Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold290
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: 778129
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29
Warning! 94969 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:271104 original size:60 final size:60
Alignment explanation
Indices: 271005--271126 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
270995 CTTCGGCTTC
* * *
271005 GGCTTCGGCTATCATACTATGAAAAGGGATGGCTTCGACTATC-AATCTATGAAAAGAGAT
1 GGCTTCGGCTATCAAACTATGAAAAGGGATGGCTACGACTATCGAA-CAATGAAAAGAGAT
* *
271065 GGCTTCGGCTATCAAATTATGAAAAGGGATGG-TGACGACTATCGAACAATGAAAAGGGAT
1 GGCTTCGGCTATCAAACTATGAAAAGGGATGGCT-ACGACTATCGAACAATGAAAAGAGAT
271125 GG
1 GG
271127 TAATGACCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.02
60 52 0.95
61 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (60 bp):
GGCTTCGGCTATCAAACTATGAAAAGGGATGGCTACGACTATCGAACAATGAAAAGAGAT
Found at i:271127 original size:30 final size:30
Alignment explanation
Indices: 271013--271154 Score: 117
Period size: 30 Copynumber: 4.7 Consensus size: 30
271003 TCGGCTTCGG
* * *
271013 CTATCATACTATGAAAAGGGATGGCTTCGA
1 CTATCAAACAATGAAAAGGGATGGCTACGA
* * * * *
271043 CTATCAATCTATGAAAAGAGATGGCTTCGG
1 CTATCAAACAATGAAAAGGGATGGCTACGA
**
271073 CTATCAAATTATGAAAAGGGATGG-TGACGA
1 CTATCAAACAATGAAAAGGGATGGCT-ACGA
* *
271103 CTATCGAACAATGAAAAGGGATGG-TAATGA
1 CTATCAAACAATGAAAAGGGATGGCT-ACGA
* *
271133 CCATCAAATAATGAAAAAGGGA
1 CTATCAAACAATG-AAAAGGGA
271155 GAGCTTCGGC
Statistics
Matches: 93, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
29 1 0.01
30 84 0.90
31 8 0.09
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (30 bp):
CTATCAAACAATGAAAAGGGATGGCTACGA
Found at i:271211 original size:30 final size:31
Alignment explanation
Indices: 271006--271212 Score: 84
Period size: 30 Copynumber: 6.9 Consensus size: 31
270996 TTCGGCTTCG
* *
271006 GCTTCGGCTATCATACTATG-AAAAGGGATG-
1 GCTTCGGCTATCAAATTATGAAAAAGGGA-GA
* *
271036 GCTTCGACTATC-AATCTATG-AAAAGAGATG-
1 GCTTCGGCTATCAAAT-TATGAAAAAGGGA-GA
271066 GCTTCGGCTATCAAATTATG-AAAAGGGATG-
1 GCTTCGGCTATCAAATTATGAAAAAGGGA-GA
* * * **
271096 G-TGACGACTATCGAACAATG-AAAAGGGATG-
1 GCT-TCGGCTATCAAATTATGAAAAAGGGA-GA
* * *
271126 G-TAAT-GACCATCAAATAATGAAAAAGGGAGA
1 GCT--TCGGCTATCAAATTATGAAAAAGGGAGA
* * *
271157 GCTTCGGCTGTCGAATTAT-TAAAAGGGTA-A
1 GCTTCGGCTATCAAATTATGAAAAAGGG-AGA
*
271187 -CTTCGGTTATCAAATTATGAAAAAGG
1 GCTTCGGCTATCAAATTATGAAAAAGG
271213 ATCTGTCAAC
Statistics
Matches: 141, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
29 17 0.12
30 101 0.72
31 22 0.16
32 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
GCTTCGGCTATCAAATTATGAAAAAGGGAGA
Found at i:271483 original size:52 final size:52
Alignment explanation
Indices: 271405--271510 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
271395 TTATATATTA
271405 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
1 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
271457 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
1 TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
271509 TA
1 TA
271511 CTTTGTGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (52 bp):
TATTGGCAAGGTTAGACTGTATGTGTTACGAACTTACTAAGCATGAAATGCT
Found at i:272482 original size:31 final size:30
Alignment explanation
Indices: 272447--272506 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
272437 GGAGGTGGGA
*
272447 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAACTTTTAGGGGAAAAG
* * *
272478 TGGGAGGGAGTAAAACTTTTGGGGGAAAA
1 TGGGAGAGAATAAAACTTTTAGGGGAAAA
272507 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAACTTTTAGGGGAAAAG
Found at i:272735 original size:9 final size:9
Alignment explanation
Indices: 272721--272757 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
272711 TATAGTTTGA
272721 TATTCGAAT
1 TATTCGAAT
272730 TATTCGAAT
1 TATTCGAAT
*
272739 TATTCGAGT
1 TATTCGAAT
272748 TATTCGAAT
1 TATTCGAAT
272757 T
1 T
272758 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:272827 original size:9 final size:9
Alignment explanation
Indices: 272810--272840 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
272800 TCGAGTTGAT
272810 TCGAATAAC
1 TCGAATAAC
*
272819 TCGATTAAC
1 TCGAATAAC
272828 TCGAATAAC
1 TCGAATAAC
272837 TCGA
1 TCGA
272841 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:273560 original size:53 final size:53
Alignment explanation
Indices: 273495--273605 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 53
273485 TGACTTGGTT
* * *
273495 GTGTAACCAAGTCAAAGAGTTACACGGGCATGGACATGGGCTAGGACATGACC
1 GTGTGACCAAGTCAAAGAGTTACACGGGCACGGACATGGGCTAGGACACGACC
* * * *
273548 GTGTGACCAAGTCAGAGAGTTACGCGGGCACGGACATGGGTTAGGACACGGCC
1 GTGTGACCAAGTCAAAGAGTTACACGGGCACGGACATGGGCTAGGACACGACC
273601 GTGTG
1 GTGTG
273606 TCCTCATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.35, T:0.17
Consensus pattern (53 bp):
GTGTGACCAAGTCAAAGAGTTACACGGGCACGGACATGGGCTAGGACACGACC
Found at i:280206 original size:45 final size:45
Alignment explanation
Indices: 280014--280613 Score: 301
Period size: 44 Copynumber: 13.3 Consensus size: 45
280004 CATAGCAAAC
* * * * *
280014 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGTTA-CTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * * * *
280058 CTTATCTCCCTGATGTTGTAGTTGAGCAGACTGAAGATAGCGAA-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CCAATT
* * **
280103 CTTATTTCCCTGAAGTTGCAGCGGAATAGATTGAAGCTA-CAAGTT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAA-TT
* * * *
280148 GCAAACCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGTTACCAATT
1 ------CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * * * *
280199 CTTATCTCCTTAAAGTTGCAGCGGAGTAGATCGAAGCTACAAATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * * * * * *
280244 -TCT-TCTCCCTAAAATTACATTAGAGCAGATTGAAACCA-CAATC
1 CT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* **
280287 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * ** * ** *
280332 CTTATCTCCTTAAAGTTGCAGAAGAGTAGATCAAAGCTA-CAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * * * * *
280376 CTCT-TCTCCTTGAAATTACATTGGAGCAGATCGAAGCCA-CAATC
1 CT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * ** **
280420 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGA-TAAAAATACACAAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAGCTAC-CAATT
* * * * *
280466 CTTATCTCCCTGAAGTTACAGTGGAGAAGGTTAAAGTTACCAATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * ** *
280511 CTTATCTCCTTGAAGTTGCAGCGGAGTAGATCAAAGCTA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
* * * * ** *
280555 CTCT-TCTCCCAGAAGTTACATTGGAGCGGATCAAAAC-ACCAATT
1 CT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
280599 CTTATAC-CCCTGAAG
1 CTTAT-CTCCCTGAAG
280614 ATGCGGTGAA
Statistics
Matches: 418, Mismatches: 113, Indels: 50
0.72 0.19 0.09
Matches are distributed among these distances:
43 9 0.02
44 190 0.45
45 144 0.34
46 37 0.09
51 35 0.08
52 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAATT
Found at i:280314 original size:44 final size:44
Alignment explanation
Indices: 280153--280541 Score: 198
Period size: 45 Copynumber: 8.7 Consensus size: 44
280143 AAGTTGCAAA
* * * **
280153 CCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGTTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTA-CAAT
* * * * * * *
280198 TCTTATCTCCTTAAAGTTGCAGCGGAGTAGATCGAAGCTACAAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTAC-AAT
* * * * * * *
280243 --TTCTTCTCCCTAAAATTACATTAGAGCAGATTGAAACCACAAT
1 CCTT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAT
* *
280286 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTA-CAAT
* * * ** * *
280331 TCTTATCTCCTTAAAGTTGCAGAAGAGTAGA-TCAAAGCTACAAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CTAC-AAT
* * * * * * *
280376 -CTCT-TCTCCTTGAAATTACATTGGAGCAGATCGAAGCCACAAT
1 CCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAT
* * * *
280419 CCTTATCTCCCTAAAGTTGCAGTGGAGCAGGA-TAAAAATACACAAG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAACT--ACAAT
* * * *
280465 CCTTATCTCCCTGAAGTTACAGTGGAGAAGGTT-AAAGTTACCAAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-CTA-CAAT
* * * *
280510 TCTTATCTCCTTGAAGTTGCAGCGGAGTAGAT
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
280542 CAAAGCTACA
Statistics
Matches: 256, Mismatches: 71, Indels: 34
0.71 0.20 0.09
Matches are distributed among these distances:
43 9 0.04
44 107 0.42
45 108 0.42
46 32 0.12
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACTACAAT
Found at i:280319 original size:133 final size:133
Alignment explanation
Indices: 280153--280449 Score: 477
Period size: 133 Copynumber: 2.2 Consensus size: 133
280143 AAGTTGCAAA
* * *
280153 CCTTATCTCCCTGAAGTTACAGTGGAGTAGGTTGAAGTTACCAATTCTTATCTCCTTAAAGTTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
** * * *
280218 AGCGGAGTAGATCGAAGCTACAAATTTCTTCTCCCTAAAATTACATTAGAGCAGATTGAAACCAC
66 AGAAGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATTACATTAGAGCAGATCGAAACCAC
280283 AAT
131 AAT
280286 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
* * * *
280351 AGAAGAGTAGATCAAAGCTACAAATCTCTTCTCCTTGAAATTACATTGGAGCAGATCGAAGCCAC
66 AGAAGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATTACATTAGAGCAGATCGAAACCAC
280416 AAT
131 AAT
*
280419 CCTTATCTCCCTAAAGTTGCAGTGGAGCAGG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGG
280450 ATAAAAATAC
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 151 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (133 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTAAAGTTGC
AGAAGAGTAGATCAAAGCTACAAATCTCTTCTCCCTAAAATTACATTAGAGCAGATCGAAACCAC
AAT
Found at i:281253 original size:22 final size:22
Alignment explanation
Indices: 281225--281267 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
281215 GAAGAAAAGT
281225 CGAATCTTACCGCTTCTTTTTG
1 CGAATCTTACCGCTTCTTTTTG
*
281247 CGAATCTTACCGCTTTTTTTT
1 CGAATCTTACCGCTTCTTTTT
281268 ACTTTTGCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.12, T:0.49
Consensus pattern (22 bp):
CGAATCTTACCGCTTCTTTTTG
Found at i:284474 original size:22 final size:21
Alignment explanation
Indices: 284423--284475 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
284413 GTTTGATGTG
*
284423 AAAAAAAATATATGGTTTGTT
1 AAAAAAAATATATGGTTTATT
* * *
284444 AAATTAAAATGTTTGGCTTTATT
1 AAA-AAAAATATATGG-TTTATT
284467 AAAAAAAAT
1 AAAAAAAAT
284476 TAAATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (21 bp):
AAAAAAAATATATGGTTTATT
Found at i:289153 original size:18 final size:18
Alignment explanation
Indices: 289110--289157 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
289100 TTTATTTAAG
*
289110 ATTATCATTATTAATTAC
1 ATTATTATTATTAATTAC
* *
289128 ATTGTTATTATT-ATTGAT
1 ATTATTATTATTAATT-AC
289146 ATTATTATTATT
1 ATTATTATTATT
289158 TATTTCAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTATTATTATTAATTAC
Found at i:291516 original size:15 final size:15
Alignment explanation
Indices: 291496--291528 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
291486 ATCCCTATAT
291496 AATGCTTAAATTTGA
1 AATGCTTAAATTTGA
291511 AATGCTTAAATTTGA
1 AATGCTTAAATTTGA
291526 AAT
1 AAT
291529 TTAATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (15 bp):
AATGCTTAAATTTGA
Found at i:302875 original size:34 final size:34
Alignment explanation
Indices: 302793--302887 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 34
302783 CAGAATAAAT
* * *
302793 CATTTGGTATGCTGAATGGATTTGCTCTTACGAG
1 CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
*
302827 CATTTGGTGTGCTGGATGGATTGGCTCTTGCGAG
1 CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
* *
302861 CATTTGGTGTGCTGGTTGGAATGGCTC
1 CATTTGGTGTGCTGGATGGATTGGCTC
302888 ACTTGAGCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.37
Consensus pattern (34 bp):
CATTTGGTGTGCTGGATGGATTGGCTCTTACGAG
Found at i:302896 original size:34 final size:33
Alignment explanation
Indices: 302793--302913 Score: 118
Period size: 34 Copynumber: 3.6 Consensus size: 33
302783 CAGAATAAAT
* * * *
302793 CATTTGGTATGCTGAATGGATTTGCTCTTACGAG
1 CATTTGGTGTGCTGGATGGAATGGCTCTT-CGAG
*
302827 CATTTGGTGTGCTGGATGGATTGGCTCTTGCGAG
1 CATTTGGTGTGCTGGATGGAATGGCTCTT-CGAG
*
302861 CATTTGGTGTGCTGGTTGGAATGGCTCACTT-GAG
1 CATTTGGTGTGCTGGATGGAATGGCT--CTTCGAG
* * *
302895 CATATAGTGTACTGGATGG
1 CATTTGGTGTGCTGGATGG
302914 TTAAATGACA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
34 72 0.96
36 3 0.04
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (33 bp):
CATTTGGTGTGCTGGATGGAATGGCTCTTCGAG
Found at i:304552 original size:47 final size:47
Alignment explanation
Indices: 304483--304577 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
304473 ACAACCATCC
* *
304483 ATTTTACAACAAACTCGAATATGTTCGAACTCGTTAGCCCGAAGCTT
1 ATTTTACAACAAACCCAAATATGTTCGAACTCGTTAGCCCGAAGCTT
*
304530 ATTTTACAACGAACCCAAATATGTTCGAACTCGTTAGCCCGAAGCTT
1 ATTTTACAACAAACCCAAATATGTTCGAACTCGTTAGCCCGAAGCTT
304577 A
1 A
304578 GTTTCACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (47 bp):
ATTTTACAACAAACCCAAATATGTTCGAACTCGTTAGCCCGAAGCTT
Found at i:306422 original size:230 final size:230
Alignment explanation
Indices: 306019--306478 Score: 902
Period size: 230 Copynumber: 2.0 Consensus size: 230
306009 GATTAGCCAA
306019 TACACCCCTAATCCGTGGGCCCCACTTAAGCCCCTCTTAAGCAGGTGTTTGGTTCAATGTATTGC
1 TACACCCCTAATCCGTGGGCCCCACTTAAGCCCCTCTTAAGCAGGTGTTTGGTTCAATGTATTGC
306084 CTAATACACCCCTAATACGTTACGCCCCTAATCCCCGAAATTCTCTATTTTCTAATCCCTGCCTT
66 CTAATACACCCCTAATACGTTACGCCCCTAATCCCCGAAATTCTCTATTTTCTAATCCCTGCCTT
306149 CTCCTCAGTTTACATCCGTTTTAGTTTTCACGCCCTAATTTGCCCTCTGTCCCCTAACTCTCCTT
131 CTCCTCAGTTTACATCCGTTTTAGTTTTCACGCCCTAATTTGCCCTCTGTCCCCTAACTCTCCTT
306214 TATCTCCTTCATTGCTTGCTTCGCCTTCGGCCAGT
196 TATCTCCTTCATTGCTTGCTTCGCCTTCGGCCAGT
306249 TACACCCCTAATCCGTGGGCCCCACTTAAGCCCCTCTTAAGCAGGTGTTTGGTTCAATGTATTGC
1 TACACCCCTAATCCGTGGGCCCCACTTAAGCCCCTCTTAAGCAGGTGTTTGGTTCAATGTATTGC
306314 CTAATACACCCCTAATACGTTACGCCCCTAATCCCCGAAATTCTCTATTTTCTAATCCCTGCCTT
66 CTAATACACCCCTAATACGTTACGCCCCTAATCCCCGAAATTCTCTATTTTCTAATCCCTGCCTT
* *
306379 CTCCTCAGTTTTCCTCCGTTTTAGTTTTCACGCCCTAATTTGCCCTCTGTCCCCTAACTCTCCTT
131 CTCCTCAGTTTACATCCGTTTTAGTTTTCACGCCCTAATTTGCCCTCTGTCCCCTAACTCTCCTT
306444 TATCTCCTTCATTGCTTGCTTCGCCTTCGGCCAGT
196 TATCTCCTTCATTGCTTGCTTCGCCTTCGGCCAGT
306479 AGCCCCAAAT
Statistics
Matches: 228, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
230 228 1.00
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.35
Consensus pattern (230 bp):
TACACCCCTAATCCGTGGGCCCCACTTAAGCCCCTCTTAAGCAGGTGTTTGGTTCAATGTATTGC
CTAATACACCCCTAATACGTTACGCCCCTAATCCCCGAAATTCTCTATTTTCTAATCCCTGCCTT
CTCCTCAGTTTACATCCGTTTTAGTTTTCACGCCCTAATTTGCCCTCTGTCCCCTAACTCTCCTT
TATCTCCTTCATTGCTTGCTTCGCCTTCGGCCAGT
Found at i:309206 original size:229 final size:227
Alignment explanation
Indices: 308799--309310 Score: 963
Period size: 229 Copynumber: 2.3 Consensus size: 227
308789 CCTGAAGAAC
* *
308799 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
308863 AAAATACCTTAACCAAAACGCAGCGTTGGTTCAATGTATATTAGAATTCATGGCGTTTTTTATAA
66 AAAATACCTTAACCAAAACGCAGCGTTGGTTCAATGTATATTAGAATTCATGGCGTTTTTTATAA
308928 AAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAA
131 AAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAA
308993 ACGCACCGTTTTATCTTGAGGTAGATTAATAT
196 ACGCACCGTTTTATCTTGAGGTAGATTAATAT
*
309025 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
*
309090 AAAATACCTTAACCAAAACGCAGCGTTGGTTCAATTGTATATTAGAATTCGTGGCGTTTTTTATA
66 AAAATACCTTAACCAAAACGCAGCGTTGGTTCAA-TGTATATTAGAATTCATGGCGTTTTTTAT-
309155 AAAAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGA
129 AAAAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGA
309220 AAACGCACCGTTTTATCTTGAGGTAGATTAATAT
194 AAACGCACCGTTTTATCTTGAGGTAGATTAATAT
309254 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGA
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGA
309311 NNNNNNNNNN
Statistics
Matches: 279, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
226 50 0.18
227 45 0.16
228 28 0.10
229 156 0.56
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (227 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGAAGCGCCGC
AAAATACCTTAACCAAAACGCAGCGTTGGTTCAATGTATATTAGAATTCATGGCGTTTTTTATAA
AAAACGCCGCGAAAGAATAGTATTAGCGGCGTTTAACAAAAAGCGCCGCAAATATCTTAAGGAAA
ACGCACCGTTTTATCTTGAGGTAGATTAATAT
Found at i:309260 original size:116 final size:113
Alignment explanation
Indices: 308799--309304 Score: 453
Period size: 113 Copynumber: 4.5 Consensus size: 113
308789 CCTGAAGAAC
* * * ****
308799 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTT-ATTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATAATTAGCGGCGTTTAACAAAAAGCGCCGC
* ** * * * * *
308863 AAAATACCTTAACCAAAACGCAGCGTTGGT-TC--AATGTATATTAGA-AT
66 -AAATATCTTAAGGAAAACGCACCGTT-TTATCTTGAGGTAGATTA-ATAT
* *
308910 TCA-TGGCGTTTTTTATAAAAAACGCCGCGAAAGAATAGT-ATTAGCGGCGTTTAACAAAAAGCG
1 T-AGTGGCG-TTTTTA-AAAAAACGCCGCAAAAGAACA-TAATTAGCGGCGTTTAACAAAAAGCG
308973 CCGCAAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
62 CCGCAAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
* * ***** *
309025 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTTGGATGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATAATTAGCGGCGTTTAACAAAAAGCGCCGC
* ** * * *
309090 AAAATACCTTAACCAAAACGCAGCGTTGGTTCA-ATT---GTATATTAGA-AT
66 -AAATATCTTAAGGAAAACGCACCGTT--TT-ATCTTGAGGTAGATTA-ATAT
* * *
309138 TCGTGGCGTTTTTTATAAAAAAACGCCGCGAAAGAATAGT-ATTAGCGGCGTTTAACAAAAAGCG
1 TAGTGGCG--TTTT-TAAAAAAACGCCGCAAAAGAACA-TAATTAGCGGCGTTTAACAAAAAGCG
309202 CCGCAAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
62 CCGCAAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
* *
309254 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTA
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATAATTAGCGGCGTTTA
309305 TTTGGANNNN
Statistics
Matches: 314, Mismatches: 55, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
111 6 0.02
112 10 0.03
113 146 0.46
114 46 0.15
115 43 0.14
116 61 0.19
117 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (113 bp):
TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATAATTAGCGGCGTTTAACAAAAAGCGCCGC
AAATATCTTAAGGAAAACGCACCGTTTTATCTTGAGGTAGATTAATAT
Found at i:309703 original size:16 final size:16
Alignment explanation
Indices: 309682--309749 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
309672 GATTTGCTAT
309682 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
309698 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
309714 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
309730 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
309746 TACA
1 TACA
309750 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:318367 original size:29 final size:29
Alignment explanation
Indices: 318324--318387 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
318314 TTGGATTTAT
* * * *
318324 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGA-TCTATTTAATAATAGAGGAACTAAA
*
318354 TTGATCTATTTAATAATAGAGGAACTAAT
1 TTGATCTATTTAATAATAGAGGAACTAAA
318383 TTGAT
1 TTGAT
318388 ACACTCCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (29 bp):
TTGATCTATTTAATAATAGAGGAACTAAA
Found at i:329476 original size:13 final size:14
Alignment explanation
Indices: 329456--329493 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
329446 ATGGGGGTAA
329456 GATTCTGTATATTT
1 GATTCTGTATATTT
*
329470 G-TTCTGTTTATTT
1 GATTCTGTATATTT
329483 GATTCTG-ATAT
1 GATTCTGTATAT
329494 GTGCATCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.58
Consensus pattern (14 bp):
GATTCTGTATATTT
Found at i:329842 original size:13 final size:13
Alignment explanation
Indices: 329824--329849 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329814 CACTTACGCA
329824 AACAAATGGTTTT
1 AACAAATGGTTTT
329837 AACAAATGGTTTT
1 AACAAATGGTTTT
329850 GGGAAACACT
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:336280 original size:97 final size:100
Alignment explanation
Indices: 336023--336371 Score: 327
Period size: 97 Copynumber: 3.5 Consensus size: 100
336013 GATGGTACCG
* * * * * * * * *
336023 TTCTTACCCTTGGCTCAAACACACTCCTTTGTAAATCAAATCAAGTGCTCATAATGGTGGATTCG
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATC-AATGAAATCCTCGTAATGGTGGATTCA
* ** *
336088 TAATGGGGTCCACCATTTGATAATGAAACCAATCGGTAATA
65 TAATGGAGTCCA-CA-TTGGCAATG-AACCAA--GGTACTA
* * * * *
336129 TTATTACCTTTGGCTC-AA-ACACCCCTTTCTGAATCAATGAAATGCTCGTTATGGTGGATTTGA
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGA-TTCA
*
336192 -AATGGAGTCCACATAT-TCAATGAA-C-A-GTACTA
65 TAATGGAGTCCACAT-TGGCAATGAACCAAGGTACTA
* *
336224 TTCTTGCCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTTGTAATGGTGGATTCAT
1 TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGATTCAT
*
336289 AATGGAGTTCACATTGGCAATGAACCGAATGGTACTA
66 AATGGAGTCCACATTGGCAATGAACC-AA-GGTACTA
* *
336326 TTCTTACCTTTGG-TCCAATCACACCCCTTTATGAATCAATGGAATC
1 TTCTTACCTTTGGCT-CAAACACACCCCTTTATGAATCAATGAAATC
336372 TGTTTTAAAC
Statistics
Matches: 204, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
95 19 0.09
96 6 0.03
97 56 0.27
98 2 0.01
99 1 0.00
100 3 0.01
101 6 0.03
102 50 0.25
103 29 0.14
104 16 0.08
105 2 0.01
106 14 0.07
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (100 bp):
TTCTTACCTTTGGCTCAAACACACCCCTTTATGAATCAATGAAATCCTCGTAATGGTGGATTCAT
AATGGAGTCCACATTGGCAATGAACCAAGGTACTA
Found at i:340959 original size:13 final size:13
Alignment explanation
Indices: 340943--340967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340933 TTTTTTTTAA
340943 TTTTTAATTAATC
1 TTTTTAATTAATC
340956 TTTTTAATTAAT
1 TTTTTAATTAAT
340968 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:344592 original size:17 final size:18
Alignment explanation
Indices: 344561--344607 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
344551 CCAATTTTTT
344561 TTTTATGCTTCTTTCTT-C
1 TTTT-TGCTTCTTTCTTGC
*
344579 TTTTTGCTTGTTTCTTGC
1 TTTTTGCTTCTTTCTTGC
*
344597 TTCTTGCTTCT
1 TTTTTGCTTCT
344608 CCTCCTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.02, C:0.21, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTTGCTTCTTTCTTGC
Found at i:346883 original size:20 final size:22
Alignment explanation
Indices: 346860--346900 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
346850 CGAAAAAAAG
346860 ATAATTT-TTTT-TAAAATAAT
1 ATAATTTATTTTATAAAATAAT
346880 ATAATTTATTTTATAAAATAA
1 ATAATTTATTTTATAAAATAA
346901 AAATACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTTATTTTATAAAATAAT
Found at i:352235 original size:3 final size:3
Alignment explanation
Indices: 352227--352269 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
352217 CGCAAGGACT
*
352227 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
352270 TGTCATCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:355431 original size:17 final size:19
Alignment explanation
Indices: 355401--355441 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
355391 ACATTTATCT
355401 CTATTTTCATTTTA-TTAAA
1 CTATTTTCA-TTTACTTAAA
355420 CTATTTTC-TTTACTTAAA
1 CTATTTTCATTTACTTAAA
355438 -TATT
1 CTATT
355442 AAAATTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (19 bp):
CTATTTTCATTTACTTAAA
Found at i:360222 original size:58 final size:58
Alignment explanation
Indices: 360153--360265 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
360143 TACTTGGATG
*
360153 CCATAACATCTTTCA-TCTATGGTCTTACACCGTATACCTCATACATTATACCATGCCA
1 CCATAACATCTTTCATTC-ATGGTCTTACACCATATACCTCATACATTATACCATGCCA
* * * * *
360211 CCATTACATCTTTCATTCATGGTCTTACGCCATATACCTTATACCTTGTACCATG
1 CCATAACATCTTTCATTCATGGTCTTACACCATATACCTCATACATTATACCATG
360266 TTGTTATGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (58 bp):
CCATAACATCTTTCATTCATGGTCTTACACCATATACCTCATACATTATACCATGCCA
Found at i:365679 original size:77 final size:77
Alignment explanation
Indices: 365551--365701 Score: 257
Period size: 77 Copynumber: 2.0 Consensus size: 77
365541 AAGTTTGTTT
* *
365551 ATGTTGTTCAGTTTTTCTACGTTTGTTGAGGCTAGCTAAATGAGAAGTATCCACTATCTTCAAAC
1 ATGTTGTTCAGTTTTTCTACGTTTGCTGAGGCTAGCTAAATGAGAAATATCCACTATCTTCAAAC
365616 ACTTACAACTTG
66 ACTTACAACTTG
* * *
365628 ATGTTGTTCAGTTTTTCTACGTTTGCTGAGGTTAGCTCAGTGAGAAATATCCACTATCTTCAAAC
1 ATGTTGTTCAGTTTTTCTACGTTTGCTGAGGCTAGCTAAATGAGAAATATCCACTATCTTCAAAC
365693 ACTTACAAC
66 ACTTACAAC
365702 AAGTGATCCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (77 bp):
ATGTTGTTCAGTTTTTCTACGTTTGCTGAGGCTAGCTAAATGAGAAATATCCACTATCTTCAAAC
ACTTACAACTTG
Found at i:368088 original size:424 final size:420
Alignment explanation
Indices: 367281--368105 Score: 1113
Period size: 424 Copynumber: 1.9 Consensus size: 420
367271 AAACATTTAC
* * *
367281 TTTTAAAATTTATTCAACAATAATCGTAAGTGGACTGATAAAAAATTTGTATATAAAATTTATTA
1 TTTTAAAATTTATTCAACAATAACCATAAGTGGACTGATAAAAAACTTGTATATAAAATTTATTA
* * *
367346 AACATGTTTTGAATACGTGGTGATTAATTTTTTATTTAAAAATTATATAAAAGTATAAAAAGATA
66 AACATGTTTTCAATACGAGGTGATTAATTTTTTATTTAAAAATTATATAAAAATATAAAAAGATA
*
367411 AAAGTACTATAATAATATTAGTTAACATTATTGAGTTGGTACCTATTATATTGCTTTAGTTGAAA
131 AAAGTACTATAATAATATTAGTTAACATTATTGAGTTGGTACCTATTATATTACTTTAGTTGAAA
* *
367476 TCATAAAGTTTATCGTAACTTTTTGGGTTTAACTCCCGTTAAGTAAAAGTATTTGTTCTAAATTT
196 TCAT-AA---TATCG--A--TTTTGGGTTCAACTCCCGATAAGTAAAAGTATTTGTTCTAAATTT
* * * * *
367541 TATGTAAAAAAGGTGAAATTACCCTCAAAATAATATCTATTGCTTTGTATAAGTAAGAGACTTTT
253 TATATAAAAAAGATGAAATTACCCTCAAAATAATATCTATTACTTTGTAAAAATAAGAGACTTTT
* * * * * *
367606 GGTAACTTTATAACTGAGTTAGAACTTGATTATGAATGTCATCAACTCAATCAAAATTTTAACTA
318 GGTAACTTTATAACTAAGTTAGAACTCGATTATGAATGACACCAAATCAATCAAAATTTTAAATA
*
367671 TACATTAGATTATGTCACTGGGTAGAAAAAAAATTTCT
383 TACATAAGATTATGTCACTGGGTAGAAAAAAAATTTCT
* * * * *
367709 TTTTAAAATTTATTCAACAATAACCATAGGTGGAGTGGTAAAAAGCTTGTATATACAATTTATTA
1 TTTTAAAATTTATTCAACAATAACCATAAGTGGACTGATAAAAAACTTGTATATAAAATTTATTA
* *
367774 AACATGTTTTCAATTTTTGGACACGCAGG-GTTTAATTTTTTATTTAAAGATTATATAAAAATAT
66 AACATGTTTTCAA----T----ACG-AGGTGATTAATTTTTTATTTAAAAATTATATAAAAATAT
**
367838 AAAAAGATAAAAGTACTATAATAATATTAGTTAACATTATTGAGTTGGTAGTTATTATATTACTT
122 AAAAAGATAAAAGTACTATAATAATATTAGTTAACATTATTGAGTTGGTACCTATTATATTACTT
*
367903 TAGTTGAAATCAT-A-AT-G-TTTTGGGTTCAACTCCCGATAGGTAAAAGTATTTGTTCTAAATT
187 TAGTTGAAATCATAATATCGATTTTGGGTTCAACTCCCGATAAGTAAAAGTATTTGTTCTAAATT
*
367964 TTATATGAAAAAA-ATGAAATTACCCTCAAAATAATATCTATTACTTTGTAAAAATAAGAGATTT
252 TTATAT-AAAAAAGATGAAATTACCCTCAAAATAATATCTATTACTTTGTAAAAATAAGAGACTT
* ** *
368028 TTTGTAACTTTATAACTAAGTTAGAACTCGATTATGGTTGACACCAAATCAATTAAAATTTTAAA
316 TTGGTAACTTTATAACTAAGTTAGAACTCGATTATGAATGACACCAAATCAATCAAAATTTTAAA
*
368093 TATATATAAGATT
381 TATACATAAGATT
368106 TTATCAACTA
Statistics
Matches: 350, Mismatches: 37, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
424 158 0.45
425 6 0.02
428 69 0.20
429 1 0.00
430 2 0.01
432 1 0.00
434 1 0.00
436 110 0.31
437 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (420 bp):
TTTTAAAATTTATTCAACAATAACCATAAGTGGACTGATAAAAAACTTGTATATAAAATTTATTA
AACATGTTTTCAATACGAGGTGATTAATTTTTTATTTAAAAATTATATAAAAATATAAAAAGATA
AAAGTACTATAATAATATTAGTTAACATTATTGAGTTGGTACCTATTATATTACTTTAGTTGAAA
TCATAATATCGATTTTGGGTTCAACTCCCGATAAGTAAAAGTATTTGTTCTAAATTTTATATAAA
AAAGATGAAATTACCCTCAAAATAATATCTATTACTTTGTAAAAATAAGAGACTTTTGGTAACTT
TATAACTAAGTTAGAACTCGATTATGAATGACACCAAATCAATCAAAATTTTAAATATACATAAG
ATTATGTCACTGGGTAGAAAAAAAATTTCT
Found at i:369337 original size:3 final size:3
Alignment explanation
Indices: 369331--369356 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
369321 ACGGTGGTGA
369331 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
369357 ATGGTGCCGT
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:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:376314 original size:21 final size:21
Alignment explanation
Indices: 376268--376377 Score: 138
Period size: 21 Copynumber: 5.3 Consensus size: 21
376258 ATGTTTTACT
*
376268 TTCTGTTAAACTCTTAT-GAG-
1 TTCTGTTAAGCTCTT-TCGAGC
*
376288 TCTCTGTTAAGCTCTTTCAAGC
1 T-TCTGTTAAGCTCTTTCGAGC
376310 TTCTGTTAAGCTCTTTCGAGC
1 TTCTGTTAAGCTCTTTCGAGC
* *
376331 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTAAGCTCTTTCGAGC
376352 TTCTGTTAAG--CTTTCGAGC
1 TTCTGTTAAGCTCTTTCGAGC
376371 TTCTGTT
1 TTCTGTT
376378 GGCGTATTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.19
20 2 0.03
21 62 0.77
22 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCTGTTAAGCTCTTTCGAGC
Found at i:381966 original size:21 final size:21
Alignment explanation
Indices: 381942--381986 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
381932 TAATTTAGCC
*
381942 ATTTTTTATTTTAATT-TTAAT
1 ATTTTTTAATTTAATTATT-AT
381963 ATTTTTTAATTTAATTATTAT
1 ATTTTTTAATTTAATTATTAT
381984 ATT
1 ATT
381987 CTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTTAATTTAATTATTAT
Found at i:405352 original size:13 final size:13
Alignment explanation
Indices: 405334--405359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
405324 ACTTTACGCA
405334 AACAAATGGTTTT
1 AACAAATGGTTTT
405347 AACAAATGGTTTT
1 AACAAATGGTTTT
405360 TGGAAACACC
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:407194 original size:12 final size:12
Alignment explanation
Indices: 407177--407201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407167 GGTGTGCATT
407177 CGGTTAACCGAC
1 CGGTTAACCGAC
407189 CGGTTAACCGAC
1 CGGTTAACCGAC
407201 C
1 C
407202 CGAATTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:407335 original size:9 final size:9
Alignment explanation
Indices: 407321--407413 Score: 132
Period size: 9 Copynumber: 10.3 Consensus size: 9
407311 TGGTTAAAAA
407321 TTAACCGAT
1 TTAACCGAT
*
407330 TTAACCGAC
1 TTAACCGAT
407339 TTAACCGAT
1 TTAACCGAT
*
407348 TTAACTGAT
1 TTAACCGAT
*
407357 TTAACCGAC
1 TTAACCGAT
*
407366 TTAACCAAT
1 TTAACCGAT
407375 TTAACCGAT
1 TTAACCGAT
*
407384 TTAACCGAC
1 TTAACCGAT
*
407393 TTAACCGAC
1 TTAACCGAT
407402 TTAACCGAT
1 TTAACCGAT
407411 TTA
1 TTA
407414 GTTCAACTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (9 bp):
TTAACCGAT
Found at i:407351 original size:27 final size:27
Alignment explanation
Indices: 407321--407413 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
407311 TGGTTAAAAA
407321 TTAACCGATTTAACCGACTTAACCGAT
1 TTAACCGATTTAACCGACTTAACCGAT
* *
407348 TTAACTGATTTAACCGACTTAACCAAT
1 TTAACCGATTTAACCGACTTAACCGAT
*
407375 TTAACCGATTTAACCGACTTAACCGAC
1 TTAACCGATTTAACCGACTTAACCGAT
407402 TTAACCGATTTA
1 TTAACCGATTTA
407414 GTTCAACTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (27 bp):
TTAACCGATTTAACCGACTTAACCGAT
Found at i:413567 original size:24 final size:23
Alignment explanation
Indices: 413535--413610 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 23
413525 AAACAAATAT
413535 AGATGCAATTTCATATACAGAATC
1 AGATGCAATTTCA-ATACAGAATC
413559 AGATGCAATTTCAGATACA-AAGTC
1 AGATGCAATTTCA-ATACAGAA-TC
*
413583 AGATGCAATATCAACTACAGAATC
1 AGATGCAATTTCAA-TACAGAATC
413607 AGAT
1 AGAT
413611 CTTACCCTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.06
24 42 0.89
25 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (23 bp):
AGATGCAATTTCAATACAGAATC
Found at i:415893 original size:27 final size:27
Alignment explanation
Indices: 415862--415948 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
415852 ATACATATTA
415862 TGAAAATAAATACATATTGTTCTAGTC
1 TGAAAATAAATACATATTGTTCTAGTC
* * * * *
415889 TG-AAATCATATTACCT-TGGGCTT-TATTA
1 TGAAAAT-A-AATACATAT-TG-TTCTAGTC
415917 TGAAAATAAATACATATTGTTCTAGTC
1 TGAAAATAAATACATATTGTTCTAGTC
415944 TGAAA
1 TGAAA
415949 TCAAAACCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 6 0.14
27 18 0.42
28 13 0.30
29 6 0.14
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (27 bp):
TGAAAATAAATACATATTGTTCTAGTC
Found at i:422574 original size:11 final size:12
Alignment explanation
Indices: 422556--422589 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
422546 ACTCACCTAT
422556 TATAAAATATAA
1 TATAAAATATAA
422568 T-TAAAATA-AA
1 TATAAAATATAA
422578 TATAAAATATAA
1 TATAAAATATAA
422590 ATGTACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.15
11 14 0.70
12 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:424719 original size:6 final size:6
Alignment explanation
Indices: 424708--424738 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
424698 AATTAATAAT
424708 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA G
1 GGTGAA GGTGAA GGTGAA GGTGAA GGTGAA G
424739 CTTCGTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGTGAA
Found at i:425650 original size:126 final size:124
Alignment explanation
Indices: 425396--425704 Score: 340
Period size: 126 Copynumber: 2.5 Consensus size: 124
425386 GGTTGTCAAG
* * * *
425396 ACTTGAT-TTGGGATGGACGATTTTGCTTCAAGGGT-TTTCTAAGCTTGATATTGAAGAATGGGT
1 ACTTGATCTT-GGATGGAAGATTCTGCTTCAAGGGTCTTT-TAAGCTTGATCTTAAAGAATGGGT
* * *
425459 TTTATCTTCTTTGAGTTGGTGCAACTAGATCGGAAAAAGCTTTTATCCAAGGTTATTTGAG
64 TTTATCTTCTTTGAGTTGGTGCAACTAGATCGGAAAAAGCTTTTAACCAAGGGTATTTGAA
*
425520 ACTTGATCTTGGATGGAAGATTCTGCTTCAAGGGTCTTTT-AGACTTGATCCTAAAGAATGGGTT
1 ACTTGATCTTGGATGGAAGATTCTGCTTCAAGGGTCTTTTAAG-CTTGATCTTAAAGAATGGG-T
* * * * ** *
425584 TTTATCTTTTTTTATGTTGGTGTAACTAGATTGGGGAAAGCTTTTAACCAAGGGTCTTTGAA
64 TTTATCTTCTTTGA-GTTGGTGCAACTAGATCGGAAAAAGCTTTTAACCAAGGGTATTTGAA
* * * * * *
425646 ACTTG-TCCTTGGATTGATGATTC-ACTTCAAAGGCCTTTTAAGCTTGATCTTTAAGAATG
1 ACTTGAT-CTTGGATGGAAGATTCTGCTTCAAGGGTCTTTTAAGCTTGATCTTAAAGAATG
425705 AATTTAGCCT
Statistics
Matches: 156, Mismatches: 22, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
123 2 0.01
124 47 0.30
125 47 0.30
126 60 0.38
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (124 bp):
ACTTGATCTTGGATGGAAGATTCTGCTTCAAGGGTCTTTTAAGCTTGATCTTAAAGAATGGGTTT
TATCTTCTTTGAGTTGGTGCAACTAGATCGGAAAAAGCTTTTAACCAAGGGTATTTGAA
Found at i:429394 original size:16 final size:17
Alignment explanation
Indices: 429373--429406 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
429363 CTAGTGATAG
429373 AATTCAAACAACC-TAT
1 AATTCAAACAACCATAT
429389 AATTCAAACAACCATAT
1 AATTCAAACAACCATAT
429406 A
1 A
429407 TGCCTCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTCAAACAACCATAT
Found at i:432245 original size:56 final size:56
Alignment explanation
Indices: 432155--432264 Score: 166
Period size: 56 Copynumber: 2.0 Consensus size: 56
432145 TAAAACTAAC
* *
432155 TCCTATATATCAAGAGTACACCAAAACAGCAAACAAGAGCAAAGAAATTTGAAATA
1 TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATA
* * * *
432211 TCCTATATATCAGGAGTACATCAAAATAGAAAACAAAAGTAAAGAAATTTGAAA
1 TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGCAAAGAAATTTGAAA
432265 CACAAACAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.20
Consensus pattern (56 bp):
TCCTATATATCAAGAGTACACCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATA
Found at i:438766 original size:8 final size:8
Alignment explanation
Indices: 438749--438790 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
438739 AAAGATTTAT
438749 AAAT-AAA
1 AAATAAAA
438756 AAATAAAA
1 AAATAAAA
438764 AAATAAAA
1 AAATAAAA
438772 AAATGAAATA
1 AAAT-AAA-A
438782 AAATAAAA
1 AAATAAAA
438790 A
1 A
438791 TGAATAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 4 0.12
8 17 0.53
9 6 0.19
10 5 0.16
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (8 bp):
AAATAAAA
Found at i:440360 original size:10 final size:10
Alignment explanation
Indices: 440347--440374 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
440337 CACTATTATT
440347 TTTTATTTGG
1 TTTTATTTGG
440357 TTTTATTTGG
1 TTTTATTTGG
440367 TTTTATTT
1 TTTTATTT
440375 TTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (10 bp):
TTTTATTTGG
Found at i:441011 original size:43 final size:44
Alignment explanation
Indices: 440804--441193 Score: 181
Period size: 44 Copynumber: 8.9 Consensus size: 44
440794 GGATTACTGG
* * * * *
440804 CTTCAATCTGCTCTATTACTGCCTAGGGAGATAAGATCTGCCAT
1 CTTCAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCAT
* ** *
440848 ATT-AGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
1 CTTCA-ATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCA-T
** * * ** *
440893 CTTCGGTCTGCTCCACTGCAACCTTAGGGAGATAAGACCTG--A-
1 CTTCAATCCGCTCCACTAC-TGCTTAGGGAGATAAGATCTGTCAT
* ** * * * * *
440935 -TGCAATCTACTCTACTGAC-ACTTCAGAGAGATAAGATCTTTTAT
1 CTTCAATCCGCTCCACT-ACTGCTT-AGGGAGATAAGATCTGTCAT
*
440979 -TTTAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCAT
1 CTTCAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCAT
* * *
441022 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
1 CTTCAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCA-T
** * * * ** * *
441067 CTTCGGTCTGCTCCGCTGCAACCTCAGGGAGATAAGA-CT-TGA-
1 CTTCAATCCGCTCCACTAC-TGCTTAGGGAGATAAGATCTGTCAT
* * ** * * ** * * *
441109 -TGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCAT
1 CTTCAATCCGCTCCACTACTGCTT-AGGGAGATAAGATCTGTCAT
* *
441153 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 CTTCAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGT
441194 AATTTTTCAA
Statistics
Matches: 263, Mismatches: 65, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
40 6 0.02
41 48 0.18
42 2 0.01
43 22 0.08
44 103 0.39
45 50 0.19
46 32 0.12
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
CTTCAATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGTCAT
Found at i:441070 original size:174 final size:175
Alignment explanation
Indices: 440764--441193 Score: 589
Period size: 174 Copynumber: 2.5 Consensus size: 175
440754 CTATTATTTT
* * * * * *** * * * *
440764 AATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTACTGGCTTCAATCTGCTCTATTACTGCCT
1 AATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCAATCCGCTCCACTACTGCTT
*
440828 AGGGAGATAAGATCTGCCATATTAGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
66 AGGGAGATAAGATCTGTCATATTAGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
*
440893 CTTCGGTCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGC
131 CTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGC
** *
440938 AATCTACTCTACTG-ACACTTCAGAGAGATAAGATCTT-TTAT-TTTAATCCGCTCCACTACTGC
1 AATCTACTCTACTGCA-ACTTCAGAGAGATAAGAT-TTGCCATCTTCAATCCGCTCCACTACTGC
* * *
441000 TTAGGGAGATAAGATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
64 TTAGGGAGATAAGATCTGTCATATTAGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAA
* *
441065 TTCTTCGGTCTGCTCCGCTGCAACCTCAGGGAGATAAGACTTGATGC
129 TTCTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGC
* * *
441112 GATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCAATCCGCTCCACTACTGCTT
441177 AGGGAGATAAGATCTGT
66 AGGGAGATAAGATCTGT
441194 AATTTTTCAA
Statistics
Matches: 225, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
173 3 0.01
174 181 0.80
175 39 0.17
176 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (175 bp):
AATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCAATCCGCTCCACTACTGCTT
AGGGAGATAAGATCTGTCATATTAGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATT
CTTCGGTCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGC
Found at i:441140 original size:41 final size:42
Alignment explanation
Indices: 440903--441316 Score: 171
Period size: 44 Copynumber: 9.6 Consensus size: 42
440893 CTTCGGTCTG
* *
440903 CTCCACTGCAACCTT-AGGGAGATAAGACCTGA-TGCAATCTA
1 CTCCACTGCAA-CTTCAGGGAGATAAGACTTGATTGCGATCTA
* * * *** **
440944 CTCTACTG-ACACTTCAGAGAGATAAGATCTTTTATTTTAATCCG
1 CTCCACTGCA-ACTTCAGGGAGATAAGA-C-TTGATTGCGATCTA
* ** * * *
440988 CTCCACTACTGCTT-AGGGAGATAAGATCTGTCATCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGAT-TGCGATCTA
* ** * * * *
441032 CTCCACTACTGCTT-AGGGAGATAAGATCTGTAATTCTTCGGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGA-T-TGCGATCTA
* *
441077 CTCCGCTGCAACCTCAGGGAGATAAGACTTGA-TGCGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTGCGATCTA
* * * * *
441118 CTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG--AT-TGCGATCTA
* ** * * * *
441163 CTCCACTACTGCTT-AGGGAGATAAGATCTGTAATTTTTCAACCTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGA--TTGCGATCTA
*
441208 CTCCACTGCAACTTCAGGGAGATAAGACCTGA-TGCGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGATTGCGATCTA
* * * *** *
441249 CTCTACTGCAACTTCAGAGAGATAAGATCTTTTATTTTAAT-TCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-C-TTGATTGCGATCT-A
441293 CTCCACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
441317 GGATTACTGG
Statistics
Matches: 287, Mismatches: 63, Indels: 43
0.73 0.16 0.11
Matches are distributed among these distances:
40 4 0.01
41 82 0.29
42 3 0.01
43 22 0.08
44 93 0.32
45 57 0.20
46 26 0.09
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGATTGCGATCTA
Found at i:441155 original size:131 final size:131
Alignment explanation
Indices: 441005--441278 Score: 458
Period size: 131 Copynumber: 2.1 Consensus size: 131
440995 ACTGCTTAGG
*
441005 GAGATAAGATCTGTCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTT
1 GAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTT
*** * * *
441070 CGGTCTGCTCCGCTGCAACCTCAGGGAGATAAGACTTGATGCGATCTACTCTACTGCAACTTCAG
66 CAACCTACTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAG
441135 A
131 A
* *
441136 GAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTT
1 GAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTT
*
441201 CAACCTACTCCACTGCAACTTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAG
66 CAACCTACTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAG
441266 A
131 A
441267 GAGATAAGATCT
1 GAGATAAGATCT
441279 TTTATTTTAA
Statistics
Matches: 132, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (131 bp):
GAGATAAGATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCTT
CAACCTACTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTCAG
A
Found at i:441371 original size:174 final size:171
Alignment explanation
Indices: 440692--441370 Score: 539
Period size: 174 Copynumber: 3.9 Consensus size: 171
440682 TGCTCCGCTG
* * * * * *
440692 CAACTTCAGGGAGATGAGGTCTG-A-TGCGATCTATTCCTACTGCAACGTCAGATAGATAAAATC
1 CAACTT-AGGGAGATAAGATCTGAATTGCGATCTACTCC-ACTGCAACTTCAGAGAGATAAGA-C
* ** * * * * *
440755 TATTATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTTCAATCTGCTCTAT
63 T-TGA-TGCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTACTGGCTTCAATCTGCTCCAC
* **
440820 TACTGCCTAGGGAGATAAGATCTGCCATATT-AGATCTACTCCACTA
126 TACTGCTTAGGGAGATAAGATCTGTAATATTCA-ATCTACTCCACTA
** * * * *
440866 CTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCACTGCAACCTT-AGGGAGATAAGA
1 CAACTTAGGGAGATAAGATCTG-AA-T-TGCGATCTACTCCACTGCAA-CTTCAGAGAGATAAGA
* * * *** * *
440930 CCTGATGCAATCTACTCTACTG-ACACTTCAGAGAGATAAGATCT-TTTATTTTAATCCGCTCCA
62 CTTGATGCAATCTACTCCACTGCA-ACTTCAGAGAGATAAGAT-TACTGGCTTCAATCTGCTCCA
* * * *
440993 CTACTGCTTAGGGAGATAAGATCTGTCATCTTCGATCTGCTCCACTA
125 CTACTGCTTAGGGAGATAAGATCTGTAATATTCAATCTACTCCACTA
** * * * * * *
441040 CTGCTTAGGGAGATAAGATCTGTAATTCTTCGGTCTGCTCCGCTGCAACCTCAGGGAGATAAGAC
1 CAACTTAGGGAGATAAGATCTG-AA-T-TGCGATCTACTCCACTGCAACTTCAGAGAGATAAGAC
* * * *** *
441105 TTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCCATCTTCGATCTGCTCCACT
63 TTGATGCAATCTACTCCACTGCAACTTCAGAGAGATAAGA-TTACTGGCTTCAATCTGCTCCACT
* * *
441170 ACTGCTTAGGGAGATAAGATCTGTAATTTTTCAACCTACTCCACTG
127 ACTGCTTAGGGAGATAAGATCTGTAA-TATTCAATCTACTCCACTA
* *
441216 CAACTTCAGGGAGATAAGACCTG-A-TGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCT
1 CAACTT-AGGGAGATAAGATCTGAATTGCGATCTACTCCACTGCAACTTCAGAGAGATAAGA-C-
* ** * * *
441279 TTTATTTTAAT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTTCAATCTGCTCCAC
63 TTGA-TGCAATCT-ACTCCACTGCAACTTCAGAGAGATAAGATTACTGGCTTCAATCTGCTCCAC
*
441343 TACTGCTTAGGGAGATAAGATTTGTAAT
126 TACTGCTTAGGGAGATAAGATCTGTAAT
441371 TCTTCGTAGG
Statistics
Matches: 411, Mismatches: 75, Indels: 39
0.78 0.14 0.07
Matches are distributed among these distances:
172 29 0.07
173 19 0.05
174 230 0.56
175 72 0.18
176 19 0.05
177 31 0.08
178 11 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (171 bp):
CAACTTAGGGAGATAAGATCTGAATTGCGATCTACTCCACTGCAACTTCAGAGAGATAAGACTTG
ATGCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTACTGGCTTCAATCTGCTCCACTACTG
CTTAGGGAGATAAGATCTGTAATATTCAATCTACTCCACTA
Found at i:441723 original size:9 final size:9
Alignment explanation
Indices: 441709--441744 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
441699 TACCCAATTG
441709 ATTCGGTTA
1 ATTCGGTTA
441718 ATTCGGTTA
1 ATTCGGTTA
*
441727 ATTCAGTTA
1 ATTCGGTTA
441736 ATTCGGTTA
1 ATTCGGTTA
441745 GTTTTTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (9 bp):
ATTCGGTTA
Found at i:442312 original size:11 final size:11
Alignment explanation
Indices: 442296--442321 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
442286 CTAACCAGAC
442296 ATGTGTGAATG
1 ATGTGTGAATG
442307 ATGTGTGAATG
1 ATGTGTGAATG
442318 ATGT
1 ATGT
442322 TTAGGATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (11 bp):
ATGTGTGAATG
Found at i:443302 original size:42 final size:42
Alignment explanation
Indices: 443253--443366 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
443243 AGATCGTCAT
* * * *
443253 ATGCCCCAATCTAATCAAAATTTGAACTGTTCAGATCACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
* *
443295 ATGCCCCATTCTGATCAATATTTGAGCCGCTCAGATCACCTC
1 ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
* *
443337 ATGCCCCGTTCTAATCAATATTTGAGCCGC
1 ATGCCCCATTCTAATCAATATTTGAACCGC
443367 CTTTTTTGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (42 bp):
ATGCCCCATTCTAATCAATATTTGAACCGCTCAGATCACCTC
Found at i:443499 original size:3 final size:3
Alignment explanation
Indices: 443491--443516 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
443481 GTCTTTTCCT
443491 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
443517 TTTTAGACTC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:450245 original size:21 final size:21
Alignment explanation
Indices: 450206--450245 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
450196 ATTGCCCTAA
* *
450206 ATTTCTCTTCAATCCATTTCC
1 ATTTCTCCTCAAACCATTTCC
*
450227 ATTTCTCCTCAAACTATTT
1 ATTTCTCCTCAAACCATTT
450246 TGGCCATTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTCTCCTCAAACCATTTCC
Found at i:458697 original size:31 final size:32
Alignment explanation
Indices: 458659--458720 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
458649 AATTATACAC
*
458659 ATGAAACTTTGATTGTGATTCAA-ATGTATAT
1 ATGAAACTTTAATTGTGATTCAATATGTATAT
*
458690 ATGAAACTTTAATTTTGATTCAATATGTATA
1 ATGAAACTTTAATTGTGATTCAATATGTATA
458721 CTTAAAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (32 bp):
ATGAAACTTTAATTGTGATTCAATATGTATAT
Found at i:459145 original size:16 final size:16
Alignment explanation
Indices: 459124--459178 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
459114 GTTTGGTTCA
459124 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
459140 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
459156 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAG
459172 CTGTAAT
1 CTGTAAT
459179 AGTAATTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:459214 original size:45 final size:44
Alignment explanation
Indices: 459160--459252 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
459150 ATAGAGCTGT
459160 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-A-TCAATGTGTTTGGTTGAATGG
**
459205 AATGGAATAGAACTGTAATAGTATCCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATCAATGTGTTTGGTTGAATGG
459249 AATG
1 AATG
459253 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 3 0.07
44 20 0.44
45 22 0.49
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATCAATGTGTTTGGTTGAATGG
Found at i:465039 original size:64 final size:65
Alignment explanation
Indices: 464915--465045 Score: 183
Period size: 64 Copynumber: 2.0 Consensus size: 65
464905 ATTTTATGCC
* * *
464915 AAAATCATGGTAGATTAGTGGTCCTCAAATTTATTTTCATTTAATATTAAAATTAACGTAATTTG
1 AAAATCATGGTAGATTAGTGGTCCTC--A-GTATTTTCATTTAATATCAAAATTAACGTAACTTG
464980 TGG
63 TGG
* *
464983 AAAATTATGGTAGATTAGTGGTCCTC-GTATTTTCATTTAATATCAAATTTAACGTAACTTGTG
1 AAAATCATGGTAGATTAGTGGTCCTCAGTATTTTCATTTAATATCAAAATTAACGTAACTTGTG
465046 AAACCTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 33 0.57
68 25 0.43
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (65 bp):
AAAATCATGGTAGATTAGTGGTCCTCAGTATTTTCATTTAATATCAAAATTAACGTAACTTGTGG
Found at i:471665 original size:17 final size:17
Alignment explanation
Indices: 471645--471677 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
471635 CCATTTGGTG
*
471645 AACTCTAGGTTTTGGCA
1 AACTCTAGGGTTTGGCA
471662 AACTCTAGGGTTTGGC
1 AACTCTAGGGTTTGGC
471678 GGACAGTTAT
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:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (17 bp):
AACTCTAGGGTTTGGCA
Found at i:476661 original size:21 final size:21
Alignment explanation
Indices: 476636--476699 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
476626 AAATTAAAAA
476636 TATACAAATCAATAAAATAAT
1 TATACAAATCAATAAAATAAT
*
476657 TATACACAGATCAACAAAATAA-
1 TATACA-A-ATCAATAAAATAAT
* *
476679 GA-ACAAACCACATAAAATAAT
1 TATACAAATCA-ATAAAATAAT
476700 AACGCAAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
21 9 0.26
22 2 0.06
23 12 0.34
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.20
Consensus pattern (21 bp):
TATACAAATCAATAAAATAAT
Found at i:476921 original size:21 final size:21
Alignment explanation
Indices: 476884--476938 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
476874 TCTAATATCT
476884 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
476903 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
476924 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
476939 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 11 0.33
21 22 0.67
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:477267 original size:29 final size:28
Alignment explanation
Indices: 477225--477294 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
477215 AAGCAATCCC
* *
477225 TAAAATCTCCAAAATCAGAAATCCTAAACA
1 TAAAATCCCCAAAATCA-AAAACCT-AACA
*
477255 -AAAATCCCCAAAATCAAAAACCTTACA
1 TAAAATCCCCAAAATCAAAAACCTAACA
477282 TAAAATCCCCAAA
1 TAAAATCCCCAAA
477295 TTCGACCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 18 0.50
29 15 0.42
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.17
Consensus pattern (28 bp):
TAAAATCCCCAAAATCAAAAACCTAACA
Found at i:480094 original size:28 final size:28
Alignment explanation
Indices: 480062--480118 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
480052 TAATACATCA
480062 AATCAT-TCAAAAGAATTTATGCTCACAT
1 AATCATATCAAAA-AATTTATGCTCACAT
*
480090 AATCATGCATCAACAAATTTATGCTCACA
1 AATCAT--ATCAAAAAATTTATGCTCACA
480119 AACTCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (28 bp):
AATCATATCAAAAAATTTATGCTCACAT
Found at i:487674 original size:20 final size:20
Alignment explanation
Indices: 487649--487688 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
487639 AGTTTGATTT
487649 GTTAAAAGAC-TTTTAACTTG
1 GTTAAAA-ACATTTTAACTTG
*
487669 GTTAAAATCATTTTAACTTG
1 GTTAAAAACATTTTAACTTG
487689 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
GTTAAAAACATTTTAACTTG
Found at i:488336 original size:20 final size:20
Alignment explanation
Indices: 488262--488336 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
488252 TATACTTTTT
488262 TTAACATTAA-TTAATCTTAA
1 TTAACA-TAAGTTAATCTTAA
* * *
488282 TTAA-TTAAACTAAATCTTAA
1 TTAACAT-AAGTTAATCTTAA
488302 TTAAC-T-AGTCATAATCTTAA
1 TTAACATAAGT--TAATCTTAA
488322 TTAACATAAGTTAAT
1 TTAACATAAGTTAAT
488337 GGGAACATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 35 0.80
21 1 0.02
22 3 0.07
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAACATAAGTTAATCTTAA
Found at i:502437 original size:30 final size:30
Alignment explanation
Indices: 502401--502469 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
502391 AATATGATGT
* **
502401 TCACACAAGCTGACAGTATATCAGGGTTGC
1 TCACACAAGCTGACAGTATAACAGAATTGC
* *
502431 TCACACAAACTGACATTATAACAGAATTGC
1 TCACACAAGCTGACAGTATAACAGAATTGC
*
502461 TCAAACAAG
1 TCACACAAG
502470 TTGAAATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (30 bp):
TCACACAAGCTGACAGTATAACAGAATTGC
Found at i:503825 original size:25 final size:26
Alignment explanation
Indices: 503757--503841 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 26
503747 AATAAAAAAG
*
503757 ATATAAATAAGTAAATAATAATATTAAT
1 ATATAAATAAGTAAAT-AT-ATATTAAA
*
503785 ATAT-AATAAGACAAATATAT-TTAAA
1 ATATAAATAAG-TAAATATATATTAAA
* *
503810 ATTTAAATAAGTAAATATA-AATATAA
1 ATATAAATAAGTAAATATATATTA-AA
503836 ATATAA
1 ATATAA
503842 TAATAATAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
25 16 0.34
26 15 0.32
27 8 0.17
28 8 0.17
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (26 bp):
ATATAAATAAGTAAATATATATTAAA
Found at i:503846 original size:3 final size:3
Alignment explanation
Indices: 503838--503877 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
503828 AAATATAAAT
* *
503838 ATA ATA ATA ATA GTA ATG ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
503878 CATCAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:507049 original size:3 final size:3
Alignment explanation
Indices: 507030--507094 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
507020 ATTATGTTAT
* *
507030 ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
507078 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
507095 GTGGATGCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:508371 original size:20 final size:19
Alignment explanation
Indices: 508342--508381 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
508332 GAATTGAATT
508342 ATGAGAAATGAGATATGAA
1 ATGAGAAATGAGATATGAA
*
508361 ATGATGAAATGAGATGTGAA
1 ATGA-GAAATGAGATATGAA
508381 A
1 A
508382 CTTGAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
ATGAGAAATGAGATATGAA
Found at i:515263 original size:35 final size:35
Alignment explanation
Indices: 515224--515293 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
515214 AATTTTCTCG
*
515224 AGAAAATTATTAATATATTTTAGGGAAGAGGAGAT
1 AGAAAATGATTAATATATTTTAGGGAAGAGGAGAT
515259 AGAAAATGATTAATATATTTTAGGGAAGAGGAGAT
1 AGAAAATGATTAATATATTTTAGGGAAGAGGAGAT
515294 TTGGGTGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (35 bp):
AGAAAATGATTAATATATTTTAGGGAAGAGGAGAT
Found at i:516161 original size:18 final size:19
Alignment explanation
Indices: 516121--516185 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
516111 TATTAGCATC
*
516121 TTTTATATTTTTAAAAATA
1 TTTTTTATTTTTAAAAATA
*
516140 TTTTTTATTTTTAAAGAGT-
1 TTTTTTATTTTTAAA-AATA
* *
516159 TTTTTATTTTTTTAAATATA
1 TTTTT-TATTTTTAAAAATA
516179 TTTTTTA
1 TTTTTTA
516186 AAACTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTTATTTTTAAAAATA
Found at i:516447 original size:21 final size:21
Alignment explanation
Indices: 516416--516455 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
516406 AATTTTTATA
*
516416 ATTTTTCAATAGTTTTATTTTT
1 ATTTTTCAATA-ATTTATTTTT
516438 ATTTTT-AATAATTTATTT
1 ATTTTTCAATAATTTATTT
516456 GCTTTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTTTCAATAATTTATTTTT
Found at i:517582 original size:42 final size:42
Alignment explanation
Indices: 517527--517610 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
517517 TACAAAGTGT
*
517527 ATTGACATCTAAATATT-ATTATAATTTAATTTAGATTTATTA
1 ATTGACATCTAAAT-TTAATTATAAATTAATTTAGATTTATTA
* *
517569 ATTGACATTTAAATTTAATTATAAATTAATTTAGGTTTATTA
1 ATTGACATCTAAATTTAATTATAAATTAATTTAGATTTATTA
517611 GACTTAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (42 bp):
ATTGACATCTAAATTTAATTATAAATTAATTTAGATTTATTA
Found at i:518282 original size:25 final size:25
Alignment explanation
Indices: 518241--518293 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
518231 ACAAATCTTG
* **
518241 TAATATATATTTTTAAATTTTAAAA
1 TAATATATATTTATAAATTAAAAAA
518266 TAATAT-TATTTAATAAATTAAAAAA
1 TAATATATATTT-ATAAATTAAAAAA
518291 TAA
1 TAA
518294 GTACGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAATATATATTTATAAATTAAAAAA
Found at i:520745 original size:24 final size:25
Alignment explanation
Indices: 520717--520774 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 25
520707 TATCTAGATA
520717 TTAATAT-GAGATATTAAATTTAAT
1 TTAATATCGAGATATTAAATTTAAT
*
520741 TTAATATTTATCTAGATATTAAATTTAAT
1 TT-A-A--TATCGAGATATTAAATTTAAT
520770 TTAAT
1 TTAAT
520775 GTTTATCTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
24 2 0.07
25 2 0.07
26 1 0.04
27 1 0.04
28 4 0.14
29 18 0.64
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATATCGAGATATTAAATTTAAT
Found at i:520763 original size:29 final size:29
Alignment explanation
Indices: 520725--520787 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
520715 TATTAATATG
520725 AGATATTAAATTTAATTTAATATTTATCT
1 AGATATTAAATTTAATTTAATATTTATCT
*
520754 AGATATTAAATTTAATTTAATGTTTATCT
1 AGATATTAAATTTAATTTAATATTTATCT
520783 AGATA
1 AGATA
520788 ATATTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
AGATATTAAATTTAATTTAATATTTATCT
Found at i:524028 original size:23 final size:23
Alignment explanation
Indices: 523997--524048 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
523987 TAAGATATCT
*
523997 ATATATAAATTATAAATAA-ATAA
1 ATAT-TAAATTAAAAATAATATAA
524020 AGTATTAAATTAAAAATAATATAA
1 A-TATTAAATTAAAAATAATATAA
524044 ATATT
1 ATATT
524049 TTCAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATTAAATTAAAAATAATATAA
Found at i:527697 original size:12 final size:12
Alignment explanation
Indices: 527680--527724 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
527670 AAGTTTCCAA
527680 AAATGAAAATGG
1 AAATGAAAATGG
*
527692 AAATGAGAATGG
1 AAATGAAAATGG
* * *
527704 GAATGGAAATGA
1 AAATGAAAATGG
527716 AAATGAAAA
1 AAATGAAAA
527725 CTTGCAATTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.16
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:531192 original size:8 final size:7
Alignment explanation
Indices: 531181--531220 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
531171 CAATTTTTAC
531181 TTTTTCA
1 TTTTTCA
531188 TTTTTTCA
1 -TTTTTCA
531196 TTTTTCA
1 TTTTTCA
531203 -TTTTCA
1 TTTTTCA
531209 TTTTTCA
1 TTTTTCA
531216 TTTTT
1 TTTTT
531221 TTACTCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:531206 original size:13 final size:13
Alignment explanation
Indices: 531190--531219 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
531180 CTTTTTCATT
531190 TTTTCATTTTTCA
1 TTTTCATTTTTCA
531203 TTTTCATTTTTCA
1 TTTTCATTTTTCA
531216 TTTT
1 TTTT
531220 TTTACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:537102 original size:27 final size:28
Alignment explanation
Indices: 537050--537108 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
537040 AGAATAATTT
*
537050 TAAAATTAATATATAAAGCGACTAAAAA
1 TAAAATTAATATATAAAGCAACTAAAAA
*
537078 TAAAA-TAATATATAAA-TAACTTAAAAA
1 TAAAATTAATATATAAAGCAAC-TAAAAA
537105 TAAA
1 TAAA
537109 TCATTTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 21 0.75
28 5 0.18
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.27
Consensus pattern (28 bp):
TAAAATTAATATATAAAGCAACTAAAAA
Found at i:537190 original size:15 final size:16
Alignment explanation
Indices: 537172--537212 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
537162 AAGATGAAAT
537172 TTTAAAATAAATCA-A
1 TTTAAAATAAATCACA
*
537187 TTTAAGGAT-AATCACA
1 TTTAA-AATAAATCACA
537203 TTTAAAATAA
1 TTTAAAATAA
537213 CATATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (16 bp):
TTTAAAATAAATCACA
Found at i:537758 original size:10 final size:10
Alignment explanation
Indices: 537743--537791 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
537733 TTTCGCATAT
537743 AGAGAAAAAA
1 AGAGAAAAAA
*
537753 AGAGAAAGAA
1 AGAGAAAAAA
*
537763 A-A-AAAAAG
1 AGAGAAAAAA
537771 AGAGAAAAAA
1 AGAGAAAAAA
537781 AGAAGAAAAAA
1 AG-AGAAAAAA
537792 CCAAGAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 17 0.53
11 8 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:537764 original size:14 final size:14
Alignment explanation
Indices: 537745--537788 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
537735 TCGCATATAG
537745 AGAAAAAAAGAGAA
1 AGAAAAAAAGAGAA
* *
537759 AGAAAAAAAAAGAG
1 AGAAAAAAAGAGAA
537773 AGAAAAAAAGAAGAA
1 AGAAAAAAAG-AGAA
537788 A
1 A
537789 AAACCAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAGAA
Found at i:537778 original size:11 final size:11
Alignment explanation
Indices: 537757--537791 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
537747 AAAAAAAGAG
537757 AAAGAA-AAAA
1 AAAGAAGAAAA
537767 AAAGAGAGAAAA
1 AAAGA-AGAAAA
537779 AAAGAAGAAAA
1 AAAGAAGAAAA
537790 AA
1 AA
537792 CCAAGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 9 0.39
12 9 0.39
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:537797 original size:26 final size:26
Alignment explanation
Indices: 537743--537791 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
537733 TTTCGCATAT
537743 AGAGAAAAAAAGAGAAAGAAAAAAAA
1 AGAGAAAAAAAGAGAAAGAAAAAAAA
537769 AGAGAGAAAAAA-AG-AAGAAAAAA
1 AGAGA-AAAAAAGAGAAAGAAAAAA
537792 CCAAGAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (26 bp):
AGAGAAAAAAAGAGAAAGAAAAAAAA
Found at i:544074 original size:31 final size:31
Alignment explanation
Indices: 544038--544111 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
544028 GGATAATTTC
*
544038 TTAACCACTCACATCCCACTAAGTCCCATAA
1 TTAACCACTCACATCCCACTAAGTCCCACAA
* *
544069 TTAACCACCCACATCCCTCTAAGTCCCACAA
1 TTAACCACTCACATCCCACTAAGTCCCACAA
*
544100 ATAACCACTCAC
1 TTAACCACTCAC
544112 CAGATTCCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.42, G:0.03, T:0.20
Consensus pattern (31 bp):
TTAACCACTCACATCCCACTAAGTCCCACAA
Found at i:549129 original size:19 final size:20
Alignment explanation
Indices: 549101--549146 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
549091 NNNNNNATAA
* * *
549101 TTTATAATTTTTAATAT-TT
1 TTTATGATTTTGAATATCCT
549120 TTTATGATTTTGAATATCCT
1 TTTATGATTTTGAATATCCT
549140 TTTATGA
1 TTTATGA
549147 GAAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTATGATTTTGAATATCCT
Found at i:549525 original size:18 final size:18
Alignment explanation
Indices: 549485--549527 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
549475 TTTTATTTTA
*
549485 AAAAATATATAAAAATAT
1 AAAAATATATAAAAAAAT
*
549503 GAAAATATA-AAAAAAAT
1 AAAAATATATAAAAAAAT
549520 CAAAAATA
1 -AAAAATA
549528 GTAATAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAATATATAAAAAAAT
Found at i:549735 original size:22 final size:22
Alignment explanation
Indices: 549707--549751 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
549697 ACTTGAACTT
549707 TCAAAATGCATCAAAAAGACCC
1 TCAAAATGCATCAAAAAGACCC
549729 TCAAAATGCATCAAAAAGACCC
1 TCAAAATGCATCAAAAAGACCC
549751 T
1 T
549752 TAAACTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.27, G:0.09, T:0.16
Consensus pattern (22 bp):
TCAAAATGCATCAAAAAGACCC
Found at i:549853 original size:108 final size:110
Alignment explanation
Indices: 549630--549843 Score: 299
Period size: 108 Copynumber: 2.0 Consensus size: 110
549620 TTAATGGTGT
* * * *
549630 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATCAAGCCCCTCAATTTTTTTTGCACTTAATTGA
1 AAAAAGCCCTCAAACTTCTTAAAAAAAAGCAATCAAGCCCCTC-ATTTTTTTTCCACTCAATTGA
549695 GCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATGCATC
65 GCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATGCATC
* * *
549741 AAAAAGACCCTTAAACTTCTTAAAAAAAAGTAATTAAG-CCC-C-TTTTTTTTCCACTCAATTGA
1 AAAAAG-CCCTCAAACTTCTTAAAAAAAAGCAATCAAGCCCCTCATTTTTTTTCCACTCAATTGA
* * *
549803 GTATTTGAACTTTCAAAATGCATCACAAAGACCCTCAAAAT
65 GCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAAT
549844 TTTTCAAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
108 56 0.61
110 1 0.01
111 9 0.10
112 26 0.28
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (110 bp):
AAAAAGCCCTCAAACTTCTTAAAAAAAAGCAATCAAGCCCCTCATTTTTTTTCCACTCAATTGAG
CACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATGCATC
Found at i:549909 original size:18 final size:18
Alignment explanation
Indices: 549878--549927 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
549868 TGCTCTTATT
* *
549878 AAAAAGTAAAAAATAATA
1 AAAAAATAATAAATAATA
**
549896 AAAAAATAATAAATTTTA
1 AAAAAATAATAAATAATA
*
549914 GAAAAATAATAAAT
1 AAAAAATAATAAAT
549928 TTTAGAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAAAATAATAAATAATA
Found at i:549928 original size:18 final size:18
Alignment explanation
Indices: 549897--549940 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
549887 AAAATAATAA
549897 AAAAATAATAAATTTTAG
1 AAAAATAATAAATTTTAG
549915 AAAAATAATAAATTTTAG
1 AAAAATAATAAATTTTAG
549933 AAAAATAA
1 AAAAATAA
549941 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATAATAAATTTTAG
Found at i:551603 original size:284 final size:283
Alignment explanation
Indices: 551058--551606 Score: 965
Period size: 284 Copynumber: 1.9 Consensus size: 283
551048 TGGGTTTCCC
551058 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
1 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
* * *
551123 AAGATGAACTTGTGGGTCAAAGTTGAGATACAGTTAGTAATTTATCTTTGAATTTGCCTAGTTTT
66 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTACTAATTTATCTTTGAATTTGCCTAGTTGT
* *
551188 AAAGCTGAGCTATGGAGTGCTAAAGATTTATATAACTGTTTTGTTTTCAATGTTGTTACTGATAG
131 AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
551253 TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACCAAAAAAA
196 TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACC-AAAAAA
551318 AAAAAAAAGAGAAATTGCTAAAGA
260 AAAAAAAAGAGAAATTGCTAAAGA
*
551342 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGTAAG
1 TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
*
551407 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTACTAATTTATCTTTGAATTTGTCTAGTTGT
66 AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTACTAATTTATCTTTGAATTTGCCTAGTTGT
551472 AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
131 AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
* * *
551537 TTTTGCTCTTTGCTTTCCTCTTTCTT-ACGAAATTGCTATGAGTAAATATTTTATTTGACCAAAA
196 TTTTGCTATTTGC--TCCACTTTCTTGA-GAAATTGCTATGAGTAAATATCTTATTTGACCAAAA
551601 AAAAAA
258 AAAAAA
551607 TGGACACATT
Statistics
Matches: 252, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
284 200 0.79
285 11 0.04
286 41 0.16
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41
Consensus pattern (283 bp):
TTTATTGTCTGTTATATTAATTTTGGATGGGTGATTTGAAGTGGGATTTTAATTTGTTATGGAAG
AAGATAAACTTGTGGGTCAAAGTTGAGATACAGTTACTAATTTATCTTTGAATTTGCCTAGTTGT
AAAGCTGAGCTATGGAGCGCTAAAGATTTATATAACTGTTCTGTTTTCAATGTTGTTACTGATAG
TTTTGCTATTTGCTCCACTTTCTTGAGAAATTGCTATGAGTAAATATCTTATTTGACCAAAAAAA
AAAAAAAGAGAAATTGCTAAAGA
Found at i:554248 original size:2 final size:2
Alignment explanation
Indices: 554241--554271 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
554231 ATTGTCCCAA
*
554241 TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
554272 ATCGCTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:565960 original size:13 final size:13
Alignment explanation
Indices: 565942--565974 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
565932 TGAAGTTTGC
565942 TCTAAAATCTCGA
1 TCTAAAATCTCGA
*
565955 TGT-AAATCTCGA
1 TCTAAAATCTCGA
565967 TCTAAAAT
1 TCTAAAAT
565975 AATAGATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (13 bp):
TCTAAAATCTCGA
Found at i:571276 original size:21 final size:21
Alignment explanation
Indices: 571243--571302 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
571233 GAAACACGCC
*
571243 AACAGAAGTTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
571264 AATAGAAGCTCATAAAAACTG
1 AACAGAAGCTCATAAGAGCTG
*
571285 AACAAAAGCTCATAAGAG
1 AACAGAAGCTCATAAGAG
571303 TTGATCCACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:574779 original size:35 final size:35
Alignment explanation
Indices: 574740--574884 Score: 168
Period size: 35 Copynumber: 4.1 Consensus size: 35
574730 TTTCTCTTGC
*
574740 AAGCCTCCGCCATGTGTTGGGAGCAAGATCTCTC-T
1 AAGCCTCC-CCATGTGTTGGGAGCAAGACCTCTCAT
*
574775 AAGCCTCCCTCATGTGTTGGAAGCAAGACCTCTCAT
1 AAGCCTCCC-CATGTGTTGGGAGCAAGACCTCTCAT
* * *
574811 AAGCCTCCCCCTTTGTGTTGGGAGCAGGACCTCCCAT
1 AAGCCT-CCCC-ATGTGTTGGGAGCAAGACCTCTCAT
* * *
574848 AAGCC-CCCTATGTGTTGGGAGCAGGACCCCTCAT
1 AAGCCTCCCCATGTGTTGGGAGCAAGACCTCTCAT
574882 AAG
1 AAG
574885 TGCCCTCCAT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
34 26 0.27
35 33 0.34
36 8 0.08
37 29 0.30
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (35 bp):
AAGCCTCCCCATGTGTTGGGAGCAAGACCTCTCAT
Found at i:574842 original size:37 final size:37
Alignment explanation
Indices: 574740--574884 Score: 167
Period size: 34 Copynumber: 4.1 Consensus size: 37
574730 TTTCTCTTGC
* *
574740 AAGCCTCCGCC-ATGTGTTGGGAGCAAGATCTCTC-T
1 AAGCCTCCCCCTATGTGTTGGGAGCAAGACCTCTCAT
* *
574775 AAGCCTCCCTC-ATGTGTTGGAAGCAAGACCTCTCAT
1 AAGCCTCCCCCTATGTGTTGGGAGCAAGACCTCTCAT
* * *
574811 AAGCCTCCCCCTTTGTGTTGGGAGCAGGACCTCCCAT
1 AAGCCTCCCCCTATGTGTTGGGAGCAAGACCTCTCAT
* *
574848 AAG---CCCCCTATGTGTTGGGAGCAGGACCCCTCAT
1 AAGCCTCCCCCTATGTGTTGGGAGCAAGACCTCTCAT
574882 AAG
1 AAG
574885 TGCCCTCCAT
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
34 31 0.32
35 30 0.31
36 11 0.11
37 24 0.25
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (37 bp):
AAGCCTCCCCCTATGTGTTGGGAGCAAGACCTCTCAT
Found at i:574861 original size:71 final size:72
Alignment explanation
Indices: 574752--574884 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 72
574742 GCCTCCGCCA
* * *
574752 TGTGTTGGGAGCAAGATCTCTCTAAGCCTCCCTCATGTGTTGGAAGCAAGACCTCTCATAAGCCT
1 TGTGTTGGGAGCAAGACCTCCCTAAGCCTCCCTCATGTGTTGGAAGCAAGACCCCTCATAAGCCT
574817 CCCCCTT
66 CCCCCTT
* * *
574824 TGTGTTGGGAGCAGGACCTCCCATAAGCC-CCCT-ATGTGTTGGGAGCAGGACCCCTCATAAG
1 TGTGTTGGGAGCAAGACCTCCC-TAAGCCTCCCTCATGTGTTGGAAGCAAGACCCCTCATAAG
574885 TGCCCTCCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
71 25 0.46
72 23 0.43
73 6 0.11
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (72 bp):
TGTGTTGGGAGCAAGACCTCCCTAAGCCTCCCTCATGTGTTGGAAGCAAGACCCCTCATAAGCCT
CCCCCTT
Found at i:591544 original size:25 final size:25
Alignment explanation
Indices: 591516--591571 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
591506 ACTTGTCACC
*
591516 AAGGCTCTCCAGATA-ATATACCACA
1 AAGGCTCTCCAGAGAGAT-TACCACA
* *
591541 AAGGCTTTCCAGAGAGATTGCCACA
1 AAGGCTCTCCAGAGAGATTACCACA
591566 AAGGCT
1 AAGGCT
591572 TTTTAGAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (25 bp):
AAGGCTCTCCAGAGAGATTACCACA
Found at i:591572 original size:25 final size:25
Alignment explanation
Indices: 591536--591593 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
591526 AGATAATATA
*
591536 CCACAAAGGCTTTCCAGAGAGATTG
1 CCACAAAGGCTTTCCAGAGAGATCG
**
591561 CCACAAAGGCTTTTTAGAGAGATCG
1 CCACAAAGGCTTTCCAGAGAGATCG
*
591586 CCATAAAG
1 CCACAAAG
591594 AATTTACAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (25 bp):
CCACAAAGGCTTTCCAGAGAGATCG
Found at i:607429 original size:23 final size:23
Alignment explanation
Indices: 607398--607473 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
607388 AGTGTTATTG
607398 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
*
607421 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
*
607444 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTTGGCTACAT
607467 ATCAGTG
1 ATCAGTG
607474 TGACACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTTGGCTACAT
Found at i:612970 original size:113 final size:113
Alignment explanation
Indices: 612840--613062 Score: 430
Period size: 113 Copynumber: 2.0 Consensus size: 113
612830 AACTAATTTT
612840 TTTATTATACCAATCACTATTAATTATTTAATATATGAAATAAAAAATTTAAATA-TTTTTAAGC
1 TTTATTATACCAATCACTATTAATTATTTAATATATGAAATAAAAAATTTAAATATTTTTTAAGC
612904 AATTACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAATTAAAA
66 AA-TACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAATTAAAA
612953 TTTATTATACCAATCACTATTAATTATTTAATATATGAAATAAAAAATTTAAATATTTTTTAAGC
1 TTTATTATACCAATCACTATTAATTATTTAATATATGAAATAAAAAATTTAAATATTTTTTAAGC
613018 AATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAATTA
66 AATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAATTA
613063 TATTTTTAAG
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
113 98 0.90
114 11 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (113 bp):
TTTATTATACCAATCACTATTAATTATTTAATATATGAAATAAAAAATTTAAATATTTTTTAAGC
AATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAATTAAAA
Found at i:612976 original size:60 final size:59
Alignment explanation
Indices: 612888--613062 Score: 181
Period size: 60 Copynumber: 3.1 Consensus size: 59
612878 AATAAAAAAT
*
612888 TTAAATATTT-TTAAGCAATTACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAA
1 TTAAATATTTATTAACCAA-TACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAA
* * *
612947 TTAAA-ATTTATTATACCAATCACTATTAATTA-TT-T-AA---T-ATATGAA-ATAAAAAA
1 TTAAATATTTATTA-ACCAAT-ACTGTTAATTATTTGTAAATTTTAATTTGAATAT-ATAAA
* *
613000 TTTAAATATTTTTTAAGCAATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAA
1 -TTAAATATTTATTAACCAATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAA
613060 TTA
1 TTA
613063 TATTTTTAAG
Statistics
Matches: 93, Mismatches: 9, Indels: 28
0.72 0.07 0.22
Matches are distributed among these distances:
52 2 0.02
53 20 0.22
54 13 0.14
55 8 0.09
56 2 0.02
57 2 0.02
58 5 0.05
59 15 0.16
60 24 0.26
61 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (59 bp):
TTAAATATTTATTAACCAATACTGTTAATTATTTGTAAATTTTAATTTGAATATATAAA
Found at i:613157 original size:24 final size:22
Alignment explanation
Indices: 613124--613169 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
613114 TATCACTCTG
*
613124 TAACATTTTATACAATTAATATTT
1 TAACAATTTA-ACAATT-ATATTT
*
613148 TAACAATTTAACTATTATATTT
1 TAACAATTTAACAATTATATTT
613170 CATGTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (22 bp):
TAACAATTTAACAATTATATTT
Found at i:613158 original size:16 final size:17
Alignment explanation
Indices: 613124--613163 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
613114 TATCACTCTG
613124 TAAC-ATTTTATACAAT
1 TAACTATTTTATACAAT
613140 TAA-TATTTTA-ACAATT
1 TAACTATTTTATACAA-T
613156 TAACTATT
1 TAACTATT
613164 ATATTTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (17 bp):
TAACTATTTTATACAAT
Found at i:614554 original size:19 final size:18
Alignment explanation
Indices: 614530--614569 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
614520 AAAAAAATAA
614530 AAAAATAAAAATATTTTAT
1 AAAAATAAAAATATTTT-T
614549 AAAAATAAAAATATTTTT
1 AAAAATAAAAATATTTTT
614567 AAA
1 AAA
614570 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATAAAAATATTTTT
Found at i:620189 original size:43 final size:43
Alignment explanation
Indices: 620154--620236 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
620144 TTATTCGATG
* *
620154 ATGCATTATGTGTACCAGTATGATTGCTTCGGTTTATCCAATA
1 ATGCACTATCTGTACCAGTATGATTGCTTCGGTTTATCCAATA
* *
620197 ATGCACTATCTGTGCCAGTATGATTGCTTCGGTTTTTCCA
1 ATGCACTATCTGTACCAGTATGATTGCTTCGGTTTATCCA
620237 GTGACGCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (43 bp):
ATGCACTATCTGTACCAGTATGATTGCTTCGGTTTATCCAATA
Found at i:620254 original size:43 final size:43
Alignment explanation
Indices: 620160--620266 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
620150 GATGATGCAT
* *
620160 TATGTGTACCAGTATGATTGCTTCGGTTTATCCAATAATGCAC
1 TATGTGTGCCAGTATGATTGCTTCGGTTTATCCAATAACGCAC
* * * *
620203 TATCTGTGCCAGTATGATTGCTTCGGTTTTTCCAGTGACGCACC
1 TATGTGTGCCAGTATGATTGCTTCGGTTTATCCAATAACGCA-C
* *
620247 T-TGTGTGCTAGTATAATTGC
1 TATGTGTGCCAGTATGATTGC
620267 CTCAGTTTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 52 0.96
44 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (43 bp):
TATGTGTGCCAGTATGATTGCTTCGGTTTATCCAATAACGCAC
Found at i:622706 original size:41 final size:41
Alignment explanation
Indices: 622626--622723 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
622616 AATCTTTTAA
* * *
622626 AAAACTTAGTATTT-AAATCTAGAATCTAAAAATCCAATTT
1 AAAACTTAATATTTAAAATCTAAAATCTAAAAAGCCAATTT
* * *
622666 AAAACTTAATATTTAAAATCTAAAATTTAAAGAGCTAATTT
1 AAAACTTAATATTTAAAATCTAAAATCTAAAAAGCCAATTT
* * *
622707 AAAGCCTAATATATAAA
1 AAAACTTAATATTTAAA
622724 GTAAAAAAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (41 bp):
AAAACTTAATATTTAAAATCTAAAATCTAAAAAGCCAATTT
Found at i:627054 original size:16 final size:15
Alignment explanation
Indices: 627024--627058 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
627014 TTCTATTGTC
627024 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
627039 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
627055 TATA
1 TATA
627059 CAAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:629569 original size:69 final size:69
Alignment explanation
Indices: 629458--629686 Score: 314
Period size: 69 Copynumber: 3.3 Consensus size: 69
629448 GCTCCGACAC
* * ** * *
629458 AGCTAGCGGACCTATGCTCCCAGTTTATGTCATAAAGGTTTGACGATTTAATATCGCAACCTCTA
1 AGCTAGCAGACCTACGCTCCCAACTGATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTA
629523 AAGT
66 AAGT
* * * *
629527 AGCTAGCAGACCTACGCTCCCAACTGATGTCATAAAGGTTTGACAATATAAGATCACAACCTCCA
1 AGCTAGCAGACCTACGCTCCCAACTGATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTA
629592 AAGT
66 AAGT
* * *
629596 AGCTAACGGACCTACGTTCCCAACTGATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTA
1 AGCTAGCAGACCTACGCTCCCAACTGATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTA
*
629661 AAGC
66 AAGT
* *
629665 AGCTAGTAGACCTATGCTCCCA
1 AGCTAGCAGACCTACGCTCCCA
629687 GTTGACATTA
Statistics
Matches: 137, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 137 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (69 bp):
AGCTAGCAGACCTACGCTCCCAACTGATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTA
AAGT
Done.