Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold313
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1192932
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 126135 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:924323 original size:42 final size:41
Alignment explanation
Indices: 924277--924703 Score: 435
Period size: 42 Copynumber: 10.4 Consensus size: 41
924267 TTATTTCATG
* *
924277 TGAAGATGGTGCTTTTATTTATGAAGACGGTGCTTTATTATA
1 TGAAGATGGTGCTTTT-TTTATGAAGATGGTGCTTTGTTATA
* * *
924319 TGAAGATGGTGCTTTTTTATATGAATATGGTGCTTTATTTTA
1 TGAAGATGGTGCTTTTTT-TATGAAGATGGTGCTTTGTTATA
* * * * * *
924361 AGAAGATGGTGC-TTTTTAATG-TGAAGGTGCTTTTTTATG
1 TGAAGATGGTGCTTTTTTTATGAAGATGGTGCTTTGTTATA
* *
924400 TGAAGATGGTGCATTGTTATATGAAGATGGTGCTTTGTTATA
1 TGAAGATGGTGC-TTTTTTTATGAAGATGGTGCTTTGTTATA
* *
924442 TGAAGATGGTGCTTTAATATATGAAGATGGTGCTTT-TT-TA
1 TGAAGATGGTGCTTT-TTTTATGAAGATGGTGCTTTGTTATA
* *
924482 TG-TGAAGGTGCTTTTTTTATGTGAAGATGGTGCTTTGTTATA
1 TGAAGATGGTGCTTTTTTTA--TGAAGATGGTGCTTTGTTATA
* * *
924524 TGAAGATGGTGCTTTGTTATATGAAGATGGTGCTTTTTTATG
1 TGAAGATGGTGCTTT-TTTTATGAAGATGGTGCTTTGTTATA
* *
924566 TGAAGATGATGCTTTTTTATGTGAAGATGGTGCTTTGTTATA
1 TGAAGATGGTGCTTTTTT-TATGAAGATGGTGCTTTGTTATA
* *
924608 TGAAGATGGTGCTTTATTATT-TGAAGATGGTGCTTTTTTAGA
1 TGAAGATGGTGCTTT-TT-TTATGAAGATGGTGCTTTGTTATA
* * *
924650 TAAAGATGGTGCTTTTTTATATG-TGATAGTGCTTT-TTATA
1 TGAAGATGGTGCTTTTTT-TATGAAGATGGTGCTTTGTTATA
924690 T---GATGGTGCTTTTT
1 TGAAGATGGTGCTTTTT
924704 AATGTGAAGG
Statistics
Matches: 327, Mismatches: 42, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
37 13 0.04
38 3 0.01
39 33 0.10
40 28 0.09
41 34 0.10
42 198 0.61
43 13 0.04
44 5 0.02
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (41 bp):
TGAAGATGGTGCTTTTTTTATGAAGATGGTGCTTTGTTATA
Found at i:924349 original size:63 final size:62
Alignment explanation
Indices: 924277--924717 Score: 479
Period size: 63 Copynumber: 7.2 Consensus size: 62
924267 TTATTTCATG
*
924277 TGAAGATGGTGCTTTTATTTATGAAGACGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
1 TGAAGATGGTGCTTTT-TTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
* * * * *
924340 TGAATATGGTGCTTTATTTTAAGAAGATGGTGCTTT-TTA-ATG-TGAAGGTGCTTTTTTATG
1 TGAAGATGGTGCTTT-TTTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
* * * **
924400 TGAAGATGGTGCATTGTTATATGAAGATGGTGCTTTGTTATATGAAGATGGTGCTTTAATATA
1 TGAAGATGGTGC-TTTTTTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
* * * * *
924463 TGAAGATGGTGC-TTTTTTATG-TGAAGGTGCTTTTTTTATGTGAAGATGGTGCTTTGTTATA
1 TGAAGATGGTGCTTTTTTTATGAAGATGGTGC-TTTATTATATGAAGATGGTGCTTTTTTATA
* * * * *
924524 TGAAGATGGTGCTTTGTTATATGAAGATGGTGCTTTTTTATGTGAAGATGATGCTTTTTTATG
1 TGAAGATGGTGCTTT-TTTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
* * *
924587 TGAAGATGGTGCTTTGTTATATGAAGATGGTGCTTTATTATTTGAAGATGGTGCTTTTTTAGA
1 TGAAGATGGTGCTTT-TTTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
* * * * *
924650 TAAAGATGGTGCTTTTTTATATG-TGATAGTGCTTT-TTATAT---GATGGTGCTTTTTAATG
1 TGAAGATGGTGCTTTTTT-TATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
*
924708 TGAAGGTGGT
1 TGAAGATGGT
924718 CACTCGGAAC
Statistics
Matches: 324, Mismatches: 44, Indels: 25
0.82 0.11 0.06
Matches are distributed among these distances:
58 22 0.07
60 51 0.16
61 58 0.18
62 20 0.06
63 165 0.51
64 8 0.02
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (62 bp):
TGAAGATGGTGCTTTTTTTATGAAGATGGTGCTTTATTATATGAAGATGGTGCTTTTTTATA
Found at i:925302 original size:20 final size:21
Alignment explanation
Indices: 925253--925302 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
925243 TTTCAAATTA
*
925253 CCTATAGG-AATATTGATTTT
1 CCTATAGGAAAAATTGATTTT
* *
925273 CCCATGGGAAAAATT-ATTTT
1 CCTATAGGAAAAATTGATTTT
925293 CCTATAGGAA
1 CCTATAGGAA
925303 TTTATTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (21 bp):
CCTATAGGAAAAATTGATTTT
Found at i:926378 original size:60 final size:63
Alignment explanation
Indices: 926274--926427 Score: 199
Period size: 60 Copynumber: 2.5 Consensus size: 63
926264 GTTCCGAGTG
* *
926274 ACCATCTTCATATAAAAAA-TCACCATCTTCATATAACAAAGCACCGTCTTCACATAAAAAAGC
1 ACCATCTTCATATAAAAAAGT-ACCATCTTCATATAACAAAGCACCATCTTCACATAAAAAAAC
* * * **
926337 A-C-T-TTCACATAAAAAAGTACCATCTTCATGTAATAAAGCACCATCTTCTTATAAAAAAAC
1 ACCATCTTCATATAAAAAAGTACCATCTTCATATAACAAAGCACCATCTTCACATAAAAAAAC
*
926397 ACCATCTTCATATAAAAAAGCACCATCTTCA
1 ACCATCTTCATATAAAAAAGTACCATCTTCA
926428 CAAGAAATAG
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
60 49 0.63
61 3 0.04
62 2 0.03
63 24 0.31
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.26
Consensus pattern (63 bp):
ACCATCTTCATATAAAAAAGTACCATCTTCATATAACAAAGCACCATCTTCACATAAAAAAAC
Found at i:926404 original size:18 final size:21
Alignment explanation
Indices: 926274--926427 Score: 197
Period size: 21 Copynumber: 7.5 Consensus size: 21
926264 GTTCCGAGTG
*
926274 ACCATCTTCATATAAAAAATC
1 ACCATCTTCATATAAAAAAGC
*
926295 ACCATCTTCATATAACAAAGC
1 ACCATCTTCATATAAAAAAGC
* *
926316 ACCGTCTTCACATAAAAAAGC
1 ACCATCTTCATATAAAAAAGC
* *
926337 A-C-T-TTCACATAAAAAAGT
1 ACCATCTTCATATAAAAAAGC
* *
926355 ACCATCTTCATGTAATAAAGC
1 ACCATCTTCATATAAAAAAGC
* *
926376 ACCATCTTCTTATAAAAAAAC
1 ACCATCTTCATATAAAAAAGC
926397 ACCATCTTCATATAAAAAAGC
1 ACCATCTTCATATAAAAAAGC
926418 ACCATCTTCA
1 ACCATCTTCA
926428 CAAGAAATAG
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.13
19 2 0.02
20 2 0.02
21 95 0.83
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.26
Consensus pattern (21 bp):
ACCATCTTCATATAAAAAAGC
Found at i:936844 original size:2 final size:2
Alignment explanation
Indices: 936837--936888 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
936827 TTGACATTCA
936837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
936879 TC TC TC TC TC
1 TC TC TC TC TC
936889 CTTATTCTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:944964 original size:2 final size:2
Alignment explanation
Indices: 944957--945015 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
944947 GCAGCACAGC
944957 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
944999 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
945016 ATATATATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:947563 original size:2 final size:2
Alignment explanation
Indices: 947556--947617 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
947546 ATGACGCACA
947556 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
947598 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
947618 ATTAAGATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:959984 original size:193 final size:191
Alignment explanation
Indices: 959656--960040 Score: 734
Period size: 193 Copynumber: 2.0 Consensus size: 191
959646 TGAGCTGATT
*
959656 TGGGGTTTCAGAGGAAAATATTTTATGTTCAATGGGGCTTTACGGGTGTATGTATGAACGGGGTA
1 TGGGGTTTCAGAGGAAAATATTTTATGTTCAATGGGGCTTTACGGGTGTATGTATGAACGGAGTA
959721 CCTTACCCATTTTTGTTTTAACATTTTAGCGTCCTTGGTCAACACACGTTGAACGTTGTCGTGTC
66 CCTTACCCATTTTTGTTTTAACATTTTAGCGTCCTTGGTCAACACACGTTGAACGTTGTCGTGTC
959786 ACCTGTTCCAAACAGTCGCCACCTACGCACGGCATCTGGGGGAATAAGAGATATCTACCAG
131 ACCTGTTCCAAACAGTCGCCACCTACGCACGGCATCTGGGGGAATAAGAGATATCTACCAG
959847 NTGGGGTTTCAGAGGAAAATATTTTTATGTTCAATGGGGCTTTACGGGTGTATGTATGAACGGAG
1 -TGGGGTTTCAGAGGAAAATA-TTTTATGTTCAATGGGGCTTTACGGGTGTATGTATGAACGGAG
*
959912 TACCTTACCCATTTTTGTTTTAACATTTTAGCGTCCTTGGTCAACACACGTTGTACGTTGTCGTG
64 TACCTTACCCATTTTTGTTTTAACATTTTAGCGTCCTTGGTCAACACACGTTGAACGTTGTCGTG
959977 TCACCTGTTCCAAACAGTCGCCACCTACGCACGGCATCTGGGGGAATAAGAGATATCTACCAG
129 TCACCTGTTCCAAACAGTCGCCACCTACGCACGGCATCTGGGGGAATAAGAGATATCTACCAG
960040 T
1 T
960041 TCCTTGCTTC
Statistics
Matches: 190, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
192 21 0.11
193 169 0.89
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (191 bp):
TGGGGTTTCAGAGGAAAATATTTTATGTTCAATGGGGCTTTACGGGTGTATGTATGAACGGAGTA
CCTTACCCATTTTTGTTTTAACATTTTAGCGTCCTTGGTCAACACACGTTGAACGTTGTCGTGTC
ACCTGTTCCAAACAGTCGCCACCTACGCACGGCATCTGGGGGAATAAGAGATATCTACCAG
Found at i:960909 original size:2 final size:2
Alignment explanation
Indices: 960902--960943 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
960892 TATTCCATAT
960902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
960944 ATTCATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:962263 original size:22 final size:22
Alignment explanation
Indices: 962247--962290 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
962237 CACATATATC
962247 CATGTTTATTCTTACATTCACA
1 CATGTTTATTCTTACATTCACA
*
962269 CATGTTTTTTCTTACATTCACA
1 CATGTTTATTCTTACATTCACA
962291 TATTCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.48
Consensus pattern (22 bp):
CATGTTTATTCTTACATTCACA
Found at i:964610 original size:2 final size:2
Alignment explanation
Indices: 964603--964652 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
964593 AATAATTCAT
964603 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
964645 GA GA GA GA
1 GA GA GA GA
964653 AACTAGATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:965269 original size:2 final size:2
Alignment explanation
Indices: 965262--965293 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
965252 ATTGAAAAAT
965262 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
965294 TATTTTGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:965669 original size:2 final size:2
Alignment explanation
Indices: 965662--965742 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
965652 TTGTTTGTCA
965662 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
965704 TC TC TC TC TC TC TC TC TC TC TC 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 TC TC TC TC T
965743 GATACTCTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:980135 original size:1 final size:1
Alignment explanation
Indices: 980131--980173 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
980121 CCCCCCCCCC
* ** *
980131 AAAAAAAAAAAACAAAAAAAAAAAATCAATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
980174 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.05, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:980148 original size:13 final size:14
Alignment explanation
Indices: 980130--980170 Score: 66
Period size: 13 Copynumber: 2.9 Consensus size: 14
980120 CCCCCCCCCC
980130 CAAAAAAAAAAAA-
1 CAAAAAAAAAAAAT
980143 CAAAAAAAAAAAAT
1 CAAAAAAAAAAAAT
980157 CAATAAAAAAAAAA
1 CAA-AAAAAAAAAA
980171 AAANNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 3 0.12
15 10 0.38
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (14 bp):
CAAAAAAAAAAAAT
Found at i:980150 original size:14 final size:14
Alignment explanation
Indices: 980131--980171 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
980121 CCCCCCCCCC
980131 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
*
980145 AAAAAAAAAAATCA
1 AAAAAAAAAAAACA
980159 ATAAAAAAAAAAA
1 A-AAAAAAAAAAA
980172 AANNNNNNNN
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.90, C:0.05, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:981563 original size:2 final size:2
Alignment explanation
Indices: 981556--981606 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
981546 TGTTAACTCT
981556 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
981598 GA GA GA GA G
1 GA GA GA GA G
981607 NNNNNNNNNN
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:984420 original size:24 final size:24
Alignment explanation
Indices: 984368--984412 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
984358 AAAACGACAG
* *
984368 GAAGAGGAAAGGAAGCGAAAGGAT
1 GAAGAGGAAAAGAAGCAAAAGGAT
984392 GAAGAGGAAAAGAAG-AAAAGG
1 GAAGAGGAAAAGAAGCAAAAGG
984413 GCTGAAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.40, T:0.02
Consensus pattern (24 bp):
GAAGAGGAAAAGAAGCAAAAGGAT
Found at i:984495 original size:21 final size:21
Alignment explanation
Indices: 984461--984501 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
984451 AAGGAAAGAT
984461 GAGGAAGAAAAAAGAAGGAAA
1 GAGGAAGAAAAAAGAAGGAAA
* * *
984482 GAGGAGGAACAAAGACGGAA
1 GAGGAAGAAAAAAGAAGGAA
984502 GGAAGAACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.37, T:0.00
Consensus pattern (21 bp):
GAGGAAGAAAAAAGAAGGAAA
Found at i:986444 original size:4 final size:4
Alignment explanation
Indices: 986435--986475 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
986425 GATTTCAGGG
*
986435 TATC TATC TATC TATC TATC TATC TATC TATC TATT TATC T
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC T
986476 GTACCTTCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (4 bp):
TATC
Found at i:987292 original size:26 final size:26
Alignment explanation
Indices: 987244--987296 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
987234 GCGGGACATT
*
987244 TGAGTGGGTGTTTTATAATGGCAATA
1 TGAGTGGGTGTTTTATAAAGGCAATA
*
987270 TGAGT-GGTTTTTTATCAAAGGCAATA
1 TGAGTGGGTGTTTTAT-AAAGGCAATA
987296 T
1 T
987297 AATGGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (26 bp):
TGAGTGGGTGTTTTATAAAGGCAATA
Found at i:987302 original size:25 final size:25
Alignment explanation
Indices: 987254--987310 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
987244 TGAGTGGGTG
* *
987254 TTTTATAATGGCAATATGAGTGGTT
1 TTTTATAAAGGCAATATGAATGGTT
987279 TTTTATCAAAGGCAATAT-AATGG-T
1 TTTTAT-AAAGGCAATATGAATGGTT
*
987303 GTTTATAA
1 TTTTATAA
987311 TGAAGGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 6 0.21
25 10 0.36
26 10 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTATAAAGGCAATATGAATGGTT
Found at i:990590 original size:160 final size:160
Alignment explanation
Indices: 990326--990646 Score: 642
Period size: 160 Copynumber: 2.0 Consensus size: 160
990316 ATATATATAA
990326 ATCTGAAATTATGTAGACTTTAAAATTTTTCAATTAAATAGGAATTCTTTCCAACAACGGCATTG
1 ATCTGAAATTATGTAGACTTTAAAATTTTTCAATTAAATAGGAATTCTTTCCAACAACGGCATTG
990391 AAGAACTCAGTAAACATATTCACGACAAATGGGAAGCTGTCGCTCAGAATCTTGGTATTGAAAGA
66 AAGAACTCAGTAAACATATTCACGACAAATGGGAAGCTGTCGCTCAGAATCTTGGTATTGAAAGA
990456 GATGATGTCGAGGCCATCAAAATTGATTTT
131 GATGATGTCGAGGCCATCAAAATTGATTTT
990486 ATCTGAAATTATGTAGACTTTAAAATTTTTCAATTAAATAGGAATTCTTTCCAACAACGGCATTG
1 ATCTGAAATTATGTAGACTTTAAAATTTTTCAATTAAATAGGAATTCTTTCCAACAACGGCATTG
990551 AAGAACTCAGTAAACATATTCACGACAAATGGGAAGCTGTCGCTCAGAATCTTGGTATTGAAAGA
66 AAGAACTCAGTAAACATATTCACGACAAATGGGAAGCTGTCGCTCAGAATCTTGGTATTGAAAGA
990616 GATGATGTCGAGGCCATCAAAATTGATTTT
131 GATGATGTCGAGGCCATCAAAATTGATTTT
990646 A
1 A
990647 AAGATGATGA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (160 bp):
ATCTGAAATTATGTAGACTTTAAAATTTTTCAATTAAATAGGAATTCTTTCCAACAACGGCATTG
AAGAACTCAGTAAACATATTCACGACAAATGGGAAGCTGTCGCTCAGAATCTTGGTATTGAAAGA
GATGATGTCGAGGCCATCAAAATTGATTTT
Found at i:1001249 original size:30 final size:31
Alignment explanation
Indices: 1001215--1001298 Score: 73
Period size: 36 Copynumber: 2.6 Consensus size: 31
1001205 AATACGTTGC
1001215 CGGTC-CAATAGATCGCAGTCTATTGACCGG
1 CGGTCACAATAGATCGCAGTCTATTGACCGG
*
1001245 CGGTCTAATTATAATAGATCGCAGTCTATTGACCGG
1 CGGTC-----ACAATAGATCGCAGTCTATTGACCGG
* *
1001281 CAGTTCAAAATAGA-CGCA
1 C-GGTCACAATAGATCGCA
1001299 AACATTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
30 5 0.11
31 4 0.09
32 7 0.16
36 25 0.57
37 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (31 bp):
CGGTCACAATAGATCGCAGTCTATTGACCGG
Found at i:1008239 original size:12 final size:12
Alignment explanation
Indices: 1008222--1008263 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
1008212 TGAAAAGTTT
1008222 ACGGACAGACGG
1 ACGGACAGACGG
1008234 ACGGACAGACGG
1 ACGGACAGACGG
* *
1008246 ACAGACAGACAG
1 ACGGACAGACGG
1008258 ACGGAC
1 ACGGAC
1008264 GACAGACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (12 bp):
ACGGACAGACGG
Found at i:1008258 original size:16 final size:15
Alignment explanation
Indices: 1008225--1008271 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 15
1008215 AAAGTTTACG
1008225 GACAGACGGACG---
1 GACAGACGGACGACA
1008237 GACAGACGGACAGACA
1 GACAGACGGAC-GACA
1008253 GACAGACGGACGACA
1 GACAGACGGACGACA
1008268 GACA
1 GACA
1008272 AAATGTGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.35
13 1 0.03
15 8 0.26
16 11 0.35
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (15 bp):
GACAGACGGACGACA
Found at i:1008271 original size:4 final size:4
Alignment explanation
Indices: 1008225--1008271 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
1008215 AAAGTTTACG
* * * *
1008225 GACA GACG GACG GACA GACG GACA GACA GACA GACG GAC- GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1008272 AAATGTGATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1015592 original size:21 final size:21
Alignment explanation
Indices: 1015568--1015613 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1015558 TCCCGGTGAT
*
1015568 AGTACCATCATGTAATGTTAA
1 AGTACCAGCATGTAATGTTAA
*
1015589 AGTATCAGCATGTAATGTTAA
1 AGTACCAGCATGTAATGTTAA
1015610 AGTA
1 AGTA
1015614 TTAGCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTACCAGCATGTAATGTTAA
Found at i:1015636 original size:21 final size:21
Alignment explanation
Indices: 1015576--1015637 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1015566 ATAGTACCAT
*
1015576 CATGTAATGTTAAAGTATCAG
1 CATGTAATGTTAAAGTATTAG
1015597 CATGTAATGTTAAAGTATTAG
1 CATGTAATGTTAAAGTATTAG
* * *
1015618 CTTTTAATGTTTAAGTATTA
1 CATGTAATGTTAAAGTATTA
1015638 TCATATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (21 bp):
CATGTAATGTTAAAGTATTAG
Found at i:1018048 original size:2 final size:2
Alignment explanation
Indices: 1018041--1018093 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1018031 AATATTTTGT
1018041 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1018083 AC AC AC AC AC A
1 AC AC AC AC AC A
1018094 GAGTTAGCGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1024593 original size:336 final size:335
Alignment explanation
Indices: 1023980--1024611 Score: 1246
Period size: 336 Copynumber: 1.9 Consensus size: 335
1023970 TTTTAGGAAC
1023980 TAGCTCCAAAAATGTTATGTTTAAAAAATGTCAGATGCCTTCAAATGGTCAGACCAACCTAAGTG
1 TAGCTCCAAAAATGTTATGTTTAAAAAATGTCAGATGCCTTCAAATGGTCAGACCAACCTAAGTG
1024045 TGGCCAATGATGACCGAAAACTGTTCCGCATCCTAAATTAGCATTACCTGCACAATCTGTATATA
66 TGGCCAATGATGACCGAAAACTGTTCCGCATCCTAAATTAGCATTACCTGCACAATCTGTATATA
1024110 AATGGAGATCAAACTCTTTGAATTGATTTACTAATCTATAAGATGCAACTCCACTGATATTTTCC
131 AATGGAGATCAAACTCTTTGAATTGATTTACTAATCTATAAGATGCAACTCCACTGATATTTTCC
1024175 AAAAACATTAACCAAGTGTCAATGTCCTTTCTCATTTTCTCAGTAATTCTAAGCCTGTGATTAGG
196 AAAAACATTAACCAAGTGTCAATGTCCTTTCTCATTTTCTCAGTAATTCTAAGCCTGTGATTAGG
1024240 ACGCGAAAGCCCAAAGGATGCATCATACTACAACCTNACGAAAATTGAGCCACCACGAAATCTAA
261 ACGCGAAAGCCCAAAGGATGCATCATACTACAACCT-ACGAAAATTGAGCCACCACGAAATCTAA
1024305 TGATTCCACAG
325 TGATTCCACAG
1024316 TAGCTCCAAAAATGTTATGTTTAAAAAATGTCAGATGCCTTCAAATGGTCAGACCAACCTAAGTG
1 TAGCTCCAAAAATGTTATGTTTAAAAAATGTCAGATGCCTTCAAATGGTCAGACCAACCTAAGTG
1024381 TGGCCAATGATGACCGAAAACTGTTCCGCATCCTAAATTAGCATTACCTGCACAATCTGTATATA
66 TGGCCAATGATGACCGAAAACTGTTCCGCATCCTAAATTAGCATTACCTGCACAATCTGTATATA
1024446 AATGGAGATCAAACTCTTTGAATTGATTTACTAATCTATAAGATGCAACTCCACTGATATTTTCC
131 AATGGAGATCAAACTCTTTGAATTGATTTACTAATCTATAAGATGCAACTCCACTGATATTTTCC
1024511 AAAAACATTAACCAAGTGTCAATGTCCTTTCTCATTTTCTCAGTAATTCTAAGCCTGTGATTAGG
196 AAAAACATTAACCAAGTGTCAATGTCCTTTCTCATTTTCTCAGTAATTCTAAGCCTGTGATTAGG
*
1024576 ACGCGAAAGCGCAAAGGATGCATCATACTACAACCT
261 ACGCGAAAGCCCAAAGGATGCATCATACTACAACCT
1024612 TCTAACAAAT
Statistics
Matches: 295, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 295 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (335 bp):
TAGCTCCAAAAATGTTATGTTTAAAAAATGTCAGATGCCTTCAAATGGTCAGACCAACCTAAGTG
TGGCCAATGATGACCGAAAACTGTTCCGCATCCTAAATTAGCATTACCTGCACAATCTGTATATA
AATGGAGATCAAACTCTTTGAATTGATTTACTAATCTATAAGATGCAACTCCACTGATATTTTCC
AAAAACATTAACCAAGTGTCAATGTCCTTTCTCATTTTCTCAGTAATTCTAAGCCTGTGATTAGG
ACGCGAAAGCCCAAAGGATGCATCATACTACAACCTACGAAAATTGAGCCACCACGAAATCTAAT
GATTCCACAG
Found at i:1025344 original size:10 final size:10
Alignment explanation
Indices: 1025299--1025352 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
1025289 GCGTCTTTCT
*
1025299 ACCACGTTCC
1 ACCACGATCC
*
1025309 ACCACTATCC
1 ACCACGATCC
*
1025319 ACCACGTTCC
1 ACCACGATCC
1025329 ACCACGATCC
1 ACCACGATCC
*
1025339 ACCACGCTCC
1 ACCACGATCC
1025349 ACCA
1 ACCA
1025353 AAATCCACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 38 1.00
ACGTcount: A:0.26, C:0.52, G:0.07, T:0.15
Consensus pattern (10 bp):
ACCACGATCC
Found at i:1025358 original size:20 final size:20
Alignment explanation
Indices: 1025299--1025361 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1025289 GCGTCTTTCT
*
1025299 ACCACGTTCCACCACTATCC
1 ACCACGTTCCACCACAATCC
*
1025319 ACCACGTTCCACCACGATCC
1 ACCACGTTCCACCACAATCC
* *
1025339 ACCACGCTCCACCAAAATCC
1 ACCACGTTCCACCACAATCC
1025359 ACC
1 ACC
1025362 CCGTCCCCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.29, C:0.51, G:0.06, T:0.14
Consensus pattern (20 bp):
ACCACGTTCCACCACAATCC
Found at i:1029459 original size:11 final size:11
Alignment explanation
Indices: 1029443--1029485 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1029433 CGTGTGTCTG
1029443 CTTTGGGTTTA
1 CTTTGGGTTTA
**
1029454 CTTTGGGTCCA
1 CTTTGGGTTTA
**
1029465 CTCCGGGTTTA
1 CTTTGGGTTTA
1029476 CTTTGGGTTT
1 CTTTGGGTTT
1029486 TCTTGGGGCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.47
Consensus pattern (11 bp):
CTTTGGGTTTA
Found at i:1031842 original size:81 final size:81
Alignment explanation
Indices: 1031704--1031877 Score: 303
Period size: 81 Copynumber: 2.1 Consensus size: 81
1031694 ATATGCATAG
* *
1031704 ACAATTTCTTTTATAGAATTGACTGTGAAATTGTTTCTTGAAAAACCACCAGAATTTGACAATCT
1 ACAATTTATTTTAAAGAATTGACTGTGAAATTGTTTCTTGAAAAACCACCAGAATTTGACAATCT
1031769 AGATTTATTTACATCA
66 AGATTTATTTACATCA
* *
1031785 ACAATTTATTTTAAAGAATTGACTGTGAAATTGTTTCTTGAAAAACCACCTGCATTTGACAATCT
1 ACAATTTATTTTAAAGAATTGACTGTGAAATTGTTTCTTGAAAAACCACCAGAATTTGACAATCT
1031850 AGATTTATTTACATCA
66 AGATTTATTTACATCA
*
1031866 ATAATTTATTTT
1 ACAATTTATTTT
1031878 TTTTCATCTA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (81 bp):
ACAATTTATTTTAAAGAATTGACTGTGAAATTGTTTCTTGAAAAACCACCAGAATTTGACAATCT
AGATTTATTTACATCA
Found at i:1033291 original size:13 final size:13
Alignment explanation
Indices: 1033273--1033306 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1033263 TTAATATTGG
* *
1033273 TAATAATTTATGT
1 TAATAATATAAGT
1033286 TAATAATATAAGT
1 TAATAATATAAGT
1033299 TAATAATA
1 TAATAATA
1033307 ATGGAAGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (13 bp):
TAATAATATAAGT
Found at i:1037458 original size:20 final size:20
Alignment explanation
Indices: 1037411--1037621 Score: 237
Period size: 21 Copynumber: 10.2 Consensus size: 20
1037401 TGTTCCTTCT
*
1037411 TATTTGTTCGGACGAATAAG
1 TATTTGTTCGGACGAATTAG
1037431 TTATTTGTTCGGACGAATTAG
1 -TATTTGTTCGGACGAATTAG
*
1037452 GATTTGTTCGGACGAATTACG
1 TATTTGTTCGGACGAATTA-G
*
1037473 TATTTGTTCGGAC-ATATAAG
1 TATTTGTTCGGACGA-ATTAG
1037493 TTATTTGTTCGGACGAATTAG
1 -TATTTGTTCGGACGAATTAG
*
1037514 GATTTGTTCGGACGAATTAG
1 TATTTGTTCGGACGAATTAG
* *
1037534 GATTTGTTCGGACGAATAAG
1 TATTTGTTCGGACGAATTAG
* * *
1037554 CTATTTATTCGGAC-ATATAAAT
1 -TATTTGTTCGGACGA-AT-TAG
1037576 TATTTGTTCGGACGAATTAG
1 TATTTGTTCGGACGAATTAG
* *
1037596 GATTTGTTCGGACGAAATAG
1 TATTTGTTCGGACGAATTAG
1037616 CTATTT
1 -TATTT
1037622 TTCATTTTTT
Statistics
Matches: 165, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
20 78 0.47
21 83 0.50
22 4 0.02
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (20 bp):
TATTTGTTCGGACGAATTAG
Found at i:1037492 original size:62 final size:61
Alignment explanation
Indices: 1037412--1037611 Score: 296
Period size: 62 Copynumber: 3.2 Consensus size: 61
1037402 GTTCCTTCTT
*
1037412 ATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTACGT
1 ATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTA-GG
1037474 ATTTGTTCGGAC-ATATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGA-ATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGG
* * * **
1037535 ATTTGTTCGGACGAATAAGCTATTTATTCGGAC-ATATAAATTATTTGTTCGGACGAATTAGG
1 ATTTGTTCGGACGAATAAGTTATTTGTTCGGACGA-AT-TAGGATTTGTTCGGACGAATTAGG
1037597 ATTTGTTCGGACGAA
1 ATTTGTTCGGACGAA
1037612 ATAGCTATTT
Statistics
Matches: 128, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
60 1 0.01
61 33 0.26
62 94 0.73
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (61 bp):
ATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGG
Found at i:1037532 original size:82 final size:82
Alignment explanation
Indices: 1037410--1037611 Score: 334
Period size: 82 Copynumber: 2.5 Consensus size: 82
1037400 CTGTTCCTTC
* * *
1037410 TTATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTA-CGT
1 TTATTTGTTCGGACGAATTAG-GATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATAAGC-T
* *
1037474 ATTTGTTCGGACATATAAG
64 ATTTATTCGGACATATAAA
1037493 TTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATAAGCTAT
1 TTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATAAGCTAT
1037558 TTATTCGGACATATAAA
66 TTATTCGGACATATAAA
1037575 TTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAA
1 TTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAA
1037612 ATAGCTATTT
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
82 92 0.81
83 21 0.19
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (82 bp):
TTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATAAGCTAT
TTATTCGGACATATAAA
Found at i:1037593 original size:17 final size:18
Alignment explanation
Indices: 1037573--1037611 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1037563 CGGACATATA
1037573 AATT-ATTTGTTCGGACG
1 AATTGATTTGTTCGGACG
1037590 AATTAGGATTTGTTCGGACG
1 AATT--GATTTGTTCGGACG
1037610 AA
1 AA
1037612 ATAGCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
20 15 0.79
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
AATTGATTTGTTCGGACG
Found at i:1044079 original size:54 final size:54
Alignment explanation
Indices: 1043994--1044156 Score: 247
Period size: 54 Copynumber: 3.0 Consensus size: 54
1043984 ACAGCGTAAG
* *
1043994 ACGAGACATTCCTACAGACAATAATTGAATCATAGGAATACTTTCTATCATTTC
1 ACGAGACATTCCTACAGAAAATAATCGAATCATAGGAATACTTTCTATCATTTC
* *
1044048 ACGAGACATTCCTACAGAAAATAATCAAATCATAGGAATAATTTCTATCATTTC
1 ACGAGACATTCCTACAGAAAATAATCGAATCATAGGAATACTTTCTATCATTTC
* * *
1044102 ACAAGACATTCCTA-AAAACAATAATCGAATCATAGGAATACTCTCTATCATTTC
1 ACGAGACATTCCTACAGAA-AATAATCGAATCATAGGAATACTTTCTATCATTTC
1044156 A
1 A
1044157 ATAAAGGCCT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 3 0.03
54 96 0.97
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (54 bp):
ACGAGACATTCCTACAGAAAATAATCGAATCATAGGAATACTTTCTATCATTTC
Found at i:1044692 original size:46 final size:44
Alignment explanation
Indices: 1044621--1044708 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
1044611 AAGTCCTTTG
**
1044621 TTACAGCTTGCTGTAAAATTCAAATTTCTTAACTGTAAACAACACA
1 TTACAGCTTGCCATAAAATTCAAA-TTCTT-ACTGTAAACAACACA
1044667 TTACAGCTTGCCATAAAA-TCAAAATTCTTACTGTAAACAACA
1 TTACAGCTTGCCATAAAATTC-AAATTCTTACTGTAAACAACA
1044709 AATTTTAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 13 0.33
45 7 0.18
46 19 0.49
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (44 bp):
TTACAGCTTGCCATAAAATTCAAATTCTTACTGTAAACAACACA
Found at i:1045740 original size:46 final size:44
Alignment explanation
Indices: 1045669--1045756 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
1045659 AAGTCCTTTG
**
1045669 TTACAGCTTGCTGTAAAATTCAAATTTCTTAACTGTAAACAACACA
1 TTACAGCTTGCCATAAAATTCAAA-TTCTT-ACTGTAAACAACACA
1045715 TTACAGCTTGCCATAAAA-TCAAAATTCTTACTGTAAACAACA
1 TTACAGCTTGCCATAAAATTC-AAATTCTTACTGTAAACAACA
1045757 AATTTTAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 13 0.33
45 7 0.18
46 19 0.49
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (44 bp):
TTACAGCTTGCCATAAAATTCAAATTCTTACTGTAAACAACACA
Found at i:1050365 original size:2 final size:2
Alignment explanation
Indices: 1050358--1050398 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1050348 NNNNNNNNNN
1050358 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1050399 CTCCATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1054697 original size:2 final size:2
Alignment explanation
Indices: 1054690--1054719 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1054680 NNNNNNNNNN
1054690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1054720 GGAGGGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1055233 original size:2 final size:2
Alignment explanation
Indices: 1055228--1055259 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1055218 GACACCCCCC
1055228 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1055260 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1055966 original size:2 final size:2
Alignment explanation
Indices: 1055959--1056028 Score: 104
Period size: 2 Copynumber: 35.0 Consensus size: 2
1055949 TCTTTACCAT
* * * *
1055959 TC TC TC TC TC TG TC TC TC TC TC TC CC CC CC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1056001 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1056029 GTCATTACAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.53, G:0.01, T:0.46
Consensus pattern (2 bp):
TC
Found at i:1059225 original size:2 final size:2
Alignment explanation
Indices: 1059218--1059250 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1059208 TCGTAAAAGA
1059218 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1059251 CTCAATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1064227 original size:17 final size:17
Alignment explanation
Indices: 1064205--1064239 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1064195 CATACAGTCA
*
1064205 TTTGACTAGTTCCGAAT
1 TTTGACCAGTTCCGAAT
*
1064222 TTTGACCAGTTCTGAAT
1 TTTGACCAGTTCCGAAT
1064239 T
1 T
1064240 GTTCATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (17 bp):
TTTGACCAGTTCCGAAT
Found at i:1072837 original size:62 final size:62
Alignment explanation
Indices: 1072740--1072866 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
1072730 AAATACACTT
** *
1072740 TATTGCAGATGCATGGGATGGTAAGGGGCATAACTACTGTACAACAACAGAAAATTCATTCA
1 TATTGCAGATGCATGGGAAAGTAAGGGGCATAACTACTGTACAACAACAGAAAAGTCATTCA
1072802 TATTGCAGATGCATGGGAAAGTAAGGGGCATAACTACTGTACAACAACAGAAAAGTCATTCA
1 TATTGCAGATGCATGGGAAAGTAAGGGGCATAACTACTGTACAACAACAGAAAAGTCATTCA
1072864 TAT
1 TAT
1072867 AACTGTTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (62 bp):
TATTGCAGATGCATGGGAAAGTAAGGGGCATAACTACTGTACAACAACAGAAAAGTCATTCA
Found at i:1074209 original size:2 final size:2
Alignment explanation
Indices: 1074202--1074262 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1074192 AACCAGATTT
1074202 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1074244 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
1074263 TTTGGTTTGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1084743 original size:16 final size:17
Alignment explanation
Indices: 1084713--1084746 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1084703 TCTCGAGTTC
1084713 TTTTTTGTTTATTTAAA
1 TTTTTTGTTTATTTAAA
*
1084730 TTTTTT-TTTTTTTAAA
1 TTTTTTGTTTATTTAAA
1084746 T
1 T
1084747 GTTTACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTGTTTATTTAAA
Found at i:1086127 original size:2 final size:2
Alignment explanation
Indices: 1086122--1086166 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1086112 ATATACATGT
1086122 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1086164 AG A
1 AG A
1086167 ACTTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1086240 original size:39 final size:40
Alignment explanation
Indices: 1086166--1086243 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
1086156 AGAGAGAGAG
* *
1086166 AACTTAAATGAATAAAAACACAAAGTCAAAGTAAAACAAC
1 AACTTAAATCAATAAAAACAAAAAGTCAAAGTAAAACAAC
* *
1086206 AACTTAAATCAAT-AAAACAAAAAGTCAGATTAAAACAA
1 AACTTAAATCAATAAAAACAAAAAGTCAAAGTAAAACAA
1086244 TATTTTACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 22 0.65
40 12 0.35
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.17
Consensus pattern (40 bp):
AACTTAAATCAATAAAAACAAAAAGTCAAAGTAAAACAAC
Found at i:1100329 original size:2 final size:2
Alignment explanation
Indices: 1100324--1100348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1100314 GAGAGGACAC
1100324 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
1100349 GTGGCGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1102376 original size:2 final size:2
Alignment explanation
Indices: 1102369--1102421 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1102359 TCGTTTTGCT
1102369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1102411 TC TC TC TC TC T
1 TC TC TC TC TC T
1102422 ACATGTGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1102778 original size:2 final size:2
Alignment explanation
Indices: 1102771--1102820 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1102761 TATCAACATC
1102771 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1102813 CT CT CT CT
1 CT CT CT CT
1102821 TTTCACACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1105677 original size:20 final size:21
Alignment explanation
Indices: 1105639--1105680 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1105629 GTGTTCTTGA
*
1105639 TTTACAGTATTTTCAGTATTT
1 TTTACAGTATTTACAGTATTT
1105660 TTTACAGT-TTTACAGTATTT
1 TTTACAGTATTTACAGTATTT
1105680 T
1 T
1105681 CGTTATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTACAGTATTTACAGTATTT
Found at i:1111068 original size:24 final size:24
Alignment explanation
Indices: 1111041--1111113 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1111031 TTTTTGCAAC
*
1111041 TTATTACATGAAATATGTCACAAG
1 TTATTACATGAAAGATGTCACAAG
* *
1111065 TTATTACGTGAAAGATGTTACAAG
1 TTATTACATGAAAGATGTCACAAG
* * * *
1111089 TAATTGCATGAAAGACGTTACAAG
1 TTATTACATGAAAGATGTCACAAG
1111113 T
1 T
1111114 AATAACATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (24 bp):
TTATTACATGAAAGATGTCACAAG
Found at i:1113637 original size:72 final size:74
Alignment explanation
Indices: 1113441--1113644 Score: 306
Period size: 78 Copynumber: 2.7 Consensus size: 74
1113431 TATAATTCAT
* *
1113441 AGTAATAAGAAATATTGGAACTCTTTATAACATCATTTGATTACATGCAAGTATTATAAACTTCC
1 AGTAATAAGAAATATTGGAACTTTTTATAACATCATTTGATTACATGCAAGTATGATAAACTTCC
1113506 CAATTAAGG
66 CAATTAAGG
*
1113515 TACATGTAATAAGAAATATTGGAA-TTTTTAATAGCATCATTTGATTACATGCAAGTATGATAAA
1 ---A-GTAATAAGAAATATTGGAACTTTTT-ATAACATCATTTGATTACATGCAAGTATGATAAA
1113579 CTTCCCAATTAA-G
61 CTTCCCAATTAAGG
*
1113592 -GTAATAGGAAATATTGGAACTTTTTATAACATCATTTGATTACATGCAAGTAT
1 AGTAATAAGAAATATTGGAACTTTTTATAACATCATTTGATTACATGCAAGTAT
1113645 CCATGAATTT
Statistics
Matches: 119, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
72 45 0.38
73 5 0.04
77 6 0.05
78 63 0.53
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (74 bp):
AGTAATAAGAAATATTGGAACTTTTTATAACATCATTTGATTACATGCAAGTATGATAAACTTCC
CAATTAAGG
Found at i:1115566 original size:2 final size:2
Alignment explanation
Indices: 1115559--1115608 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1115549 GTTCGTACTA
1115559 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1115601 TC TC TC TC
1 TC TC TC TC
1115609 GTTCTCATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1116314 original size:2 final size:2
Alignment explanation
Indices: 1116307--1116350 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1116297 AACTTTATTT
1116307 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1116349 GA
1 GA
1116351 TTTGGGTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1118262 original size:15 final size:15
Alignment explanation
Indices: 1118242--1118272 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1118232 TTAAAATTTG
1118242 TTATCTCAAACATCA
1 TTATCTCAAACATCA
*
1118257 TTATCTCAAATATCA
1 TTATCTCAAACATCA
1118272 T
1 T
1118273 GATTATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (15 bp):
TTATCTCAAACATCA
Found at i:1126140 original size:15 final size:15
Alignment explanation
Indices: 1126120--1126199 Score: 115
Period size: 15 Copynumber: 5.3 Consensus size: 15
1126110 CAGCTGCACC
1126120 AAAGAAACCAGAGGA
1 AAAGAAACCAGAGGA
1126135 AAAGAAACCAGAGGA
1 AAAGAAACCAGAGGA
*
1126150 AAAGAAACCGGAGGA
1 AAAGAAACCAGAGGA
* *
1126165 AAAGAAACCGGAAGA
1 AAAGAAACCAGAGGA
* *
1126180 AAAGAAACCTGAGGT
1 AAAGAAACCAGAGGA
1126195 AAAGA
1 AAAGA
1126200 TTTAAAACTG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.57, C:0.12, G:0.28, T:0.03
Consensus pattern (15 bp):
AAAGAAACCAGAGGA
Found at i:1127159 original size:30 final size:30
Alignment explanation
Indices: 1127123--1127334 Score: 316
Period size: 30 Copynumber: 7.1 Consensus size: 30
1127113 AGTTGAAACA
1127123 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
*
1127153 CCTAAGGCTCCTGAAAAGCCTAAAGAAGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
* * * *
1127183 CCTAAGGCTCCCGAAAAACCCAAGGAAGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
* *
1127213 CCTAAGGCTCCTGAAAAACCTAAAGAAGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
1127243 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
* *
1127273 CCTAAGGCTCCTGAAAAGCCTAAAGAACAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
* * *
1127303 CCTAAGGCTCCAGAAAAACCCAAAGAGGAG
1 CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
1127333 CC
1 CC
1127335 CAAACCAGAG
Statistics
Matches: 165, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 165 1.00
ACGTcount: A:0.42, C:0.26, G:0.22, T:0.10
Consensus pattern (30 bp):
CCTAAGGCTCCAGAAAAGCCTAAAGAAGAG
Found at i:1129435 original size:26 final size:25
Alignment explanation
Indices: 1129406--1129473 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
1129396 AGGCTCTCAC
* *
1129406 GATATAGTGACTTTGTCGGCTGTAA
1 GATATAGTGACTATGTCGGCTCTAA
*
1129431 TGATATAGTTACTATGTCGGCTCTAA
1 -GATATAGTGACTATGTCGGCTCTAA
*
1129457 CAGTATAGTGACTATGT
1 GA-TATAGTGACTATGT
1129474 TGTGAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (25 bp):
GATATAGTGACTATGTCGGCTCTAA
Found at i:1133456 original size:15 final size:15
Alignment explanation
Indices: 1133436--1133466 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1133426 TTGTCGAACG
*
1133436 AAATTCTGTGTGCAT
1 AAATTCTATGTGCAT
1133451 AAATTCTATGTGCAT
1 AAATTCTATGTGCAT
1133466 A
1 A
1133467 GATGAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (15 bp):
AAATTCTATGTGCAT
Found at i:1159086 original size:3 final size:3
Alignment explanation
Indices: 1159080--1159121 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1159070 GTGGTGGTGG
*
1159080 TGA TGA TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1159122 AAGTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1167878 original size:25 final size:25
Alignment explanation
Indices: 1167844--1167994 Score: 293
Period size: 25 Copynumber: 6.0 Consensus size: 25
1167834 CTGCATCTGC
1167844 TCCTATTGTCACATGGTAAGTGTTA
1 TCCTATTGTCACATGGTAAGTGTTA
1167869 TCCTATTGTCACATGGTAAGTGTTA
1 TCCTATTGTCACATGGTAAGTGTTA
*
1167894 TCCTATTGTCACATGGTAAGTGTAA
1 TCCTATTGTCACATGGTAAGTGTTA
1167919 TCCTATTGTCACATGGTAAGTGTTA
1 TCCTATTGTCACATGGTAAGTGTTA
1167944 TCCTATTGTCACATGGTAAGTGTTA
1 TCCTATTGTCACATGGTAAGTGTTA
1167969 TCCTATTGTCACATGGTAAGTGTTA
1 TCCTATTGTCACATGGTAAGTGTTA
1167994 T
1 T
1167995 NNNNNNNNNN
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 124 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (25 bp):
TCCTATTGTCACATGGTAAGTGTTA
Found at i:1178147 original size:13 final size:13
Alignment explanation
Indices: 1178129--1178153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1178119 GTTTAATCGT
1178129 TCGCCATTTTGAA
1 TCGCCATTTTGAA
1178142 TCGCCATTTTGA
1 TCGCCATTTTGA
1178154 CCTACTTAAC
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:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
TCGCCATTTTGAA
Found at i:1182542 original size:14 final size:14
Alignment explanation
Indices: 1182520--1182564 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
1182510 TTTTCCTTCC
* *
1182520 CTCCCTCTCTCTCT
1 CTCCTTCTCTCTAT
1182534 CTCCTTCTCTCTAT
1 CTCCTTCTCTCTAT
1182548 CTCCTTCTCTCTAT
1 CTCCTTCTCTCTAT
1182562 CTC
1 CTC
1182565 TCCCCATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.04, C:0.49, G:0.00, T:0.47
Consensus pattern (14 bp):
CTCCTTCTCTCTAT
Found at i:1183909 original size:33 final size:33
Alignment explanation
Indices: 1183839--1183909 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1183829 AAAATAAGAT
* * * * *
1183839 CTTTGATCCGCTCCGACTATTTTGATATCGCTT
1 CTTTGATCCGCTCCGACAAATTCGATATCGATA
*
1183872 CTTTGATCCGCTCCGACAAATTCGATGTCGATA
1 CTTTGATCCGCTCCGACAAATTCGATATCGATA
1183905 CTTTG
1 CTTTG
1183910 TGTAGCGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (33 bp):
CTTTGATCCGCTCCGACAAATTCGATATCGATA
Found at i:1190361 original size:253 final size:253
Alignment explanation
Indices: 1189908--1190418 Score: 1013
Period size: 253 Copynumber: 2.0 Consensus size: 253
1189898 GGTCTCTGGT
1189908 CTACAGGTTCACAACAACTTCGTATAAAATCAATTTCAAAATCATTAATATATACTGAAAAAAGA
1 CTACAGGTTCACAACAACTTCGTATAAAATCAATTTCAAAATCATTAATATATACTGAAAAAAGA
1189973 AAAGGCAACAAAGCCTCTCCTTTCGTAAGTCCAGTTGTAGACGAAAGATATTTTAACTCACAATT
66 AAAGGCAACAAAGCCTCTCCTTTCGTAAGTCCAGTTGTAGACGAAAGATATTTTAACTCACAATT
1190038 AAAATCCTTAAGAATGCTTAACAACTTTCCCGTGACGCTTTTCTATGCTATGATCAACAAAACAA
131 AAAATCCTTAAGAATGCTTAACAACTTTCCCGTGACGCTTTTCTATGCTATGATCAACAAAACAA
1190103 GCGTATCATTAAATTTTCTTTTCCTTCTTCAAATACTAAATTCGTAAGTGCGAAATTC
196 GCGTATCATTAAATTTTCTTTTCCTTCTTCAAATACTAAATTCGTAAGTGCGAAATTC
*
1190161 CTACNGGTTCACAACAACTTCGTATAAAATCAATTTCAAAATCATTAATATATACTGAAAAAAGA
1 CTACAGGTTCACAACAACTTCGTATAAAATCAATTTCAAAATCATTAATATATACTGAAAAAAGA
1190226 AAAGGCAACAAAGCCTCTCCTTTCGTAAGTCCAGTTGTAGACGAAAGATATTTTAACTCACAATT
66 AAAGGCAACAAAGCCTCTCCTTTCGTAAGTCCAGTTGTAGACGAAAGATATTTTAACTCACAATT
1190291 AAAATCCTTAAGAATGCTTAACAACTTTCCCGTGACGCTTTTCTATGCTATGATCAACAAAACAA
131 AAAATCCTTAAGAATGCTTAACAACTTTCCCGTGACGCTTTTCTATGCTATGATCAACAAAACAA
1190356 GCGTATCATTAAATTTTCTTTTCCTTCTTCAAATACTAAATTCGTAAGTGCGAAATTC
196 GCGTATCATTAAATTTTCTTTTCCTTCTTCAAATACTAAATTCGTAAGTGCGAAATTC
1190414 CTACA
1 CTACA
1190419 ATATCCCTTG
Statistics
Matches: 256, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
253 256 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (253 bp):
CTACAGGTTCACAACAACTTCGTATAAAATCAATTTCAAAATCATTAATATATACTGAAAAAAGA
AAAGGCAACAAAGCCTCTCCTTTCGTAAGTCCAGTTGTAGACGAAAGATATTTTAACTCACAATT
AAAATCCTTAAGAATGCTTAACAACTTTCCCGTGACGCTTTTCTATGCTATGATCAACAAAACAA
GCGTATCATTAAATTTTCTTTTCCTTCTTCAAATACTAAATTCGTAAGTGCGAAATTC
Found at i:1192161 original size:80 final size:80
Alignment explanation
Indices: 1192042--1192208 Score: 307
Period size: 80 Copynumber: 2.1 Consensus size: 80
1192032 TAGCAGCAAC
* *
1192042 TAATTTTCGTGATCAAGAATGGTGATTATCTTGAACGTACTCTAAAATGTCGAAACATTTTTCGA
1 TAATTTTCGTGATCAAGAATGGTGATTATCTTGAACGTACTCTAAAATGTCGAAACATTTTACAA
1192107 CTGGTTCACGGCGAG
66 CTGGTTCACGGCGAG
*
1192122 TAATTTTCGTTATCAAGAATGGTGATTATCTTGAACGTACTCTAAAATGTCGAAACATTTTACAA
1 TAATTTTCGTGATCAAGAATGGTGATTATCTTGAACGTACTCTAAAATGTCGAAACATTTTACAA
1192187 CTGGTTCACGGCGAG
66 CTGGTTCACGGCGAG
1192202 TAATTTT
1 TAATTTT
1192209 TGCGGCGACA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (80 bp):
TAATTTTCGTGATCAAGAATGGTGATTATCTTGAACGTACTCTAAAATGTCGAAACATTTTACAA
CTGGTTCACGGCGAG
Done.