Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 114 of 202
Found at i:35130734 original size:26 final size:27
Alignment explanation
Indices: 35130679--35130735 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
35130669 AGGTTTTTAG
*
35130679 TTTATCGATAACTGAATATTTTATTAA
1 TTTATCGATAAATGAATATTTTATTAA
*
35130706 TTTATCGATAAATTAATA-TTTATTAA
1 TTTATCGATAAATGAATATTTTATTAA
35130732 TTTA
1 TTTA
35130736 GAGAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (27 bp):
TTTATCGATAAATGAATATTTTATTAA
Found at i:35130862 original size:35 final size:38
Alignment explanation
Indices: 35130820--35130893 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 38
35130810 TGAATCAAAG
*
35130820 TTAATTGGTTCATG-AAACAAAAA-AAA-AAGAGTTAA
1 TTAATTGGTTCATGTAAACAAAAAGAAAGAAGACTTAA
*
35130855 TTAATTGGTTCATGTAACCAAAAAGAAAGAAGACTTAA
1 TTAATTGGTTCATGTAAACAAAAAGAAAGAAGACTTAA
35130893 T
1 T
35130894 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 14 0.41
36 8 0.24
37 3 0.09
38 9 0.26
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (38 bp):
TTAATTGGTTCATGTAAACAAAAAGAAAGAAGACTTAA
Found at i:35131712 original size:12 final size:13
Alignment explanation
Indices: 35131695--35131723 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35131685 TTGGTTAGTT
35131695 TGCTAATCCT-AA
1 TGCTAATCCTAAA
35131707 TGCTAATCCTAAA
1 TGCTAATCCTAAA
35131720 TGCT
1 TGCT
35131724 TTAAACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (13 bp):
TGCTAATCCTAAA
Found at i:35134745 original size:24 final size:24
Alignment explanation
Indices: 35134694--35134745 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
35134684 ATTTCTCTCA
* * *
35134694 CCCTTTTCAACATATACCTATAAT
1 CCCTTTTCAACATATACATAAAAG
35134718 CCCTTTTGC-ACATATACATAAAAG
1 CCCTTTT-CAACATATACATAAAAG
35134742 CCCT
1 CCCT
35134746 CAAAAGGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (24 bp):
CCCTTTTCAACATATACATAAAAG
Found at i:35136100 original size:27 final size:29
Alignment explanation
Indices: 35136043--35136117 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 29
35136033 TATGTACATG
*
35136043 TCATGATACATATTATTATCTTACCATTTCA
1 TCAT-ATACATA-TATCATCTTACCATTTCA
35136074 TCATATACATATATCATC-T-CCATTTCA
1 TCATATACATATATCATCTTACCATTTCA
35136101 --ATATATCAATATATCAT
1 TCATATA-C-ATATATCAT
35136118 GTACCATCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 5 0.12
26 1 0.02
27 17 0.41
28 1 0.02
29 6 0.15
30 7 0.17
31 4 0.10
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (29 bp):
TCATATACATATATCATCTTACCATTTCA
Found at i:35136321 original size:24 final size:23
Alignment explanation
Indices: 35136294--35136348 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
35136284 TATGCTCATA
35136294 CGAGCTATAAACGGTAAGCTCCTC
1 CGAGCTAT-AACGGTAAGCTCCTC
* * *
35136318 CGAGCTGATAATGGTAAGCTTCTT
1 CGAGCT-ATAACGGTAAGCTCCTC
35136342 CGAGCTA
1 CGAGCTA
35136349 AATAGTGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.89
25 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
CGAGCTATAACGGTAAGCTCCTC
Found at i:35136383 original size:25 final size:24
Alignment explanation
Indices: 35136287--35136398 Score: 95
Period size: 25 Copynumber: 4.6 Consensus size: 24
35136277 GTACATGTAT
*
35136287 GCTCATACGAGCT-ATAAACGGTAA
1 GCTCATACGAGCTGAT-AATGGTAA
* *
35136311 GCTCCTCCGAGCTGATAATGGTAA
1 GCTCATACGAGCTGATAATGGTAA
* * *
35136335 GCTTC-TTCGAGCTAAATAGTGGTAA
1 GC-TCATACGAGCT-GATAATGGTAA
35136360 GCTCATACGAGCTGAGT-ATCGGTAA
1 GCTCATACGAGCTGA-TAAT-GGTAA
*
35136385 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
35136399 GAATTGGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
24 31 0.43
25 41 0.57
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGCTGATAATGGTAA
Found at i:35142251 original size:45 final size:45
Alignment explanation
Indices: 35142182--35142267 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
35142172 AGATACTCGA
* *
35142182 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCTGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTGG
*
35142227 TGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
35142268 TCGGTTCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTGG
Found at i:35142341 original size:51 final size:50
Alignment explanation
Indices: 35142269--35142464 Score: 232
Period size: 51 Copynumber: 3.9 Consensus size: 50
35142259 TAATGATGTT
* * * *
35142269 CGGTTCACATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * *
35142320 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
35142371 TGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
35142421 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
35142465 CACTTTCACT
Statistics
Matches: 119, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 75 0.63
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:35142452 original size:101 final size:101
Alignment explanation
Indices: 35142276--35142460 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 101
35142266 GTTCGGTTCA
* *
35142276 CATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
35142341 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* *
35142378 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
35142442 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
35142461 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:35144451 original size:23 final size:23
Alignment explanation
Indices: 35144425--35144470 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
35144415 TTTGCCCAAT
35144425 AACCACTCTCACATTTCCCTTAC
1 AACCACTCTCACATTTCCCTTAC
35144448 AACCACTCTCACATTTCCCTTAC
1 AACCACTCTCACATTTCCCTTAC
35144471 TTTACCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCACTCTCACATTTCCCTTAC
Found at i:35144717 original size:19 final size:20
Alignment explanation
Indices: 35144685--35144722 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
35144675 TAAAATTAAA
35144685 TTTTCAAAAATATT-TTTAT
1 TTTTCAAAAATATTGTTTAT
* *
35144704 TTTTCCAAATTATTGTTTA
1 TTTTCAAAAATATTGTTTA
35144723 ATCAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTCAAAAATATTGTTTAT
Found at i:35145186 original size:13 final size:13
Alignment explanation
Indices: 35145160--35145217 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
35145150 AATGTATAAA
* *
35145160 ATGAAATAGATAT
1 ATGAAATTGTTAT
*
35145173 AAGAAATTGTTAT
1 ATGAAATTGTTAT
* *
35145186 ATGAAATAGATAT
1 ATGAAATTGTTAT
*
35145199 ACGAAATTGTTAT
1 ATGAAATTGTTAT
35145212 ATGAAA
1 ATGAAA
35145218 ATAGATATAC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.33
Consensus pattern (13 bp):
ATGAAATTGTTAT
Found at i:35145189 original size:26 final size:26
Alignment explanation
Indices: 35145160--35145231 Score: 117
Period size: 26 Copynumber: 2.7 Consensus size: 26
35145150 AATGTATAAA
35145160 ATGAAATAGATATAAGAAATTGTTAT
1 ATGAAATAGATATAAGAAATTGTTAT
*
35145186 ATGAAATAGATATACGAAATTGTTAT
1 ATGAAATAGATATAAGAAATTGTTAT
35145212 ATGAAAATAGATATACAGAA
1 ATG-AAATAGATATA-AGAA
35145232 TGATTTTATG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 28 0.67
27 11 0.26
28 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (26 bp):
ATGAAATAGATATAAGAAATTGTTAT
Found at i:35145279 original size:40 final size:40
Alignment explanation
Indices: 35145208--35145283 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
35145198 TACGAAATTG
35145208 TTATATGAAAATAGATATACAGAATGATTTTATGAATCGA
1 TTATATGAAAATAGATATACAGAATGATTTTATGAATCGA
* * * *
35145248 TTATATGGAAATAGTTATA-TGAAGTGTTTTTATGAA
1 TTATATGAAAATAGATATACAGAA-TGATTTTATGAA
35145284 ATGTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.10
40 28 0.90
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (40 bp):
TTATATGAAAATAGATATACAGAATGATTTTATGAATCGA
Found at i:35158316 original size:22 final size:22
Alignment explanation
Indices: 35158254--35158325 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
35158244 ATTGTTCAAA
* **
35158254 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
35158276 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
35158298 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
35158320 CATGAG
1 CATGAG
35158326 GGTCGGGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:35164597 original size:21 final size:19
Alignment explanation
Indices: 35164560--35164634 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
35164550 AATCATATCT
35164560 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
35164579 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
35164600 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
* *
35164619 TCTAAGATTGTATATC
1 TCCAAGATTGCATATC
35164635 CTTCAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:35165172 original size:44 final size:44
Alignment explanation
Indices: 35165079--35165254 Score: 255
Period size: 44 Copynumber: 4.0 Consensus size: 44
35165069 AGGAAAGTAA
* * *
35165079 GATTCGCAATCTTCAACCTATTCCAC-GCTAACCAGAGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
*
35165122 GATTCACAATCTTCAACCTATTCCACTGTTGACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* *
35165166 GATTCACAATCTTCAGCCTATTCCACTGCTGACCCGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * * *
35165210 GATTCACAATCTTTATCCTATTCCACTGCTGTCTAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
35165254 G
1 G
35165255 GTTGGGGTTA
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 25 0.21
44 95 0.79
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
Found at i:35165368 original size:43 final size:42
Alignment explanation
Indices: 35165315--35165456 Score: 104
Period size: 43 Copynumber: 3.3 Consensus size: 42
35165305 TATTTTTAAC
35165315 CTGCTCCGCTGCAACCTAGGGAGGCAAGGCTGGTGTCTTTGAT
1 CTGCTCCGCTGCAACC-AGGGAGGCAAGGCTGGTGTCTTTGAT
* *** * ** * * * * *
35165358 CTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAAC
1 CTGCTCCGCTG-C-AACCAGGGAGGCAAG-GCTGGTGTCTTTGAT
* *
35165403 CTACTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTCCGCTGCAA-CCAGGGAGGCAAGGCTGGTGTCTTTGAT
*
35165446 CTGCTTCGCTG
1 CTGCTCCGCTG
35165457 TTGGTGCAGG
Statistics
Matches: 67, Mismatches: 28, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 26 0.39
44 23 0.34
45 18 0.27
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (42 bp):
CTGCTCCGCTGCAACCAGGGAGGCAAGGCTGGTGTCTTTGAT
Found at i:35165394 original size:88 final size:88
Alignment explanation
Indices: 35165265--35165530 Score: 460
Period size: 88 Copynumber: 3.0 Consensus size: 88
35165255 GTTGGGGTTA
*
35165265 TCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
35165330 CTAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* * *
35165353 TTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
35165418 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
* *
35165441 TCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
35165506 CCAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTGGTGTCT
35165529 TC
1 TC
35165531 AATATAGGAA
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 167 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCT
Found at i:35165516 original size:44 final size:44
Alignment explanation
Indices: 35165292--35165518 Score: 152
Period size: 44 Copynumber: 5.2 Consensus size: 44
35165282 CGGTGTAGGA
* *
35165292 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCTAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAGGG
* * * * * * * **** *
35165336 AGGCAAG-GCTGGTGTCTTTGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGT-AACCCAGGG
* * *
35165380 AGGCAAGATTTGCTATTTTTAACCTACTCCGCTGCAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAGGG
* * * * ** * * **** *
35165424 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTTGGTGCAGGA
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-TAACCCAGGG
35165468 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAGGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAGGG
35165512 AGGCAAG
1 AGGCAAG
35165519 GCTAGTGTCT
Statistics
Matches: 121, Mismatches: 58, Indels: 8
0.65 0.31 0.04
Matches are distributed among these distances:
43 35 0.29
44 51 0.42
45 35 0.29
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAGGG
Found at i:35165594 original size:44 final size:44
Alignment explanation
Indices: 35165530--35165823 Score: 274
Period size: 44 Copynumber: 6.7 Consensus size: 44
35165520 CTAGTGTCTT
* *
35165530 CAATATAGGAAGACATGATCTGCTATCTTCGATCTACTTCACGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACAC
* * * * * *
35165574 CAATACATGAAGACAAGATCTTCTTTCTTCGATCTACTCCGCCAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACAC
* * *
35165619 CAATATGGGAAGACAAGATTTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-AC
* * * * *
35165662 CAATATAGGAAGACAGGACCTGCTATCTTTGATCTACGTCACGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACAC
* ** *
35165706 CAATACATAAAGACAAGATCTGCTTTCTTCGATCTAC-TCTACCAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-A-CAC
* * * *
35165751 CAATATGGGGAGACAAAATCTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-AC
* *
35165794 CAATATAGGAAGACAGGACCTGCTATCTTC
1 CAATATAGGAAGACAAGATCTGCTATCTTC
35165824 ACTGATATGC
Statistics
Matches: 196, Mismatches: 45, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
42 2 0.01
43 43 0.22
44 109 0.56
45 42 0.21
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (44 bp):
CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACAC
Found at i:35165775 original size:132 final size:132
Alignment explanation
Indices: 35165530--35165823 Score: 489
Period size: 132 Copynumber: 2.2 Consensus size: 132
35165520 CTAGTGTCTT
* * * *
35165530 CAATATAGGAAGACATGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACGTCACGCCAATACATAAAGACAAGATCT
* * * *
35165595 TCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATTTGCATCTTCGATCCACTTCCT
66 GCTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAAATCTGCATCTTCGATCCACTTCCT
35165660 AC
131 AC
*
35165662 CAATATAGGAAGACAGGACCTGCTATCTTTGATCTACGTCACGCCAATACATAAAGACAAGATCT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACGTCACGCCAATACATAAAGACAAGATCT
* *
35165727 GCTTTCTTCGATCTACTCTACCACCAATATGGGGAGACAAAATCTGCATCTTCGATCCACTTCCT
66 GCTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAAATCTGCATCTTCGATCCACTTCCT
35165792 AC
131 AC
35165794 CAATATAGGAAGACAGGACCTGCTATCTTC
1 CAATATAGGAAGACAGGACCTGCTATCTTC
35165824 ACTGATATGC
Statistics
Matches: 150, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 150 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (132 bp):
CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACGTCACGCCAATACATAAAGACAAGATCT
GCTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAAATCTGCATCTTCGATCCACTTCCT
AC
Found at i:35167060 original size:15 final size:15
Alignment explanation
Indices: 35167037--35167067 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35167027 CACCTTGGCC
35167037 TTTCCTTTTTCTTTT
1 TTTCCTTTTTCTTTT
*
35167052 TTTCTTTTTTCTTTT
1 TTTCCTTTTTCTTTT
35167067 T
1 T
35167068 GAAATATTCT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCCTTTTTCTTTT
Found at i:35167468 original size:15 final size:16
Alignment explanation
Indices: 35167429--35167467 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
35167419 CTAGTAGAGT
35167429 TTTTTTTTGCGCCATC
1 TTTTTTTTGCGCCATC
35167445 TTTTTTTTGCGCCATC
1 TTTTTTTTGCGCCATC
35167461 TTTTTTT
1 TTTTTTT
35167468 GGGCAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.10, T:0.64
Consensus pattern (16 bp):
TTTTTTTTGCGCCATC
Found at i:35171939 original size:9 final size:9
Alignment explanation
Indices: 35171925--35171973 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
35171915 GTTAAATGAA
35171925 TCGAGTTAT
1 TCGAGTTAT
*
35171934 TCGAGTTAA
1 TCGAGTTAT
35171943 TCGAGTTAT
1 TCGAGTTAT
*
35171952 TCGAGTTAA
1 TCGAGTTAT
35171961 TCGAGTTAT
1 TCGAGTTAT
35171970 TCGA
1 TCGA
35171974 ATCAACTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:35171946 original size:18 final size:18
Alignment explanation
Indices: 35171923--35171973 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
35171913 GAGTTAAATG
35171923 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
35171941 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
35171959 AATCGAGTTATTCGA
1 AATCGAGTTATTCGA
35171974 ATCAACTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:35172044 original size:9 final size:9
Alignment explanation
Indices: 35172027--35172063 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
35172017 TGAGTTTTCG
35172027 AATTCGAAT
1 AATTCGAAT
*
35172036 AACTCGAAT
1 AATTCGAAT
35172045 AATTCGAAT
1 AATTCGAAT
35172054 AATTCGAAT
1 AATTCGAAT
35172063 A
1 A
35172064 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35172170 original size:29 final size:29
Alignment explanation
Indices: 35172114--35172170 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
35172104 ACTTTTTTAC
*
35172114 TTTTCCCTCAAAACTTTTACTCCTTCCCA
1 TTTTCCCTCAAAACTTTTACTCCCTCCCA
*
35172143 TTTTCCC-CAACACTTTTACTCCCCTCCC
1 TTTTCCCTCAAAACTTTTACT-CCCTCCC
35172171 CTCCCAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.18, C:0.44, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTTCCCTCAAAACTTTTACTCCCTCCCA
Found at i:35172323 original size:30 final size:31
Alignment explanation
Indices: 35172275--35172334 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
35172265 AAACCTTTTA
* *
35172275 TTTTCCCCCCAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
35172305 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
35172335 TCTCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:35173877 original size:22 final size:22
Alignment explanation
Indices: 35173807--35173877 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
35173797 AAATTCAATA
*
35173807 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
35173829 TC-AATTCCGTTCAAAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
*
35173851 TCAAATTCCTTCCAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
35173873 TCAAA
1 TCAAA
35173878 CTCTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.11
22 34 0.76
23 6 0.13
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:35173883 original size:30 final size:30
Alignment explanation
Indices: 35173848--35173906 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
35173838 TTCAAAAATT
*
35173848 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
35173878 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
35173907 TTTCCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:35173898 original size:52 final size:51
Alignment explanation
Indices: 35173826--35173928 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
35173816 TTCAAAAATT
* * *
35173826 CTCTCAATTCCGTTCAAAAATTCTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTC-CAAA
* *
35173878 CTCTCAAATTCC-TTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
35173929 TCCATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 35 0.78
53 6 0.13
ACGTcount: A:0.34, C:0.32, G:0.01, T:0.33
Consensus pattern (51 bp):
CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
Found at i:35173917 original size:21 final size:22
Alignment explanation
Indices: 35173878--35173919 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35173868 TTCTCTCAAA
35173878 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
35173900 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
35173920 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:35174146 original size:14 final size:15
Alignment explanation
Indices: 35174117--35174150 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35174107 AAATTTTAAA
35174117 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
35174132 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
35174146 TTTTA
1 TTTTA
35174151 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:35176320 original size:23 final size:23
Alignment explanation
Indices: 35176294--35176479 Score: 147
Period size: 28 Copynumber: 7.2 Consensus size: 23
35176284 TTTTGACATT
*
35176294 ATTTGATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
*
35176317 ATTTAGTTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACC-----TA
35176345 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
35176368 ATTTAACTTAATTAAAAACCCTAACCTAA
1 A--T---TTAATTAAAAACCCTAACCT-A
*
35176397 CCTATTTTAATTAAAAACCCTAACTTA
1 ---A-TTTAATTAAAAACCCTAACCTA
**
35176424 ACCTAATTAAAAACCCTAACCTAGTTTA
1 ATTTAATTAAAAACCCTAACC-----TA
35176452 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
35176475 ATTTA
1 ATTTA
35176480 CCCTAGCCCT
Statistics
Matches: 135, Mismatches: 9, Indels: 38
0.74 0.05 0.21
Matches are distributed among these distances:
23 46 0.34
24 1 0.01
25 1 0.01
27 1 0.01
28 82 0.61
29 1 0.01
31 2 0.01
32 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:35176346 original size:28 final size:28
Alignment explanation
Indices: 35176315--35176479 Score: 223
Period size: 28 Copynumber: 6.1 Consensus size: 28
35176305 AACCCTAACC
*
35176315 TAATTTAGTTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
35176343 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
* **
35176371 TAACTTAATTAAAAACCCTAACCTAACC
1 TAATTTAATTAAAAACCCTAACCTAATT
*
35176399 TATTTTAATTAAAAACCCTAA-C----T
1 TAATTTAATTAAAAACCCTAACCTAATT
** *
35176422 TAACCTAATTAAAAACCCTAACCTAGTT
1 TAATTTAATTAAAAACCCTAACCTAATT
35176450 TAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCTAATT
35176478 TA
1 TA
35176480 CCCTAGCCCT
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
23 18 0.15
24 1 0.01
27 1 0.01
28 99 0.83
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (28 bp):
TAATTTAATTAAAAACCCTAACCTAATT
Found at i:35176359 original size:51 final size:51
Alignment explanation
Indices: 35176294--35176521 Score: 255
Period size: 51 Copynumber: 4.4 Consensus size: 51
35176284 TTTTGACATT
* *
35176294 ATTTGATTAAAAACCCTAACCTAATTTAGTTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
**
35176345 ATTTAATTAAAAACCCTAACCTAATTTAACTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAA--T---TTAATTAAAAACCCTAACCTAATTTA
* * ** *
35176401 TTTTAATTAAAAACCCTAACTTAACCTAATTAAAAACCCTAACCTAGTTTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
** *
35176452 ATTTAATTAAAAACCCTAACCTAATTTACCCT---AGCCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAATTTA-ATTAAAAACCCTAACCTAATTTA
* *
35176501 ACTTAATTAAAATCCCTAACC
1 ATTTAATTAAAAACCCTAACC
35176522 CTAACCTAAT
Statistics
Matches: 150, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
49 34 0.23
51 69 0.46
52 1 0.01
53 1 0.01
56 45 0.30
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (51 bp):
ATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
Found at i:35176518 original size:34 final size:34
Alignment explanation
Indices: 35176479--35176554 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
35176469 AACCTAATTT
*
35176479 ACCCTAGCCCTAACCTAATTTAACTTAAT-TAAAA
1 ACCCTAACCCTAACCTAATTTAA-TTAATGTAAAA
*
35176513 TCCCTAACCCTAACCTAATTTAATTAATGTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAATGTAAAA
35176547 ACCCTAAC
1 ACCCTAAC
35176555 AAAATTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 5 0.13
34 33 0.87
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.29
Consensus pattern (34 bp):
ACCCTAACCCTAACCTAATTTAATTAATGTAAAA
Found at i:35180032 original size:124 final size:124
Alignment explanation
Indices: 35179822--35180054 Score: 378
Period size: 124 Copynumber: 1.9 Consensus size: 124
35179812 GATTTGACAC
* * *
35179822 TATTTGCTCAGAAACGTCAAAAAAAAATATTTCCTACATGACCAATTGTAGCGAAATCGCGTCCA
1 TATTTGCTAAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCGAAATCGCATCCA
* * *
35179887 CGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAGTGATTTTATAA
66 CGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAGTGATTTTATAA
* *
35179946 TATTTGCTAAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGCGAAATCGCATCC
1 TATTTGCTAAG-AAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCGAAATCGCATCC
35180010 ACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
65 ACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
35180055 GAAGCGATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 70 0.70
125 30 0.30
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
TATTTGCTAAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCGAAATCGCATCCA
CGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAGTGATTTTATAA
Found at i:35180074 original size:124 final size:124
Alignment explanation
Indices: 35179810--35180075 Score: 372
Period size: 124 Copynumber: 2.1 Consensus size: 124
35179800 CCACGAGGGC
* * *
35179810 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCCTACATGACCAATTGTAGCG
1 GCGATTTCACACTATTTGCTAAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCG
* * * * **
35179875 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * * * *
35179934 GTGATTTTATAATATTTGCTAAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTCACACTATTTGCTAAG-AAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGC
35179998 GAAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
65 GAAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
*
35180058 GCGATTTCCCACTATTTG
1 GCGATTTCACACTATTTG
35180076 ACCAGATACA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
124 92 0.75
125 30 0.25
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTCACACTATTTGCTAAGAAACGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCG
AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:35181440 original size:27 final size:27
Alignment explanation
Indices: 35181408--35181484 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
35181398 GCTTTGAAGA
35181408 GCCACTATCACTGAATTTCACCAAAGT
1 GCCACTATCACTGAATTTCACCAAAGT
* * * *
35181435 GTCACTATCACTGAGTTGT-ATCGAAGT
1 GCCACTATCACTGAATT-TCACCAAAGT
35181462 GCCACTATCACTG-ATTTGCACCA
1 GCCACTATCACTGAATTT-CACCA
35181485 CTATGCACAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
25 1 0.03
26 2 0.05
27 35 0.90
28 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (27 bp):
GCCACTATCACTGAATTTCACCAAAGT
Found at i:35182972 original size:40 final size:40
Alignment explanation
Indices: 35182923--35183003 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
35182913 ACCAAATCAC
*
35182923 AATCATTTTTAATCAAGGTTTATTTATTTATTAAATCCGT
1 AATCATTTTTAATCAAGGGTTATTTATTTATTAAATCCGT
35182963 AATCATTTTTAATCAAGGGTTATTTATTTATTAAATCCGT
1 AATCATTTTTAATCAAGGGTTATTTATTTATTAAATCCGT
35183003 A
1 A
35183004 CTAACACGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (40 bp):
AATCATTTTTAATCAAGGGTTATTTATTTATTAAATCCGT
Found at i:35186235 original size:43 final size:43
Alignment explanation
Indices: 35186135--35186249 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
35186125 CAATGTCATA
* *
35186135 TCCCAGATATGGTCTTACATGTTATCACATATCGATGCCATTG
1 TCCCAGATATGGTCTTACACGTAATCACATATCGATGCCATTG
** * * *
35186178 TCTTAGATAGGGTCTTACACGTAATCGCATATCGATTCCAATT-
1 TCCCAGATATGGTCTTACACGTAATCACATATCGATGCC-ATTG
* *
35186221 TCCCAGACATGGTCTTACACGAAATCACA
1 TCCCAGATATGGTCTTACACGTAATCACA
35186250 CCTCAGGAGT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 55 0.95
44 3 0.05
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (43 bp):
TCCCAGATATGGTCTTACACGTAATCACATATCGATGCCATTG
Found at i:35188254 original size:30 final size:30
Alignment explanation
Indices: 35188220--35188287 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
35188210 CGACCATTGG
** *
35188220 AAAGGGATAGTTTCGGCTGTCAAAATATGA
1 AAAGGGATAGCCTCAGCTGTCAAAATATGA
*
35188250 AAAGGGATAGCCTCAGCTGTCAAATTATGA
1 AAAGGGATAGCCTCAGCTGTCAAAATATGA
35188280 AAAGGGAT
1 AAAGGGAT
35188288 TGTGATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (30 bp):
AAAGGGATAGCCTCAGCTGTCAAAATATGA
Found at i:35188326 original size:29 final size:30
Alignment explanation
Indices: 35188276--35188341 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
35188266 CTGTCAAATT
* * *
35188276 ATGAAAAGGGATTGTGATGACCATC-AACA
1 ATGAAAAGGGATGGTAACGACCATCGAACA
*
35188305 ATGAAAAGGGATGGTAACGACCATCGAACC
1 ATGAAAAGGGATGGTAACGACCATCGAACA
35188335 ATGAAAA
1 ATGAAAA
35188342 TGGGTAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (30 bp):
ATGAAAAGGGATGGTAACGACCATCGAACA
Found at i:35188371 original size:89 final size:89
Alignment explanation
Indices: 35188239--35188471 Score: 288
Period size: 89 Copynumber: 2.6 Consensus size: 89
35188229 GTTTCGGCTG
* * * * * * *
35188239 TCAAAATATGAAAAGGGATAGCCTCAGCTGTCAAATTATGAAAAGGGATTGTGATGACCATCAAC
1 TCAAAACATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGAACATCAAC
* * *
35188304 AATGAAAAGGGATGGTAACGACCA
66 AATGAAAAAGGATAGTAACAACCA
* * * *
35188328 TCGAACCATGAAAATGGG-TAGCTTCGGCTATCAAATTATGAAAAGGAATGGTGACGAACATTAA
1 TCAAAACATGAAAA-GGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGAACATCAA
* *
35188392 CTATGAAAAAGGATAGTGACAACCA
65 CAATGAAAAAGGATAGTAACAACCA
* *
35188417 TCAAAATATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGGATGGTGAC
1 TCAAAACATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGAC
35188472 AACCATCGTG
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
88 3 0.02
89 115 0.95
90 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (89 bp):
TCAAAACATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGGGATGGTGACGAACATCAAC
AATGAAAAAGGATAGTAACAACCA
Found at i:35192837 original size:30 final size:30
Alignment explanation
Indices: 35192803--35192873 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
35192793 GCTTTAGCTG
*
35192803 TCAAAATATGAAAAGAGATAGCTTCGACTC
1 TCAAATTATGAAAAGAGATAGCTTCGACTC
* * *
35192833 TCAAATTATGAAAAGGGATAGCTTCGGCTG
1 TCAAATTATGAAAAGAGATAGCTTCGACTC
35192863 TCAAATTATGA
1 TCAAATTATGA
35192874 TTCGACTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (30 bp):
TCAAATTATGAAAAGAGATAGCTTCGACTC
Found at i:35192882 original size:49 final size:49
Alignment explanation
Indices: 35192825--35192922 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
35192815 AAGAGATAGC
35192825 TTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGA
1 TTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGA
35192874 TTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGA
1 TTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGA
35192923 AATGGGATAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (49 bp):
TTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGA
Found at i:35192918 original size:30 final size:30
Alignment explanation
Indices: 35192882--35193049 Score: 139
Period size: 30 Copynumber: 5.6 Consensus size: 30
35192872 GATTCGACTC
* *
35192882 TCAAATTATGAAAAGGGATAGCTTCGGCTG
1 TCAAATTATGAAAAGGGATAGCTTCAGCTA
*
35192912 TCAAATTATGAAATGGGATAGCTTCAGCTA
1 TCAAATTATGAAAAGGGATAGCTTCAGCTA
* * ** *
35192942 TCAAATTATGGAAAGGGAT-GGTGAAGACCA
1 TCAAATTATGAAAAGGGATAGCTTCAG-CTA
* * *
35192972 TCAACA--ATGAAAAGGGAT-G-GTGACGACCA
1 TCAA-ATTATGAAAAGGGATAGCTTCA-G-CTA
* * *
35193001 TCGAACTATGAAAAGGGATAGCTTCGGCTA
1 TCAAATTATGAAAAGGGATAGCTTCAGCTA
35193031 TCAAATTATGAAAAGGGAT
1 TCAAATTATGAAAAGGGAT
35193050 GGTGACGACC
Statistics
Matches: 111, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
28 2 0.02
29 24 0.22
30 81 0.73
31 3 0.03
32 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (30 bp):
TCAAATTATGAAAAGGGATAGCTTCAGCTA
Found at i:35192934 original size:79 final size:79
Alignment explanation
Indices: 35192803--35192951 Score: 235
Period size: 79 Copynumber: 1.9 Consensus size: 79
35192793 GCTTTAGCTG
* *
35192803 TCAAAATATGAAAAGAGATAGCTTCGACTCTCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAA
1 TCAAAATATGAAAAGAGATAGCTTCGACTCTCAAATTATGAAAAGGGATAGCTTCAGCTATCAAA
35192868 TTATGATTCGACTC
66 TTATGATTCGACTC
* * * * *
35192882 TCAAATTATGAAAAGGGATAGCTTCGGCTGTCAAATTATGAAATGGGATAGCTTCAGCTATCAAA
1 TCAAAATATGAAAAGAGATAGCTTCGACTCTCAAATTATGAAAAGGGATAGCTTCAGCTATCAAA
35192947 TTATG
66 TTATG
35192952 GAAAGGGATG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (79 bp):
TCAAAATATGAAAAGAGATAGCTTCGACTCTCAAATTATGAAAAGGGATAGCTTCAGCTATCAAA
TTATGATTCGACTC
Found at i:35193064 original size:30 final size:30
Alignment explanation
Indices: 35192941--35193073 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
35192931 AGCTTCAGCT
* * *
35192941 ATCAAATTATGGAAAGGGATGGTGAAGACC
1 ATCAAACTATGAAAAGGGATGGTGACGACC
*
35192971 ATC-AACAATGAAAAGGGATGGTGACGACC
1 ATCAAACTATGAAAAGGGATGGTGACGACC
* * * * *
35193000 ATCGAACTATGAAAAGGGATAGCT-TCGGCT
1 ATCAAACTATGAAAAGGGAT-GGTGACGACC
*
35193030 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAACTATGAAAAGGGATGGTGACGACC
35193060 ATC-AACTATGAAAA
1 ATCAAACTATGAAAA
35193074 TATGAAAAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
29 37 0.44
30 45 0.54
31 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (30 bp):
ATCAAACTATGAAAAGGGATGGTGACGACC
Found at i:35197264 original size:51 final size:52
Alignment explanation
Indices: 35197187--35197326 Score: 196
Period size: 50 Copynumber: 2.8 Consensus size: 52
35197177 ATGTTCGGTT
35197187 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA-TCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATA
* * * *
35197238 TACATAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATA
* * *
35197288 CACGTAGTAGCCTGCACATATTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
35197327 CACTTTCACT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
49 4 0.05
50 38 0.49
51 35 0.45
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.24
Consensus pattern (52 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATA
Found at i:35197317 original size:50 final size:50
Alignment explanation
Indices: 35197182--35197326 Score: 184
Period size: 51 Copynumber: 2.9 Consensus size: 50
35197172 CAATGATGTT
* *
35197182 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATC
* * *
35197233 CGATATACATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TC
* * * *
35197283 CGGTACACGTAGTAGCCTGCACATATTACTACACACGTGACCAT
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCAT
35197327 CACTTTCACT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
49 4 0.05
50 38 0.47
51 39 0.48
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATC
Found at i:35207081 original size:14 final size:14
Alignment explanation
Indices: 35207073--35207101 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35207063 TATAAAGATT
35207073 AAAAAATAAAAATA
1 AAAAAATAAAAATA
35207087 AAAAAAT-AAAATA
1 AAAAAATAAAAATA
35207100 AA
1 AA
35207102 TGTAAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:35209915 original size:54 final size:54
Alignment explanation
Indices: 35209844--35210042 Score: 319
Period size: 54 Copynumber: 3.7 Consensus size: 54
35209834 ATATGGTAAG
35209844 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATAGA-ATCATATGGGGAAA
1 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTAT-GACATCATATGGGGAAA
* *
35209898 TGAATACCATATAGTGTAAGACCTAGTCTAGGACTATGACATCATATGGGGAAA
1 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGAAA
* * * * *
35209952 TGAAGACTATATACTATAAGACCTAGCCTGAGACTATGACATCATATGGGGAAA
1 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGAAA
35210006 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTAT
1 TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTAT
35210043 TGCGTCATGT
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.02
54 128 0.98
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (54 bp):
TGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGACATCATATGGGGAAA
Found at i:35210209 original size:29 final size:29
Alignment explanation
Indices: 35210167--35210263 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
35210157 AAAGTGATGT
35210167 CTTTGTGGCTGAATTTGTTATATGTAAGC
1 CTTTGTGGCTGAATTTGTTATATGTAAGC
* * * *
35210196 CTTTGTGGTTGAATCTGTTACATGTGAGC
1 CTTTGTGGCTGAATTTGTTATATGTAAGC
* *
35210225 CCTAGTGGCTGAACTTT-TTATATGTGAAAGC
1 CTTTGTGGCTGAA-TTTGTTATATGT--AAGC
35210256 CTTTGTGG
1 CTTTGTGG
35210264 TTGCTCTAGG
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 42 0.79
30 2 0.04
31 9 0.17
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (29 bp):
CTTTGTGGCTGAATTTGTTATATGTAAGC
Found at i:35213731 original size:45 final size:44
Alignment explanation
Indices: 35213681--35213774 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
35213671 GAATAGAGGC
* *
35213681 GTAATGGATTAGAGGTGTAATAGCAAATTAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG--AATTAATATGTTTGGTTGAAT
* **
35213726 GTAATGGAATAGAGGCGTAATAGTATTCTTATGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTAATATGTTTGGTTGAAT
35213770 GTAAT
1 GTAAT
35213775 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.09
44 18 0.42
45 21 0.49
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTAATATGTTTGGTTGAAT
Found at i:35213952 original size:16 final size:16
Alignment explanation
Indices: 35213915--35213956 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35213905 TTAATCATAT
*
35213915 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
35213931 TT-AAATATATTATAA
1 TTAAAATATATTATAA
35213946 TTAAAATATAT
1 TTAAAATATAT
35213957 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:35213963 original size:14 final size:15
Alignment explanation
Indices: 35213924--35213965 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35213914 TTTAAACATA
*
35213924 ATTATTATTAAATAT
1 ATTATAATTAAATAT
35213939 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
35213953 A-TATAATTTAATA
1 ATTATAATTAAATA
35213966 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:35214083 original size:14 final size:15
Alignment explanation
Indices: 35214034--35214085 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35214024 ATAAAATATA
35214034 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35214049 TATTAAATATATTAT
1 AATTAAATATATTAT
35214064 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35214077 AATTTAATA
1 AATTAAATA
35214086 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35214323 original size:14 final size:15
Alignment explanation
Indices: 35214274--35214325 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35214264 ATAAAATATA
35214274 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35214289 TATTAAATATATTAT
1 AATTAAATATATTAT
35214304 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35214317 AATTTAATA
1 AATTAAATA
35214326 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35214443 original size:14 final size:15
Alignment explanation
Indices: 35214394--35214445 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35214384 ATAAAGGATA
35214394 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35214409 TATTAAATATATTAT
1 AATTAAATATATTAT
35214424 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35214437 AATTTAATA
1 AATTAAATA
35214446 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35214563 original size:14 final size:15
Alignment explanation
Indices: 35214514--35214565 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35214504 ATAAAATATA
35214514 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35214529 TATTAAATATATTAT
1 AATTAAATATATTAT
35214544 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35214557 AATTTAATA
1 AATTAAATA
35214566 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35214701 original size:120 final size:120
Alignment explanation
Indices: 35213918--35214690 Score: 1422
Period size: 120 Copynumber: 6.4 Consensus size: 120
35213908 ATCATATTTA
35213918 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
35213983 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
35214038 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
35214103 TATTCTTATATGAATTTACTCAAATCGTAATATATGATACTATAAAAGATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
*
35214158 AACATAATTATTATTAAATATATTAGAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
35214223 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
35214278 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
35214343 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAGGATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
35214398 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
35214463 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
35214518 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
35214583 TATTCTTATATGAATTTACTCAAATCGTAATATATGATACTATAAAAGATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
* * *
35214638 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
35214691 TAAAATAATT
Statistics
Matches: 634, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
120 632 1.00
121 2 0.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
Found at i:35214790 original size:27 final size:26
Alignment explanation
Indices: 35214734--35214790 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
35214724 GAATTTGTAT
* *
35214734 AATTTAAAATAATTATTATTACATAT
1 AATTTAAAATAATTATAATTACATAA
*
35214760 AATTTAATAATAA-TATAAATTTCATAA
1 AATTTAA-AATAATTAT-AATTACATAA
35214787 AATT
1 AATT
35214791 CTTGATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTTAAAATAATTATAATTACATAA
Found at i:35214800 original size:90 final size:91
Alignment explanation
Indices: 35214706--35214893 Score: 288
Period size: 90 Copynumber: 2.1 Consensus size: 91
35214696 TAATTATAAC
* * * *
35214706 TAATAAATTATATTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
35214771 AATATA-AATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAACTCTTAA
* *
35214796 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
35214861 GATATATAATTTCATAAAACTCTTAA
66 AATATATAATTTCATAAAACTCTTAA
35214887 TAATAAA
1 TAATAAA
35214894 ATGTTCTTAT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 64 0.73
91 24 0.27
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAACTCTTAA
Found at i:35216303 original size:11 final size:11
Alignment explanation
Indices: 35216289--35216315 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35216279 AAAAATCAAT
35216289 ACAAAAGTTTC
1 ACAAAAGTTTC
35216300 ACAAAAGTTTC
1 ACAAAAGTTTC
35216311 ACAAA
1 ACAAA
35216316 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:35218080 original size:6 final size:6
Alignment explanation
Indices: 35218069--35218094 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35218059 TAGTTTGGAC
35218069 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
35218095 ATAATTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:35224943 original size:18 final size:18
Alignment explanation
Indices: 35224916--35224961 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
35224906 ATGTTTAGTT
35224916 ATTT-ATTTTTTAATTTA
1 ATTTAATTTTTTAATTTA
** *
35224933 ATTTAATTTTTTTGTTTT
1 ATTTAATTTTTTAATTTA
35224951 ATTTAATTTTT
1 ATTTAATTTTT
35224962 CAGGTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTAATTTTTTAATTTA
Found at i:35229394 original size:2 final size:2
Alignment explanation
Indices: 35229389--35229423 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35229379 ACACACACAC
35229389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35229424 AAATCCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35231250 original size:84 final size:85
Alignment explanation
Indices: 35231136--35231299 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 85
35231126 ATTAAAAATT
* * *
35231136 TTTTTTCACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAA-A-TTCTTAAACTTTTTTA
1 TTTTTACACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAATACCT-TTAAACTTTTTCA
35231199 A-AGAAAATAATTAAGCCTTTC
65 ATA-AAAATAATTAAGCCTTTC
* * *
35231220 TTTTTACACTTAATTGGATAATTT-AATTTTTAAAATACATTAAAAATACCTTTAAACTTTTTCA
1 TTTTTACACTCAATTAGAT-ATTTGAATTTTTAAAATACATAAAAAATACCTTTAAACTTTTTCA
*
35231284 ATAAAAGTAATTAAGC
65 ATAAAAATAATTAAGC
35231300 TCCTAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
84 37 0.54
85 30 0.43
86 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (85 bp):
TTTTTACACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAATACCTTTAAACTTTTTCAA
TAAAAATAATTAAGCCTTTC
Found at i:35231299 original size:85 final size:81
Alignment explanation
Indices: 35231117--35231299 Score: 208
Period size: 85 Copynumber: 2.2 Consensus size: 81
35231107 AAAAAACAAA
**
35231117 AAAAAAGTAATTAAAAATTTTTTTTCACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAA
1 AAAAAAGTAATTAAGCATTTTTTTTCACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAA
* *
35231182 ATTCTTAAACTTTTTT
66 ACTCTTAAACTTTTTC
* * * *
35231198 AAAGAAAATAATTAAGCCTTTCTTTTTACACTTAATTGGATAATTT-AATTTTTAAAATACATTA
1 AAA-AAAGTAATTAAGCATTT-TTTTT-CACTCAATTAGAT-ATTTGAATTTTTAAAATACA-TA
*
35231262 AAAATAC-CTTTAAACTTTTTC
61 AAAAAACTC-TTAAACTTTTTC
35231283 AATAAAAGTAATTAAGC
1 AA-AAAAGTAATTAAGC
35231300 TCCTAAATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
81 3 0.04
82 13 0.15
83 5 0.06
84 27 0.32
85 36 0.42
86 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (81 bp):
AAAAAAGTAATTAAGCATTTTTTTTCACTCAATTAGATATTTGAATTTTTAAAATACATAAAAAA
ACTCTTAAACTTTTTC
Found at i:35231543 original size:18 final size:19
Alignment explanation
Indices: 35231504--35231555 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
35231494 AAATTTTAAT
35231504 AAAAATAATAAAATAGAAA
1 AAAAATAATAAAATAGAAA
* *
35231523 AAAAATAATAAAATCGTAA
1 AAAAATAATAAAATAGAAA
35231542 AAAAAT-ATAAAATA
1 AAAAATAATAAAATA
35231556 TTGTAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAAATAATAAAATAGAAA
Found at i:35231915 original size:19 final size:20
Alignment explanation
Indices: 35231834--35231918 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 20
35231824 TCCTTACGAC
*
35231834 TTTATAAAATTTTATA-ATT
1 TTTATAAAATTTTACATATT
* * *
35231853 TTT-TCTATATTTCTATATATT
1 TTTAT-AAAATTT-TACATATT
*
35231874 TTATAAAAAATTTTAC-TATT
1 TT-TATAAAATTTTACATATT
35231894 TTTATAAAATTTTACAT-TT
1 TTTATAAAATTTTACATATT
35231913 TTTATA
1 TTTATA
35231919 TGTTTTTAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 28 0.53
20 11 0.21
21 7 0.13
22 6 0.11
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAAAATTTTACATATT
Found at i:35231944 original size:19 final size:18
Alignment explanation
Indices: 35231881--35231944 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
35231871 ATTTTATAAA
*
35231881 AAATTTTACTATTTTTAT
1 AAATTTTACAATTTTTAT
*
35231899 AAAATTTTACATTTTTTAT
1 -AAATTTTACAATTTTTAT
**
35231918 ATGTTTTTAACAATTTTTAT
1 A-AATTTT-ACAATTTTTAT
*
35231938 AACTTTT
1 AAATTTT
35231945 TTTTTCTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 1 0.03
19 24 0.67
20 11 0.31
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (18 bp):
AAATTTTACAATTTTTAT
Found at i:35231944 original size:20 final size:19
Alignment explanation
Indices: 35231834--35231945 Score: 62
Period size: 20 Copynumber: 5.7 Consensus size: 19
35231824 TCCTTACGAC
* *
35231834 TTTATAAAATTTTATAATTT
1 TTTATAAATTTTTACAA-TT
* * * *
35231854 TTTCTATATTTCTATATATT
1 TTTATAAATTTTTACA-ATT
* * *
35231874 TTATAAAAAATTTTACTATT
1 TT-TATAAATTTTTACAATT
* *
35231894 TTTATAAAATTTTACATTT
1 TTTATAAATTTTTACAATT
**
35231913 TTTATATGTTTTTAACAATT
1 TTTATAAATTTTT-ACAATT
*
35231933 TTTATAACTTTTT
1 TTTATAAATTTTT
35231946 TTTTCTAATT
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
19 24 0.35
20 37 0.54
21 8 0.12
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTATAAATTTTTACAATT
Found at i:35231997 original size:19 final size:17
Alignment explanation
Indices: 35231882--35231997 Score: 51
Period size: 19 Copynumber: 6.4 Consensus size: 17
35231872 TTTTATAAAA
*
35231882 AATTTTACTATTTTTAT
1 AATTTTAATATTTTTAT
35231899 AAAATTTTACAT-TTTTTAT
1 --AATTTTA-ATATTTTTAT
* *
35231918 ATGTTTTTAACAATTTTTAT
1 A--ATTTTAA-TATTTTTAT
* *
35231938 AACTTT--T-TTTTTCT
1 AATTTTAATATTTTTAT
35231952 AATTTTAAATATTTTTATT
1 AATTTT-AATATTTTTA-T
*
35231971 AAAATTTAATCATTTTTAT
1 -AATTTTAAT-ATTTTTAT
35231990 AACTTTTA
1 AA-TTTTA
35231998 TTGATTTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 26
0.66 0.10 0.24
Matches are distributed among these distances:
14 11 0.15
17 2 0.03
18 11 0.15
19 28 0.38
20 21 0.29
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (17 bp):
AATTTTAATATTTTTAT
Found at i:35238368 original size:39 final size:39
Alignment explanation
Indices: 35238314--35238532 Score: 314
Period size: 39 Copynumber: 5.6 Consensus size: 39
35238304 AACATGTTTT
* *
35238314 TGAGTATTGCGATATATGTTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
35238353 TGAGTATTGTGATATATGTTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
35238392 TAAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
35238431 TGA-TAATTATGATATATGCTTAAATGTTATGTGATTATA
1 TGAGT-ATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
35238470 TGAGTATTATGGTATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
35238509 TGTGTAATGTGATATATACTTAAA
1 TGAGTATTGTGATATATGCTTAAA
35238533 AGTGAAAATG
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
38 1 0.01
39 163 0.99
40 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:35238434 original size:8 final size:8
Alignment explanation
Indices: 35238418--35238510 Score: 50
Period size: 8 Copynumber: 11.9 Consensus size: 8
35238408 TGCTTGAATG
*
35238418 TTATGTGA
1 TTATATGA
35238426 TTATATGA
1 TTATATGA
*
35238434 TAATTATGA
1 TTA-TATGA
*
35238443 -TATATGC
1 TTATATGA
*
35238450 TTAAATG-
1 TTATATGA
*
35238457 TTATGTGA
1 TTATATGA
35238465 TTATATGA
1 TTATATGA
*
35238473 GTATTATG-
1 TTA-TATGA
* *
35238481 GTATATGC
1 TTATATGA
*
35238489 TTAAATG-
1 TTATATGA
*
35238496 TTATGTGA
1 TTATATGA
35238504 TTATATG
1 TTATATG
35238511 TGTAATGTGA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
7 18 0.28
8 38 0.58
9 9 0.14
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.47
Consensus pattern (8 bp):
TTATATGA
Found at i:35241507 original size:13 final size:13
Alignment explanation
Indices: 35241486--35241516 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35241476 ACTAATGACA
*
35241486 CAATTCCCAAAAC
1 CAATACCCAAAAC
35241499 CAATACCCAAAAC
1 CAATACCCAAAAC
35241512 CAATA
1 CAATA
35241517 GGTAACTTGT
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:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (13 bp):
CAATACCCAAAAC
Found at i:35245958 original size:36 final size:36
Alignment explanation
Indices: 35245911--35245982 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
35245901 GCTCTAGGTT
* * *
35245911 AGTTTAAGCTCTTGTTGCTATAATTGTCTGCAAAGG
1 AGTTTAAGCTCTCGTTACTATAATCGTCTGCAAAGG
35245947 AGTTTAAGCTCTCGTTACTATAATCGTCTGCAAAGG
1 AGTTTAAGCTCTCGTTACTATAATCGTCTGCAAAGG
35245983 GGAACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (36 bp):
AGTTTAAGCTCTCGTTACTATAATCGTCTGCAAAGG
Found at i:35250715 original size:30 final size:29
Alignment explanation
Indices: 35250679--35250746 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 29
35250669 CCCTGTTAAG
*
35250679 AAACATTTAGACCCCAAAATTAAAAAATAA
1 AAACATTTAGACCCCAAAACTAAAAAAT-A
*
35250709 AAACATTTAGACCCCAAAACTAAATAATA
1 AAACATTTAGACCCCAAAACTAAAAAATA
35250738 AAACATTTA
1 AAACATTTA
35250747 ACAAAGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.57, C:0.18, G:0.03, T:0.22
Consensus pattern (29 bp):
AAACATTTAGACCCCAAAACTAAAAAATA
Found at i:35256234 original size:50 final size:50
Alignment explanation
Indices: 35256157--35256398 Score: 243
Period size: 50 Copynumber: 4.7 Consensus size: 50
35256147 TTTCTGTACT
* * * * **
35256157 GCCAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGC
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
** * *
35256207 GCTC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GC-CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
* * * *
35256257 GCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
* * * **
35256307 GCCAACGCCATGTCCCGGACATGGTCTTACATAGGACCTCTCATAATCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGC
35256363 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
35256399 TCTCATTCCC
Statistics
Matches: 162, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 124 0.77
51 1 0.01
53 1 0.01
56 35 0.22
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
Found at i:35256285 original size:100 final size:102
Alignment explanation
Indices: 35256177--35256398 Score: 270
Period size: 100 Copynumber: 2.2 Consensus size: 102
35256167 TATCCCAAAT
** * * *
35256177 ATGGTCTTACATGGGAGTTCTCATATCGGCGCTC-ATGCCATGTCCCAGACATGGTCTTACGGGG
1 ATGGTCTTACATGGGACCTCTCATATCGGCGC-CAACGCCATGTCCCAGACATGGTCTTACAGAG
*
35256241 GACCTCTC-ATCTC-GGTGCCAACGCCATGTCCCAGAC
65 GACCTCTCAATCTCAGATGCCAACGCCATGTCCCAGAC
* * * * *
35256277 ATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCGGACATGGTCTTACATAGG
1 ATGGTCTTACATGGGACCTCTCATATCGGCGCCAACGCCATGTCCCAGACATGGTCTTACAGAGG
*
35256342 ACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGAC
66 ACCTCTC--AATCTC-A-GATGCCAACGCCATGTCCCAGAC
35256383 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
35256399 TCTCATTCCC
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
99 1 0.01
100 60 0.58
103 5 0.05
106 37 0.36
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (102 bp):
ATGGTCTTACATGGGACCTCTCATATCGGCGCCAACGCCATGTCCCAGACATGGTCTTACAGAGG
ACCTCTCAATCTCAGATGCCAACGCCATGTCCCAGAC
Found at i:35259193 original size:17 final size:17
Alignment explanation
Indices: 35259171--35259213 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
35259161 ACTGCAAGGG
35259171 TCACACGGCTATGTGAC
1 TCACACGGCTATGTGAC
*
35259188 TCACACGGCTGTGTGAC
1 TCACACGGCTATGTGAC
35259205 TCACACGGC
1 TCACACGGC
35259214 CAAGAGACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (17 bp):
TCACACGGCTATGTGAC
Found at i:35260676 original size:25 final size:25
Alignment explanation
Indices: 35260626--35260765 Score: 131
Period size: 25 Copynumber: 5.6 Consensus size: 25
35260616 GTACATGTAT
* * *
35260626 GCTCATACAAGCTGTA-AACGATAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
35260650 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
35260675 GCTCCT-CTAAGCTGAATAACGGTAA
1 GCTCATAC-GAGCTGAATAACGGTAA
* * * *
35260700 GCTTATACGAGCTGAGTATCGATAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
35260725 GCTCATACGAGCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
35260750 GCTCATAAGAGCTGAA
1 GCTCATACGAGCTGAA
35260766 ATCTGTAACC
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.13
25 83 0.86
26 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:35262020 original size:30 final size:30
Alignment explanation
Indices: 35261986--35262249 Score: 157
Period size: 30 Copynumber: 8.9 Consensus size: 30
35261976 ATAACTTTAG
*
35261986 CTATCAAAATATGAAAAGGGATAGAT-TCGA
1 CTATCAAAATATGAAAAGGGAT-GGTGTCGA
* * * *
35262016 CTATC-TATTCATGAAAAGGGATGGTGACAA
1 CTATCAAAAT-ATGAAAAGGGATGGTGTCGA
** * *
35262046 CCGTCAATA-ATGAAAAGGGATGGTGACGA
1 CTATCAAAATATGAAAAGGGATGGTGTCGA
* * * *
35262075 CCATCGAAATATAAAAAGGGATAGCT-TCGA
1 CTATCAAAATATGAAAAGGGAT-GGTGTCGA
* * * *
35262105 ATATCGAAATATGAAAAGGGATAGCT-TCGG
1 CTATCAAAATATGAAAAGGGAT-GGTGTCGA
* * *
35262135 CTACCGAATTATGAAAAGGGATGGTGAT-GA
1 CTATCAAAATATGAAAAGGGATGGTG-TCGA
* * *
35262165 CCATCAACA-ATGAAAAGGGATGGTGACGA
1 CTATCAAAATATGAAAAGGGATGGTGTCGA
* * * * *
35262194 CCATCGAACTATGAAAAGGGATAGGT-TTGG
1 CTATCAAAATATGAAAAGGGAT-GGTGTCGA
*
35262224 CTATCAAACTATGAAAAGGGATGGTG
1 CTATCAAAATATGAAAAGGGATGGTG
35262250 ACAACCATCG
Statistics
Matches: 183, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
29 58 0.32
30 119 0.65
31 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (30 bp):
CTATCAAAATATGAAAAGGGATGGTGTCGA
Found at i:35262121 original size:89 final size:89
Alignment explanation
Indices: 35261992--35262185 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 89
35261982 TTAGCTATCA
* * *
35261992 AAATATGAAAAGGGATAGATTCGACTATCTATTCATGAAAAGGGAT-G-GT-GACAACCGTCAAT
1 AAATATGAAAAGGGATAGATTCGAATATCAAATCATGAAAAGGGATAGCGTCGACAACCG--AAT
35262054 AATGAAAAGGGATGGTGACGACCATC
64 AATGAAAAGGGATGGTGACGACCATC
* * * * *
35262080 GAAATATAAAAAGGGATAGCTTCGAATATCGAAAT-ATGAAAAGGGATAGCTTCGGCTACCGAAT
1 -AAATATGAAAAGGGATAGATTCGAATATC-AAATCATGAAAAGGGATAGCGTCGACAACCGAAT
* *
35262144 TATGAAAAGGGATGGTGATGACCATC
64 AATGAAAAGGGATGGTGACGACCATC
35262170 AACA-ATGAAAAGGGAT
1 AA-ATATGAAAAGGGAT
35262186 GGTGACGACC
Statistics
Matches: 89, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
89 51 0.57
90 31 0.35
91 1 0.01
92 6 0.07
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.21
Consensus pattern (89 bp):
AAATATGAAAAGGGATAGATTCGAATATCAAATCATGAAAAGGGATAGCGTCGACAACCGAATAA
TGAAAAGGGATGGTGACGACCATC
Found at i:35262181 original size:119 final size:118
Alignment explanation
Indices: 35261987--35262245 Score: 349
Period size: 119 Copynumber: 2.2 Consensus size: 118
35261977 TAACTTTAGC
* * *
35261987 TATCAAAATATGAAAAGGGATAGATTCGACTATCTATTCATGAAAAGGGATGGTGACAACCGTCA
1 TATC-AAATATGAAAAGGGATAGATTCGACTACCAATTCATGAAAAGGGATGGTGACAACCATCA
*
35262052 ATAATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTTCGAA
65 ACAATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTTCGAA
* * **
35262106 TATCGAAATATGAAAAGGGATAGCTTCGGCTACCGAATT-ATGAAAAGGGATGGTGATGACCATC
1 TATC-AAATATGAAAAGGGATAGATTCGACTACC-AATTCATGAAAAGGGATGGTGACAACCATC
* * * * **
35262170 AACAATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGGATAGGTTTGGC
64 AACAATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTTCGAA
35262225 TATCAAACTATGAAAAGGGAT
1 TATCAAA-TATGAAAAGGGAT
35262246 GGTGACAACC
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
118 3 0.02
119 117 0.95
120 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (118 bp):
TATCAAATATGAAAAGGGATAGATTCGACTACCAATTCATGAAAAGGGATGGTGACAACCATCAA
CAATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTTCGAA
Found at i:35262200 original size:89 final size:90
Alignment explanation
Indices: 35262055--35262259 Score: 254
Period size: 89 Copynumber: 2.3 Consensus size: 90
35262045 ACCGTCAATA
* *
35262055 ATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTTCGAATATCGAAATATGAA
1 ATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTACGAACATCGAAATATGAA
* *
35262120 AAGGGATAGCTTCGGCTACCGAATT
66 AAGGGATAGCTTCGGCTACCAAACT
* * * * *
35262145 ATGAAAAGGGATGGTGATGACCATC-AACA-ATGAAAAGGGAT-GGTGACGACCATCGAACTATG
1 ATGAAAAGGGATGGTGACGACCATCGAA-ATATAAAAAGGGATAGCT-ACGAACATCGAAATATG
* * *
35262207 AAAAGGGATAGGTTTGGCTATCAAACT
64 AAAAGGGATAGCTTCGGCTACCAAACT
*
35262234 ATGAAAAGGGATGGTGACAACCATCG
1 ATGAAAAGGGATGGTGACGACCATCG
35262260 TGATTTTACT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
88 2 0.02
89 71 0.72
90 25 0.26
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (90 bp):
ATGAAAAGGGATGGTGACGACCATCGAAATATAAAAAGGGATAGCTACGAACATCGAAATATGAA
AAGGGATAGCTTCGGCTACCAAACT
Found at i:35264711 original size:39 final size:37
Alignment explanation
Indices: 35264668--35264763 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 37
35264658 TCGAATATAA
*
35264668 TAAATATTTTTTATTTTTTTATTTTTAAAATACTTTTTT
1 TAAAT-TTTTTTATTTTTATATTTTTAAAATAC-TTTTT
*
35264707 TAAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
1 TAAATTTTTTT-ATTTT--TATATTTTTAAAATACTTTTT
*
35264747 T-AATTTTTTTAATTTTA
1 TAAATTTTTTTATTTTTA
35264764 AAATACTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
36 1 0.02
38 10 0.20
39 19 0.38
40 6 0.12
41 14 0.28
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (37 bp):
TAAATTTTTTTATTTTTATATTTTTAAAATACTTTTT
Found at i:35264716 original size:29 final size:28
Alignment explanation
Indices: 35264669--35264753 Score: 93
Period size: 30 Copynumber: 3.0 Consensus size: 28
35264659 CGAATATAAT
*
35264669 AAATA-TTTTTT-ATTTTTTTATTTTTA
1 AAATATTTTTTTAATTTTTTTAATTTTA
35264695 AAATACTTTTTTTAAATTTTTTTAATTTTA
1 AAATA-TTTTTTT-AATTTTTTTAATTTTA
**
35264725 AAATATTTTTAAAATACTTTTTTAATTTT
1 AAATATTTTTTTAAT--TTTTTTAATTTT
35264754 TTTAATTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.10
28 9 0.18
29 5 0.10
30 31 0.62
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
AAATATTTTTTTAATTTTTTTAATTTTA
Found at i:35264746 original size:30 final size:30
Alignment explanation
Indices: 35264682--35264782 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
35264672 TATTTTTTAT
* *
35264682 TTTTTTATTTTTAAAATACTTTTTTTAAAT--
1 TTTTTTAATTTTAAAATA--TTTTTAAAATAC
35264712 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
** *
35264742 TTTTTTAATTTT--TTTAATTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAC
35264770 TTTTTTTAATTTT
1 -TTTTTTAATTTT
35264783 TGTTTTAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 22 0.35
29 12 0.19
30 29 0.46
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:35264762 original size:28 final size:32
Alignment explanation
Indices: 35264729--35264801 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 32
35264719 ATTTTAAAAT
35264729 ATTTTTAAAATAC-TTTTTTAA-TTT-TTTTA
1 ATTTTTAAAATACTTTTTTTAATTTTGTTTTA
35264758 A-TTTTAAAATACTTTTTTTAATTTTTGTTTTA
1 ATTTTTAAAATACTTTTTTTAA-TTTTGTTTTA
35264790 ATTTTTAAAATA
1 ATTTTTAAAATA
35264802 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
28 11 0.28
29 9 0.23
31 3 0.08
32 6 0.15
33 10 0.26
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (32 bp):
ATTTTTAAAATACTTTTTTTAATTTTGTTTTA
Found at i:35264775 original size:41 final size:41
Alignment explanation
Indices: 35264687--35264774 Score: 153
Period size: 39 Copynumber: 2.2 Consensus size: 41
35264677 TTTATTTTTT
35264687 TATTTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAA
1 TATTTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAA
35264728 TATTTTTAAAATAC-TTTTTT-AATTTTTTTAATTTTAAAA
1 TATTTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAA
35264767 TACTTTTT
1 TA-TTTTT
35264775 TTAATTTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
39 21 0.46
40 11 0.24
41 14 0.30
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (41 bp):
TATTTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAA
Found at i:35266594 original size:25 final size:25
Alignment explanation
Indices: 35266560--35266609 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
35266550 ACATGTACGC
* *
35266560 TTGCAGTAAAATTGAGGTTTAAAAA
1 TTGCAGTAAAATCGAGCTTTAAAAA
35266585 TTGCAGTAAAATCGAGCTTTAAAAA
1 TTGCAGTAAAATCGAGCTTTAAAAA
35266610 CTGACATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (25 bp):
TTGCAGTAAAATCGAGCTTTAAAAA
Found at i:35275545 original size:9 final size:9
Alignment explanation
Indices: 35275523--35275582 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
35275513 AATTTTGAAT
*
35275523 TTTTATGAAT
1 TTTTAT-AAA
35275533 TTTTATAAA
1 TTTTATAAA
35275542 TTTTATAAA
1 TTTTATAAA
* *
35275551 TACTGATAAA
1 T-TTTATAAA
*
35275561 TATTATAAA
1 TTTTATAAA
35275570 TTATTAT-AA
1 TT-TTATAAA
35275579 TTTT
1 TTTT
35275583 TTATAGGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.05
9 23 0.55
10 17 0.40
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTTATAAA
Found at i:35275574 original size:10 final size:10
Alignment explanation
Indices: 35275520--35275578 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
35275510 AACAATTTTG
* *
35275520 AATTTTTATG
1 AATTATTATA
*
35275530 AATTTTTATA
1 AATTATTATA
35275540 AATT-TTATA
1 AATTATTATA
*
35275549 AA-TACTGATA
1 AATTA-TTATA
35275559 AA-TATTATA
1 AATTATTATA
35275568 AATTATTATA
1 AATTATTATA
35275578 A
1 A
35275579 TTTTTTATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
8 1 0.02
9 13 0.30
10 29 0.67
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (10 bp):
AATTATTATA
Found at i:35275578 original size:19 final size:19
Alignment explanation
Indices: 35275525--35275578 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
35275515 TTTTGAATTT
* * *
35275525 TTATGAATTTTTATAAATT
1 TTATAAATTATTATAAATA
*
35275544 TTATAAA-TACTGATAAATA
1 TTATAAATTA-TTATAAATA
35275563 TTATAAATTATTATAA
1 TTATAAATTATTATAA
35275579 TTTTTTATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 25 0.89
20 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
TTATAAATTATTATAAATA
Found at i:35277415 original size:13 final size:13
Alignment explanation
Indices: 35277397--35277444 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
35277387 CACCAACAAA
35277397 TTTCCATAACTTT
1 TTTCCATAACTTT
35277410 TTTCCATAAC--T
1 TTTCCATAACTTT
35277421 TTT--ATAA-TTT
1 TTTCCATAACTTT
35277431 TTTCCATAACTTT
1 TTTCCATAACTTT
35277444 T
1 T
35277445 ATAATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
9 4 0.13
10 4 0.13
11 4 0.13
12 4 0.13
13 14 0.47
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTCCATAACTTT
Found at i:35277432 original size:22 final size:21
Alignment explanation
Indices: 35277402--35277452 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
35277392 ACAAATTTCC
35277402 ATAACTTTTTTCCATAACTTTT
1 ATAA-TTTTTTCCATAACTTTT
35277424 ATAATTTTTTCCATAACTTTT
1 ATAATTTTTTCCATAACTTTT
35277445 ATAATTTT
1 ATAATTTT
35277453 GTCTCTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATTTTTTCCATAACTTTT
Found at i:35283085 original size:41 final size:38
Alignment explanation
Indices: 35283032--35283133 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 38
35283022 TTTTCAAATC
* * *
35283032 AATGAATAGGTTGAAAAGGATGTCTCCTGAAAAGGATATCA
1 AATGAAAAGGTTGAAAAGGAT-TATCC-AAAAAGGATAT-A
35283073 AATGAAAAGGTTGAAAAGGGTATTATCCAAAAAGGATATA
1 AATGAAAAGGTTGAAAA-GG-ATTATCCAAAAAGGATATA
* *
35283113 AAAGAAAAGGTCGAAAAGGAT
1 AATGAAAAGGTTGAAAAGGAT
35283134 ATCAATGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
38 2 0.04
39 2 0.04
40 16 0.30
41 26 0.48
42 6 0.11
43 2 0.04
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.21
Consensus pattern (38 bp):
AATGAAAAGGTTGAAAAGGATTATCCAAAAAGGATATA
Found at i:35283132 original size:24 final size:24
Alignment explanation
Indices: 35283100--35283153 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
35283090 GGGTATTATC
35283100 CAAAAAGGATATAAAAGAAAAGGT
1 CAAAAAGGATATAAAAGAAAAGGT
* * * *
35283124 CGAAAAGGATATCAATGAAAATGT
1 CAAAAAGGATATAAAAGAAAAGGT
35283148 CAAAAA
1 CAAAAA
35283154 TGTAACACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.15
Consensus pattern (24 bp):
CAAAAAGGATATAAAAGAAAAGGT
Found at i:35283231 original size:21 final size:21
Alignment explanation
Indices: 35283207--35283273 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
35283197 GAGTATTACT
35283207 ATACAATTTGAACATTAAATC
1 ATACAATTTGAACATTAAATC
* * *
35283228 ATACAA-TT-CATATT-ACT-
1 ATACAATTTGAACATTAAATC
*
35283245 ATAGAATTTGAACATTAAATC
1 ATACAATTTGAACATTAAATC
35283266 ATACAATT
1 ATACAATT
35283274 CATACATTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
17 5 0.15
18 4 0.12
19 8 0.24
20 4 0.12
21 13 0.38
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.36
Consensus pattern (21 bp):
ATACAATTTGAACATTAAATC
Found at i:35283253 original size:38 final size:38
Alignment explanation
Indices: 35283200--35283277 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
35283190 GGTTACGGAG
35283200 TATTACTATACAATTTGAACATTAAATCATACAATTCA
1 TATTACTATACAATTTGAACATTAAATCATACAATTCA
*
35283238 TATTACTATAGAATTTGAACATTAAATCATACAATTCA
1 TATTACTATACAATTTGAACATTAAATCATACAATTCA
35283276 TA
1 TA
35283278 CATTGACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (38 bp):
TATTACTATACAATTTGAACATTAAATCATACAATTCA
Found at i:35283280 original size:21 final size:21
Alignment explanation
Indices: 35283218--35283281 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
35283208 TACAATTTGA
35283218 ACATTAAATCATACAATTCAT
1 ACATTAAATCATACAATTCAT
* * *
35283239 --ATT-ACT-ATAGAATTTGA-
1 ACATTAAATCATACAA-TTCAT
35283256 ACATTAAATCATACAATTCAT
1 ACATTAAATCATACAATTCAT
35283277 ACATT
1 ACATT
35283282 GACATAACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 5 0.16
18 5 0.16
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (21 bp):
ACATTAAATCATACAATTCAT
Found at i:35286754 original size:7 final size:7
Alignment explanation
Indices: 35286742--35286767 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35286732 TTAAATGGTA
35286742 GATGTGT
1 GATGTGT
35286749 GATGTGT
1 GATGTGT
35286756 GATGTGT
1 GATGTGT
35286763 GATGT
1 GATGT
35286768 AAGTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GATGTGT
Found at i:35290449 original size:29 final size:29
Alignment explanation
Indices: 35290394--35290449 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
35290384 ACCATTTCTA
*
35290394 TTTTAAAAAAACAAAAATTAGTTGTCGAC
1 TTTTAAAAAAACAAAAATTAGTAGTCGAC
35290423 TTTTAAAAAAACAAAAATTGAG-AGTCG
1 TTTTAAAAAAACAAAAATT-AGTAGTCG
35290450 TCACCAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (29 bp):
TTTTAAAAAAACAAAAATTAGTAGTCGAC
Found at i:35292284 original size:22 final size:21
Alignment explanation
Indices: 35292249--35292325 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
35292239 AAAAGGTATC
* * *
35292249 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
35292270 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
35292293 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
35292312 TACATATCATATCT
1 TACAAATCATATCT
35292326 AAAATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.39
21 4 0.09
22 15 0.33
23 9 0.20
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:35292309 original size:19 final size:19
Alignment explanation
Indices: 35292285--35292357 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
35292275 AATCATATCT
35292285 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
35292304 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
35292323 TCTAAAATTGCATATCATA
1 TCTAAGATTGCATATCATA
35292342 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
35292358 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:35301554 original size:42 final size:41
Alignment explanation
Indices: 35301492--35301654 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 41
35301482 GTACATAAGT
* * * *
35301492 GCTAAACAGAAACCCGTAAGGGTTAAATGGAAGCTCATAGGA
1 GCTAAACTGAAACCCATAAGGGTTAAAT-GAAGCTCAAAAGA
* * *
35301534 GCTAAACGGAAACCCATAAGGGTTAATCTGAAGATCAGAAA-A
1 GCTAAACTGAAACCCATAAGGGTTAA-ATGAAGCTCA-AAAGA
*
35301576 GCTAAACTGAAACCCATTAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACTGAAACCCATAAGGGTTAAA-TGAAGCTCAAAAGA
* * * *
35301618 GCTGAACTAAAACCCAGAAGGGTTAAACTGAAACTCA
1 GCTAAACTGAAACCCATAAGGGTTAAA-TGAAGCTCA
35301655 TATGAGTTAA
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.03
42 97 0.95
43 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.17
Consensus pattern (41 bp):
GCTAAACTGAAACCCATAAGGGTTAAATGAAGCTCAAAAGA
Found at i:35301620 original size:84 final size:84
Alignment explanation
Indices: 35301492--35301649 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
35301482 GTACATAAGT
* * * * *
35301492 GCTAAACAGAAACCCGTAAGGGTTAAATGGAAGCTCATAGGAGCTAAACGGAAACCCATAAGGGT
1 GCTAAACAGAAACCCATAAGGGTTAAATGGAAGCTCAAAAGAGCTAAACGAAAACCCAGAAGGGT
*
35301557 TAATCTGAAGATCAGAAAA
66 TAAACTGAAGATCAGAAAA
* * * *
35301576 GCTAAACTGAAACCCATTAGGGTTAAACT-GAAGCTCAAAAGAGCTGAACTAAAACCCAGAAGGG
1 GCTAAACAGAAACCCATAAGGGTTAAA-TGGAAGCTCAAAAGAGCTAAACGAAAACCCAGAAGGG
35301640 TTAAACTGAA
65 TTAAACTGAA
35301650 ACTCATATGA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 62 0.98
85 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (84 bp):
GCTAAACAGAAACCCATAAGGGTTAAATGGAAGCTCAAAAGAGCTAAACGAAAACCCAGAAGGGT
TAAACTGAAGATCAGAAAA
Found at i:35301625 original size:21 final size:21
Alignment explanation
Indices: 35301485--35301687 Score: 97
Period size: 21 Copynumber: 9.7 Consensus size: 21
35301475 CAATGAAGTA
* * *
35301485 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTAAACTGAAACT
* * * *
35301506 CGTAAGGGTTAAA-TGGAAGCT
1 CATAAGAGCTAAACT-GAAACT
* * *
35301527 CATAGGAGCTAAACGGAAACC
1 CATAAGAGCTAAACTGAAACT
* * *
35301548 CATAAGGGTTAATCTGAAGA-T
1 CATAAGAGCTAAACTGAA-ACT
* * *
35301569 CAGAAAAGCTAAACTGAAACC
1 CATAAGAGCTAAACTGAAACT
* * * *
35301590 CATTAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
* * * *
35301611 CAAAAGAGCTGAACTAAAACC
1 CATAAGAGCTAAACTGAAACT
* * *
35301632 CAGAAGGGTTAAACTGAAACT
1 CATAAGAGCTAAACTGAAACT
* * *
35301653 CATATGAG-TTAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
35301673 CATAAGAGCTAAACT
1 CATAAGAGCTAAACT
35301688 AAAAGCAAGC
Statistics
Matches: 124, Mismatches: 53, Indels: 10
0.66 0.28 0.05
Matches are distributed among these distances:
20 18 0.15
21 105 0.85
22 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (21 bp):
CATAAGAGCTAAACTGAAACT
Found at i:35303991 original size:28 final size:27
Alignment explanation
Indices: 35303934--35303992 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
35303924 AAGCCCTTTT
*
35303934 TTTTTTAAATTTACCGAAATAGGCAGG
1 TTTTTTAAATTTACCGAAATAGGCACG
* *
35303961 TTTTTTAATTATTTACCGGAATGGGC-CG
1 TTTTTTAA--ATTTACCGAAATAGGCACG
35303989 TTTT
1 TTTT
35303993 CCCCGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCACG
Found at i:35304258 original size:22 final size:22
Alignment explanation
Indices: 35304233--35304301 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
35304223 ACAAATCCTA
*
35304233 TCTCAATTTCATTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
**
35304255 TCTCAAAGTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
35304277 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
35304299 TCT
1 TCT
35304302 TAAACTCTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:35304336 original size:52 final size:51
Alignment explanation
Indices: 35304254--35304359 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 51
35304244 TTCAAAAATT
* * * *
35304254 CTCTCAAAGTCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTC-TAAA
* * *
35304306 CTCTCGAATTCCTTCCAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
1 CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
35304357 CTC
1 CTC
35304360 CATATTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 7 0.15
52 40 0.85
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (51 bp):
CTCTCAAAGTCCTTCAAAAATCCTCACAATTTCCTTCAAAAAATCTCTAAA
Found at i:35304446 original size:18 final size:18
Alignment explanation
Indices: 35304403--35304455 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
35304393 TTTTTTAAAG
*
35304403 AAAATTTTAAATATTTTT
1 AAAATTTTAAATAATTTT
***
35304421 ATTTTTTTAAATAATTTT
1 AAAATTTTAAATAATTTT
*
35304439 AAAATTTTTAAT-ATTTT
1 AAAATTTTAAATAATTTT
35304456 CTGCAATGGC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAAATTTTAAATAATTTT
Found at i:35305549 original size:7 final size:7
Alignment explanation
Indices: 35305537--35305568 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
35305527 AGTGGATTGA
35305537 TATTTAG
1 TATTTAG
35305544 TATTTAG
1 TATTTAG
35305551 TATTTAG
1 TATTTAG
35305558 TATTTAG
1 TATTTAG
35305565 TATT
1 TATT
35305569 ATGTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:35306819 original size:28 final size:28
Alignment explanation
Indices: 35306737--35307583 Score: 704
Period size: 28 Copynumber: 28.9 Consensus size: 28
35306727 ATATTATTTG
*
35306737 ATTTAATTATAAACCCTAACACTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACCTA
*
35306766 ATTCAATTATTATAAAACCCTAACCTAACCTA
1 ATT---TAATTA-AAAACCCTAACCTAACCTA
*
35306798 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
35306826 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
35306854 ATTTAATTAAAAACCCTAAACTCTAACCTA
1 ATTTAATTAAAAACCCT-AAC-CTAACCTA
* **
35306884 ATTTAATTTAATTAGCCTAAAACCTAACCTAATTTA
1 ATTTAA-TT-A--A----AAACCCTAACCTAACCTA
* * **
35306920 ATTTAATTAAAAACCCAAACCCAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
35306948 ATTTAATTATAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTA
*
35306977 ATTCAATTATAAAACCCTAACCTAACCTA
1 ATTTAATTA-AAAACCCTAACCTAACCTA
*
35307006 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
35307034 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AA-CCTAACCTA
*
35307064 ATTTAATTTAATTAGCCTAAACCCTAACCT-ACTTCA
1 ATTTAA-TT-A--A----AAACCCTAACCTAACCT-A
35307100 ATTTAATT-AAAACCCTAA-C---CCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
* *
35307123 ATTCAATTATAAAA--CAAACCCTAACCCTA
1 ATTTAATTA-AAAACCCTAA-CCTAA-CCTA
* *
35307152 ATTCAATTATAAAACCCTAACCTAACATA
1 ATTTAATTA-AAAACCCTAACCTAACCTA
*
35307181 ATTTAATTAAAAACCCTAAAACCTAACATA
1 ATTTAATTAAAAACCCT--AACCTAACCTA
35307211 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AA-CCTAACCTA
**
35307241 ATTTAATTTAATTAGCCTAAACCCTAACCTAATTTA
1 ATTTAA-TT-A--A----AAACCCTAACCTAACCTA
* * **
35307277 ATTTAATTAAAAACCCAAACCCAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
35307305 ATTTAATTATAAACCCTAA-C---CCT-
1 ATTTAATTAAAAACCCTAACCTAACCTA
* *
35307328 ATTTAATTTAAAACCTTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
35307351 ATTTAATTTAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
*
35307379 ATTTAATTAAAAACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTA
35307407 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
35307435 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AA-CCTAACCTA
* **
35307465 ATTTAATTTAATTAGCCTAAACCCTAAACTAATTTA
1 ATTTAA-TT-A--A----AAACCCTAACCTAACCTA
* * **
35307501 ATTTAATTAAAAACCCAAACCCAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTA
35307529 ATTTAATTATATAAACCCTAACCCTAACCTA
1 ATTTAATTA-A-AAACCCTAA-CCTAACCTA
*
35307560 ATTTAATTTAAAACCCTAACCTAA
1 ATTTAATTAAAAACCCTAACCTAA
35307584 TTTGATAATC
Statistics
Matches: 696, Mismatches: 55, Indels: 135
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.00
23 47 0.07
24 4 0.01
25 5 0.01
26 1 0.00
27 11 0.02
28 272 0.39
29 88 0.13
30 107 0.15
31 26 0.04
32 23 0.03
33 10 0.01
34 7 0.01
35 11 0.02
36 47 0.07
37 9 0.01
38 27 0.04
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.31
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACCTA
Done.