Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 133 of 214
Found at i:40350701 original size:88 final size:88
Alignment explanation
Indices: 40350580--40350841 Score: 332
Period size: 88 Copynumber: 3.0 Consensus size: 88
40350570 GATAGGACTG
** *
40350580 GTATCTTCGATCTGCTTCGCTGTTGATGCAGGAAGGCTAGATTTGCTATTTTTAACCTGCTCCAC
1 GTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCTAGATCTGCTATTTTTAACCTGCTCCAC
40350645 TGCAACCGAGGGAGGCAAGGCTA
66 TGCAACCGAGGGAGGCAAGGCTA
* * * * * *
40350668 GTATCTTCGATCTGCTTTGCTGTCAATGTAGGAAGG-TAAGATCTACTATCTTTATCCCGCTCCA
1 GTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCT-AGATCTGCTATTTTTAACCTGCTCCA
* * *
40350732 CTGTAACCAAGGGAGGCAAGGCTTT
65 CTGCAACCGAGGGAGGCAAGGC-TA
* * * **
40350757 GT-T-TTCGATCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATTTTCAATTTGCTCCAC
1 GTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCTAGATCTGCTATTTTTAACCTGCTCCAC
40350820 TGCAACCGAGGGAGGCAAGGCT
66 TGCAACCGAGGGAGGCAAGGCT
40350842 GGTGATTTCA
Statistics
Matches: 146, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
86 1 0.01
87 68 0.47
88 74 0.51
89 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (88 bp):
GTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCTAGATCTGCTATTTTTAACCTGCTCCAC
TGCAACCGAGGGAGGCAAGGCTA
Found at i:40352071 original size:6 final size:6
Alignment explanation
Indices: 40352062--40352113 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
40352052 TATTTTTACT
* *
40352062 TTTTCA TTTTTCA TTTTCA TTTTCA TTTTTTCA TTTTTCA TATTCT TTTTCA
1 TTTTCA -TTTTCA TTTTCA TTTTCA --TTTTCA -TTTTCA TTTTCA TTTTCA
40352114 ACTTAAAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
6 20 0.51
7 13 0.33
8 6 0.15
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTCA
Found at i:40352071 original size:7 final size:7
Alignment explanation
Indices: 40352061--40352102 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
40352051 CTATTTTTAC
40352061 TTTTTCA
1 TTTTTCA
40352068 TTTTTCA
1 TTTTTCA
40352075 -TTTTCA
1 TTTTTCA
40352081 -TTTTCA
1 TTTTTCA
40352087 TTTTTTCA
1 -TTTTTCA
40352095 TTTTTCA
1 TTTTTCA
40352102 T
1 T
40352103 ATTCTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.36
7 15 0.45
8 6 0.18
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTTCA
Found at i:40352083 original size:27 final size:27
Alignment explanation
Indices: 40352053--40352111 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
40352043 TAGCCTCTCT
*
40352053 ATTTTTACTTTTTCATTTTTCATTTTC
1 ATTTTTACTTTTTCATTTTTCATATTC
* *
40352080 ATTTTCATTTTTTCATTTTTCATATTC
1 ATTTTTACTTTTTCATTTTTCATATTC
40352107 -TTTTT
1 ATTTTT
40352112 CAACTTAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.15, C:0.14, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTTTACTTTTTCATTTTTCATATTC
Found at i:40352111 original size:21 final size:20
Alignment explanation
Indices: 40352064--40352111 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40352054 TTTTTACTTT
*
40352064 TTCA-TTTTTCATTTTCATT
1 TTCATTTTTTCATTTTCATA
40352083 TTCATTTTTTCATTTTTCATA
1 TTCATTTTTTCA-TTTTCATA
40352104 TTC-TTTTT
1 TTCATTTTT
40352112 CAACTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 10 0.38
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (20 bp):
TTCATTTTTTCATTTTCATA
Found at i:40352112 original size:27 final size:27
Alignment explanation
Indices: 40352061--40352113 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
40352051 CTATTTTTAC
*
40352061 TTTTTCATTTTTCATTTTCATTTTCAT
1 TTTTTCATTTTTCATATTCATTTTCAT
*
40352088 TTTTTCATTTTTCATATTCTTTTTCA
1 TTTTTCATTTTTCATATTCATTTTCA
40352114 ACTTAAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTCATTTTTCATATTCATTTTCAT
Found at i:40353058 original size:29 final size:28
Alignment explanation
Indices: 40353026--40353095 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
40353016 CTTTTTATCA
* *
40353026 TTTTCATATTTTTTATTTTGACTTTGATT
1 TTTTCAT-TTTTTTATTCTAACTTTGATT
* * * *
40353055 TTTTCCTTTTTTTTCTTCTAATTTTGTTT
1 TTTT-CATTTTTTTATTCTAACTTTGATT
40353084 TTTTCATTTTTT
1 TTTTCATTTTTT
40353096 CGTTCTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 7 0.21
29 24 0.73
30 2 0.06
ACGTcount: A:0.11, C:0.10, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTCATTTTTTTATTCTAACTTTGATT
Found at i:40357952 original size:17 final size:18
Alignment explanation
Indices: 40357919--40357954 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40357909 TAATGAATAC
*
40357919 ATAAAATAATATTATATA
1 ATAAAAGAATATTATATA
40357937 ATAAAAGAAT-TTATATA
1 ATAAAAGAATATTATATA
40357954 A
1 A
40357955 AAATTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAGAATATTATATA
Found at i:40364349 original size:23 final size:22
Alignment explanation
Indices: 40364306--40364349 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40364296 TTTCAAGTCA
40364306 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
40364329 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
40364350 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:40364474 original size:23 final size:23
Alignment explanation
Indices: 40364448--40364523 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
40364438 ATAAGTGCCA
*
40364448 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
*
40364471 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
40364494 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCTGAAGCTAC
40364517 CACTGAT
1 CACTGAT
40364524 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCTGAAGCTAC
Found at i:40369471 original size:94 final size:93
Alignment explanation
Indices: 40369223--40369483 Score: 271
Period size: 94 Copynumber: 2.8 Consensus size: 93
40369213 CAATCAAGAG
* * **
40369223 AGTTCGCTAGGACATTAAACATAGGGTTACATGTGTAAGACCTTAGTTCAGCTATAAAAACATGT
1 AGTTCGCCAGGACATTAAACATAGGGTTACATGTGTAAAACCTTAGTTCAGCTATAGCAACATGT
* * * *
40369288 GGAGTCCATCGGGATAGTAAACCCGGGGT
66 AGAATCCA-CGGGATAGTAAACACAGGGT
* ** * *
40369317 AGTTCGCCAGGACATTAAACATAGGGTTACTTGTGTAACGCCTTA-TCTCAACTATGGCAACATG
1 AGTTCGCCAGGACATTAAACATAGGGTTACATGTGTAAAACCTTAGT-TCAGCTATAGCAACATG
*
40369381 TAGAATCTGCA-GTGATAGTAAACACAGGGT
65 TAGAATC--CACGGGATAGTAAACACAGGGT
* * *
40369411 AG-TCTGCCAGGACATTAAACA-AGGGGTTACATGTGTAAAACCATAGTTCGGTTATAGCAACAT
1 AGTTC-GCCAGGACATTAAACATA-GGGTTACATGTGTAAAACCTTAGTTCAGCTATAGCAACAT
40369474 GT-GAAGTCCA
64 GTAGAA-TCCA
40369484 TAGATCAGTA
Statistics
Matches: 139, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
92 2 0.01
93 7 0.05
94 127 0.91
95 1 0.01
96 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (93 bp):
AGTTCGCCAGGACATTAAACATAGGGTTACATGTGTAAAACCTTAGTTCAGCTATAGCAACATGT
AGAATCCACGGGATAGTAAACACAGGGT
Found at i:40373789 original size:41 final size:41
Alignment explanation
Indices: 40373744--40373859 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 41
40373734 ATCAGCACTT
* *
40373744 AGCCTGCTAGACATATAGTCTGAAATGTTTCACAAGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACAAGCATTA
* **
40373785 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAAA-TGTTTCACAAGCATTA
40373827 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCAC
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCAC
40373860 TGGCAATAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 30 0.44
42 38 0.56
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACAAGCATTA
Found at i:40381526 original size:30 final size:30
Alignment explanation
Indices: 40381475--40381532 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
40381465 AGACTTTATC
* * *
40381475 ACTTTTTGAATTTATCAATTTTAGTCCTAT
1 ACTTTTTCAATTTATAAATTTTAATCCTAT
40381505 ACTTTTTCAATTT-TAATATTTTAATCCT
1 ACTTTTTCAATTTATAA-ATTTTAATCCT
40381533 GACCCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.55
Consensus pattern (30 bp):
ACTTTTTCAATTTATAAATTTTAATCCTAT
Found at i:40384389 original size:4 final size:4
Alignment explanation
Indices: 40384380--40384415 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
40384370 CCAAGGTACT
*
40384380 CATA CATA CATA CATA CATA CATA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
40384416 TATGAGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:40388603 original size:6 final size:6
Alignment explanation
Indices: 40388594--40388622 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40388584 ATGGTAATGG
40388594 TTTGGT TTTGGT TTTGGT TTTGGT TTTGG
1 TTTGGT TTTGGT TTTGGT TTTGGT TTTGG
40388623 ACAGCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (6 bp):
TTTGGT
Found at i:40393310 original size:9 final size:10
Alignment explanation
Indices: 40393295--40393353 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
40393285 TTTATATACT
*
40393295 TTTTTTTGAA
1 TTTTTTAGAA
40393305 TTTTTTAGAA
1 TTTTTTAGAA
*
40393315 -TTTTTAAAA
1 TTTTTTAGAA
* *
40393324 ATTTATA-AA
1 TTTTTTAGAA
* *
40393333 ATTTTTAGAT
1 TTTTTTAGAA
40393343 TTTTTTAGAA
1 TTTTTTAGAA
40393353 T
1 T
40393354 ATATAAACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 16 0.40
10 24 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (10 bp):
TTTTTTAGAA
Found at i:40393358 original size:28 final size:28
Alignment explanation
Indices: 40393306--40393360 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
40393296 TTTTTTGAAT
*
40393306 TTTTTAGAATTTTTAAAAATTTATAAAA
1 TTTTTAGAATTTTTAAAAATATATAAAA
* * *
40393334 TTTTTAGATTTTTTTAGAATATATAAA
1 TTTTTAGAATTTTTAAAAATATATAAA
40393361 CATTGAGACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTTTAGAATTTTTAAAAATATATAAAA
Found at i:40397209 original size:20 final size:19
Alignment explanation
Indices: 40397184--40397230 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40397174 AATGGAATCG
*
40397184 ACTTTTTTACAAAAAAAAA
1 ACTTTTTGACAAAAAAAAA
* *
40397203 TACTTTTTGGCAGAAAAAAA
1 -ACTTTTTGACAAAAAAAAA
40397223 ACTTTTTG
1 ACTTTTTG
40397231 GACTAATTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (19 bp):
ACTTTTTGACAAAAAAAAA
Found at i:40398204 original size:9 final size:9
Alignment explanation
Indices: 40398187--40398223 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40398177 TGAGTTTTTG
40398187 AATTCGAAT
1 AATTCGAAT
*
40398196 AACTCGAAT
1 AATTCGAAT
40398205 AATTCGAAT
1 AATTCGAAT
40398214 AATTCGAAT
1 AATTCGAAT
40398223 A
1 A
40398224 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40398619 original size:17 final size:18
Alignment explanation
Indices: 40398593--40398635 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
40398583 ACTTTTCCTC
40398593 AAAC-TTTTA-TTCCCCA
1 AAACTTTTTATTTCCCCA
*
40398609 AAACTTTTTATTTTCCCCT
1 AAACTTTTTA-TTTCCCCA
40398628 AAACTTTT
1 AAACTTTT
40398636 ACTTCTCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
19 14 0.61
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.47
Consensus pattern (18 bp):
AAACTTTTTATTTCCCCA
Found at i:40404441 original size:35 final size:34
Alignment explanation
Indices: 40404395--40404491 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
40404385 GTAATTGATA
* *
40404395 TCGTCAATTTATTCGACTAGCGCTGGGCACAACTT
1 TCGTCAGTTTATTCGACTAGCGCTGGGCAC-ACAT
*
40404430 TCGTCAGTTTA-TCTGACTAGTGCTGGGCACACAT
1 TCGTCAGTTTATTC-GACTAGCGCTGGGCACACAT
**
40404464 TCGTTGGTTTATTCGACTAGCGCTGGGC
1 TCGTCAGTTTATTCGACTAGCGCTGGGC
40404492 GCGAACATCG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 27 0.50
35 27 0.50
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.33
Consensus pattern (34 bp):
TCGTCAGTTTATTCGACTAGCGCTGGGCACACAT
Found at i:40404474 original size:34 final size:36
Alignment explanation
Indices: 40404402--40404511 Score: 131
Period size: 35 Copynumber: 3.2 Consensus size: 36
40404392 ATATCGTCAA
* **
40404402 TTTAT-TCGACTAGCGCTGGGCACAACTTTCGTCAG
1 TTTATCTCGACTAGCGCTGGGCACAACATTCGTTGG
*
40404437 TTTATCT-GACTAGTGCTGGGCAC-ACATTCGTTGG
1 TTTATCTCGACTAGCGCTGGGCACAACATTCGTTGG
*
40404471 TTTAT-TCGACTAGCGCTGGGCGCGAACA-TCGTTGG
1 TTTATCTCGACTAGCGCTGGGCAC-AACATTCGTTGG
40404506 TTTATC
1 TTTATC
40404512 CAACTAGAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
33 1 0.02
34 27 0.42
35 32 0.50
36 4 0.06
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (36 bp):
TTTATCTCGACTAGCGCTGGGCACAACATTCGTTGG
Found at i:40412554 original size:17 final size:18
Alignment explanation
Indices: 40412513--40412547 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40412503 CTCAAACATA
40412513 TACATC-AACCAATTCAT
1 TACATCAAACCAATTCAT
*
40412530 TACATCAAACCGATTCAT
1 TACATCAAACCAATTCAT
40412548 ATATCAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (18 bp):
TACATCAAACCAATTCAT
Found at i:40416192 original size:25 final size:24
Alignment explanation
Indices: 40416154--40416201 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
40416144 ATCCAAGCAA
40416154 TATAACGAGAAGCTCACAAAGAGCT
1 TATAACGAGAAGCTC-CAAAGAGCT
* * *
40416179 TATAACGGGTAGCTCCGAAGAGC
1 TATAACGAGAAGCTCCAAAGAGC
40416202 AATTAATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.17
Consensus pattern (24 bp):
TATAACGAGAAGCTCCAAAGAGCT
Found at i:40422151 original size:20 final size:19
Alignment explanation
Indices: 40422117--40422154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
40422107 AATCAAAGAA
40422117 GGTTTCTAAGAAAATTTGG
1 GGTTTCTAAGAAAATTTGG
*
40422136 GGTTTTTAATGAAAATTTG
1 GGTTTCTAA-GAAAATTTG
40422155 AGAGGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.42
Consensus pattern (19 bp):
GGTTTCTAAGAAAATTTGG
Found at i:40424395 original size:22 final size:22
Alignment explanation
Indices: 40424370--40424426 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
40424360 TTTCTTGTTG
*
40424370 TTTTCTCCTTATTTTGCTACCA
1 TTTTCTCATTATTTTGCTACCA
* *
40424392 TTTTACT-ATTATGTTGCTACTA
1 TTTT-CTCATTATTTTGCTACCA
* *
40424414 TTTTGTCGTTATT
1 TTTTCTCATTATT
40424427 GTTCGAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (22 bp):
TTTTCTCATTATTTTGCTACCA
Found at i:40427307 original size:7 final size:7
Alignment explanation
Indices: 40427295--40427351 Score: 69
Period size: 7 Copynumber: 7.4 Consensus size: 7
40427285 TCAACCTTTA
40427295 ATTTAAT
1 ATTTAAT
40427302 ATTTAAT
1 ATTTAAT
40427309 ATTTAAT
1 ATTTAAT
40427316 ATTTAAT
1 ATTTAAT
40427323 ATTTTTTACAT
1 A---TTTA-AT
40427334 AATTTAAT
1 -ATTTAAT
40427342 ATTTAAT
1 ATTTAAT
40427349 ATT
1 ATT
40427352 ATTTAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
7 32 0.71
8 2 0.04
9 4 0.09
10 4 0.09
11 2 0.04
12 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTAAT
Found at i:40428255 original size:25 final size:24
Alignment explanation
Indices: 40428227--40428280 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
40428217 AACTTGAACA
* * *
40428227 TAAAATAACTCAAATTTATTAAATT
1 TAAAAAAACT-AAATTCATCAAATT
40428252 TAAAAAAAACTAAATTCATCAAATT
1 T-AAAAAAACTAAATTCATCAAATT
40428277 TAAA
1 TAAA
40428281 CTAATCCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.56
26 8 0.32
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAAAACTAAATTCATCAAATT
Found at i:40433032 original size:29 final size:27
Alignment explanation
Indices: 40432968--40433034 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
40432958 GAGTTTCACG
*
40432968 TGTATAATTACATCAAATTAAAGTTTA
1 TGTATAATTACATCAAATTAAAGTTCA
* *
40432995 TGTACATAATTGCACATTACATTAAAGTTCA
1 TGT--ATAATT--ACATCAAATTAAAGTTCA
40433026 TGTATAATT
1 TGTATAATT
40433035 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 3 0.09
29 12 0.36
31 18 0.55
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (27 bp):
TGTATAATTACATCAAATTAAAGTTCA
Found at i:40435118 original size:11 final size:11
Alignment explanation
Indices: 40435102--40435127 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40435092 TATGTGTTCT
40435102 ATTTATTTTTA
1 ATTTATTTTTA
40435113 ATTTATTTTTA
1 ATTTATTTTTA
40435124 ATTT
1 ATTT
40435128 TTAAATCCAT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTTTA
Found at i:40440335 original size:15 final size:15
Alignment explanation
Indices: 40440309--40440347 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
40440299 GATATAAACT
40440309 TGATTGAAAAACTTGA
1 TGATT-AAAAACTTGA
40440325 TGATTAAAAACTTGA
1 TGATTAAAAACTTGA
40440340 TGATTAAA
1 TGATTAAA
40440348 TGAACAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (15 bp):
TGATTAAAAACTTGA
Found at i:40452554 original size:15 final size:16
Alignment explanation
Indices: 40452534--40452564 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40452524 TCTGACTGAC
40452534 AAACTTG-AATAACTT
1 AAACTTGAAATAACTT
40452549 AAACTTGAAATAACTT
1 AAACTTGAAATAACTT
40452565 GAATCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (16 bp):
AAACTTGAAATAACTT
Found at i:40478796 original size:23 final size:22
Alignment explanation
Indices: 40478744--40478796 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
40478734 TCCTTGTCTT
*
40478744 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
40478766 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
40478789 TTTCTTTT
1 TTTCTTTT
40478797 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40487218 original size:3 final size:3
Alignment explanation
Indices: 40487175--40487200 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40487165 ACTTTATCCC
40487175 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40487201 TGAGTGGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40499802 original size:12 final size:12
Alignment explanation
Indices: 40499785--40499824 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
40499775 CAAATTTTTC
40499785 ATTTTAATATAT
1 ATTTTAATATAT
40499797 ATTTTAATATAT
1 ATTTTAATATAT
*
40499809 GTTTTAA-ATAT
1 ATTTTAATATAT
40499820 -TTTTA
1 ATTTTA
40499825 TATTATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (12 bp):
ATTTTAATATAT
Found at i:40501717 original size:22 final size:21
Alignment explanation
Indices: 40501691--40501741 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
40501681 ATTTTTTATT
*
40501691 TAAAAATTAACCATAAAAAATC
1 TAAAAATTAA-CATAAAAAAAC
*
40501713 T-AAAATTAATATAAAAAAAC
1 TAAAAATTAACATAAAAAAAC
40501733 TAATAAATT
1 TAA-AAATT
40501742 CGTGATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 9 0.36
22 6 0.24
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAAATTAACATAAAAAAAC
Found at i:40501728 original size:20 final size:21
Alignment explanation
Indices: 40501693--40501735 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40501683 TTTTTATTTA
*
40501693 AAAATTAACCATAAAAAATCT
1 AAAATTAACCATAAAAAAACT
*
40501714 AAAATTAA-TATAAAAAAACT
1 AAAATTAACCATAAAAAAACT
40501734 AA
1 AA
40501736 TAAATTCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATTAACCATAAAAAAACT
Found at i:40510266 original size:21 final size:22
Alignment explanation
Indices: 40510242--40510285 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
40510232 TAAAAAAAGA
40510242 AAAAAATAGAAA-AAAAAGTTT
1 AAAAAATAGAAAGAAAAAGTTT
40510263 AAAAAATAGAAAGAAAAAGTTT
1 AAAAAATAGAAAGAAAAAGTTT
40510285 A
1 A
40510286 GATCTTTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAAATAGAAAGAAAAAGTTT
Found at i:40511259 original size:21 final size:22
Alignment explanation
Indices: 40511234--40511300 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
40511224 ATTTTATGTA
40511234 ATTATATTATTATCATAC-ATT
1 ATTATATTATTATCATACTATT
*
40511255 TTTATATTATT-TC--ACTATT
1 ATTATATTATTATCATACTATT
*
40511274 ATTATCATTATTATCATA-TAGT
1 ATTAT-ATTATTATCATACTATT
40511296 ATTAT
1 ATTAT
40511301 TAATTGAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 8 0.21
21 12 0.32
22 8 0.21
23 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.55
Consensus pattern (22 bp):
ATTATATTATTATCATACTATT
Found at i:40511276 original size:3 final size:3
Alignment explanation
Indices: 40511270--40511346 Score: 64
Period size: 3 Copynumber: 24.3 Consensus size: 3
40511260 ATTATTTCAC
* * * *
40511270 TAT TAT TAT CAT TAT TAT CAT ATAG TAT TAT TAAT TGAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T-AT TAT TAT TAT
* *
40511318 TAT TAT TGT TAT TAT TATT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
40511347 GTATTCACTA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
3 50 0.86
4 8 0.14
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:40517635 original size:44 final size:44
Alignment explanation
Indices: 40517572--40517686 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
40517562 TACAATGGTG
40517572 AATCTTAT-CTCCTTGAAGTTGCAGTGGAACAAGA-TGAAGCTACA
1 AATCTTATAC-CCTTGAAGTTGCAGTGGAAC-AGATTGAAGCTACA
** *
40517616 AATCTTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACA
1 AATCTTATACCCTTGAAGTTGCAGTGGAACAGATTGAAGCTACA
* * * * *
40517660 ATTCCTATACCCCTAAAGTTGTAGTGG
1 AATCTTATACCCTTGAAGTTGCAGTGG
40517687 GTAGGAATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 58 0.95
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATACCCTTGAAGTTGCAGTGGAACAGATTGAAGCTACA
Found at i:40517669 original size:138 final size:138
Alignment explanation
Indices: 40517490--40517798 Score: 392
Period size: 138 Copynumber: 2.2 Consensus size: 138
40517480 TTTCGGTCTT
* *** * * *
40517490 CCTGAAGTTGTAGTGAAACGGA-TGAAGCTACAATTCCTATACCCTTGAAGTTACCGTGGGTCA-
1 CCTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATTCCTATACCCCTAAAGTTACAGTGGGT-AG
* * * *
40517553 GAAT-AAAATTACAATGGTGAATCTTATCTCCTTGAAGTTGCAGTGGAACAAGA-TGAAGCTACA
65 GAATGAAAA-TACAATGGTGAATCTTATCTCCTTGAAATTACAGTAGAACAA-ACTAAAGCTACA
*
40517616 AATCTTATACC
128 AATCCTATACC
* **
40517627 CTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATTCCTATACCCCTAAAGTTGTAGTGGGTAGG
1 CCTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATTCCTATACCCCTAAAGTTACAGTGGGTAGG
*
40517692 AATGAAAATACAATGGTGAATCTTATCTCCTTGAAATTACAGTAGAGCAAACTAAAGCTACAAAT
66 AATGAAAATACAATGGTGAATCTTATCTCCTTGAAATTACAGTAGAACAAACTAAAGCTACAAAT
40517757 CCTATACC
131 CCTATACC
* * *
40517765 CCTGAAGTTGTAGTGGGTCAGATTGAAACTACAA
1 CCTGAAGTTGCAGTGGGTCGGATTGAAGCTACAA
40517799 ATGACAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
137 19 0.13
138 125 0.84
139 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (138 bp):
CCTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATTCCTATACCCCTAAAGTTACAGTGGGTAGG
AATGAAAATACAATGGTGAATCTTATCTCCTTGAAATTACAGTAGAACAAACTAAAGCTACAAAT
CCTATACC
Found at i:40517687 original size:44 final size:44
Alignment explanation
Indices: 40517605--40517697 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
40517595 GTGGAACAAG
* * * *
40517605 ATGAAGCTACAAATCTTATACCCTTGAAGTTGCAGTGGGTCGGA
1 ATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTAGGA
* * *
40517649 TTGAAGCTACAATTCCTATACCCCTAAAGTTGTAGTGGGTAGGA
1 ATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTAGGA
40517693 ATGAA
1 ATGAA
40517698 AATACAATGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (44 bp):
ATGAAGCTACAAATCCTATACCCCTAAAGTTGCAGTGGGTAGGA
Found at i:40517714 original size:94 final size:93
Alignment explanation
Indices: 40517613--40518107 Score: 478
Period size: 94 Copynumber: 5.3 Consensus size: 93
40517603 AGATGAAGCT
* * * * *
40517613 ACAAATCTTATAC-CCTTGAAGTTGCAGTGGGTC-GGATTGAAGCTACAATTCCTATACCCCTAA
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTGGG-CAAGA-TAAAGCTACAAATCCTATACCCCTGA
* *
40517676 AGTTGTAGTGGGT-AGGAATGAAAATACAATG
63 AGTTGCAGTGGGTCA-GAATGAAACTACAATG
*** * * * *
40517707 GTGAATCTTATCTCCTTGAAATTACAGTAGAGCAA-ACTAAAGCTACAAATCCTATACCCCTGAA
1 ACAAATCTTATCTCCCTGAAGTTGCAGT-GGGCAAGA-TAAAGCTACAAATCCTATACCCCTGAA
* *
40517771 GTTGTAGTGGGTCAGATTGAAACTACAAATG
64 GTTGCAGTGGGTCAGAATGAAACTAC-AATG
* * * *
40517802 ACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAGATGAAGCTACAAGTCCTATACCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGG-GCAAGATAAAGCTACAAATCCTATACCCCTGAAG
* *
40517867 TTACAATGGGTC-GAATTGAAACTACAATG
65 TTGCAGTGGGTCAGAA-TGAAACTACAATG
* * *
40517896 GCAAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGT-GGGCAAGATAAAGCTACAAATCCTATACCCCTGAAG
* * *
40517961 TTGCAGTTGGTCAGATTGAAACTATAATG
65 TTGCAGTGGGTCAGAATGAAACTACAATG
** * * * * * *
40517990 ATGAATCTTATCTCCCTGAAATTGCAGTGGAGCAAGATAAAGCTACAATTTCTATGCCTCTGAAC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGG-GCAAGATAAAGCTACAAATCCTATACCCCTGAAG
** * **
40518055 TTGCAGTGGGTTGGAATAAAACTACAACA
65 TTGCAGTGGGTCAGAATGAAACTACAATG
*
40518084 ACAAATCTTATCTCCTTGAAGTTG
1 ACAAATCTTATCTCCCTGAAGTTG
40518108 AAATAGAGCA
Statistics
Matches: 331, Mismatches: 59, Indels: 22
0.80 0.14 0.05
Matches are distributed among these distances:
93 2 0.01
94 248 0.75
95 80 0.24
96 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (93 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGGCAAGATAAAGCTACAAATCCTATACCCCTGAAGT
TGCAGTGGGTCAGAATGAAACTACAATG
Found at i:40517845 original size:189 final size:187
Alignment explanation
Indices: 40517650--40518121 Score: 576
Period size: 189 Copynumber: 2.5 Consensus size: 187
40517640 TGGGTCGGAT
* * **
40517650 TGAAGCTACAATTCCTATACCCCTAAAGTTGTAGTGGGTAGGAATGAAAATACAATGGTGAATCT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGT-GGAATGAAAATACAATGGCAAATCT
* *
40517715 TATCTCCTTGAAA-TTACAGTAGAGCAA-ACTAAAGCTACAAATCCTATACCCCTGAAGTTGTAG
65 TATCTCCCT-AAAGTTACAGTAGAGCAAGA-TAAAGCTACAAATCCTATACCCCTGAAGTTGCAG
40517778 TGGGTCAGATTGAAACTACAAATGACAAATCTTATCTCCCT-AAAGTTACAGTGGAGCAAGA
128 TGGGTCAGATTGAAACTA-AAATGACAAATCTTATCTCCCTGAAA-TTACAGTGGAGCAAGA
* * * * *
40517839 TGAAGCTACAAGTCCTATACCCCTGAAGTTACAATGGGTCGAATTGAAACTACAATGGCAAATCT
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTGGAA-TGAAAATACAATGGCAAATCT
* *
40517904 TATCTCCCTAAAGTTGCAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTGCAGTT
65 TATCTCCCTAAAGTTACAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTGCAGTG
* ** *
40517969 GGTCAGATTGAAACTATAATGATGAATCTTATCTCCCTGAAATTGCAGTGGAGCAAGA
130 GGTCAGATTGAAACTAAAATGACAAATCTTATCTCCCTGAAATTACAGTGGAGCAAGA
* * * * * ***
40518027 TAAAGCTACAATTTCTATGCCTCTGAACTTGCAGTGGGTTGGAAT-AAAACTACAACAACAAATC
1 TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGG-TGGAATGAAAA-TACAATGGCAAATC
* * *
40518091 TTATCTCCTTGAAGTTGA-AATAGAGCAAGAT
64 TTATCTCCCTAAAGTT-ACAGTAGAGCAAGAT
40518122 GAAACTTTGA
Statistics
Matches: 242, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
187 3 0.01
188 108 0.45
189 130 0.54
190 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (187 bp):
TGAAGCTACAATTCCTATACCCCTGAAGTTGCAGTGGGTGGAATGAAAATACAATGGCAAATCTT
ATCTCCCTAAAGTTACAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGG
GTCAGATTGAAACTAAAATGACAAATCTTATCTCCCTGAAATTACAGTGGAGCAAGA
Found at i:40518117 original size:188 final size:189
Alignment explanation
Indices: 40517710--40518121 Score: 537
Period size: 188 Copynumber: 2.2 Consensus size: 189
40517700 TACAATGGTG
*
40517710 AATCTTATCTCCTTGAAATT-ACAGTAGAGCAA-ACTAAAGCTACAAATCCTATACCCCTGAAGT
1 AATCTTATCTCCTTGAAGTTGA-AGTAGAGCAAGA-TAAAGCTACAAATCCTATACCCCTGAAGT
*
40517773 TGTAGTGGGTCAGATTGAAACTACAAATGACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAG
64 TGCAGTGGGTCAGATTGAAACTACAAATGACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAG
* * * ***
40517838 ATGAAGCTACAAGTCCTATACCCCTGAAGTTACAATGGGTCGAATTGAAACTACAATGGCA
129 ATAAAGCTACAAGTCCTATACCCCTGAACTTACAATGGGTCGAATTAAAACTACAACAACA
* * *
40517899 AATCTTATCTCCCTAAAGTTGCAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGTTGAAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
* * ** *
40517964 CAGTTGGTCAGATTGAAACTA-TAATGATGAATCTTATCTCCCTGAAA-TTGCAGTGGAGCAAGA
66 CAGTGGGTCAGATTGAAACTACAAATGACAAATCTTATCTCCCT-AAAGTTACAGTGGAGCAAGA
* * * * * * *
40518027 TAAAGCTACAATTTCTATGCCTCTGAACTTGCAGTGGGTTGGAA-TAAAACTACAACAACA
130 TAAAGCTACAAGTCCTATACCCCTGAACTTACAATGGG-TCGAATTAAAACTACAACAACA
*
40518087 AATCTTATCTCCTTGAAGTTGAAATAGAGCAAGAT
1 AATCTTATCTCCTTGAAGTTGAAGTAGAGCAAGAT
40518122 GAAACTTTGA
Statistics
Matches: 192, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
188 107 0.56
189 84 0.44
190 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (189 bp):
AATCTTATCTCCTTGAAGTTGAAGTAGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
CAGTGGGTCAGATTGAAACTACAAATGACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAAGAT
AAAGCTACAAGTCCTATACCCCTGAACTTACAATGGGTCGAATTAAAACTACAACAACA
Found at i:40518722 original size:29 final size:31
Alignment explanation
Indices: 40518660--40518725 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
40518650 AAGAACAGAG
*
40518660 AGCAGAGAACAGCAGAAACACAAAAGTAGAAA
1 AGCA-AGAACAGCAGAAACACAAAAGGAGAAA
*
40518692 AGCAAGAATAGCAGAAACA-AAAAGGAG-AA
1 AGCAAGAACAGCAGAAACACAAAAGGAGAAA
40518721 AGCAA
1 AGCAA
40518726 AAAAAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 7 0.22
30 7 0.22
31 14 0.44
32 4 0.12
ACGTcount: A:0.61, C:0.14, G:0.23, T:0.03
Consensus pattern (31 bp):
AGCAAGAACAGCAGAAACACAAAAGGAGAAA
Found at i:40519288 original size:13 final size:13
Alignment explanation
Indices: 40519257--40519285 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40519247 TTGAAACAGG
40519257 TTTTAAAATGATT
1 TTTTAAAATGATT
40519270 TTTTAAAAT-ATT
1 TTTTAAAATGATT
40519282 TTTT
1 TTTT
40519286 TAACTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTTAAAATGATT
Found at i:40534219 original size:27 final size:27
Alignment explanation
Indices: 40534167--40534243 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
40534157 AATAAACGAA
*
40534167 TAATAATAATAATAAATAGATAAATAAGAG
1 TAATAATAATAAT-AATAG-T-AATAACAG
*
40534197 TAATAATAATAATAATAGTAATAACCG
1 TAATAATAATAATAATAGTAATAACAG
*
40534224 TATTAA-ACATAATAATAGTA
1 TAATAATA-ATAATAATAGTA
40534244 GTAAAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.02
27 23 0.53
28 1 0.02
29 5 0.12
30 13 0.30
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (27 bp):
TAATAATAATAATAATAGTAATAACAG
Found at i:40534240 original size:3 final size:3
Alignment explanation
Indices: 40534165--40534220 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
40534155 TTAATAAACG
* *
40534165 AAT AAT AAT AAT AAT AAAT AGAT AAAT AAG AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT
*
40534213 AGT AAT AA
1 AAT AAT AA
40534221 CCGTATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 36 0.82
4 7 0.16
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40536529 original size:19 final size:18
Alignment explanation
Indices: 40536505--40536553 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40536495 TTTTATTGTC
*
40536505 TTTAAATTATTGTTGAAAT
1 TTTAAATTATT-TTCAAAT
40536524 TTTAAATTGA-TTTCAAAT
1 TTTAAATT-ATTTTCAAAT
*
40536542 TTTAAAATATTT
1 TTTAAATTATTT
40536554 AAATTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 15 0.58
19 9 0.35
20 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTAAATTATTTTCAAAT
Found at i:40537690 original size:15 final size:15
Alignment explanation
Indices: 40537670--40537703 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40537660 AAAATAAAAG
40537670 AATTTATTATATTTA
1 AATTTATTATATTTA
* *
40537685 AATTTATTTTATTTG
1 AATTTATTATATTTA
40537700 AATT
1 AATT
40537704 AAAAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTTATTATATTTA
Found at i:40538621 original size:20 final size:20
Alignment explanation
Indices: 40538584--40538622 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40538574 CTTCATTTCT
* *
40538584 ATGTTTGTACAAATATGAAA
1 ATGTTTATACAAACATGAAA
*
40538604 ATGTTTATACTAACATGAA
1 ATGTTTATACAAACATGAA
40538623 TTATGTATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTTTATACAAACATGAAA
Found at i:40539154 original size:21 final size:22
Alignment explanation
Indices: 40539129--40539170 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40539119 TTAAAAAATT
40539129 GGAGAAGT-GAAGAAAATAGAG
1 GGAGAAGTGGAAGAAAATAGAG
*
40539150 GGAGAAGTGGAAGAGAATAGA
1 GGAGAAGTGGAAGAAAATAGA
40539171 ATATAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (22 bp):
GGAGAAGTGGAAGAAAATAGAG
Found at i:40548941 original size:106 final size:107
Alignment explanation
Indices: 40548800--40549002 Score: 345
Period size: 106 Copynumber: 1.9 Consensus size: 107
40548790 TGGATTAAGA
* * *
40548800 TTTAAGAGGATATTTGGCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
1 TTTAAGAGGATATTTGGCTATTTAGTCAAACGAAAAAATCGAAACCCAACACATTAGGACACGTT
*
40548865 TCCTCGAATTTCCAAATGCAAAATATTGCCTTACTTTAAAAT
66 TCCTCGAATTCCCAAATGCAAAATATTGCCTTACTTTAAAAT
*
40548907 TTTAA-AGGATATTTGGCTATTTAGTCGAACGAAAAAATCGAAACCCAACACATTAGGACACGTT
1 TTTAAGAGGATATTTGGCTATTTAGTCAAACGAAAAAATCGAAACCCAACACATTAGGACACGTT
*
40548971 TTCTCGAATTCCCAAATGCAAAATATTGCCTT
66 TCCTCGAATTCCCAAATGCAAAATATTGCCTT
40549003 TATTATTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
106 85 0.94
107 5 0.06
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (107 bp):
TTTAAGAGGATATTTGGCTATTTAGTCAAACGAAAAAATCGAAACCCAACACATTAGGACACGTT
TCCTCGAATTCCCAAATGCAAAATATTGCCTTACTTTAAAAT
Found at i:40549895 original size:27 final size:27
Alignment explanation
Indices: 40549865--40549930 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
40549855 TTTTAAAGCA
40549865 TAAAAGTATATATAAAATAAAAT-ATTT
1 TAAAAGTATATATAAAATAAAATCA-TT
40549892 TAAAAATGTAT-TATAAAATAAAATCATT
1 T-AAAA-GTATATATAAAATAAAATCATT
40549920 TAAAA-TATATA
1 TAAAAGTATATA
40549931 GACAATATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 5 0.14
28 20 0.57
29 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (27 bp):
TAAAAGTATATATAAAATAAAATCATT
Found at i:40549897 original size:28 final size:28
Alignment explanation
Indices: 40549866--40549924 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
40549856 TTTAAAGCAT
40549866 AAAA-GTATATATAAAATAAAAT-ATTTTA
1 AAAATGTAT-TATAAAATAAAATCA-TTTA
40549894 AAAATGTATTATAAAATAAAATCATTTA
1 AAAATGTATTATAAAATAAAATCATTTA
40549922 AAA
1 AAA
40549925 TATATAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATGTATTATAAAATAAAATCATTTA
Found at i:40550104 original size:3 final size:3
Alignment explanation
Indices: 40550096--40550143 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
40550086 TAAAATGACG
* *
40550096 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ATA ATA A-A ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
40550143 A
1 A
40550144 TAGAAAAGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.69, C:0.27, G:0.00, T:0.04
Consensus pattern (3 bp):
ACA
Found at i:40553460 original size:15 final size:14
Alignment explanation
Indices: 40553430--40553457 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40553420 TACATTCTCC
40553430 TTCAAAAATATCAA
1 TTCAAAAATATCAA
40553444 TTCAAAAATATCAA
1 TTCAAAAATATCAA
40553458 ATTTATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCAAAAATATCAA
Found at i:40558464 original size:21 final size:21
Alignment explanation
Indices: 40558414--40558464 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
40558404 AGTTCGGGCC
40558414 CAAATAA-AAAAATAAACAAA
1 CAAATAATAAAAATAAACAAA
40558434 CAGAAT-ATAAAAATAAA-AAA
1 CA-AATAATAAAAATAAACAAA
40558454 TCAAATAATAA
1 -CAAATAATAA
40558465 GAGTCCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAATAATAAAAATAAACAAA
Found at i:40558843 original size:15 final size:16
Alignment explanation
Indices: 40558823--40558852 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40558813 TTTTCAAAAA
40558823 AGAG-AAATTGAATAC
1 AGAGAAAATTGAATAC
40558838 AGAGAAAATTGAATA
1 AGAGAAAATTGAATA
40558853 TATTCGAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (16 bp):
AGAGAAAATTGAATAC
Found at i:40564582 original size:19 final size:20
Alignment explanation
Indices: 40564543--40564582 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40564533 CAAGGTCGTA
*
40564543 TATGTAAAATGTATCCGTTT
1 TATGTAAAAAGTATCCGTTT
*
40564563 TATGTAAAAAG-ATTCGTTT
1 TATGTAAAAAGTATCCGTTT
40564582 T
1 T
40564583 CTAGTAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (20 bp):
TATGTAAAAAGTATCCGTTT
Found at i:40571921 original size:45 final size:45
Alignment explanation
Indices: 40571821--40572182 Score: 256
Period size: 44 Copynumber: 7.8 Consensus size: 45
40571811 CACCGTAGTG
* * * **
40571821 AATCTTATCCCCCTGAAGTTGCAG-CAGAGTAGATTAAAGCCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGATAGCA
**
40571865 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATCGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGATAGCA
* *
40571910 AATCTTATCTCCCTGAAGTTGGAGT-AGAGCAGATTAAAGATAGAA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGATAGCA
* * * * *
40571955 AATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAAGTTA-CG
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGATAGCA
* *
40571999 AATCTTATTTCCCTGAAGTTGCAGTGGAA-CATATTAAAGCTACTAGTCACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATTAAAG--A-TAG---CA
* * * * * *
40572050 AATCTTATCTCCTTAAAGTTACA-TCAGAGCAAATTAAAGTTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGATAGCA
* * * *
40572094 AATCTTATTTCCCT-AGAGTTACATTGGAA-CAGATTAAAGCTACAAGTTGCA
1 AATCTTATCTCCCTGA-AGTTGCAGT-GAAGCAGATTAAAG-----A-TAGCA
*
40572145 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAA
40572183 ACGAACTTTA
Statistics
Matches: 251, Mismatches: 41, Indels: 45
0.74 0.12 0.13
Matches are distributed among these distances:
43 1 0.00
44 95 0.38
45 83 0.33
46 1 0.00
47 2 0.01
48 2 0.01
49 1 0.00
50 5 0.02
51 60 0.24
52 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGATAGCA
Found at i:40571944 original size:89 final size:89
Alignment explanation
Indices: 40571821--40572178 Score: 263
Period size: 95 Copynumber: 3.9 Consensus size: 89
40571811 CACCGTAGTG
* * * *
40571821 AATCTTATCCCCCTGAAGTTGCAGCAGAGTAGATTAAAGCCA-CAAATCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAGAAAATCTTATCTCCCTGAAGTT
* *
40571885 GCAGTGAAGCAGATCGAAGATAGCA
66 GCAATGAAGCAGATCAAAGATA-CA
* **
40571910 AATCTTATCTCCCTGAAGTTGGAGTAGAGCAGATTAAAGATAGAAAATCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAGAAAATCTTATCTCCCTGAAGTT
* * * * *
40571975 GTAATGGAGCAGATTAAAGTTACG
66 GCAATGAAGCAGATCAAAGATACA
* * * * *
40571999 AATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTACTAGTCACAAATCTTATCTCCTT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGC--C-AG--A-AAATCTTATCTCCCT
* * * * * *
40572064 AAAGTTAC-ATCAGAGCAAATTAAAGTTACA
60 GAAGTTGCAATGA-AGCAGATCAAAGATACA
* * * * * *
40572094 AATCTTATTTCCCT-AGAGTTACATTGGAACAGATTAAAGCTACAAGTTGCAAATCTTATCTCCC
1 AATCTTATCTCCCTGA-AGTTGCAGTAGAGCAGATTAAAGC--C-A---GAAAATCTTATCTCCC
* *
40572158 TGAAGTTGCAGTGGAGCAGAT
59 TGAAGTTGCAATGAAGCAGAT
40572179 TAAAACGAAC
Statistics
Matches: 215, Mismatches: 41, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
89 71 0.33
90 37 0.17
92 2 0.01
94 4 0.02
95 99 0.46
96 1 0.00
98 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAGAAAATCTTATCTCCCTGAAGTT
GCAATGAAGCAGATCAAAGATACA
Found at i:40572175 original size:95 final size:94
Alignment explanation
Indices: 40571861--40572182 Score: 334
Period size: 95 Copynumber: 3.4 Consensus size: 94
40571851 AGATTAAAGC
* ** * *
40571861 CACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATCGAAGATAGCAAATCTTATCTCCCTGA
1 CACAAATCTTATCTCCCTGAAGTTGCA-TGGAGCAGATTAAAGTTA-CAAATCTTATTTCCCTGA
** * * *
40571926 AGTTGGAGTAGAGCAGATTAAAG--A-TAG-
64 AGTTACAGTGGAACAGATTAAAGCTACAAGT
* *
40571953 -A-AAATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAAGTTACGAATCTTATTTCCCTGAA
1 CACAAATCTTATCTCCCTGAAGTTG-CATGGAGCAGATTAAAGTTACAAATCTTATTTCCCTGAA
* * *
40572016 GTTGCAGTGGAACATATTAAAGCTACTAGT
65 GTTACAGTGGAACAGATTAAAGCTACAAGT
* * * * *
40572046 CACAAATCTTATCTCCTTAAAGTTACATCAGAGCAAATTAAAGTTACAAATCTTATTTCCCT-AG
1 CACAAATCTTATCTCCCTGAAGTTGCAT-GGAGCAGATTAAAGTTACAAATCTTATTTCCCTGA-
*
40572110 AGTTACATTGGAACAGATTAAAGCTACAAGT
64 AGTTACAGTGGAACAGATTAAAGCTACAAGT
**
40572141 TGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 CACAAATCTTATCTCCCTGAAGTTGCA-TGGAGCAGATTAAA
40572183 ACGAACTTTA
Statistics
Matches: 191, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
89 35 0.18
90 36 0.19
91 3 0.02
92 3 0.02
94 4 0.02
95 109 0.57
96 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (94 bp):
CACAAATCTTATCTCCCTGAAGTTGCATGGAGCAGATTAAAGTTACAAATCTTATTTCCCTGAAG
TTACAGTGGAACAGATTAAAGCTACAAGT
Found at i:40572178 original size:51 final size:51
Alignment explanation
Indices: 40571991--40572182 Score: 175
Period size: 51 Copynumber: 3.9 Consensus size: 51
40571981 GAGCAGATTA
* * * *
40571991 AAGTTACGAATCTTATTTCCCTGAAGTTGCAGTGGAACATATTAAAGCTAC
1 AAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTAC
* * * * ** *
40572042 TAGTCACAAATCTTATCTCCTTAAAGTTACA-T----CAGAGCAAA-TTA-
1 AAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTAC
* *
40572086 AAGTTACAAATCTTATTTCCCT-AGAGTTACATTGGAACAGATTAAAGCTAC
1 AAGTTACAAATCTTATCTCCCTGA-AGTTACAGTGGAACAGATTAAAGCTAC
* * *
40572137 AAGTTGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAA
40572183 ACGAACTTTA
Statistics
Matches: 109, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
43 1 0.01
44 25 0.23
45 3 0.03
46 6 0.06
49 7 0.06
50 3 0.03
51 63 0.58
52 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (51 bp):
AAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTAAAGCTAC
Found at i:40573775 original size:4 final size:4
Alignment explanation
Indices: 40573766--40573864 Score: 80
Period size: 4 Copynumber: 24.8 Consensus size: 4
40573756 ATTGTTTCCT
* *
40573766 TTTA TTTA TTTA TTTA TTTA -TTA TTCCT- TTTA TTTTA TTCA TTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA -TTTA TTTA TTTA TTTA
* * * *
40573815 CTTA TTTA CTTA TTTA TTTA TATA -TTA TTCA TTTA TTTA CTTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
40573862 TTT
1 TTT
40573865 TAATTCCTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
3 9 0.12
4 58 0.75
5 9 0.12
6 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:40578537 original size:9 final size:9
Alignment explanation
Indices: 40578531--40578555 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40578521 TAAGATAATC
40578531 ATAATAACA
1 ATAATAACA
40578540 ATAATAACA
1 ATAATAACA
40578549 ATAATAA
1 ATAATAA
40578556 GGATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:40583458 original size:9 final size:9
Alignment explanation
Indices: 40583434--40583478 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
40583424 ATTTTACAAT
*
40583434 TCGAATAGC
1 TCGAATAAC
*
40583443 TCAAATAAC
1 TCGAATAAC
*
40583452 TCGAATAAT
1 TCGAATAAC
40583461 TCGAATAAC
1 TCGAATAAC
*
40583470 TCAAATAAC
1 TCGAATAAC
40583479 AAATTTGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40585467 original size:3 final size:3
Alignment explanation
Indices: 40585459--40585504 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40585449 TATATAAAAC
40585459 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40585505 GGACTAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40586094 original size:10 final size:10
Alignment explanation
Indices: 40586079--40586110 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
40586069 ACGTTTTTAA
40586079 TATATATATG
1 TATATATATG
40586089 TATATATATG
1 TATATATATG
*
40586099 TATGTATATG
1 TATATATATG
40586109 TA
1 TA
40586111 AAAAAACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:40586097 original size:14 final size:14
Alignment explanation
Indices: 40586078--40586107 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40586068 AACGTTTTTA
40586078 ATATATATATGTAT
1 ATATATATATGTAT
*
40586092 ATATATGTATGTAT
1 ATATATATATGTAT
40586106 AT
1 AT
40586108 GTAAAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:40591069 original size:25 final size:25
Alignment explanation
Indices: 40591035--40591086 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
40591025 ATGAATGTCA
*
40591035 TTAAAAAGGTCCACTAGAGAAAGGG
1 TTAAAAAGGTCAACTAGAGAAAGGG
40591060 TTAAAAAGGTCAACTAGAGAAAGGG
1 TTAAAAAGGTCAACTAGAGAAAGGG
40591085 TT
1 TT
40591087 TCTAATTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (25 bp):
TTAAAAAGGTCAACTAGAGAAAGGG
Found at i:40593795 original size:11 final size:11
Alignment explanation
Indices: 40593781--40593824 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
40593771 AAATAAATAT
40593781 TATTTTATTAA
1 TATTTTATTAA
*
40593792 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
40593805 TATTTTATTAT
1 TATTTTATTAA
40593816 TATTTTATT
1 TATTTTATT
40593825 TAGTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:40595814 original size:33 final size:33
Alignment explanation
Indices: 40595772--40596036 Score: 149
Period size: 33 Copynumber: 7.9 Consensus size: 33
40595762 GCAATGTTTA
40595772 AATGTAAGACCATAGCTGGGCTATGGCA-TTTT
1 AATGTAAGACCATAGCTGGGCTATGGCACTTTT
* * * * * *
40595804 AATGAAAAGACCATAACTGAGTTATGGCACTATG
1 AATG-TAAGACCATAGCTGGGCTATGGCACTTTT
* * * * * ** *
40595838 AACGTAAGACCATGGTTGGACCATGATAGTGTTT
1 AATGTAAGACCATAGCTGGGCTATGGCACT-TTT
* *
40595872 ATATGTAAGACCATAGTTGGGCTATGGCA-TTCT
1 A-ATGTAAGACCATAGCTGGGCTATGGCACTTTT
* ** * * *
40595905 GATGATAAGACCATAATTGGGTTATGGCACTATG
1 AATG-TAAGACCATAGCTGGGCTATGGCACTTTT
* * * * * *
40595939 AACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 AATGTAAGACCATAGCTGGGCTATGGCACT-TTT
*
40595973 ATATGTAAGACCATAGCTGGGCTATGGCA-TTCT
1 A-ATGTAAGACCATAGCTGGGCTATGGCACTTTT
* * * *
40596006 GATGATAAGATCATAACTGGGTTATGGCACT
1 AATG-TAAGACCATAGCTGGGCTATGGCACT
40596037 ACGAATGTAA
Statistics
Matches: 170, Mismatches: 53, Indels: 18
0.71 0.22 0.07
Matches are distributed among these distances:
32 10 0.06
33 102 0.60
34 15 0.09
35 43 0.25
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (33 bp):
AATGTAAGACCATAGCTGGGCTATGGCACTTTT
Found at i:40595917 original size:101 final size:101
Alignment explanation
Indices: 40595742--40596046 Score: 493
Period size: 101 Copynumber: 3.0 Consensus size: 101
40595732 ATTGACGGAG
* * * *
40595742 AAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* *
40595807 GAAAAGACCATAACTGAGTTATGGCACTATGAACGT
66 GATAAGACCATAACTGGGTTATGGCACTATGAACGT
** *
40595843 AAGACCATGGTTGGACCATGATAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
*
40595908 GATAAGACCATAATTGGGTTATGGCACTATGAACGT
66 GATAAGACCATAACTGGGTTATGGCACTATGAACGT
40595944 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* * *
40596009 GATAAGATCATAACTGGGTTATGGCACTACGAATGT
66 GATAAGACCATAACTGGGTTATGGCACTATGAACGT
40596045 AA
1 AA
40596047 AGGATGAATT
Statistics
Matches: 187, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 187 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (101 bp):
AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
GATAAGACCATAACTGGGTTATGGCACTATGAACGT
Found at i:40596630 original size:9 final size:9
Alignment explanation
Indices: 40596537--40596639 Score: 143
Period size: 9 Copynumber: 11.4 Consensus size: 9
40596527 TTTGGTTAAA
40596537 AATTAACCG
1 AATTAACCG
*
40596546 AATTACCCG
1 AATTAACCG
40596555 AATTAACCG
1 AATTAACCG
*
40596564 AATTACCCG
1 AATTAACCG
40596573 AATTAACCG
1 AATTAACCG
*
40596582 AATTACCCG
1 AATTAACCG
*
40596591 AATTACCCG
1 AATTAACCG
40596600 AATTAACCG
1 AATTAACCG
*
40596609 AATTACCCG
1 AATTAACCG
*
40596618 AATTAACCA
1 AATTAACCG
*
40596627 AATTAACCA
1 AATTAACCG
40596636 AATT
1 AATT
40596640 GAATCACTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 85 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:40596786 original size:18 final size:18
Alignment explanation
Indices: 40596743--40596789 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
40596733 ATTTAATTTT
*
40596743 ATAATTGGGTTGGGTTGG
1 ATAATTGGGTTGGGTTGA
*
40596761 GTAATTGGGTTGGGTTGA
1 ATAATTGGGTTGGGTTGA
*
40596779 ATACTTGGGTT
1 ATAATTGGGTT
40596790 TAGATTGGGT
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:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (18 bp):
ATAATTGGGTTGGGTTGA
Found at i:40604530 original size:24 final size:24
Alignment explanation
Indices: 40604503--40604554 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40604493 TTAGTAAGTC
*
40604503 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40604527 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40604551 AAAT
1 AAAT
40604555 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40606499 original size:24 final size:24
Alignment explanation
Indices: 40606472--40606523 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40606462 TTAGTAAGTC
*
40606472 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40606496 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40606520 AAAT
1 AAAT
40606524 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40608085 original size:21 final size:23
Alignment explanation
Indices: 40608061--40608105 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
40608051 GTTTGCAGGT
*
40608061 GAGCAGTTG-GGCGATGG-CAGA
1 GAGCAGGTGCGGCGATGGTCAGA
*
40608082 GAGCAGGTGCGGCGCTGGTCAGA
1 GAGCAGGTGCGGCGATGGTCAGA
40608105 G
1 G
40608106 GCGGTGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.20, C:0.18, G:0.49, T:0.13
Consensus pattern (23 bp):
GAGCAGGTGCGGCGATGGTCAGA
Found at i:40608095 original size:22 final size:22
Alignment explanation
Indices: 40608061--40608112 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
40608051 GTTTGCAGGT
*
40608061 GAGCAGTTGGGCGATGG-CAGA
1 GAGCAGGTGGGCGATGGTCAGA
*
40608082 GAGCAGGTGCGGCGCTGGTCAGA
1 GAGCAGGTG-GGCGATGGTCAGA
40608105 G-GC-GGTGG
1 GAGCAGGTGG
40608113 CAGGGGGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 9 0.33
23 5 0.19
ACGTcount: A:0.17, C:0.17, G:0.52, T:0.13
Consensus pattern (22 bp):
GAGCAGGTGGGCGATGGTCAGA
Found at i:40614985 original size:41 final size:41
Alignment explanation
Indices: 40614926--40615171 Score: 145
Period size: 41 Copynumber: 5.8 Consensus size: 41
40614916 GTATCTTTGG
* *
40614926 TCTACTCCACTGTGACTTCAGGGAGATAAGACCTGATGCGA
1 TCTACTCCACTGTAACTTCAGGGAGATAAGACCTGATTCGA
* * * * **
40614967 TCTACTCCGCTGTAACTTCAGAGAGATGAGATCCCTTATTTTAA
1 TCTACTCCACTGTAACTTCAGGGAGATAAGA--CCTGA-TTCGA
* * * * ** *
40615011 TCTGCCCCACTGTAAAC-TCGGGGAGATAGGATAGTGTCTTCGA
1 TCTACTCCACTGT-AACTTCAGGGAGATAAGA-CCTG-ATTCGA
* * * *
40615054 TCTACTCCGCTGTAA-TCTCAGGGAGACAAGATCTGAAATTCTTCGG
1 TCTACTCCACTGTAACT-TCAGGGAGATAAGACCTG--A---TTCGA
* *
40615100 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATACGA
1 TCTACTCCACTGTAACTTCAGGGAGATAAGACCTGATTCGA
* * * *
40615141 TCTTCTCTACTATAACTTCAGAGAGATAAGA
1 TCTACTCCACTGTAACTTCAGGGAGATAAGA
40615172 TCCTTTATTT
Statistics
Matches: 149, Mismatches: 44, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
41 56 0.38
42 4 0.03
43 29 0.19
44 23 0.15
45 3 0.02
46 34 0.23
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTACTCCACTGTAACTTCAGGGAGATAAGACCTGATTCGA
Found at i:40615105 original size:46 final size:46
Alignment explanation
Indices: 40615047--40615135 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
40615037 TAGGATAGTG
* * *
40615047 TCTTCGATCTACTCCGCTGTAATCTCAGGGAGACAAGATCTGAAAT
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGAAAT
* *
40615093 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGA
1 TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGA
40615136 TACGATCTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (46 bp):
TCTTCGATCTACTCCACTGTAACCTCAGGGAGACAAGACCTGAAAT
Found at i:40615306 original size:175 final size:174
Alignment explanation
Indices: 40614919--40615453 Score: 756
Period size: 174 Copynumber: 3.1 Consensus size: 174
40614909 AATACTTGTA
* * * **
40614919 TCTTTGGTCTACTCCACTGTGACTTCAGGGAGATAAGACCTGATGCGATCTACTCCGCTGTAACT
1 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACT
* * * * * *
40614984 TCAGAGAGATGAGATCCCTTATTTTAATCTGCCCCACTGTAAACTCGGGGAGATAGGA-TAGT-G
66 TCAGAGAGATAAGAT-CCTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAG
* * *
40615047 TCTTCGATCTACTCCGCTGTAATCTCAGGGAGACAAGATCTGAAAT
130 -CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
* * *
40615093 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATACGATCTTCTCTACTATAACT
1 TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACT
* *
40615158 TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTATAATCTCAGGGAGATAGGATTACTAG
66 TCAGAGAGATAAGATCC-TTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAG
*
40615223 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAAT
130 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
** *
40615268 TCTTCGGTCTGTTCCACTGTAATCTCAGGG-GAATAAGACCT-AGTGCGATCTACTCTACTGTAA
1 TCTTCGGTCTACTCCACTGTAACCTCAGGGAG-ATAAGACCTGA-TGCGATCTACTCTACTGTAA
**
40615331 CTTCAGAGAGATAAGATCCTTGGTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTA
64 CTTCAGAGAGATAAGATCCTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTA
40615396 GCTTCAATCTGCTCCGCTGTAATCTCA-GGAGATAAGATCTGAAAT
129 GCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
*
40615441 TCTTCGATCTACT
1 TCTTCGGTCTACT
40615454 TCGTTGTCGA
Statistics
Matches: 322, Mismatches: 34, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
173 29 0.09
174 176 0.55
175 116 0.36
176 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (174 bp):
TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACT
TCAGAGAGATAAGATCCTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
Found at i:40615372 original size:43 final size:42
Alignment explanation
Indices: 40615280--40615434 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 42
40615270 TTCGGTCTGT
* * * **
40615280 TCCACTGTAATCTCAGGGGAATAAGA-CCTAG-TGCGATCTAC
1 TCCACTGTAATCTCAGGAG-ATAAGATCCTAGCTTCAATCCGC
* * * *
40615321 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTGGTTTAATCCGC
1 TCCACTGTAATC-TCAG-GAGATAAGATCCTAGCTTCAATCCGC
* * *
40615364 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC
1 TCCACTGTAATCTCA-GGAGATAAGA-TCCTAGCTTCAATCCGC
*
40615408 TCCGCTGTAATCTCAGGAGATAAGATC
1 TCCACTGTAATCTCAGGAGATAAGATC
40615435 TGAAATTCTT
Statistics
Matches: 89, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.01
41 19 0.21
42 7 0.08
43 34 0.38
44 28 0.31
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
TCCACTGTAATCTCAGGAGATAAGATCCTAGCTTCAATCCGC
Found at i:40615416 original size:44 final size:44
Alignment explanation
Indices: 40615183--40615433 Score: 194
Period size: 44 Copynumber: 5.8 Consensus size: 44
40615173 CCTTTATTTT
* * * *
40615183 AATCCGCTCCATTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
40615227 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTA-GCTTC
** * * *
40615273 GGTCTGTTCCACTGTAATCTCAGGG-GAATAAGA--CCTAG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAG-ATAAGATTACTAGCTTC
* * * * * * * *
40615314 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTGGTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTAGCTTC
* *
40615357 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
*
40615401 AATCTGCTCCGCTGTAATCTCA-GGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
40615434 CTGAAATTCT
Statistics
Matches: 160, Mismatches: 36, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
40 1 0.01
41 26 0.16
42 5 0.03
43 37 0.23
44 55 0.34
45 4 0.03
46 32 0.20
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:40615416 original size:87 final size:87
Alignment explanation
Indices: 40614966--40615434 Score: 288
Period size: 87 Copynumber: 5.4 Consensus size: 87
40614956 ACCTGATGCG
* * * * * *
40614966 ATCTACTCCGCTGTAA-CTTCAGAGAGATGAGATCCCTTATTTTAATCTGCCCCACTGTAAACTC
1 ATCTGCTCCGCTGTAATC-TCAGAGAGATAAGAT-CCTTGTTTTAATCCGCTCCACTGTAATCTC
* * *
40615030 GGGGAGATAGGA-TAGT-GTCTTCG
64 AGGGAGATAGGATTACTAG-CTTCA
* * * ** ** *
40615053 ATCTACTCCGCTGTAATCTCAGGGAGACAAGAT-C-TGAAATTCTTCGGTCTACTCCACTGTAAC
1 ATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCCTTG---TT-TT-AATCCGCTCCACTGTAAT
* * * * *
40615116 CTCAGGGAGATAAGA--CCT-GATACG
61 CTCAGGGAGATAGGATTACTAGCTTCA
* ** * * * *
40615140 ATCTTCTCTACTATAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTATAATCTC
1 ATCTGCTCCGCTGTAATC-TCAGAGAGATAAGATCC-TTGTTTTAATCCGCTCCACTGTAATCTC
40615204 AGGGAGATAGGATTACTAGCTTCA
64 AGGGAGATAGGATTACTAGCTTCA
* ** * *
40615228 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT--TTGAAATTCTTCGGTCTGTTCCACTGTAAT
1 ATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCCTTG---TT-TT-AATCCGCTCCACTGTAAT
* * * *
40615291 CTCAGGG-GAATAAGA--CCTAG-TGCG
61 CTCAGGGAG-ATAGGATTACTAGCTTCA
* ** *
40615315 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTGGTTTAATCCGCTCCACTGTAATCTCA
1 ATCTGCTCCGCTGTAATC-TCAGAGAGATAAGATCCTTGTTTTAATCCGCTCCACTGTAATCTCA
40615379 GGGAGATAGGATTACTAGCTTCA
65 GGGAGATAGGATTACTAGCTTCA
40615402 ATCTGCTCCGCTGTAATCTCAG-GAGATAAGATC
1 ATCTGCTCCGCTGTAATCTCAGAGAGATAAGATC
40615435 TGAAATTCTT
Statistics
Matches: 288, Mismatches: 66, Indels: 57
0.70 0.16 0.14
Matches are distributed among these distances:
84 27 0.09
85 31 0.11
86 20 0.07
87 110 0.38
88 42 0.15
89 33 0.11
90 25 0.09
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (87 bp):
ATCTGCTCCGCTGTAATCTCAGAGAGATAAGATCCTTGTTTTAATCCGCTCCACTGTAATCTCAG
GGAGATAGGATTACTAGCTTCA
Found at i:40616762 original size:1 final size:1
Alignment explanation
Indices: 40616756--40616796 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
40616746 CTCTCCAAAG
40616756 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40616797 AGGAAGCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40627705 original size:22 final size:22
Alignment explanation
Indices: 40627677--40627732 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40627667 TTAAGTATAA
40627677 AAGATATATATAGACATGAACT
1 AAGATATATATAGACATGAACT
* * * *
40627699 AAGATATGTGTATACATGAATT
1 AAGATATATATAGACATGAACT
* *
40627721 AACAAATATATA
1 AAGATATATATA
40627733 AAGTATATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (22 bp):
AAGATATATATAGACATGAACT
Found at i:40628166 original size:15 final size:16
Alignment explanation
Indices: 40628128--40628168 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
40628118 AAATAAAATC
40628128 AATAA-AATAATAGGT
1 AATAATAATAATAGGT
40628143 AAT--TAATAATA-GT
1 AATAATAATAATAGGT
40628156 AATAATAATAATA
1 AATAATAATAATA
40628169 ATAGGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (16 bp):
AATAATAATAATAGGT
Found at i:40629701 original size:19 final size:19
Alignment explanation
Indices: 40629666--40629706 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40629656 CTATTAATAC
40629666 ATATAATATAACTATTATT
1 ATATAATATAACTATTATT
*
40629685 ATATTATATAA-TA--ATT
1 ATATAATATAACTATTATT
40629701 ATATAA
1 ATATAA
40629707 AAGATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATATAACTATTATT
Found at i:40630992 original size:16 final size:17
Alignment explanation
Indices: 40630973--40631018 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
40630963 AAAATTCTTT
40630973 AAAAATTCAAAAATA-G
1 AAAAATTCAAAAATATG
**
40630989 AAAAATAGAAAAATATG
1 AAAAATTCAAAAATATG
40631006 AAAAATTTCAAAA
1 AAAAA-TTCAAAA
40631019 TTCAATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 13 0.54
17 6 0.25
18 5 0.21
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAAATTCAAAAATATG
Found at i:40630993 original size:9 final size:8
Alignment explanation
Indices: 40630981--40631011 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
40630971 TTAAAAATTC
40630981 AAAAATAG
1 AAAAATAG
40630989 AAAAATAG
1 AAAAATAG
40630997 AAAAATATG
1 AAAAATA-G
40631006 AAAAAT
1 AAAAAT
40631012 TTCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (8 bp):
AAAAATAG
Found at i:40631440 original size:21 final size:22
Alignment explanation
Indices: 40631413--40631470 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
40631403 TGAATTTTAG
40631413 AATTTTTTTATATTTTAAAATT
1 AATTTTTTTATATTTTAAAATT
* *
40631435 -ATTTTTATATATTTAAAAATT
1 AATTTTTTTATATTTTAAAATT
40631456 AATTTTTTTA-ATTTT
1 AATTTTTTTATATTTT
40631471 TATGTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTTTTTTATATTTTAAAATT
Found at i:40643554 original size:46 final size:46
Alignment explanation
Indices: 40643487--40643649 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
40643477 TTTGAGTACT
* * *
40643487 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
40643533 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
40643579 TCTCATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
40643625 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
40643650 ATCATACGTA
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
44 12 0.11
45 5 0.05
46 94 0.85
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:40657532 original size:13 final size:12
Alignment explanation
Indices: 40657505--40657530 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40657495 TTAGAAAAGG
40657505 TTAATTCAATTT
1 TTAATTCAATTT
40657517 TTAATTCAATTT
1 TTAATTCAATTT
40657529 TT
1 TT
40657531 TACAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAATTCAATTT
Found at i:40657849 original size:16 final size:17
Alignment explanation
Indices: 40657828--40657868 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40657818 GATCAAAATA
40657828 TAATTTTATAA-TGTAT
1 TAATTTTATAATTGTAT
*
40657844 TAATTTT-TAATTTTAT
1 TAATTTTATAATTGTAT
40657860 TAAATTTTA
1 T-AATTTTA
40657869 AGCGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTTTATAATTGTAT
Found at i:40658889 original size:27 final size:29
Alignment explanation
Indices: 40658830--40658900 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 29
40658820 AAAAATAAAA
40658830 ATTTACCAAAATAT-TACAACTTTTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
*
40658858 ATTTACCAAAACATATA-AAC-TTTTTTT
1 ATTTACCAAAATATATACAACTTTTTTTT
40658885 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
40658901 CAAATAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.55
28 16 0.40
29 2 0.05
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTACCAAAATATATACAACTTTTTTTT
Found at i:40659069 original size:4 final size:4
Alignment explanation
Indices: 40659060--40659149 Score: 65
Period size: 4 Copynumber: 20.2 Consensus size: 4
40659050 CAGAAGGAGG
*
40659060 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA GAAAA GGAAA GGAGAA GAAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA G-AAA -GAAA -GA-AA G-AAA
*
40659111 GGAGAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA G
1 -GA-AA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
40659150 GGAAAGGAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
3 3 0.04
4 38 0.52
5 24 0.33
6 8 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40659087 original size:14 final size:14
Alignment explanation
Indices: 40659060--40659149 Score: 80
Period size: 16 Copynumber: 6.4 Consensus size: 14
40659050 CAGAAGGAGG
40659060 GAAAG-AAA-GAAA
1 GAAAGAAAAGGAAA
* *
40659072 GAAAGGAGAGGAAA
1 GAAAGAAAAGGAAA
40659086 GAAAGAAAAGGAAA
1 GAAAGAAAAGGAAA
40659100 GGAGAAGAAAAGGAGAA
1 -GA-AAGAAAAGGA-AA
*
40659117 GAGAAGAAAAAAGAAA
1 GA-AAG-AAAAGGAAA
40659133 GAAAG--AAGGAAA
1 GAAAGAAAAGGAAA
40659145 GAAAG
1 GAAAG
40659150 GGAAAGGAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
12 16 0.24
13 2 0.03
14 16 0.24
15 5 0.07
16 20 0.30
17 8 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAGGAAA
Found at i:40659109 original size:16 final size:15
Alignment explanation
Indices: 40659080--40659181 Score: 76
Period size: 16 Copynumber: 6.9 Consensus size: 15
40659070 AAGAAAGGAG
40659080 AGGAAAGA-AAGAAA
1 AGGAAAGAGAAGAAA
40659094 AGGAAAGGAGAAGAAA
1 AGGAAA-GAGAAGAAA
40659110 AGGAGAAGAGAAGAAAA
1 AGGA-AAGAGAAG-AAA
*
40659127 AAGAAAGA-AAG--A
1 AGGAAAGAGAAGAAA
*
40659139 AGGAAAGA-AAGGGAA
1 AGGAAAGAGAA-GAAA
40659154 AGGAGAAGAGAA-AAA
1 AGGA-AAGAGAAGAAA
40659169 A--AAAGAAGAAGAA
1 AGGAAAG-AGAAGAA
40659182 GAGGGAAGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
12 13 0.18
13 6 0.08
14 8 0.11
15 13 0.18
16 24 0.32
17 10 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AGGAAAGAGAAGAAA
Found at i:40659154 original size:22 final size:21
Alignment explanation
Indices: 40659059--40659155 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 21
40659049 CCAGAAGGAG
40659059 GGAAAGAAA-GAAAGAAAGGAGA
1 GGAAAGAAAGGAAAGAAA-GA-A
* *
40659081 GGAAAGAAAGAAAAG-GA-AA
1 GGAAAGAAAGGAAAGAAAGAA
40659100 GGAGAAGAAAAGG--AGAAGAGAA
1 GGA-AAG-AAAGGAAAGAA-AGAA
40659122 -GAAA-AAA-GAAAGAAAGAA
1 GGAAAGAAAGGAAAGAAAGAA
40659140 GGAAAGAAAGGGAAAG
1 GGAAAGAAA-GGAAAG
40659156 GAGAAGAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
17 1 0.02
18 7 0.12
19 14 0.24
20 9 0.15
21 7 0.12
22 17 0.29
23 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
GGAAAGAAAGGAAAGAAAGAA
Found at i:40659160 original size:39 final size:38
Alignment explanation
Indices: 40659064--40659179 Score: 107
Period size: 39 Copynumber: 3.0 Consensus size: 38
40659054 AGGAGGGAAA
* *
40659064 GAAAGAAA-GAAAGGAGAGGAAAGAAAG-AA-AAGGAAAG
1 GAAAGAAAGGAAAGGAGAAGAAA-AAAGAAAGAAAG-AAG
40659101 GAGAAGAAAAGGAGAA-GAGAAGAAAAAAGAAAGAAAGAAG
1 GA-AAG-AAAGGA-AAGGAGAAGAAAAAAGAAAGAAAGAAG
*
40659141 GAAAGAAAGGGAAAGGAGAAGAGAAAAAAAAAG-AAGAAG
1 GAAAGAAA-GGAAAGGAGAAGA-AAAAAGAAAGAAAGAAG
40659180 AAGAGGGAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
37 2 0.03
38 8 0.12
39 26 0.39
40 26 0.39
41 5 0.07
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (38 bp):
GAAAGAAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAG
Found at i:40659173 original size:18 final size:18
Alignment explanation
Indices: 40659063--40659180 Score: 53
Period size: 18 Copynumber: 6.1 Consensus size: 18
40659053 AAGGAGGGAA
*
40659063 AGAAAGAAAGAAAGGAGAGG
1 AGAAA-AAA-AAAGGAGAAG
40659083 A-AAGAAAGAAAAGGA-AAG
1 AGAA-AAA-AAAAGGAGAAG
* *
40659101 -GAGAAGAAAAGGAGAAG
1 AGAAAAAAAAAGGAGAAG
* *
40659118 AGAAGAAAAAAGAAAGAAAG
1 AGAAAAAAAAAG-GAG-AAG
40659138 AAGGAAAGAAAGGGAAAGGAGAAG
1 -A-GAAA-AAA---AAAGGAGAAG
*
40659162 AGAAAAAAAAAGAAGAAG
1 AGAAAAAAAAAGGAGAAG
40659180 A
1 A
40659181 AGAGGGAAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
16 7 0.09
17 5 0.07
18 21 0.28
19 12 0.16
20 6 0.08
21 4 0.05
22 7 0.09
23 4 0.05
24 3 0.04
25 2 0.03
26 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAGGAGAAG
Found at i:40659193 original size:60 final size:61
Alignment explanation
Indices: 40659060--40659183 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 61
40659050 CAGAAGGAGG
**
40659060 GAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAAAAGGAGAAGAGAA
1 GAAA-AAAGAAAGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAAAAAAAGAAGAGAA
*
40659122 GAAAAAAGAAAGAAA-GA-AGGAAAGAAAGGGAAAGGAGAA-GAGAA-AAAAAAAGAAGAAGAA
1 GAAAAAAGAAAGAAAGGAGAGGAAAGAAA-GAAAAGGA-AAGGAGAAGAAAAAAAGAAG-AGAA
40659182 GA
1 GA
40659184 GGGAAGAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
59 19 0.34
60 20 0.36
61 13 0.23
62 4 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (61 bp):
GAAAAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAAAAAAAGAAGAGAA
Found at i:40659194 original size:44 final size:44
Alignment explanation
Indices: 40659083--40659182 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
40659073 AAAGGAGAGG
* *
40659083 AAAGAAAG-AA-AAGGAAAGGAGAA-GAAAAGGAGAAGAGAAGAAA
1 AAAGAAAGAAAGAAGGAAA-GA-AAGGGAAAGGAGAAGAGAAAAAA
40659126 AAAGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
40659170 AAAG-AAG-AAGAAG
1 AAAGAAAGAAAGAAG
40659183 AGGGAAGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
42 6 0.12
43 13 0.25
44 26 0.50
45 7 0.13
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (44 bp):
AAAGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA
Found at i:40659237 original size:19 final size:19
Alignment explanation
Indices: 40659213--40659250 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40659203 GGAAAAAGGT
40659213 AATTTTATTTATAA-ATTTG
1 AATTTT-TTTATAATATTTG
*
40659232 AATTTTTTTGTAATATTTG
1 AATTTTTTTATAATATTTG
40659251 TGTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AATTTTTTTATAATATTTG
Found at i:40660783 original size:10 final size:10
Alignment explanation
Indices: 40660768--40660794 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40660758 AGTGCACGGT
40660768 GACGTTGGAG
1 GACGTTGGAG
40660778 GACGTTGGAG
1 GACGTTGGAG
40660788 GACGTTG
1 GACGTTG
40660795 CAGTGCAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.48, T:0.22
Consensus pattern (10 bp):
GACGTTGGAG
Found at i:40664622 original size:15 final size:12
Alignment explanation
Indices: 40664579--40664615 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40664569 ATTACTTAAA
* *
40664579 AAAATTATACTC
1 AAAATAATACAC
40664591 AAAATAATACAC
1 AAAATAATACAC
40664603 AAAATAATACAC
1 AAAATAATACAC
40664615 A
1 A
40664616 CTAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAATACAC
Found at i:40664858 original size:3 final size:3
Alignment explanation
Indices: 40664850--40664887 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40664840 TCTTCATACT
40664850 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
40664888 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40664987 original size:19 final size:21
Alignment explanation
Indices: 40664963--40665001 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40664953 ACTAAAACAA
*
40664963 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
40664982 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
40665002 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:40665269 original size:27 final size:28
Alignment explanation
Indices: 40665238--40665311 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
40665228 TTTGTTTTTT
40665238 TTTATATATTTTGGTAAAT-AAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
40665265 TTTATATATTTTGGTAAATAAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
40665293 TTGTA-ATATTTTGGTAAAT
1 TT-TATATATTTTGGTAAAT
40665312 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 19 0.42
28 24 0.53
29 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (28 bp):
TTTATATATTTTGGTAAATAAAAAAAAG
Found at i:40674136 original size:28 final size:27
Alignment explanation
Indices: 40674088--40674142 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
40674078 AATTTAAAAG
* * *
40674088 AATTAAAAAAATATAATTATGTTTAAA
1 AATTAAAAAAATAAAAATATGGTTAAA
*
40674115 AATTTAAAAAATAAAAAATATGGTTAAA
1 AATTAAAAAAAT-AAAAATATGGTTAAA
40674143 TTTTTAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (27 bp):
AATTAAAAAAATAAAAATATGGTTAAA
Found at i:40679924 original size:36 final size:33
Alignment explanation
Indices: 40679840--40679929 Score: 83
Period size: 36 Copynumber: 2.6 Consensus size: 33
40679830 TCCACTCATA
*
40679840 TATTT-TTAAAATTTTTATTTTAAAAAATATATT
1 TATTTATTAAAATTTATA-TTTAAAAAATATATT
** *
40679873 TATATTATTTTAATTTAATATTTAATAATATATTATT
1 TAT-TTATTAAAATTT-ATATTTAA-AAAATA-TATT
40679910 TATTTATTAAAATTTTATAT
1 TATTTATTAAAA-TTTATAT
40679930 ATAGGGATCT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
33 3 0.07
34 2 0.04
35 12 0.27
36 18 0.40
37 10 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TATTTATTAAAATTTATATTTAAAAAATATATT
Found at i:40681623 original size:31 final size:32
Alignment explanation
Indices: 40681582--40681647 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
40681572 AAAATAATAC
* * *
40681582 TAAATTATTGTATAAGGACTAAAATTTGAATT
1 TAAATTATTGTAAAAGGACCAAAATTAGAATT
40681614 TAAA-TATTGTAAAAGGACCAAAATTAGAATT
1 TAAATTATTGTAAAAGGACCAAAATTAGAATT
40681645 TAA
1 TAA
40681648 CCTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (32 bp):
TAAATTATTGTAAAAGGACCAAAATTAGAATT
Found at i:40684330 original size:4 final size:4
Alignment explanation
Indices: 40684321--40684399 Score: 158
Period size: 4 Copynumber: 19.8 Consensus size: 4
40684311 CCCATCCGTG
40684321 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
40684369 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
40684400 GGTGAAACCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:40688914 original size:161 final size:155
Alignment explanation
Indices: 40688650--40688964 Score: 459
Period size: 161 Copynumber: 2.0 Consensus size: 155
40688640 ATATACTATC
* * *
40688650 CTTTTTTTGCTTCTAGTTCTTGTACTCGTACGAGACTAAGGAAAAAATCACAACCCCAAATTAGA
1 CTTTTTTTGCTTCTAGTTCTTGTACTCATACCAGACTAAGGAAAAAATCACAAACCCAAATTAGA
* *
40688715 TTTAAATATTTTGAAACTTGACAGTAAAAAAATGTTTATAATATACTTGTGATCCAGTTGTATTA
66 TTTAAATATTTTGAAACTTGACAATAAAAAAATGTTTAT-ATATACCTGTGATCCAGTTGTATTA
* * *
40688780 GGTTGAATGCATGGTCTTTTGTTGTT
130 GGTTGAAGGCATGATCTTCTGTTGTT
* *
40688806 CTTTTTTTGGCTTCTAGTTCTTGTACTTATACCAGACTAAGACAATAAAAAATCACAAACCCAAA
1 CTTTTTTT-GCTTCTAGTTCTTGTACTCATACCAGACTAAG----GAAAAAATCACAAACCCAAA
* *
40688871 TTAGATTTAAATATTTTGAAACTTGACAATGAAAAAGTGTTTATATATACCTGTGATCCAGTTGT
61 TTAGATTTAAATATTTTGAAACTTGACAATAAAAAAATGTTTATATATACCTGTGATCCAGTTGT
*
40688936 GTTAGGTTGAAGGCATGATCTTCTGTTGT
126 ATTAGGTTGAAGGCATGATCTTCTGTTGT
40688965 GACCCTCACC
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
156 8 0.06
157 29 0.21
160 45 0.32
161 59 0.42
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (155 bp):
CTTTTTTTGCTTCTAGTTCTTGTACTCATACCAGACTAAGGAAAAAATCACAAACCCAAATTAGA
TTTAAATATTTTGAAACTTGACAATAAAAAAATGTTTATATATACCTGTGATCCAGTTGTATTAG
GTTGAAGGCATGATCTTCTGTTGTT
Found at i:40691266 original size:18 final size:18
Alignment explanation
Indices: 40691243--40691277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40691233 AAACCTTTAA
*
40691243 CACCCTTACCACATTCAC
1 CACCCTCACCACATTCAC
*
40691261 CACCCTCACCACCTTCA
1 CACCCTCACCACATTCA
40691278 TTGCCAGCAA
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:0.26, C:0.54, G:0.00, T:0.20
Consensus pattern (18 bp):
CACCCTCACCACATTCAC
Found at i:40691340 original size:57 final size:57
Alignment explanation
Indices: 40691256--40691515 Score: 270
Period size: 57 Copynumber: 4.7 Consensus size: 57
40691246 CCTTACCACA
* * *
40691256 TTCACCACCCTCACCACCTTCATTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
1 TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
* * * * ** *
40691313 TTCAACACCCTCACCACATTTACTGCCAGCAACCTCAGCACACTCTCCATTTAGACC
1 TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
* *
40691370 TTCAACACCCTTACCACCTTTACTGCCAACAACCTCAACACCCT-CCCACCTAAACC
1 TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
* * **
40691426 TT--------T-ACCACCTTCACTGCCAGCAACCTCAACACCCTTCCCATTTAAACC
1 TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
* * **
40691474 TTCAACACCCTTACCACTTTTACTGCCAGCAATTTCAACACC
1 TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACC
40691516 TTCATTACCA
Statistics
Matches: 166, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
47 30 0.18
48 13 0.08
56 11 0.07
57 112 0.67
ACGTcount: A:0.28, C:0.45, G:0.04, T:0.22
Consensus pattern (57 bp):
TTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAAACC
Done.