Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 72 of 316
Found at i:21318683 original size:21 final size:21
Alignment explanation
Indices: 21318659--21318700 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
21318649 AAAAACAATC
21318659 ATGTTGAAATGGAGTTTCATA
1 ATGTTGAAATGGAGTTTCATA
21318680 ATGTTGAAATGGAGTTTCATA
1 ATGTTGAAATGGAGTTTCATA
21318701 TTTCATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (21 bp):
ATGTTGAAATGGAGTTTCATA
Found at i:21333437 original size:11 final size:11
Alignment explanation
Indices: 21333421--21333445 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21333411 ATATCTAGAA
21333421 TTCTCTTCATT
1 TTCTCTTCATT
21333432 TTCTCTTCATT
1 TTCTCTTCATT
21333443 TTC
1 TTC
21333446 ATCAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:21334724 original size:25 final size:25
Alignment explanation
Indices: 21334695--21334746 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
21334685 AAGAATAATT
*
21334695 TGAATATTTGATATTGCCTAATAAA
1 TGAATATTCGATATTGCCTAATAAA
* *
21334720 TGAATATTCGATATTGCTTAGTAAA
1 TGAATATTCGATATTGCCTAATAAA
21334745 TG
1 TG
21334747 TTAAGCCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (25 bp):
TGAATATTCGATATTGCCTAATAAA
Found at i:21335414 original size:10 final size:10
Alignment explanation
Indices: 21335399--21335426 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
21335389 ATATTACATG
21335399 TTTACTTTGT
1 TTTACTTTGT
21335409 TTTACTTTGT
1 TTTACTTTGT
21335419 TTTACTTT
1 TTTACTTT
21335427 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:21339952 original size:17 final size:18
Alignment explanation
Indices: 21339914--21339956 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21339904 TGGCCAATAT
21339914 CCCACACGCCCGTGTGGG
1 CCCACACGCCCGTGTGGG
* *
21339932 CCCACATGCCCTTGT-GG
1 CCCACACGCCCGTGTGGG
21339949 CCCACACG
1 CCCACACG
21339957 ACCCAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.14, C:0.47, G:0.26, T:0.14
Consensus pattern (18 bp):
CCCACACGCCCGTGTGGG
Found at i:21343638 original size:30 final size:30
Alignment explanation
Indices: 21343602--21343659 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
21343592 TGGCAAACAT
21343602 TGCCCTGACGTATAGAATTATTATTTAATA
1 TGCCCTGACGTATAGAATTATTATTTAATA
21343632 TGCCCTGACGTATAGAATTATTATTTAA
1 TGCCCTGACGTATAGAATTATTATTTAA
21343660 CATCGCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (30 bp):
TGCCCTGACGTATAGAATTATTATTTAATA
Found at i:21350431 original size:11 final size:11
Alignment explanation
Indices: 21350417--21350441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21350407 TCTTTCTAAA
21350417 TTCTCTCAAAT
1 TTCTCTCAAAT
21350428 TTCTCTCAAAT
1 TTCTCTCAAAT
21350439 TTC
1 TTC
21350442 ATCAAAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:21350431 original size:22 final size:21
Alignment explanation
Indices: 21350393--21350447 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
21350383 GTCCTTTCAC
* * *
21350393 AATTCTCTTTAAATTCTTTCTA
1 AATTCTCATCAAATTCTCTC-A
21350415 AATTCTC-TCAAATTTCTCTCA
1 AATTCTCATCAAA-TTCTCTCA
21350436 AATT-TCATCAAA
1 AATTCTCATCAAA
21350448 GCTGTCTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 14 0.48
22 13 0.45
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTCTCATCAAATTCTCTCA
Found at i:21352161 original size:9 final size:9
Alignment explanation
Indices: 21352142--21352172 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
21352132 CGAGCCTAGG
21352142 GGTAA-TTT
1 GGTAATTTT
21352150 GGTAATTTT
1 GGTAATTTT
21352159 GGTAATTTT
1 GGTAATTTT
21352168 GGTAA
1 GGTAA
21352173 AATATAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (9 bp):
GGTAATTTT
Found at i:21354085 original size:7 final size:7
Alignment explanation
Indices: 21354072--21354104 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
21354062 TAGTTGTTTC
21354072 GTATTTA
1 GTATTTA
*
21354079 ATATTTA
1 GTATTTA
21354086 GTATTTA
1 GTATTTA
21354093 GTATTTA
1 GTATTTA
21354100 GTATT
1 GTATT
21354105 ACCTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:21354954 original size:22 final size:21
Alignment explanation
Indices: 21354922--21354972 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
21354912 CCAACACCCA
21354922 CAACCA-AATCCCCTACCGGAG
1 CAACCACAATCCCC-ACCGGAG
* *
21354943 GAACCACAATCCCCACTGGAG
1 CAACCACAATCCCCACCGGAG
21354964 CAACCACAA
1 CAACCACAA
21354973 CCCTCGCCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.37, C:0.41, G:0.14, T:0.08
Consensus pattern (21 bp):
CAACCACAATCCCCACCGGAG
Found at i:21355306 original size:127 final size:128
Alignment explanation
Indices: 21355087--21355459 Score: 660
Period size: 127 Copynumber: 2.9 Consensus size: 128
21355077 TTGTAGAAAC
21355087 ATTTTTATATAGTTTT-ATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
1 ATTTTTATATAGTTTTAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
*
21355151 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATGTTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
*
21355215 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTT-TTTTTAATATTTTAATTGTACTTTAATTT
1 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
21355279 TTTTAATTTTATTAAAATAAATATTCTTTTAAATTGGCCAATATTTTTATTATTTTTATATTT
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
21355342 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
21355407 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAATTTTTATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAAT-ATTTTTATTA
21355460 AAATAAATGT
Statistics
Matches: 233, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
127 123 0.53
128 98 0.42
129 12 0.05
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (128 bp):
ATTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
Found at i:21355465 original size:39 final size:39
Alignment explanation
Indices: 21355413--21355494 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
21355403 CTTTTTTTAA
* *
21355413 TTTTAATACAATAAATGTTCTTTTAAAT-TAGCCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATATAG-CAATAAT
* * *
21355452 TTTTATTAAAATAAATGTTATTTTGAATATAGCAATATT
1 TTTTAATAAAATAAATGTTATTTTAAATATAGCAATAAT
21355491 TTTT
1 TTTT
21355495 TATATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.92
40 3 0.08
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (39 bp):
TTTTAATAAAATAAATGTTATTTTAAATATAGCAATAAT
Found at i:21358779 original size:126 final size:125
Alignment explanation
Indices: 21358550--21358856 Score: 497
Period size: 126 Copynumber: 2.4 Consensus size: 125
21358540 GTTTAAGGCG
* *
21358550 TTTTCAGATACTACTGTAGCAAAAGAGTGTCCACGTGGGAGCTTTTTCCGTAATTTTGCTGACAG
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCGTAATTTTACTGACAG
*
21358615 TGCATCATTCTTAAAGCATTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATT
66 TGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
* * * * *
21358675 TTTTCAAATACTACTGTAGCAAAATAGCATCCATGTGGGAGCTTTTTCTTGTAATTTTACTGACA
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTC-CGTAATTTTACTGACA
* *
21358740 GTGCATCATTCTTGAAGCGTTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
65 GTGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
*
21358801 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCCGTAATT
1 TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGC-TTTTTCCGTAATT
21358857 AATAGTTAAT
Statistics
Matches: 164, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
125 43 0.26
126 115 0.70
127 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (125 bp):
TTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCGTAATTTTACTGACAG
TGCATCATTCTTAAAGCATTTTTGACACTATTTATTCAGAAACATCTTCTCAAAATTATT
Found at i:21359011 original size:16 final size:16
Alignment explanation
Indices: 21358982--21359019 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21358972 CTTAAAAAAT
*
21358982 ACTAAAATCCTAAACC
1 ACTAAAAACCTAAACC
21358998 -CTAAAAACCATAAACC
1 ACTAAAAACC-TAAACC
21359014 ACTAAA
1 ACTAAA
21359020 CCGTAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (16 bp):
ACTAAAAACCTAAACC
Found at i:21359089 original size:171 final size:171
Alignment explanation
Indices: 21358877--21359377 Score: 722
Period size: 171 Copynumber: 2.9 Consensus size: 171
21358867 TTAATTAATA
*
21358877 AACCCTAAAAAACCCTAAACCCTAATTTAATT-ATTTTTTAATTTAATAGTTAATTTAATTAATT
1 AACCCTAAAAAACCCTAAACCCTAATTTAATTGATTTTTTAATTTCATAGTTAATTTAATTAATT
*
21358941 AACCCTCAAGTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAATCCTAAACCCTAAAAAC
66 AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAA-CCTAAACCCTAAAAAC
* * *
21359006 CATAAACCACTAAACCGTAACCCTAAAATAATAAAAAACCTT
130 CATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
* *
21359048 AACCCT-AAAACCCCTAAACCCTAATTTAATTGATTTTTTAATTTCATGGTTAATTTAATTAATT
1 AACCCTAAAAAACCCTAAACCCTAATTTAATTGATTTTTTAATTTCATAGTTAATTTAATTAATT
* *
21359112 AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAGAAAACACTAAAACCATAAACCCTAAAAAC
66 AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAACC-TAAACCCTAAAAAC
* * ** ** *
21359177 CCTAAACCATTAAACATTAACTTTAAAACAATCAAAAACCCT
130 CATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
* *
21359219 AACCTTAAAAAACCCTAAACTCTAATTTAATTGATTTTTTTTAATTTCATAGTTAATTTAATTAA
1 AACCCTAAAAAACCCTAAACCCTAATTTAATTGA--TTTTTTAATTTCATAGTTAATTTAATTAA
* * *
21359284 TTAACTCTGAACTCTAATTAAATTAATTTTTCCCTT-AAAAATACTAAAACCCTAAACCCTAAAA
64 TTAACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAA-CCTAAACCCTAAAA
*
21359348 A-CACTAAACCACTAAACCCTAATCCTAAAA
128 ACCA-TAAACCACTAAACCCTAACCCTAAAA
21359378 AAAAGGGTCA
Statistics
Matches: 292, Mismatches: 31, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
170 26 0.09
171 133 0.46
172 26 0.09
173 44 0.15
174 63 0.22
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (171 bp):
AACCCTAAAAAACCCTAAACCCTAATTTAATTGATTTTTTAATTTCATAGTTAATTTAATTAATT
AACCCTCAACTCTAATTAAATTAATTTTTTCCTTAAAAAATACTAAAACCTAAACCCTAAAAACC
ATAAACCACTAAACCCTAACCCTAAAACAATAAAAAACCCT
Found at i:21359346 original size:24 final size:24
Alignment explanation
Indices: 21359319--21359369 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
21359309 ATTTTTCCCT
*
21359319 TAAAAATACTAAAACC-CTAAACCC
1 TAAAAACACT-AAACCACTAAACCC
21359343 TAAAAACACTAAACCACTAAACCC
1 TAAAAACACTAAACCACTAAACCC
21359367 TAA
1 TAA
21359370 TCCTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (24 bp):
TAAAAACACTAAACCACTAAACCC
Found at i:21359354 original size:16 final size:17
Alignment explanation
Indices: 21359329--21359363 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21359319 TAAAAATACT
*
21359329 AAAACCCTAAACC-CTA
1 AAAACACTAAACCACTA
21359345 AAAACACTAAACCACTA
1 AAAACACTAAACCACTA
21359362 AA
1 AA
21359364 CCCTAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.31, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAACACTAAACCACTA
Found at i:21360449 original size:22 final size:23
Alignment explanation
Indices: 21360410--21360491 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 23
21360400 CACTATTAAA
*
21360410 CAGAGAGTACTGAA-GTGCTATA-
1 CAGAGAGCACT-AATGTGCTATAG
21360432 CAGAGAGCA-TAGATGTGCTA-AG
1 CAGAGAGCACTA-ATGTGCTATAG
* *
21360454 CGGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCT-AT-AG
21360479 CAGAGAGCACTAA
1 CAGAGAGCACTAA
21360492 CGTACTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 3 0.06
22 29 0.59
23 3 0.06
25 13 0.27
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (23 bp):
CAGAGAGCACTAATGTGCTATAG
Found at i:21360489 original size:25 final size:25
Alignment explanation
Indices: 21360456--21360507 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
21360446 GTGCTAAGCG
* *
21360456 GAGAGCACTAATGTGCTAATAATCA
1 GAGAGCACTAACGTACTAATAATCA
21360481 GAGAGCACTAACGTACTAATAATCA
1 GAGAGCACTAACGTACTAATAATCA
21360506 GA
1 GA
21360508 TAGCGCGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (25 bp):
GAGAGCACTAACGTACTAATAATCA
Found at i:21361427 original size:169 final size:170
Alignment explanation
Indices: 21361132--21361438 Score: 413
Period size: 169 Copynumber: 1.8 Consensus size: 170
21361122 TATCTTTAAT
* * * *
21361132 CAAATCATGAACCTTTGGTTCAAGCTTTCAATCACATATCTCAATTTCAATTCACATTTCAATTC
1 CAAATCATGAACCTTAGGTTCAAGCTTTCAATCACACATCTCAATTTCAATTCACAATTCAACTC
* * *
21361197 ATAATTCCACTTTTTCATACTTTCAATAGTTCAATCGATCAAATTCATTCAATTTTCTCATTTCA
66 ATAATT-CACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTCA
*
21361262 TTTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
130 GTTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
* * *
21361303 CAAATTCATGAACCTTAGGTTTATGC-TTCAAATCTCACATCTCAA-TTCAATTCACAATTCAAC
1 CAAA-TCATGAACCTTAGGTTCAAGCTTTC-AATCACACATCTCAATTTCAATTCACAATTCAAC
* * * * * *
21361366 TCATAATT-TCTTTCTCATATTTTTAATAGTACGATCAATCAAATTTATTTAATTTTCTCATTTC
64 TCATAATTCACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTC
21361430 AGTTATTCA
129 AGTTATTCA
21361439 CCCTATTAAC
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
169 55 0.47
171 31 0.26
172 31 0.26
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (170 bp):
CAAATCATGAACCTTAGGTTCAAGCTTTCAATCACACATCTCAATTTCAATTCACAATTCAACTC
ATAATTCACTTTCTCATACTTTCAATAGTACAATCAATCAAATTCATTCAATTTTCTCATTTCAG
TTATTCAACTGATTTCAATATCAACAATTTGATATTTTAG
Found at i:21361606 original size:23 final size:23
Alignment explanation
Indices: 21361561--21361658 Score: 128
Period size: 23 Copynumber: 4.3 Consensus size: 23
21361551 AGTGCATGAA
* *
21361561 ACGACACACGAGGTGCCT--CAT
1 ACGACACACGAGGTGCTTGAAAT
*
21361582 ACGACACACGAGATGCTTGAAAT
1 ACGACACACGAGGTGCTTGAAAT
21361605 ACGACACACGAGGTGCTTGAAAT
1 ACGACACACGAGGTGCTTGAAAT
* *
21361628 ACGACACACGAGGTGCCTAAAAT
1 ACGACACACGAGGTGCTTGAAAT
*
21361651 ATGACACA
1 ACGACACA
21361659 TAAAGTGCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.24
23 52 0.76
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
ACGACACACGAGGTGCTTGAAAT
Found at i:21362028 original size:44 final size:44
Alignment explanation
Indices: 21361938--21362029 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
21361928 CCCATGTAAC
* * * *
21361938 AGTAGCAGTACGACACACATGGTGCCTCATCGACTAGATGTTGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACTAGAGGTCGA
**
21361982 AGTAACAGTACGACACTTATAGTGCCTCATCGACTCA-AGGTCGA
1 AGTAACAGTACGACACACATAGTGCCTCATCGACT-AGAGGTCGA
21362026 AGTA
1 AGTA
21362030 TCCTTGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (44 bp):
AGTAACAGTACGACACACATAGTGCCTCATCGACTAGAGGTCGA
Found at i:21368229 original size:25 final size:25
Alignment explanation
Indices: 21368201--21368270 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
21368191 TTTTTAATTC
21368201 TCTTAACAATAATTGTAAAAGAAAA
1 TCTTAACAATAATTGTAAAAGAAAA
* *
21368226 TCTTAAACTAA-AAAT-TAATAGAAAA
1 TCTT-AAC-AATAATTGTAAAAGAAAA
*
21368251 TCTATAAAAATAATTG-AAAA
1 TCT-TAACAATAATTGTAAAA
21368271 TTCATAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
24 2 0.06
25 24 0.69
26 7 0.20
27 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.29
Consensus pattern (25 bp):
TCTTAACAATAATTGTAAAAGAAAA
Found at i:21371053 original size:4 final size:4
Alignment explanation
Indices: 21371044--21371124 Score: 81
Period size: 4 Copynumber: 19.8 Consensus size: 4
21371034 GTAAGTTAAA
* *** * *
21371044 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G
*
21371094 TAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
21371125 TAGAAAAGGG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
4 58 0.92
5 4 0.06
6 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.25, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:21371953 original size:47 final size:47
Alignment explanation
Indices: 21371889--21371999 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
21371879 GACATTGAGT
*
21371889 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
21371936 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
21371983 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
21372000 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:21385115 original size:12 final size:13
Alignment explanation
Indices: 21385079--21385116 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
21385069 AAATATTTGA
21385079 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
21385092 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
21385106 CTTG-TCTTAAT
1 CTTGTTCTTAAT
21385117 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:21404015 original size:34 final size:34
Alignment explanation
Indices: 21403977--21404044 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
21403967 TTGAGGAAGT
21403977 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
1 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
21404011 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
1 ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
21404045 CAACACCGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.29
Consensus pattern (34 bp):
ATGTGCAGTGGTGTGGCCACCTTTGAGTCCCTCG
Found at i:21406527 original size:17 final size:17
Alignment explanation
Indices: 21406501--21406534 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21406491 TATATAATTG
*
21406501 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
21406518 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
21406535 TTAAGTGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:21407701 original size:24 final size:24
Alignment explanation
Indices: 21407669--21407824 Score: 201
Period size: 24 Copynumber: 6.5 Consensus size: 24
21407659 GAAATGACAT
21407669 TGGCACTATGTGTGCGGATTTAAA
1 TGGCACTATGTGTGCGGATTTAAA
*
21407693 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTAAA
*
21407717 TGGCACTATGTGTGCAGATTTAAA
1 TGGCACTATGTGTGCGGATTTAAA
* *
21407741 TAGCACTATGTGTGC-GATTTGAA
1 TGGCACTATGTGTGCGGATTTAAA
* **
21407764 TGGCACTATGTGTGCAGATTTGGA
1 TGGCACTATGTGTGCGGATTTAAA
*
21407788 TGGCACTACGTGTGCGGA-TTAGCAA
1 TGGCACTATGTGTGCGGATTTA--AA
21407813 -GGCACTATGTGT
1 TGGCACTATGTGT
21407825 ACGGGTTAGC
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
23 23 0.20
24 93 0.79
25 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTAAA
Found at i:21407725 original size:48 final size:48
Alignment explanation
Indices: 21407669--21407824 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
21407659 GAAATGACAT
*
21407669 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
*
21407717 TGGCACTATGTGTGCAGATTTAAATAGCACTATGTGTGC-GATTTGAA
1 TGGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
** * *
21407764 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA
1 TGGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTG-AA
21407813 -GGCACTATGTGT
1 TGGCACTATGTGT
21407825 ACGGGTTAGC
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 43 0.43
48 54 0.55
49 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (48 bp):
TGGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
Found at i:21407770 original size:71 final size:72
Alignment explanation
Indices: 21407671--21407807 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 72
21407661 AATGACATTG
* *
21407671 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGAT
1 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
21407736 TTAAATA
66 TTAAATA
* * *
21407743 GCACTATGTGTGC-GATTTGAATGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGAT
1 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
21407807 T
66 T
21407808 AGCAAGGCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
71 47 0.78
72 13 0.22
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (72 bp):
GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
TTAAATA
Found at i:21407818 original size:71 final size:72
Alignment explanation
Indices: 21407669--21407824 Score: 219
Period size: 71 Copynumber: 2.2 Consensus size: 72
21407659 GAAATGACAT
* *
21407669 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAG
1 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAG
21407734 ATTTAAA
66 ATTTAAA
* * * *
21407741 TAGCACTATGTGTGC-GATTTGAATGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGG
1 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAG
21407805 A-TTAGCAA
66 ATTTA--AA
21407813 -GGCACTATGTGT
1 TGGCACTATGTGT
21407825 ACGGGTTAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
70 3 0.04
71 56 0.75
72 16 0.21
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (72 bp):
TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAG
ATTTAAA
Found at i:21407833 original size:24 final size:24
Alignment explanation
Indices: 21407670--21407849 Score: 95
Period size: 24 Copynumber: 7.5 Consensus size: 24
21407660 AAATGACATT
*
21407670 GGCACTATGTGTGCGGATTTA--AA
1 GGCACTATGTGTACGGA-TTAGCAA
* *
21407693 TGGCACTATGTGTGCGGATTTG-AA
1 -GGCACTATGTGTACGGATTAGCAA
* *
21407717 TGGCACTATGTGTGCAGATTTA--AA
1 -GGCACTATGTGTACGGA-TTAGCAA
* * *
21407741 TAGCACTATGTGTGC-GATTTG-AA
1 -GGCACTATGTGTACGGATTAGCAA
* * * * *
21407764 TGGCACTATGTGTGCAGATTTGGAT
1 -GGCACTATGTGTACGGATTAGCAA
* *
21407789 GGCACTACGTGTGCGGATTAGCAA
1 GGCACTATGTGTACGGATTAGCAA
* *
21407813 GGCACTATGTGTACGGGTTAGCAT
1 GGCACTATGTGTACGGATTAGCAA
*
21407837 GGCAATATGTGTA
1 GGCACTATGTGTA
21407850 TGAATTTCCT
Statistics
Matches: 134, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
22 2 0.01
23 20 0.15
24 109 0.81
25 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (24 bp):
GGCACTATGTGTACGGATTAGCAA
Found at i:21407839 original size:48 final size:47
Alignment explanation
Indices: 21407669--21407848 Score: 202
Period size: 48 Copynumber: 3.8 Consensus size: 47
21407659 GAAATGACAT
21407669 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGG-TTTAAATGGCACTATGTGTGCGGATTTGAA
* *
21407717 TGGCACTATGTGTGCAGATTTAAATAGCACTATGTGTGC-GATTTGAA
1 TGGCACTATGTGTGC-GGTTTAAATGGCACTATGTGTGCGGATTTGAA
* ** * *
21407764 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA
1 TGGCACTATGTGTGC-GGTTTAAATGGCACTATGTGTGCGGATTTG-AA
* * * *
21407813 -GGCACTATGTGTACGGGTTAGCATGGCAATATGTGT
1 TGGCACTATGTGTGCGGTTTA-AATGGCACTATGTGT
21407849 ATGAATTTCC
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
47 46 0.40
48 65 0.57
49 3 0.03
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.32
Consensus pattern (47 bp):
TGGCACTATGTGTGCGGTTTAAATGGCACTATGTGTGCGGATTTGAA
Found at i:21407846 original size:95 final size:95
Alignment explanation
Indices: 21407669--21407848 Score: 229
Period size: 95 Copynumber: 1.9 Consensus size: 95
21407659 GAAATGACAT
* * * *
21407669 TGGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAG
1 TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAGAATGGCACTATGTGTACAG
* *
21407734 ATTTAAATAGCACTATGTGTGCGATTTGAA
66 AGTTAAATAGCAATATGTGTGCGATTTGAA
**
21407764 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA-GGCACTATGTGTAC-
1 TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAG-AATGGCACTATGTGTACA
* * *
21407827 GGGTTAGCATGGCAATATGTGT
65 GAGTTA-AATAGCAATATGTGT
21407849 ATGAATTTCC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
94 4 0.06
95 66 0.92
96 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.32
Consensus pattern (95 bp):
TGGCACTATGTGTGCAGATTTAAATGGCACTACGTGTGCGGATTAGAATGGCACTATGTGTACAG
AGTTAAATAGCAATATGTGTGCGATTTGAA
Found at i:21411448 original size:17 final size:18
Alignment explanation
Indices: 21411422--21411455 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21411412 TTTTTGTTTA
21411422 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
21411439 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
21411456 ATATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:21411464 original size:23 final size:23
Alignment explanation
Indices: 21411437--21411487 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
21411427 ATTAATAGCA
21411437 TTAATAATTTAATATGCATATAT
1 TTAATAATTTAATATGCATATAT
21411460 TTAATAATTTAATATGCATATAT
1 TTAATAATTTAATATGCATATAT
21411483 TTAAT
1 TTAAT
21411488 TATTAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAATAATTTAATATGCATATAT
Found at i:21416228 original size:19 final size:19
Alignment explanation
Indices: 21416197--21416242 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
21416187 GGTATAGAGC
*
21416197 ACACGCCCGTGTGCTAGGG
1 ACACGCCCATGTGCTAGGG
*
21416216 ACATGCCCATGTGCTAGGG
1 ACACGCCCATGTGCTAGGG
21416235 ACACGCCC
1 ACACGCCC
21416243 GTGTCCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (19 bp):
ACACGCCCATGTGCTAGGG
Found at i:21418270 original size:46 final size:46
Alignment explanation
Indices: 21418131--21418483 Score: 208
Period size: 46 Copynumber: 7.5 Consensus size: 46
21418121 AGGCTGACGC
* * * * **
21418131 CATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCCGTGTTGATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCT-CGAGCCGATG
* *
21418180 CCATGTCCTAGACATGGTCTTACACTGAC--ACATCTCGTAGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCG-AGCCGATG
* *
21418226 AATGTCCTAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGA-GCCGATG
* * * * *
21418272 CATGTCCCAGACAT-GTCTTACAATAGCTCT-CGTCTCAATACCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-TACATCTCGA-GCCGATG
* * *
21418318 CCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCT-TACAT-CTCG-AGCCGATG
* * * * * *
21418366 CATGTCCCAGAC-TTGCCTTACACTAGCTCT-CATCTCAATGTCGATAC
1 CATGTCCCAGACATGGTCTTACACTGGCT-TACATCTCGA-GCCGAT-G
* * * *
21418413 CATGTCTCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCAATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-TACAT-CTCG-AGCCGATG
21418460 CATGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
21418484 AGCACACACA
Statistics
Matches: 244, Mismatches: 44, Indels: 34
0.76 0.14 0.11
Matches are distributed among these distances:
44 12 0.05
45 17 0.07
46 95 0.39
47 51 0.21
48 43 0.18
49 2 0.01
50 24 0.10
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAGCCGATG
Found at i:21418338 original size:94 final size:94
Alignment explanation
Indices: 21418130--21418486 Score: 372
Period size: 94 Copynumber: 3.8 Consensus size: 94
21418120 GAGGCTGACG
* * * ** *
21418130 CCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCCGT-GTTGATGCCATGTCCTAGACA
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT--GTGGCCGATG-CATGTCCCAGACA
* * *
21418194 TGGTCTTACACT-G-ACACATCTC-GTAGCCGATGA
62 T-GTCTTACACTAGCTCTCATCTCAATA-CCGAT-A
* * *
21418227 --ATGTCCTAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGACATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGACATG
* * *
21418287 TCTTACAATAGCTCTCGTCTCAATACCGATG
64 TCTTACACTAGCTCTCATCTCAATACCGATA
* * *
21418318 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTCGATGCATGTCCCAGACTTGCC
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
**
21418383 TTACACTAGCTCTCATCTCAATGTCGATA
66 TTACACTAGCTCTCATCTCAATACCGATA
* *
21418412 CCATGTCTCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCAATGCATGTCCCAGACATGTC
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
21418477 TTACACTAGC
66 TTACACTAGC
21418487 ACACACACAT
Statistics
Matches: 219, Mismatches: 31, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
90 9 0.04
91 16 0.07
92 17 0.08
93 15 0.07
94 149 0.68
95 13 0.06
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (94 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTC
TTACACTAGCTCTCATCTCAATACCGATA
Found at i:21418386 original size:140 final size:140
Alignment explanation
Indices: 21418176--21418444 Score: 312
Period size: 140 Copynumber: 1.9 Consensus size: 140
21418166 TATCCGTGTT
* *
21418176 GATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCTAGACATG
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATG
* * * *
21418241 TCTTACACTGGCT-TACATCTCGAGGCCGAT-GCATGTCCCAGACAT-GTCTTACAATAGCTCTC
66 CCTTACACTAGCTCT-CATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTCTC
21418303 GTCTCAATACC
130 GTCTCAATACC
* * * * * *
21418314 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGGTCGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACATC-T--CGTAGCCGATGAATGTCCCAGAC
* * * * * *
21418378 TTGCCTTACACTAGCTCTCATCTCAATGTCGATACCATGTCTCAGACATGGTCTTACACTGGCTC
63 ATGCCTTACACTAGCTCTCATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTC
21418443 TC
128 TC
21418445 ATAATGTGGC
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
137 2 0.02
138 33 0.31
140 43 0.40
141 14 0.13
142 15 0.14
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (140 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACATCTCGTAGCCGATGAATGTCCCAGACATG
CCTTACACTAGCTCTCATCTCAAGGCCGATACCATGTCCCAGACATGGTCTTACAATAGCTCTCG
TCTCAATACC
Found at i:21427918 original size:7 final size:7
Alignment explanation
Indices: 21427906--21427940 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
21427896 ATAAAATAAT
21427906 ATTTTTA
1 ATTTTTA
21427913 ATTTTTA
1 ATTTTTA
21427920 ATTTTTA
1 ATTTTTA
21427927 ATTTTTA
1 ATTTTTA
21427934 ATTTTTA
1 ATTTTTA
21427941 TATATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTA
Found at i:21428480 original size:131 final size:130
Alignment explanation
Indices: 21428174--21428570 Score: 392
Period size: 131 Copynumber: 3.0 Consensus size: 130
21428164 TGAAATTCAT
* * * *
21428174 GTTCGATTCCTTTCTTACTCACATTTGCATTTTTTATTTCAT-ATGCTTTAAGCTTTTTAAAATT
1 GTTCGATTCTTTTC-TACTCACATTTGTATTTTTTATTTCATGTTGCTTTAA-CTTTTTTAAATT
* * *
21428238 TTAATT-A-ATTTTTTATCATATTAGTTCTTTGGTTAGATAGTTAGATAATTGTAATTACATATT
64 TTAATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTAC-----
21428301 TAAGTCTCAA
124 --A-TCTCAA
* * * * *
21428311 GGTT-GATTTCTCTCCTACTCATATGTGTATTTTTTATTTCATGTTACTTTAACTTTTTTAAATT
1 -GTTCGA-TTCTTTTCTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAACTTTTTTAAATT
* * * *
21428375 TTGAATTAATATTTTTTAACATTTTAGTT-TTTCCTTAGATGGTTAAATAGTTGTAATTACATCT
64 TT-AATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTACATCT
21428439 CAA
128 CAA
* * * * *
21428442 GTTCGATTCTTTTACTAATCACATTTGTATTTTTTATTTTATGTTGCTTTAATTATTTTTTTATT
1 GTTCGATTCTTTT-CTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAA--CTTTTTTAAAT
* *
21428507 TTTAATTAATA-TTTTTAACATATTAATTCATTTCGTTAGATGGTTAGATAATTGTGATTACATC
63 TTTAATTAATATTTTTTAACATATTAGTTC-TTTCGTTAGATGGTTAGATAATTGTAATTACATC
21428571 CTTAAGACTA
Statistics
Matches: 216, Mismatches: 32, Indels: 27
0.79 0.12 0.10
Matches are distributed among these distances:
130 8 0.04
131 56 0.26
132 9 0.04
133 41 0.19
137 39 0.18
138 19 0.09
139 27 0.12
140 17 0.08
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.53
Consensus pattern (130 bp):
GTTCGATTCTTTTCTACTCACATTTGTATTTTTTATTTCATGTTGCTTTAACTTTTTTAAATTTT
AATTAATATTTTTTAACATATTAGTTCTTTCGTTAGATGGTTAGATAATTGTAATTACATCTCAA
Found at i:21428683 original size:23 final size:22
Alignment explanation
Indices: 21428655--21428714 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
21428645 TTTATTTTTA
21428655 ATTATTTTTATAAGCATATTATT
1 ATTATTTTTATAAGCA-ATTATT
**
21428678 ATTATTTTATATTTGCAATTATT
1 ATTATTTT-TATAAGCAATTATT
*
21428701 ATTTAATTTTATAA
1 A-TTATTTTTATAA
21428715 ATAAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (22 bp):
ATTATTTTTATAAGCAATTATT
Found at i:21435864 original size:31 final size:31
Alignment explanation
Indices: 21435796--21435865 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
21435786 TTAATCAATA
*
21435796 ATTGTTTTGTAATTTTTTCATAAAGTTAGTG
1 ATTGTTTTATAATTTTTTCATAAAGTTAGTG
* *
21435827 ACTGTTTTATTATTTTTT-A-AAAGTTAAAGTG
1 ATTGTTTTATAATTTTTTCATAAAGTT--AGTG
21435858 ATTGTTTT
1 ATTGTTTT
21435866 GTTAGCTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.18
30 1 0.03
31 26 0.79
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (31 bp):
ATTGTTTTATAATTTTTTCATAAAGTTAGTG
Found at i:21446068 original size:12 final size:12
Alignment explanation
Indices: 21446051--21446099 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
21446041 TTTTTTAATA
21446051 AAATTTAATATT
1 AAATTTAATATT
*
21446063 AAATTTAAT-CT
1 AAATTTAATATT
21446074 AATATTT-ATATT
1 AA-ATTTAATATT
21446086 -AATTTAATATT
1 AAATTTAATATT
21446097 AAA
1 AAA
21446100 GTGATTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 11 0.35
12 16 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTTAATATT
Found at i:21446078 original size:17 final size:18
Alignment explanation
Indices: 21446056--21446099 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
21446046 TAATAAAATT
21446056 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
21446073 TAATATT-TATATTAATT
1 TAATATTAAATATTAATC
21446090 TAATATTAAA
1 TAATATTAAA
21446100 GTGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:21457921 original size:8 final size:9
Alignment explanation
Indices: 21457898--21457923 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21457888 AGGAGTTAAG
21457898 ACAAAAATA
1 ACAAAAATA
21457907 ACAAAAATA
1 ACAAAAATA
21457916 ACAAAAAT
1 ACAAAAAT
21457924 TCAAAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (9 bp):
ACAAAAATA
Found at i:21461199 original size:22 final size:21
Alignment explanation
Indices: 21461148--21461200 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
21461138 AAAGAGTTTT
21461148 CAATCAAAAAAAGTAAAAAAA
1 CAATCAAAAAAAGTAAAAAAA
21461169 -AAGTCCAAATAAACAG-AAAAAAA
1 CAA-T-CAAA-AAA-AGTAAAAAAA
21461192 CAATCAAAA
1 CAATCAAAA
21461201 GCAATCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 8 0.30
23 11 0.41
24 4 0.15
ACGTcount: A:0.72, C:0.13, G:0.06, T:0.09
Consensus pattern (21 bp):
CAATCAAAAAAAGTAAAAAAA
Found at i:21461295 original size:25 final size:25
Alignment explanation
Indices: 21461261--21461319 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
21461251 GGCAAACAAA
**
21461261 ATCACAACAC-AGATCGGAGGAATTT
1 ATCA-AACACTAGATCAAAGGAATTT
*
21461286 ATCATAACACTGGATCAAAGGAATTT
1 ATCA-AACACTAGATCAAAGGAATTT
21461312 ATCAAACA
1 ATCAAACA
21461320 AAATCCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (25 bp):
ATCAAACACTAGATCAAAGGAATTT
Found at i:21465418 original size:21 final size:20
Alignment explanation
Indices: 21465391--21465430 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21465381 CTTATGAAGC
21465391 CAAAAAAATTGTTTGGGGAA
1 CAAAAAAATTGTTTGGGGAA
21465411 CAAAAAAATTGTTTGGGGAA
1 CAAAAAAATTGTTTGGGGAA
21465431 AAGATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (20 bp):
CAAAAAAATTGTTTGGGGAA
Found at i:21477392 original size:33 final size:33
Alignment explanation
Indices: 21477354--21477452 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
21477344 AACTGAGTGG
*
21477354 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
21477387 GAGTGTTTTGCTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
*
21477420 GGGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
21477453 CAAGAAGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.17, C:0.10, G:0.41, T:0.31
Consensus pattern (33 bp):
GAGTGTTTTGTTGCTGGACAGGAGCTGGAATGT
Found at i:21479796 original size:189 final size:189
Alignment explanation
Indices: 21479476--21479853 Score: 729
Period size: 189 Copynumber: 2.0 Consensus size: 189
21479466 GTAGATGAAA
** *
21479476 TCTTAGTCTTTTTTTCATAGATTTGAGCAGCATCTCGGACTTTAGAATAAGTCTGTTTCACAGCT
1 TCTTAGTCTTGATTTCATAGATTTGAGCAGCATCTCGAACTTTAGAATAAGTCTGTTTCACAGCT
21479541 TCCCATATTTCTTTGGATGTGTTAAGAAACATGCATGTATCACTGATTTATGGCATCATAGAGTT
66 TCCCATATTTCTTTGGATGTGTTAAGAAACATGCATGTATCACTGATTTATGGCATCATAGAGTT
21479606 CCATAACCAAGACATTACCATAGAGTCTTGTTCATCCCAAGCATCAAAATTAGGATCTC
131 CCATAACCAAGACATTACCATAGAGTCTTGTTCATCCCAAGCATCAAAATTAGGATCTC
21479665 TCTTAGTCTTGATTTCATAGATTTGAGCAGCATCTCGAACTTTAGAATAAGTCTGTTTCACAGCT
1 TCTTAGTCTTGATTTCATAGATTTGAGCAGCATCTCGAACTTTAGAATAAGTCTGTTTCACAGCT
21479730 TCCCATATTTCTTTGGATGTGTTAAGAAACATGCATGTATCACTGATTTATGGCATCATAGAGTT
66 TCCCATATTTCTTTGGATGTGTTAAGAAACATGCATGTATCACTGATTTATGGCATCATAGAGTT
21479795 CCATAACCAAGACATTACCATAGAGTCTTGTTCATCCCAAGCATCAAAATTAGGATCTC
131 CCATAACCAAGACATTACCATAGAGTCTTGTTCATCCCAAGCATCAAAATTAGGATCTC
21479854 CTTCTTTAGG
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 186 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (189 bp):
TCTTAGTCTTGATTTCATAGATTTGAGCAGCATCTCGAACTTTAGAATAAGTCTGTTTCACAGCT
TCCCATATTTCTTTGGATGTGTTAAGAAACATGCATGTATCACTGATTTATGGCATCATAGAGTT
CCATAACCAAGACATTACCATAGAGTCTTGTTCATCCCAAGCATCAAAATTAGGATCTC
Found at i:21483158 original size:43 final size:43
Alignment explanation
Indices: 21483076--21483177 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 43
21483066 CAATGTGTTT
*
21483076 GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTGTAGATG-C
1 GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTATAGATGTC
* *
21483118 GCAAAACTGAGATGATAATAAGAACAA-GAAAACAC-ATAGATGTTT
1 GCAAAACTGAGAAGAT-ATAAGAA-AAGGAAAAC-CTATAGATG-TC
21483163 GCAAAACTGAGAAGA
1 GCAAAACTGAGAAGA
21483178 ACATATTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 15 0.29
43 19 0.37
44 3 0.06
45 14 0.27
ACGTcount: A:0.51, C:0.12, G:0.22, T:0.16
Consensus pattern (43 bp):
GCAAAACTGAGAAGATATAAGAAAAGGAAAACCTATAGATGTC
Found at i:21484285 original size:94 final size:94
Alignment explanation
Indices: 21484124--21484311 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
21484114 ACATCAAGAA
*
21484124 TGTTTCTCATAGTAATGATCTAGAGGAGCCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
1 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
21484189 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
66 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
21484218 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
1 TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
21484283 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
66 GCTATAAGGTGGGCTTTTTTTTTTTTTTT
21484312 GTAGTTACTG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.44
Consensus pattern (94 bp):
TGTTTCTCATAGTAATGATCTAGAGGAACCAATAAGCATTACTGGTCTTGAGACATTTTCCTTGA
GCTATAAGGTGGGCTTTTTTTTTTTTTTT
Found at i:21487539 original size:2 final size:2
Alignment explanation
Indices: 21487532--21487561 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21487522 AAAATTACTT
21487532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21487562 AAGCACCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21487896 original size:28 final size:28
Alignment explanation
Indices: 21487857--21487951 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 28
21487847 TTTATTTCTT
21487857 TTAAAATATTATAAATTTGTAAAAAATTA
1 TTAAAA-ATTATAAATTTGTAAAAAATTA
* *
21487886 TTAAAAATTATAAA-ATGTTAAATAAAAT-
1 TTAAAAATTATAAATTTG-TAAA-AAATTA
* * * * *
21487914 TTAAAAATAAAAAATTTATTAAAAATCA
1 TTAAAAATTATAAATTTGTAAAAAATTA
21487942 TTCAAAAATT
1 TT-AAAAATT
21487952 TAATTTTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
27 5 0.10
28 29 0.57
29 17 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TTAAAAATTATAAATTTGTAAAAAATTA
Found at i:21488482 original size:31 final size:31
Alignment explanation
Indices: 21488447--21488509 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
21488437 TTTAAAACTT
21488447 TATATAATTTAAAAAAATCTTCTTGAATGAA
1 TATATAATTTAAAAAAATCTTCTTGAATGAA
21488478 TATATAATTTAAAAAAATCTTCTTGAATGAA
1 TATATAATTTAAAAAAATCTTCTTGAATGAA
21488509 T
1 T
21488510 TTGGACATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (31 bp):
TATATAATTTAAAAAAATCTTCTTGAATGAA
Found at i:21488959 original size:27 final size:27
Alignment explanation
Indices: 21488929--21489004 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
21488919 GACTAATCGA
* *
21488929 GCCTTTCTCTGAGGCGCAAATGATTGT
1 GCCTATCTCAGAGGCGCAAATGATTGT
*
21488956 GCCTATCTCAGAGGCGCAAATGGTTGT
1 GCCTATCTCAGAGGCGCAAATGATTGT
* *
21488983 GCCTATCCCAAAGGCGCAAATG
1 GCCTATCTCAGAGGCGCAAATG
21489005 GTGGGGCCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (27 bp):
GCCTATCTCAGAGGCGCAAATGATTGT
Found at i:21494465 original size:31 final size:31
Alignment explanation
Indices: 21494427--21494485 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
21494417 ATTAAATATT
*
21494427 TTTAATACAGGTAACACAATATGATTGGCTC
1 TTTAATACACGTAACACAATATGATTGGCTC
** *
21494458 TTTAATACACGTGGCATAATATGATTGG
1 TTTAATACACGTAACACAATATGATTGG
21494486 TTGACATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (31 bp):
TTTAATACACGTAACACAATATGATTGGCTC
Found at i:21495413 original size:29 final size:29
Alignment explanation
Indices: 21495369--21495425 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
21495359 TGAGACAACA
** *
21495369 AAAATAAAAGGGAAAGAAAGGAAAGAAAG
1 AAAATAAAAGAAAAAGAAAGAAAAGAAAG
*
21495398 AAAATAAAAGAAAAAGAGAGAAAAGAAA
1 AAAATAAAAGAAAAAGAAAGAAAAGAAA
21495426 ATAAAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (29 bp):
AAAATAAAAGAAAAAGAAAGAAAAGAAAG
Found at i:21495419 original size:20 final size:20
Alignment explanation
Indices: 21495390--21495431 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21495380 GAAAGAAAGG
*
21495390 AAAGAAAGAAAATAAAAGAA
1 AAAGAAAGAAAAGAAAAGAA
* *
21495410 AAAGAGAGAAAAGAAAATAA
1 AAAGAAAGAAAAGAAAAGAA
21495430 AA
1 AA
21495432 GTTTTCATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAGAAAGAAAAGAAAAGAA
Found at i:21499204 original size:45 final size:44
Alignment explanation
Indices: 21499122--21499251 Score: 131
Period size: 45 Copynumber: 2.9 Consensus size: 44
21499112 AGACATCATG
*
21499122 ATAAAGATGAGTAAGACCATAACTGAAAGATGTTATGGAATCACC
1 ATAAAGATGAGTAAGACCATAACTGAAAGATGCTATGGAATCA-C
* * *
21499167 ATAAAGATCAGTAAGACCATAGAC-GAAACG-TGCTATGGCATCAT
1 ATAAAGATGAGTAAGACCATA-ACTGAAA-GATGCTATGGAATCAC
** **
21499211 ATATAA-ATGAGTAAGACCATGGCTGAAAGACACTATGGAAT
1 ATA-AAGATGAGTAAGACCATAACTGAAAGATGCTATGGAAT
21499252 TATGGTAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
43 2 0.03
44 28 0.40
45 37 0.53
46 3 0.04
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.22
Consensus pattern (44 bp):
ATAAAGATGAGTAAGACCATAACTGAAAGATGCTATGGAATCAC
Found at i:21499412 original size:27 final size:27
Alignment explanation
Indices: 21499382--21499452 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
21499372 ACAGTTCGCA
*
21499382 GGGACATTAAACACGGGACAGTCCGAT
1 GGGACACTAAACACGGGACAGTCCGAT
** *
21499409 GGGACACTAAACATC-GGATGGTCCGCT
1 GGGACACTAAACA-CGGGACAGTCCGAT
*
21499436 GGGACAGTAAACACGGG
1 GGGACACTAAACACGGG
21499453 GTTATATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.03
27 35 0.95
28 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.14
Consensus pattern (27 bp):
GGGACACTAAACACGGGACAGTCCGAT
Found at i:21503221 original size:38 final size:38
Alignment explanation
Indices: 21503179--21503252 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
21503169 CCAGTTGACC
* *
21503179 CCTTAGTAGGGGATAAAATACTTGAAAATGAGTATACT
1 CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATACT
*
21503217 CCTTAGTTGGGGACAAAATACTTGAAAAGGAGTATA
1 CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATA
21503253 TTTTACACGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (38 bp):
CCTTAGTAGGGGACAAAATACTTGAAAAGGAGTATACT
Found at i:21504138 original size:45 final size:43
Alignment explanation
Indices: 21504071--21504291 Score: 178
Period size: 45 Copynumber: 4.9 Consensus size: 43
21504061 AGTTGTAAGC
*
21504071 ATAAAATGAGTAAGACCATAGCTAAATGATTCTATGTCATCATG
1 ATAAAATGAGTAAGACCATAGCTAAA-GATTCTATGACATCATG
* *
21504115 ATAAAGATGAGTAAGATCGTAGCTAAAAGATGT-TATGACATCACT-
1 ATAAA-ATGAGTAAGACCATAGCT-AAAGAT-TCTATGACATCA-TG
* * *
21504160 ATAAAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATG
1 AT-AAAATGAGTAAGACCATAGCT-AAAGATTCTATGACATCATG
* * * *
21504205 ATATAAATGAATAAGACCATGGCTGAAAGATGCCATTG-CATCATG
1 ATA-AAATGAGTAAGACCATAGCT-AAAGATTCTA-TGACATCATG
* * * **
21504250 GTAAACAAGACTAAGACCATAGCTGAAAGACACTATGACATC
1 ATAAA-ATGAGTAAGACCATAGCT-AAAGATTCTATGACATC
21504292 CTAGTAGTCT
Statistics
Matches: 146, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
44 11 0.08
45 125 0.86
46 10 0.07
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (43 bp):
ATAAAATGAGTAAGACCATAGCTAAAGATTCTATGACATCATG
Found at i:21504247 original size:90 final size:90
Alignment explanation
Indices: 21504073--21504279 Score: 226
Period size: 90 Copynumber: 2.3 Consensus size: 90
21504063 TTGTAAGCAT
* * * * *
21504073 AAAATGAGTAAGACCATAGCT-AAATGATTCTATGTCATCATGATAAAGATGAGTAAGATCGTAG
1 AAAATGAGTAAGACCATAGCTGAAA-GATGCTATGGCATCATGATAAAGATGAATAAGACCATAG
**
21504137 CTAAAAGATGTTATGACATCACT-ATA
65 CTAAAAGATGCCATGACATCA-TGATA
* *
21504163 AAAATGAGTAAAACCATAGCTGAAAGATGCTATGGCATCATGATATAA-ATGAATAAGACCATGG
1 AAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATA-AAGATGAATAAGACCATAG
* *
21504227 CTGAAAGATGCCATTG-CATCATGGTA
65 CTAAAAGATGCCA-TGACATCATGATA
*
21504253 AACAA-GACTAAGACCATAGCTGAAAGA
1 AA-AATGAGTAAGACCATAGCTGAAAGA
21504280 CACTATGACA
Statistics
Matches: 99, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
89 1 0.01
90 89 0.90
91 9 0.09
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (90 bp):
AAAATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATAAAGATGAATAAGACCATAGC
TAAAAGATGCCATGACATCATGATA
Found at i:21506666 original size:18 final size:18
Alignment explanation
Indices: 21506638--21506684 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21506628 AATTGATCGG
* *
21506638 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTAAA
*
21506656 TTATTCGGTAACAGTAAA
1 TTATTCAGTAACAGTAAA
21506674 TTATTCAGTAA
1 TTATTCAGTAA
21506685 TAATCAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAGTAAA
Found at i:21508970 original size:68 final size:67
Alignment explanation
Indices: 21508898--21509047 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
21508888 CATCATGTGT
* * * *
21508898 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
21508960 ATGTAG
62 ATGTAG
** * *
21508966 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
21509031 AG
66 AG
21509033 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
21509048 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:21509003 original size:64 final size:64
Alignment explanation
Indices: 21508922--21509105 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
21508912 AGACATTATG
* * *
21508922 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
21508986 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGAGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
21509051 AA
63 AA
* * * *
21509053 ACTG--GCTAGGTCACATGAGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
21509106 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:21511803 original size:27 final size:27
Alignment explanation
Indices: 21511755--21511859 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
21511745 GCGAGGCTGC
* *
21511755 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
21511782 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
21511808 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
21511835 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
21511860 GACGCTTCCT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 8 0.11
27 60 0.85
28 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:21513490 original size:26 final size:26
Alignment explanation
Indices: 21513459--21513592 Score: 223
Period size: 26 Copynumber: 5.2 Consensus size: 26
21513449 TGAAATGCCC
* *
21513459 ATCATGAAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
21513485 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
21513511 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
21513537 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21513563 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
21513589 ATCA
1 ATCA
21513593 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 100 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:21518940 original size:27 final size:27
Alignment explanation
Indices: 21518896--21518974 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
21518886 GTCACTAGAT
21518896 ACAGATAT-TGTGGCAGAGCCACCAGA
1 ACAGATATATGTGGCAGAGCCACCAGA
*
21518922 ACAGATATATGTGGTAGAGCCACCA-A
1 ACAGATATATGTGGCAGAGCCACCAGA
*
21518948 ATCAGATA-ATTGTGGCATAGCCACCAG
1 A-CAGATATA-TGTGGCAGAGCCACCAG
21518975 GACGCTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 11 0.24
27 35 0.76
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
ACAGATATATGTGGCAGAGCCACCAGA
Found at i:21520605 original size:26 final size:26
Alignment explanation
Indices: 21520576--21520705 Score: 215
Period size: 26 Copynumber: 5.0 Consensus size: 26
21520566 ATGCCCATCG
*
21520576 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
21520602 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* * *
21520628 TGGAATATATACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
*
21520654 TGAAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
21520680 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
21520706 ATTTGTATCA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 95 1.00
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Found at i:21522501 original size:15 final size:18
Alignment explanation
Indices: 21522473--21522514 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
21522463 TCATCCTTTC
21522473 TTTCTTTATCTATT-CTT
1 TTTCTTTATCTATTCCTT
21522490 TTTCTTT-T-TATTCCTT
1 TTTCTTTATCTATTCCTT
*
21522506 TTACTTTAT
1 TTTCTTTAT
21522515 ATATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTATCTATTCCTT
Found at i:21525938 original size:38 final size:38
Alignment explanation
Indices: 21525896--21525972 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
21525886 GGTTTTAGGT
*
21525896 ACAAGAATGGCTCTCATACTTTCTTATAATCCATTGGG
1 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
21525934 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
1 ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
21525972 A
1 A
21525973 TCCCAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (38 bp):
ACAAGAATGGCTCCCATACTTTCTTATAATCCATTGGG
Found at i:21531112 original size:62 final size:62
Alignment explanation
Indices: 21531012--21531137 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
21531002 TAGATTCTTA
21531012 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
1 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
* * *
21531074 GTATCGCTCAGCAAGGTTCCTTGTGGTCTATTATGAAGCTCCGTAGTTAACTGACCCATTTG
1 GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
21531136 GT
1 GT
21531138 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (62 bp):
GTATCGCTCAGCAAGGTTCCTTGTGGTATATTACGAAGCTCCGTAGCTAACTGACCCATTTG
Found at i:21534301 original size:131 final size:131
Alignment explanation
Indices: 21534173--21534429 Score: 284
Period size: 131 Copynumber: 2.0 Consensus size: 131
21534163 AGTTTTTAAT
* *
21534173 AAACATGAGTGAAAACCTAAAGGAATATTCGATTGTTTTGAGCAAACG-AGAAATCACAACCCAG
1 AAACATGAGTGAAAACCTAAAGGAATATTCGATTATTTTGAGCAAACGCA-AAATCACAACCCAA
* * * *
21534237 CACGGTAGGGCATGATTCC-CGAATTGTCAAACGCCAAATATTGCCTTCGTTTTAAATGAATTTT
65 CACGGTAGAGCACGATTCCACGAATTGTCAAACACCAAATATCGCCTTCGTTTTAAAT-AATTTT
21534301 AGA
129 AGA
* *** * * * * * **
21534304 AGACATGAGTGAAATTTTGAAGGGATATTTGATTATTTTGAGTAAGCGCAAAATTGCAACCCAAC
1 AAACATGAGTGAAAACCTAAAGGAATATTCGATTATTTTGAGCAAACGCAAAATCACAACCCAAC
* * * * *
21534369 ACGTTAGAGCACGATTCCACGAATTTTCAAATATCGAATATCGCCTTCGTTTTAAATAATT
66 ACGGTAGAGCACGATTCCACGAATTGTCAAACACCAAATATCGCCTTCGTTTTAAATAATT
21534430 GTGAAACTAG
Statistics
Matches: 102, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
131 69 0.68
132 33 0.32
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (131 bp):
AAACATGAGTGAAAACCTAAAGGAATATTCGATTATTTTGAGCAAACGCAAAATCACAACCCAAC
ACGGTAGAGCACGATTCCACGAATTGTCAAACACCAAATATCGCCTTCGTTTTAAATAATTTTAG
A
Found at i:21535212 original size:23 final size:23
Alignment explanation
Indices: 21535168--21535212 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21535158 AAGAGACATT
*
21535168 CAAAAATAATAATTTTATAATTA
1 CAAAAATAATAATTTTAAAATTA
*
21535191 CAAAAATGA-AATTTCTAAAATT
1 CAAAAATAATAATTT-TAAAATT
21535213 GTTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CAAAAATAATAATTTTAAAATTA
Found at i:21549700 original size:23 final size:23
Alignment explanation
Indices: 21549656--21549700 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21549646 AGGAGACATT
*
21549656 CAAAAATAATAATTTTATAATTA
1 CAAAAATAATAATTTTAAAATTA
*
21549679 CAAAAATGA-AATTTCTAAAATT
1 CAAAAATAATAATTT-TAAAATT
21549701 GTTTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
CAAAAATAATAATTTTAAAATTA
Found at i:21555076 original size:30 final size:29
Alignment explanation
Indices: 21555042--21555101 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
21555032 TCCTTAACTC
21555042 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTT-GAAAAATTACAATTTTGCCCCT
* * * *
21555072 AAACTTTTAATATTTACACTTTTGCCCCT
1 AAACTTTGAAAAATTACAATTTTGCCCCT
21555101 A
1 A
21555102 GCTCGGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (29 bp):
AAACTTTGAAAAATTACAATTTTGCCCCT
Found at i:21560590 original size:40 final size:41
Alignment explanation
Indices: 21560532--21560613 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
21560522 GCATGACTGT
21560532 TACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGA
1 TACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGA
21560573 TACTG-TACTGTGATGGGCTAAGGCCCTACTGCATATTTGA
1 TACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGA
21560613 T
1 T
21560614 TGTGCACTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (41 bp):
TACTGATACTGTGATGGGCTAAGGCCCTACTGCATATTTGA
Found at i:21561069 original size:23 final size:23
Alignment explanation
Indices: 21561025--21561069 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
21561015 TTATATTAAA
***
21561025 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAACAAATATG
*
21561048 ATTAAAAATAAAAAACATATAT
1 ATTAAAAATAAAAAACAAATAT
21561070 TTAATATATA
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:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
ATTAAAAATAAAAAACAAATATG
Found at i:21567630 original size:42 final size:42
Alignment explanation
Indices: 21567567--21567667 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
21567557 TATGGATGCC
* *
21567567 ACACGGGTGTGTGGTCGCCCGTGTGGTAGGCCGTGTGCCCTA
1 ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
* *
21567609 ACACGGGCGTGTGGTCACCCGTGTTGTAGGCTGTGTGCCCTA
1 ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
* *
21567651 ACACGAGCGTGTAGTCA
1 ACACGGGCGTGTGGTCA
21567668 ACGAGACTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.14, C:0.26, G:0.37, T:0.24
Consensus pattern (42 bp):
ACACGGGCGTGTGGTCACCCGTGTGGTAGGCCGTGTGCCCTA
Found at i:21568336 original size:34 final size:35
Alignment explanation
Indices: 21568293--21568362 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
21568283 ACTGATGATA
21568293 TGATAGGCTAAGGCCCTAATGCATA-CTGATACTG
1 TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
* * * *
21568327 TGATGGGCTAAGGCTCTACTGCATATTTGATACTG
1 TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
21568362 T
1 T
21568363 ATTGAGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (35 bp):
TGATAGGCTAAGGCCCTAATGCATATCTGATACTG
Found at i:21568864 original size:18 final size:18
Alignment explanation
Indices: 21568841--21568882 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
21568831 TCGACTAAAT
*
21568841 AAATAAAATGATTTTTGG
1 AAATAAAACGATTTTTGG
*
21568859 AAATAATACGATTTTTGG
1 AAATAAAACGATTTTTGG
21568877 AAATAA
1 AAATAA
21568883 TAAGATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (18 bp):
AAATAAAACGATTTTTGG
Found at i:21568883 original size:18 final size:18
Alignment explanation
Indices: 21568850--21568884 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21568840 TAAATAAAAT
21568850 GATTTTTGGAAATAATAC
1 GATTTTTGGAAATAATAC
21568868 GATTTTTGGAAATAATA
1 GATTTTTGGAAATAATA
21568885 AGATCTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (18 bp):
GATTTTTGGAAATAATAC
Found at i:21576516 original size:43 final size:43
Alignment explanation
Indices: 21576468--21576574 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
21576458 GATAAACGGA
**
21576468 TCTCCAAAAACAACCAATATAATGTGTAGCATAAAGCTATCAC
1 TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
* *
21576511 TCTCCAAGCACAGCTAATATAATGTGTAGCATAAAGCTATCAC
1 TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
* *
21576554 ACTCTAAGCACAACCAATATA
1 TCTCCAAGCACAACCAATATA
21576575 CCCTCCAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23
Consensus pattern (43 bp):
TCTCCAAGCACAACCAATATAATGTGTAGCATAAAGCTATCAC
Found at i:21576616 original size:65 final size:65
Alignment explanation
Indices: 21576512--21576660 Score: 253
Period size: 65 Copynumber: 2.3 Consensus size: 65
21576502 AGCTATCACT
* * **
21576512 CTCCAAGCACAGCTAATATAATGTGTAGCATAAAGCTATCACACTCTAAGCACAACCAATATACC
1 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCTAAGCACAACCAATATACC
*
21576577 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACCCTCTAAGCACAACCAATATACC
1 CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCTAAGCACAACCAATATACC
21576642 CTCCAAACACAACTAATAT
1 CTCCAAACACAACTAATAT
21576661 CTCCTCCACA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 79 1.00
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.21
Consensus pattern (65 bp):
CTCCAAACACAACTAATATAACATGTAGCATAAAGCTATCACACTCTAAGCACAACCAATATACC
Found at i:21576642 original size:22 final size:22
Alignment explanation
Indices: 21576555--21576660 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
21576545 AGCTATCACA
21576555 CTCTAAGCACAACCAATATACC
1 CTCTAAGCACAACCAATATACC
* * * *
21576577 CTCCAAACACAACTAATATAAC
1 CTCTAAGCACAACCAATATACC
* * * *
21576599 ATGT-AGCATAA--AGCTATCACC
1 CTCTAAGCACAACCA-ATAT-ACC
21576620 CTCTAAGCACAACCAATATACC
1 CTCTAAGCACAACCAATATACC
* * *
21576642 CTCCAAACACAACTAATAT
1 CTCTAAGCACAACCAATAT
21576661 CTCCTCCACA
Statistics
Matches: 61, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 9 0.15
22 44 0.72
23 3 0.05
24 1 0.02
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.20
Consensus pattern (22 bp):
CTCTAAGCACAACCAATATACC
Found at i:21576666 original size:22 final size:22
Alignment explanation
Indices: 21576617--21576678 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
21576607 TAAAGCTATC
* *
21576617 ACCCTCTAAGCACAACCAATAT
1 ACCCTCCAAACACAACCAATAT
*
21576639 ACCCTCCAAACACAACTAATAT
1 ACCCTCCAAACACAACCAATAT
*
21576661 -CTCCTCCACACACAACCA
1 AC-CCTCCAAACACAACCA
21576679 TAAAGTGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.16
Consensus pattern (22 bp):
ACCCTCCAAACACAACCAATAT
Found at i:21576995 original size:19 final size:19
Alignment explanation
Indices: 21576945--21576995 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
21576935 TGACATTTTC
*
21576945 ACATCACATATAATCATAT
1 ACATCACATATAAACATAT
* **
21576964 -CAACTTATCATAAACATAT
1 ACATCACAT-ATAAACATAT
21576983 ACATCACATATAA
1 ACATCACATATAA
21576996 GCTTTATTTG
Statistics
Matches: 23, Mismatches: 7, Indels: 4
0.68 0.21 0.12
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (19 bp):
ACATCACATATAAACATAT
Found at i:21579561 original size:127 final size:127
Alignment explanation
Indices: 21579330--21579592 Score: 472
Period size: 127 Copynumber: 2.1 Consensus size: 127
21579320 TTCCTCCCTT
* *
21579330 TTTCAAATCAGTCCTTTTGTTTAATTAAAATATATATTCTTAATTATTTTCAAATTGGGTTCCGT
1 TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
21579395 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
66 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
* *
21579457 TTTCTAATCAGTCCTTTTGTTTAATTAAGACATATATTCTTAATTATTTTCAAATTGGGTTTCGT
1 TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
* *
21579522 TTTTAAAATCCATTTTAAACAAATGAATTCCCGAACACTTAATTTTAATTTTCCCTATTAAA
66 TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
21579584 TTTCTAATC
1 TTTCTAATC
21579593 CCAAATATTA
Statistics
Matches: 130, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 130 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (127 bp):
TTTCTAATCAGTCCTTTTGTTTAATTAAAACATATATTCTTAATTATTTTCAAATTGGGTTCCGT
TTTTAAAATCCATTTTAAACAAATAAATTCCCGAACACTTAATTTTAATTTCCCCTATTAAA
Found at i:21582846 original size:22 final size:22
Alignment explanation
Indices: 21582821--21582864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21582811 TAGTCATATA
21582821 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
21582843 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
21582865 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:21582900 original size:13 final size:14
Alignment explanation
Indices: 21582884--21582925 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
21582874 TTTCAATTTT
21582884 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
21582897 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
21582912 ATTTTACATAATAT
1 ATTTTA-ATAATAT
21582926 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 9 0.38
16 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:21583519 original size:15 final size:14
Alignment explanation
Indices: 21583474--21583519 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
21583464 CTAGAAAAAT
21583474 AAATTATTTTCTA-A
1 AAATTATTTT-TAGA
*
21583488 AAATTATTTTTCGA
1 AAATTATTTTTAGA
21583502 AAATTATTTTTAGTA
1 AAATTATTTTTAG-A
21583517 AAA
1 AAA
21583520 CAAATGGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 1 0.04
14 23 0.82
15 4 0.14
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (14 bp):
AAATTATTTTTAGA
Found at i:21584303 original size:7 final size:7
Alignment explanation
Indices: 21584291--21584344 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
21584281 GATCAGTTTT
21584291 TTTTTAA
1 TTTTTAA
21584298 TTTTTAA
1 TTTTTAA
21584305 -TTTTAA
1 TTTTTAA
21584311 TTATTGTAA
1 TT-TT-TAA
21584320 TTTTTGAA
1 TTTTT-AA
*
21584328 TTTTAAA
1 TTTTTAA
*
21584335 ATTTTAA
1 TTTTTAA
21584342 TTT
1 TTT
21584345 CAATTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.15
7 18 0.46
8 10 0.26
9 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (7 bp):
TTTTTAA
Found at i:21584342 original size:22 final size:22
Alignment explanation
Indices: 21584292--21584357 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
21584282 ATCAGTTTTT
*
21584292 TTTTAATTTTTAATTTTAATTA
1 TTTTAATTTTTAATTTTAATAA
*
21584314 TTGTAATTTTTGAATTTTAA-AA
1 TTTTAATTTTT-AATTTTAATAA
* *
21584336 TTTTAA-TTTCAATTTAAATAA
1 TTTTAATTTTTAATTTTAATAA
21584357 T
1 T
21584358 AGTAAACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.19
21 6 0.16
22 16 0.43
23 8 0.22
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTTAATTTTTAATTTTAATAA
Found at i:21588564 original size:24 final size:24
Alignment explanation
Indices: 21588537--21588585 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
21588527 TTAAATTCTT
* *
21588537 TAAAATATAATTATATGGATTAAA
1 TAAAATATAAATATACGGATTAAA
21588561 TAAAATATAAATATACGGATTAAA
1 TAAAATATAAATATACGGATTAAA
21588585 T
1 T
21588586 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
TAAAATATAAATATACGGATTAAA
Found at i:21594446 original size:18 final size:18
Alignment explanation
Indices: 21594413--21594447 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21594403 TACAAGGTGC
*
21594413 GTATCCTAGCCATTATAT
1 GTATCCTAACCATTATAT
*
21594431 GTATCCTAACCCTTATA
1 GTATCCTAACCATTATA
21594448 AGTTTTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (18 bp):
GTATCCTAACCATTATAT
Found at i:21594742 original size:21 final size:22
Alignment explanation
Indices: 21594706--21594748 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
21594696 CAACCAGAAT
*
21594706 AACCACAACATTCGCCA-AAGC
1 AACCACAACATCCGCCAGAAGC
*
21594727 AACCACAACCTCCGCCAGAAGC
1 AACCACAACATCCGCCAGAAGC
21594749 TGAATCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.42, G:0.12, T:0.07
Consensus pattern (22 bp):
AACCACAACATCCGCCAGAAGC
Found at i:21598228 original size:126 final size:126
Alignment explanation
Indices: 21597990--21598517 Score: 664
Period size: 126 Copynumber: 4.2 Consensus size: 126
21597980 TAAGGCTAAG
* **
21597990 CAGGAACTACTGTAGAAAAGGAGCGTCCACATGGAAGCTTTTTTTTTTTGTAATTTTGCTGACAG
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATGGAAGC---TTTTTTCAGTAATTTTGCTGACAG
* *
21598055 TGCATCCTGCTTGAAGCGTTTTTTAAACTATTTTTTCATAA-TCGTCTTCTCAAAATTATTTTTT
63 TGCATCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACT-GTCTTCTCAAAATTATTTTTT
* * * * *
21598119 CAAGAACTACTGTAGAAAAAGAACGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
21598184 ATCCTGCTTGAAGCCTTTTTTACACTATTTTCTCAAAACTGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * * * * * *
21598245 CAGGAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGCGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * *
21598310 ATCTTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTATTTTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * *
21598371 TAGGAACTACTGTAGAGAAAGAGCGTTCACATGGAAGCTTTTTTCAGTAATTTTGCTGACAGTTG
1 CAGGAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTCAGTAATTTTGCTGACAG-TG
* * * * * * * *
21598436 CATCCTGCTTGAAACATTCTTAACATTATCTTTTT-AGAACCGTCTTCTCAAAATTAATTTTT
65 CATCCTGCTTGAAGCGTTTTTTACACTAT-TTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* *
21598498 CTGAAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
21598518 AAAACAAAAT
Statistics
Matches: 345, Mismatches: 51, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
126 245 0.71
127 63 0.18
128 5 0.01
129 32 0.09
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAGCGTCCACATGGAAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTTTTTTACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
Found at i:21598653 original size:33 final size:33
Alignment explanation
Indices: 21598603--21598733 Score: 126
Period size: 33 Copynumber: 3.9 Consensus size: 33
21598593 CAAACACAAA
*
21598603 AATTATTTTTTTAAAAAAAACTAAACCCTAATTT
1 AATTAATTTTTT-AAAAAAACTAAACCCTAATTT
*
21598637 AATTAATTTTTT-AAAAAACTTAAACCTTAATTT
1 AATTAATTTTTTAAAAAAAC-TAAACCCTAATTT
***
21598670 AATTAATTTATTTAAAACCCCTCAAA-CCTAATTT
1 AATTAATTT-TTTAAAAAAACT-AAACCCTAATTT
*
21598704 AATTAA--TTTAAAAAAAACTCTAAACCCTAA
1 AATTAATTTTTTAAAAAAA--CTAAACCCTAA
21598734 ATTTTTATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
31 6 0.08
32 11 0.14
33 28 0.35
34 28 0.35
35 7 0.09
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (33 bp):
AATTAATTTTTTAAAAAAACTAAACCCTAATTT
Found at i:21598808 original size:22 final size:23
Alignment explanation
Indices: 21598783--21598828 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
21598773 TTATTTTAAC
21598783 AAAACACTAACAC-CAC-AACCCT
1 AAAACACTAA-ACTCACAAACCCT
*
21598805 AAAACCCTAAACTCACAAACCCT
1 AAAACACTAAACTCACAAACCCT
21598828 A
1 A
21598829 GGCACTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 12 0.57
23 7 0.33
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (23 bp):
AAAACACTAAACTCACAAACCCT
Found at i:21609852 original size:18 final size:18
Alignment explanation
Indices: 21609817--21609859 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21609807 CGCATAAAAA
* * *
21609817 GAAAGCAAATAAATAAAT
1 GAAAGAAAAGAAACAAAT
21609835 GAAAGAAAAGAAACAAAT
1 GAAAGAAAAGAAACAAAT
21609853 GAAAGAA
1 GAAAGAA
21609860 GGGGGAAAGA
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:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (18 bp):
GAAAGAAAAGAAACAAAT
Found at i:21609946 original size:5 final size:5
Alignment explanation
Indices: 21609936--21609967 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
21609926 AAGCTGTGAA
21609936 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
21609968 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:21609961 original size:9 final size:9
Alignment explanation
Indices: 21609937--21609967 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
21609927 AGCTGTGAAA
21609937 AAATAAAAT
1 AAATAAAAT
21609946 AAAATAAAAT
1 -AAATAAAAT
21609956 AAATAAAAT
1 AAATAAAAT
21609965 AAA
1 AAA
21609968 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:21613910 original size:47 final size:47
Alignment explanation
Indices: 21613857--21614335 Score: 741
Period size: 47 Copynumber: 10.2 Consensus size: 47
21613847 AATTCTAAAT
21613857 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
21613904 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
21613951 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTGTATATA
*
21614000 TGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
21614045 TGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTG--TATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
21614090 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
21614137 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA
* * *
21614186 TGTGATAAGGCTTAACGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
21614233 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
21614280 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
21614327 TGTGATAAG
1 TGTGATAAG
21614336 TCCCGAAGGG
Statistics
Matches: 400, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
45 87 0.22
47 224 0.56
49 89 0.22
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:21614038 original size:96 final size:94
Alignment explanation
Indices: 21613857--21614335 Score: 741
Period size: 96 Copynumber: 5.1 Consensus size: 94
21613847 AATTCTAAAT
21613857 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
21613922 CCGATGTGATGAATGTGAAAGTGTATATA
66 CCGATGTGATGAATGTGAAAGTGTATATA
*
21613951 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCTTAAT
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTGTATATATGTGATAAGGCCTAAT
21614016 GGCCGATGTGATGAATGTGAAAGTG--TATA
64 GGCCGATGTGATGAATGTGAAAGTGTATATA
*
21614045 TGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCTAATGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
*
21614108 CCGATGTGATGAATGTGAAAGTGTATATG
66 CCGATGTGATGAATGTGAAAGTGTATATA
* * *
21614137 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAAC
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAAT
*
21614202 GGCCGATGTGATGAATGTGAAAGTGTATATG
64 GGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * *
21614233 CGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
* * * *
21614298 CCAATGTGATGGATGTGAAAGTGCATAAA
66 CCGATGTGATGAATGTGAAAGTGTATATA
21614327 TGTGATAAG
1 TGTGATAAG
21614336 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 23, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
90 44 0.12
92 45 0.13
94 129 0.36
96 136 0.38
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.29
Consensus pattern (94 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATA
Found at i:21614249 original size:233 final size:234
Alignment explanation
Indices: 21613852--21614335 Score: 767
Period size: 233 Copynumber: 2.1 Consensus size: 234
21613842 ATGTGAATTC
21613852 TAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 TAAA-TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* *
21613917 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
65 AATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCGATGTGATGAA
*
21613982 TGTGAAAGTGTGTATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG-TATAT
130 TGTGAAAG-GTGTATATACGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGATATAT
* * *
21614046 GTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTG-
194 GTGACAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGA
* *
21614086 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTA
1 TAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
21614151 ATAGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTTAACGGCCGATGTGATGA
66 ATAGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAACGGCCGATGTGATGA
*
21614216 ATGTGAAA-GTGTATATGCGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
129 ATGTGAAAGGTGTATATACGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTG-ATATA
* * * *
21614280 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCA
193 TGTGACAAGGCCGAATGACCAATGTGATGAATGTGAAAGTG-A
21614323 TAAATGTGATAAG
1 TAAATGTGATAAG
21614336 TCCCGAAGGG
Statistics
Matches: 229, Mismatches: 15, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
233 134 0.59
234 3 0.01
235 80 0.35
237 12 0.05
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (234 bp):
TAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
ATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCGATGTGATGAAT
GTGAAAGGTGTATATACGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGATATATGT
GACAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGA
Found at i:21614510 original size:37 final size:37
Alignment explanation
Indices: 21614454--21614532 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
21614444 CCGAGTTCTA
* * *
21614454 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
21614491 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
21614528 AAGAC
1 AAGAC
21614533 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:21618718 original size:9 final size:9
Alignment explanation
Indices: 21618704--21618733 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
21618694 ATTTGTGAAA
21618704 AAATAAAAT
1 AAATAAAAT
21618713 AAATAAAAT
1 AAATAAAAT
21618722 AAATAAAAT
1 AAATAAAAT
21618731 AAA
1 AAA
21618734 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:21620763 original size:2 final size:2
Alignment explanation
Indices: 21620756--21620814 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
21620746 TAAATAAGTG
* * *
21620756 CT CT CT CT CT CT CT CT CT CT CT CC CC CT CT CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
21620798 CT CT CT CC CT CC CT CT C
1 CT CT CT CT CT CT CT CT C
21620815 CCTCCCCCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (2 bp):
CT
Found at i:21620775 original size:14 final size:14
Alignment explanation
Indices: 21620756--21620826 Score: 92
Period size: 14 Copynumber: 5.2 Consensus size: 14
21620746 TAAATAAGTG
*
21620756 CTCTCTCTCTCTCT
1 CTCTCTCTCTCCCT
*
21620770 CTCTCTCTCCCCCT
1 CTCTCTCTCTCCCT
21620784 CTCTCTCTCTCCCT
1 CTCTCTCTCTCCCT
*
21620798 CTCTCTCCCTCCCT
1 CTCTCTCTCTCCCT
*
21620812 CTC-C-CTCCCCCT
1 CTCTCTCTCTCCCT
21620824 CTC
1 CTC
21620827 CCTCAGATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
12 9 0.18
13 1 0.02
14 41 0.80
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
CTCTCTCTCTCCCT
Found at i:21620815 original size:6 final size:6
Alignment explanation
Indices: 21620758--21620830 Score: 56
Period size: 6 Copynumber: 11.5 Consensus size: 6
21620748 AATAAGTGCT
* * * * *
21620758 CTCTCT CTCTCT CTCTCT CTCCCC CTCTCTC TCTCTCC CTCTCTC TCCCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTC-C -CTCTCC CTCTC-C -CTCTCC
*
21620810 CTCTCC CTCCCC CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTC
21620831 AGATCAAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
6 43 0.77
7 4 0.07
8 9 0.16
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CTCTCC
Found at i:21620815 original size:10 final size:10
Alignment explanation
Indices: 21620760--21620830 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
21620750 TAAGTGCTCT
* *
21620760 CTCTCTCTCT
1 CTCTCCCTCC
*
21620770 CTCTCTCTCC
1 CTCTCCCTCC
* * *
21620780 CCCTCTCTCT
1 CTCTCCCTCC
*
21620790 CTCTCCCTCT
1 CTCTCCCTCC
21620800 CTCTCCCTCC
1 CTCTCCCTCC
21620810 CTCTCCCTCCCC
1 CTCTCCCT--CC
21620822 CTCTCCCTC
1 CTCTCCCTC
21620831 AGATCAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
10 43 0.81
12 10 0.19
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (10 bp):
CTCTCCCTCC
Found at i:21622147 original size:2 final size:2
Alignment explanation
Indices: 21622140--21622206 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
21622130 CTTATTTGTA
* * * * *
21622140 CT CT CT CT CT CC CT CC CC CC CT CT CT CT CT CT CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
21622182 CT CT CT CT CT CT CT CC CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
21622207 ATGCAAAAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
CT
Found at i:21626968 original size:20 final size:20
Alignment explanation
Indices: 21626922--21626959 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
21626912 CCAATTTTTT
*
21626922 TTACTTTCATTTGCATTTCA
1 TTACTTTCAATTGCATTTCA
21626942 TTACTTTCAATTGCATTT
1 TTACTTTCAATTGCATTT
21626960 ACTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (20 bp):
TTACTTTCAATTGCATTTCA
Found at i:21630160 original size:25 final size:20
Alignment explanation
Indices: 21630112--21630151 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21630102 CTCTTTTCCA
21630112 TAACTTTTCATCTAATCTAT
1 TAACTTTTCATCTAATCTAT
21630132 TAACTTTTCATCTAATCTAT
1 TAACTTTTCATCTAATCTAT
21630152 ACATTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (20 bp):
TAACTTTTCATCTAATCTAT
Done.