Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2792_ERROPOS1793843
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: 513059
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 18467 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:249652 original size:176 final size:176
Alignment explanation
Indices: 249312--250038 Score: 970
Period size: 176 Copynumber: 4.1 Consensus size: 176
249302 AACCATTAAT
* * *
249312 ACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACAC
1 ACCCTTAACTTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACC-AATTAAATTAAAAACCC
* ** *
249377 TAA-CAATTAAATTAAAAACCCTAACCTAATTAAATTCAAAACCCTAACCCTTAACTTAAAAACC
63 TAACCAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAACC
* * *
249441 CTAACCTAATTAAATTAAGAACCCTAACTTAATTAAATTAAAAATCCTA
128 CTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * * **
249490 ACCCGTT-ACTTAAAAACTCTAACCCTTAGCTTAAAAACCCTAACC-CTTAACGTAAAAACCCTA
1 ACCC-TTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCAATTAAATTAAAAACCCTA
*
249553 ACCTAATTAAATTAAGAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAACCC
65 ACC-AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAACCC
* * *
249618 TAACATAATTAAATTAAAAACTCTAACCTAATTAAATTAAAAATCCTA
129 TAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* ** * *
249666 ACCCTTAGCTTAAAAACCCTAACAATTAAATTAAAAACCCTAACCTAATTAAATTTAAAACCCTA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACC-AATTAAATTAAAAACCCTA
* * *
249731 ACC-CTTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCTTAACAATTAAATTAAAAACCCT
65 ACCAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAACCCT
* * *
249795 AACC--CTTAACTTAAAAACCCTAACCTAATGAAATTAAAAACCCTA
130 AACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
* * *
249840 ACCTAATTAAATTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCTAATTAAATTAAAACCCC
1 ACC--CTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACC-AATTAAATTAAAAACCC
249905 TAACCTAATTAAATTAAAAACCCTAA-C-AATTAAATTAAAAACCCTAACAATTAAATTAAAAAC
63 TAACC-AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAAC
* *
249968 CCTAACCTAATTAAATTAAAAACCCTAAACC--CTTAACTTAAAAACCCTA
127 CCTAACCTAATTAAATTAAAAACCCT-AACCTAATTAAATTAAAAACCCTA
250017 ACCCTTAACTTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
250039 ACTAAGTTAA
Statistics
Matches: 481, Mismatches: 55, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
174 54 0.11
175 20 0.04
176 313 0.65
177 19 0.04
178 69 0.14
179 6 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (176 bp):
ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCAATTAAATTAAAAACCCTAA
CCAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACAATTAAATTAAAAACCCTA
ACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
Found at i:250072 original size:23 final size:23
Alignment explanation
Indices: 249316--250071 Score: 689
Period size: 23 Copynumber: 34.2 Consensus size: 23
249306 ATTAATACCC
* *
249316 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
*
249339 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
*
249362 TTAAATTAAAAACACT-AAC-AA
1 TTAAATTAAAAACCCTAAACTAA
*
249383 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* **
249406 TTAAATTCAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
* *
249427 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
*
249450 TTAAATTAAGAACCCT-AACTTAA
1 TTAAATTAAAAACCCTAAAC-TAA
* ***
249473 TTAAATTAAAAATCCT-AACCCG
1 TTAAATTAAAAACCCTAAACTAA
* * **
249495 TT-ACTTAAAAACTCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
** **
249515 TTAGCTTAAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
** *
249536 TTAACGTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* *
249559 TTAAATTAAGAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
249582 TTAAATTAAAAACCCT-AAC-AA
1 TTAAATTAAAAACCCTAAACTAA
249603 TTAAATTAAAAACCCT-AACATAA
1 TTAAATTAAAAACCCTAAAC-TAA
* *
249626 TTAAATTAAAAACTCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* **
249649 TTAAATTAAAAATCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
**
249670 TTAGCTTAAAAACCCT-AAC-AA
1 TTAAATTAAAAACCCTAAACTAA
*
249691 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* **
249714 TTAAATTTAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
* *
249735 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
*
249758 TTAAATTAAAAA-CCTTAAC-AA
1 TTAAATTAAAAACCCTAAACTAA
**
249779 TTAAATTAAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
* *
249800 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* *
249823 TGAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
**
249846 TTAAATTAAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
* *
249867 TTAACTTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
* *
249890 TTAAATTAAAACCCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
249913 TTAAATTAAAAACCCT-AAC-AA
1 TTAAATTAAAAACCCTAAACTAA
249934 TTAAATTAAAAACCCT-AAC-AA
1 TTAAATTAAAAACCCTAAACTAA
*
249955 TTAAATTAAAAACCCTAACCTAA
1 TTAAATTAAAAACCCTAAACTAA
**
249978 TTAAATTAAAAACCCTAAAC-CC
1 TTAAATTAAAAACCCTAAACTAA
* **
250000 TTAACTTAAAAACCCT-AAC-CC
1 TTAAATTAAAAACCCTAAACTAA
*
250021 TTAACTTAAAAACCCTAAACTAA
1 TTAAATTAAAAACCCTAAACTAA
250044 GTT-AATTAAAAACCCTAAACTAA
1 -TTAAATTAAAAACCCTAAACTAA
250067 GTTAA
1 -TTAA
250072 TAATTTTACT
Statistics
Matches: 614, Mismatches: 93, Indels: 51
0.81 0.12 0.07
Matches are distributed among these distances:
20 3 0.00
21 246 0.40
22 60 0.10
23 300 0.49
24 5 0.01
ACGTcount: A:0.50, C:0.23, G:0.01, T:0.26
Consensus pattern (23 bp):
TTAAATTAAAAACCCTAAACTAA
Found at i:250627 original size:17 final size:18
Alignment explanation
Indices: 250605--250644 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
250595 TGTTTTTGTT
250605 TTTTTATT-TTTATTTCA
1 TTTTTATTCTTTATTTCA
* *
250622 TTTTTATTCTTTCTTTCG
1 TTTTTATTCTTTATTTCA
250640 TTTTT
1 TTTTT
250645 TTTACATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTATTCTTTATTTCA
Found at i:251345 original size:3 final size:3
Alignment explanation
Indices: 251339--251410 Score: 67
Period size: 3 Copynumber: 23.0 Consensus size: 3
251329 TTTAGCAATT
*
251339 TTA TTA TTTA GTTAA TTA TT- TTA TTA TTG TT- TTCA TTA TTA TTA TTA
1 TTA TTA -TTA -TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
*
251386 TCA TTA TTA TTA TTAA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA
251411 GTTTTATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.07
3 42 0.71
4 12 0.20
5 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:251483 original size:16 final size:17
Alignment explanation
Indices: 251459--251492 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
251449 AATATATTAA
*
251459 TTAGTTTTA-TTTTATT
1 TTAGCTTTATTTTTATT
251475 TTAGCTTTATTTTTATT
1 TTAGCTTTATTTTTATT
251492 T
1 T
251493 CATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (17 bp):
TTAGCTTTATTTTTATT
Found at i:256311 original size:46 final size:46
Alignment explanation
Indices: 256247--256428 Score: 346
Period size: 46 Copynumber: 4.0 Consensus size: 46
256237 GGCAAAATGT
*
256247 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
256293 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
256339 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
*
256385 GAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGTT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTT
256429 ATAGCAATGT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 134 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (46 bp):
GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
Found at i:264030 original size:46 final size:46
Alignment explanation
Indices: 263963--264101 Score: 260
Period size: 46 Copynumber: 3.0 Consensus size: 46
263953 CATGGCAAAA
263963 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
264009 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
264055 TGCGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
264101 T
1 T
264102 ATAGCAATGT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:266469 original size:123 final size:123
Alignment explanation
Indices: 266249--266611 Score: 582
Period size: 123 Copynumber: 2.9 Consensus size: 123
266239 CTACTATAGA
*
266249 AAAAGCGCGTCCACGAGGGTGCGATTTTCACAAATCCTTCTCAAATAGCATCCTGCTAGAAGCGA
1 AAAAGCGCGTCCACGAGGGTGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGA
* *
266314 TTTTATACTATTTGCTCAGAAACATCAAAAAAATTATTTCTTCCATGACCAACTGTAGC
65 TTTTATACTATTTGCTTAGAAACGTCAAAAAAATTATTTCTTCCATGACCAACTGTAGC
*
266373 AAAAGCGCGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTATAAGCGAT
1 AAAAGCGCGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAT
* *
266438 TTTATATTATTTGCTTAGAAACGTCAAAAAAATTATTTCTTCCATGACCTACTGTAGC
66 TTTATACTATTTGCTTAGAAACGTCAAAAAAATTATTTCTTCCATGACCAACTGTAGC
* * *
266496 AAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGTTAGAAGCGAT
1 AAAAGCGCGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAT
* ** *
266561 TTTATACTATTTGATTAGAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 TTTATACTATTTGCTTAGAAACGTCAA--AAAAATTATTTCTTCCATGACC
266612 TAAAAACCCT
Statistics
Matches: 222, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
123 175 0.79
124 28 0.13
125 19 0.09
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (123 bp):
AAAAGCGCGTCCACGAGGGTGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAT
TTTATACTATTTGCTTAGAAACGTCAAAAAAATTATTTCTTCCATGACCAACTGTAGC
Found at i:266812 original size:28 final size:28
Alignment explanation
Indices: 266748--266812 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
266738 CAATTTGCTG
* *
266748 AAAAATGGACCATTCCGGTAATAATTAA
1 AAAAAGGGCCCATTCCGGTAATAATTAA
* * * **
266776 ATAATGGGCCCATTTCGGTAATTTTTAA
1 AAAAAGGGCCCATTCCGGTAATAATTAA
266804 AAAAAGGGC
1 AAAAAGGGC
266813 TCTTTTGGTA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (28 bp):
AAAAAGGGCCCATTCCGGTAATAATTAA
Found at i:267724 original size:55 final size:55
Alignment explanation
Indices: 267648--267787 Score: 210
Period size: 55 Copynumber: 2.5 Consensus size: 55
267638 ACAAATGATC
* * *
267648 TAAACATATAAACAATCGATTCAAAAGAAGTAGTATTCCAACATAACAATCAATT
1 TAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACACAACAACCAATT
* * *
267703 TGAACATATAAACAATGGATTCAAAAGCAA-CAGTATTCCAACACAACAACCGATT
1 TAAACATATAAACAATCGATTCAAAAG-AAGCAGTATTCCAACACAACAACCAATT
267758 TAAACATATAAACAATCGATTCAAAAGAAG
1 TAAACATATAAACAATCGATTCAAAAGAAG
267788 AAAAAGTAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
54 2 0.03
55 71 0.95
56 2 0.03
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (55 bp):
TAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACACAACAACCAATT
Found at i:268824 original size:21 final size:20
Alignment explanation
Indices: 268776--268824 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
268766 TAGGAGTTTG
* **
268776 AATCAATTCAAACAATAATG
1 AATCAATTCAAACAACAAAC
*
268796 AATTAATTCAAAACAACAAAC
1 AATCAATTC-AAACAACAAAC
268817 AATCAATT
1 AATCAATT
268825 GAAATAAGCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.24
Consensus pattern (20 bp):
AATCAATTCAAACAACAAAC
Found at i:269102 original size:55 final size:55
Alignment explanation
Indices: 269006--269236 Score: 264
Period size: 55 Copynumber: 4.2 Consensus size: 55
268996 ATGTGTTATG
* * * *
269006 TAACAATCGATTTAAACATATAAACAATCGATTCAAGAGAAGTAGTATTCCAACA
1 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTATTCCAACA
* * *
269061 TAACAATCAATTTAATCATATACACAATCAATTAAAAAGAAGCAGTATTCCAACA
1 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTATTCCAACA
* * **
269116 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTGTTCTAATT
1 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTATTCCAACA
* * * * * * * * *
269171 TGACAATCGATTTAAACATACAAAGAATCGACTCAAAAGAAGCACTATTCCAACA
1 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTATTCCAACA
* *
269226 TGATAATCAAT
1 TAACAATCAAT
269237 CCAAAAGAAG
Statistics
Matches: 147, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (55 bp):
TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTATTCCAACA
Found at i:270654 original size:26 final size:26
Alignment explanation
Indices: 270623--270679 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
270613 GCCCTTTTTT
* **
270623 AATAAACACAAAAAATTTATTTTAAA
1 AATAAAAACAAAAAAAGTATTTTAAA
*
270649 AATAAAAAATAAAAAAAGTATTTTAAA
1 AAT-AAAAACAAAAAAAGTATTTTAAA
270676 AATA
1 AATA
270680 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (26 bp):
AATAAAAACAAAAAAAGTATTTTAAA
Found at i:283516 original size:14 final size:16
Alignment explanation
Indices: 283487--283523 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
283477 TCTCTTCTTA
283487 AAAAAAACAAAGAGAG
1 AAAAAAACAAAGAGAG
283503 AAAAAAA-AAA-AGAG
1 AAAAAAACAAAGAGAG
283517 AAAAAAA
1 AAAAAAA
283524 GAAGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAGAGAG
Found at i:286547 original size:114 final size:114
Alignment explanation
Indices: 286347--286772 Score: 457
Period size: 114 Copynumber: 3.7 Consensus size: 114
286337 GTTTACTACC
** * * * * *
286347 AAGCGCCGCAAAAGCTCTTATCCAAAACGCAGCGCTTTGGTCTTGATGTATAGTAGCCTTAGTGG
1 AAGCGCCGC-AAATTTCTTAACCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGG
* * *
286412 CGCTTATATTCAAACGTCGCTAAAGTATAGTATTAGCGGCGAGTACTGAA
65 CGCTTATATTAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTACTGAA
* *
286462 AAGCGCCGCAATATTTCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTACATTAGGATTAGTGG
1 AAGCGCCGCAA-ATTTCTTAACCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGG
* * * ** * *
286526 CGCTTAT-TTAAAAACGCCGCTAACGCATAGTAGTAGCGGCGCTTATTGTA
65 CGCTTATATT-AAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTACTGAA
* * * * * * * *
286576 AAGCGTCGCAAA-ATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTACCAGTAGTGGC
1 AAGCGCCGCAAATTTCTTAACCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGC
* ** * *
286640 ACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAA
66 GCTTATATTAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTACTGAA
* *
286689 AAGCGCCGCAAGATTTCTTAACCAAAACGCAGAG-TTTGGTCTTGCGGTATATTAGGATTAGTGG
1 AAGCGCCGCAA-ATTTCTTAACCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGG
*
286753 CGCTTAT-TGGAAAACGCCGC
65 CGCTTATAT-TAAAACGCCGC
286773 AAAATATTAA
Statistics
Matches: 251, Mismatches: 53, Indels: 15
0.79 0.17 0.05
Matches are distributed among these distances:
112 17 0.07
113 74 0.29
114 116 0.46
115 44 0.18
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (114 bp):
AAGCGCCGCAAATTTCTTAACCAAAACGCAGAGCTTTGGTCTTGAGGTATATTAGCATTAGTGGC
GCTTATATTAAAACGCCGCTAAAGAATAGTATTAGCGGCGAGTACTGAA
Found at i:286880 original size:188 final size:188
Alignment explanation
Indices: 286563--286965 Score: 698
Period size: 188 Copynumber: 2.1 Consensus size: 188
286553 TAGTAGTAGC
* * *
286563 GGCGCTTATTGTAAAGCGTCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
1 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
286628 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
66 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
* * *
286693 GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGCGGTATATTAGGATTAGT
131 GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
286751 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
1 GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
* * *
286816 AGCAGTAGTGGCACTTATATTAAAACGCTGCTAAAGAATAGTATTAGCGGCGAGTAGTGAAAAGC
66 ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
*
286881 GCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
131 GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
* *
286939 GGCGCTTATTTGAAAACGCCGCTAAAT
1 GGCGCTTATTGGAAAACGCCGCAAAAT
286966 CATAGTATTA
Statistics
Matches: 203, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
188 203 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (188 bp):
GGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACT
ACCAGTAGTGGCACTTATATTAAAACGCTACTAAAGAATAGTATTAGCAGCGAGTAGTGAAAAGC
GCCGCAAGATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACATTACGATTAGT
Found at i:287088 original size:113 final size:112
Alignment explanation
Indices: 286745--287095 Score: 406
Period size: 113 Copynumber: 3.1 Consensus size: 112
286735 GTATATTAGG
* *
286745 ATTAGTGGCGCTTATTGGAAAA-CGCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGAT
1 ATTAGCGGCGCTTATT-GAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGAT
* * * *
286809 GTATACTAGCAGTAGTGGCACTTATATTAAAACGCTGCTAAAGA-ATAGT
65 GTATACTACCAGTTGTGGCGCTTAT-TTAAAACGCCGCTAAA-ACATAGT
** * * *
286858 ATTAGCGGCGAGTAGTGAAAAGCGCCGCAATATTTC-TTAACCAAAACGCAGAG-TTTGGTCTTG
1 ATTAGCGGCGCTTATTGAAAAGCGCCGCAA-A--ACATTAACCAAAACGCAGCGCTTTGGTCTTG
* * * * *
286921 AGGTACATTACGA-TTAGTGGCGCTTATTTGAAAACGCCGCTAAATCATAGT
63 ATGTATACTACCAGTT-GTGGCGCTTATTT-AAAACGCCGCTAAAACATAGT
*
286972 ATTAGCGGCGCTTATTGTAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
1 ATTAGCGGCGCTTATTGAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
* * *
287037 TATACTACCAGTTGTGGCGCTTATGGTAAAACGCCGGTAAAACATATT
66 TATACTACCAGTTGTGGCGCTTAT-TTAAAACGCCGCTAAAACATAGT
287085 ATTAGCGGCGC
1 ATTAGCGGCGC
287096 GTTGTGGGAA
Statistics
Matches: 197, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
111 1 0.01
112 21 0.11
113 83 0.42
114 76 0.39
115 16 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
ATTAGCGGCGCTTATTGAAAAGCGCCGCAAAACATTAACCAAAACGCAGCGCTTTGGTCTTGATG
TATACTACCAGTTGTGGCGCTTATTTAAAACGCCGCTAAAACATAGT
Found at i:287148 original size:17 final size:17
Alignment explanation
Indices: 287117--287166 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
287107 CGCCGCTAGA
*
287117 TTATTATAT-ATGTAGT
1 TTATTATATAATGTAGG
287133 TTATTATATAATGTAGG
1 TTATTATATAATGTAGG
287150 TTATTATATAATGTAGG
1 TTATTATATAATGTAGG
287167 AAATAGGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATTATATAATGTAGG
Found at i:287218 original size:7 final size:7
Alignment explanation
Indices: 287206--287282 Score: 57
Period size: 7 Copynumber: 11.0 Consensus size: 7
287196 TTTGAATTCT
287206 GGTTTAG
1 GGTTTAG
287213 GGTTTAG
1 GGTTTAG
*
287220 AGTTTAG
1 GGTTTAG
*
287227 GGTTTAA
1 GGTTTAG
*
287234 GGTTTAC
1 GGTTTAG
* *
287241 GATGTA-
1 GGTTTAG
287247 GGTTTAG
1 GGTTTAG
* **
287254 TGTTTTT
1 GGTTTAG
287261 GGTTTAG
1 GGTTTAG
287268 GGTTTGAG
1 GGTTT-AG
*
287276 AGTTTAG
1 GGTTTAG
287283 TGATTAAGGT
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
6 4 0.08
7 43 0.81
8 6 0.11
ACGTcount: A:0.18, C:0.01, G:0.35, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:289243 original size:11 final size:11
Alignment explanation
Indices: 289206--289245 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
289196 GAATATCTCA
289206 AACT-ATGGGT
1 AACTAATGGGT
*
289216 AACTAGTGGGT
1 AACTAATGGGT
289227 AACTAATGGGT
1 AACTAATGGGT
289238 AACTAATG
1 AACTAATG
289246 TATTATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:290608 original size:17 final size:17
Alignment explanation
Indices: 290586--290884 Score: 161
Period size: 17 Copynumber: 16.6 Consensus size: 17
290576 GTTAAATTTA
290586 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
290603 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
290620 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
290643 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
290660 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
* *
290677 TTACATAAATTTGTTTAAATTTA-
1 TTAC-TAAA-----ATACA-TTAC
*
290700 TTTCTAAAATACATTAC
1 TTACTAAAATACATTAC
*
290717 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
290740 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
290757 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
290774 TTACTAAAAT---TT-G
1 TTACTAAAATACATTAC
** *
290787 TT--T-AAATTTATTAA
1 TTACTAAAATACATTAC
*
290801 TTACTTAAATACATTAC
1 TTACTAAAATACATTAC
*
290818 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
290841 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
290858 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
290875 TTACTAAAAT
1 TTACTAAAAT
290885 TTGTTTAAAT
Statistics
Matches: 225, Mismatches: 18, Indels: 78
0.70 0.06 0.24
Matches are distributed among these distances:
10 4 0.02
11 1 0.00
13 4 0.02
14 4 0.02
16 13 0.06
17 136 0.60
18 4 0.02
22 4 0.02
23 43 0.19
24 12 0.05
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.43
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:290659 original size:40 final size:40
Alignment explanation
Indices: 290603--290766 Score: 157
Period size: 40 Copynumber: 3.7 Consensus size: 40
290593 AATACATTAC
*
290603 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
290643 TTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGTTTAAA
1 TTACTAAAATACATTACTTACTAAAAT---TT-GTT---TAAA----TTT--A
290696 TTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 -TTA---CTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
290740 TTACTAAAATACATTACTTACTAAAAT
1 TTACTAAAATACATTACTTACTAAAAT
290767 ACATTACTTA
Statistics
Matches: 104, Mismatches: 3, Indels: 34
0.74 0.02 0.24
Matches are distributed among these distances:
40 50 0.48
43 5 0.05
44 3 0.03
46 3 0.03
47 4 0.04
50 4 0.04
51 3 0.03
53 3 0.03
54 5 0.05
57 24 0.23
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:290665 original size:57 final size:57
Alignment explanation
Indices: 290577--290726 Score: 266
Period size: 57 Copynumber: 2.6 Consensus size: 57
290567 CGATTGAATG
290577 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTAC-TAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACAT-AAATTTGT
*
290634 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
*
290691 TTAAATTTATTTCTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
290727 TTGTTTAAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
57 89 0.99
58 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACATAAATTTGT
Found at i:290722 original size:97 final size:97
Alignment explanation
Indices: 290606--290917 Score: 518
Period size: 97 Copynumber: 3.2 Consensus size: 97
290596 ACATTACTTA
*
290606 CTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
290671 CATTACTTAC-ATAAATTTGTTTAAATTTATTT
66 CATTACTTACTA-AAATTTGTTTAAATTTATTT
290703 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
290768 CATTACTTACTAAAATTTGTTTAAATTTATTAATT
66 CATTACTTACTAAAATTTGTTTAAATTTA-T--TT
*
290803 ACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAAT
1 -CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAAT
*
290868 ACATTACTTACTAAAATTTGTTTAAATTTATTA
65 ACATTACTTACTAAAATTTGTTTAAATTTATTT
* **
290901 CTTAAATATGTTACTTA
1 CTAAAATACATTACTTA
290918 AATTTATTAC
Statistics
Matches: 205, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
97 106 0.52
98 3 0.01
100 3 0.01
101 93 0.45
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (97 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATA
CATTACTTACTAAAATTTGTTTAAATTTATTT
Found at i:290764 original size:57 final size:60
Alignment explanation
Indices: 290703--290827 Score: 211
Period size: 57 Copynumber: 2.1 Consensus size: 60
290693 AAATTTATTT
290703 CTAAAATACATTACTTACTAAAATTTGTTTAAA-T-TT-ATTACTAAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
*
290760 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAA-TTATTAATTACTAAAATACATTACTTA
290821 CTAAAAT
1 CTAAAAT
290828 TTGTTTAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
57 33 0.52
59 1 0.02
60 2 0.03
61 27 0.43
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (60 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
Found at i:290835 original size:101 final size:100
Alignment explanation
Indices: 290598--290900 Score: 533
Period size: 101 Copynumber: 3.0 Consensus size: 100
290588 ACTAAAATAC
*
290598 ATTACTTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
1 ATTA-TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
290663 CTAAAATACATTACTTAC-ATAAATTTGTTTAAATTT
65 CTAAAATACATTACTTACTA-AAATTTGTTTAAATTT
290699 A-T-TT-CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
1 ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
290761 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
66 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
290796 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
1 ATT-ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
290861 CTAAAATACATTACTTACTAAAATTTGTTTAAATTT
65 CTAAAATACATTACTTACTAAAATTTGTTTAAATTT
290897 ATTA
1 ATTA
290901 CTTAAATATG
Statistics
Matches: 195, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
97 91 0.47
98 4 0.02
100 4 0.02
101 96 0.49
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (100 bp):
ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
TAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:290844 original size:40 final size:43
Alignment explanation
Indices: 290752--290867 Score: 184
Period size: 44 Copynumber: 2.7 Consensus size: 43
290742 ACTAAAATAC
*
290752 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAA-TT
*
290796 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAA-T
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
290838 -TT-ATTACTAAAATACATTACTTACTAAAAT
1 ATTAATTACTAAAATACATTACTTACTAAAAT
290868 ACATTACTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 27 0.39
41 2 0.03
42 1 0.01
44 39 0.57
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (43 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATT
Found at i:290871 original size:57 final size:57
Alignment explanation
Indices: 290796--290917 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
290786 GTTTAAATTT
* *
290796 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
* *
290853 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTTAAATAT
1 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
*
290910 GTTACTTA
1 ATTACTTA
290918 AATTTATTAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATAC
Found at i:290907 original size:13 final size:13
Alignment explanation
Indices: 290889--290959 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
290879 TAAAATTTGT
290889 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
290902 TTAAATATGTTAC
1 TTAAATTTATTAC
290915 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
290928 TTAAATATGTTAC
1 TTAAATTTATTAC
290941 TTAAATTTATTAC
1 TTAAATTTATTAC
290954 TTAAAT
1 TTAAAT
290960 AATTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:290925 original size:26 final size:26
Alignment explanation
Indices: 290889--290960 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
290879 TAAAATTTGT
290889 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
290915 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
290941 TTAAATTTATTACTTAAATA
1 TTAAATTTATTACTTAAATA
290961 ATTATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAATTTATTACTTAAATATGTTAC
Found at i:291189 original size:73 final size:73
Alignment explanation
Indices: 291106--291255 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
291096 TAAAATAAAA
291106 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
291171 TTAATAAT
66 TTAATAAT
291179 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
291244 TTAATAAT
66 TTAATAAT
291252 TATA
1 TATA
291256 TTAGTAATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (73 bp):
TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
TTAATAAT
Found at i:291222 original size:38 final size:38
Alignment explanation
Indices: 291107--291223 Score: 118
Period size: 38 Copynumber: 3.2 Consensus size: 38
291097 AAAATAAAAT
291107 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
*** * * * *
291145 ATAAAATGTTAT-T---TTATTAAATATT-ATTAATAATT
1 ATAAAAAAATATGTGGAATATTAAA-ATTGACTATTAA-A
291180 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
1 ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
291218 ATAAAA
1 ATAAAA
291224 TGTTATTTTA
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
34 13 0.22
35 12 0.21
36 1 0.02
37 1 0.02
38 18 0.31
39 13 0.22
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (38 bp):
ATAAAAAAATATGTGGAATATTAAAATTGACTATTAAA
Found at i:291320 original size:19 final size:19
Alignment explanation
Indices: 291296--291618 Score: 110
Period size: 19 Copynumber: 17.5 Consensus size: 19
291286 TATTAAATAA
291296 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
291315 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
*
291333 TACAT--T-ACTTACATA-A
1 TACATAATAACTTACA-ACT
291349 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
291368 TACATAATACATTTAACTTACAACT
1 TAC---ATA-A--TAACTTACAACT
**
291393 TACATAAT-ACATT-TGACT
1 TACATAATAAC-TTACAACT
* *
291411 GACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* *
291429 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
291443 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* *
291462 TACATAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
* *
291481 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
291495 TACATAATAACTTACAACTTACAT
1 TACATAATAACTTAC-A---AC-T
291519 AATACATAATAACTTACAACT
1 --TACATAATAACTTACAACT
*
291540 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* * *
291558 TGCA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
*
291572 TACATAATAACTTAC-ACAA
1 TACATAATAACTTACAAC-T
291591 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
291610 TACATAATA
1 TACATAATA
291619 CATTTAACTT
Statistics
Matches: 232, Mismatches: 27, Indels: 90
0.66 0.08 0.26
Matches are distributed among these distances:
14 11 0.05
15 14 0.06
16 17 0.07
17 13 0.06
18 55 0.24
19 77 0.33
20 2 0.01
21 3 0.01
22 8 0.03
23 1 0.00
25 16 0.07
26 15 0.06
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:291334 original size:18 final size:18
Alignment explanation
Indices: 291311--291432 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
291301 AATAACTTAC
291311 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
291329 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
291347 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
291364 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--T---TT
291387 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
* *
291407 GACTGACATAATACATTT
1 AACTTACATAATACATTT
291425 AACTTACA
1 AACTTACA
291433 ACTTACACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 2 0.03
16 4 0.05
17 2 0.03
18 33 0.41
19 11 0.14
20 7 0.09
21 1 0.01
23 1 0.01
24 1 0.01
25 15 0.19
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:291375 original size:26 final size:26
Alignment explanation
Indices: 291292--291690 Score: 516
Period size: 26 Copynumber: 16.1 Consensus size: 26
291282 ATTTTATTAA
291292 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291318 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
291345 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291371 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
291396 ATAATAC---AT---TT--GACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
291414 ATAATACATT-TAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291439 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
291465 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291491 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
291517 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
291543 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291568 ACAATACATAATAACTT---AC--AC
1 ATAATACATAATAACTTACAACTTAC
291589 --AATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
291613 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
291638 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
291663 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
291689 AT
1 AT
291691 TTAACTTACA
Statistics
Matches: 331, Mismatches: 21, Indels: 42
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.04
19 15 0.05
20 3 0.01
21 2 0.01
22 2 0.01
23 5 0.02
24 2 0.01
25 113 0.34
26 153 0.46
27 15 0.05
28 9 0.03
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:291698 original size:11 final size:10
Alignment explanation
Indices: 291682--291735 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
291672 AATAACTTAC
291682 AACTTACATTT
1 AACTTACA-TT
291693 AACTTACA-T
1 AACTTACATT
291702 AA--TACATTT
1 AACTTACA-TT
291711 AACTTACA-T
1 AACTTACATT
291720 AACTTACA-T
1 AACTTACATT
291729 AACTTAC
1 AACTTAC
291736 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:291719 original size:18 final size:18
Alignment explanation
Indices: 291656--291721 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
291646 TTTAACTTAC
*
291656 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
291675 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
291693 AACTTACATAATACATTT
1 AACTTACATAATACATTT
291711 AACTTACATAA
1 AACTTACATAA
291722 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:291731 original size:18 final size:18
Alignment explanation
Indices: 291597--291735 Score: 65
Period size: 18 Copynumber: 8.0 Consensus size: 18
291587 ACAATACATA
291597 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
291613 ATAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
291631 --AACTTACACAA--TAC
1 ATAACTTACATAACTTAC
291645 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
291663 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
291682 --AACTTACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
291700 ATAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
291718 ATAACTTACATAACTTAC
1 ATAACTTACATAACTTAC
291736 CATTGCAATT
Statistics
Matches: 97, Mismatches: 3, Indels: 44
0.67 0.02 0.31
Matches are distributed among these distances:
14 6 0.06
15 4 0.04
16 13 0.13
17 1 0.01
18 60 0.62
19 7 0.07
20 6 0.06
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:297210 original size:21 final size:21
Alignment explanation
Indices: 297184--297254 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
297174 CTACAACTTA
* *
297184 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
297205 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
297226 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
297247 AAGCAGAG
1 AAGCAGAG
297255 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:297497 original size:14 final size:14
Alignment explanation
Indices: 297478--297511 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
297468 ATTGCTATTG
297478 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
297492 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
*
297506 TTTGCT
1 GTTGCT
297512 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (14 bp):
GTTGCTTTTGAAAT
Found at i:297720 original size:126 final size:125
Alignment explanation
Indices: 297580--297867 Score: 362
Period size: 126 Copynumber: 2.3 Consensus size: 125
297570 TTTTGTATAA
* * * *
297580 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAAAAATGCCACTAAAGAACATGTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAACGCCACTAAAGAACATGGTCT
297645 TTAGCGGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCAT-T
66 TTAGCGGC-ATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-CATCT
* ** * *
297706 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGGTC
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAAAAAACGCCACTAAAGAACATGGTC
* ***** * **
297771 TTTAGTGGCATTTTTTTACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
65 TTTAGCGGCATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCATCT
* *
297832 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT
297868 TTGTTTGTAA
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
125 4 0.03
126 104 0.74
127 32 0.23
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAACGCCACTAAAGAACATGGTCT
TTAGCGGCATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCATCT
Found at i:297731 original size:42 final size:40
Alignment explanation
Indices: 297580--297868 Score: 256
Period size: 42 Copynumber: 6.9 Consensus size: 40
297570 TTTTGTATAA
* * **
297580 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTT-TATT
** * ** **
297621 AAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TT--TTATT
* *
297664 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCATT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT--ATT
297706 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT-TT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTATT
* * * *
297745 CCAAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTT
1 ---AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTATT
* * *
297788 ACAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 --AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTAT-T
* *
297832 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTT
297869 TGTTTGTAAA
Statistics
Matches: 211, Mismatches: 26, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
39 2 0.01
41 34 0.16
42 133 0.63
43 41 0.19
44 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (40 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTATT
Found at i:297755 original size:84 final size:82
Alignment explanation
Indices: 297565--297868 Score: 320
Period size: 84 Copynumber: 3.6 Consensus size: 82
297555 CAAAAATAGT
* * * * ** * *
297565 GGCGTTTTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAAAAATGCCAC
1 GGCGTTTTT-TA-CAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-TATTAAACGCCGC
297630 TAAAGAACATGTTCTTTAGC
63 TAAAGAACATGTTCTTTAGC
**** * * * *
297650 GGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCATTAAGCGCCGC
1 GGCG-TTTTTTACAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTT--ATTAAACGCCGC
297715 TAAAGAACATGTTCTTTAGC
63 TAAAGAACATGTTCTTTAGC
* * * *
297735 GGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCT
1 GGCGTTTTTTACAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTATT--AAACGCCGCT
*
297800 AAAGAACATGATCTTTAGC
64 AAAGAACATGTTCTTTAGC
* * *
297819 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTT
1 GGCGTTTTTTACAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTT
297869 TGTTTGTAAA
Statistics
Matches: 183, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
82 2 0.01
83 1 0.01
84 142 0.78
85 36 0.20
86 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (82 bp):
GGCGTTTTTTACAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTATTAAACGCCGCTAA
AGAACATGTTCTTTAGC
Found at i:297869 original size:42 final size:42
Alignment explanation
Indices: 297667--297869 Score: 275
Period size: 42 Copynumber: 4.8 Consensus size: 42
297657 AGAAAAAAAA
**
297667 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCAT-TAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTTCTAAG
* * *
297709 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCAAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * *
297751 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAG
297793 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
297835 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
297870 GTTTGTAAAC
Statistics
Matches: 142, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
41 1 0.01
42 140 0.99
43 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:314996 original size:18 final size:19
Alignment explanation
Indices: 314973--315010 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
314963 GGAAGCAAGC
*
314973 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
314991 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
315010 A
1 A
315011 CTGGAGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:320625 original size:110 final size:110
Alignment explanation
Indices: 320428--320745 Score: 455
Period size: 110 Copynumber: 2.9 Consensus size: 110
320418 AAGGAAATTT
* * * *
320428 TTTCTAAATAAGGCAATGTTTAGCTTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTT
320493 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTT-TCAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
* * *
320537 TTTCAAAATAAGGCAATGTTTTGCCGTTTAGAAATTCTAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTCAAAATAAGGCAATGTTTTG-CGTTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTT
* * *
320602 TCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTTAAAAA
65 TCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
* * *
320648 TTTCAAAATAAGGCAATGTTTTGCGTTTGGGAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTT
* * *
320712 CGA--TTTCTCGTTTAACCAAATTGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
320746 ATTGAATTTA
Statistics
Matches: 187, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
107 27 0.14
109 46 0.25
110 85 0.45
111 29 0.16
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (110 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
Found at i:324268 original size:7 final size:7
Alignment explanation
Indices: 324258--324308 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
324248 AAAAAAAGGG
324258 AAAAAAT
1 AAAAAAT
324265 AAAAAA-
1 AAAAAAT
*
324271 AAACAAAA
1 AAA-AAAT
324279 ACAAAAAT
1 A-AAAAAT
*
324287 CAAAAAT
1 AAAAAAT
*
324294 CAAAAAT
1 AAAAAAT
324301 AAAAAAT
1 AAAAAAT
324308 A
1 A
324309 GAAGTCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
6 3 0.08
7 29 0.76
8 4 0.11
9 2 0.05
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:324290 original size:13 final size:13
Alignment explanation
Indices: 324265--324305 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
324255 GGGAAAAAAT
324265 AAAA-AAAAA-CA
1 AAAACAAAAATCA
324276 AAAACAAAAATCA
1 AAAACAAAAATCA
324289 AAAATCAAAAAT-A
1 AAAA-CAAAAATCA
324302 AAAA
1 AAAA
324306 ATAGAAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 11 0.41
14 7 0.26
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAACAAAAATCA
Found at i:327064 original size:125 final size:125
Alignment explanation
Indices: 326915--327441 Score: 975
Period size: 125 Copynumber: 4.2 Consensus size: 125
326905 CTCACTTCCC
* * * *
326915 CATTGCAATTTAAAAGATTGAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATTTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
*
326980 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCTAAATTGGTGAATCTTGTTTCTCCGA
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
327040 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
327105 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
*
327165 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTCATTAAAGCTACAACAGCGAATCTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
327230 ACG-CCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
* *
327289 CATTGCAGTTAAAAAGATTAAAGCCACACCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
327354 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
327414 CATTGCAGTTAAAAAGATTAAAGCCACA
1 CATTGCAGTTAAAAAGATTAAAGCCACA
327442 ATGGCGAATC
Statistics
Matches: 393, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
124 122 0.31
125 271 0.69
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (125 bp):
CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTT
ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
Found at i:327101 original size:25 final size:25
Alignment explanation
Indices: 327055--327104 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
327045 CAGTTAAAAA
* * *
327055 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
327080 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
327105 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:327453 original size:249 final size:250
Alignment explanation
Indices: 326915--327441 Score: 975
Period size: 249 Copynumber: 2.1 Consensus size: 250
326905 CTCACTTCCC
* * * * *
326915 CATTGCAATTTAAAAGATTGAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATTTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTCATTAAAGCTACAACAGCGAATCTT
*
326980 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCTAAATTGGTGAATCTTGTTTCTCCGACATTG
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTG
* *
327045 CAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTGATTAAAGCTACAACAGCGAATCTTACGCC
131 CAGTTAAAAAGATTAAAGCCACACCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTTACGCC
327110 CCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
196 CCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
327165 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTCATTAAAGCTACAACAGCGAATCTT
1 CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTCATTAAAGCTACAACAGCGAATCTT
327230 ACG-CCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTG
66 ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTG
327294 CAGTTAAAAAGATTAAAGCCACACCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTTACGCC
131 CAGTTAAAAAGATTAAAGCCACACCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTTACGCC
327359 CCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
196 CCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
327414 CATTGCAGTTAAAAAGATTAAAGCCACA
1 CATTGCAGTTAAAAAGATTAAAGCCACA
327442 ATGGCGAATC
Statistics
Matches: 269, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
249 206 0.77
250 63 0.23
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (250 bp):
CATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTTCATTAAAGCTACAACAGCGAATCTT
ACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGACATTG
CAGTTAAAAAGATTAAAGCCACACCGGTGAATCTTAATTAAAGCTACAACAGCGAATCTTACGCC
CCAAGCGATGCAGTGGAATAGATTAAAGCCAAATTGGTGAATCTTGTTTCTCCGA
Found at i:330518 original size:110 final size:109
Alignment explanation
Indices: 330331--330647 Score: 451
Period size: 110 Copynumber: 2.9 Consensus size: 109
330321 AAGGAAAATT
* * * *
330331 TTTCTAAATAAGGCAATGTTTAGCTTTTGGAAATTCGAGAAACGTGCCCTAATGTGCTGGGTTTC
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTC
330396 GATTTTTCTCGTTCAACCAAATAGCTAAATATCCTT-TCAAAAA
66 GATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
* * *
330439 TTTCAAAATAAGGCAATGTTTTGCCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTCAAAATAAGGCAATGTTTTG-CGTTTGGAAATTCGAG-AAACGTGCCCTAAGGTGCTGGGTT
* * *
330504 TCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTGAAAAA
64 TCGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
* * *
330550 TTTCAAAATAAGGCAATGTTTTACGTTTGGGAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTC
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTC
* * *
330615 GA--TTTCTCGTTTAACCAAATTGCCAAATATCCT
66 GATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
330648 ATTGAATTTA
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
107 27 0.15
108 21 0.11
109 39 0.21
110 71 0.38
111 28 0.15
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTTC
GATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTCAAAAA
Found at i:334444 original size:17 final size:17
Alignment explanation
Indices: 334422--334455 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
334412 ATCCACTAAT
*
334422 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
334439 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
334456 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:339074 original size:17 final size:17
Alignment explanation
Indices: 339052--339085 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
339042 ATCCACTAAT
*
339052 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
339069 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
339086 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:341439 original size:14 final size:14
Alignment explanation
Indices: 341420--341451 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
341410 TTTTAATGCA
341420 TGTTAAACATATTT
1 TGTTAAACATATTT
341434 TGTTAAACATATTT
1 TGTTAAACATATTT
341448 TGTT
1 TGTT
341452 CACAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (14 bp):
TGTTAAACATATTT
Found at i:342690 original size:42 final size:42
Alignment explanation
Indices: 342629--342709 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
342619 AAGTCGTCTA
342629 CGTAGTTTATAGATGTTCTTATATGATTCTATGGTGTCGCAT
1 CGTAGTTTATAGATGTTCTTATATGATTCTATGGTGTCGCAT
* *
342671 CGTAGTTTGTAGATTTTCTTATATGATTCTATGGTGTCG
1 CGTAGTTTATAGATGTTCTTATATGATTCTATGGTGTCG
342710 ATGCTTGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (42 bp):
CGTAGTTTATAGATGTTCTTATATGATTCTATGGTGTCGCAT
Found at i:343263 original size:48 final size:48
Alignment explanation
Indices: 343189--343285 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
343179 GTGGAATGTC
*
343189 ATGGAAAAAATTTGTTGATGCGAAGAATAATTTGTTTAAGACTAATAA
1 ATGGAAAAAATTTGTTGATGCAAAGAATAATTTGTTTAAGACTAATAA
** *
343237 ATGGAAAAGGTTTGTTGATGCAAAGAATAATTTGTTTAAGACTGATAA
1 ATGGAAAAAATTTGTTGATGCAAAGAATAATTTGTTTAAGACTAATAA
343285 A
1 A
343286 GTATTTGGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (48 bp):
ATGGAAAAAATTTGTTGATGCAAAGAATAATTTGTTTAAGACTAATAA
Found at i:357631 original size:7 final size:6
Alignment explanation
Indices: 357615--357670 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
357605 TGTTTTCTGC
* *
357615 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
*
357665 AGAAAT
1 AAAAAT
357671 TTTTTTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 5 0.12
6 25 0.60
7 7 0.17
8 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:357670 original size:19 final size:19
Alignment explanation
Indices: 357616--357670 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
357606 GTTTTCTGCA
*
357616 AAAAT-AAA-AATGAAAAT
1 AAAATAAAATAATAAAAAT
*
357633 AAAATAAAATAGTAAAAAT
1 AAAATAAAATAATAAAAAT
*
357652 -AAATAATAATAATAGAAAT
1 AAAATAA-AATAATAAAAAT
357671 TTTTTTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 5 0.16
18 9 0.29
19 17 0.55
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAATAAAAAT
Found at i:364201 original size:20 final size:20
Alignment explanation
Indices: 364176--364236 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
364166 ATTTAGAAAA
*
364176 TAAATAATTTTTTGAAAATT
1 TAAATAATTTTTTGATAATT
364196 TAAATAATTTTTTGATAATT
1 TAAATAATTTTTTGATAATT
364216 TAAATAATTTTTTGATAATT
1 TAAATAATTTTTTGATAATT
364236 T
1 T
364237 TTTTAGAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TAAATAATTTTTTGATAATT
Found at i:364240 original size:12 final size:11
Alignment explanation
Indices: 364199--364239 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
364189 GAAAATTTAA
364199 ATAATTTTTTG
1 ATAATTTTTTG
**
364210 ATAA--TTTAA
1 ATAATTTTTTG
364219 ATAATTTTTTG
1 ATAATTTTTTG
364230 ATAATTTTTT
1 ATAATTTTTT
364240 TAGAATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 7 0.29
11 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (11 bp):
ATAATTTTTTG
Found at i:364413 original size:21 final size:21
Alignment explanation
Indices: 364388--364430 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
364378 TTGTGGGACA
*
364388 TGTCACTCTTGCCCAATCAGT
1 TGTCACTCTTACCCAATCAGT
*
364409 TGTCATTCTTACCCAATCAGT
1 TGTCACTCTTACCCAATCAGT
364430 T
1 T
364431 CTCCTAGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (21 bp):
TGTCACTCTTACCCAATCAGT
Found at i:375946 original size:42 final size:42
Alignment explanation
Indices: 375900--376036 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
375890 TAGAAAAGAC
** *
375900 AAACTGAAGCTGGAGAAGGATGAAGCTGACTTAAAAGAGAAG
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
375942 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
* * *
375984 AAACTGAAGCTGGATCAGGACGAAGCTGAGTTAAAAGAAAAC
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
*
376026 CAACTGAAGCT
1 AAACTGAAGCT
376037 AGCCAGGTTG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.15
Consensus pattern (42 bp):
AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
Found at i:376220 original size:74 final size:75
Alignment explanation
Indices: 376089--376283 Score: 293
Period size: 74 Copynumber: 2.6 Consensus size: 75
376079 TTTGAAATAC
* * * *
376089 AATCTCAATGGTTTATTGGGATGTTTATAAACTGAAGATACTGCCAGTATGCATTTGTGTGATGG
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
376154 -TTGTGTTTG
66 TTTGTGTTTG
* * **
376163 AATGTCAATGGTTTATTGGGATGTTTATGAACTGAAGATGCAGACAATATGTGTTTGTGTGATGG
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
376228 TTTTGTGTTTG
66 -TTTGTGTTTG
*
376239 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGAC
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGAC
376284 TGTATTTGTG
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 57 0.53
76 51 0.47
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (75 bp):
AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
TTTGTGTTTG
Found at i:377014 original size:33 final size:31
Alignment explanation
Indices: 376971--377039 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
376961 CATATTATTT
*
376971 TTTTAAAATTTATTTATATTATTT-TTAATAC
1 TTTTAAAATTTATATATATTATTTATTAA-AC
*
377002 TATTTAATAATTTATATATTTTATTTATTAAAC
1 T-TTTAA-AATTTATATATATTATTTATTAAAC
377035 TTTTA
1 TTTTA
377040 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 9 0.27
33 19 0.58
34 4 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTAAAATTTATATATATTATTTATTAAAC
Found at i:377664 original size:11 final size:11
Alignment explanation
Indices: 377648--377673 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
377638 TACCATAATT
377648 ATTCAATTACA
1 ATTCAATTACA
377659 ATTCAATTACA
1 ATTCAATTACA
377670 ATTC
1 ATTC
377674 TATTTATTTC
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:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTCAATTACA
Found at i:380316 original size:21 final size:20
Alignment explanation
Indices: 380268--380316 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
380258 TAGGAGTTTG
* **
380268 AATCAATTCAAACAATAATG
1 AATCAATTCAAACAACAAAC
*
380288 AATTAATTCAAAACAACAAAC
1 AATCAATTC-AAACAACAAAC
380309 AATCAATT
1 AATCAATT
380317 GAAATAAGCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.24
Consensus pattern (20 bp):
AATCAATTCAAACAACAAAC
Found at i:381764 original size:3 final size:3
Alignment explanation
Indices: 381756--381782 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
381746 AATTAAAAAG
381756 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
381783 GGACTAGATT
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:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:382859 original size:15 final size:16
Alignment explanation
Indices: 382833--382862 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
382823 TAGTGTTTAG
382833 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
382849 GTGGG-TATTGGGTT
1 GTGGGTTATTGGGTT
382863 CTTTTGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.47, T:0.47
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:382995 original size:55 final size:55
Alignment explanation
Indices: 382902--383122 Score: 280
Period size: 55 Copynumber: 4.0 Consensus size: 55
382892 GTTTGTACAG
*
382902 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGTAGTATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
* * * * *
382957 TAACAATCGATTTAATCATATACACAATCAATTAAAAAGAAGCAGTATTCCAACT
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
* * * * * *
383012 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTGTTCCAACT
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
** * * * *
383067 TGGCAATCGATTTAAAGATATAAAGAATCGACTCAAAAGAAGCACTATTCCAACA
1 TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
383122 T
1 T
383123 GATAATTGAC
Statistics
Matches: 143, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 143 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACA
Found at i:384493 original size:39 final size:36
Alignment explanation
Indices: 384448--384525 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 36
384438 TTATACTTTT
384448 AAAAAATATAAATTTAAATTTTAAAGATGATATTATTG
1 AAAAAA-A-AAATTTAAATTTTAAAGATGATATTATTG
384486 ---AAAAAAATTTAAATTTTAAAGATGATATTATTG
1 AAAAAAAAAATTTAAATTTTAAAGATGATATTATTG
384519 AAAAAAA
1 AAAAAAA
384526 CAATCACGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
33 29 0.78
34 1 0.03
35 3 0.08
36 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (36 bp):
AAAAAAAAAATTTAAATTTTAAAGATGATATTATTG
Found at i:384495 original size:33 final size:33
Alignment explanation
Indices: 384457--384525 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
384447 TAAAAAATAT
384457 AAATTTAAATTTTAAAGATGATATTATTGAAAA
1 AAATTTAAATTTTAAAGATGATATTATTGAAAA
384490 AAATTTAAATTTTAAAGATGATATTATTGAAAA
1 AAATTTAAATTTTAAAGATGATATTATTGAAAA
384523 AAA
1 AAA
384526 CAATCACGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.38
Consensus pattern (33 bp):
AAATTTAAATTTTAAAGATGATATTATTGAAAA
Found at i:387132 original size:15 final size:13
Alignment explanation
Indices: 387096--387128 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
387086 CATTCTTTAT
387096 TTGGGTGTATTGTG
1 TTGGG-GTATTGTG
387110 TTGGGGTATTGTG
1 TTGGGGTATTGTG
387123 TTGGGG
1 TTGGGG
387129 GGTAATGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.06, C:0.00, G:0.48, T:0.45
Consensus pattern (13 bp):
TTGGGGTATTGTG
Found at i:390247 original size:20 final size:20
Alignment explanation
Indices: 390222--390271 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
390212 TGGCTTAAAA
390222 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
390242 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
390259 GTGGTAGTGGATT
1 TTGGTAGTGGATT
390272 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:394875 original size:20 final size:20
Alignment explanation
Indices: 394850--394899 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
394840 TGGCTTAAAA
394850 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
394870 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
394887 GTGGTAGTGGATT
1 TTGGTAGTGGATT
394900 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:399174 original size:3 final size:3
Alignment explanation
Indices: 399166--399223 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
399156 TTTTAGTGTC
* * *
399166 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ACT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
399214 AATT ATT ATT
1 -ATT ATT ATT
399224 GGCTTTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:403656 original size:12 final size:12
Alignment explanation
Indices: 403641--403698 Score: 116
Period size: 12 Copynumber: 4.8 Consensus size: 12
403631 ATTCCAAGAA
403641 CAGATGCAAGCT
1 CAGATGCAAGCT
403653 CAGATGCAAGCT
1 CAGATGCAAGCT
403665 CAGATGCAAGCT
1 CAGATGCAAGCT
403677 CAGATGCAAGCT
1 CAGATGCAAGCT
403689 CAGATGCAAG
1 CAGATGCAAG
403699 AAAAACTAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (12 bp):
CAGATGCAAGCT
Found at i:414121 original size:13 final size:13
Alignment explanation
Indices: 414103--414133 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
414093 TTTATGTGTC
414103 ATTATTAATTATT
1 ATTATTAATTATT
*
414116 ATTATTATTTATT
1 ATTATTAATTATT
414129 ATTAT
1 ATTAT
414134 CATTACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTATTAATTATT
Found at i:414124 original size:16 final size:16
Alignment explanation
Indices: 414103--414156 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
414093 TTTATGTGTC
414103 ATTATTAATTATTATT
1 ATTATTAATTATTATT
* *
414119 ATTATTTATTATTATC
1 ATTATTAATTATTATT
* * *
414135 ATTACTACTGATTATT
1 ATTATTAATTATTATT
414151 A-TATTA
1 ATTATTA
414157 TGGCTTTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
15 4 0.13
16 26 0.87
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTATTAATTATTATT
Found at i:433423 original size:43 final size:43
Alignment explanation
Indices: 433373--433483 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
433363 TTAATCCCCT
* * * *
433373 CACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTC
1 CACTGTAACTTCAGGGAGATAAGATACTGGCTTCAATCTGCTC
* *
433416 CGCTGTAA-TCTCAGGGAGATAAGATTCTGGCTTCAATCTGCTC
1 CACTGTAACT-TCAGGGAGATAAGATACTGGCTTCAATCTGCTC
*
433459 CACTGTAACCTCAGGGAGATAAGAT
1 CACTGTAACTTCAGGGAGATAAGAT
433484 CTGAATTCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 57 0.98
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
CACTGTAACTTCAGGGAGATAAGATACTGGCTTCAATCTGCTC
Found at i:445916 original size:28 final size:28
Alignment explanation
Indices: 445885--445959 Score: 64
Period size: 28 Copynumber: 2.6 Consensus size: 28
445875 AGACATAAAC
* *
445885 TAAAATATGTATATATTAACAA-AATATA
1 TAAAATATGTATATATTAA-AAGAAAAAA
* *
445913 TAAAGTATATTTAAATATATAAAAGAAAAAA
1 TAAA--ATATGTATATAT-TAAAAGAAAAAA
445944 T-AAATATGTATATATT
1 TAAAATATGTATATATT
445960 TATGAAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.38
30 14 0.38
31 8 0.22
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.36
Consensus pattern (28 bp):
TAAAATATGTATATATTAAAAGAAAAAA
Found at i:446088 original size:23 final size:22
Alignment explanation
Indices: 446047--446090 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
446037 CATATATGTT
* *
446047 ACAAAAATAATGTATATATATC
1 ACAAAAATAATGCACATATATC
446069 ACAAAAATATATGCACATATAT
1 ACAAAAATA-ATGCACATATAT
446091 ATATACCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (22 bp):
ACAAAAATAATGCACATATATC
Found at i:446137 original size:3 final size:3
Alignment explanation
Indices: 446129--446158 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
446119 AAATAAGTAG
446129 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
446159 GGACTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:454942 original size:17 final size:18
Alignment explanation
Indices: 454920--454955 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
454910 GAAGCAAGCA
*
454920 ATGATTGAAGA-AATCAG
1 ATGATTGAAAAGAATCAG
454937 ATGATTGAAAAGAATCAG
1 ATGATTGAAAAGAATCAG
454955 A
1 A
454956 CCTGGAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGATTGAAAAGAATCAG
Found at i:476651 original size:19 final size:20
Alignment explanation
Indices: 476629--476667 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
476619 ATCTATAGAT
476629 GCAATTTTTAGTC-AATTTC
1 GCAATTTTTAGTCAAATTTC
476648 GCAATTTTTAGTCAAATTTC
1 GCAATTTTTAGTCAAATTTC
476668 ACTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
GCAATTTTTAGTCAAATTTC
Found at i:476849 original size:6 final size:6
Alignment explanation
Indices: 476838--476866 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
476828 ATTAATCATG
476838 TTTATC TTTATC TTTATC TTTATC TTTAT
1 TTTATC TTTATC TTTATC TTTATC TTTAT
476867 ATAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATC
Found at i:481577 original size:33 final size:34
Alignment explanation
Indices: 481534--481602 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
481524 CCCCTCACTT
*
481534 TAAATTCATATTTCACTACACT-ATATCATTGGC
1 TAAATCCATATTTCACTACACTAATATCATTGGC
481567 TAAATCCATATTTCACTACACTAATATCATTGGC
1 TAAATCCATATTTCACTACACTAATATCATTGGC
481601 TA
1 TA
481603 TCATTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.38
Consensus pattern (34 bp):
TAAATCCATATTTCACTACACTAATATCATTGGC
Found at i:484108 original size:16 final size:16
Alignment explanation
Indices: 484075--484108 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
484065 TGAGTTTGTT
* *
484075 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
484091 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
484107 AA
1 AA
484109 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:486937 original size:21 final size:21
Alignment explanation
Indices: 486911--486951 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
486901 AGACGAGCAA
* *
486911 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
486932 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
486952 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:488888 original size:16 final size:16
Alignment explanation
Indices: 488855--488888 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
488845 GGAGATTGTT
* *
488855 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
488871 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
488887 AA
1 AA
488889 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:497206 original size:2 final size:2
Alignment explanation
Indices: 497201--497253 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
497191 TATATATATA
* * * * * *
497201 TG TG TG TG TG TG TA TA TG TA TG TA TG TA TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
497243 TG TG TG TG TG T
1 TG TG TG TG TG T
497254 ATGCATCACC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.11, C:0.00, G:0.38, T:0.51
Consensus pattern (2 bp):
TG
Found at i:509307 original size:30 final size:30
Alignment explanation
Indices: 509261--509354 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
509251 TTTTATTATG
*
509261 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
509292 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
509322 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
509352 CCA
1 CCA
509355 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:509316 original size:15 final size:15
Alignment explanation
Indices: 509271--509348 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
509261 CCAATATCTC
509271 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
509286 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
509301 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
509316 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
509331 GATACCCATATCTTT
1 GATACCCATATCTTT
509346 GAT
1 GAT
509349 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Done.