Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 40 of 216
Found at i:11370167 original size:48 final size:48
Alignment explanation
Indices: 11370088--11370181 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
11370078 AGGGAATTCT
* *
11370088 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
11370136 GTTGAATCCATTATTGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCATTATTGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
11370182 AGCCAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:11374669 original size:3 final size:3
Alignment explanation
Indices: 11374661--11374688 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11374651 TACAGCTTTG
11374661 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
11374689 ACATTCTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:11378081 original size:19 final size:21
Alignment explanation
Indices: 11378029--11378081 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 21
11378019 CTTTCAACAC
*
11378029 CAAAAATAGAGTTTTTCTCTAA
1 CAAAAATA-AGTTTTTCTCAAA
*
11378051 -AAAAATTA-TTTTT-T-AAA
1 CAAAAATAAGTTTTTCTCAAA
11378068 CAAAAATAAGTTTT
1 CAAAAATAAGTTTT
11378082 AGTCCGGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
19 9 0.35
20 1 0.04
21 6 0.23
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (21 bp):
CAAAAATAAGTTTTTCTCAAA
Found at i:11389296 original size:16 final size:16
Alignment explanation
Indices: 11389275--11389326 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
11389265 TTTGGTTCGC
11389275 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11389291 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
11389307 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
11389323 TGTA
1 TGTA
11389327 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:11389373 original size:45 final size:44
Alignment explanation
Indices: 11389307--11389401 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
11389297 GGATTAGAGG
* *
11389307 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
11389352 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
11389396 TGTAAT
1 TGTAAT
11389402 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:11389580 original size:16 final size:16
Alignment explanation
Indices: 11389543--11389584 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11389533 TTAATCATAT
*
11389543 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
11389559 TT-AAATATATTATAA
1 TTAAAATATATTATAA
11389574 TTAAAATATAT
1 TTAAAATATAT
11389585 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:11389591 original size:14 final size:15
Alignment explanation
Indices: 11389552--11389593 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11389542 TTTAAACATA
*
11389552 ATTATTATTAAATAT
1 ATTATAATTAAATAT
11389567 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
11389581 A-TATAATTTAATA
1 ATTATAATTAAATA
11389594 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:11389766 original size:47 final size:46
Alignment explanation
Indices: 11389715--11389875 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
11389705 GATTTAATAA
11389715 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
11389762 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
11389803 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
11389850 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
11389876 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:11394590 original size:29 final size:30
Alignment explanation
Indices: 11394534--11394612 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
11394524 AATCTTAAAA
* *
11394534 TTATAAATCAATTTTGATTTAACGTGTAATT
1 TTATATATAAATTTTGATTT-ACGTGTAATT
* *
11394565 TTATATATGAATTTTGATTT-GGTGTAATT
1 TTATATATAAATTTTGATTTACGTGTAATT
*
11394594 ATATATATAAAATTTTGAT
1 TTATATAT-AAATTTTGAT
11394613 CGTGGTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.36
30 9 0.21
31 18 0.43
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (30 bp):
TTATATATAAATTTTGATTTACGTGTAATT
Found at i:11405882 original size:34 final size:35
Alignment explanation
Indices: 11405828--11405894 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11405818 CAAACACCAG
*
11405828 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
11405863 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11405895 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11411204 original size:4 final size:4
Alignment explanation
Indices: 11411195--11411222 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
11411185 CATCTTATGC
11411195 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
11411223 GAGGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:11412094 original size:16 final size:16
Alignment explanation
Indices: 11412073--11412104 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11412063 GATCCTCACT
11412073 ATATTTTCTTTCTTTC
1 ATATTTTCTTTCTTTC
*
11412089 ATATTTTCTTTGTTTC
1 ATATTTTCTTTCTTTC
11412105 TTTTTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.69
Consensus pattern (16 bp):
ATATTTTCTTTCTTTC
Found at i:11413345 original size:21 final size:22
Alignment explanation
Indices: 11413303--11413345 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11413293 TAGACGAAGT
* *
11413303 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTAAATAA
11413325 ACAATATAATTT-ACTAAATAA
1 ACAATATAATTTAACTAAATAA
11413346 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATAATTTAACTAAATAA
Found at i:11414425 original size:20 final size:21
Alignment explanation
Indices: 11414392--11414431 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11414382 ATGACTAAGC
11414392 CTATCTTCAGTTTTACTTGAT
1 CTATCTTCAGTTTTACTTGAT
*
11414413 CTAT-TTCATTTTTACTTGA
1 CTATCTTCAGTTTTACTTGA
11414432 ACTTGGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.55
Consensus pattern (21 bp):
CTATCTTCAGTTTTACTTGAT
Found at i:11417304 original size:14 final size:13
Alignment explanation
Indices: 11417273--11417311 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
11417263 TAAGTCCTTT
11417273 ACAGATACAGAT-A
1 ACAGA-ACAGATAA
11417286 ACAGAATCAGATAA
1 ACAGAA-CAGATAA
11417300 ACAGAACAGATA
1 ACAGAACAGATA
11417312 CAATGAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 16 0.67
14 7 0.29
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.13
Consensus pattern (13 bp):
ACAGAACAGATAA
Found at i:11417506 original size:13 final size:14
Alignment explanation
Indices: 11417488--11417525 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
11417478 ATCCCACCCC
11417488 AAATACAGATACA-
1 AAATACAGATACAG
*
11417501 AAATACAAATACAG
1 AAATACAGATACAG
11417515 AAATAACAGAT
1 AAAT-ACAGAT
11417526 TTAACAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (14 bp):
AAATACAGATACAG
Found at i:11420385 original size:42 final size:42
Alignment explanation
Indices: 11420322--11420439 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 42
11420312 TGTGATTACG
*
11420322 TGTAAGACCATGTCTGAGACATTGGCATTGATATAAGATTCA
1 TGTAAGACCATGTCTGAGACATTGGCATCGATATAAGATTCA
* * *
11420364 TGTAAGACCATGTCT-AGGACATTGGCATCGATTTGAGATTCG
1 TGTAAGACCATGTCTGA-GACATTGGCATCGATATAAGATTCA
11420406 TGTAAGACCATAG-CTG-G-CTATTGGCATCGATATA
1 TGTAAGACCAT-GTCTGAGAC-ATTGGCATCGATATA
11420440 TGATAGTTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 49 0.74
43 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGAGACATTGGCATCGATATAAGATTCA
Found at i:11420473 original size:42 final size:40
Alignment explanation
Indices: 11420322--11420473 Score: 128
Period size: 42 Copynumber: 3.6 Consensus size: 40
11420312 TGTGATTACG
* * * * *
11420322 TGTAAGACCATGTCTGAGACATTGGCATTGATATAAGATTC
1 TGTAAGACCATATCTG-GATATTGGCATCGATTTGAGATTC
* *
11420363 ATGTAAGACCATGTCTAGGACATTGGCATCGATTTGAGATTC
1 -TGTAAGACCATATCT-GGATATTGGCATCGATTTGAGATTC
* * *
11420405 GTGTAAGACCATAGCTGGCTATTGGCATCGATATATGATAGTT-
1 -TGTAAGACCATATCTGGATATTGGCATCGAT-T-TGAGA-TTC
11420448 TGTAAGACCATATCTGGGATA-TGGCA
1 TGTAAGACCATATCT-GGATATTGGCA
11420474 CTGTGCGAGT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
41 14 0.15
42 69 0.73
43 9 0.10
44 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (40 bp):
TGTAAGACCATATCTGGATATTGGCATCGATTTGAGATTC
Found at i:11426630 original size:42 final size:43
Alignment explanation
Indices: 11426524--11426637 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 43
11426514 TTATGTAGAA
* *
11426524 AAATGCCGCTATAGAATATGACCTTTAGCGGTGCTTTTCCCAC
1 AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
* ** * * * *
11426567 AAACGCCATTAAAGAAGATGACATTTAGCGTTG-ATTTCCCAC
1 AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
*
11426609 AAATGACGCTATAGAACATGACCTTTAGC
1 AAATGCCGCTATAGAACATGACCTTTAGC
11426638 AGCATGTTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
42 30 0.54
43 26 0.46
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
Found at i:11429113 original size:24 final size:24
Alignment explanation
Indices: 11429069--11429115 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11429059 AACAAAATAT
*
11429069 AAATGAAAACATAAATCAATAAAC
1 AAATGAAAACATAAATAAATAAAC
*
11429093 AAATGAAGGACATAAA-AAATAAA
1 AAATGAA-AACATAAATAAATAAA
11429116 AAAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.15
Consensus pattern (24 bp):
AAATGAAAACATAAATAAATAAAC
Found at i:11429780 original size:19 final size:19
Alignment explanation
Indices: 11429750--11429824 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
11429740 AATCATATCT
*
11429750 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
11429769 TCCAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
11429790 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
11429809 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
11429825 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 33 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:11429787 original size:21 final size:21
Alignment explanation
Indices: 11429761--11429823 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
11429751 CTAATATTGC
*
11429761 ATATCATATCCAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
11429782 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
11429801 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
11429822 AT
1 AT
11429824 CCTTGAAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 19 0.49
21 20 0.51
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:11431641 original size:108 final size:108
Alignment explanation
Indices: 11431497--11432001 Score: 784
Period size: 107 Copynumber: 4.7 Consensus size: 108
11431487 GTCAAACGGG
** *
11431497 AAATCGAAACCCAGCACATTAGCACACGTTTCCTCGAATTTCTAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
* * *
11431562 TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAA
66 TTGAAATTTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAA
* *
11431605 AAATCGAAACCCAGCACATTAGGGCACATTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
* * *
11431670 TTGAATTTTTAAAAGAATATTTAGCTATTTGATCGAAC-AAAA
66 TTGAAATTTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAA
11431712 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
* *
11431777 TTGAAATTTTAAAAGGATATTTAGCTATTTAGTCGAATG-AAA
66 TTGAAATTTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAA
* * * *
11431819 AAATCGAAACCTAACACATTAGGGCACGTTTTCTCGAATTTCTAAACACAAAATATTCCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
*
11431884 TTGAAATTTTAAAAGGATATTTAGCTATTTGGTTGAAC-AAAA
66 TTGAAATTTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAA
* *
11431926 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGTAAAATATTGCCTTA-T
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
11431990 TTAGAAAATTTT
66 TT-G-AAATTTT
11432002 TCCTTTTTTG
Statistics
Matches: 362, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
106 3 0.01
107 259 0.72
108 100 0.28
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (108 bp):
AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCTAAACGCAAAATATTGCCTTACT
TTGAAATTTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAA
Found at i:11432067 original size:20 final size:21
Alignment explanation
Indices: 11432024--11432068 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
11432014 GTAAGGTGTT
*
11432024 AATATGCATAATGTAATAATA
1 AATATGCATAATGTAACAATA
11432045 AATATG-ATAATGTGAACAA-A
1 AATATGCATAATGT-AACAATA
11432065 AATA
1 AATA
11432069 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (21 bp):
AATATGCATAATGTAACAATA
Found at i:11432227 original size:30 final size:27
Alignment explanation
Indices: 11432193--11432251 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
11432183 TATCATCAAG
*
11432193 TAAAACAATAATAACAATA-AAGAAACTAGA
1 TAAAAAAAT-ATAA-AATATAA-AAA-TAGA
11432223 TAAAAAAATATAAAATATAAAAATAGA
1 TAAAAAAATATAAAATATAAAAATAGA
11432250 TA
1 TA
11432252 TGTACACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.22
28 7 0.26
29 6 0.22
30 8 0.30
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (27 bp):
TAAAAAAATATAAAATATAAAAATAGA
Found at i:11441710 original size:86 final size:85
Alignment explanation
Indices: 11441566--11441730 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
11441556 AGCTCTTACA
* * * *
11441566 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAG-GG
1 ATGCCAACGTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGAC-GTGG
*
11441630 TCTTACACGAAATCATATACG
65 TCTTACACAAAATCATATACG
* * *
11441651 ATGCCAATGTCCCAAACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGACGT
1 ATGCCAACGTCCCAAACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTATCCCAGACGT
11441714 GGTCTTACACAAAATCA
63 GGTCTTACACAAAATCA
11441731 CATATCGGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 27 0.40
86 37 0.54
87 4 0.06
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (85 bp):
ATGCCAACGTCCCAAACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGACGTGGT
CTTACACAAAATCATATACG
Found at i:11443901 original size:15 final size:15
Alignment explanation
Indices: 11443881--11443911 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11443871 TTATTGTTAA
11443881 AAAAAATAAAATTTT
1 AAAAAATAAAATTTT
11443896 AAAAAATAAAATTTT
1 AAAAAATAAAATTTT
11443911 A
1 A
11443912 TATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAATAAAATTTT
Found at i:11444446 original size:16 final size:14
Alignment explanation
Indices: 11444401--11444436 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
11444391 TGGAGAATAT
*
11444401 TTTTAATTAATTCAA
1 TTTTAATTAATT-TA
11444416 TTTTAATTAATTTA
1 TTTTAATTAATTTA
11444430 TTTTAAT
1 TTTTAAT
11444437 ATTATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATTAATTTA
Found at i:11444682 original size:14 final size:14
Alignment explanation
Indices: 11444641--11444683 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
11444631 AGTACTTAAA
*
11444641 TTTTTAATATTTAAT
1 TTTTTAAT-TTTATT
*
11444656 TTTTTAACCTTTATT
1 TTTTTAA-TTTTATT
11444671 TTTTTAATTTTAT
1 TTTTTAATTTTAT
11444684 AATTTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTTATT
Found at i:11454136 original size:31 final size:32
Alignment explanation
Indices: 11454117--11454187 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
11454107 TATAATTTAT
11454117 TATATTATTTATAAGTTTTTATAAAATTTTAAA
1 TATATT-TTTATAAGTTTTTATAAAATTTTAAA
* *
11454150 TATATTTTTATTAG-TTTTATAAATTTTTAGAA
1 TATATTTTTATAAGTTTTTATAAAATTTTA-AA
*
11454182 TTTATT
1 TATATT
11454188 AGAATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 14 0.41
32 14 0.41
33 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (32 bp):
TATATTTTTATAAGTTTTTATAAAATTTTAAA
Found at i:11454177 original size:19 final size:18
Alignment explanation
Indices: 11454104--11454419 Score: 79
Period size: 19 Copynumber: 17.2 Consensus size: 18
11454094 ATGACTTTTT
*
11454104 TTTTATAATTTATTATATTA
1 TTTTATAAATT-TT-TATTA
* *
11454124 -TTTATAAGTTTTTATAAAA
1 TTTTATAAATTTTTAT--TA
*
11454143 TTTTAAATATATTTTTATTA
1 TTTT--ATAAATTTTTATTA
*
11454163 GTTTTATAAATTTTTA-GA
1 -TTTTATAAATTTTTATTA
*
11454181 ATTTATTAGAATTTTTA-TA
1 TTTTA-TA-AATTTTTATTA
* *
11454200 TTTT-TATGATATTTATTA
1 TTTTATA-AATTTTTATTA
* *
11454218 GTTTT-TATATTTTTATAA
1 -TTTTATAAATTTTTATTA
* *
11454236 TTTTA-AAAGTTTATGTTA
1 TTTTATAAA-TTTTTATTA
* *
11454254 ATTT-T-AATTTTTA-AA
1 TTTTATAAATTTTTATTA
* **
11454269 TTTT-TATGATTTATTAGAA
1 TTTTATA-AATTT-TTATTA
* *
11454288 TTTTTATACATTTTTATAAAA
1 -TTTTATAAATTTTTAT--TA
11454309 TTTTA-AATATTTTTATTTA
1 TTTTATAA-ATTTTTA-TTA
*
11454328 TTTTATAATTTTTTATATA
1 TTTTATAAATTTTTAT-TA
* *
11454347 TTTTTTAAATTTTTATAA
1 TTTTATAAATTTTTATTA
* *
11454365 GTTTATATCAA-TTTTAATA
1 -TTT-TATAAATTTTTATTA
* *
11454384 TTTT-T-AATCTTTAATA
1 TTTTATAAATTTTTATTA
*
11454400 ATTTAT-AATTTTTA-TA
1 TTTTATAAATTTTTATTA
11454416 TTTT
1 TTTT
11454420 TTCTGATTTG
Statistics
Matches: 225, Mismatches: 42, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
15 7 0.03
16 20 0.09
17 36 0.16
18 32 0.14
19 81 0.36
20 30 0.13
21 9 0.04
22 10 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTATAAATTTTTATTA
Found at i:11454222 original size:27 final size:26
Alignment explanation
Indices: 11454156--11454238 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 26
11454146 TAAATATATT
*
11454156 TTTATTAGTTTTATAAATTTTTA-GAA
1 TTTATTAGTTTT-TATATTTTTATGAA
11454182 TTTATTAGAATTTTTATATTTTTATGATA
1 TTTATTAG--TTTTTATATTTTTATGA-A
11454211 TTTATTAGTTTTTATATTTTTAT-AA
1 TTTATTAGTTTTTATATTTTTATGAA
11454236 TTT
1 TTT
11454239 TAAAAGTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
25 4 0.08
26 9 0.17
27 24 0.46
28 6 0.12
29 9 0.17
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (26 bp):
TTTATTAGTTTTTATATTTTTATGAA
Found at i:11454274 original size:26 final size:27
Alignment explanation
Indices: 11454236--11454304 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
11454226 ATTTTTATAA
** **
11454236 TTTTAAAAGTTTATG-TTAATTTTAAT
1 TTTTAAATTTTTATGATTAATTAGAAT
*
11454262 TTTTAAATTTTTATGATTTATTAGAAT
1 TTTTAAATTTTTATGATTAATTAGAAT
11454289 TTTTATACATTTTTAT
1 TTTTA-A-ATTTTTAT
11454305 AAAATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 13 0.37
27 13 0.37
28 1 0.03
29 8 0.23
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (27 bp):
TTTTAAATTTTTATGATTAATTAGAAT
Found at i:11454378 original size:29 final size:27
Alignment explanation
Indices: 11454261--11454379 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 27
11454251 TTAATTTTAA
* *
11454261 TTTTTAAATTTTTATGATTTATTAGAAT
1 TTTTTAAATTTTTATAATTTA-TATAAT
*
11454289 TTTTATACATTTTTATAAAATTT-TA-AAT
1 TTTT-TAAATTTTTAT--AATTTATATAAT
** *
11454317 ATTTTTATTTATTTTATAATTTTTTATATAT
1 -TTTTTAAAT-TTTTATAA-TTTATATA-AT
11454348 TTTTTAAATTTTTATAAGTTTATATCAAT
1 TTTTTAAATTTTTATAA-TTTATAT-AAT
11454377 TTT
1 TTT
11454380 AATATTTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
27 2 0.03
28 13 0.18
29 43 0.59
30 9 0.12
31 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTTTAAATTTTTATAATTTATATAAT
Found at i:11454408 original size:17 final size:16
Alignment explanation
Indices: 11454377--11454418 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11454367 TTATATCAAT
*
11454377 TTTAATATTTTTAATC
1 TTTAATATTTATAATC
11454393 TTTAATAATTTATAAT-
1 TTTAAT-ATTTATAATC
*
11454409 TTTTATATTT
1 TTTAATATTT
11454419 TTTCTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAATATTTATAATC
Found at i:11454415 original size:9 final size:9
Alignment explanation
Indices: 11454103--11454439 Score: 157
Period size: 10 Copynumber: 36.6 Consensus size: 9
11454093 AATGACTTTT
11454103 TTTTTATAA
1 TTTTTATAA
11454112 TTTATTAT-A
1 TTT-TTATAA
11454121 TTATTTATAA
1 TT-TTTATAA
11454131 GTTTTTATAAAA
1 -TTTTTAT--AA
*
11454143 TTTTAAATATA
1 TTTT-TATA-A
*
11454154 TTTTTATTA
1 TTTTTATAA
*
11454163 GTTTTATAAA
1 TTTTTAT-AA
*
11454173 TTTTTAGAA
1 TTTTTATAA
*
11454182 TTTATTAGAA
1 TTT-TTATAA
11454192 TTTTTAT-A
1 TTTTTATAA
*
11454200 TTTTTATGA
1 TTTTTATAA
* *
11454209 TATTTATTAG
1 TTTTTA-TAA
11454219 TTTTTAT-A
1 TTTTTATAA
11454227 TTTTTATAA
1 TTTTTATAA
*
11454236 -TTTTAAAA
1 TTTTTATAA
11454244 GTTTATGT-TAA
1 -TTT-T-TATAA
11454255 --TTT-TAA
1 TTTTTATAA
11454261 TTTTTA-AA
1 TTTTTATAA
*
11454269 TTTTTATGA
1 TTTTTATAA
*
11454278 TTTATTAGAA
1 TTT-TTATAA
11454288 TTTTTATACA
1 TTTTTATA-A
11454298 TTTTTATAAA
1 TTTTTAT-AA
* *
11454308 ATTTTAAATA
1 TTTTTATA-A
*
11454318 TTTTTAT-T
1 TTTTTATAA
11454326 TATTTTATAA
1 T-TTTTATAA
11454336 TTTTTTATATA
1 -TTTTTATA-A
11454347 TTTTT-TAAA
1 TTTTTAT-AA
11454356 TTTTTATAA
1 TTTTTATAA
*
11454365 GTTTATATCAA
1 -TTTTTAT-AA
*
11454376 TTTTAAT-A
1 TTTTTATAA
11454384 -TTTT-TAA
1 TTTTTATAA
*
11454391 TCTTTAATAA
1 T-TTTTATAA
11454401 --TTTATAA
1 TTTTTATAA
*
11454408 TTTTTATAT
1 TTTTTATAA
* *
11454417 TTTTTCTGA
1 TTTTTATAA
*
11454426 TTTGTATAA
1 TTTTTATAA
11454435 TTTTT
1 TTTTT
11454440 TTTCTTTTTT
Statistics
Matches: 250, Mismatches: 39, Indels: 78
0.68 0.11 0.21
Matches are distributed among these distances:
6 5 0.02
7 11 0.04
8 36 0.14
9 82 0.33
10 92 0.37
11 19 0.08
12 5 0.02
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11454858 original size:21 final size:20
Alignment explanation
Indices: 11454824--11454874 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
11454814 TAAATTTAAA
*
11454824 TAAAAAATATATTTATATATTT
1 TAAAAAATAT-TTTAT-TAATT
11454846 TAATAAAATATTTTATTAATT
1 TAA-AAAATATTTTATTAATT
11454867 TAAAAAAT
1 TAAAAAAT
11454875 TATACAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 7 0.26
22 8 0.30
23 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAAAATATTTTATTAATT
Found at i:11456783 original size:18 final size:18
Alignment explanation
Indices: 11456757--11456791 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11456747 GTTAATCAAA
*
11456757 TTGAGTTATTCGAGTTAT
1 TTGAATTATTCGAGTTAT
11456775 TTGAATTATTCGAGTTA
1 TTGAATTATTCGAGTTA
11456792 ATTCAAAAAA
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:0.26, C:0.06, G:0.20, T:0.49
Consensus pattern (18 bp):
TTGAATTATTCGAGTTAT
Found at i:11456984 original size:19 final size:19
Alignment explanation
Indices: 11456943--11456985 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
11456933 TTGCAAAAAG
**
11456943 AAATTCAAAATGATTTTTG
1 AAATTCAAAATGATTTTAA
11456962 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATGATTT-TAA
11456981 AAATT
1 AAATT
11456986 TCAGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATGATTTTAA
Found at i:11462045 original size:69 final size:69
Alignment explanation
Indices: 11461944--11462105 Score: 189
Period size: 69 Copynumber: 2.3 Consensus size: 69
11461934 ATATATACAC
* *** * *
11461944 TGCCATGGTCCAACCATGACCTTATGTATGAAAAACTATTATAGCCTCGCTATGGTCTTACGTGA
1 TGCCATGGTCCAACCATGGCCTTGCATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
*
11462009 ATAT
66 ACAT
* * * ** *
11462013 TGCCACGGTCCAACCATGGCCTTGCATCTGAAAAACTATCATAGTCTCTTTATGGTCTTATGTAA
1 TGCCATGGTCCAACCATGGCCTTGCATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
11462078 ACAT
66 ACAT
* *
11462082 TACCATGGTCCAACCATGGTCTTG
1 TGCCATGGTCCAACCATGGCCTTG
11462106 TACATCTTTA
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (69 bp):
TGCCATGGTCCAACCATGGCCTTGCATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
ACAT
Found at i:11464595 original size:14 final size:17
Alignment explanation
Indices: 11464563--11464600 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
11464553 AATTATAAAG
11464563 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
11464580 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
11464594 TATATTA
1 TATATTA
11464601 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:11464599 original size:28 final size:27
Alignment explanation
Indices: 11464536--11464601 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
11464526 CTTAGATATT
*
11464536 TATATAATAAATTAATTAATTATAAAG
1 TATATATTAAATTAATTAATTATAAAG
11464563 TATATTATTAAATTAATTATATTATAAA-
1 TATA-TATTAAATTAATTA-ATTATAAAG
11464591 TATTATATTAA
1 TA-TATATTAA
11464602 GAAATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
27 4 0.11
28 21 0.60
29 10 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TATATATTAAATTAATTAATTATAAAG
Found at i:11464837 original size:15 final size:17
Alignment explanation
Indices: 11464819--11464850 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11464809 CAGAATAGAA
11464819 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
11464834 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
11464851 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:11465524 original size:3 final size:3
Alignment explanation
Indices: 11465516--11465590 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
11465506 ATGTGAGGTA
11465516 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
11465564 ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11465591 TAAATGAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11465783 original size:24 final size:22
Alignment explanation
Indices: 11465745--11465789 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
11465735 CGGATTAATT
11465745 ATTGATTGAAATGTGAAAAATG
1 ATTGATTGAAATGTGAAAAATG
*
11465767 ATTGAATTGAAAATGTGAGAAAT
1 ATTG-ATTG-AAATGTGAAAAAT
11465790 TGGGATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (22 bp):
ATTGATTGAAATGTGAAAAATG
Found at i:11467806 original size:26 final size:26
Alignment explanation
Indices: 11467770--11467823 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11467760 ATCGTCCCCC
11467770 CCACATGCATATGCAATGCAATCATT
1 CCACATGCATATGCAATGCAATCATT
11467796 CCACATGCATATGCAATGCAATCATT
1 CCACATGCATATGCAATGCAATCATT
11467822 CC
1 CC
11467824 TTAATGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (26 bp):
CCACATGCATATGCAATGCAATCATT
Found at i:11471614 original size:2 final size:2
Alignment explanation
Indices: 11471607--11471635 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11471597 TAAATGTAAC
11471607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11471636 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11471810 original size:30 final size:30
Alignment explanation
Indices: 11471773--11471839 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
11471763 AGGGGCTTGA
**
11471773 TTAAAATTTTTTGAGA-TTAATGAAAATTT
1 TTAAAATTTTAAGAGAGTTAATGAAAATTT
*
11471802 TCTAAAATTTTAAGAGAGTTTAATTAAAATTT
1 T-TAAAATTTTAAGAGAG-TTAATGAAAATTT
11471834 TTAAAA
1 TTAAAA
11471840 AAATGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 13 0.41
31 5 0.16
32 13 0.41
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (30 bp):
TTAAAATTTTAAGAGAGTTAATGAAAATTT
Found at i:11476164 original size:18 final size:17
Alignment explanation
Indices: 11476141--11476193 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
11476131 ATATATTATG
*
11476141 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
11476159 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
11476176 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
11476194 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:11476406 original size:44 final size:46
Alignment explanation
Indices: 11476357--11476445 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
11476347 ACTTCTATTA
* *
11476357 CATTCAACCAAACACAAGA-ATA-CCATTATGCCTCTATTCCATTC
1 CATTCAACCAAACAAAAGATATATCCATTACGCCTCTATTCCATTC
* *
11476401 CATTCAACCAAACAAAAGATTTATCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGATATATCCATTACGCCTCTATTCCATT
11476446 ACGCATCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 18 0.46
45 2 0.05
46 19 0.49
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.30
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGATATATCCATTACGCCTCTATTCCATTC
Found at i:11476448 original size:16 final size:16
Alignment explanation
Indices: 11476427--11476479 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
11476417 AGATTTATCT
11476427 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
11476443 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
* *
11476459 ATTACACCTCTATTTC
1 ATTACGCCTCTATTCC
11476475 ATTAC
1 ATTAC
11476480 AGCGAACCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:11478223 original size:2 final size:2
Alignment explanation
Indices: 11478216--11478254 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11478206 TCAACTTTTA
11478216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11478255 ATGTAGGGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11484328 original size:29 final size:31
Alignment explanation
Indices: 11484265--11484329 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
11484255 ATATGTTGCT
* *
11484265 AGTCCCTATACTTTGAAAAAATTCAAGATTT
1 AGTCCCTATACTTTGAAAAAATTCAAAATTA
*
11484296 AGTCCCTATAC-TT-AAAAAGTT-AGAAATTA
1 AGTCCCTATACTTTGAAAAAATTCA-AAATTA
11484325 AGTCC
1 AGTCC
11484330 TCCAAGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 16 0.53
30 2 0.07
31 11 0.37
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (31 bp):
AGTCCCTATACTTTGAAAAAATTCAAAATTA
Found at i:11492713 original size:21 final size:21
Alignment explanation
Indices: 11492687--11492728 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11492677 ACAATCCTAT
*
11492687 TTAAGCTTTTAGACAAGTGGC
1 TTAAGCTTTGAGACAAGTGGC
11492708 TTAAGCTTTGAGACAAGTGGC
1 TTAAGCTTTGAGACAAGTGGC
11492729 CTTTGTCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (21 bp):
TTAAGCTTTGAGACAAGTGGC
Found at i:11494833 original size:87 final size:86
Alignment explanation
Indices: 11494687--11494850 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 86
11494677 TTTAAGTTCG
* * * *
11494687 GTGAATTCATCAAGTTAGTATCAATAGGACCACCCAAACTTTGGGATATTAACTGATTAAGAGTA
1 GTGAATTCATAAAGTTAGTATCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
*
11494752 AGAAACTTAACTTCACATGTCA
66 AG-AACTCAACTTCACATGTCA
* * * *
11494774 GTGAATTCATAAAGTTTGTCTCAATAGGATCACCCAAACTCTGGGATATGAATTCATTAAGAGTA
1 GTGAATTCATAAAGTTAGTATCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
11494839 AGAACTCAACTT
66 AGAACTCAACTT
11494851 TATGCATGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 9 0.13
87 59 0.87
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (86 bp):
GTGAATTCATAAAGTTAGTATCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
AGAACTCAACTTCACATGTCA
Found at i:11494871 original size:30 final size:30
Alignment explanation
Indices: 11494837--11494897 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
11494827 TCATTAAGAG
11494837 TAAGAACTCAACTTTATGCATGTAAATCAT
1 TAAGAACTCAACTTTATGCATGTAAATCAT
11494867 TAAGAACTCAACTTTATGCATGTAAATCAT
1 TAAGAACTCAACTTTATGCATGTAAATCAT
11494897 T
1 T
11494898 TGCCATAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (30 bp):
TAAGAACTCAACTTTATGCATGTAAATCAT
Found at i:11496103 original size:30 final size:30
Alignment explanation
Indices: 11496067--11496127 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
11496057 GCTTTGGAGC
11496067 TTGTTTGAGACAATAGAAAGATTTTTTTAG
1 TTGTTTGAGACAATAGAAAGATTTTTTTAG
11496097 TTGTTTGAGACAATAGAAAGATTTTTTTAG
1 TTGTTTGAGACAATAGAAAGATTTTTTTAG
11496127 T
1 T
11496128 CTGCAAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (30 bp):
TTGTTTGAGACAATAGAAAGATTTTTTTAG
Found at i:11502284 original size:28 final size:27
Alignment explanation
Indices: 11502241--11502296 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
11502231 TTCTGATCAA
11502241 ATTATATATAAA-TTTTGATTTAATAT
1 ATTATATATAAATTTTTGATTTAATAT
11502267 ATTATATGATAAAATTTTTTGATTTAATAT
1 ATTATAT-AT-AAA-TTTTTGATTTAATAT
11502297 GTAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
27 2 0.08
28 3 0.12
30 14 0.54
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (27 bp):
ATTATATATAAATTTTTGATTTAATAT
Found at i:11508722 original size:14 final size:15
Alignment explanation
Indices: 11508698--11508742 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
11508688 GTTTTTTTGA
11508698 ATTTTTATT-AATCTT
1 ATTTTTATTAAAT-TT
11508713 ATTTTT-TTAAATTT
1 ATTTTTATTAAATTT
*
11508727 ATTTTTATAAAATTT
1 ATTTTTATTAAATTT
11508742 A
1 A
11508743 AATTATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTTATTAAATTT
Found at i:11513396 original size:25 final size:24
Alignment explanation
Indices: 11513368--11513436 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 24
11513358 AGAATACGTG
11513368 GTTGTCGCTTACAAATTGTAATATT
1 GTTGT-GCTTACAAATTGTAATATT
* ****
11513393 GTTGT--TCATGTTTTGTAATATT
1 GTTGTGCTTACAAATTGTAATATT
11513415 GTTGTTGCTTACAAATTGTAAT
1 GTTG-TGCTTACAAATTGTAAT
11513437 GGGAGAATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
22 16 0.52
23 1 0.03
25 14 0.45
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (24 bp):
GTTGTGCTTACAAATTGTAATATT
Found at i:11514116 original size:21 final size:21
Alignment explanation
Indices: 11514071--11514149 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
11514061 CAGTTTGTAA
* * * *
11514071 CTGAGTGGGGGTAGCTTCCTA
1 CTGAGTTGGGGTAGCCTCTTG
11514092 CTGAGTTGGGGTA-CTCTCTTG
1 CTGAGTTGGGGTAGC-CTCTTG
* *
11514113 CTGATTTGGGGTAGCCTGTTG
1 CTGAGTTGGGGTAGCCTCTTG
*
11514134 TTGAGTTGGGGTAGCC
1 CTGAGTTGGGGTAGCC
11514150 ACTTAGTTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.38, T:0.34
Consensus pattern (21 bp):
CTGAGTTGGGGTAGCCTCTTG
Found at i:11515850 original size:15 final size:15
Alignment explanation
Indices: 11515832--11515867 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11515822 ACTTTCAGAT
11515832 ACATCACTAACAAAC
1 ACATCACTAACAAAC
* *
11515847 ACATCATTACCAAAC
1 ACATCACTAACAAAC
11515862 ACATCA
1 ACATCA
11515868 AAATTAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (15 bp):
ACATCACTAACAAAC
Found at i:11516459 original size:16 final size:16
Alignment explanation
Indices: 11516418--11516461 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11516408 AAATAGAAAT
11516418 AATCCAAAATAAACCTA
1 AATCCAAAA-AAACCTA
** *
11516435 AATTGAAAAAACCCTA
1 AATCCAAAAAAACCTA
11516451 AATCCAAAAAA
1 AATCCAAAAAA
11516462 TAAAAAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.16
Consensus pattern (16 bp):
AATCCAAAAAAACCTA
Found at i:11517608 original size:22 final size:22
Alignment explanation
Indices: 11517580--11517628 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11517570 TGTTTTGTTG
* * *
11517580 TTTTGCTATCATTTTGTTGCTA
1 TTTTGCTATCATATTGCTACTA
*
11517602 TTTTGCTATTATATTGCTACTA
1 TTTTGCTATCATATTGCTACTA
11517624 TTTTG
1 TTTTG
11517629 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (22 bp):
TTTTGCTATCATATTGCTACTA
Found at i:11518268 original size:1 final size:1
Alignment explanation
Indices: 11518262--11518287 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11518252 AAATTGAACC
11518262 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
11518288 ATCCACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11521141 original size:15 final size:16
Alignment explanation
Indices: 11521121--11521157 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11521111 CGGATTCAGA
11521121 TAATTT-TAAA-ATTT
1 TAATTTATAAATATTT
11521135 CTAATTTATAAATATTT
1 -TAATTTATAAATATTT
11521152 TAATTT
1 TAATTT
11521158 CAAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTATAAATATTT
Found at i:11521162 original size:15 final size:16
Alignment explanation
Indices: 11521121--11521164 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
11521111 CGGATTCAGA
11521121 TAATTTTAAA-ATTTC
1 TAATTTTAAATATTTC
11521136 TAATTTATAAATATTT-
1 TAATTT-TAAATATTTC
*
11521152 TAATTTCAAATAT
1 TAATTTTAAATAT
11521165 AATAATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 10 0.38
17 4 0.15
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTTAAATATTTC
Found at i:11530757 original size:7 final size:7
Alignment explanation
Indices: 11530733--11530773 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
11530723 AAGATGTTTG
11530733 TAGTAGT
1 TAGTAGT
11530740 TAGATTAGT
1 TAG--TAGT
*
11530749 TACTAGT
1 TAGTAGT
11530756 TAGTAGT
1 TAGTAGT
11530763 TAGTAGT
1 TAGTAGT
11530770 TAGT
1 TAGT
11530774 TGAACATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 24 0.80
9 6 0.20
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (7 bp):
TAGTAGT
Found at i:11533399 original size:28 final size:27
Alignment explanation
Indices: 11533362--11533421 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
11533352 ATAACTTGTA
* *
11533362 ATAATTATTAATAATATTATTTAAATT
1 ATAATTATTAATAATAATATTTAAATC
* *
11533389 ATAATATATTAATATTAATATTTGAATC
1 ATAAT-TATTAATAATAATATTTAAATC
11533417 ATAAT
1 ATAAT
11533422 GAATTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATAATTATTAATAATAATATTTAAATC
Found at i:11535301 original size:19 final size:19
Alignment explanation
Indices: 11535269--11535306 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11535259 GATTGTACTA
*
11535269 GTCAACATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
11535288 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
11535307 AAGTGGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Found at i:11551020 original size:50 final size:50
Alignment explanation
Indices: 11550904--11551144 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
11550894 AATAATAACA
* * ** * *
11550904 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
11550955 TGCTC-ATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGC-CAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11551005 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
11551055 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
11551110 ATGCCAATGCCATGTCTCAAACATGGTCTTACATG
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATG
11551145 AGATCTCTTT
Statistics
Matches: 168, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.01
50 96 0.57
51 32 0.19
52 1 0.01
53 4 0.02
55 2 0.01
56 32 0.19
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:11557686 original size:21 final size:21
Alignment explanation
Indices: 11557654--11557694 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11557644 GAACATTTGG
11557654 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
11557675 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
11557695 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:11567279 original size:18 final size:19
Alignment explanation
Indices: 11567253--11567289 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11567243 TTTTAACCTT
*
11567253 TTAATATAAA-AATAAAAG
1 TTAAAATAAATAATAAAAG
11567271 TTAAAATAAATAATAAAAG
1 TTAAAATAAATAATAAAAG
11567290 AAAAACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
TTAAAATAAATAATAAAAG
Found at i:11567942 original size:40 final size:40
Alignment explanation
Indices: 11567887--11567968 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
11567877 AAACCGAACC
11567887 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACAAA
1 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACAAA
* * *
11567927 AGGTGGGTAATGAGAAACCTGAAAATCAGTAAACTACGAA
1 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACAAA
11567967 AG
1 AG
11567969 CTGAAATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (40 bp):
AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACAAA
Found at i:11571439 original size:27 final size:27
Alignment explanation
Indices: 11571408--11571463 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
11571398 AAGTATGTCA
11571408 AACGTTTTTCAATTAAAATGGACTTTT
1 AACGTTTTTCAATTAAAATGGACTTTT
11571435 AACGTTTTTCAATTAAAATGGACTTTT
1 AACGTTTTTCAATTAAAATGGACTTTT
11571462 AA
1 AA
11571464 ATTAAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (27 bp):
AACGTTTTTCAATTAAAATGGACTTTT
Found at i:11571897 original size:28 final size:28
Alignment explanation
Indices: 11571857--11571911 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
11571847 AATATGATAG
11571857 AGCTTTCTATCCCAATCCTATAGATGCC
1 AGCTTTCTATCCCAATCCTATAGATGCC
11571885 AGCTTTCTATCCCAATCCTATAGATGC
1 AGCTTTCTATCCCAATCCTATAGATGC
11571912 TATGGCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.31, G:0.11, T:0.33
Consensus pattern (28 bp):
AGCTTTCTATCCCAATCCTATAGATGCC
Found at i:11575610 original size:3 final size:3
Alignment explanation
Indices: 11575602--11575641 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
11575592 AGTCATTCTG
11575602 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11575642 CAACATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11575788 original size:14 final size:13
Alignment explanation
Indices: 11575772--11575797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11575762 TTTGTATAGT
11575772 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
11575785 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
11575798 ATATGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTTTC
Found at i:11578021 original size:19 final size:20
Alignment explanation
Indices: 11577977--11578021 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
11577967 AACGTCTCTT
*
11577977 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
11577996 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
11578015 TATGCAT
1 TATGCAT
11578022 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:11580769 original size:49 final size:49
Alignment explanation
Indices: 11580715--11580823 Score: 132
Period size: 48 Copynumber: 2.2 Consensus size: 49
11580705 TACTCTGCTT
* * * * * *
11580715 AAAAAAGGTGGGACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAA
1 AAAAAAGGAGAGACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGT-AAA
*
11580765 AAAAAA--AGAGACCAGGGTGAAACCCTACAAAAGGAGCCTTGAGTAAA
1 AAAAAAGGAGAGACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGTAAA
11580812 AAAAAAGGAGAG
1 AAAAAAGGAGAG
11580824 GCTAATGTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
47 9 0.18
48 31 0.62
49 4 0.08
50 6 0.12
ACGTcount: A:0.47, C:0.15, G:0.28, T:0.11
Consensus pattern (49 bp):
AAAAAAGGAGAGACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGTAAA
Found at i:11580835 original size:49 final size:48
Alignment explanation
Indices: 11580726--11580822 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
11580716 AAAAAGGTGG
* * * *
11580726 GACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAAGA
1 GACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGTCAAAAAAAAAAGA
* *
11580774 GACCAGGGTGAAACCCTACAAAAGGAGCCTTGAGT-AAAAAAAAAGGA
1 GACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGTCAAAAAAAAAAGA
11580821 GA
1 GA
11580823 GGCTAATGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 13 0.30
48 30 0.70
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.11
Consensus pattern (48 bp):
GACCAAGGTGAAACCCTACAAAAGGAGCCTTGAGTCAAAAAAAAAAGA
Found at i:11582203 original size:46 final size:45
Alignment explanation
Indices: 11582135--11582282 Score: 128
Period size: 45 Copynumber: 3.3 Consensus size: 45
11582125 GTACTGGCGT
* *
11582135 GAAGTAGATC-AAAGATAACAGATCTCGCCTTCCCATGCTGGTGGC
1 GAAGCAGATCGAAATAT-ACAGATCTCGCCTTCCCATGCTGGTGGC
* * * *
11582180 GAAGCAGATCGAAGGA-ATACAGATCTTGTCTT--CATGTACTGG-CGT
1 GAAGCAGATCGAA--ATATACAGATCTCGCCTTCCCATG--CTGGTGGC
* * *
11582225 GAAGTAGATC-AAATATACAGATCTCGCATTCCCATACTGGTGGC
1 GAAGCAGATCGAAATATACAGATCTCGCCTTCCCATGCTGGTGGC
11582269 GAAGCAGATCGAAA
1 GAAGCAGATCGAAA
11582283 AAAAGTAGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
42 1 0.01
43 17 0.21
44 16 0.20
45 25 0.31
46 18 0.22
47 2 0.03
48 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (45 bp):
GAAGCAGATCGAAATATACAGATCTCGCCTTCCCATGCTGGTGGC
Found at i:11582281 original size:89 final size:87
Alignment explanation
Indices: 11582107--11582592 Score: 550
Period size: 89 Copynumber: 5.5 Consensus size: 87
11582097 GTTGAAAAGC
* * *
11582107 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATG
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AA-ATAACAGATCTTGTCTTCCCATA
11582172 CTGGTGGCGAAGCAGATCGAAGGAA
64 CTGGTGGCGAAGCAGATCGAA-GAA
*
11582197 TA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTCG-CATTCCCAT
1 -AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATA-ACAGATCTTGTC-TTCCCAT
*
11582260 ACTGGTGGCGAAGCAGATCGAAAAAA
63 ACTGGTGGCGAAGCAGATCG-AAGAA
* * * *
11582286 AGTAGATATTGTCTTCATGTA-TCAGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCAT
1 AGCAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAA-T-AACAGATCTTGTCTTCCCAT
* * * **
11582350 ACTGGTGGTGGAGTAGATAAAAGAA
63 ACTGGTGGCGAAGCAGATCGAAGAA
*
11582375 AGCAAATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTTCCCAT
1 AGCAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAA-T-AACAGATCTTGTCTTCCCAT
* * *
11582439 ATTGGTGGCGTAGCAGATCAAAGAA
63 ACTGGTGGCGAAGCAGATCGAAGAA
* *
11582464 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATAC
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAA-TAACAGATCTTGTCTTCCCATAC
* * * * *
11582529 TGGTGGTGGAGTAGGTTGAAGAA
65 TGGTGGCGAAGCAGATCGAAGAA
** *
11582552 AATAGATCGTGTCTTCATGTACTGGCGTGAAAG-AGATCAAA
1 AGCAGATCTTGTCTTCATGTACTGGCGTG-AAGTAGATCAAA
11582593 GATAGTAGGT
Statistics
Matches: 349, Mismatches: 36, Indels: 23
0.86 0.09 0.06
Matches are distributed among these distances:
88 77 0.22
89 199 0.57
90 70 0.20
91 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (87 bp):
AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATAACAGATCTTGTCTTCCCATACT
GGTGGCGAAGCAGATCGAAGAA
Found at i:11582367 original size:45 final size:44
Alignment explanation
Indices: 11582109--11582542 Score: 281
Period size: 44 Copynumber: 9.8 Consensus size: 44
11582099 TGAAAAGCAG
*** *
11582109 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGA-AA
* * * * * *
11582153 CAGATCTCGCCTTCCCATGCTGGTGGCGAAGCAGATCGAAGGAATA
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AAAGAA-A
*** * * *
11582199 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAATATA
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* * * *
11582242 CAGATCTCG-CATTCCCATACTGGTGGCGAAGCAGATCGAAAAAAA
1 CAGATCTTGTC-TTCCCATACTGGTGGTGAAGTAGATC-AAAGAAA
* * *** * * *
11582287 GTAGATATTGTCTTCATGTA-TCAG-CGTGAAGTAGATCAAAGTCAA
1 -CAGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCAAAG-AAA
* * *
11582332 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATAAAAGAAA
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* *** * *
11582376 GCAAATCTTGTCTTCATGTA-TCGG-CGTGAAGTAGATCAAAGTCAA
1 -CAGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCAAAG-AAA
* * * *
11582421 CAGATCTTGTCTTCCCATATTGGTGGCGTAGCAGATCAAAGAAA
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
*** *
11582465 GCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAA
1 -CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
* *
11582509 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAG
1 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAG
11582543 GTTGAAGAAA
Statistics
Matches: 285, Mismatches: 86, Indels: 38
0.70 0.21 0.09
Matches are distributed among these distances:
42 1 0.00
43 37 0.13
44 107 0.38
45 105 0.37
46 34 0.12
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAAA
Found at i:11582426 original size:179 final size:176
Alignment explanation
Indices: 11582107--11582593 Score: 617
Period size: 179 Copynumber: 2.7 Consensus size: 176
11582097 GTTGAAAAGC
* * * *
11582107 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATG
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAG-TAACAGATCTTGTCTCCCCATA
* * * * *
11582172 CTGGTGGCGAAGCAGATCGAAGGAATACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
65 CTGGTGGTGGAGTAGAT-AAAAGAA-ACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
11582237 A-TATACAGATCTCG-CATTCCCATACTGGTGGCGAAGCAGATCGAAAAAA
128 AGTATACAGATCTCGTC-TTCCCATACTGGTGGCGAAGCAGATC-AAAAAA
* * *
11582286 AGTAGATATTGTCTTCATGTA-TCAGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCAT
1 AGCAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAGT-AACAGATCTTGTCTCCCCAT
*
11582350 ACTGGTGGTGGAGTAGATAAAAGAAAGCAAATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCA
64 ACTGGTGGTGGAGTAGATAAAAGAAA-CAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCA
* * * *
11582414 AAGTCA-ACAGATCTTGTCTTCCCATATTGGTGGCGTAGCAGATCAAAGAA
127 AAGT-ATACAGATCTCGTCTTCCCATACTGGTGGCGAAGCAGATCAAAAAA
*
11582464 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATAC
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGTAACAGATCTTGTCTCCCCATAC
* ** * *
11582529 TGGTGGTGGAGTAGGTTGAAGAAAATAGATCGTGTCTTCATGTACTGGCGTGAAAG-AGATCAAA
66 TGGTGGTGGAGTAGATAAAAG-AAACAGATCTTGTCTTCATGTACTGGCGTG-AAGTAGATCAAA
11582593 G
129 G
11582594 ATAGTAGGTC
Statistics
Matches: 270, Mismatches: 27, Indels: 24
0.84 0.08 0.07
Matches are distributed among these distances:
177 73 0.27
178 92 0.34
179 103 0.38
180 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (176 bp):
AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGTAACAGATCTTGTCTCCCCATAC
TGGTGGTGGAGTAGATAAAAGAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGT
ATACAGATCTCGTCTTCCCATACTGGTGGCGAAGCAGATCAAAAAA
Found at i:11582675 original size:177 final size:177
Alignment explanation
Indices: 11582107--11582701 Score: 470
Period size: 177 Copynumber: 3.3 Consensus size: 177
11582097 GTTGAAAAGC
* ** * * * * * *
11582107 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATG
1 AGCAGATCTTATCTTCACATACCGGCGCGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATA
* * * * * * * *
11582172 CTGGTGGCGAAGCAGATCGAAGGAATACAGATCTTGTCTTCATGTA-CTGGCGTGAAGTAGATCA
65 CTGGTGGTGGAGTAGAT-AAAAGAAAACAAATCGTGTCTTCATGTATC-GGCGTGAAGTAGATCA
* * *
11582236 AA-T-ATACAGATC-TCG-CATTCCCATACTGGTGGCGAAGCAGATCGAAAAAA
128 AAGTCA-ACAGATCAT-GTC-TTCCCATATTGGTAGCGAAGCAGATC-AAAGAA
* * * ** * * * *
11582286 AGTAGATATTGTCTTCATGTATCAGCGTGAAGTAGATCAAAGTCAACAGATCTTGTCTCCCCATA
1 AGCAGATCTTATCTTCACATACCGGCGCGAAGTAGATCAAAG-AAACAGATCTTGTCTCCCCATA
* *
11582351 CTGGTGGTGGAGTAGATAAAAGAAAGCAAATCTTGTCTTCATGTATCGGCGTGAAGTAGATCAAA
65 CTGGTGGTGGAGTAGATAAAAGAAAACAAATCGTGTCTTCATGTATCGGCGTGAAGTAGATCAAA
* * *
11582416 GTCAACAGATCTTGTCTTCCCATATTGGTGGCGTAGCAGATCAAAGAA
130 GTCAACAGATCATGTCTTCCCATATTGGTAGCGAAGCAGATCAAAGAA
* ** * *
11582464 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATAC
1 AGCAGATCTTATCTTCACATACCGGCGCGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATAC
* ** * *
11582529 TGGTGGTGGAGTAGGTTGAAGAAAATAGATCGTGTCTTCATGTA-CTGGCGTGAAAG-AGATCAA
66 TGGTGGTGGAGTAGATAAAAGAAAACAAATCGTGTCTTCATGTATC-GGCGTG-AAGTAGATCAA
** * * ** * * *
11582592 AGAT-AGTAGGTCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATAT
129 AG-TCAACAGATCATGTCTTCCCATATTGGTAGCGAAGCAGATCAAAGAA
* * * ** * *
11582641 A-CATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGATCTTGCCTCCC
1 AGCAGATCTTATCTTCACATACCGGC-GCGAAGTAGATCAAAGA-AACAGATCTTGTCTCCC
11582702 TAAGCAGTAG
Statistics
Matches: 347, Mismatches: 58, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
176 18 0.05
177 122 0.35
178 102 0.29
179 102 0.29
180 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (177 bp):
AGCAGATCTTATCTTCACATACCGGCGCGAAGTAGATCAAAGAAACAGATCTTGTCTCCCCATAC
TGGTGGTGGAGTAGATAAAAGAAAACAAATCGTGTCTTCATGTATCGGCGTGAAGTAGATCAAAG
TCAACAGATCATGTCTTCCCATATTGGTAGCGAAGCAGATCAAAGAA
Found at i:11583032 original size:264 final size:264
Alignment explanation
Indices: 11582562--11583111 Score: 983
Period size: 264 Copynumber: 2.1 Consensus size: 264
11582552 AATAGATCGT
* *
11582562 GTCTTCATGTACTGGCGTGAAAGAGATCAAAGATAGTAGGTCATGTCTTCCTATATTGGTAGCGA
1 GTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCATGTCTTCCTATATTGGTAGCAA
*
11582627 AGTGGATCGAATATACATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGAT
66 AGTGGATCAAATATACATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGAT
*
11582692 CTTGCCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAG
131 CTTGCCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
*
11582757 TGGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTCGGCAGTGGAATCGATTGAAAAAGCAGA
196 TGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAATCGATTGAAAAAGCAGA
11582822 TCCC
261 TCCC
* * * *
11582826 GTCTTCATGTACTGGCATGAAGGAGATCAAAGTTAGTAGGTCCTGTCTTCCTGTATTGGTAGCAA
1 GTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCATGTCTTCCTATATTGGTAGCAA
11582891 AGTGGATCAAATATACATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGAT
66 AGTGGATCAAATATACATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGAT
*
11582956 CTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
131 CTTGCCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
11583021 TGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAATCGATTGAAAAAGCAGA
196 TGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAATCGATTGAAAAAGCAGA
**
11583086 TCTT
261 TCCC
*
11583090 GTCTTCATGTATTGGCGTGAAG
1 GTCTTCATGTACTGGCGTGAAG
11583112 TATATCGAAG
Statistics
Matches: 272, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
264 272 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (264 bp):
GTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCATGTCTTCCTATATTGGTAGCAA
AGTGGATCAAATATACATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTGAAGATTACAGAT
CTTGCCTCCCTAAGCAGTAGTGAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
TGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAATCGATTGAAAAAGCAGA
TCCC
Found at i:11584653 original size:3 final size:3
Alignment explanation
Indices: 11584645--11584687 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
11584635 AGTCATTCTG
11584645 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11584688 CAACATGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11584836 original size:14 final size:13
Alignment explanation
Indices: 11584820--11584845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11584810 TTTGTATAGT
11584820 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
11584833 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
11584846 ATATGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTTTC
Found at i:11589507 original size:22 final size:22
Alignment explanation
Indices: 11589482--11589524 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11589472 CGCCACTTGC
*
11589482 TCTGCCATCGTCGGACCTAACT
1 TCTGCCATCGCCGGACCTAACT
* *
11589504 TCTGTCATCGCCGTACCTAAC
1 TCTGCCATCGCCGGACCTAAC
11589525 CCCTTCCCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.37, G:0.16, T:0.28
Consensus pattern (22 bp):
TCTGCCATCGCCGGACCTAACT
Found at i:11590641 original size:20 final size:18
Alignment explanation
Indices: 11590599--11590643 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
11590589 ATACGTTTCT
11590599 TTTTATAATATATACATA
1 TTTTATAATATATACATA
* *
11590617 ATTTATAATTCATATATATA
1 TTTTATAA-T-ATATACATA
11590637 TTTTATA
1 TTTTATA
11590644 TTTATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTATAATATATACATA
Found at i:11590797 original size:28 final size:27
Alignment explanation
Indices: 11590723--11590797 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
11590713 TATACATACT
11590723 TATATATTTTTCATAATTTTTATGTACA
1 TATATATTTTTCAT-ATTTTTATGTACA
* * * * *
11590751 TATATA-TATGCATACTTTTATATTCAA
1 TATATATTTTTCATATTTTTATGTAC-A
11590778 TAATATATTTTTCATATTTT
1 T-ATATATTTTTCATATTTT
11590798 CATAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
26 9 0.25
27 7 0.19
28 11 0.31
29 9 0.25
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (27 bp):
TATATATTTTTCATATTTTTATGTACA
Found at i:11594803 original size:19 final size:17
Alignment explanation
Indices: 11594754--11594804 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
11594744 AATGAAGATG
11594754 ATGAAAAA-TAAAAGAA
1 ATGAAAAAGTAAAAGAA
* *
11594770 AAGAAAAAGAAAAAAGAGA
1 ATGAAAAAG-TAAAAGA-A
11594789 ATGAAAAAGTCAAAAG
1 ATGAAAAAGT-AAAAG
11594805 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.08
Consensus pattern (17 bp):
ATGAAAAAGTAAAAGAA
Found at i:11596127 original size:50 final size:49
Alignment explanation
Indices: 11596052--11596328 Score: 234
Period size: 50 Copynumber: 5.6 Consensus size: 49
11596042 GTGGAGTAGG
* * *
11596052 TTGAAGCTACAACGGTGAATCTTACTTCCCTGACTTTGCAATTAAAAAGA
1 TTGAAGCCACAAC-GCGAATCTTACTTCCCTGACATTGCAATTAAAAAGA
* * * ** *
11596102 TTGAAGCCATAACAGCAAATCTTACTTCCCTGACGA-TGCAGTGGAACAGA
1 TTGAAGCCACAAC-GCGAATCTTACTTCCCTGAC-ATTGCAATTAAAAAGA
* * * * * *
11596152 TTAAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAATTAAAAATA
1 TTGAAGCCACAACG-CGAATCTTACTTCCCTGACATTGCAATTAAAAAGA
* * * ** * *
11596202 TTGAAGCCACAACGACGAATCTTACTTCCCTGGCAGTGCAGTGGAATATA
1 TTGAAGCCACAACG-CGAATCTTACTTCCCTGACATTGCAATTAAAAAGA
* * * *
11596252 TTGAAGCTA-AACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGA
1 TTGAAGCCACAAC-GCGAATCTTACTTCCCTGACATTGCAATTAAAAAGA
*
11596301 TTGAAGCCACAATAGCGAATCTTACTTC
1 TTGAAGCCACAA-CGCGAATCTTACTTC
11596329 TCTAGCGGCG
Statistics
Matches: 173, Mismatches: 48, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
49 38 0.22
50 135 0.78
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (49 bp):
TTGAAGCCACAACGCGAATCTTACTTCCCTGACATTGCAATTAAAAAGA
Found at i:11596307 original size:99 final size:100
Alignment explanation
Indices: 11596030--11596387 Score: 445
Period size: 99 Copynumber: 3.6 Consensus size: 100
11596020 TACCTATACT
* * * * * * *
11596030 CCTGGCAGTGTAGTGGAGTAGGTTGAAGCTACAACGGTGAATCTTACTTCCCTGACTTTGCAATT
1 CCTGGCAGTGCAGTGGAATAGATTGAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAATT
* *
11596095 AAAAAGATTGAAGCCATAACAGCAAATCTTACTTC
66 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * *
11596130 CCTGAC-GATGCAGTGGAACAGATTAAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAAT
1 CCTGGCAG-TGCAGTGGAATAGATTGAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAAT
*
11596194 TAAAAATATTGAAGCCACAAC-GACGAATCTTACTTC
65 TAAAAAGATTGAAGCCACAACAG-CGAATCTTACTTC
* *
11596230 CCTGGCAGTGCAGTGGAATATATTGAAGCTA-AACGGTGAATCTTGCTTCCCCGACATTGCAATT
1 CCTGGCAGTGCAGTGGAATAGATTGAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAATT
*
11596294 AAAAAGATTGAAGCCACAATAGCGAATCTTACTTC
66 AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
* * * * * * * * *
11596329 TCTAGCGGCGCAATAGAATAGATTGAAG-TACAACGACGAATCTTGTTTCCCTGACATTG
1 CCTGGCAGTGCAGTGGAATAGATTGAAGCTACAACGATGAATCTTGCTTCCCCGACATTG
11596388 TAGTTAATCA
Statistics
Matches: 222, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
98 2 0.01
99 110 0.50
100 109 0.49
101 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (100 bp):
CCTGGCAGTGCAGTGGAATAGATTGAAGCTACAACGATGAATCTTGCTTCCCCGACATTGCAATT
AAAAAGATTGAAGCCACAACAGCGAATCTTACTTC
Found at i:11596935 original size:44 final size:44
Alignment explanation
Indices: 11596827--11596936 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 44
11596817 GATCACACCA
* *
11596827 CAACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAG
1 CAACAAGTCTTATCTCCCTGAAGCTGCAGTGAAGCAGACTGAAG
** * *
11596871 -ATATCAAACCTTATCTCCCTGAAGCTGCAGTGGAGCA-AGTTGAAG
1 CA-A-CAAGTCTTATCTCCCTGAAGCTGCAGTGAAGCAGA-CTGAAG
11596916 CAACAAGTCTTATCTCCCTGA
1 CAACAAGTCTTATCTCCCTGA
11596937 CGTTATAGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.02
44 18 0.33
45 34 0.63
46 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (44 bp):
CAACAAGTCTTATCTCCCTGAAGCTGCAGTGAAGCAGACTGAAG
Found at i:11597406 original size:22 final size:22
Alignment explanation
Indices: 11597381--11597423 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11597371 CGCCACTTGC
11597381 TCTGCCATCGCCGCACCTAACT
1 TCTGCCATCGCCGCACCTAACT
* *
11597403 TCTGTCATCGTCGCACCTAAC
1 TCTGCCATCGCCGCACCTAAC
11597424 CCCTGCCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.42, G:0.14, T:0.26
Consensus pattern (22 bp):
TCTGCCATCGCCGCACCTAACT
Found at i:11598512 original size:18 final size:20
Alignment explanation
Indices: 11598489--11598533 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11598479 GCATACGTTT
11598489 TTTTATAA-T-ATATACATA
1 TTTTATAATTCATATACATA
*
11598507 TTTTATAATTCATATATATA
1 TTTTATAATTCATATACATA
11598527 TTTTATA
1 TTTTATA
11598534 TTTTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAATTCATATACATA
Found at i:11598540 original size:18 final size:18
Alignment explanation
Indices: 11598489--11598540 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
11598479 GCATACGTTT
*
11598489 TTTTATAATATATACATA
1 TTTTATATTATATACATA
*
11598507 TTTTATAATTCATATATATA
1 TTTTAT-ATT-ATATACATA
*
11598527 TTTTATATTTTATA
1 TTTTATATTATATA
11598541 ATTTCTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATTATATACATA
Found at i:11607012 original size:28 final size:28
Alignment explanation
Indices: 11606980--11607051 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
11606970 TTTAATAAGT
*
11606980 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
11607008 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
11607036 TCGTACACTTAGTGCT
1 TCGCACACTTAGTGCT
11607052 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:11612336 original size:9 final size:9
Alignment explanation
Indices: 11612322--11612379 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
11612312 GCAACCCAAT
11612322 TTTTATTTA
1 TTTTATTTA
11612331 TTTTATTT-
1 TTTTATTTA
11612339 TATTTACTTTA
1 T-TTTA-TTTA
11612350 -TTTA-TTA
1 TTTTATTTA
*
11612357 CTTTATTTTA
1 TTTTA-TTTA
11612367 TTTTA-TTA
1 TTTTATTTA
11612375 TTTTA
1 TTTTA
11612380 CAACTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.07
8 13 0.31
9 16 0.38
10 10 0.24
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:11612337 original size:5 final size:5
Alignment explanation
Indices: 11612322--11612373 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
11612312 GCAACCCAAT
* *
11612322 TTTTA -TTTA TTTTA TTTTA -TTTA CTTTA TTTATTA CTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
11612372 TT
1 TT
11612374 ATTTTACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 2 0.05
7 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:11613800 original size:16 final size:15
Alignment explanation
Indices: 11613781--11613819 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
11613771 AATCAAAATC
11613781 AAAATAAATAAAAAAG
1 AAAA-AAATAAAAAAG
*
11613797 AAAAAAA-GAAAAAG
1 AAAAAAATAAAAAAG
11613811 AAAAAAATA
1 AAAAAAATA
11613820 TAATTTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 13 0.65
15 3 0.15
16 4 0.20
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAAAAATAAAAAAG
Found at i:11613810 original size:14 final size:14
Alignment explanation
Indices: 11613791--11613817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11613781 AAAATAAATA
11613791 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
11613805 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
11613818 TATAATTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:11614385 original size:15 final size:15
Alignment explanation
Indices: 11614360--11614394 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11614350 GACTCTATTT
*
11614360 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
11614374 TAATTAATATTAAGA
1 TAATTAATATTAAGA
11614389 TAATTA
1 TAATTA
11614395 TTAACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:11617321 original size:35 final size:35
Alignment explanation
Indices: 11617282--11617351 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
11617272 TAGATGGTAT
11617282 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
11617317 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
11617352 CATCTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (35 bp):
ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
Found at i:11618268 original size:33 final size:33
Alignment explanation
Indices: 11618226--11618294 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
11618216 TTAACATGTG
*
11618226 TTTCAATTGTACTAAATTGTAACAAATTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
* *
11618259 TTTCAATTGTACTTAATTGTAATAAACTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
11618292 TTT
1 TTT
11618295 TACTATCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TTTCAATTGTACTAAATTGTAACAAACTAATAA
Found at i:11619276 original size:42 final size:44
Alignment explanation
Indices: 11619204--11619303 Score: 134
Period size: 42 Copynumber: 2.3 Consensus size: 44
11619194 CATCATGAAC
*
11619204 ATGGTTTCTTCCACGTTACATTGTCTTGTCA-AGTCATTGATTTA
1 ATGGTTGCTTCCACGTTACATTGTCTTGTCACA-TCATTGATTTA
*
11619248 ATGGTTGCTTCCAC-TT-CATTGTCTTGTCACATTATTGATTTA
1 ATGGTTGCTTCCACGTTACATTGTCTTGTCACATCATTGATTTA
* *
11619290 ATGTTTGTTTCCAC
1 ATGGTTGCTTCCAC
11619304 ATTGCAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 35 0.69
43 3 0.06
44 13 0.25
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (44 bp):
ATGGTTGCTTCCACGTTACATTGTCTTGTCACATCATTGATTTA
Found at i:11629893 original size:17 final size:17
Alignment explanation
Indices: 11629871--11629904 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11629861 ATCCACTAAT
*
11629871 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
11629888 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
11629905 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:11634521 original size:17 final size:17
Alignment explanation
Indices: 11634499--11634532 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11634489 ATCCACTAAT
*
11634499 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
11634516 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
11634533 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:11635858 original size:12 final size:11
Alignment explanation
Indices: 11635831--11635860 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11635821 TTTTAAAAAA
11635831 TAAAAATATTT
1 TAAAAATATTT
11635842 TAAAAATATTT
1 TAAAAATATTT
11635853 TAAAAATA
1 TAAAAATA
11635861 AAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:11655003 original size:89 final size:87
Alignment explanation
Indices: 11654852--11655183 Score: 300
Period size: 89 Copynumber: 3.8 Consensus size: 87
11654842 ACAGATCGAG
* * * *
11654852 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAGGCAAGTCTTATCCACCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGT-GGTAA-TCCTAT-CTCCTGAAGTTGC
*
11654916 AGTGAGGCAGACTGAAGGTGGCAAA
63 AGTGAGGCAGACTGAAGATGGCAAA
11654941 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCTC-CTGAAGTTGCA
* * * **** *
11655006 GTGA-GCGGA-TTAAAACCTTAGA
64 GTGAGGCAGACTGAAGATGGCAAA
* * ** * * * * * *
11655028 TCTTATCTCTCTGAAGTTGCA-AAGAACAGATCACA-T-CTAGTCTTATCCTCCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTAT-CTCCTGAAGTTGCAG
11655090 TGAGGCAGACTGAAGATGGCAAA
65 TGAGGCAGACTGAAGATGGCAAA
* * * *
11655113 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCTC-CTGAAGTTGCA
11655178 GT-AGGC
64 GTGAGGC
11655184 GGATTAAAAC
Statistics
Matches: 189, Mismatches: 43, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
83 22 0.12
84 8 0.04
85 26 0.14
86 18 0.10
87 24 0.13
88 12 0.06
89 71 0.38
90 7 0.04
91 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTATCTCCTGAAGTTGCAGT
GAGGCAGACTGAAGATGGCAAA
Found at i:11655142 original size:172 final size:172
Alignment explanation
Indices: 11654894--11655263 Score: 591
Period size: 172 Copynumber: 2.2 Consensus size: 172
11654884 TAAGTAGGCA
* *
11654894 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* * *
11654959 ACAGTGGAGCAGATTAAAGCTGGTAATCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAAAACC
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAG-GCGGATTAAAACC
11655023 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
11655066 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* *
11655131 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGTAGTAGGCGGATTAAAACCT
66 ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCT
* * * * *
11655196 TATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
131 TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
*
11655238 AGTCTTAT-CTCCCTGAAGTTGTAGTG
1 AGTCTTATCCT-CCTGAAGTTGCAGTG
11655264 GAACGGACTA
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 2 0.01
172 180 0.98
173 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
ACAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:11655290 original size:216 final size:216
Alignment explanation
Indices: 11655068--11655474 Score: 733
Period size: 216 Copynumber: 1.9 Consensus size: 216
11655058 TCACATCTAG
*
11655068 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGC
*
11655133 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGTAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
11655198 TATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGT
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGT
11655263 GGAACGGACTAAGTAAGCAAA
196 GGAACGGACTAAGTAAGCAAA
* *
11655284 TCTTATCCTCCTGAATTTGCTGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGC
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGC
*
11655349 AGTGGAGCAGATTAAAGTCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCTTA
66 AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCTTA
* *
11655414 GATCTTATCTCTCTGAAGTTGCAGAGAGCGGATCGCATTTAGTCTTATCTCCCTGAAGTTG
131 GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTG
11655475 CACCAGGAGC
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 182 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (216 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGC
AGTGGAGCAGATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCAGTAGGCGGATTAAAACCTTA
GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGT
GGAACGGACTAAGTAAGCAAA
Found at i:11655345 original size:172 final size:172
Alignment explanation
Indices: 11654894--11655364 Score: 537
Period size: 172 Copynumber: 2.7 Consensus size: 172
11654884 TAAGTAGGCA
* * * *
11654894 AGTCTTATCCACCTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
* * * *
11654959 ACAGTGGAGCAGATTAAAG-CTGGTAATCCTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACC
66 GCAGTGGAGCAGACTAAAGAC-GGAAATCCTATCTCCCTGAAGTTGCAGTGAGCGGATTAAAACC
11655023 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
130 TTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
* *
11655066 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
* * * *
11655131 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATC-CCACTGAAGTTGTAGT-AGGCGGATTAAAAC
66 GCAGTGGAGCAGACTAAAGACGGAAATCCTATCTCC-CTGAAGTTGCAGTGA-GCGGATTAAAAC
* * * * *
11655194 CTTATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCT
129 CTTAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
* *
11655238 AGTCTTAT-CTCCCTGAAGTTGTAGTG-GAACGGACT-AAG-TAAGCAAATCTTATC-CTCCTGA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGAG-ACAGACTGAAGAT-AGCAAATCTTATCTC-CCTGA
* * * * * * *
11655298 ATTTGCTGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTGGCAGTGGAGCAGATT
62 AGTTGCAGTGGA-GCAGACTAAAGACGG-AAATCCTATCTCCCTGAAGTTGCAGT-GAGCGGATT
11655362 AAA
124 AAA
11655365 GTCGGTAATC
Statistics
Matches: 262, Mismatches: 25, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
170 4 0.02
171 43 0.16
172 202 0.77
173 12 0.05
174 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGACTAAAGACGGAAATCCTATCTCCCTGAAGTTGCAGTGAGCGGATTAAAACCT
TAGATCTTATCTCTCTGAAGTTGCAAAGAACAGATCACATCT
Found at i:11655359 original size:45 final size:44
Alignment explanation
Indices: 11654852--11655359 Score: 188
Period size: 44 Copynumber: 11.7 Consensus size: 44
11654842 ACAGATCGAG
* * *
11654852 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAGGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
11654896 TCTTATC-CACCTGAAGTTGCAGT-GAGGCAGACTGAAGGT-GGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AA-GTAAGCAAA
* * **
11654941 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCT--GGTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCAAA
* * * * * *
11654985 TCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAA--AACCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC--AAA
* ** * * * * * *
11655028 TCTTATCTCTCTGAAGTTGCA-AAGAACAGA-TCA--CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
*
11655068 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAA
* ** **
11655113 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCGGTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAA
* * * * * * *
11655157 TCCTATC-CCACTGAAGTTGTAGTAG-GCGGATTAA--AACCTTATA
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTAAGTAAGC--AAA
** * * * * * *
11655200 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-T-CG-CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
* * *
11655240 TCTTATCTCCCTGAAGTTGTAGTGGAACGGACTAAGTAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
* * *
11655284 TCTTATC-CTCCTGAATTTGCTGT-GAGGCAGACTGAAG-ATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAA
*
11655329 TCTTATCTCCCTGAAGTGGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
11655360 TTAAAGTCGG
Statistics
Matches: 345, Mismatches: 82, Indels: 73
0.69 0.16 0.15
Matches are distributed among these distances:
39 1 0.00
40 39 0.11
41 9 0.03
42 15 0.04
43 70 0.20
44 101 0.29
45 99 0.29
46 11 0.03
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA
Found at i:11656872 original size:19 final size:20
Alignment explanation
Indices: 11656831--11656872 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
11656821 GTTTCTATGC
* *
11656831 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
11656851 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
11656870 CAT
1 CAT
11656873 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:11659068 original size:21 final size:21
Alignment explanation
Indices: 11659024--11659061 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11659014 TAACTTGTAA
11659024 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
11659045 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
11659062 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:11659083 original size:28 final size:28
Alignment explanation
Indices: 11659029--11659083 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
11659019 TGTAATAAAT
* *
11659029 TATTAATAATATTATTTAAATTATAATA
1 TATTAATAATAATATTTAAATCATAATA
* *
11659057 TATTAATATTAATATTTGAATCATAAT
1 TATTAATAATAATATTTAAATCATAAT
11659084 GAGTTTTTGT
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:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTAATAATAATATTTAAATCATAATA
Found at i:11661086 original size:19 final size:19
Alignment explanation
Indices: 11661062--11661099 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11661052 GATTGTACTG
11661062 GTCAAAATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
11661081 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
11661100 AAGTGGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Done.