAG
**
427292 TTTTTGATCCAACAGTTTGACCATGACTATTTGCATATAA
1 TTTTTGATCCAACAGGCTGACCATGACTATTTGCATATAA
427332 TTTTTGATCCAACAGGCTGACCATGACTATTTGCATATA
1 TTTTTGATCCAACAGGCTGACCATGACTATTTGCATATA
427371 CTTTGACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (40 bp):
TTTTTGATCCAACAGGCTGACCATGACTATTTGCATATAA
Found at i:427591 original size:33 final size:34
Alignment explanation
Indices: 427543--427610 Score: 113
Period size: 33 Copynumber: 2.0 Consensus size: 34
427533 AAATTAACAA
427543 TGTTTTCCCCATAAACG-TCGCTAATGCTCTGACC
1 TGTTTTCCCCATAAACGCT-GCTAATGCTCTGACC
427577 TGTTTT-CCCATAAACGCTGCTAATGCTCTGACC
1 TGTTTTCCCCATAAACGCTGCTAATGCTCTGACC
427610 T
1 T
427611 TTAGCAGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.34
Consensus pattern (34 bp):
TGTTTTCCCCATAAACGCTGCTAATGCTCTGACC
Found at i:427622 original size:16 final size:16
Alignment explanation
Indices: 427601--427634 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
427591 CGCTGCTAAT
427601 GCTCTGACCTTTAGCA
1 GCTCTGACCTTTAGCA
427617 GCTCTGACCTTTAGCA
1 GCTCTGACCTTTAGCA
427633 GC
1 GC
427635 GCTTTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (16 bp):
GCTCTGACCTTTAGCA
Found at i:429951 original size:17 final size:18
Alignment explanation
Indices: 429924--429977 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
429914 AACCCTTTTT
429924 AATTT-ATTTTAAATTTA
1 AATTTAATTTTAAATTTA
*
429941 GA-TTAATTTTAAATTTA
1 AATTTAATTTTAAATTTA
* *
429958 AATTTGATTTTAAAATTA
1 AATTTAATTTTAAATTTA
429976 AA
1 AA
429978 AAGTCCATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
AATTTAATTTTAAATTTA
Found at i:431975 original size:60 final size:60
Alignment explanation
Indices: 431882--432012 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
431872 TCCAACCTCG
* * * *
431882 AACTTCC-AAAAATCCCATTTTTTACCCTAAAACTTCCAAAAATTCAATTTTTACCCCCA
1 AACTTCCAAAAAATCCCATTCTTGACCCCAAAACTTCCAAAAAATCAATTTTTACCCCCA
* * ** * *
431941 AACTTCCAAAAAATCTCATTCTTGACCCCGAAACTTCCAAAAAATCCTTTTTTACCCTCG
1 AACTTCCAAAAAATCCCATTCTTGACCCCAAAACTTCCAAAAAATCAATTTTTACCCCCA
432001 AACTTCCAAAAA
1 AACTTCCAAAAA
432013 TTACATTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 7 0.11
60 54 0.89
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.30
Consensus pattern (60 bp):
AACTTCCAAAAAATCCCATTCTTGACCCCAAAACTTCCAAAAAATCAATTTTTACCCCCA
Found at i:432042 original size:29 final size:29
Alignment explanation
Indices: 431877--432055 Score: 150
Period size: 29 Copynumber: 6.1 Consensus size: 29
431867 AAAAATCCAA
* **
431877 CCTCGAACTTCCAAAAATCCCATTTTTTAC
1 CCTCAAACTTCCAAAAATTACA-TTTTTAC
*
431907 CCTAAAACTTCCAAAAATT-CAATTTTTAC
1 CCTCAAACTTCCAAAAATTAC-ATTTTTAC
* *
431936 CCCCAAACTTCCAAAAAATCT-CATTCTTGAC
1 CCTCAAACTTCC-AAAAAT-TACATT-TTTAC
* * *
431967 CC-CGAAACTTCCAAAAAATCCTTTTTTAC
1 CCTC-AAACTTCCAAAAATTACATTTTTAC
*
431996 CCTCGAACTTCCAAAAATTACATTTTTAC
1 CCTCAAACTTCCAAAAATTACATTTTTAC
* **
432025 CCTCAAAAC-TCCCAAAATTACCCTTTTAC
1 CCTC-AAACTTCCAAAAATTACATTTTTAC
432054 CC
1 CC
432056 CCGAATGTCT
Statistics
Matches: 124, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
29 69 0.56
30 39 0.31
31 16 0.13
ACGTcount: A:0.35, C:0.32, G:0.02, T:0.31
Consensus pattern (29 bp):
CCTCAAACTTCCAAAAATTACATTTTTAC
Found at i:432050 original size:60 final size:58
Alignment explanation
Indices: 431877--432060 Score: 153
Period size: 59 Copynumber: 3.1 Consensus size: 58
431867 AAAAATCCAA
* * **
431877 CCTCGAACTTCCAAAAATCCCATTTTTTACCCT-AAAACTTCCAAAAATT-CAATTTTTAC
1 CCTCGAACTTCCAAAAAT-TCA-TTTTTACCCTCAAAAC-TCCCAAAATTACCTTTTTTAC
* * * * * *
431936 CCCCAAACTTCCAAAAAATCTCATTCTTGACCC-CGAAACTTCCAAAA-AATCCTTTTTTAC
1 CCTCGAACTTCC-AAAAAT-TCATT-TTTACCCTCAAAACTCCCAAAATTA-CCTTTTTTAC
*
431996 CCTCGAACTTCCAAAAATTACATTTTTACCCTCAAAACTCCCAAAATTACC-CTTTTAC
1 CCTCGAACTTCCAAAAATT-CATTTTTACCCTCAAAACTCCCAAAATTACCTTTTTTAC
*
432054 CCCCGAA
1 CCTCGAA
432061 TGTCTAAAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
58 19 0.19
59 42 0.42
60 38 0.38
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (58 bp):
CCTCGAACTTCCAAAAATTCATTTTTACCCTCAAAACTCCCAAAATTACCTTTTTTAC
Found at i:443421 original size:23 final size:21
Alignment explanation
Indices: 443387--443433 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
443377 GTCAATCAAT
**
443387 AAATAAATTAAAATTTATAAA
1 AAATAAATTAAAAACTATAAA
443408 AAATCAAATTTAAAAACTATAAA
1 AAAT-AAA-TTAAAAACTATAAA
443431 AAA
1 AAA
443434 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAATTAAAAACTATAAA
Found at i:444262 original size:21 final size:22
Alignment explanation
Indices: 444222--444263 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
444212 AAGTCCAATT
*
444222 CTTTTGAGCCTTTGAATTGTGC
1 CTTTTGAGCCATTGAATTGTGC
*
444244 CTTTTGTGCCATT-AATTGTG
1 CTTTTGAGCCATTGAATTGTG
444264 GATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (22 bp):
CTTTTGAGCCATTGAATTGTGC
Found at i:445095 original size:47 final size:47
Alignment explanation
Indices: 445022--445116 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
445012 TTTCCTGTCT
445022 AATTTTGCATTCCATCTCTTTAACCATGGTCCTTTGATATTTCAAGA
1 AATTTTGCATTCCATCTCTTTAACCATGGTCCTTTGATATTTCAAGA
* *
445069 AATTTTGCATTCCGTCTCTTTCACCATGGTCCTTTGATATTTCAAGA
1 AATTTTGCATTCCATCTCTTTAACCATGGTCCTTTGATATTTCAAGA
445116 A
1 A
445117 CAGAGCATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (47 bp):
AATTTTGCATTCCATCTCTTTAACCATGGTCCTTTGATATTTCAAGA
Found at i:445533 original size:20 final size:20
Alignment explanation
Indices: 445495--445534 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
445485 CTATTAAAAT
*
445495 AATTATTTTTATTTAATTTA
1 AATTATTTTTAATTAATTTA
445515 AATTATATTTTAATT-ATTTA
1 AATTAT-TTTTAATTAATTTA
445535 TGTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTATTTTTAATTAATTTA
Found at i:445565 original size:15 final size:15
Alignment explanation
Indices: 445517--445568 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
445507 TTAATTTAAA
*
445517 TTATATTTTAATTAT
1 TTATATTTTAATAAT
* * * *
445532 TTATGTTTGAAAAAG
1 TTATATTTTAATAAT
*
445547 TTATATTTTAATCAT
1 TTATATTTTAATAAT
445562 TTATATT
1 TTATATT
445569 AATAAACTGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (15 bp):
TTATATTTTAATAAT
Found at i:456903 original size:17 final size:17
Alignment explanation
Indices: 456881--456914 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
456871 ATGTGAATAA
456881 AAAATAATT-TTTTTTTT
1 AAAAT-ATTGTTTTTTTT
456898 AAAATATTGTTTTTTTT
1 AAAATATTGTTTTTTTT
456915 TTTAAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
AAAATATTGTTTTTTTT
Found at i:456912 original size:16 final size:17
Alignment explanation
Indices: 456881--456913 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
456871 ATGTGAATAA
*
456881 AAAATAATTTTTTTTTT
1 AAAATAATTGTTTTTTT
456898 AAAAT-ATTGTTTTTTT
1 AAAATAATTGTTTTTTT
456914 TTTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
AAAATAATTGTTTTTTT
Found at i:457939 original size:15 final size:14
Alignment explanation
Indices: 457907--457933 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
457897 TTCGAGAAAA
457907 AAAAATAATTTTTC
1 AAAAATAATTTTTC
457921 AAAAATAATTTTT
1 AAAAATAATTTTT
457934 TGAAAACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAATAATTTTTC
Found at i:464045 original size:3 final size:3
Alignment explanation
Indices: 464037--464063 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
464027 AACCCAAAAG
464037 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
464064 AGACAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:465383 original size:7 final size:7
Alignment explanation
Indices: 465371--465414 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
465361 TACTTACTCT
465371 ATCTGCA
1 ATCTGCA
465378 ATCTGCA
1 ATCTGCA
465385 ATCTGCA
1 ATCTGCA
465392 ATCTGCA
1 ATCTGCA
465399 ATCTGCA
1 ATCTGCA
*
465406 ATCTTCA
1 ATCTGCA
465413 AT
1 AT
465415 TCCTTTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (7 bp):
ATCTGCA
Found at i:470371 original size:78 final size:78
Alignment explanation
Indices: 470242--470399 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
470232 AAGCTCAGAG
470242 CTTCCACTTGTTTACACCAACAAGAAATCATCACCCTTGTTATTGATCAAATTAGCACCAGTTAA
1 CTTCCACTTGTTTACACCAACAAGAAATCATCACCCTTGTTATTGATCAAATTAGCACCAGTTAA
470307 ATCTTACTCGTTA
66 ATCTTACTCGTTA
470320 CTTCCACTTGTTTACACCAACAAGAAATCATCACCCTTGTTATTGATCAAATTAGCACCAGTTAA
1 CTTCCACTTGTTTACACCAACAAGAAATCATCACCCTTGTTATTGATCAAATTAGCACCAGTTAA
470385 ATCTTACTCGTTA
66 ATCTTACTCGTTA
470398 CT
1 CT
470400 CCCAGTAACC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.34
Consensus pattern (78 bp):
CTTCCACTTGTTTACACCAACAAGAAATCATCACCCTTGTTATTGATCAAATTAGCACCAGTTAA
ATCTTACTCGTTA
Found at i:473420 original size:10 final size:9
Alignment explanation
Indices: 473395--473438 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
473385 TGCTTTTTTT
473395 TTATAAAAA
1 TTATAAAAA
473404 TTATAAAAA
1 TTATAAAAA
* *
473413 TTATTAAAT
1 TTATAAAAA
*
473422 TTAAAAAAA
1 TTATAAAAA
473431 TT-TAAAAA
1 TTATAAAAA
473439 AATTAAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TTATAAAAA
Found at i:473439 original size:10 final size:10
Alignment explanation
Indices: 473418--473446 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
473408 AAAAATTATT
473418 AAATTTAAAA
1 AAATTTAAAA
473428 AAATTTAAAA
1 AAATTTAAAA
473438 AAA-TTAAAA
1 AAATTTAAAA
473447 TGATTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:473446 original size:18 final size:18
Alignment explanation
Indices: 473394--473446 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
473384 CTGCTTTTTT
473394 TTTATAAAAATTATAAAAA
1 TTTATAAAAATTA-AAAAA
* *
473413 -TTATTAAATTTAAAAAAA
1 TTTATAAAAATT-AAAAAA
*
473431 TTTAAAAAAATTAAAA
1 TTTATAAAAATTAAAA
473447 TGATTCAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTATAAAAATTAAAAAA
Found at i:475095 original size:23 final size:23
Alignment explanation
Indices: 475065--475121 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
475055 GTCATAAGAC
*
475065 AAAAGCGTGCCACAAGGTAGAGG
1 AAAAGCGTGCCACAAGGTAGAGA
*
475088 AAAAGCGTACCACAAGGTAGAGA
1 AAAAGCGTGCCACAAGGTAGAGA
475111 AAAAGCGTGCC
1 AAAAGCGTGCC
475122 GTAAAGGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.30, T:0.09
Consensus pattern (23 bp):
AAAAGCGTGCCACAAGGTAGAGA
Found at i:476308 original size:22 final size:23
Alignment explanation
Indices: 476251--476310 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
476241 GGGGACGGTG
* *
476251 TTAAATTATAATTTTTACGATAA
1 TTAAATTATAATTTTTACAAAAA
* *
476274 TAAAAATATAATTTTTA-AAAAA
1 TTAAATTATAATTTTTACAAAAA
*
476296 TTAAATTAAAATTTT
1 TTAAATTATAATTTT
476311 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAATTATAATTTTTACAAAAA
Found at i:478279 original size:24 final size:24
Alignment explanation
Indices: 478252--478304 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
478242 CCTTGGGTGG
478252 TGGTGCTG-GACTTGGAGCTTTGTA
1 TGGTGCTGAG-CTTGGAGCTTTGTA
*
478276 TGGTGCTGAGTTTGGAGCTTTGTA
1 TGGTGCTGAGCTTGGAGCTTTGTA
478300 TGGTG
1 TGGTG
478305 GTGCAGAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.11, C:0.09, G:0.40, T:0.40
Consensus pattern (24 bp):
TGGTGCTGAGCTTGGAGCTTTGTA
Found at i:478350 original size:12 final size:12
Alignment explanation
Indices: 478332--478361 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
478322 CTCACTGGGA
478332 CTGGAGTTGGAG
1 CTGGAGTTGGAG
*
478344 TTGGAGTTGGAG
1 CTGGAGTTGGAG
478356 CTGGAG
1 CTGGAG
478362 CTAGTATGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.27
Consensus pattern (12 bp):
CTGGAGTTGGAG
Found at i:481414 original size:6 final size:6
Alignment explanation
Indices: 481403--481443 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
481393 AAAAGGTGGT
481403 ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA ATGGG
1 ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA ATGGGA ATGGG
481444 CATTGCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.17
Consensus pattern (6 bp):
ATGGGA
Found at i:483742 original size:24 final size:23
Alignment explanation
Indices: 483694--483789 Score: 78
Period size: 24 Copynumber: 4.3 Consensus size: 23
483684 TAAATTTATT
*
483694 TTAAAATTAAATTT-GTTTAA-A
1 TTAAATTTAAATTTAGTTTAAAA
*
483715 --AAATTTAAATTTATTTTAAAA
1 TTAAATTTAAATTTAGTTTAAAA
483736 TTTAAATTT-AATTTGAGTTTAAAA
1 -TTAAATTTAAATTT-AGTTTAAAA
**
483760 TTATTTTTAAATTTAAAGTTTAAAA
1 TTAAATTTAAATTT--AGTTTAAAA
483785 -TAAAT
1 TTAAAT
483790 AAAACCCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
19 11 0.19
20 5 0.08
21 1 0.02
23 11 0.19
24 22 0.37
25 9 0.15
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAAATTTAAATTTAGTTTAAAA
Found at i:483774 original size:18 final size:18
Alignment explanation
Indices: 483682--483781 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
483672 CCATACTCCT
483682 TTTAAATTTA-TTTTAAA
1 TTTAAATTTATTTTTAAA
* * **
483699 ATTAAATTTGTTTAAAAAA
1 TTTAAATTTATTT-TTAAA
*
483718 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTTAAA
* * *
483736 TTTAAATTTA-ATTTGAG
1 TTTAAATTTATTTTTAAA
*
483753 TTTAAAATTATTTTTAAA
1 TTTAAATTTATTTTTAAA
483771 TTTAAAGTTTA
1 TTTAAA-TTTA
483782 AAATAAATAA
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
17 20 0.32
18 26 0.41
19 17 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:483783 original size:7 final size:6
Alignment explanation
Indices: 483715--483783 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
483705 TTTGTTTAAA
* * * *
483715 AAATTT AAATTT -ATTTT AAAATTT AAATTT -AATTT GAGTTT AAAATT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
**
483762 ATTTTT AAATTT AAAGTTT AAA
1 AAATTT AAATTT AAA-TTT AAA
483784 ATAAATAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
5 9 0.19
6 29 0.60
7 10 0.21
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:484454 original size:18 final size:19
Alignment explanation
Indices: 484420--484461 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
484410 AAAACGTTTC
*
484420 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
484439 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
484457 AATAA
1 AATAA
484462 TAACACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:485707 original size:59 final size:59
Alignment explanation
Indices: 485631--485924 Score: 489
Period size: 59 Copynumber: 5.0 Consensus size: 59
485621 CCCTAGATTG
* * * * *
485631 TCCAGAAATCCCATTTTTTACCCCTAACCTTCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
* *
485690 TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCTCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
485749 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAAATTACCATTTCACCCCCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCC-AAAAATTACCATTTCACCCCCGAACT
485809 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
* * *
485868 TCCAACAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCTCCGAA
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAA
485925 TGTTTGGAAT
Statistics
Matches: 224, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
59 166 0.74
60 58 0.26
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (59 bp):
TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
Found at i:485722 original size:30 final size:31
Alignment explanation
Indices: 485641--485915 Score: 282
Period size: 30 Copynumber: 9.2 Consensus size: 31
485631 TCCAGAAATC
* *
485641 CCATTTTTTACCCCTAACCTTCCAAAAATTA
1 CCATTTTTGACCCCGAACCTTCCAAAAATTA
*
485672 CCA-TTTT-ACCCCCGAA-CTTCCAAAAA-TC
1 CCATTTTTGA-CCCCGAACCTTCCAAAAATTA
485700 CCATTTTTGACCCCGAACCTTCCAAAAATTA
1 CCATTTTTGACCCCGAACCTTCCAAAAATTA
*
485731 CCA--TTTCACCCTCGAA-CTTCCAAAAA-T-
1 CCATTTTTGACCC-CGAACCTTCCAAAAATTA
485758 CTCATTTTTGACCCCGAACCTTCCAAAAAATTA
1 C-CATTTTTGACCCCGAACCTTCC-AAAAATTA
*
485791 CCA--TTTCACCCCCGAA-CTTCCAAAAA-T-
1 CCATTTTTGA-CCCCGAACCTTCCAAAAATTA
485818 CTCATTTTTGACCCCGAACCTTCCAAAAATTA
1 C-CATTTTTGACCCCGAACCTTCCAAAAATTA
* *
485850 CCA--TTTCACCCCCGAA-CTTCCAACAA-T-
1 CCATTTTTGA-CCCCGAACCTTCCAAAAATTA
485877 CTCATTTTTGACCCCGAACCTTCCAAAAATTA
1 C-CATTTTTGACCCCGAACCTTCCAAAAATTA
485909 CCATTTT
1 CCATTTT
485916 ACCTCCGAAT
Statistics
Matches: 206, Mismatches: 11, Indels: 54
0.76 0.04 0.20
Matches are distributed among these distances:
27 3 0.01
28 13 0.06
29 75 0.36
30 80 0.39
31 29 0.14
32 5 0.02
33 1 0.00
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (31 bp):
CCATTTTTGACCCCGAACCTTCCAAAAATTA
Found at i:485846 original size:119 final size:118
Alignment explanation
Indices: 485631--485924 Score: 498
Period size: 119 Copynumber: 2.5 Consensus size: 118
485621 CCCTAGATTG
* * * *
485631 TCCAGAAATCCCATTTTTTACCCCTAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAA
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAA
*
485696 AATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCTCGAACT
66 AATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
*
485749 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAAATTACCATTTCACCCCCGAACTTCCAA
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCC-AAAAATTACCATTTTACCCCCGAACTTCCAA
*
485814 AAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
65 AAATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
* *
485868 TCCAACAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCTCCGAA
1 TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
485925 TGTTTGGAAT
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
118 51 0.31
119 114 0.69
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (118 bp):
TCCAAAAATCTCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAA
AATCCCATTTTTGACCCCGAACCTTCCAAAAATTACCATTTCACCCCCGAACT
Found at i:485924 original size:30 final size:29
Alignment explanation
Indices: 485646--485924 Score: 274
Period size: 29 Copynumber: 9.4 Consensus size: 29
485636 AAATCCCATT
*
485646 TTTTACCCCTAACCTTCCAAAAATTACCA
1 TTTTACCCCGAACCTTCCAAAAATTACCA
*
485675 TTTTACCCCCGAA-CTTCCAAAAA-TCCCA
1 TTTTA-CCCCGAACCTTCCAAAAATTACCA
485703 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTT-ACCCCGAACCTTCCAAAAATTACCA
*
485734 TTTCACCCTCGAA-CTTCCAAAAA-T-CTCA
1 TTTTACCC-CGAACCTTCCAAAAATTAC-CA
485762 TTTTTGACCCCGAACCTTCCAAAAAATTACCA
1 -TTTT-ACCCCGAACCTTCC-AAAAATTACCA
*
485794 TTTCACCCCCGAA-CTTCCAAAAA-T-CTCA
1 TTTTA-CCCCGAACCTTCCAAAAATTAC-CA
485822 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTT-ACCCCGAACCTTCCAAAAATTACCA
* *
485853 TTTCACCCCCGAA-CTTCCAACAA-T-CTCA
1 TTTTA-CCCCGAACCTTCCAAAAATTAC-CA
485881 TTTTTGACCCCGAACCTTCCAAAAATTACCA
1 -TTTT-ACCCCGAACCTTCCAAAAATTACCA
485912 TTTTACCTCCGAA
1 TTTTACC-CCGAA
485925 TGTTTGGAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 55
0.76 0.04 0.20
Matches are distributed among these distances:
27 3 0.01
28 13 0.06
29 85 0.40
30 79 0.37
31 25 0.12
32 5 0.02
33 1 0.00
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (29 bp):
TTTTACCCCGAACCTTCCAAAAATTACCA
Found at i:488658 original size:9 final size:9
Alignment explanation
Indices: 488644--488768 Score: 84
Period size: 10 Copynumber: 13.7 Consensus size: 9
488634 AATATTTTTC
488644 ATAAAAATT
1 ATAAAAATT
488653 ATAAAAA--
1 ATAAAAATT
488660 ATAAAATATAT
1 ATAAAA-AT-T
*
488671 ATTAAAATT
1 ATAAAAATT
*
488680 ATATAAACTT
1 ATA-AAAATT
488690 AATAAAAA-T
1 -ATAAAAATT
488699 ATAAAATATT
1 ATAAAA-ATT
*
488709 ATAAATATT
1 ATAAAAATT
488718 AT-AAAA-T
1 ATAAAAATT
488725 AT-AAAATT
1 ATAAAAATT
*
488733 CTAATAAATT
1 ATAA-AAATT
488743 ATAAACAAATT
1 AT-AA-AAATT
488754 AT-AAAATT
1 ATAAAAATT
488762 AATAAAA
1 -ATAAAA
488769 CTTGTTTAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
7 13 0.14
8 17 0.18
9 21 0.23
10 25 0.27
11 17 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:488686 original size:38 final size:38
Alignment explanation
Indices: 488647--488768 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 38
488637 ATTTTTCATA
488647 AAAATT-ATAAAAA-ATAAAATATATATTAAA-ATTATAT
1 AAAATTAATAAAAATATAAAATAT-TA-TAAATATTATAT
*
488684 AAACTTAATAAAAATATAAAATATTATAAATA-T-TAT
1 AAAATTAATAAAAATATAAAATATTATAAATATTATAT
* * * *
488720 AAAA-T-ATAAAATTCTAATAA-ATTATAAACA-AATTAT
1 AAAATTAATAAAAATATAA-AATATTATAAATATTA-TAT
488756 AAAATTAATAAAA
1 AAAATTAATAAAA
488769 CTTGTTTAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
34 19 0.27
35 3 0.04
36 13 0.18
37 11 0.15
38 16 0.23
39 9 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (38 bp):
AAAATTAATAAAAATATAAAATATTATAAATATTATAT
Found at i:488703 original size:27 final size:26
Alignment explanation
Indices: 488647--488767 Score: 81
Period size: 27 Copynumber: 4.5 Consensus size: 26
488637 ATTTTTCATA
* * *
488647 AAAATTATAAAAAATAA-AATATATATT
1 AAAATTATATAAATTAATAA-AAATA-T
488674 AAAATTATATAAACTTAATAAAAATAT
1 AAAATTATATAAA-TTAATAAAAATAT
*
488701 AAAA-TATTATAAA-TATTATAAAATAT
1 AAAATTA-TATAAATTAATA-AAAATAT
*
488727 AAAATTCTAATAAATT-ATAAACAAATTAT
1 AAAATTAT-ATAAATTAAT-AA-AAA-TAT
488756 AAAATTA-ATAAA
1 AAAATTATATAAA
488768 ACTTGTTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
25 4 0.05
26 14 0.18
27 36 0.47
28 12 0.16
29 11 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATTATATAAATTAATAAAAATAT
Found at i:488720 original size:19 final size:18
Alignment explanation
Indices: 488644--488726 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 18
488634 AATATTTTTC
*
488644 ATAAAA-ATTATAAAA-A
1 ATAAAATATTATAAAATT
488660 ATAAAATATATATTAAAATT
1 ATAAAATAT-TA-TAAAATT
* *
488680 ATATAAACT-TAATAAAAAT
1 ATA-AAA-TATTATAAAATT
488699 ATAAAATATTATAAATATT
1 ATAAAATATTATAAA-ATT
488718 ATAAAATAT
1 ATAAAATAT
488727 AAAATTCTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
16 6 0.11
17 3 0.06
18 11 0.20
19 25 0.46
20 4 0.07
21 4 0.07
22 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAAATATTATAAAATT
Found at i:489390 original size:16 final size:15
Alignment explanation
Indices: 489359--489392 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
489349 AATTATTAGA
489359 ATTTTATATATATAT
1 ATTTTATATATATAT
*
489374 ATTTTATAATATTTAT
1 ATTTTAT-ATATATAT
489390 ATT
1 ATT
489393 ATTTTTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTATATATATAT
Found at i:491813 original size:30 final size:31
Alignment explanation
Indices: 491762--491820 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
491752 AATTTTTTAA
*
491762 ATTTTAAAAAAGTCAAAAAATTATAAAAACCT
1 ATTTTAAAAAAAT-AAAAAATTATAAAAACCT
*
491794 ATTTTAAAAAAAT-AAAAATTATTAAAA
1 ATTTTAAAAAAATAAAAAATTATAAAAA
491821 TTATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
32 12 0.48
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (31 bp):
ATTTTAAAAAAATAAAAAATTATAAAAACCT
Found at i:491849 original size:39 final size:39
Alignment explanation
Indices: 491778--491860 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
491768 AAAAAGTCAA
** * *
491778 AAAATTATAAAAACCTATTTTAAAAAAATAAAAATTATT
1 AAAATTATAAAAAAATATTTTAAAAAAATAAAAAATAAT
* *
491817 AAAATTATTAAAAAAATATTTT-TAAAATTAAAAAATAAT
1 AAAATTA-TAAAAAAATATTTTAAAAAAATAAAAAATAAT
491856 AAAAT
1 AAAAT
491861 ATTGACGTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (39 bp):
AAAATTATAAAAAAATATTTTAAAAAAATAAAAAATAAT
Found at i:492841 original size:22 final size:22
Alignment explanation
Indices: 492815--492862 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
492805 ATAAATTTTA
*
492815 TTTTCTATAAAGCTCAAAAGTT
1 TTTTCTACAAAGCTCAAAAGTT
* *
492837 TTTTCTGCAAAGCTCAGAAGTT
1 TTTTCTACAAAGCTCAAAAGTT
492859 TTTT
1 TTTT
492863 TGTTCACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (22 bp):
TTTTCTACAAAGCTCAAAAGTT
Found at i:496044 original size:3 final size:3
Alignment explanation
Indices: 496036--496061 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
496026 GGTTTGTTCT
496036 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
496062 TATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:502009 original size:22 final size:22
Alignment explanation
Indices: 501958--502017 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
501948 ATTAAACTAT
*
501958 TAAATATAATTAAAATATATTAA
1 TAAATA-AATTTAAATATATTAA
**
501981 TTTATAAATTTAAATAT-TATAA
1 TAAATAAATTTAAATATAT-TAA
502003 TAAAT-AATTTCAAAT
1 TAAATAAATTT-AAAT
502018 CATTTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATAAATTTAAATATATTAA
Found at i:505497 original size:2 final size:2
Alignment explanation
Indices: 505490--505547 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
505480 TATATTAACC
**
505490 TA TA TA TA CC 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 TA TA TA
505532 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
505548 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:506668 original size:67 final size:67
Alignment explanation
Indices: 506588--506742 Score: 229
Period size: 67 Copynumber: 2.3 Consensus size: 67
506578 GCCTTATTAC
* * *
506588 CTAGTATGTTAGGCTGGTTGCTGAGCTCTGATTTGGTGTTTGAACTGAGTCTGGTTCACTCTTTT
1 CTAGTATGTTAGGCTGGTTGCTGAGCTCTGATTTAGTGTTTAAACTGAGTCTCGTTCACTCTTTT
*
506653 AG
66 AA
* * *
506655 CTAGTATGTTAGGCTAGTTGTTGAGCTCTGATTTAGTGTTTAAATTGAGTCTCGTTCACTCTTTT
1 CTAGTATGTTAGGCTGGTTGCTGAGCTCTGATTTAGTGTTTAAACTGAGTCTCGTTCACTCTTTT
506720 AA
66 AA
* *
506722 CTAATATGTTAGGCTGATTGC
1 CTAGTATGTTAGGCTGGTTGC
506743 ACGGTGTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.43
Consensus pattern (67 bp):
CTAGTATGTTAGGCTGGTTGCTGAGCTCTGATTTAGTGTTTAAACTGAGTCTCGTTCACTCTTTT
AA
Found at i:507751 original size:17 final size:18
Alignment explanation
Indices: 507729--507775 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
507719 TGAGTACTAT
507729 TATATATTTAATGT-AAA
1 TATATATTTAATGTAAAA
507746 TATATATTTAATGTAAAA
1 TATATATTTAATGTAAAA
*
507764 TATAAATTTAAT
1 TATATATTTAAT
507776 AGATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATATTTAATGTAAAA
Found at i:507973 original size:15 final size:16
Alignment explanation
Indices: 507943--507979 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
507933 ACTTCTCGAA
507943 AAAATAATTCATTTTTC
1 AAAA-AATTCATTTTTC
507960 AAAAAATT-ATTTTTC
1 AAAAAATTCATTTTTC
507975 AAAAA
1 AAAAA
507980 CTATTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.60
16 4 0.20
17 4 0.20
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATTCATTTTTC
Found at i:507984 original size:14 final size:15
Alignment explanation
Indices: 507953--507986 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
507943 AAAATAATTC
*
507953 ATTTTTCAAAAAATT
1 ATTTTTCAAAAAACT
507968 ATTTTTC-AAAAACT
1 ATTTTTCAAAAAACT
507982 ATTTT
1 ATTTT
507987 CAATCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTCAAAAAACT
Found at i:515729 original size:16 final size:16
Alignment explanation
Indices: 515682--515732 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
515672 GAAATTATGA
* *
515682 TTTCCATCTTTCTATT
1 TTTCCATCTTTCCAAT
* *
515698 TTTCTACCCTTT-CAAT
1 TTTCCA-TCTTTCCAAT
515714 TTTCCATCTTTCCAAT
1 TTTCCATCTTTCCAAT
515730 TTT
1 TTT
515733 TCTTTACTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 4 0.15
16 19 0.70
17 4 0.15
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTCCATCTTTCCAAT
Found at i:519538 original size:19 final size:19
Alignment explanation
Indices: 519516--519558 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
519506 TATAAGTTTA
519516 AAAATAAAAAT-AAAAACAT
1 AAAATAAAAATAAAAAAC-T
*
519535 AAAAT-TAAATAAAAAACT
1 AAAATAAAAATAAAAAACT
519553 AAAATA
1 AAAATA
519559 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATAAAAATAAAAAACT
Found at i:520843 original size:21 final size:20
Alignment explanation
Indices: 520819--520858 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
520809 TCATACTATT
520819 ATGTCTTTGGGTGTTTTTATA
1 ATGTCTTT-GGTGTTTTTATA
* *
520840 ATGTGTTTGGTTTTTTTAT
1 ATGTCTTTGGTGTTTTTAT
520859 TTGCATAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.03, G:0.23, T:0.62
Consensus pattern (20 bp):
ATGTCTTTGGTGTTTTTATA
Found at i:524580 original size:14 final size:13
Alignment explanation
Indices: 524555--524602 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
524545 TTTATTTATT
*
524555 TTATTCTTATTTC
1 TTATTTTTATTTC
*
524568 TTAGTTTTTATTTT
1 TTA-TTTTTATTTC
524582 TTATTTTTATTT-
1 TTATTTTTATTTC
*
524594 TTAATTTTA
1 TTATTTTTA
524603 ACAATTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 8 0.26
13 12 0.39
14 11 0.35
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (13 bp):
TTATTTTTATTTC
Found at i:524588 original size:5 final size:6
Alignment explanation
Indices: 524549--524602 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
524539 ATTTCATTTA
* *
524549 TTTA-T TTTATT CTTATT TCTTAGTT TTTATTT TTTATT TTTATT TTTAAT
1 TTTATT TTTATT TTTATT T-TTA-TT TTTA-TT TTTATT TTTATT TTTATT
524599 TTTA
1 TTTA
524603 ACAATTAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.10
6 23 0.55
7 12 0.29
8 3 0.07
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:542050 original size:35 final size:35
Alignment explanation
Indices: 541978--542074 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 35
541968 AATAATAGAA
* *
541978 AAAATAGCAACAAAAAATAACAATAAAAACAACACC
1 AAAATAGTAA-AAAAAATAACAACAAAAACAACACC
*
542014 AAAATAGTAAAAAAAATAAC-ACAAAACCAACAACC
1 AAAATAGTAAAAAAAATAACAACAAAAACAAC-ACC
* * *
542049 AAAATAAT-AAAAACACAACAACAAAA
1 AAAATAGTAAAAAAAATAACAACAAAA
542075 CAGCAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 18 0.34
35 26 0.49
36 9 0.17
ACGTcount: A:0.71, C:0.19, G:0.02, T:0.08
Consensus pattern (35 bp):
AAAATAGTAAAAAAAATAACAACAAAAACAACACC
Found at i:542052 original size:23 final size:22
Alignment explanation
Indices: 542026--542083 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
542016 AATAGTAAAA
542026 AAAATAACACAAAAC-CAACAACC
1 AAAATAACA-AAAACACAACAA-C
*
542049 AAAATAATAAAAACACAACAAC
1 AAAATAACAAAAACACAACAAC
* *
542071 AAAACAGCAAAAA
1 AAAATAACAAAAA
542084 ATAGCAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.71, C:0.22, G:0.02, T:0.05
Consensus pattern (22 bp):
AAAATAACAAAAACACAACAAC
Found at i:542082 original size:22 final size:22
Alignment explanation
Indices: 542036--542101 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
542026 AAAATAACAC
* * **
542036 AAAACCAACAACCAAAATAATA
1 AAAAACAACAACCAAAACAGCA
542058 AAAACACAACAA-CAAAACAGCA
1 AAAA-ACAACAACCAAAACAGCA
* *
542080 AAAAATAGCAACCAAAACAGCA
1 AAAAACAACAACCAAAACAGCA
542102 TCAAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 5 0.14
22 25 0.69
23 6 0.17
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.05
Consensus pattern (22 bp):
AAAAACAACAACCAAAACAGCA
Found at i:546399 original size:10 final size:10
Alignment explanation
Indices: 546384--546415 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
546374 AGATCAGCCT
546384 AATATTTGGA
1 AATATTTGGA
546394 AATATTTGGA
1 AATATTTGGA
*
546404 AAGATTTGGA
1 AATATTTGGA
546414 AA
1 AA
546416 AAATATTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (10 bp):
AATATTTGGA
Found at i:548659 original size:30 final size:31
Alignment explanation
Indices: 548625--548685 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
548615 ATAATTTTTT
*
548625 AATATTTTAATG-ATTTTT-AAATTTAAAAAA
1 AATATTTT-ATGAATTTTTAAAAATTAAAAAA
*
548655 AATATTTTTTGAATTTTTAAAAATTAAAAAA
1 AATATTTTATGAATTTTTAAAAATTAAAAAA
548686 TAATTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 14 0.52
31 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
AATATTTTATGAATTTTTAAAAATTAAAAAA
Found at i:558439 original size:17 final size:18
Alignment explanation
Indices: 558402--558444 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
558392 ACATTAAAAA
*
558402 AAAACTTAAAAACATAATT
1 AAAATTTAAAAACA-AATT
558421 AAAATTTAAAAAC-AATT
1 AAAATTTAAAAACAAATT
558438 AAAATTT
1 AAAATTT
558445 TTTTGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.48
19 12 0.52
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTTAAAAACAAATT
Found at i:562765 original size:10 final size:10
Alignment explanation
Indices: 562750--562775 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
562740 CACGGGGAGA
562750 GAGAGAGAGG
1 GAGAGAGAGG
562760 GAGAGAGAGG
1 GAGAGAGAGG
562770 GAGAGA
1 GAGAGA
562776 AAGAGACGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Done.