Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 56 of 199
Found at i:16276328 original size:20 final size:20
Alignment explanation
Indices: 16276303--16276342 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16276293 CGTAAAATGA
*
16276303 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
16276323 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16276343 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16276332 original size:34 final size:35
Alignment explanation
Indices: 16276288--16276354 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
16276278 CAATAAAATG
*
16276288 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
16276322 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
16276355 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:16276358 original size:14 final size:15
Alignment explanation
Indices: 16276282--16276358 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
16276272 AATTGCCAAT
* *
16276282 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
16276296 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
16276310 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
16276330 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
16276345 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
16276359 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:16278189 original size:33 final size:33
Alignment explanation
Indices: 16278151--16278217 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
16278141 TGTAATCGTT
*
16278151 AGGGTGAAGAGAGTGAAAAGAGGAGTTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
* *
16278184 AGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAA
1 AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
16278217 A
1 A
16278218 ATGTCTTACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.01, G:0.45, T:0.15
Consensus pattern (33 bp):
AGGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAA
Found at i:16278645 original size:33 final size:33
Alignment explanation
Indices: 16278608--16278673 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16278598 GTAATCGTTT
16278608 GGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAAA
1 GGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAAA
* * *
16278641 GGGTGAAGAGAGTGAAGAGATGAGTTGTGGAAA
1 GGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAAA
16278674 ATGTCTTACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.45, T:0.15
Consensus pattern (33 bp):
GGGTGAAGAGAGTGAAAAGAGGAGCTGTGGAAA
Found at i:16278781 original size:456 final size:444
Alignment explanation
Indices: 16277915--16278805 Score: 1462
Period size: 456 Copynumber: 2.0 Consensus size: 444
16277905 GACAAGAAGT
16277915 TTCAAAACCCAAAAAAAAGAGGGAGAAAAAAAAAGGAAAAAAACCCTAATTCACATTACTCTTGA
1 TTCAAAACCCAAAAAAAAGAGGGAGAAAAAAAAAGGAAAAAAACCCTAATTCACATTACTCTTGA
* *
16277980 AATTTCAGAAATTACTCAAGAAAAACTTATCAAGAGCAAAAAGGGTATTGAAACCTCTAACCTAG
66 AATTTCAGAAATTACTCAAGAAAAACTTATCAAGAACAAAAAGGGTATTGAAACCCCTAACCTAG
*
16278045 AGCTTGCAATTTTACCTTCGATAAACCAGCAGAGGTGAACCACCACGCTATCGAGGCAAGCAAAG
131 AGCTTGCAATTTTACCTTCGATAAACCAGCAGAGGTGAACCACCACGCTAACGAGGCAAGCAAAG
*
16278110 AGAATAGGTGAACTAGCAGAGATGATGAGGCTGTAATCGTTAGGGTGAAGAGAGTGAAAAGAGGA
196 AGAAGAGGTGAACTAGCAGAGATGATGAGGCTGTAATCGTTAGGGTGAAGAGAGTGAAAAGAGGA
*
16278175 GTTGTGGAAAGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAAAATGTCTTACCCCTTAGAAATCG
261 GCTGTGGAAAGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAAAATGTCTTACCCCTTAGAAATCG
* * *
16278240 GTAAGACATTTTCCCTAAAATGTAACCTATTTTCCCGTGTTTTGGAGTTCATTTTCCAAATGGAA
326 GTAAGACATTTCCCCTAAAATGTAACCCATTTTCCCGTGTTTTGGAGTTCATTTTCCAAATGAAA
* *
16278305 AATGTTTTTCGCCAATCAAACACTGGAAAAGTTGGAAATGATTTTCCGGAAAAG
391 AATGTTTTCCGCCAATCAAACACTGGAAAAGTTAGAAATGATTTTCCGGAAAAG
* *
16278359 TTCAAAACCCAAAAAAAAGAGGGAG-AAAAAAAAGG-GAAAAATCCTAATTCACATTACTCTTGA
1 TTCAAAACCCAAAAAAAAGAGGGAGAAAAAAAAAGGAAAAAAACCCTAATTCACATTACTCTTGA
16278422 AATTTCAGAAATTACTCAAGAAAAACTTATCAAGAACAAAAAGGGTATTGAAACCCCTAACCTAG
66 AATTTCAGAAATTACTCAAGAAAAACTTATCAAGAACAAAAAGGGTATTGAAACCCCTAACCTAG
* *
16278487 AGCTTGCAATTTTACCTTCGATAAACCAGCAGAGGTGAACTAGCACGCTAACGAGGCAAGCAAAG
131 AGCTTGCAATTTTACCTTCGATAAACCAGCAGAGGTGAACCACCACGCTAACGAGGCAAGCAAAG
* *
16278552 AGAAGATGTGAACTAGCAGAGAAGATGAGGTAGAGATGATGAGGCTGTAATCGTTTGGGTGAAGA
196 AGAAGAGGTGAACTAGC--------------AGAGATGATGAGGCTGTAATCGTTAGGGTGAAGA
*
16278617 GAGTGAAAAGAGGAGCTGTGGAAAGGGTGAAGAGAGTGAAGAGATGAGTTGTGGAAAATGTCTTA
247 GAGTGAAAAGAGGAGCTGTGGAAAGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAAAATGTCTTA
*
16278682 CCCCTTAGAAATCGGTAAGGCATTTCCCCTAAAATGTAACCCATTTTCCCGTGTTTTGGAGTTCA
312 CCCCTTAGAAATCGGTAAGACATTTCCCCTAAAATGTAACCCATTTTCCCGTGTTTTGGAGTTCA
* *
16278747 TTTTCTAAATGAAAAATGTTTTCCGCCAATCAAACGCTGGAAAAGTTAGAAATGATTTT
377 TTTTCCAAATGAAAAATGTTTTCCGCCAATCAAACACTGGAAAAGTTAGAAATGATTTT
16278806 TCGAAAAATC
Statistics
Matches: 413, Mismatches: 20, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
442 166 0.40
443 10 0.02
444 25 0.06
456 212 0.51
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (444 bp):
TTCAAAACCCAAAAAAAAGAGGGAGAAAAAAAAAGGAAAAAAACCCTAATTCACATTACTCTTGA
AATTTCAGAAATTACTCAAGAAAAACTTATCAAGAACAAAAAGGGTATTGAAACCCCTAACCTAG
AGCTTGCAATTTTACCTTCGATAAACCAGCAGAGGTGAACCACCACGCTAACGAGGCAAGCAAAG
AGAAGAGGTGAACTAGCAGAGATGATGAGGCTGTAATCGTTAGGGTGAAGAGAGTGAAAAGAGGA
GCTGTGGAAAGGGTGAAGAGAGTGAAGAGATGAGCTGTGGAAAATGTCTTACCCCTTAGAAATCG
GTAAGACATTTCCCCTAAAATGTAACCCATTTTCCCGTGTTTTGGAGTTCATTTTCCAAATGAAA
AATGTTTTCCGCCAATCAAACACTGGAAAAGTTAGAAATGATTTTCCGGAAAAG
Found at i:16279576 original size:10 final size:11
Alignment explanation
Indices: 16279561--16279606 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
16279551 AACTAAATCC
16279561 TTTCTCTC-AA
1 TTTCTCTCAAA
*
16279571 TTTCTCTCTAA
1 TTTCTCTCAAA
16279582 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
16279594 TTTCTATCAAA
1 TTTCTCTCAAA
16279605 TT
1 TT
16279607 CCTATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 10 0.31
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:16279587 original size:12 final size:10
Alignment explanation
Indices: 16279561--16279603 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
16279551 AACTAAATCC
16279561 TTTCTCTCAA
1 TTTCTCTCAA
16279571 TTTCTCTCTAA
1 TTTCTCTC-AA
16279582 TATTCTCTCAAA
1 T-TTCTCTC-AA
*
16279594 TTTCTATCAA
1 TTTCTCTCAA
16279604 ATTCCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
12 10 0.34
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:16281476 original size:18 final size:18
Alignment explanation
Indices: 16281440--16281482 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
16281430 TGCCAGGTGC
* * *
16281440 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCATTATAT
16281458 GTATCCTAACCATTATAT
1 GTATCCTAACCATTATAT
*
16281476 GTTTCCT
1 GTATCCT
16281483 TTTCCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCATTATAT
Found at i:16281917 original size:49 final size:49
Alignment explanation
Indices: 16281862--16282031 Score: 286
Period size: 49 Copynumber: 3.5 Consensus size: 49
16281852 GTTTATATTA
*
16281862 ATGTAATAAAGTACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
16281911 ATGTAATAAAATACAAAATAATTTATTTTGAATATTTTGATATAATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
16281960 ATGTAATAAAATACAAAATAGTTTTTTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
16282009 ATTTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
16282032 AATATTCTTA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 113 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:16285397 original size:125 final size:124
Alignment explanation
Indices: 16285128--16285414 Score: 459
Period size: 125 Copynumber: 2.3 Consensus size: 124
16285118 CCCAAACATG
*
16285128 CTACTGTAGCAAAAGCGCATCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
*
16285193 TTGAAGCGTTTTTATACTATTTGCTAAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAACGTTTTTATACTATTTGCTAAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
* *
16285252 CTACTGTAGCAAAAGTGCGTCCACTTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
16285317 TTGAAACTTTTTTTATACTATTTGCTCAGAAACA-TCAAGTCGAAATTATTTTTTCAGGAC
66 TTGAAAC-GTTTTTATACTATTTGCTAAGAAA-AGTCAACTCGAAATTATTTTTTCAGGAC
* * *
16285377 CTACTGTATCAAAAACGCGTCCACGTAGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
16285415 CTTAATAAAT
Statistics
Matches: 149, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
124 68 0.46
125 80 0.54
126 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAACGTTTTTATACTATTTGCTAAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:16285619 original size:21 final size:22
Alignment explanation
Indices: 16285581--16285621 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16285571 TTAAAAATCT
* *
16285581 TAAAAACCTTAAACCCTAACCC
1 TAAAAACCTCAAAACCTAACCC
16285603 TAAAAACC-CAAAACCTAAC
1 TAAAAACCTCAAAACCTAAC
16285622 GTGGGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (22 bp):
TAAAAACCTCAAAACCTAACCC
Found at i:16286008 original size:24 final size:24
Alignment explanation
Indices: 16285976--16286025 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
16285966 TTTGCTTCTT
16285976 TTAGCATAATTTACATTTAATATA
1 TTAGCATAATTTACATTTAATATA
16286000 TTAGCATAATTTACATTTAATATA
1 TTAGCATAATTTACATTTAATATA
16286024 TT
1 TT
16286026 TTATTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (24 bp):
TTAGCATAATTTACATTTAATATA
Found at i:16290094 original size:22 final size:22
Alignment explanation
Indices: 16290052--16290098 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
16290042 TTCCCTTTGC
16290052 TTGTTTCTGCTAGTTCTATTTCT
1 TTGTTTCTGCTAGTTCTATTT-T
*
16290075 TTGTTT-TGCTTGTT-TCATTTT
1 TTGTTTCTGCTAGTTCT-ATTTT
16290096 TTG
1 TTG
16290099 GTGCTAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
23 6 0.27
ACGTcount: A:0.06, C:0.13, G:0.15, T:0.66
Consensus pattern (22 bp):
TTGTTTCTGCTAGTTCTATTTT
Found at i:16295137 original size:11 final size:11
Alignment explanation
Indices: 16295121--16295147 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16295111 TAGAAATTAG
16295121 TTTGTGAAACT
1 TTTGTGAAACT
16295132 TTTGTGAAACT
1 TTTGTGAAACT
16295143 TTTGT
1 TTTGT
16295148 ATTGATTTTT
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:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:16296474 original size:26 final size:26
Alignment explanation
Indices: 16296439--16296492 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
16296429 TTTTTGATGT
*
16296439 TGTAAAACTATATAACATATGGATTA
1 TGTAAAACTAGATAACATATGGATTA
16296465 TGTAAAACTAGATAACATATGGATTA
1 TGTAAAACTAGATAACATATGGATTA
16296491 TG
1 TG
16296493 ATGTAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (26 bp):
TGTAAAACTAGATAACATATGGATTA
Found at i:16296748 original size:120 final size:120
Alignment explanation
Indices: 16296575--16297027 Score: 757
Period size: 120 Copynumber: 3.8 Consensus size: 120
16296565 ATTTATATAT
* * * * * *
16296575 TGATTTTAGTAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTCTATATCATT-
1 TGATTTGAGTAAATTCATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATAT-TTTA
* * * * *
16296639 ATTA-AATTATATGTAATAATTATTATTTTAATTTAAAATTTACAGTATCATATATTA
64 ATTATAA-TATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
16296696 TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
1 TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
16296761 TATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
66 TATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
16296816 TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
1 TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
16296881 TATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
66 TATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
*
16296936 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAAT
1 TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
16297001 TATAATATATTTAATAATAATTATGTT
66 TATAATATATTTAATAATAATTATGTT
16297028 TAAATATGAT
Statistics
Matches: 318, Mismatches: 12, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
119 2 0.01
120 289 0.91
121 27 0.08
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAAT
TATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCATATATTA
Found at i:16296754 original size:61 final size:61
Alignment explanation
Indices: 16296688--16296995 Score: 275
Period size: 61 Copynumber: 5.1 Consensus size: 61
16296678 TTACAGTATC
16296688 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
16296749 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-AATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
16296807 C
61 T
16296808 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
16296869 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-AATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
16296927 C
61 T
*
16296928 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
16296989 ATATATT
1 ATATATT
16296996 TTAATTATAA
Statistics
Matches: 190, Mismatches: 33, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
57 22 0.12
58 16 0.08
59 38 0.20
60 32 0.17
61 45 0.24
62 15 0.08
63 22 0.12
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:16296775 original size:15 final size:15
Alignment explanation
Indices: 16296740--16296791 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
16296730 TTAAGAATTT
*
16296740 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16296754 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16296768 TATTTAATAATAAT-
1 TATTTAATTATAATA
16296782 TATGTTAATT
1 TAT-TTAATT
16296792 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16296800 original size:59 final size:59
Alignment explanation
Indices: 16296727--16297027 Score: 269
Period size: 59 Copynumber: 5.0 Consensus size: 59
16296717 AGAATATTAA
16296727 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
* * * * * * *
16296786 TTAATTTA-AATTTTA-TAGTATCATATATTATGATTTGAGTAA-ATTCATATAAGAAT-ATTA-
1 TT-ATTAAGAATTTTATTA-AATTATATATT-TTAATT-A-TAATA-T-ATTTAATAATAATTAT
*
16296846 A
59 G
16296847 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
* * * * * * * * *
16296906 TTAATTTA-AATTTTA-TAGTATCATATATTATGATT-TGAGTAAATTCATATAAGAA-TATTG
1 TT-ATTAAGAATTTTATTA-AATTATATATTTTAATTAT-AATATATTTA-ATAATAATTA-TG
16296966 ATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
1 -TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
16297026 TT
1 TT
16297028 TAAATATGAT
Statistics
Matches: 186, Mismatches: 34, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
57 8 0.04
58 13 0.07
59 53 0.28
60 40 0.22
61 51 0.27
62 13 0.07
63 8 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (59 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG
Found at i:16296895 original size:15 final size:15
Alignment explanation
Indices: 16296860--16296911 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
16296850 TTAAGAATTT
*
16296860 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16296874 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16296888 TATTTAATAATAAT-
1 TATTTAATTATAATA
16296902 TATGTTAATT
1 TAT-TTAATT
16296912 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16297010 original size:16 final size:16
Alignment explanation
Indices: 16296989--16297030 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
16296979 TTATTAAATT
*
16296989 ATATATTTTAATTATA
1 ATATATTTTAATAATA
16297005 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
16297020 AT-TATGTTTAA
1 ATATAT-TTTAA
16297031 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:16297015 original size:15 final size:15
Alignment explanation
Indices: 16296980--16297021 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16296970 TTAAGAATTT
*
16296980 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16296994 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16297008 TATTTAATAATAAT
1 TATTTAATTATAAT
16297022 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16297201 original size:39 final size:40
Alignment explanation
Indices: 16297158--16297262 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
16297148 TTCCATTATG
16297158 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
16297197 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
16297242 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
16297263 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:16297256 original size:45 final size:44
Alignment explanation
Indices: 16297156--16297265 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
16297146 TTTTCCATTA
16297156 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
16297195 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
16297240 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
16297266 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:16297265 original size:16 final size:16
Alignment explanation
Indices: 16297244--16297313 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
16297234 TTGATTTGCT
*
16297244 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
16297260 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
16297276 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
16297292 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
16297308 AATACA
1 ATTACA
16297314 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:16297285 original size:32 final size:32
Alignment explanation
Indices: 16297244--16297313 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
16297234 TTGATTTGCT
16297244 ATTACACCTCTATTCCATTACACCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
16297276 ATTACACCTCTATTCCATTACGCCTCTAATCC
1 ATTACACCTCTATTCCATTACACCTCTAATCC
*
16297308 AATACA
1 ATTACA
16297314 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.33
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACACCTCTAATCC
Found at i:16298321 original size:107 final size:107
Alignment explanation
Indices: 16298196--16298410 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
16298186 TAAATATAAT
16298196 CGACCAATGTACTTAGCTAATCATTAAATAAGATATAACATAACACATACCTGATTATTATAATT
1 CGACCAATGTACTTAGCTAATCATTAAATAAGATATAACATAACACATACCTGATTATTATAATT
16298261 TTGCAATCCATTTGATATTAGATTAGATTGACAAGGAACTTA
66 TTGCAATCCATTTGATATTAGATTAGATTGACAAGGAACTTA
16298303 CGACCAATGTACTTAGCTAATCATTAAATAAGATATAACATAACACATACCTGATTATTATAATT
1 CGACCAATGTACTTAGCTAATCATTAAATAAGATATAACATAACACATACCTGATTATTATAATT
16298368 TTGCAATCCATTTGATATTAGATTAGATTGACAAGGAACTTA
66 TTGCAATCCATTTGATATTAGATTAGATTGACAAGGAACTTA
16298410 C
1 C
16298411 TAAACACATG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (107 bp):
CGACCAATGTACTTAGCTAATCATTAAATAAGATATAACATAACACATACCTGATTATTATAATT
TTGCAATCCATTTGATATTAGATTAGATTGACAAGGAACTTA
Found at i:16298741 original size:67 final size:65
Alignment explanation
Indices: 16298665--16298867 Score: 227
Period size: 67 Copynumber: 3.1 Consensus size: 65
16298655 AAACCATATA
* * * *
16298665 TATATATAATTCACAAAATTAAATTCAGCTCACAGAGATTGAAACATATATTCGAACCACATGTA
1 TATATATAATTCATAACATTAAATTCAGCTCA-AGAAATTGAAACATACATTCGAACCACATGTA
16298730 T
65 T
* * * * * * *
16298731 GTATATATAATTCATGACATTAAGTTCAGCTAAAAAAATTTGTAACATACATTCCAA-C-C-T-C
1 -TATATATAATTCATAACATTAAATTCAGCTCAAGAAA-TTGAAACATACATTCGAACCACATGT
16298792 A-
64 AT
16298793 TATATATAATTCATAACATTAAATTCAGCTCAAGGAAATTGAAACATACATTCGAACCACATGTA
1 TATATATAATTCATAACATTAAATTCAGCTCAA-GAAATTGAAACATACATTCGAACCACATGTA
16298858 T
65 T
16298859 ATATATATA
1 -TATATATA
16298868 TTATACTATT
Statistics
Matches: 110, Mismatches: 18, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
61 46 0.42
62 4 0.04
63 2 0.02
64 2 0.02
65 2 0.02
66 4 0.04
67 50 0.45
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (65 bp):
TATATATAATTCATAACATTAAATTCAGCTCAAGAAATTGAAACATACATTCGAACCACATGTAT
Found at i:16298839 original size:61 final size:60
Alignment explanation
Indices: 16298664--16298861 Score: 198
Period size: 61 Copynumber: 3.1 Consensus size: 60
16298654 CAAACCATAT
* * * * *
16298664 ATATATATAATTCACAAAATTAAATTCAGCTCACAGAGATTGAAACATATATTCGAACCACATGT
1 ATATATATAATTCATAACATTAAATTCAGCTCA-AGAAATTGAAACATACATTCGAA-C-C-T-C
* * * * * *
16298729 ATGTATATATAATTCATGACATTAAGTTCAGCTAAAAAAATTTGTAACATACATTCCAACCTC
1 A--TATATATAATTCATAACATTAAATTCAGCTCAAGAAA-TTGAAACATACATTCGAACCTC
*
16298792 ATATATATAATTCATAACATTAAATTCAGCTCAAGGAAATTGAAACATACATTCGAACCAC
1 ATATATATAATTCATAACATTAAATTCAGCTCAA-GAAATTGAAACATACATTCGAACCTC
*
16298853 ATGTATATA
1 ATATATATA
16298862 TATATATTAT
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
61 57 0.52
62 3 0.03
63 1 0.01
64 1 0.01
65 2 0.02
66 4 0.04
67 42 0.38
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.31
Consensus pattern (60 bp):
ATATATATAATTCATAACATTAAATTCAGCTCAAGAAATTGAAACATACATTCGAACCTC
Found at i:16300547 original size:126 final size:126
Alignment explanation
Indices: 16300319--16300570 Score: 468
Period size: 126 Copynumber: 2.0 Consensus size: 126
16300309 AAACAACTTG
* *
16300319 TAGGCAAAGGTTTTAAAGAAAATTTTCAAAATTTTGACTAAGTTTAGGTAACCTCCTACAAGAAA
1 TAGGCAAAGGGTTTAAAGAAAATTTTCAAAATTTTGACTAAGTTTAGGCAACCTCCTACAAGAAA
*
16300384 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTCAACCAATAATTTGATAAA
66 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
16300445 TAGGCAAAGGGTTTAAAGAAAATTTTCAAAATTTTGACTAAGTTTAGGCAACCTCCTACAAGAAA
1 TAGGCAAAGGGTTTAAAGAAAATTTTCAAAATTTTGACTAAGTTTAGGCAACCTCCTACAAGAAA
*
16300510 ATACAATATATAGGTTCCAAATAAACCTAAAACCATAATTTTAAACCAATAATTTGATAAA
66 ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
16300571 AATTCAACAA
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (126 bp):
TAGGCAAAGGGTTTAAAGAAAATTTTCAAAATTTTGACTAAGTTTAGGCAACCTCCTACAAGAAA
ATACAATATATAGGTTCCAAATAAACCTAAAAACATAATTTTAAACCAATAATTTGATAAA
Found at i:16302609 original size:16 final size:15
Alignment explanation
Indices: 16302561--16302611 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
16302551 AATTATTTTC
16302561 CTATTATTTATTATA
1 CTATTATTTATTATA
*
16302576 CTATT-TTT-TTACA
1 CTATTATTTATTATA
16302589 CTATTATTTATTATA
1 CTATTATTTATTATA
16302604 CTTATTAT
1 C-TATTAT
16302612 ATCATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 9 0.29
14 6 0.19
15 10 0.32
16 6 0.19
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTATTTATTATA
Found at i:16304848 original size:23 final size:23
Alignment explanation
Indices: 16304804--16304848 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16304794 TCTTATTTTG
* *
16304804 TTGATTTGTGTATACTTTATTTA
1 TTGATTTGTATATACTTGATTTA
**
16304827 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATACTTGATTT
16304849 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATACTTGATTTA
Found at i:16305211 original size:36 final size:38
Alignment explanation
Indices: 16305131--16305211 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 38
16305121 GTATACATAC
16305131 ATATA-TTTTATAATATATACATATACGAACACATTTT
1 ATATATTTTTATAATATATACATATACGAACACATTTT
* * *
16305168 TTA-ATTTTTATAA-ATATATATATAC--ACATACTTTT
1 ATATATTTTTATAATATATACATATACGAACACA-TTTT
16305203 ATATATTTT
1 ATATATTTT
16305212 CTATGTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
34 4 0.11
35 6 0.16
36 17 0.46
37 10 0.27
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (38 bp):
ATATATTTTTATAATATATACATATACGAACACATTTT
Found at i:16305291 original size:15 final size:15
Alignment explanation
Indices: 16305271--16305299 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16305261 AATATGTATA
16305271 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
16305286 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
16305300 AATTCACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTATTTTTTATT
Found at i:16305337 original size:23 final size:22
Alignment explanation
Indices: 16305308--16305350 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16305298 ATAATTCACA
*
16305308 TACATATATATTTTTCTTATACG
1 TACATATATATATTT-TTATACG
16305331 TACATATATATATTTTTATA
1 TACATATATATATTTTTATA
16305351 TTTTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TACATATATATATTTTTATACG
Found at i:16311478 original size:56 final size:57
Alignment explanation
Indices: 16311366--16311503 Score: 172
Period size: 56 Copynumber: 2.4 Consensus size: 57
16311356 TTTAATTCAT
* * * *
16311366 ATAATAATTATATTAAGAATGTTATTAAATTATATTTTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGATTAAATTATATTTTATTTTAATAAAATATATTTA
*
16311424 ATAATAATTATGTTAAAATATGATTAAATTAT-TTATT-TTTTAATAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTATATT-TTATTTTAATAAAATATATTTA
* * *
16311480 ACAATAATTTTATTAAAATTTGAT
1 ATAATAATTATATTAAAATATGAT
16311504 AACAAACAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 39 0.56
57 16 0.23
58 15 0.21
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAATTATATTTTATTTTAATAAAATATATTTA
Found at i:16312973 original size:16 final size:17
Alignment explanation
Indices: 16312938--16312972 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16312928 CGCATAATAT
* *
16312938 AATAAGCATTTTTAAAA
1 AATAAACATTTATAAAA
16312955 AATAAACATTTATAAAA
1 AATAAACATTTATAAAA
16312972 A
1 A
16312973 TTTAATTTTG
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:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
AATAAACATTTATAAAA
Found at i:16319332 original size:3 final size:3
Alignment explanation
Indices: 16319324--16319357 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
16319314 CTTTAAAAAC
16319324 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
16319358 CATGATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16323678 original size:3 final size:3
Alignment explanation
Indices: 16323670--16323703 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
16323660 GCGCTGAGAA
16323670 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16323704 ACTACGTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16327540 original size:2 final size:2
Alignment explanation
Indices: 16327533--16327558 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16327523 TAAAAATTCA
16327533 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16327559 TGGTGTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16329741 original size:78 final size:78
Alignment explanation
Indices: 16329639--16329802 Score: 310
Period size: 78 Copynumber: 2.1 Consensus size: 78
16329629 AGGGTTACGG
* *
16329639 AGCATTATCGAAATTTACAGAACAAATAATAGACATTTCATATCATTTAGCACTCATATCAGAAA
1 AGCATAATCGAAATTTACAAAACAAATAATAGACATTTCATATCATTTAGCACTCATATCAGAAA
16329704 CCAGTTGTAATCA
66 CCAGTTGTAATCA
16329717 AGCATAATCGAAATTTACAAAACAAATAATAGACATTTCATATCATTTAGCACTCATATCAGAAA
1 AGCATAATCGAAATTTACAAAACAAATAATAGACATTTCATATCATTTAGCACTCATATCAGAAA
16329782 CCAGTTGTAATCA
66 CCAGTTGTAATCA
16329795 AGCATAAT
1 AGCATAAT
16329803 GTCCCTTATG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (78 bp):
AGCATAATCGAAATTTACAAAACAAATAATAGACATTTCATATCATTTAGCACTCATATCAGAAA
CCAGTTGTAATCA
Found at i:16331134 original size:25 final size:24
Alignment explanation
Indices: 16331105--16331213 Score: 92
Period size: 25 Copynumber: 4.4 Consensus size: 24
16331095 GAATCTCTTT
*
16331105 CGAGCCATGTAACAAGAAGCTCATG
1 CGAGCCAT-TATCAAGAAGCTCATG
* * *
16331130 TGAGCCATTTATCGAGAAGCTCTTG
1 CGAGCCA-TTATCAAGAAGCTCATG
* *
16331155 CGAGCCAATTATCAGGAAGCTCATA
1 CGAGCC-ATTATCAAGAAGCTCATG
* * * *
16331180 CGAGCCATAATCGAGAAACTCAAG
1 CGAGCCATTATCAAGAAGCTCATG
*
16331204 AGAGCCATTA
1 CGAGCCATTA
16331214 ATCGGGAACT
Statistics
Matches: 65, Mismatches: 17, Indels: 5
0.75 0.20 0.06
Matches are distributed among these distances:
24 20 0.31
25 43 0.66
26 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (24 bp):
CGAGCCATTATCAAGAAGCTCATG
Found at i:16331174 original size:50 final size:49
Alignment explanation
Indices: 16331090--16331273 Score: 137
Period size: 50 Copynumber: 3.7 Consensus size: 49
16331080 TACTCATATA
* ** * * *
16331090 ATCGAGAATCTCTTTCGAGCCATGTAACAAGAAGCTCATGTGAGCCATTT
1 ATCGAGAAGCTCTTGAGAGCCAT-TATCAGGAAGCTCATGAGAGCCATTT
* *
16331140 ATCGAGAAGCTCTTGCGAGCCAATTATCAGGAAGCTCAT-ACGAGCCA-TA
1 ATCGAGAAGCTCTTGAGAGCC-ATTATCAGGAAGCTCATGA-GAGCCATTT
* ** * *
16331189 ATCGAGAAACTCAAGAGAGCCATTAATCGGGAA-CT-ACGGAGAGCCATTT
1 ATCGAGAAGCTCTTGAGAGCCATT-ATCAGGAAGCTCA-TGAGAGCCATTT
*
16331238 ATCG-GAAGCTCATT-AGAGCCAATTATTAGGAAGCTC
1 ATCGAGAAGCTC-TTGAGAGCC-ATTATCAGGAAGCTC
16331274 CGAAGAGCTA
Statistics
Matches: 106, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
47 1 0.01
48 29 0.27
49 36 0.34
50 38 0.36
51 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (49 bp):
ATCGAGAAGCTCTTGAGAGCCATTATCAGGAAGCTCATGAGAGCCATTT
Found at i:16331223 original size:24 final size:24
Alignment explanation
Indices: 16331181--16331244 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
16331171 AAGCTCATAC
16331181 GAGCCA-TAATCGAGAAACT-CAAGA
1 GAGCCATTAATCG-GAAACTAC-AGA
* *
16331205 GAGCCATTAATCGGGAACTACGGA
1 GAGCCATTAATCGGAAACTACAGA
*
16331229 GAGCCATTTATCGGAA
1 GAGCCATTAATCGGAA
16331245 GCTCATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (24 bp):
GAGCCATTAATCGGAAACTACAGA
Found at i:16331255 original size:24 final size:24
Alignment explanation
Indices: 16331120--16331273 Score: 86
Period size: 25 Copynumber: 6.3 Consensus size: 24
16331110 CATGTAACAA
16331120 GAAGCTCATGT-GAGCCATTTATCG
1 GAAGCTCAT-TAGAGCCATTTATCG
* *
16331144 AGAAGCTC-TTGCGAGCCAATTATCAG
1 -GAAGCTCATT-AGAGCCATTTATC-G
*
16331170 GAAGCTCA-TACGAGCCA-TAATCG
1 GAAGCTCATTA-GAGCCATTTATCG
* ** *
16331193 AGAAACTCAAGAGAGCCATTAATCGG
1 -GAAGCTCATTAGAGCCATTTATC-G
**
16331219 GAA-CT-ACGGAGAGCCATTTATCG
1 GAAGCTCA-TTAGAGCCATTTATCG
* *
16331242 GAAGCTCATTAGAGCCAATTATTAG
1 GAAGCTCATTAGAGCCATTTA-TCG
16331267 GAAGCTC
1 GAAGCTC
16331274 CGAAGAGCTA
Statistics
Matches: 105, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
23 7 0.07
24 45 0.43
25 51 0.49
26 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (24 bp):
GAAGCTCATTAGAGCCATTTATCG
Found at i:16331648 original size:21 final size:21
Alignment explanation
Indices: 16331624--16331665 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16331614 TGAATTTATC
*
16331624 TCAACTTAATACAATTCACAT
1 TCAACTTAATACAATACACAT
* *
16331645 TCAATTTAATCCAATACACAT
1 TCAACTTAATACAATACACAT
16331666 CTTTGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
TCAACTTAATACAATACACAT
Found at i:16334309 original size:26 final size:26
Alignment explanation
Indices: 16334256--16334337 Score: 107
Period size: 26 Copynumber: 3.3 Consensus size: 26
16334246 AAGTTCAAGC
16334256 GAGCCA-T-ATCAGGAAGCTC-CGGA
1 GAGCCATTAATCAGGAAGCTCACGGA
*
16334279 GAGCCATTAATTAGGAAGCTCACGGA
1 GAGCCATTAATCAGGAAGCTCACGGA
* * *
16334305 GAGCCTTTAATCGGGAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACGGA
16334331 GAGCCAT
1 GAGCCAT
16334338 GTAACGGGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 6 0.12
24 1 0.02
25 11 0.22
26 32 0.64
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACGGA
Found at i:16334345 original size:26 final size:26
Alignment explanation
Indices: 16334267--16334346 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
16334257 AGCCATATCA
**
16334267 GGAAGCTC-CGGAGAGCCATTAATTA
1 GGAAGCTCACGGAGAGCCATTAATCG
*
16334292 GGAAGCTCACGGAGAGCCTTTAATCG
1 GGAAGCTCACGGAGAGCCATTAATCG
*
16334318 GGAAGCTCACGAAGAGCCATGTAA-CG
1 GGAAGCTCACGGAGAGCCAT-TAATCG
16334344 GGA
1 GGA
16334347 CGCTAATAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
25 8 0.17
26 37 0.77
27 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.16
Consensus pattern (26 bp):
GGAAGCTCACGGAGAGCCATTAATCG
Found at i:16334437 original size:24 final size:23
Alignment explanation
Indices: 16334410--16334481 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 23
16334400 GGATGCTCCG
16334410 AAGAGCTATTAACGGGACGCTCT
1 AAGAGCTATTAACGGGACGCTCT
* * *
16334433 CAAGAACCATATAATGGAGA-GCTCAT
1 -AAGAGCTAT-TAACGG-GACGCTC-T
* *
16334459 GAGAGCTAATAACGGGACGCTCT
1 AAGAGCTATTAACGGGACGCTCT
16334482 TTCGAGCTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
23 3 0.08
24 16 0.44
25 14 0.39
26 3 0.08
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (23 bp):
AAGAGCTATTAACGGGACGCTCT
Found at i:16342336 original size:17 final size:19
Alignment explanation
Indices: 16342316--16342352 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16342306 ATATTTATAG
16342316 TTTTATA-A-TTTTTATTT
1 TTTTATATATTTTTTATTT
16342333 TTTTATATATTTTTTATTT
1 TTTTATATATTTTTTATTT
16342352 T
1 T
16342353 GTATAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATATATTTTTTATTT
Found at i:16342357 original size:18 final size:19
Alignment explanation
Indices: 16342319--16342357 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16342309 TTTATAGTTT
*
16342319 TATAATTTTTATTTTTTTA
1 TATAATTTTTATTTTTGTA
*
16342338 TATATTTTTTA-TTTTGTA
1 TATAATTTTTATTTTTGTA
16342356 TA
1 TA
16342358 AATGTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TATAATTTTTATTTTTGTA
Found at i:16342365 original size:24 final size:24
Alignment explanation
Indices: 16342338--16342398 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
16342328 TATTTTTTTA
16342338 TATATTTTTTATTTTGTATAAAT-G
1 TATATTTTTTATTTTGTA-AAATAG
* * * *
16342362 TATATATTATATTTTTTAAAATAT
1 TATATTTTTTATTTTGTAAAATAG
16342386 TATAGTTTTTTAT
1 TATA-TTTTTTAT
16342399 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 4 0.14
24 19 0.66
25 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
TATATTTTTTATTTTGTAAAATAG
Found at i:16342454 original size:17 final size:17
Alignment explanation
Indices: 16342291--16342454 Score: 70
Period size: 17 Copynumber: 9.3 Consensus size: 17
16342281 CAAAAGGTGT
*
16342291 TTTTTAATAATTTATATA
1 TTTTT-ATATTTTATATA
16342309 --TTTATAGTTTTATA-A
1 TTTTTATA-TTTTATATA
*
16342324 TTTTTATTTTTTTATATA
1 TTTTTA-TATTTTATATA
*
16342342 TTTTT-TATTTTGTATA
1 TTTTTATATTTTATATA
** * *
16342358 AATGTATATATTATAT-
1 TTTTTATATTTTATATA
* * *
16342374 TTTTTAAAATATTATAGTT
1 TTTTT-ATATTTTATA-TA
*
16342393 TTTTATATATTTTTAATTCTA
1 TTTT-TATA-TTTT-A-TATA
16342414 CTTAGTTTATATTTT-TATA
1 -TT--TTTATATTTTATATA
*
16342433 ATTTTATATTTTATATA
1 TTTTTATATTTTATATA
16342450 TTTTT
1 TTTTT
16342455 CAAACTAATA
Statistics
Matches: 109, Mismatches: 20, Indels: 35
0.66 0.12 0.21
Matches are distributed among these distances:
15 4 0.04
16 32 0.29
17 36 0.33
18 9 0.08
19 9 0.08
20 4 0.04
21 2 0.02
22 7 0.06
23 4 0.04
24 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTATATTTTATATA
Found at i:16347121 original size:43 final size:41
Alignment explanation
Indices: 16347029--16347135 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 41
16347019 GATGGCTCTA
* *
16347029 TCCCAGACAGGGTCTTACACGAATCATATACGGTGCCAATG
1 TCCCAGACATGGTCTTACACGAATCATATACGATGCCAATG
* * *
16347070 TCCTAGACATGGTCTTACACATAATC-TCATATCGATGTCAATG
1 TCCCAGACATGGTCTTACAC-GAATCAT-ATA-CGATGCCAATG
*
16347113 TCCCAGACATGGTCCTACACGAA
1 TCCCAGACATGGTCTTACACGAA
16347136 ACCACACCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 19 0.35
42 9 0.16
43 27 0.49
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (41 bp):
TCCCAGACATGGTCTTACACGAATCATATACGATGCCAATG
Found at i:16348640 original size:30 final size:30
Alignment explanation
Indices: 16348594--16348657 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
16348584 TCAATTAGAC
** *
16348594 TAAGGAAATGTGTAGGTTTGTCTACTAATA
1 TAAGGAAATGTGTAGGTTCATCTACCAATA
* *
16348624 TAAGGACATGTTTAGGTTCATCTACCAATA
1 TAAGGAAATGTGTAGGTTCATCTACCAATA
16348654 TAAG
1 TAAG
16348658 TTGTCTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (30 bp):
TAAGGAAATGTGTAGGTTCATCTACCAATA
Found at i:16354438 original size:23 final size:23
Alignment explanation
Indices: 16354395--16354438 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
16354385 ATTCTAAATA
*
16354395 ATTTAATAAATTTAACCATTTAC
1 ATTTAATAAATTTAACAATTTAC
*
16354418 ATTT-ATAAATTCTATCAATTT
1 ATTTAATAAATT-TAACAATTT
16354439 GACTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATAAATTTAACAATTTAC
Found at i:16362781 original size:17 final size:17
Alignment explanation
Indices: 16362748--16362781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16362738 ACTACAAAAT
*
16362748 CAAATCTTCTAATATTA
1 CAAATCTTCTAAGATTA
*
16362765 CAAATCTTTTAAGATTA
1 CAAATCTTCTAAGATTA
16362782 GTTTTCATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:16367151 original size:15 final size:15
Alignment explanation
Indices: 16367131--16367164 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
16367121 CTCGGATACC
16367131 ATTTCATGAACCTTA
1 ATTTCATGAACCTTA
16367146 ATTTCATGAACCTTA
1 ATTTCATGAACCTTA
16367161 ATTT
1 ATTT
16367165 GAAAGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTCATGAACCTTA
Found at i:16369119 original size:35 final size:34
Alignment explanation
Indices: 16369052--16369119 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
16369042 CTATTGAATT
*
16369052 AAATTTTAAATTATATTCTAATTCAATGCATATG
1 AAATTTTAAATTATATTCCAATTCAATGCATATG
* *
16369086 AAATATTTAAATTTTATTTCCAATTTAAT-CATAT
1 AAAT-TTTAAATTATA-TTCCAATTCAATGCATAT
16369120 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 15 0.52
36 10 0.34
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (34 bp):
AAATTTTAAATTATATTCCAATTCAATGCATATG
Found at i:16372256 original size:21 final size:23
Alignment explanation
Indices: 16372230--16372272 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16372220 TATTGTTTTC
16372230 AAAAAAA-CCAAAAGTT-TGTTA
1 AAAAAAAGCCAAAAGTTGTGTTA
*
16372251 AAAAAAAGTCAAAAGTTGTGTT
1 AAAAAAAGCCAAAAGTTGTGTT
16372273 TTGAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (23 bp):
AAAAAAAGCCAAAAGTTGTGTTA
Found at i:16388222 original size:43 final size:43
Alignment explanation
Indices: 16388090--16388267 Score: 173
Period size: 43 Copynumber: 4.1 Consensus size: 43
16388080 TGTTAGTATG
* * * *
16388090 ATTG-TTTCGGTTTATCTAATGGTGCACTAT-GTGTGCCAGTATA
1 ATTGCTTT-GGTTCATCCAATGATGCACT-TCGTGTGCCAATATA
* ** * * *
16388133 ATTACTTCAGTTTATCTAATGATG-AATTACGTGTGCCAATATA
1 ATTGCTTTGGTTCATCCAATGATGCACTT-CGTGTGCCAATATA
16388176 ATTGCTTTGGTTCATCCAATGATGCACTTCGTGTGCCAATATA
1 ATTGCTTTGGTTCATCCAATGATGCACTTCGTGTGCCAATATA
* * * * *
16388219 ATTGCTTTGGTTCATTCGATGATACACCTCGTGTGCCAATACA
1 ATTGCTTTGGTTCATCCAATGATGCACTTCGTGTGCCAATATA
16388262 ATTGCT
1 ATTGCT
16388268 CTGACTTGCT
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 106 0.93
44 5 0.04
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (43 bp):
ATTGCTTTGGTTCATCCAATGATGCACTTCGTGTGCCAATATA
Found at i:16388281 original size:43 final size:42
Alignment explanation
Indices: 16388162--16388284 Score: 122
Period size: 43 Copynumber: 2.9 Consensus size: 42
16388152 TGATGAATTA
* * * * * *
16388162 CGTGTGCCAATATAATTGCTTTGGTTCATCCAATGATGCACTT
1 CGTGTGCCAATACAATTGCTCTGCTTCAT-CGATGATACACCT
* * *
16388205 CGTGTGCCAATATAATTGCTTTGGTTCATTCGATGATACACCT
1 CGTGTGCCAATACAATTGCTCTGCTTCA-TCGATGATACACCT
16388248 CGTGTGCCAATACAATTGCTCTGACTTGC-TCGATGAT
1 CGTGTGCCAATACAATTGCTCTG-CTT-CATCGATGAT
16388285 GCATTATGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 67 0.94
44 3 0.04
45 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (42 bp):
CGTGTGCCAATACAATTGCTCTGCTTCATCGATGATACACCT
Found at i:16391098 original size:18 final size:18
Alignment explanation
Indices: 16391075--16391117 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16391065 ACTCAATCCA
**
16391075 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
16391093 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
16391111 AACCCAA
1 AACCCAA
16391118 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:16391235 original size:9 final size:9
Alignment explanation
Indices: 16391221--16391269 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
16391211 GTAGTGATTC
16391221 AATTCGGTT
1 AATTCGGTT
16391230 AATTCGGTT
1 AATTCGGTT
*
16391239 AATTCGGGT
1 AATTCGGTT
*
16391248 AATTCGATT
1 AATTCGGTT
16391257 AATTCGGTT
1 AATTCGGTT
16391266 AATT
1 AATT
16391270 TTTAACCAAA
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:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:16397222 original size:7 final size:7
Alignment explanation
Indices: 16397210--16397246 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
16397200 TAATTACTAT
16397210 AATTTAA
1 AATTTAA
16397217 AATTTAA
1 AATTTAA
16397224 AATTTAA
1 AATTTAA
16397231 AATTTAA
1 AATTTAA
16397238 AATTTAA
1 AATTTAA
16397245 AA
1 AA
16397247 AATTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTTAA
Found at i:16420085 original size:103 final size:104
Alignment explanation
Indices: 16419906--16420170 Score: 424
Period size: 103 Copynumber: 2.6 Consensus size: 104
16419896 AACCGTTATT
* * * *
16419906 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
16419971 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
16420009 GGTGGATATCGCACTTAGCACCACCAATGAATTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
16420074 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
16420113 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
16420171 TTATGTACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:16428441 original size:30 final size:31
Alignment explanation
Indices: 16428402--16428461 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
16428392 GGAGGTGGGA
*
16428402 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
16428433 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
16428462 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:16428689 original size:9 final size:9
Alignment explanation
Indices: 16428675--16428711 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16428665 TATAGTTTGA
16428675 TATTCGAAT
1 TATTCGAAT
16428684 TATTCGAAT
1 TATTCGAAT
*
16428693 TATTCGAGT
1 TATTCGAAT
16428702 TATTCGAAT
1 TATTCGAAT
16428711 T
1 T
16428712 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16428781 original size:9 final size:9
Alignment explanation
Indices: 16428764--16428794 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16428754 TCGAGTTGAT
16428764 TCGAATAAC
1 TCGAATAAC
*
16428773 TCGATTAAC
1 TCGAATAAC
16428782 TCGAATAAC
1 TCGAATAAC
16428791 TCGA
1 TCGA
16428795 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:16432975 original size:19 final size:19
Alignment explanation
Indices: 16432948--16432990 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
16432938 CATAAAAATC
*
16432948 ATATATAAGA-AATTGGTAT
1 ATATATAAGATAA-TGATAT
*
16432967 ATATGTAAGATAATGATAT
1 ATATATAAGATAATGATAT
16432986 ATATA
1 ATATA
16432991 AAATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
ATATATAAGATAATGATAT
Found at i:16447731 original size:34 final size:35
Alignment explanation
Indices: 16447686--16447753 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
16447676 CCAGTAAAAT
* *
16447686 ATTTTCCGTAAAATGA-TTTCGGGAAAATGTTTTA
1 ATTTTCCGTAAAATGACTTACGGGAAAATATTTTA
* *
16447720 ATTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGACTTACGGGAAAATATTTT
16447754 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.43
Consensus pattern (35 bp):
ATTTTCCGTAAAATGACTTACGGGAAAATATTTTA
Found at i:16449222 original size:14 final size:14
Alignment explanation
Indices: 16449203--16449229 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16449193 TAACCAAATT
16449203 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
16449217 ATAAAAATAAAAA
1 ATAAAAATAAAAA
16449230 GATAGTTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:16449801 original size:22 final size:22
Alignment explanation
Indices: 16449776--16449843 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
16449766 TTAAAATTCA
16449776 AAATATATGTTATAATTTTTTT
1 AAATATATGTTATAATTTTTTT
* ***
16449798 AAATATAT-ATAT-ATTTTAAA
1 AAATATATGTTATAATTTTTTT
*
16449818 AAATATGTGCTT-TAATTTTTTT
1 AAATATATG-TTATAATTTTTTT
16449840 AAAT
1 AAAT
16449844 TATTAAATTT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 12 0.35
21 4 0.12
22 18 0.53
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (22 bp):
AAATATATGTTATAATTTTTTT
Found at i:16449834 original size:42 final size:39
Alignment explanation
Indices: 16449754--16449858 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 39
16449744 CAATTAATTA
* * *
16449754 TTTTTTAAATTTTTAAAATT-CAAAATATATGTTATAAT
1 TTTTTTAAATTATTAAATTTAAAAAATATATGTTATAAT
* *
16449792 TTTTTTAAATATATATATATTTTAAAAAATATGTGCTT-TAAT
1 TTTTTTAAAT-TAT-TA-AATTTAAAAAATATATG-TTATAAT
16449834 TTTTTTAAATTATTAAATTTAAAAA
1 TTTTTTAAATTATTAAATTTAAAAA
16449859 TCTATGTGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
38 10 0.18
39 11 0.20
40 4 0.07
41 6 0.11
42 23 0.41
43 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (39 bp):
TTTTTTAAATTATTAAATTTAAAAAATATATGTTATAAT
Found at i:16449865 original size:40 final size:39
Alignment explanation
Indices: 16449754--16449866 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 39
16449744 CAATTAATTA
* * *
16449754 TTTTTTAAATTTTTAAAATTCAAAATATATGT-TATAAT
1 TTTTTTAAATTATTAAATTTAAAAATATATGTGTATAAT
* *
16449792 TTTTTTAAATATATATATATTTTAAAAA-ATATGTGCTTTAAT
1 TTTTTTAAAT-TAT-TA-AATTTAAAAATATATGTG-TATAAT
*
16449834 TTTTTTAAATTATTAAATTTAAAAATCTATGTG
1 TTTTTTAAATTATTAAATTTAAAAATATATGTG
16449867 GTAATATTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
38 10 0.16
39 11 0.18
40 16 0.26
41 10 0.16
42 15 0.24
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTTTTAAATTATTAAATTTAAAAATATATGTGTATAAT
Found at i:16450108 original size:15 final size:16
Alignment explanation
Indices: 16450078--16450110 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16450068 CATGTGTCTC
16450078 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
*
16450094 TTTTTTAATAT-TTTA
1 TTTTTTAAAATATTTA
16450109 TT
1 TT
16450111 ATAGACACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:16454969 original size:22 final size:23
Alignment explanation
Indices: 16454918--16454970 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
16454908 GAATCATATA
*
16454918 TGTTCTGTATATGAAACTGAAAT
1 TGTTTTGTATATGAAACTGAAAT
* *
16454941 TGCTTTTGTATATGTAACT-AATT
1 TG-TTTTGTATATGAAACTGAAAT
16454964 TGTTTTG
1 TGTTTTG
16454971 AATCTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 14 0.54
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (23 bp):
TGTTTTGTATATGAAACTGAAAT
Found at i:16456842 original size:28 final size:28
Alignment explanation
Indices: 16456784--16456845 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
16456774 ATTGTTCTGG
* *
16456784 GAAAAATAATTTTGACAAGATGGGTTCT
1 GAAAAATAAATTTGACAAGATGGATTCT
* * * *
16456812 GAAAAATAAATTTGAGATGATGTATTTT
1 GAAAAATAAATTTGACAAGATGGATTCT
16456840 GAAAAA
1 GAAAAA
16456846 ATTATTTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (28 bp):
GAAAAATAAATTTGACAAGATGGATTCT
Found at i:16457007 original size:59 final size:59
Alignment explanation
Indices: 16456910--16457113 Score: 327
Period size: 59 Copynumber: 3.4 Consensus size: 59
16456900 CACAGCCAGT
16456910 AATATATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* *
16456970 AATAATTTGTACAAAATTATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATTAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* * *
16457029 AATAATTTTTACAAAAATATTGAAAAGAACTTCTATTTTATTAAATAAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* * *
16457088 AACAATTTGTATAAAAAAATTCAAAA
1 AATAATTTGTACAAAAATATTCAAAA
16457114 ATAAATCAAT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 128 0.97
60 4 0.03
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
Found at i:16459079 original size:19 final size:18
Alignment explanation
Indices: 16459031--16459091 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
16459021 CCGGCTATTA
16459031 TAAA-AAATTATAAAAATAT
1 TAAATAAATTAT-AAAA-AT
*
16459050 TAATTAAATTATAAAAAT
1 TAAATAAATTATAAAAAT
*
16459068 TAAATAATATTAGAAAAAT
1 TAAATAA-ATTATAAAAAT
*
16459087 AAAAT
1 TAAAT
16459092 TAACCCTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 21 0.58
20 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAATAAATTATAAAAAT
Found at i:16461274 original size:28 final size:28
Alignment explanation
Indices: 16461243--16461308 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
16461233 ATAAAAAATA
* *
16461243 ATCAAACTATTATAACTTTTTTTTATTT
1 ATCAAAATATTATAAATTTTTTTTATTT
16461271 ATCAAAATATTATAAATTTTTTTTATTT
1 ATCAAAATATTATAAATTTTTTTTATTT
16461299 A-CTAAAATAT
1 ATC-AAAATAT
16461309 ATCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (28 bp):
ATCAAAATATTATAAATTTTTTTTATTT
Found at i:16461727 original size:19 final size:19
Alignment explanation
Indices: 16461703--16461768 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
16461693 ATTAAAATAG
16461703 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
16461722 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
16461740 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
16461759 TTTAATTTAA
1 TTTAATTTAA
16461769 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:16462033 original size:18 final size:19
Alignment explanation
Indices: 16461994--16462052 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
16461984 ATTTTATATT
16461994 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
16462013 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
16462031 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
16462050 TTA
1 TTA
16462053 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:16490025 original size:58 final size:62
Alignment explanation
Indices: 16489963--16490112 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 62
16489953 GGATACGACA
* * * *
16489963 TAATAATTCTTGAAAGCAAGCAAGATTGAAA-TGTTCATCCCTTCGTA-AA-GTTA-T-TAAG
1 TAATAATTCTTGAAAGTAAGCAAGATTCAAAGCGCTCATCCCTT-GTATAAGGTTATTATAAG
* * *
16490021 TAATAACTCTTGAAAGTAAGCATGA-TCAAAGCGCTCATCCCTTTTATAAGGTTATTATAAG
1 TAATAATTCTTGAAAGTAAGCAAGATTCAAAGCGCTCATCCCTTGTATAAGGTTATTATAAG
*
16490082 TAATAATTCTAGAAAGTAAGCAAGA-TCAAAG
1 TAATAATTCTTGAAAGTAAGCAAGATTCAAAG
16490113 TGTTAGAGGT
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.08
58 34 0.44
59 4 0.05
60 1 0.01
61 32 0.42
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (62 bp):
TAATAATTCTTGAAAGTAAGCAAGATTCAAAGCGCTCATCCCTTGTATAAGGTTATTATAAG
Found at i:16491330 original size:32 final size:32
Alignment explanation
Indices: 16491289--16491354 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
16491279 TTGATACTTC
16491289 CAATCAATATCGACATTTCAGCCATGCACCCG
1 CAATCAATATCGACATTTCAGCCATGCACCCG
16491321 CAATCAATATCGACATTTCAGCCATGCACCCG
1 CAATCAATATCGACATTTCAGCCATGCACCCG
16491353 CA
1 CA
16491355 TTACTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.35, G:0.12, T:0.21
Consensus pattern (32 bp):
CAATCAATATCGACATTTCAGCCATGCACCCG
Found at i:16496816 original size:19 final size:20
Alignment explanation
Indices: 16496776--16496817 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
16496766 TTTTTTTAAC
*
16496776 TTTTTATAATTTTTTGAATA
1 TTTTTATAATTTTTTAAATA
16496796 TTTTTAT-A-TTTTTAAATTA
1 TTTTTATAATTTTTTAAA-TA
16496815 TTT
1 TTT
16496818 ATTGATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATAATTTTTTAAATA
Found at i:16500628 original size:126 final size:126
Alignment explanation
Indices: 16500403--16500652 Score: 455
Period size: 126 Copynumber: 2.0 Consensus size: 126
16500393 TGACAAACGA
16500403 GTTTGGATTCAAGTCCTAACTGTAACATCCCAAATACCCACTGAGTCAAGAACAATGATAAATCG
1 GTTTGGATTCAAGTCCTAACTGTAACATCCCAAATACCCACTGAGTCAAGAACAATGATAAATCG
*
16500468 AGAGTAGATATGTTAGAAACTGAGATGGTAATAACATAAAAATTATTACTATTAGTAGTGG
66 AGAGTAGATATGTTAGAAACTGAGATGGTAATAACACAAAAATTATTACTATTAGTAGTGG
* *
16500529 GTTTGGATTCAAGTCCTAACTGTAACATCCCCAATACCCACTGAGTCGAGAACAATGATAAATCG
1 GTTTGGATTCAAGTCCTAACTGTAACATCCCAAATACCCACTGAGTCAAGAACAATGATAAATCG
* *
16500594 ATAGTAGATATGTTAGAAACTGATATGGTAATAACACAAAAATTATTACTATTAGTAGT
66 AGAGTAGATATGTTAGAAACTGAGATGGTAATAACACAAAAATTATTACTATTAGTAGT
16500653 AGGTAAAGAT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (126 bp):
GTTTGGATTCAAGTCCTAACTGTAACATCCCAAATACCCACTGAGTCAAGAACAATGATAAATCG
AGAGTAGATATGTTAGAAACTGAGATGGTAATAACACAAAAATTATTACTATTAGTAGTGG
Found at i:16502693 original size:104 final size:104
Alignment explanation
Indices: 16502562--16502785 Score: 369
Period size: 104 Copynumber: 2.2 Consensus size: 104
16502552 AATGGATATC
*
16502562 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCAGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
16502627 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
16502666 GCACTTAGCAACCCCTCAGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCAGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
16502731 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
16502770 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
16502786 TTTATATACA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCAGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:16503147 original size:29 final size:29
Alignment explanation
Indices: 16503114--16503177 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
16503104 TAATCCACCA
16503114 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
16503143 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
16503173 CCCAA
1 CCCAA
16503178 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:16503151 original size:30 final size:30
Alignment explanation
Indices: 16503121--16503177 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16503111 CCACCCAACT
16503121 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
16503150 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
16503178 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:16504358 original size:25 final size:25
Alignment explanation
Indices: 16504328--16504376 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
16504318 ATTAGATGTA
16504328 TTAATATTTACATGTTTTTAATTAT
1 TTAATATTTACATGTTTTTAATTAT
16504353 TTAATATTTACATGTTTTTAATTA
1 TTAATATTTACATGTTTTTAATTA
16504377 CTAACTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
TTAATATTTACATGTTTTTAATTAT
Found at i:16504385 original size:25 final size:25
Alignment explanation
Indices: 16504329--16504385 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
16504319 TTAGATGTAT
*
16504329 TAATATTTACATGTTTTTAATTATT
1 TAATATTTACATGTTTTTAATTATC
16504354 TAATATTTACATGTTTTTAATTA-C
1 TAATATTTACATGTTTTTAATTATC
16504378 TAACTATT
1 TAA-TATT
16504386 GTGTTATGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (25 bp):
TAATATTTACATGTTTTTAATTATC
Found at i:16509993 original size:18 final size:18
Alignment explanation
Indices: 16509970--16510011 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
16509960 TAATAAGTTT
*
16509970 TTAATTTAATAAATTT-AA
1 TTAATTGAA-AAATTTAAA
*
16509988 TTAATTGAAAATTTTAAA
1 TTAATTGAAAAATTTAAA
16510006 TTAATT
1 TTAATT
16510012 ACACTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTGAAAAATTTAAA
Found at i:16510382 original size:18 final size:20
Alignment explanation
Indices: 16510341--16510382 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
16510331 TTATACTAAC
*
16510341 TATTTAAAATGTATTTACAA
1 TATTTAAAATGTATGTACAA
16510361 -ATTT-AAATGTATGTA-AA
1 TATTTAAAATGTATGTACAA
16510378 TATTT
1 TATTT
16510383 CATCTATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 2 0.10
18 14 0.70
19 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TATTTAAAATGTATGTACAA
Found at i:16510604 original size:28 final size:27
Alignment explanation
Indices: 16510572--16510662 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 27
16510562 ATAATTATAT
16510572 TTAAAATTCTAAAATATTTCATGTATCA
1 TTAAAATTCTAAAATATTT-ATGTATCA
*
16510600 TTAAAATTCTAAAGTATCATTTAT-TATTATA
1 TTAAAATTCTAAA--AT-ATTTATGTA-T-CA
16510631 TTTAAAATTCTAAAATATTTTATGTATCA
1 -TTAAAATTCTAAAATA-TTTATGTATCA
16510660 TTA
1 TTA
16510663 GATTTATAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
28 16 0.30
29 4 0.08
30 13 0.25
31 7 0.13
32 13 0.25
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (27 bp):
TTAAAATTCTAAAATATTTATGTATCA
Found at i:16510629 original size:60 final size:60
Alignment explanation
Indices: 16510533--16510662 Score: 206
Period size: 60 Copynumber: 2.2 Consensus size: 60
16510523 GCCAACACTT
16510533 TGTATCATTAAAACTCAAAAACATCATTTATAATTATATTTAAAATTCTAAAATATTTCA
1 TGTATCATTAAAACTCAAAAACATCATTTATAATTATATTTAAAATTCTAAAATATTTCA
* * ** * *
16510593 TGTATCATTAAAATTCTAAAGTATCATTTATTATTATATTTAAAATTCTAAAATATTTTA
1 TGTATCATTAAAACTCAAAAACATCATTTATAATTATATTTAAAATTCTAAAATATTTCA
16510653 TGTATCATTA
1 TGTATCATTA
16510663 GATTTATAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (60 bp):
TGTATCATTAAAACTCAAAAACATCATTTATAATTATATTTAAAATTCTAAAATATTTCA
Found at i:16510641 original size:32 final size:30
Alignment explanation
Indices: 16510555--16510650 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 30
16510545 ACTCAAAAAC
*
16510555 ATCATTTATAATTATATTTAAAATTCTAAA
1 ATCATTTATTATTATATTTAAAATTCTAAA
*
16510585 AT-ATTTCATGTA-T-CA-TTAAAATTCTAAA
1 ATCATTT-AT-TATTATATTTAAAATTCTAAA
16510613 GTATCATTTATTATTATATTTAAAATTCTAAA
1 --ATCATTTATTATTATATTTAAAATTCTAAA
16510645 AT-ATTT
1 ATCATTT
16510651 TATGTATCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
28 13 0.24
29 11 0.20
30 12 0.22
31 6 0.11
32 13 0.24
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (30 bp):
ATCATTTATTATTATATTTAAAATTCTAAA
Found at i:16514210 original size:11 final size:10
Alignment explanation
Indices: 16514194--16514229 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
16514184 CGCAAATACG
16514194 TATAAATATTA
1 TATAAATA-TA
16514205 TATAAATATA
1 TATAAATATA
16514215 TAT-AATATA
1 TATAAATATA
16514224 TATAAA
1 TATAAA
16514230 AATGTGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 7 0.29
11 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATAAATATA
Found at i:16514383 original size:16 final size:16
Alignment explanation
Indices: 16514362--16514397 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
16514352 AAATGGAAAG
16514362 TATATAGATATACATA
1 TATATAGATATACATA
16514378 TATATAGATATACATA
1 TATATAGATATACATA
16514394 TATA
1 TATA
16514398 AAAAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:16514456 original size:8 final size:8
Alignment explanation
Indices: 16514443--16514471 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
16514433 AAAAGAATAG
16514443 ATATACAT
1 ATATACAT
16514451 ATATACAT
1 ATATACAT
16514459 ATATACAT
1 ATATACAT
16514467 ATATA
1 ATATA
16514472 AGCAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:16516045 original size:46 final size:46
Alignment explanation
Indices: 16516017--16517657 Score: 2193
Period size: 46 Copynumber: 35.7 Consensus size: 46
16516007 CAATCTAATT
*
16516017 CGCTGCTAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516063 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCAATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
**
16516109 CGCTATCAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* *
16516155 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTTGA-CCCACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* * *
16516201 CACTGACAAATACAGGAAGACAAGATCTGCTATCTTTGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516247 CACTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516293 CGCTGCCAAATACAGGAAGACAAGATATGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* *
16516339 TGCTGCCAAATACAAGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* * *
16516385 TGCTGCCAAATACAGGAAGACAAGATCTACTATCTTCGATCTCTTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
** * *
16516431 TACTGCCAAATACAGGAAGACATGATCTGCTATCTTCGATC-CACAC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* * * * *
16516477 CGCAGCCAAATACAGAAAGACAAGTTCTGCTATTTTCGATC-CAATC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516523 CGTTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * * *
16516569 CGCTGCCAAATATAGGAAGACAAGATTTACTATCTTCGATATCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * * *
16516615 TGCTGCCAAATACAGGAAGATAAGATCCGCTATCTTTGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * *
16516661 CGCTGCCAAATACAGGAAGATAAGATCCGCTATCTTTGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * * * * *
16516707 TGCTGCCAAATATAGGAAGATAAGATCCGCTATTTTTGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516753 CGCTGCCAAATACAGGAAGATAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16516799 CGCTGCCAAATACAGGAAGACAAGAT-TCGCTATCTTCGATCTCCTT
1 CGCTGCCAAATACAGGAAGACAAGATCT-GCTATCTTCGATCTCCTC
* * * * * *
16516845 CGCTGCCAAATACAGGAAGAGAAGACCCGCTATCTTTGATCTCTTT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
16516891 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* *
16516937 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCTTT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
*
16516983 CGCTGCCAAATACAGGAAGACAAGAT-TCGCTATCTTCGATCTCCTT
1 CGCTGCCAAATACAGGAAGACAAGATCT-GCTATCTTCGATCTCCTC
* * * * * *
16517029 CGCTGCCAAATACAGGAAGAGAAGACCCGCTATCTTTGATCTCTTT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
16517075 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * *
16517121 CGTTGCTAAATACAGGAAGACAAGATCTGCTATCTTTGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
16517167 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
** * * *
16517213 TACTGCCAAATACAAGAAGATAAGATCTACTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * *
16517259 CGCTGCCAAATACAAGAAGATAAGAT-TCGCTATATTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCT-GCTATCTTCGATCTCCTC
* * * * *
16517305 CGCTGTCAAATACAGGAAGATAAGATCCGCTATCTTTGATCTCCTT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * *
16517351 CGCTGCCAAATACAGGAAGATAAGATCCGCTATCTTTGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
* *
16517397 CGCTGCCAAATATAAGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
*
16517443 CGCTGCCAAATATAGGAAGACAAGATCTGCTATCTTCGATC-CACTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTC-CTC
16517489 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* *
16517535 CACTGCTAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
* * * *
16517581 CACTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATTTACTT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
*
16517627 CGCTGCCAAATACAGGAAGACGAGATCTGCT
1 CGCTGCCAAATACAGGAAGACAAGATCTGCT
16517658 GCTTCTAGTC
Statistics
Matches: 1453, Mismatches: 127, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
45 7 0.00
46 1441 0.99
47 5 0.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (46 bp):
CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTC
Found at i:16519082 original size:6 final size:5
Alignment explanation
Indices: 16519057--16519114 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
16519047 CTTTGGCCTC
* *
16519057 TTCTT TT-TC TTCTT TTCTT TTCCTT TT-TT TTCTG TTC-T TT-TT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TT-CTT TTCTT TTCTT TTCTT TTCTT TTCTT
16519104 TTCTT TT-TT TT
1 TTCTT TTCTT TT
16519115 GTTCTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
4 16 0.36
5 23 0.52
6 5 0.11
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:16519082 original size:20 final size:20
Alignment explanation
Indices: 16519059--16519097 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16519049 TTGGCCTCTT
*
16519059 CTTTTTCTTCTTTTCTTTTC
1 CTTTTTCTTCTGTTCTTTTC
*
16519079 CTTTTTTTTCTGTTCTTTT
1 CTTTTTCTTCTGTTCTTTT
16519098 TTTCTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (20 bp):
CTTTTTCTTCTGTTCTTTTC
Found at i:16519085 original size:13 final size:12
Alignment explanation
Indices: 16519061--16519128 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 12
16519051 GGCCTCTTCT
16519061 TTTTCTTCTTTTC
1 TTTTCTT-TTTTC
16519074 TTTTCCTTTTTTTTC
1 TTTT-C--TTTTTTC
*
16519089 TGTTCTTTTTTTC
1 TTTTC-TTTTTTC
16519102 TTTTCTTTTTT-
1 TTTTCTTTTTTC
16519113 TTGTTCTTTTTT-
1 TT-TTCTTTTTTC
16519125 TTTT
1 TTTT
16519129 GGACATTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
11 4 0.08
12 17 0.35
13 16 0.33
14 2 0.04
15 8 0.16
16 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:16519110 original size:25 final size:27
Alignment explanation
Indices: 16519063--16519125 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
16519053 CCTCTTCTTT
*
16519063 TTCTTCTTTTCTTTTCCTTTTTTTTCTG
1 TTCTTTTTTTCTTTTCC-TTTTTTTCTG
16519091 TTCTTTTTTTCTTTT-CTTTTTTT-TG
1 TTCTTTTTTTCTTTTCCTTTTTTTCTG
16519116 TTCTTTTTTT
1 TTCTTTTTTT
16519126 TTTGGACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 12 0.35
26 7 0.21
27 1 0.03
28 14 0.41
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (27 bp):
TTCTTTTTTTCTTTTCCTTTTTTTCTG
Found at i:16519124 original size:14 final size:14
Alignment explanation
Indices: 16519079--16519129 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
16519069 TTTTCTTTTC
*
16519079 CTTTTTTTTCTGTT
1 CTTTTTTTTTTGTT
*
16519093 CTTTTTTTCTT-TT
1 CTTTTTTTTTTGTT
16519106 C--TTTTTTTTGTT
1 CTTTTTTTTTTGTT
16519118 CTTTTTTTTTTG
1 CTTTTTTTTTTG
16519130 GACATTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 3 0.10
14 18 0.58
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (14 bp):
CTTTTTTTTTTGTT
Found at i:16523698 original size:11 final size:11
Alignment explanation
Indices: 16523682--16523721 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
16523672 CGCAAATACG
16523682 TATAAATATTA
1 TATAAATATTA
16523693 TATAAATATATA
1 TATAAATAT-TA
16523705 TATATAATA-TA
1 TATA-AATATTA
16523716 TATAAA
1 TATAAA
16523722 AATGTGCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 6 0.22
13 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAAATATTA
Found at i:16523870 original size:16 final size:16
Alignment explanation
Indices: 16523849--16523884 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16523839 AAATGGAAAG
16523849 TATATAGATATAAATA
1 TATATAGATATAAATA
*
16523865 TATATAGATATACATA
1 TATATAGATATAAATA
16523881 TATA
1 TATA
16523885 AAAAAGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATAAATA
Found at i:16523943 original size:8 final size:8
Alignment explanation
Indices: 16523930--16523958 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
16523920 AAAAGAATAG
16523930 ATATACAT
1 ATATACAT
16523938 ATATACAT
1 ATATACAT
16523946 ATATACAT
1 ATATACAT
16523954 ATATA
1 ATATA
16523959 AGCAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:16523977 original size:28 final size:29
Alignment explanation
Indices: 16523936--16523990 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
16523926 ATAGATATAC
16523936 ATATATACATATA-TACATAT-ATAAGCAA
1 ATATATACATATATTA-ATATAATAAGCAA
16523964 ATATATA-ATAATATTAATATAATAAGC
1 ATATATACAT-ATATTAATATAATAAGC
16523991 CAGATACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.08
28 14 0.58
29 8 0.33
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (29 bp):
ATATATACATATATTAATATAATAAGCAA
Found at i:16524062 original size:3 final size:3
Alignment explanation
Indices: 16524054--16524091 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16524044 TGAGAATGAG
16524054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16524092 ATTTATTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16524817 original size:12 final size:12
Alignment explanation
Indices: 16524797--16524825 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16524787 TACAAAACTT
16524797 GAAAA-AAAAAA
1 GAAAAGAAAAAA
16524808 GAAAAGAAAAAA
1 GAAAAGAAAAAA
16524820 GAAAAG
1 GAAAAG
16524826 GAACCCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:16529983 original size:52 final size:52
Alignment explanation
Indices: 16529921--16530029 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
16529911 TTAACTTTAA
16529921 AAACTAAAAATCAATAAGAAGTATTAAAAAGGCTCATAAATTGCTAGAGAAT
1 AAACTAAAAATCAATAAGAAGTATTAAAAAGGCTCATAAATTGCTAGAGAAT
*
16529973 AAACTAAAAATCAATAAGAAGTATTAAAAAGGCTCGTAAATTGCTAGAGAAT
1 AAACTAAAAATCAATAAGAAGTATTAAAAAGGCTCATAAATTGCTAGAGAAT
16530025 AAACT
1 AAACT
16530030 CGTCAAGTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.23
Consensus pattern (52 bp):
AAACTAAAAATCAATAAGAAGTATTAAAAAGGCTCATAAATTGCTAGAGAAT
Found at i:16530463 original size:24 final size:24
Alignment explanation
Indices: 16530414--16530463 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
16530404 AAAATGCATC
* *
16530414 AAAATAAAATATTATATACACAAT
1 AAAATAAAATATAAAATACACAAT
*
16530438 AAAATAAAAT-TAAAATTCACATAT
1 AAAATAAAATATAAAATACACA-AT
16530462 AA
1 AA
16530464 CATTACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAAAATATAAAATACACAAT
Found at i:16538562 original size:24 final size:25
Alignment explanation
Indices: 16538535--16538587 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
16538525 TTTTTCATTG
16538535 TATTAT-TAA-ATTTATATTTAAAAA
1 TATTATATAATATTTA-ATTTAAAAA
* *
16538559 TATT-TATAATATTTAATTTAGAAT
1 TATTATATAATATTTAATTTAAAAA
16538583 TATTA
1 TATTA
16538588 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 1 0.04
24 18 0.75
25 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTATATAATATTTAATTTAAAAA
Found at i:16538707 original size:22 final size:21
Alignment explanation
Indices: 16538657--16538708 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
16538647 TCATTTGCTG
16538657 AATATGTTAAAATCGTTTTATTT
1 AATAT-TTAAAATC-TTTTATTT
*
16538680 ATTATTTAAAAT-TTTCTATTAT
1 AATATTTAAAATCTTT-TATT-T
16538702 AATATTT
1 AATATTT
16538709 GAATGGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 4 0.16
22 14 0.56
23 4 0.16
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
AATATTTAAAATCTTTTATTT
Found at i:16544297 original size:13 final size:13
Alignment explanation
Indices: 16544276--16544326 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
16544266 ACACTCAAAA
16544276 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
* *
16544289 TTCTGAAAAACAC
1 TTCTCAAAAGCAC
16544302 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
16544315 TTCTCAAAAGCA
1 TTCTCAAAAGCA
16544327 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:16546882 original size:30 final size:30
Alignment explanation
Indices: 16546846--16546913 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
16546836 AACATTGATG
*
16546846 AAATTATTATAATTTTTGATACCATACTTA
1 AAATTATTATAATTTTTGATACAATACTTA
**
16546876 AAATTATTATAATTTTTGATTGAATACTTA
1 AAATTATTATAATTTTTGATACAATACTTA
16546906 AAATTATT
1 AAATTATT
16546914 TACAATCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (30 bp):
AAATTATTATAATTTTTGATACAATACTTA
Found at i:16556128 original size:24 final size:25
Alignment explanation
Indices: 16556101--16556148 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
16556091 AAAAGAAAGT
16556101 TTAAAGAACTTAAAA-GAAAAAAAA
1 TTAAAGAACTTAAAACGAAAAAAAA
**
16556125 TTAAAGTGCTTAAAACGAAAAAAA
1 TTAAAGAACTTAAAACGAAAAAAA
16556149 TATGGGGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (25 bp):
TTAAAGAACTTAAAACGAAAAAAAA
Done.