Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 104 of 196
Found at i:31357979 original size:42 final size:43
Alignment explanation
Indices: 31357832--31358043 Score: 274
Period size: 43 Copynumber: 5.0 Consensus size: 43
31357822 TAACCGTTAC
*
31357832 ACGGTGGAATCAGCACTTAGCAACCACC-TTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
* * * *
31357874 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-ATATTCAATGAT
31357916 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
* * * *
31357959 GCGG-GGAATCAGCACATAGCAACC-CCTTTCACAATT-AAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-A-TATTCAATGAT
31358001 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
31358044 GCGGATTCAC
Statistics
Matches: 145, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.01
41 26 0.18
42 48 0.33
43 59 0.41
44 10 0.07
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (43 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGAT
Found at i:31358131 original size:51 final size:51
Alignment explanation
Indices: 31358055--31358346 Score: 285
Period size: 51 Copynumber: 5.8 Consensus size: 51
31358045 CGGATTCACA
* * *
31358055 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * * *
31358106 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTGCGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
*** *
31358157 TAGTAGCCTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
* * * * *
31358207 TAGTAGCCTACACATAGTACTACACACGTGATCGA--AGCTATCCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * *
31358258 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
* *
31358308 TAGTAGCCTACACATAGTACTACAAACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
31358347 TTCACTTTCA
Statistics
Matches: 192, Mismatches: 36, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
48 1 0.01
49 4 0.02
50 76 0.40
51 107 0.56
52 2 0.01
53 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:31358229 original size:101 final size:101
Alignment explanation
Indices: 31358053--31358338 Score: 466
Period size: 101 Copynumber: 2.8 Consensus size: 101
31358043 TGCGGATTCA
* * * * *
31358053 CATAGTAGCATGCACATAGTACTACACATGTGACC-ATCACTATCCGATACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
* *
31358117 ACATAGTACTACACACGTGATCGAAGCTATCCGGTGCG
64 ACATAGTACTACACACGTGATCGAAGCTATCCGATACG
*
31358155 CATAGTAGCCTGCACATAGTACTACACATACGACCTATCATTCTGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
31358220 ATAGTACTACACACGTGATCGAAGCTATCCGATACG
66 ATAGTACTACACACGTGATCGAAGCTATCCGATACG
31358256 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
*
31358321 ATAGTACTACAAACGTGA
66 ATAGTACTACACACGTGA
31358339 CCATCACTTT
Statistics
Matches: 173, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 136 0.79
102 33 0.19
103 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAGCTATCCGATACG
Found at i:31358368 original size:152 final size:151
Alignment explanation
Indices: 31358049--31358372 Score: 336
Period size: 152 Copynumber: 2.1 Consensus size: 151
31358039 ATGATGCGGA
* * * *
31358049 TTCACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGACCA-CACTATCCGATACACATAGTAGCC
* * * * *
31358114 TGCACATAGTACTACACACGTGATCGAAGCTATCCGGTGCGCATAGTAGCCTGCACATAGTACTA
65 TGCACATAGTACTACACACGCGATCCAAGCTATCCGGTACACATAGTAGCCTACACATAGTACTA
**
31358179 CACATACGACCTATCATTCTGG
130 CACATACGACCTATCATTCACG
* * * *
31358201 TACACGTAGTAGCCTACACATAGTACTACACACGTGATCGA-AGCTATCCGATACGCATAGTAGC
1 TTCACATAGTAGCCTACACATAGTACTACACACGTGA-CCACA-CTATCCGATACACATAGTAGC
* * * * *
31358265 CTGCACATAGTACTACACATGCGA-CCTATC-ATTCTGGTACACGTAGTAGCCTACACATAGTAC
64 CTGCACATAGTACTACACACGCGATCCAAGCTA-TCCGGTACACATAGTAGCCTACACATAGTAC
*
31358328 TACA-A-ACGTGACC-ATCACTTTCACT
128 TACACATAC--GACCTATCA--TTCACG
*
31358353 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTACACA
31358373 CAGTCCATGC
Statistics
Matches: 141, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
149 2 0.01
150 6 0.04
151 38 0.27
152 93 0.66
153 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (151 bp):
TTCACATAGTAGCCTACACATAGTACTACACACGTGACCACACTATCCGATACACATAGTAGCCT
GCACATAGTACTACACACGCGATCCAAGCTATCCGGTACACATAGTAGCCTACACATAGTACTAC
ACATACGACCTATCATTCACG
Found at i:31368684 original size:13 final size:12
Alignment explanation
Indices: 31368665--31368704 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
31368655 ACATAAATAA
31368665 TTAAATAAAAAT
1 TTAAATAAAAAT
31368677 TGTAAATAAAAAT
1 T-TAAATAAAAAT
*
31368690 TAAAATTAAAAAT
1 TTAAA-TAAAAAT
31368703 TT
1 TT
31368705 CTTTTGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
TTAAATAAAAAT
Found at i:31378390 original size:22 final size:22
Alignment explanation
Indices: 31378365--31378427 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
31378355 GTGTGTTGGT
* *
31378365 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGATATCAAGGGGG
*
31378387 AAAGTTGGGGATATCAGGGGGG
1 AAAGTTGGGGATATCAAGGGGG
31378409 AAAGTTGGGGATATCAAGG
1 AAAGTTGGGGATATCAAGG
31378428 AGAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.29, C:0.05, G:0.46, T:0.21
Consensus pattern (22 bp):
AAAGTTGGGGATATCAAGGGGG
Found at i:31379345 original size:14 final size:14
Alignment explanation
Indices: 31379328--31379418 Score: 64
Period size: 14 Copynumber: 6.4 Consensus size: 14
31379318 TCATAAATCA
31379328 TAAACCCTAACCCT
1 TAAACCCTAACCCT
*
31379342 TAAACCCATGA-CCT
1 TAAACCC-TAACCCT
31379356 CT-AACCTCTAACCCT
1 -TAAACC-CTAACCCT
*
31379371 TAAACCTTAAACCC-
1 TAAACCCT-AACCCT
* *
31379385 -CAACCCTTAAACCT
1 TAAACCC-TAACCCT
*
31379399 TAAACCCCAACCCT
1 TAAACCCTAACCCT
31379413 TAAACC
1 TAAACC
31379419 ATAAACCATG
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
13 8 0.14
14 30 0.51
15 21 0.36
ACGTcount: A:0.36, C:0.42, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCCTAACCCT
Found at i:31379378 original size:7 final size:7
Alignment explanation
Indices: 31379358--31379425 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
31379348 CATGACCTCT
31379358 AACCTCTA
1 AACCT-TA
*
31379366 ACCCTTA
1 AACCTTA
31379373 AACCTTA
1 AACCTTA
**
31379380 AACCCCA
1 AACCTTA
*
31379387 ACCCTTA
1 AACCTTA
31379394 AACCTTA
1 AACCTTA
**
31379401 AACCCCA
1 AACCTTA
*
31379408 ACCCTTA
1 AACCTTA
*
31379415 AACCATA
1 AACCTTA
31379422 AACC
1 AACC
31379426 ATGATCCATA
Statistics
Matches: 45, Mismatches: 15, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
7 41 0.91
8 4 0.09
ACGTcount: A:0.40, C:0.41, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCTTA
Found at i:31379389 original size:21 final size:21
Alignment explanation
Indices: 31379365--31379425 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
31379355 TCTAACCTCT
31379365 AACCCTTAAACCTTAAACCCC
1 AACCCTTAAACCTTAAACCCC
31379386 AACCCTTAAACCTTAAACCCC
1 AACCCTTAAACCTTAAACCCC
*
31379407 AACCCTTAAACCATAAACC
1 AACCCTTAAACCTTAAACC
31379426 ATGATCCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (21 bp):
AACCCTTAAACCTTAAACCCC
Found at i:31379451 original size:15 final size:15
Alignment explanation
Indices: 31379431--31379459 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31379421 AAACCATGAT
31379431 CCATAATCCCTAAAA
1 CCATAATCCCTAAAA
31379446 CCATAATCCCTAAA
1 CCATAATCCCTAAA
31379460 CCTTAAAATA
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:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (15 bp):
CCATAATCCCTAAAA
Found at i:31382526 original size:61 final size:61
Alignment explanation
Indices: 31382461--31382651 Score: 221
Period size: 61 Copynumber: 3.2 Consensus size: 61
31382451 ATTTTATAGT
31382461 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * ** * * * * * *
31382522 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTATTTTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATATTAAGAATTTTATTA-A
*
31382581 ATTATCTATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
31382642 ATTATATATT
1 ATTATATATT
31382652 TTTATTAAAT
Statistics
Matches: 100, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 7 0.07
59 31 0.31
60 14 0.14
61 41 0.41
62 7 0.07
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:31382531 original size:120 final size:120
Alignment explanation
Indices: 31382401--31382686 Score: 554
Period size: 120 Copynumber: 2.4 Consensus size: 120
31382391 ACGTGGGGGG
31382401 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
31382466 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
31382521 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
*
31382586 CTATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
*
31382641 AATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAAA
1 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
31382687 ATATTATTAA
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 164 1.00
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (120 bp):
AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
Found at i:31382688 original size:27 final size:28
Alignment explanation
Indices: 31382626--31382710 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
31382616 ATATTTAATA
* *
31382626 TTAAGAATTTTATTAAATT-ATATATTTTT
1 TTAA-AATATTATTAAATTAAT-TATTATT
* *
31382655 ATTAAATTA-TATTTAA-TAATTATTATT
1 -TTAAAATATTATTAAATTAATTATTATT
*
31382682 TTAAAATATTATTAAATTATTTATTATT
1 TTAAAATATTATTAAATTAATTATTATT
31382710 T
1 T
31382711 ATATTAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
26 7 0.16
27 13 0.29
28 19 0.42
29 2 0.04
30 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TTAAAATATTATTAAATTAATTATTATT
Found at i:31382711 original size:27 final size:26
Alignment explanation
Indices: 31382617--31382711 Score: 70
Period size: 27 Copynumber: 3.5 Consensus size: 26
31382607 CATATAAGAA
*
31382617 TATTTAATA-TTAAGAATTTTATTAAAT
1 TATTTATTATTTAA-AA-TTTATTAAAT
* *
31382644 TATATATT-TTTATTAAATTATATTTAA-
1 TATTTATTATTTA--AAATT-TATTAAAT
*
31382671 TAATTATTATTTTAAAATATTATTAAAT
1 TATTTATTA-TTTAAAAT-TTATTAAAT
31382699 TATTTATTATTTA
1 TATTTATTATTTA
31382712 TATTAATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
27 31 0.58
28 17 0.32
29 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
TATTTATTATTTAAAATTTATTAAAT
Found at i:31382916 original size:46 final size:44
Alignment explanation
Indices: 31382825--31382918 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
31382815 ATTACAACAT
* *
31382825 CATTCCATTCAACCAAACACAAGAATAGTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTC
* *
31382869 CATTCCATTCAATCAAACAAAAGGATTACCTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACAAAA-GAATA-CTATTACGCCTCTATTC
31382915 CATT
1 CATT
31382919 ACACCTCTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 20 0.45
45 4 0.09
46 20 0.45
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.30
Consensus pattern (44 bp):
CATTCCATTCAACCAAACAAAAGAATACTATTACGCCTCTATTC
Found at i:31382925 original size:16 final size:16
Alignment explanation
Indices: 31382900--31382935 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31382890 AGGATTACCT
*
31382900 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
31382916 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
31382932 ATTA
1 ATTA
31382936 TAGCGAACCA
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:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:31383195 original size:14 final size:14
Alignment explanation
Indices: 31383178--31383219 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
31383168 CCCTTAACGT
31383178 CTAACCCCTAAACC
1 CTAACCCCTAAACC
* *
31383192 CTAACTCCTAACCC
1 CTAACCCCTAAACC
31383206 CTAACCCCTAAACC
1 CTAACCCCTAAACC
31383220 TTAAATCCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (14 bp):
CTAACCCCTAAACC
Found at i:31383232 original size:28 final size:28
Alignment explanation
Indices: 31383178--31383233 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
31383168 CCCTTAACGT
* *
31383178 CTAACCCCTAAACCCTAACTCCTAACCC
1 CTAACCCCTAAACCCTAAATCCCAACCC
*
31383206 CTAACCCCTAAACCTTAAATCCCAACCC
1 CTAACCCCTAAACCCTAAATCCCAACCC
31383234 TTAAACCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.18
Consensus pattern (28 bp):
CTAACCCCTAAACCCTAAATCCCAACCC
Found at i:31383491 original size:14 final size:14
Alignment explanation
Indices: 31383472--31383527 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
31383462 AACCTTAAAT
31383472 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
31383486 CCCTAACGTC-TAAC
1 CCCTAAC-TCTTAAC
*
31383500 CCCTAAACACTTAAC
1 CCCT-AACTCTTAAC
* *
31383515 CCTTAACCCTTAA
1 CCCTAACTCTTAA
31383528 ACCTTAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:31383532 original size:14 final size:14
Alignment explanation
Indices: 31383496--31383584 Score: 58
Period size: 14 Copynumber: 6.2 Consensus size: 14
31383486 CCCTAACGTC
*
31383496 TAACCCCTAAACACT
1 TAACCCTTAAAC-CT
*
31383511 TAACCCTTAACCCT
1 TAACCCTTAAACCT
*
31383525 TAAACCTTAAATCC-
1 TAACCCTTAAA-CCT
* *
31383539 CAACCCTTAAACCA
1 TAACCCTTAAACCT
*
31383553 TAATCCC-TAAATCCA
1 TAA-CCCTTAAA-CCT
31383568 T-ACTCCTTAAACCT
1 TAAC-CCTTAAACCT
31383582 TAA
1 TAA
31383585 AATAGTAACT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.05
14 32 0.54
15 24 0.41
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (14 bp):
TAACCCTTAAACCT
Found at i:31383533 original size:21 final size:22
Alignment explanation
Indices: 31383496--31383560 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
31383486 CCCTAACGTC
*
31383496 TAACCCCTAAACACTTAA-CCCT
1 TAACCCTTAAAC-CTTAATCCCT
31383518 TAACCCTTAAACCTTAAATCCC-
1 TAACCCTTAAACCTT-AATCCCT
*
31383540 -AACCCTTAAACCATAATCCCT
1 TAACCCTTAAACCTTAATCCCT
31383561 AAATCCATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.16
21 16 0.42
22 13 0.34
23 3 0.08
ACGTcount: A:0.37, C:0.38, G:0.00, T:0.25
Consensus pattern (22 bp):
TAACCCTTAAACCTTAATCCCT
Found at i:31383544 original size:28 final size:27
Alignment explanation
Indices: 31383512--31383585 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
31383502 CTAAACACTT
* *
31383512 AACCCTTAACCCTTAAACCTTAAATCCC
1 AACCCTTAAACCTTAAACCCTAAAT-CC
* *
31383540 AACCCTTAAACCATAATCCCTAAATCC
1 AACCCTTAAACCTTAAACCCTAAATCC
31383567 ATACTCCTTAAACCTTAAA
1 A-AC-CCTTAAACCTTAAA
31383586 ATAGTAACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.08
28 23 0.61
29 12 0.32
ACGTcount: A:0.39, C:0.35, G:0.00, T:0.26
Consensus pattern (27 bp):
AACCCTTAAACCTTAAACCCTAAATCC
Found at i:31383816 original size:23 final size:26
Alignment explanation
Indices: 31383789--31383843 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
31383779 TAAATAATAG
*
31383789 TATTTT-AATT-TTTCCATGTGT-TT
1 TATTTTAAATTATTTCCATGTGTCAT
*
31383812 TATTTTAAATTATTTCTATGTGTCAT
1 TATTTTAAATTATTTCCATGTGTCAT
31383838 TATTTT
1 TATTTT
31383844 TTCTGAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 6 0.22
24 4 0.15
25 10 0.37
26 7 0.26
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (26 bp):
TATTTTAAATTATTTCCATGTGTCAT
Found at i:31384146 original size:123 final size:122
Alignment explanation
Indices: 31383927--31384278 Score: 465
Period size: 123 Copynumber: 2.9 Consensus size: 122
31383917 TAAAATGTTT
* * *
31383927 TTAGCGGCGCTTTTTCAAAAATGTCGCTAAAGCCCCCAGCATTAGCGGCGCTTTTCCAAAAACTC
1 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAACATTAGCGGCGCTTTT-CAAAAACAC
* * ** *
31383992 AGCTAAAACCCCCAGCATTAGCGGCGCTTTTTATAAAACGCCGTTAAAACACTGAGCA
65 CGCTAAAACCCCGAGCATTAGCGGCGCTTTTTATAAAACGCCGTTAAAACACCAAACA
* * *
31384050 TTAGCGGCGCTTTTTCAAAAATGCCACTAAAGCCCCCAATATTAGCGGCATCTTTTCAAAAACAC
1 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAACATTAGCGGC-GCTTTTCAAAAACAC
* * *
31384115 CGCTAAAACCCCGAGCATTAGCGGCGCTTTTTAAAAAATGTCGTTAAAACACCAAACA
65 CGCTAAAACCCCGAGCATTAGCGGCGCTTTTTATAAAACGCCGTTAAAACACCAAACA
* * **
31384173 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-ACCCCAAGCATTAGCGGCGCATTTTCAAAAATG
1 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAA-CATTAGCGGCGC-TTTTCAAAAACA
* *
31384237 CCGCTAAAGCCCCGAGCATTAGCGGCACTTTTT-TGAAAACGC
64 CCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTAT-AAAACGC
31384279 TGCTAAAGCC
Statistics
Matches: 199, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
122 7 0.04
123 187 0.94
124 5 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (122 bp):
TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCCAACATTAGCGGCGCTTTTCAAAAACACC
GCTAAAACCCCGAGCATTAGCGGCGCTTTTTATAAAACGCCGTTAAAACACCAAACA
Found at i:31384284 original size:41 final size:41
Alignment explanation
Indices: 31383927--31384292 Score: 385
Period size: 41 Copynumber: 8.9 Consensus size: 41
31383917 TAAAATGTTT
* * * *
31383927 TTAGCGGCGCTTTTTCAAAAATGTCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * *
31383968 TTAGCGGCGCTTTTCCAAAAACTCAGCTAAAACCCCCAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * *
31384009 TTAGCGGCGCTTTTT-ATAAAACGCCGTTAAAACACTGAGCA
1 TTAGCGGCGCTTTTTCA-AAAACGCCGCTAAAACCCCGAGCA
* * * * **
31384050 TTAGCGGCGCTTTTTCAAAAATGCCACTAAAGCCCCCAATA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* *
31384091 TTAGCGGC-ATCTTTTCAAAAACACCGCTAAAACCCCGAGCA
1 TTAGCGGCGCT-TTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * * * * * *
31384132 TTAGCGGCGCTTTTTAAAAAATGTCGTTAAAACACCAAACA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
*
31384173 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCAAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* * *
31384214 TTAGCGGCGCATTTTCAAAAATGCCGCTAAAGCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
* ** * *
31384255 TTAGCGGCACTTTTTTGAAAACGCTGCTAAAGCCCCGA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGA
31384293 AAGGTAAGAA
Statistics
Matches: 266, Mismatches: 55, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
40 2 0.01
41 262 0.98
42 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAACCCCGAGCA
Found at i:31384463 original size:12 final size:12
Alignment explanation
Indices: 31384446--31384472 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31384436 TTTTTTATCC
31384446 AAGTGCCGCTAA
1 AAGTGCCGCTAA
31384458 AAGTGCCGCTAA
1 AAGTGCCGCTAA
31384470 AAG
1 AAG
31384473 CTTATTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (12 bp):
AAGTGCCGCTAA
Found at i:31387470 original size:80 final size:78
Alignment explanation
Indices: 31387278--31387486 Score: 253
Period size: 80 Copynumber: 2.6 Consensus size: 78
31387268 AAGTGACCAT
* * * *
31387278 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAGCCCGAAGGCAGT
31387342 TGTGCGAGTTACTAA
64 TGTGCGAGTTACTAA
* *
31387357 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCAGT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAG-CCCGAAGGCAGT
31387422 TGTGCGAGTTACTATA
64 TGTGCGAGTTACTA-A
* ** *
31387438 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCC-GGTTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTAAATCCGGGTTAA
31387487 ATTCCGAAGG
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
78 1 0.01
79 53 0.46
80 58 0.51
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGCCCGAAGGCAGTTG
TGCGAGTTACTAA
Found at i:31387477 original size:40 final size:40
Alignment explanation
Indices: 31387239--31387463 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
31387229 TTGAATGATG
* * * *
31387239 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
31387279 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
31387319 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31387358 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
31387398 TCCGGGTTAAGTCCTGAAGGCAGTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31387439 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31387464 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 35 0.21
40 118 0.72
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31387485 original size:119 final size:119
Alignment explanation
Indices: 31387239--31387496 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
31387229 TTGAATGATG
* * *
31387239 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAGTT
* **
31387304 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
* * * **
31387358 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAG
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCAG
* * *
31387421 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAAA
* *
31387478 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31387497 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 5 0.04
119 81 0.69
120 32 0.27
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAGTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:31400487 original size:61 final size:61
Alignment explanation
Indices: 31400422--31400546 Score: 142
Period size: 61 Copynumber: 2.0 Consensus size: 61
31400412 TTTAAATATT
* * * ** * *
31400422 AAAAATTCAACAAATTTAGCACTCAATGTCTGCAAAATTTGTCATTTTAGTTCTAATTCTA
1 AAAAATTCAACAAAATTAGCACTCAATATCTACAAAATTTGTCAAATTAGTCCTAACTCTA
* * * * *
31400483 AAAAATTTAATAAAATTGGCCCTCAATATTTACAAAATTTGTCAAATTAGTCCTAACTCTA
1 AAAAATTCAACAAAATTAGCACTCAATATCTACAAAATTTGTCAAATTAGTCCTAACTCTA
31400544 AAA
1 AAA
31400547 TTAAAAATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (61 bp):
AAAAATTCAACAAAATTAGCACTCAATATCTACAAAATTTGTCAAATTAGTCCTAACTCTA
Found at i:31401773 original size:122 final size:124
Alignment explanation
Indices: 31401556--31401903 Score: 585
Period size: 122 Copynumber: 2.8 Consensus size: 124
31401546 TTATTTCGAG
* *
31401556 TTGACGTTTCTG-GTCAAATTGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
31401620 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAT-A-TTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* * * *
31401678 TTGACATTTCTGAGCAAATAGTATAAAATTGCTTCTACGAGGATGCTATTTGAGTAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
31401743 AAATCACGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
*
31401802 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
31401867 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
31401904 CAAGTTTGGG
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
122 106 0.51
123 2 0.01
124 100 0.48
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:31405054 original size:53 final size:53
Alignment explanation
Indices: 31404992--31405107 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
31404982 TAGTTCCAGA
31404992 CAAAACATTTTACCAAATCTAACATTATGTAAAAGTATGTAAAATTATTAAGC
1 CAAAACATTTTACCAAATCTAACATTATGTAAAAGTATGTAAAATTATTAAGC
31405045 CAAAACATTTTACCAAATCTAACATTATGTAAAAGTATGTAAAATTATTAAGC
1 CAAAACATTTTACCAAATCTAACATTATGTAAAAGTATGTAAAATTATTAAGC
*
31405098 TAAAA-ATTTT
1 CAAAACATTTT
31405108 TTGTTAATGG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 5 0.08
53 57 0.92
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (53 bp):
CAAAACATTTTACCAAATCTAACATTATGTAAAAGTATGTAAAATTATTAAGC
Found at i:31405182 original size:6 final size:6
Alignment explanation
Indices: 31405171--31405198 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31405161 AATTAAATTA
31405171 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTT
31405199 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
GGTTAG
Found at i:31405201 original size:41 final size:41
Alignment explanation
Indices: 31405148--31405227 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
31405138 TGTAAAATTA
31405148 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAG
31405189 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
31405228 TTTAATTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.42
Consensus pattern (41 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAG
Found at i:31405252 original size:29 final size:29
Alignment explanation
Indices: 31405183--31405241 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
31405173 TTAGGGTTAG
31405183 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
*
31405212 GGTTAGGGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
31405241 G
1 G
31405242 TTAATTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (29 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:31405274 original size:43 final size:43
Alignment explanation
Indices: 31405220--31405387 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
31405210 TAGGTTAGGG
31405220 TTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAAAATTAAA
1 TTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAAAATTAAA
* * * **
31405263 TTAGGGTTTTTAATTAAATTAGTTTAGGGTCAGAGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT--A--AG-TTA--GTTA-A-TTGTT-AGTAAA--A--TTA-AA
31405321 TTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAAAATTAAA
1 TTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAAAATTAAA
*
31405364 TTAGGGTTTTTAATTAAATTAGTT
1 TTAGGGTTTTTAATTAAGTTAGTT
31405388 TAGGGTTAGG
Statistics
Matches: 99, Mismatches: 11, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
43 38 0.38
44 3 0.03
45 1 0.01
46 1 0.01
47 2 0.02
48 8 0.08
49 4 0.04
50 4 0.04
51 4 0.04
52 4 0.04
53 8 0.08
54 2 0.02
55 1 0.01
56 1 0.01
57 3 0.03
58 15 0.15
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (43 bp):
TTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAAAATTAAA
Found at i:31405308 original size:101 final size:101
Alignment explanation
Indices: 31405185--31405680 Score: 938
Period size: 101 Copynumber: 4.9 Consensus size: 101
31405175 AGGGTTAGGG
31405185 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
31405250 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
66 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
* *
31405286 TTAGGGTCAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
31405351 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
66 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
31405387 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
31405452 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
66 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
*
31405488 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAATTGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
*
31405553 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGA
66 TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
31405589 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
1 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAA-T-T
31405654 GTTAGTAAAATTAAATTAGGGTTTTTA
64 GTTAGTAAAATTAAATTAGGGTTTTTA
31405681 TGACATCAAA
Statistics
Matches: 386, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
101 357 0.92
102 1 0.00
103 28 0.07
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (101 bp):
TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGT
TAGTAAAATTAAATTAGGGTTTTTAATTAAATTAGT
Found at i:31405324 original size:72 final size:70
Alignment explanation
Indices: 31405155--31405324 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 70
31405145 TTAGGTTAGG
** **
31405155 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 GTTTTTAATTAAATTAGGTTAGGGTTAGAATTAGAATTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
31405220 TTAGG
66 TCAGA
* ** *
31405225 GTTTTTAATTAAGTTA-GTTAATTGTTAGTAAAATTA-AATTAGGGTTTTTAATTAAATTAGTTT
1 GTTTTTAATTAAATTAGGTT-AGGGTTAG---AATTAGAATTAGGGTTTTTAATTAAATTAGGTT
31405288 AGGGTCAGA
62 AGGGTCAGA
31405297 GTTTTTAATTAAATTAGGTTAGGGTTAG
1 GTTTTTAATTAAATTAGGTTAGGGTTAG
31405325 GGTTTTTAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
69 3 0.04
70 21 0.26
72 52 0.63
73 6 0.07
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.45
Consensus pattern (70 bp):
GTTTTTAATTAAATTAGGTTAGGGTTAGAATTAGAATTAGGGTTTTTAATTAAATTAGGTTAGGG
TCAGA
Found at i:31405353 original size:29 final size:28
Alignment explanation
Indices: 31405263--31405345 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 28
31405253 TAAAATTAAA
31405263 TTAGGGTTTTTAATTAAATTAGTTTAGGG
1 TTAGGGTTTTTAATTAAATTAG-TTAGGG
* *
31405292 TCAGAGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GTTAGGG
*
31405321 TTAGGGTTTTTAATTAAGTTAGTTA
1 TTAGGGTTTTTAATTAAATTAGTTA
31405346 ATTGTTAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 4 0.08
29 43 0.90
30 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (28 bp):
TTAGGGTTTTTAATTAAATTAGTTAGGG
Found at i:31405398 original size:29 final size:29
Alignment explanation
Indices: 31405364--31405445 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
31405354 TAAAATTAAA
31405364 TTAGGGTTTTTAATTAAATTAGTTTAGGG
1 TTAGGGTTTTTAATTAAATTAGTTTAGGG
*
31405393 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGTTTAGGG
*
31405422 TTAGGGTTTTTAATTAAGTTAGTT
1 TTAGGGTTTTTAATTAAATTAGTT
31405446 AATTGTTAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGTTTAGGG
Found at i:31405453 original size:29 final size:28
Alignment explanation
Indices: 31405364--31405547 Score: 139
Period size: 29 Copynumber: 6.9 Consensus size: 28
31405354 TAAAATTAAA
31405364 TTAGGGTTTTTAATTAAATTAGTTTAGGG
1 TTAGGGTTTTTAATTAAATTAG-TTAGGG
31405393 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GTTAGGG
31405422 TTAGGGTTTTTAATT--A--AGTTA--G
1 TTAGGGTTTTTAATTAAATTAGTTAGGG
* * * * *
31405444 TTA--ATTGTTAGTAAAATTAAATTAGGG
1 TTAGGGTTTTTAATTAAATT-AGTTAGGG
*
31405471 TT----TTTAATTAAATT--AGT--TTAGGG
1 TTAGGGTTT--TT-AATTAAATTAGTTAGGG
31405494 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GTTAGGG
31405523 TTAGGGTTTTTAATTAAATTAGTTA
1 TTAGGGTTTTTAATTAAATTAGTTA
31405548 ATTGTTAGTA
Statistics
Matches: 125, Mismatches: 10, Indels: 41
0.71 0.06 0.23
Matches are distributed among these distances:
20 6 0.05
22 5 0.04
23 8 0.06
24 8 0.06
25 9 0.07
26 4 0.03
27 9 0.07
28 6 0.05
29 69 0.55
30 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.47
Consensus pattern (28 bp):
TTAGGGTTTTTAATTAAATTAGTTAGGG
Found at i:31405454 original size:130 final size:129
Alignment explanation
Indices: 31405263--31405544 Score: 313
Period size: 130 Copynumber: 2.2 Consensus size: 129
31405253 TAAAATTAAA
* **
31405263 TTAGGGTTTTTAATTAAATTAGTTTAGGGTCAGAGTTTTTAATTAAATTAGGTTAGGGTTAG-GG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTCAGAGTTTTTAATTAAATTAGGTTAGGGTTAGTAA
** * * *
31405327 TTTTTAATTA-AGTTAGTTAATT-GTTAGTAAAATTA-AATTAGGGTTTTTAATTAAATTAGTTT
66 AATTAAATTAGAGTT-GTTAATTAATTAGT----TTAGAATTAGGGTTTTTAATTAAATTAGGTT
31405389 AGGG
126 AGGG
* * * **
31405393 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-GTTAATTGTTAGTA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTCAGAGTTTTTAATTAAATTAGGTT-AGGGTTAGTA
* * **
31405457 AAATTAAATTAGGGTTTTTAATTAAATTAGTTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
65 AAATTAAATTAGAGTTGTTAATT-AATTAGTTTAGAATTAGGGTTTTTAATTAAATTAGGTTAGG
31405522 G
129 G
31405523 TTAGGGTTTTTAATTAAATTAG
1 TTAGGGTTTTTAATTAAATTAG
31405545 TTAATTGTTA
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
129 6 0.05
130 102 0.79
131 13 0.10
132 3 0.02
133 5 0.04
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.46
Consensus pattern (129 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTCAGAGTTTTTAATTAAATTAGGTTAGGGTTAGTAA
AATTAAATTAGAGTTGTTAATTAATTAGTTTAGAATTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:31405526 original size:72 final size:72
Alignment explanation
Indices: 31405393--31405526 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
31405383 TAGTTTAGGG
* **
31405393 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGTTAATTGTTAGTAA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAAGGGTTAGTAA
31405458 AATTAAA
66 AATTAAA
*
31405465 TTAGGGTTTTTAATTAAATTAGTTTAGGGTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GTTAAGGGTTAG
31405527 GGTTTTTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
72 54 0.95
73 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (72 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAAGGGTTAGTAA
AATTAAA
Found at i:31405555 original size:29 final size:28
Alignment explanation
Indices: 31405465--31405547 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 28
31405455 TAAAATTAAA
31405465 TTAGGGTTTTTAATTAAATTAGTTTAGGG
1 TTAGGGTTTTTAATTAAATTAG-TTAGGG
31405494 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTA-GTTAGGG
31405523 TTAGGGTTTTTAATTAAATTAGTTA
1 TTAGGGTTTTTAATTAAATTAGTTA
31405548 ATTGTTAGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
28 4 0.08
29 48 0.91
30 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (28 bp):
TTAGGGTTTTTAATTAAATTAGTTAGGG
Found at i:31405600 original size:29 final size:29
Alignment explanation
Indices: 31405566--31405645 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
31405556 TAAAATTAAA
31405566 TTAGGGTTTTTAATTAAATTAGATTAGGG
1 TTAGGGTTTTTAATTAAATTAGATTAGGG
*
31405595 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGATTAGGG
*
31405624 TTAGGGTTTTTAATTAAGTTAG
1 TTAGGGTTTTTAATTAAATTAG
31405646 TTAATTGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAATTAGATTAGGG
Found at i:31405627 original size:72 final size:72
Alignment explanation
Indices: 31405494--31405627 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
31405484 TAGTTTAGGG
* **
31405494 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGTTAATTGTTAGTAA
1 TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATTAAATTAGTTAAGGGTTAGTAA
31405559 AATTAAA
66 AATTAAA
31405566 TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTAG
1 TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATTAAATTA-GTTAAGGGTTAG
31405628 GGTTTTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 55 0.95
73 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (72 bp):
TTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTTTAATTAAATTAGTTAAGGGTTAGTAA
AATTAAA
Found at i:31406163 original size:18 final size:18
Alignment explanation
Indices: 31406140--31406174 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31406130 CGGAAAAGGA
*
31406140 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
31406158 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
31406175 AAACACACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:31406835 original size:7 final size:7
Alignment explanation
Indices: 31406825--31406849 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31406815 TTATATACAT
31406825 AATACTA
1 AATACTA
31406832 AATACTA
1 AATACTA
31406839 AATACTA
1 AATACTA
31406846 AATA
1 AATA
31406850 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:31407959 original size:11 final size:10
Alignment explanation
Indices: 31407929--31407994 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
31407919 GCCATTGATG
*
31407929 AAAATATAAA
1 AAAATTTAAA
31407939 AAAATTTAAA
1 AAAATTTAAA
* *
31407949 ATTATTTTAAA
1 A-AAATTTAAA
*
31407960 AAAATATAAA
1 AAAATTTAAA
31407970 AAAATTTAAA
1 AAAATTTAAA
** *
31407980 ATTATTTTAA
1 AAAATTTAAA
31407990 AAAAT
1 AAAAT
31407995 AAAATTGAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 35 0.81
11 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:31407964 original size:31 final size:31
Alignment explanation
Indices: 31407929--31407993 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
31407919 GCCATTGATG
31407929 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
31407960 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
31407991 AAA
1 AAA
31407994 TAAAATTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:31407976 original size:21 final size:20
Alignment explanation
Indices: 31407929--31407980 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
31407919 GCCATTGATG
* *
31407929 AAAATATAAAAAAATTTAAA
1 AAAATTTAAAAAAATATAAA
* *
31407949 ATTATTTTAAAAAAATATAAA
1 A-AAATTTAAAAAAATATAAA
31407970 AAAATTTAAAA
1 AAAATTTAAAA
31407981 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAAAAATATAAA
Found at i:31408052 original size:51 final size:51
Alignment explanation
Indices: 31407996--31408107 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
31407986 TTAAAAAATA
* * *
31407996 AAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTCGAAGG
1 AAATTGAGAGGAAATTGAAATTAAATATGGATTTCAAAGAATTTTCGAAGG
* *
31408047 AAATTGAGAGGAAATTGAAATTAAATATGGGTTTCAAAGAATTTTGGAAGG
1 AAATTGAGAGGAAATTGAAATTAAATATGGATTTCAAAGAATTTTCGAAGG
31408098 AAATTGAGAG
1 AAATTGAGAG
31408108 AATTTTGGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.43, C:0.02, G:0.27, T:0.29
Consensus pattern (51 bp):
AAATTGAGAGGAAATTGAAATTAAATATGGATTTCAAAGAATTTTCGAAGG
Found at i:31408109 original size:22 final size:22
Alignment explanation
Indices: 31408084--31408129 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
31408074 TGGGTTTCAA
31408084 AGAATTTTGGAAGGAAATTGAG
1 AGAATTTTGGAAGGAAATTGAG
31408106 AGAATTTTGGAAGGAAATTGAG
1 AGAATTTTGGAAGGAAATTGAG
31408128 AG
1 AG
31408130 GATTAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (22 bp):
AGAATTTTGGAAGGAAATTGAG
Found at i:31421039 original size:18 final size:18
Alignment explanation
Indices: 31421016--31421053 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31421006 TTTAAAAATA
31421016 TATATAAATTAA-AATTTT
1 TATAT-AATTAATAATTTT
*
31421034 TATATATTTAATAATTTT
1 TATATAATTAATAATTTT
31421052 TA
1 TA
31421054 ATTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATTAATAATTTT
Found at i:31432039 original size:19 final size:19
Alignment explanation
Indices: 31432015--31432054 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31432005 AGATGTCTAT
31432015 AATCATGGAATTCAGGACC
1 AATCATGGAATTCAGGACC
31432034 AATCATGGAATTCAGGACC
1 AATCATGGAATTCAGGACC
31432053 AA
1 AA
31432055 GGAAAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
AATCATGGAATTCAGGACC
Found at i:31436552 original size:177 final size:177
Alignment explanation
Indices: 31436256--31436613 Score: 635
Period size: 177 Copynumber: 2.0 Consensus size: 177
31436246 CGAGTGATTG
* * *
31436256 GTGAGTGTTTGGAATCGCTGTTAGTAGACATGATTCATAGTGTTAATTGGGAGCTTAGGAATAGC
1 GTGAGTGTTTGGAATCACTGCTAGTAGACACGATTCATAGTGTTAATTGGGAGCTTAGGAATAGC
* *
31436321 CTAAACCCCTATCCTAAGTTCCAAGTGTAAGCTTTCTATTTCCCCTTGATTTATTTTGGTAAAAT
66 CTAAACCCCTATCCTAAGTTCCAAGTGTAAGATTTCTATTTCCCCTTGATTTATTTTGGCAAAAT
* * *
31436386 GTGTGATTATGTGAATAATTGTGGATTGAGTAATATGATGTGTTATT
131 GTGTGATTATGTGAATAATTGTGGACTGAGTAATATGATGCGATATT
31436433 GTGAGTGTTTGGAATCACTGCTAGTAGACACGATTCATAGTGTTAATTGGGAGCTTAGGAATAGC
1 GTGAGTGTTTGGAATCACTGCTAGTAGACACGATTCATAGTGTTAATTGGGAGCTTAGGAATAGC
*
31436498 CTAAACCCGTATCCTAAGTTCCAAGTGTAAGATTTCTATTTCCCCTTGATTTATTTTGGCAAAAT
66 CTAAACCCCTATCCTAAGTTCCAAGTGTAAGATTTCTATTTCCCCTTGATTTATTTTGGCAAAAT
31436563 GTGTGATTATGTGAATAATTGTGGACTGAGTAATATGATGCGATATT
131 GTGTGATTATGTGAATAATTGTGGACTGAGTAATATGATGCGATATT
31436610 GTGA
1 GTGA
31436614 CATGAGATGT
Statistics
Matches: 172, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 172 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (177 bp):
GTGAGTGTTTGGAATCACTGCTAGTAGACACGATTCATAGTGTTAATTGGGAGCTTAGGAATAGC
CTAAACCCCTATCCTAAGTTCCAAGTGTAAGATTTCTATTTCCCCTTGATTTATTTTGGCAAAAT
GTGTGATTATGTGAATAATTGTGGACTGAGTAATATGATGCGATATT
Found at i:31439322 original size:20 final size:21
Alignment explanation
Indices: 31439284--31439322 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31439274 AGACTAAATC
31439284 GGAAACTAATAAAACTTTTTA
1 GGAAACTAATAAAACTTTTTA
31439305 GGAAA-TAATGAAAA-TTTT
1 GGAAACTAAT-AAAACTTTT
31439323 CAAAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (21 bp):
GGAAACTAATAAAACTTTTTA
Found at i:31442918 original size:15 final size:16
Alignment explanation
Indices: 31442889--31442918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31442879 CAAACATGCT
31442889 TTAACACATTATCAAA
1 TTAACACATTATCAAA
31442905 TTAACACA-TATCAA
1 TTAACACATTATCAA
31442919 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:31443402 original size:15 final size:16
Alignment explanation
Indices: 31443384--31443413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31443374 TTTCATTTTT
31443384 ATTTCA-TTACTTTCC
1 ATTTCATTTACTTTCC
31443399 ATTTCATTTACTTTC
1 ATTTCATTTACTTTC
31443414 TTTAACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTCATTTACTTTCC
Found at i:31455043 original size:115 final size:114
Alignment explanation
Indices: 31454837--31455181 Score: 528
Period size: 115 Copynumber: 3.0 Consensus size: 114
31454827 AACTTTAAGC
* *
31454837 CTCGACGTAAAGTGGTACTCGAGGAACTTTCAGGAGTGGTAGAACAATCACCAAGTTCAATTCGT
1 CTCGAGGTAAAGTGGTACTCGAGGAACTTTCGGGAGTGGTAGAACAATCACCAAGTTCAATTC-T
* * *
31454902 GAGAAATTTGCAGAAAAACCTACAAACGATCAACAACATAGAGGAATACG
65 GAGAAAGTTGTAGAAAAACCTGCAAACGATCAACAACATAGAGGAATACG
*
31454952 CTCGAGGTAAAGTGGTACTCGAGGAACTTTCGGGAGTGGTAGAACAATCACCAAGTTTAATTCTC
1 CTCGAGGTAAAGTGGTACTCGAGGAACTTTCGGGAGTGGTAGAACAATCACCAAGTTCAATTCT-
* * * *
31455017 AAAAAAGTTATAGAAAAACCTGCAAACGATCAACAACATCGAGGAATACG
65 GAGAAAGTTGTAGAAAAACCTGCAAACGATCAACAACATAGAGGAATACG
* * *
31455067 CTCAAGGTAAAGTGGTACTCGAGGAACTTTCGAGAGTGGTAGAACAATCACCAAGTTCAATCCTT
1 CTCGAGGTAAAGTGGTACTCGAGGAACTTTCGGGAGTGGTAGAACAATCACCAAGTTCAATTC-T
* *
31455132 GAGAAAGTTGTAGAAAAACCTGCAAAAGATCAACAACATAGAAGAATACG
65 GAGAAAGTTGTAGAAAAACCTGCAAACGATCAACAACATAGAGGAATACG
31455182 TCGTAGTGGG
Statistics
Matches: 208, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
114 1 0.00
115 206 0.99
116 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (114 bp):
CTCGAGGTAAAGTGGTACTCGAGGAACTTTCGGGAGTGGTAGAACAATCACCAAGTTCAATTCTG
AGAAAGTTGTAGAAAAACCTGCAAACGATCAACAACATAGAGGAATACG
Found at i:31456589 original size:45 final size:45
Alignment explanation
Indices: 31456525--31456696 Score: 208
Period size: 45 Copynumber: 3.9 Consensus size: 45
31456515 TACTGGGTAC
*
31456525 CATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCAAGTAT
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCAAGTAT
* *
31456570 CATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCCACCAGGTA-
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCAAGTAT
* * *
31456614 CTATTGATTATGAAGGTGGCTT-TTATGTGTTGATTCCACTAAGTAT
1 C-ATTGATTATAAAGGTGG-TTGTTATGTGCTGATTCCACCAAGTAT
* * * *
31456660 CATTGACTATAAGGGCGG-TGCTATGTGCTGA-TCCACC
1 CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACC
31456697 GTGTATCTGT
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
43 6 0.05
44 10 0.09
45 91 0.83
46 3 0.03
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGTTATGTGCTGATTCCACCAAGTAT
Found at i:31483957 original size:16 final size:16
Alignment explanation
Indices: 31483938--31483979 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
31483928 ATTAGTAGTT
31483938 AATAAATAATTTCGTA
1 AATAAATAATTTCGTA
* *
31483954 AATAAATAAATTGGTA
1 AATAAATAATTTCGTA
31483970 AATAAATAAT
1 AATAAATAAT
31483980 AATAAACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (16 bp):
AATAAATAATTTCGTA
Found at i:31485722 original size:6 final size:6
Alignment explanation
Indices: 31485711--31485752 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
31485701 TTTTAGTTAG
31485711 TTATTT TTATTT TTACTTT TTATTT TTA-TT TTATTT ATTATT
1 TTATTT TTATTT TTA-TTT TTATTT TTATTT TTATTT -TTATT
31485753 CTATTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.15
6 17 0.52
7 11 0.33
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:31485742 original size:12 final size:12
Alignment explanation
Indices: 31485711--31485752 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
31485701 TTTTAGTTAG
31485711 TTATTTTTATTT
1 TTATTTTTATTT
31485723 TTACTTTTTATTT
1 TTA-TTTTTATTT
31485736 TTA-TTTTATTT
1 TTATTTTTATTT
31485747 ATTATT
1 -TTATT
31485753 CTATTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.30
12 6 0.22
13 13 0.48
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:31486305 original size:299 final size:299
Alignment explanation
Indices: 31485767--31486367 Score: 1121
Period size: 299 Copynumber: 2.0 Consensus size: 299
31485757 TTTTGTTTCC
*
31485767 GCAAATAAACTTCAGATGCAATCAAGATGGGTTTTAATTTAATTTTTGGGTTTTTCTCTTATTAT
1 GCAAATAAACTTCAGATGCAATCAAGATGGGTTGTAATTTAATTTTTGGGTTTTTCTCTTATTAT
*
31485832 TTTCCTCTGATGAATGTTTTGAACAATGAGGACATTGCTCTGCTTAAGTTTGGGGGGATTGTGCC
66 TTTCCTCTGATGAATGTTTTGAACAATGAGGACATTGCTCTACTTAAGTTTGGGGGGATTGTGCC
* *
31485897 TCAATTTTTTTGAGGAAGATGACTCTTGCATGAGGCAAGTAAGTAGAAAAGGTGCTCAACATCAA
131 TCAATTTTTTTGAGGAAGATGACTCTTGCATGAGGCAAGTAAGCAAAAAAGGTGCTCAACATCAA
31485962 TCAATTTTGTATGGCATGTTAGTCCGGATTCAGGTATGATCTTCTATTTACTTCAAGTATTTTTT
196 TCAATTTTGTATGGCATGTTAGTCCGGATTCAGGTATGATCTTCTATTTACTTCAAGTATTTTTT
31486027 ATGTTAAGTAAATCATGAAATGAATGTTAATTTTAATGA
261 ATGTTAAGTAAATCATGAAATGAATGTTAATTTTAATGA
* *
31486066 GCAAATAAACTTCAGATGCAATCAAGATTGGTTGTAATTTACTTTTTGGGTTTTTCTCTTATTAT
1 GCAAATAAACTTCAGATGCAATCAAGATGGGTTGTAATTTAATTTTTGGGTTTTTCTCTTATTAT
*
31486131 TTTCCTCTGATGAATGTTTTGAACAATGAGGACATTGTTCTACTTAAGTTTGGGGGGATTGTGCC
66 TTTCCTCTGATGAATGTTTTGAACAATGAGGACATTGCTCTACTTAAGTTTGGGGGGATTGTGCC
*
31486196 TCAATTTTTTTTAGGAAGATGACTCTTGCATGAGGCAAGTAAGCAAAAAAGGTGCTCAACATCAA
131 TCAATTTTTTTGAGGAAGATGACTCTTGCATGAGGCAAGTAAGCAAAAAAGGTGCTCAACATCAA
31486261 TCAATTTTGTATGGCATGTTAGTCCGGATTCAGGTATGATCTTCTATTTACTTCAAGTATTTTTT
196 TCAATTTTGTATGGCATGTTAGTCCGGATTCAGGTATGATCTTCTATTTACTTCAAGTATTTTTT
*
31486326 ATGTTAAGTAAATCATGAAATGAATGTTGATTTTAATGA
261 ATGTTAAGTAAATCATGAAATGAATGTTAATTTTAATGA
31486365 GCA
1 GCA
31486368 TGTATAGATT
Statistics
Matches: 293, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
299 293 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (299 bp):
GCAAATAAACTTCAGATGCAATCAAGATGGGTTGTAATTTAATTTTTGGGTTTTTCTCTTATTAT
TTTCCTCTGATGAATGTTTTGAACAATGAGGACATTGCTCTACTTAAGTTTGGGGGGATTGTGCC
TCAATTTTTTTGAGGAAGATGACTCTTGCATGAGGCAAGTAAGCAAAAAAGGTGCTCAACATCAA
TCAATTTTGTATGGCATGTTAGTCCGGATTCAGGTATGATCTTCTATTTACTTCAAGTATTTTTT
ATGTTAAGTAAATCATGAAATGAATGTTAATTTTAATGA
Found at i:31487054 original size:21 final size:21
Alignment explanation
Indices: 31487030--31487069 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31487020 GTCTCATACA
31487030 TCAA-CATAAACATAGCATAAG
1 TCAATCATAAACAT-GCATAAG
*
31487051 TCAATCATATACATGCATA
1 TCAATCATAAACATGCATA
31487070 TCATCCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (21 bp):
TCAATCATAAACATGCATAAG
Found at i:31490219 original size:23 final size:22
Alignment explanation
Indices: 31490193--31490237 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31490183 AAATTGTTTA
31490193 TTTA-CCATTTAAGTCCATTTAAT
1 TTTATCCA-TTAAG-CCATTTAAT
*
31490216 TTTATTCATTAAGCCATTTAAT
1 TTTATCCATTAAGCCATTTAAT
31490238 CATTCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 9 0.45
24 2 0.10
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTATCCATTAAGCCATTTAAT
Found at i:31491297 original size:68 final size:68
Alignment explanation
Indices: 31491188--31491324 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
31491178 GGGCTTAGAC
*
31491188 AGAACAGCTTGAAGGATTCAGAACCTTTCACGTTGGGTTTCAAAGAAAACTTCATTCCAAACCCA
1 AGAACAGCTTGAAGGATTCAGAACCTATCACGTTGGGTTTCAAAGAAAACTTCATTCCAAACCCA
31491253 ATT
66 ATT
* *
31491256 AGAACAGCTTGAAGGATTCAGAACCTATCACGTTGGGTTTCAAAGCAAACTTCATTCCAGACCCA
1 AGAACAGCTTGAAGGATTCAGAACCTATCACGTTGGGTTTCAAAGAAAACTTCATTCCAAACCCA
31491321 ATT
66 ATT
31491324 A
1 A
31491325 CATGGATACT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.26
Consensus pattern (68 bp):
AGAACAGCTTGAAGGATTCAGAACCTATCACGTTGGGTTTCAAAGAAAACTTCATTCCAAACCCA
ATT
Found at i:31495642 original size:24 final size:24
Alignment explanation
Indices: 31495610--31495656 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
31495600 TTGCAGATTG
*
31495610 AAAAAAAT-ATTAGTAAATTAATT
1 AAAAAAATAATTACTAAATTAATT
*
31495633 AAAAATAATAATTACTAATTTAAT
1 AAAAA-AATAATTACTAAATTAAT
31495657 CGAGTCACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAAAATAATTACTAAATTAATT
Found at i:31503123 original size:25 final size:22
Alignment explanation
Indices: 31503067--31503125 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 22
31503057 GAGTAAAAAT
31503067 AAAATAAGAAAAAAAGAACTAC
1 AAAATAAGAAAAAAAGAACTAC
*
31503089 ATAATAAGAAAATAGAAGAAACTAC
1 AAAATAAGAAAA-A-AAG-AACTAC
*
31503114 AAAATGAGAAAA
1 AAAATAAGAAAA
31503126 GAACAAGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.35
23 1 0.03
24 3 0.10
25 16 0.52
ACGTcount: A:0.69, C:0.07, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAATAAGAAAAAAAGAACTAC
Found at i:31508176 original size:15 final size:15
Alignment explanation
Indices: 31508156--31508187 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31508146 AAAGAAATAA
31508156 TTTAATTTTTAAACT
1 TTTAATTTTTAAACT
31508171 TTTAATTTTTAAACT
1 TTTAATTTTTAAACT
31508186 TT
1 TT
31508188 GGTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTTTTAAACT
Found at i:31508935 original size:18 final size:18
Alignment explanation
Indices: 31508865--31508948 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
31508855 ATATAGGCTT
* *
31508865 ATGCACATTGTGTGTCAGG
1 ATGCAC-TTATGTGCCAGG
* * **
31508884 ATGCGCTTATGCGCCAAT
1 ATGCACTTATGTGCCAGG
*
31508902 ATGCACTTCGTGTGCCAGG
1 ATGCACTT-ATGTGCCAGG
31508921 ATGCACTTATGTGCC-GG
1 ATGCACTTATGTGCCAGG
*
31508938 AATGCGCTTAT
1 -ATGCACTTAT
31508949 ACGCCAATAT
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
17 2 0.04
18 29 0.58
19 19 0.38
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (18 bp):
ATGCACTTATGTGCCAGG
Found at i:31511027 original size:16 final size:19
Alignment explanation
Indices: 31510989--31511027 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
31510979 TTTTTCCCTA
31510989 ATTAAGTAATTTTTAAATC
1 ATTAAGTAATTTTTAAATC
31511008 -TTAAGT-A-TTTTAAA-C
1 ATTAAGTAATTTTTAAATC
31511023 ATTAA
1 ATTAA
31511028 AGGGCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.05
16 11 0.58
17 1 0.05
18 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTAAGTAATTTTTAAATC
Found at i:31511427 original size:75 final size:76
Alignment explanation
Indices: 31511276--31511450 Score: 228
Period size: 75 Copynumber: 2.3 Consensus size: 76
31511266 TAAACTCACA
** * *
31511276 TTAAATGTTACTTAAAACATTAAGGGGTTTTAAAGAAATAAAGAAACTCATAAATAACGGGAAAT
1 TTAAATGTTACTT-AAACATTAAGGACTTTTAAAGAAATAAAGAAACTCATAAATAACGAGAAAA
31511341 TTACTTAATTTC
65 TTACTTAATTTC
* * * * *
31511353 TTAAATGTTACATAAAGATTAAAGGACTTTTAAA-AAATTAAGTAACTCA-AAATAATGAGAAAA
1 TTAAATGTTACTTAAACATT-AAGGACTTTTAAAGAAATAAAGAAACTCATAAATAACGAGAAAA
31511416 TTACTTAATTTC
65 TTACTTAATTTC
31511428 TTAAATGTTACTTAAAACATTAA
1 TTAAATGTTACTT-AAACATTAA
31511451 AAATTCCTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
75 37 0.44
76 25 0.29
77 23 0.27
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (76 bp):
TTAAATGTTACTTAAACATTAAGGACTTTTAAAGAAATAAAGAAACTCATAAATAACGAGAAAAT
TACTTAATTTC
Found at i:31511484 original size:23 final size:24
Alignment explanation
Indices: 31511458--31511505 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
31511448 TAAAAATTCC
31511458 TAAATCTT-GCTAAATTACTTAAT
1 TAAATCTTGGCTAAATTACTTAAT
* *
31511481 TAAATCTTGGGTAATTTACTTAAT
1 TAAATCTTGGCTAAATTACTTAAT
31511505 T
1 T
31511506 TCTTAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.46
Consensus pattern (24 bp):
TAAATCTTGGCTAAATTACTTAAT
Found at i:31511658 original size:77 final size:77
Alignment explanation
Indices: 31511341--31511852 Score: 333
Period size: 77 Copynumber: 6.8 Consensus size: 77
31511331 AACGGGAAAT
* * * * * * **
31511341 TTACTTAATTTCTTAAATG-TTACATAAA-GATT-AAAGGACTTTTAAAAAATTAAGTAACTCAA
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGA-TTTTAAGAAATCAAATAATTTTA
** * *
31511403 AATAATGAGAAAA
65 AATCTTGGGTAAA
* * ** *
31511416 TTACTTAATTTCTTAAATG-TTACTTAAAACATTAAAA--ATTCCTAA-ATCTTGCTAAATTACT
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGATT-TTAAGA-AAT-C-AAA-TAAT
*
31511477 TAATTAAATCTTGGGTAAT
61 T--TTAAATCTTGGGTAAA
*
31511496 TTACTTAATTTCTTAAATGA-GACTTAAAAT-ATT-AAAGGATTTTTAA-AAAT-AAATTAATTT
1 TTACTTAATTTCTTAAATGATTACTT-AAATCATTAAAAGGA-TTTTAAGAAATCAAA-TAATTT
31511556 CTAAATCTTGGGTAAA
63 -TAAATCTTGGGTAAA
* * * *
31511572 TAACTTAATTTTTTAAA-GATTACTTAAATCATTAAAAGGCTTTTAAGAAATCAAATAATTCTTG
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGATTTTAAGAAATCAAATAATT-TTA
*
31511636 AATCTTGGGAAAA
65 AATCTTGGGTAAA
* * ***
31511649 TTACTTAATTTCTTAAATG-TTACTTAAAACATTAAAAGGATTTAAAGAAATCACGGAATTTTTA
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGATTTTAAGAAATCAAATAA-TTTTA
31511713 AATCTTGGGTAAA
65 AATCTTGGGTAAA
* * * * *
31511726 TTATTTAATTTCTTAAATG-TTGC------C----AAAGGAATTTAAAGAAATTAAGTAATTACT
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGG-ATTTTAAGAAATCAAATAATT--T
*
31511780 T-AATCAT-GGTAAA
63 TAAATCTTGGGTAAA
* * *
31511793 TTATTTAATTTCTTAAATG-TTACTTAAAACATTAAAGGGATTTTAAGAAATCAAATAATT
1 TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGATTTTAAGAAATCAAATAATT
31511853 CGAAAATCAA
Statistics
Matches: 351, Mismatches: 50, Indels: 71
0.74 0.11 0.15
Matches are distributed among these distances:
67 35 0.10
68 21 0.06
69 2 0.01
71 1 0.00
73 1 0.00
74 3 0.01
75 39 0.11
76 63 0.18
77 127 0.36
78 10 0.03
79 3 0.01
80 36 0.10
81 8 0.02
82 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (77 bp):
TTACTTAATTTCTTAAATGATTACTTAAATCATTAAAAGGATTTTAAGAAATCAAATAATTTTAA
ATCTTGGGTAAA
Found at i:31512302 original size:17 final size:17
Alignment explanation
Indices: 31512272--31512405 Score: 89
Period size: 17 Copynumber: 7.9 Consensus size: 17
31512262 TTTATAATTA
*
31512272 TATTTTTAGAATATTTTT
1 TATTTTTA-TATATTTTT
31512290 TATTTTTATATATTTTT
1 TATTTTTATATATTTTT
** *
31512307 TAAATTTATA-A--TTA
1 TATTTTTATATATTTTT
*
31512321 TATTTTTAGAATATTTTT
1 TATTTTTA-TATATTTTT
*
31512339 TATTTGTATATATTTTT
1 TATTTTTATATATTTTT
**
31512356 TAAATTTAT-TATTTTAT
1 TATTTTTATATATTTT-T
* * *
31512373 T-TTTTGAAAATATTTATG
1 TATTTT-TATATATTT-TT
31512391 TATTTTTATATATTT
1 TATTTTTATATATTT
31512406 CTTTTAATTT
Statistics
Matches: 87, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.09
15 1 0.01
16 10 0.11
17 33 0.38
18 30 0.34
19 5 0.06
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TATTTTTATATATTTTT
Found at i:31512317 original size:49 final size:49
Alignment explanation
Indices: 31512256--31512416 Score: 232
Period size: 49 Copynumber: 3.2 Consensus size: 49
31512246 TAAATTTAAA
31512256 TTTAAATTTATAATTATATTTTTAGAATATTTTTTATTTTTATATATTT
1 TTTAAATTTATAATTATATTTTTAGAATATTTTTTATTTTTATATATTT
*
31512305 TTTAAATTTATAATTATATTTTTAGAATATTTTTTATTTGTATATATTT
1 TTTAAATTTATAATTATATTTTTAGAATATTTTTTATTTTTATATATTT
* * * *
31512354 TTTAAATTTATTATTTTATTTTTTGAAAATATTTATGTATTTTTATATATTT
1 TTTAAATTTATAATTATA-TTTTT-AGAATATTT-TTTATTTTTATATATTT
*
31512406 CTTTTAATTTA
1 -TTTAAATTTA
31512417 CTAGAATTAG
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 64 0.63
50 5 0.05
51 8 0.08
52 15 0.15
53 9 0.09
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (49 bp):
TTTAAATTTATAATTATATTTTTAGAATATTTTTTATTTTTATATATTT
Found at i:31512321 original size:23 final size:23
Alignment explanation
Indices: 31512295--31512377 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 23
31512285 TTTTTTATTT
31512295 TTATATATTTTTTAAATTTATAA
1 TTATATATTTTTTAAATTTATAA
** * *
31512318 TTATAT-TTTTAGAATATTTTTTATT
1 TTATATATTTTTTAA-A-TTTATA-A
*
31512343 TGTATATATTTTTTAAATTTATTA
1 T-TATATATTTTTTAAATTTATAA
31512367 TT-T-TATTTTTT
1 TTATATATTTTTT
31512378 GAAAATATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 8 0.17
22 7 0.15
23 8 0.17
24 6 0.13
25 5 0.11
26 6 0.13
27 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATATATTTTTTAAATTTATAA
Found at i:31517764 original size:75 final size:77
Alignment explanation
Indices: 31517621--31517769 Score: 169
Period size: 75 Copynumber: 2.0 Consensus size: 77
31517611 TATTAATTTA
* * * * *
31517621 TTTTAAGAAATTAGGTAATTCTTAAATCATAGGAAAATTACATTAATTTTATAAAGGAAACTTAA
1 TTTTAAGAAATTAAGTAATTCCTAAATCATAGGAAAATAACATTAATTTTATAAACGAAACATAA
31517686 AACAATAAAGGT
66 AACAATAAAGGT
** * **
31517698 TTTTAAGAAA-TAAGTAATTCCTAAATTGT-GGATAAATAAC-TTAATTTTGTAAACGCTACATA
1 TTTTAAGAAATTAAGTAATTCCTAAATCATAGGA-AAATAACATTAATTTTATAAACGAAACATA
*
31517760 AAACATTAAA
65 AAACAATAAA
31517770 CGATTTTTCT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
75 29 0.48
76 21 0.35
77 10 0.17
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (77 bp):
TTTTAAGAAATTAAGTAATTCCTAAATCATAGGAAAATAACATTAATTTTATAAACGAAACATAA
AACAATAAAGGT
Found at i:31517993 original size:16 final size:16
Alignment explanation
Indices: 31517974--31518006 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31517964 TAGTTTTATT
*
31517974 AATATTTAATTTTAAA
1 AATATTTAATATTAAA
31517990 AATATTTAATATTAAA
1 AATATTTAATATTAAA
31518006 A
1 A
31518007 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTTAATATTAAA
Found at i:31520342 original size:69 final size:69
Alignment explanation
Indices: 31520225--31520447 Score: 308
Period size: 69 Copynumber: 3.3 Consensus size: 69
31520215 TTTTAAGCTA
* * *
31520225 TTAAAATTAA-TTTTTAA-AGAAAATAGTGAAGAAGTTAGCTATGAGAGTATTCTCTAGTGAATG
1 TTAAAATTAACTTTTTAATA-AAAATAGTGAAGAAGTAAGCTATGGGAGTATTCTCTAGAGAATG
31520288 TGGGG
65 TGGGG
* *
31520293 TTAAAATTAACTTTTTAATAAAAATAGTGAAGAAGTAAGCTAAGGGAGTATTCTCTAAAGAATGT
1 TTAAAATTAACTTTTTAATAAAAATAGTGAAGAAGTAAGCTATGGGAGTATTCTCTAGAGAATGT
31520358 GGGG
66 GGGG
* * * **
31520362 TTAAAATTATCTTTTTAATAAAAATAGTGAAAAAGTGAGCTATGGGAGTATTCTCTAGCCAATGT
1 TTAAAATTAACTTTTTAATAAAAATAGTGAAGAAGTAAGCTATGGGAGTATTCTCTAGAGAATGT
31520427 -GGG
66 GGGG
* *
31520430 ATAAAATTAACTGTTTAA
1 TTAAAATTAACTTTTTAA
31520448 GGAAAATAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
68 28 0.20
69 109 0.79
70 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (69 bp):
TTAAAATTAACTTTTTAATAAAAATAGTGAAGAAGTAAGCTATGGGAGTATTCTCTAGAGAATGT
GGGG
Found at i:31522101 original size:13 final size:13
Alignment explanation
Indices: 31522057--31522101 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
31522047 TAGTTATTTG
*
31522057 TTTATTTTATTTTT
1 TTTA-TTTATTTCT
*
31522071 TTTATTTATTTCA
1 TTTATTTATTTCT
*
31522084 ATTATTTATTTCT
1 TTTATTTATTTCT
31522097 TTTAT
1 TTTAT
31522102 GATTTTTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTCT
Found at i:31530962 original size:20 final size:19
Alignment explanation
Indices: 31530934--31531003 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
31530924 ATATTTAGCT
31530934 TTATATTTATTTATAATTAA
1 TTATATTTATTTATAATT-A
* ** *
31530954 TTATGTTTAAATAAAATTA
1 TTATATTTATTTATAATTA
*
31530973 TTAATATTTATTTATAAAT-
1 TT-ATATTTATTTATAATTA
31530992 TTATTATTTATT
1 TTA-TATTTATT
31531004 ATTATATTCA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.03
19 13 0.33
20 25 0.64
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TTATATTTATTTATAATTA
Found at i:31531064 original size:24 final size:24
Alignment explanation
Indices: 31531037--31531083 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31531027 CATATTATTA
* * *
31531037 TTTATCCATAGTATATAAAATATG
1 TTTATCAAAAGTAGATAAAATATG
*
31531061 TTTATTAAAAGTAGATAAAATAT
1 TTTATCAAAAGTAGATAAAATAT
31531084 TCACCTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTATCAAAAGTAGATAAAATATG
Found at i:31532769 original size:11 final size:11
Alignment explanation
Indices: 31532755--31532780 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31532745 ATTTTTTTAA
31532755 TTTTAAAATAT
1 TTTTAAAATAT
31532766 TTTTAAAATAT
1 TTTTAAAATAT
31532777 TTTT
1 TTTT
31532781 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:31532800 original size:20 final size:19
Alignment explanation
Indices: 31532763--31532801 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31532753 AATTTTAAAA
*
31532763 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATAATTTTT
31532782 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAAT-AATTTTT
31532802 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:31537223 original size:50 final size:49
Alignment explanation
Indices: 31537094--31537336 Score: 175
Period size: 50 Copynumber: 4.8 Consensus size: 49
31537084 GATATTAACA
* * * *
31537094 TGCCAAAGCCATGTTCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-TTTCATAT-CGG
* * * * * *
31537143 TGCAAATGCCATATCTCAGATATGGCCTTACATGAGAGTTTTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTTTCATATCGG
* ** * * *
31537193 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTTTCATATCGG
* * * * **
31537243 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTTTCAT-A--TC---GG
31537299 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
31537337 CTCATTCCCT
Statistics
Matches: 151, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.23
50 78 0.52
53 2 0.01
56 35 0.23
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTTTCATATCGG
Found at i:31543528 original size:24 final size:25
Alignment explanation
Indices: 31543490--31543544 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
31543480 CGGTTGGGAA
*
31543490 AGAAAAACTTAAGTTAGGGAATTGG
1 AGAAAAAATTAAGTTAGGGAATTGG
* *
31543515 GGAAAAAATT-AGTTAGGGATTTGG
1 AGAAAAAATTAAGTTAGGGAATTGG
31543539 AGAAAA
1 AGAAAA
31543545 TGATTTATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (25 bp):
AGAAAAAATTAAGTTAGGGAATTGG
Found at i:31544050 original size:20 final size:20
Alignment explanation
Indices: 31544027--31544068 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
31544017 TTAATTTATT
*
31544027 AATTTAAAT-TTTGGGGACTA
1 AATTGAAATATTT-GGGACTA
*
31544047 AATTGAAATATTTTGGACTA
1 AATTGAAATATTTGGGACTA
31544067 AA
1 AA
31544069 CTAAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
AATTGAAATATTTGGGACTA
Found at i:31548373 original size:28 final size:28
Alignment explanation
Indices: 31548337--31548392 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
31548327 ATGAATTAAA
* *
31548337 CTAATTAAATTAATTAAACTAAAATAAC
1 CTAACTAAATTAAGTAAACTAAAATAAC
**
31548365 CTAACTAAATTAAGTAGTCTAAAATAAC
1 CTAACTAAATTAAGTAAACTAAAATAAC
31548393 TTATTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (28 bp):
CTAACTAAATTAAGTAAACTAAAATAAC
Found at i:31548689 original size:4 final size:4
Alignment explanation
Indices: 31548680--31548713 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
31548670 CAATTTTAGA
*
31548680 TAAT TAAT TAAT TAAT TAAT TAAT TAAT AAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
31548714 GATCCATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:31564265 original size:3 final size:3
Alignment explanation
Indices: 31564257--31564297 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31564247 AGTGCATAAA
31564257 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
31564298 GATCTTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:31568218 original size:18 final size:18
Alignment explanation
Indices: 31568182--31568223 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31568172 GTTGGGTTGA
*
31568182 AATGGGCTGTGTGGGCTC
1 AATGGGCTGTGTGGCCTC
31568200 AATGGGCTCGT-TGGCCTC
1 AATGGGCT-GTGTGGCCTC
31568218 ACATGG
1 A-ATGG
31568224 ATGAAATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.14, C:0.21, G:0.38, T:0.26
Consensus pattern (18 bp):
AATGGGCTGTGTGGCCTC
Found at i:31568506 original size:27 final size:27
Alignment explanation
Indices: 31568446--31568617 Score: 247
Period size: 27 Copynumber: 6.4 Consensus size: 27
31568436 CCCTAAAATA
*
31568446 GGTAAAATAACCAAAATACCCC-ATAG
1 GGTAAAATGACCAAAATACCCCTATAG
31568472 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
*
31568499 GGTAAAATGATCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
*
31568526 GGTAGAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * * *
31568553 GGTAGAATGAACAAAATACCCCCACAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * *
31568580 GGTAAAATGACCGAAATACCTCAATAG
1 GGTAAAATGACCAAAATACCCCTATAG
31568607 GGTAAAATGAC
1 GGTAAAATGAC
31568618 TGTTATACCC
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
26 21 0.16
27 111 0.84
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCTATAG
Found at i:31569152 original size:34 final size:34
Alignment explanation
Indices: 31569079--31569144 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
31569069 TCACAGTATG
** *
31569079 ACTGATATCTATTACTGTTATGGGCCAAGGCCCC
1 ACTGATATCTATTACTGAAATGGGCAAAGGCCCC
31569113 ACTGATA-CTATTACTGAAATTGGGCAAAGGCC
1 ACTGATATCTATTACTGAAA-TGGGCAAAGGCC
31569145 TTACTGATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (34 bp):
ACTGATATCTATTACTGAAATGGGCAAAGGCCCC
Found at i:31571185 original size:20 final size:21
Alignment explanation
Indices: 31571162--31571201 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31571152 GGGTGAGAAG
31571162 AAAAAGTTTAGGGG-GAAAAT
1 AAAAAGTTTAGGGGAGAAAAT
*
31571182 AAAAAGTTTTGGGGAGAAAA
1 AAAAAGTTTAGGGGAGAAAA
31571202 AGTTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (21 bp):
AAAAAGTTTAGGGGAGAAAAT
Found at i:31571215 original size:23 final size:23
Alignment explanation
Indices: 31571188--31571231 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31571178 AAATAAAAAG
31571188 TTTTGG-GGAGAAAAAGTTTAATA
1 TTTTGGAGG-GAAAAAGTTTAATA
*
31571211 TTTTGGAGGGAAAATGTTTAA
1 TTTTGGAGGGAAAAAGTTTAA
31571232 AAAAATTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (23 bp):
TTTTGGAGGGAAAAAGTTTAATA
Found at i:31571534 original size:9 final size:9
Alignment explanation
Indices: 31571516--31571552 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31571506 TATAATTTTA
31571516 TATTCGAAT
1 TATTCGAAT
*
31571525 TATTCTAAT
1 TATTCGAAT
*
31571534 TATTCGAGT
1 TATTCGAAT
31571543 TATTCGAAT
1 TATTCGAAT
31571552 T
1 T
31571553 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31580504 original size:22 final size:23
Alignment explanation
Indices: 31580471--31580514 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
31580461 TCTATCGAAA
*
31580471 ATTATCAAAATTCATCAAAATTT
1 ATTATCAAAATTAATCAAAATTT
*
31580494 ATTAT-AAAATTAATTAAAATT
1 ATTATCAAAATTAATCAAAATT
31580515 CAACATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTATCAAAATTAATCAAAATTT
Found at i:31582952 original size:138 final size:137
Alignment explanation
Indices: 31582704--31582958 Score: 323
Period size: 138 Copynumber: 1.9 Consensus size: 137
31582694 GAGCCATAAA
* * * ** *
31582704 TAGGTCTCCTCACACAAGTTGATGGTCGGAATGTAACTACACGATGCCACTTGCACAAGCTGATG
1 TAGGTCTCCTCACACAAGCTGATGGTCGGAATGTAACTACACAATACCACTCACACAAGCTAATG
* * * *
31582769 AGTATTTGCAAAAAATGTTGAAACTCAGCCATCGGTAGGACATTCAGGACCAGCACCCTGAGCAT
66 AGTATTTGCAAAAAATGTAGAAACTCAGCCATCGGTAGAAAATTCAAGACCAGCACCCTGAGCAT
31582834 GGTAACC
131 GGTAACC
* * ***
31582841 TAGGTCTGCTGACACAAGCTGATGGTCGGAATGTAAGCTACACAATATTGCTCACACAAGCTAAT
1 TAGGTCTCCTCACACAAGCTGATGGTCGGAATGTAA-CTACACAATACCACTCACACAAGCTAAT
* * *
31582906 GAGTATTTGTAATAAATGTCAG-ACCTCAGCCATCGGTAGAAAATTCAAGACCA
65 GAGTATTTGCAAAAAATGT-AGAAACTCAGCCATCGGTAGAAAATTCAAGACCA
31582959 ACATCCAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
137 33 0.34
138 64 0.65
139 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (137 bp):
TAGGTCTCCTCACACAAGCTGATGGTCGGAATGTAACTACACAATACCACTCACACAAGCTAATG
AGTATTTGCAAAAAATGTAGAAACTCAGCCATCGGTAGAAAATTCAAGACCAGCACCCTGAGCAT
GGTAACC
Found at i:31589363 original size:2 final size:2
Alignment explanation
Indices: 31589358--31589382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31589348 AAATAGTAAT
31589358 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
31589383 TTAGGTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31595671 original size:17 final size:18
Alignment explanation
Indices: 31595649--31595684 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
31595639 AAGAAAAGCA
*
31595649 TAAAAATTAAAA-CAAAT
1 TAAAAATCAAAACCAAAT
31595666 TAAAAATCAAAACCAAAT
1 TAAAAATCAAAACCAAAT
31595684 T
1 T
31595685 CCTATGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAATCAAAACCAAAT
Found at i:31609937 original size:27 final size:29
Alignment explanation
Indices: 31609877--31609937 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
31609867 CATAGTTGTA
31609877 ACACCCCTAACCCATGCATAAACCGTTCAT
1 ACACCCCTAA-CCATGCATAAACCGTTCAT
* *
31609907 ACACCCCTAA-CAT-CATTAATCGTTCAT
1 ACACCCCTAACCATGCATAAACCGTTCAT
31609934 ACAC
1 ACAC
31609938 ATGCATATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 16 0.55
28 3 0.10
30 10 0.34
ACGTcount: A:0.34, C:0.38, G:0.05, T:0.23
Consensus pattern (29 bp):
ACACCCCTAACCATGCATAAACCGTTCAT
Found at i:31611181 original size:16 final size:16
Alignment explanation
Indices: 31611138--31611181 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31611128 TGATAGGTCT
*
31611138 CCGA-CGAGCTTCCAG
1 CCGACCGAGCTTCCAA
* *
31611153 CCGACTGATCTTCCAA
1 CCGACCGAGCTTCCAA
31611169 CCGACCGAGCTTC
1 CCGACCGAGCTTC
31611182 TAAAAAATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.18
Consensus pattern (16 bp):
CCGACCGAGCTTCCAA
Found at i:31617924 original size:26 final size:26
Alignment explanation
Indices: 31617872--31617926 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31617862 GGATTATTTA
* **
31617872 GTTAGCCTTTATGACGTATCCTGTAT
1 GTTAGCCTTTATGACATATCCAATAT
*
31617898 GTTAGCCTTTATGACATATTCAATAT
1 GTTAGCCTTTATGACATATCCAATAT
31617924 GTT
1 GTT
31617927 TCCTTTGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (26 bp):
GTTAGCCTTTATGACATATCCAATAT
Found at i:31619184 original size:21 final size:22
Alignment explanation
Indices: 31619159--31619202 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
31619149 TGTAAAGCCT
*
31619159 TTATGTTG-TATTCTATGATGC
1 TTATGTGGATATTCTATGATGC
31619180 TTATGTGGCATATTCTATGATGC
1 TTATGTGG-ATATTCTATGATGC
31619203 CTGTGGGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (22 bp):
TTATGTGGATATTCTATGATGC
Found at i:31619193 original size:23 final size:23
Alignment explanation
Indices: 31619167--31619218 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
31619157 CTTTATGTTG
* *
31619167 TATTCTATGATGCTTATGTGGCA
1 TATTCTATGATGCCTATGGGGCA
*
31619190 TATTCTATGATGCCTGTGGGGCA
1 TATTCTATGATGCCTATGGGGCA
31619213 TATTCT
1 TATTCT
31619219 GTAAAGCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (23 bp):
TATTCTATGATGCCTATGGGGCA
Found at i:31620911 original size:20 final size:20
Alignment explanation
Indices: 31620886--31620933 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31620876 TGCTATACAA
31620886 AGGCACTGTAATGTAAACAG
1 AGGCACTGTAATGTAAACAG
* * **
31620906 AGGCACCGTAGTGTAAATGG
1 AGGCACTGTAATGTAAACAG
31620926 AGGCACTG
1 AGGCACTG
31620934 AATTGCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (20 bp):
AGGCACTGTAATGTAAACAG
Found at i:31625202 original size:6 final size:6
Alignment explanation
Indices: 31625186--31625224 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
31625176 TGATTTTCTC
* *
31625186 AAAATG GAAATG AAAATG ACAATG AAAATG AGAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG AA
31625225 TTCATTTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:31626881 original size:23 final size:23
Alignment explanation
Indices: 31626855--31626930 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
31626845 AGGGCATTAC
31626855 AGAATACGCCATAAAGGCATCAT
1 AGAATACGCCATAAAGGCATCAT
* *
31626878 AGAATACGCCACAAAGGCATCAC
1 AGAATACGCCATAAAGGCATCAT
* *
31626901 AGAATATGCCATAAAGGAATCAT
1 AGAATACGCCATAAAGGCATCAT
31626924 AGAATAC
1 AGAATAC
31626931 ACCACAGAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (23 bp):
AGAATACGCCATAAAGGCATCAT
Found at i:31626903 original size:46 final size:46
Alignment explanation
Indices: 31626847--31626936 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
31626837 TTGCCTCAAG
* * *
31626847 GGCATTACAGAATACGCCATAAAGGCATCATAGAATACGCCACAAA
1 GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACAAA
*
31626893 GGCATCACAGAATATGCCATAAAGGAATCATAGAATACACCACA
1 GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACA
31626937 GAGCGTGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (46 bp):
GGCATCACAGAATACGCCATAAAGGAATCATAGAATACACCACAAA
Found at i:31635384 original size:20 final size:22
Alignment explanation
Indices: 31635346--31635385 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31635336 ATGCAATATT
31635346 TAAAATGCTAACTAAAATGTCC
1 TAAAATGCTAACTAAAATGTCC
31635368 TAAAATGC-AAC-AAAATGT
1 TAAAATGCTAACTAAAATGT
31635386 ACTTAAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (22 bp):
TAAAATGCTAACTAAAATGTCC
Found at i:31638729 original size:48 final size:49
Alignment explanation
Indices: 31638653--31638801 Score: 180
Period size: 48 Copynumber: 3.1 Consensus size: 49
31638643 AACAGATTTC
* * * *
31638653 TCGGTGGCCTGCACATAGTCCGTTCCACCCTTGTATCCTAACAAG-TTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCCTAACAAGAATA
* * *
31638701 TTGGTGGCCTGCACACAGTCCATGCCACCCTTATGTCAC-AAC-AGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTC-CTAACAAGAATA
* *
31638749 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAAC-AGATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCCTAACAAGAATA
31638797 TCGGT
1 TCGGT
31638802 ATGCATAGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
47 2 0.02
48 83 0.97
49 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (49 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCCTAACAAGAATA
Found at i:31646291 original size:48 final size:48
Alignment explanation
Indices: 31646222--31646428 Score: 245
Period size: 48 Copynumber: 4.3 Consensus size: 48
31646212 TTGGAATAAA
* * * * * *
31646222 AACAGATTTCTCGGTAGCCTGCACACAATCCGTACCACCTTTGTGTAAT
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
* * * * *
31646271 AACAGATTCTCGGTGGCCTGCACATAGTCCGTTCCACCCTTGTATCCT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
* * * *
31646319 AACA-AGTTATTGGTGGCCTGTACATAGTCCGTGCCACCCTTGTGTCAC
1 AACAGA-TTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
*
31646367 AACAGAATATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
1 AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
31646415 AACAGATTATCGGT
1 AACAGATTATCGGT
31646429 ACACATAGTA
Statistics
Matches: 135, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.01
48 127 0.94
49 7 0.05
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
AACAGATTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAT
Found at i:31650776 original size:6 final size:6
Alignment explanation
Indices: 31650765--31650858 Score: 68
Period size: 6 Copynumber: 15.8 Consensus size: 6
31650755 AAGAGAGAAA
** * **
31650765 AAAATC AAAATC AAAATC AAAATC AAAAAA AAAATC AAAGTC AAAAGAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC -AAA-ATC
* * * *
31650815 AAAATA AAAATC --TATC AAAACC AAAATC AAAGTC AAAAT- AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
31650859 ATGAAAAGAG
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
4 3 0.04
5 5 0.07
6 54 0.79
7 6 0.09
ACGTcount: A:0.69, C:0.13, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:31650798 original size:30 final size:30
Alignment explanation
Indices: 31650762--31650857 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
31650752 GAAAAGAGAG
31650762 AAAAAAATCAAAATCAAAATCAAAATCAAA
1 AAAAAAATCAAAATCAAAATCAAAATCAAA
* *
31650792 AAAAAAATCAAAGTCAAAA-GAAAA--AAA
1 AAAAAAATCAAAATCAAAATCAAAATCAAA
* * *
31650819 TAAAAATCTATCAAAACCAAAATCAAAGTCAAA
1 -AAAAA--AATCAAAATCAAAATCAAAATCAAA
*
31650852 ATAAAA
1 AAAAAA
31650858 TATGAAAAGA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 4 0.08
30 29 0.57
31 3 0.06
32 4 0.08
33 3 0.06
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.14
Consensus pattern (30 bp):
AAAAAAATCAAAATCAAAATCAAAATCAAA
Found at i:31652439 original size:43 final size:43
Alignment explanation
Indices: 31652392--31652522 Score: 101
Period size: 43 Copynumber: 3.0 Consensus size: 43
31652382 AGAAGTAGAT
31652392 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
** * * * * * *
31652435 CTTGCC-TCCAT-CGATT-GTAGTGGAACTGGT-TAAAA-AAGCAGAT
1 CTTGCCTTCC-TGC-ATTAACAGCGGAGCAGATCGAAAACAA--AG-C
*
31652478 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
31652521 CT
1 CT
31652523 ATCCTCCATT
Statistics
Matches: 61, Mismatches: 17, Indels: 20
0.62 0.17 0.20
Matches are distributed among these distances:
40 2 0.03
41 4 0.07
42 14 0.23
43 22 0.36
44 13 0.21
45 4 0.07
46 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
Found at i:31652478 original size:86 final size:86
Alignment explanation
Indices: 31652332--31652661 Score: 475
Period size: 86 Copynumber: 3.8 Consensus size: 86
31652322 ATCAGTGAAA
* *
31652332 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGT-GAAGCTGGTTAAAGAAGTAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAA-CTGGTTAAAAAAGCAGATCTTG
31652396 CCTTCCTGCATTAACAGCGGAG
65 CCTTCCTGCATTAACAGCGGAG
* *
31652418 CAGATCGAAAACAAAGCCTTGCCTCCATCGATTGTAGTGGAACTGGTTAAAAAAGCAGATCTTGC
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAAAAGCAGATCTTGC
*
31652483 CTTCCTGCATTAACAGCGAAG
66 CTTCCTGCATTAACAGCGGAG
* * * *
31652504 CAGATCGAAAACAAAGCCTAT-CCTCCATTGGTTGCAGTGGAGCTGGTTAAAGAAGTAGATCTTG
1 CAGATCGAAAACAAAGCCT-TGCCTCCATCGGTTGCAGTGGAACTGGTTAAAAAAGCAGATCTTG
*
31652568 CCTTCCTGCATTAACAGCGGAA
65 CCTTCCTGCATTAACAGCGGAG
* * * * *
31652590 CAGATCGAAAACAATGTCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTG
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTT-AAAAAAGCAGATCTTG
*
31652655 CCCTCCT
65 CCTTCCT
31652662 ACGTCGACAG
Statistics
Matches: 219, Mismatches: 21, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
85 1 0.00
86 196 0.89
87 22 0.10
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (86 bp):
CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAACTGGTTAAAAAAGCAGATCTTGC
CTTCCTGCATTAACAGCGGAG
Found at i:31652618 original size:172 final size:173
Alignment explanation
Indices: 31652332--31652661 Score: 538
Period size: 172 Copynumber: 1.9 Consensus size: 173
31652322 ATCAGTGAAA
31652332 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGTAGATCTTGC
1 CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGTAGATCTTGC
* *
31652397 CTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGCCTTGCCTCCATCGATTGTAGTGGAACT
66 CTTCCTGCATTAACAGCGGAACAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAACT
*
31652462 GGTT-AAAAAAGCAGATCTTGCCTTCCTGCATTAACAGCGAAG
131 GGTTGAAAAAAGCAGATCTTGCCCTCCTGCATTAACAGCGAAG
* *
31652504 CAGATCGAAAACAAAGCCTAT-CCTCCATTGGTTGCAGTGGAGCTGGTTAAAGAAGTAGATCTTG
1 CAGATCGAAAACAAAGCCT-TGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGTAGATCTTG
* * * *
31652568 CCTTCCTGCATTAACAGCGGAACAGATCGAAAACAATGTCTTGCCTCCATCGGTTGCAGTGGAGC
65 CCTTCCTGCATTAACAGCGGAACAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAAC
* *
31652633 TGGTTGAAGATAGCAGATCTTGCCCTCCT
130 TGGTTGAAAAAAGCAGATCTTGCCCTCCT
31652662 ACGTCGACAG
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 124 0.86
173 21 0.14
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (173 bp):
CAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGAAGCTGGTTAAAGAAGTAGATCTTGC
CTTCCTGCATTAACAGCGGAACAGATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAACT
GGTTGAAAAAAGCAGATCTTGCCCTCCTGCATTAACAGCGAAG
Done.