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 93 of 216
Found at i:28829260 original size:20 final size:20
Alignment explanation
Indices: 28829235--28829289 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
28829225 TGCTGATGTA
28829235 TTTTGCTATTGTTTTCATCG
1 TTTTGCTATTGTTTTCATCG
* * *
28829255 TTTTGCTGTTGTGTTTTATTG
1 TTTTGCTATTGT-TTTCATCG
* *
28829276 TTTTACTATCGTTT
1 TTTTGCTATTGTTT
28829290 CGTTATTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.09, C:0.11, G:0.16, T:0.64
Consensus pattern (20 bp):
TTTTGCTATTGTTTTCATCG
Found at i:28843961 original size:3 final size:3
Alignment explanation
Indices: 28843955--28843995 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28843945 TTATAATAAT
28843955 AAC 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 AAC AA
28843996 TAATAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:28844829 original size:25 final size:25
Alignment explanation
Indices: 28844781--28844829 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28844771 CATAATTGAA
* *
28844781 ATGAAATGAATTGATTTTGTATATT
1 ATGAAATGAATTGATTATGAATATT
28844806 ATGAAAT-ATATTGATTATGAATAT
1 ATGAAATGA-ATTGATTATGAATAT
28844830 ATGTGTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
ATGAAATGAATTGATTATGAATATT
Found at i:28846003 original size:49 final size:49
Alignment explanation
Indices: 28845915--28846008 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
28845905 TCAAAAAGGC
* * *
28845915 ATAAATAGTGATAAGAGTATAGAAAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTATAGAAAATGAAAAACCAAGTTTAGCAATGT
* *
28845964 ATAAATAGTGATAAGAGTGTA-AACAGTGAAAAACCAAGTTTAGCA
1 ATAAATAGTGATAAGAGTATAGAA-AATGAAAAACCAAGTTTAGCA
28846009 TTGCATAGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 2 0.05
49 37 0.95
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTATAGAAAATGAAAAACCAAGTTTAGCAATGT
Found at i:28859040 original size:10 final size:10
Alignment explanation
Indices: 28859025--28859055 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28859015 CAAATTTCTA
28859025 TTTCTTTTTT
1 TTTCTTTTTT
*
28859035 TTTCTTATTT
1 TTTCTTTTTT
28859045 TTTCTTTTTT
1 TTTCTTTTTT
28859055 T
1 T
28859056 GCCGATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:28859421 original size:9 final size:9
Alignment explanation
Indices: 28859409--28859433 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28859399 TATTCATTTA
28859409 TTTATTTGG
1 TTTATTTGG
28859418 TTTATTTGG
1 TTTATTTGG
28859427 TTTATTT
1 TTTATTT
28859434 CACTAACGGG
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:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (9 bp):
TTTATTTGG
Found at i:28864441 original size:44 final size:44
Alignment explanation
Indices: 28864377--28864496 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 44
28864367 TGCAGCTTCG
* * * * *
28864377 ATCTACTCCGCTGGAACTTCAAAAGATAAGAATTGGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAAAAGATAAGAACTGGTAACTTAA
* * * **
28864421 ATTTGCTCCACTGCAACTTCAAGGAGATAAG-GCTGGTGGCTTAA
1 ATCTGCTCCACTGCAACTTCAA-AAGATAAGAACTGGTAACTTAA
*
28864465 ATCTGCTCCACTGCAACTTCAGGAAGATAAGA
1 ATCTGCTCCACTGCAACTTCA-AAAGATAAGA
28864497 TCTGCCATAG
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
44 53 0.88
45 7 0.12
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAAAAGATAAGAACTGGTAACTTAA
Found at i:28864674 original size:143 final size:143
Alignment explanation
Indices: 28864424--28865498 Score: 1396
Period size: 143 Copynumber: 7.5 Consensus size: 143
28864414 AACTTCAATT
* * *
28864424 TGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * *
28864489 AGATAAGATCTGCCATAGTTTGTAGCTTTAATCTGTTCCACTGCAGCGCTAGGAAAATAAAATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
*
28864554 GCTGTCTTCAGTC
131 ACTGTCTTCAGTC
* ** * *
28864567 TACTCCGCTATAAATTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* ** * * * *
28864632 AGATAACATCCACCATAATTTTTAGCTTTAATCTATTCCACTGCAATGCCAGGGAAATAAGATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
* *
28864697 GCTATCTTCAGTC
131 ACTGTCTTCAGTC
* * * * * * * *
28864710 TGCTTCGCTGTAAATTCAGGGAGACAAGGCTGGTGGTTTCAATCTGCTCTACTGCAACTTTAGAA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
*
28864775 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
28864840 ACTGTCTTCAGTC
131 ACTGTCTTCAGTC
* *
28864853 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGTTTCAATCTGCTCCACTACAACTTCAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * * * *
28864918 AGATAATATCTGCCAAAATTTGTAGCTTTAATTTGTTCCACTACAACACTAGGGAAATAAGATTC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
* *
28864983 GCTATCTTCAGTC
131 ACTGTCTTCAGTC
* * *
28864996 TGCTCTGCTGCAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTTAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * *
28865061 AGATAAAAT-TCACCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAGATC
66 AGATAAGATCT-GCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATC
* *
28865125 TACCGTCTTCAGTC
130 CACTGTCTTCAGTC
*
28865139 TGCTCTGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * *
28865204 AGATAAGATCTGCCATGATTTGTAGCTTTAATCTGTTCCACTGCAATGCTAGGGAGATAAGATTC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
28865269 ACTGTCTTCAGTC
131 ACTGTCTTCAGTC
* * * *
28865282 TGTTTCGCTGCAACTTCAAGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * ** * ** * * *
28865347 AGATAAGATCTGTCATGATTTGTAGAGTTAATCTATTCCACTATAACTCTAGGGAGATCAGATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
* *
28865412 ACTATCTTTAGTC
131 ACTGTCTTCAGTC
* * * * * * * * * *
28865425 TACTCTGCTGTAACTTTAGGGTGATAAGGCTGGTGGCTTCAATATGCTGCACTGCGACTTTAAGA
1 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
*
28865490 AGATGAGAT
66 AGATAAGAT
28865499 TTGCTGTAAT
Statistics
Matches: 814, Mismatches: 116, Indels: 4
0.87 0.12 0.00
Matches are distributed among these distances:
142 1 0.00
143 812 1.00
144 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (143 bp):
TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCTAGGGAAATAAGATCC
ACTGTCTTCAGTC
Found at i:28865230 original size:429 final size:429
Alignment explanation
Indices: 28864424--28865493 Score: 1539
Period size: 429 Copynumber: 2.5 Consensus size: 429
28864414 AACTTCAATT
* *
28864424 TGCTCCACTGCAACTTCAAGGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * * * *
28864489 AGATAAGATCTGCCATAGTTTGTAGCTTTAATCTGTTCCACTGCAGCGCTAGGAAAATAAAATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACACTAGGGAAATAAGATCC
* * * *
28864554 GCTGTCTTCAGTCTACTCCGCTATAAATTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCAC
131 GCTATCTTCAGTCTACTCTGCTGTAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCAC
* * * *
28864619 TGCAACTTCAGGAAGATAACATCCACCATAATTTTTAGCTTTAATCTATTCCACTGCAATGCCAG
196 TGCAACTTTAGGAAGATAAAATCCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
* * * * *
28864684 GGAAATAAGATCCGCTATCTTCAGTCTGCTTCGCTGTAAATTCAGGGAGACAAGGCTGGTGGTTT
261 AGAAATAAGATCCACCATCTTCAGTCTGCTTCGCTGCAAATTCAGGGAGACAAGGCTGGTGGCTT
* *
28864749 CAATCTGCTCTACTGCAACTTTAGAAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCC
326 CAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCC
28864814 ACTGCAACGCCAGGGAAATAAGATCCACTGTCTTCAGTC
391 ACTGCAACGCCAGGGAAATAAGATCCACTGTCTTCAGTC
* * *
28864853 TGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGTTTCAATCTGCTCCACTACAACTTCAGGA
1 TGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * * *
28864918 AGATAATATCTGCCAAAATTTGTAGCTTTAATTTGTTCCACTACAACACTAGGGAAATAAGATTC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACACTAGGGAAATAAGATCC
* * * *
28864983 GCTATCTTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTGCTCCAC
131 GCTATCTTCAGTCTACTCTGCTGTAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCAC
* *
28865048 TGCAACTTTAGGAAGATAAAATTCACCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAG
196 TGCAACTTTAGGAAGATAAAATCCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
* * * *
28865113 AGAAATAAGATCTACCGTCTTCAGTCTGC-TCTGCTGCAACTTCAGGGAGATAAGGCTGGTGGCT
261 AGAAATAAGATCCACCATCTTCAGTCTGCTTC-GCTGCAAATTCAGGGAGACAAGGCTGGTGGCT
* *
28865177 TCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATGATTTGTAGCTTTAATCTGTTC
325 TCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTC
* * * *
28865242 CACTGCAATGCTAGGGAGATAAGATTCACTGTCTTCAGTC
390 CACTGCAACGCCAGGGAAATAAGATCCACTGTCTTCAGTC
* * *
28865282 TGTTTCGCTGCAACTTCAAGGAGATAAGGCTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
1 TGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
* * ** * * * * *
28865347 AGATAAGATCTGTCATGATTTGTAGAGTTAATCTATTCCACTATAACTCTAGGGAGATCAGATCC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACACTAGGGAAATAAGATCC
* * * * *
28865412 ACTATCTTTAGTCTACTCTGCTGTAACTTTAGGGTGATAAGGCTGGTGGCTTCAATATGCTGCAC
131 GCTATCTTCAGTCTACTCTGCTGTAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCAC
* *
28865477 TGCGACTTTAAGAAGAT
196 TGCAACTTTAGGAAGAT
28865494 GAGATTTGCT
Statistics
Matches: 564, Mismatches: 76, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
428 2 0.00
429 562 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (429 bp):
TGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA
AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTACAACACTAGGGAAATAAGATCC
GCTATCTTCAGTCTACTCTGCTGTAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCAC
TGCAACTTTAGGAAGATAAAATCCACCATAATTTGTAGCTTTAATCTATTCCACTGCAACGCCAG
AGAAATAAGATCCACCATCTTCAGTCTGCTTCGCTGCAAATTCAGGGAGACAAGGCTGGTGGCTT
CAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCC
ACTGCAACGCCAGGGAAATAAGATCCACTGTCTTCAGTC
Found at i:28865339 original size:44 final size:45
Alignment explanation
Indices: 28865131--28865353 Score: 141
Period size: 44 Copynumber: 4.8 Consensus size: 45
28865121 GATCTACCGT
* ** * *
28865131 CTTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAGGCT-GGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGGCTCAGTGG
*
28865175 CTTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAGATCTGCCATGATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAAGG-AGATAAG-GCT--CA-G---TG--G
* * * * ** * *
28865229 CTTTAATCTGTTCCACTGCAA-TGCTAGGGAGATAAGATTCACTGT
1 CTTCAATCTGCTCCACTGCAACTTC-AAGGAGATAAGGCTCAGTGG
* * * *
28865274 CTTCAGTCTGTTTCGCTGCAACTTCAAGGAGATAAGGCT-AGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGGCTCAGTGG
28865318 CTTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAG
1 CTTCAATCTGCTCCACTGCAACTTCAAGG-AGATAAG
28865354 ATCTGTCATG
Statistics
Matches: 136, Mismatches: 28, Indels: 30
0.70 0.14 0.15
Matches are distributed among these distances:
43 5 0.04
44 60 0.44
45 30 0.22
46 2 0.01
47 2 0.01
49 1 0.01
51 2 0.01
52 2 0.01
53 3 0.02
54 27 0.20
55 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGGCTCAGTGG
Found at i:28871705 original size:30 final size:30
Alignment explanation
Indices: 28871669--28871730 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28871659 CGGCTCAATG
*
28871669 ATGTTGGACATAAGCCTATCTCACAAAAGC
1 ATGTTGGACATAAGCCTATCCCACAAAAGC
28871699 ATGTTGGACATAAGCCTATCCCACAAAAGC
1 ATGTTGGACATAAGCCTATCCCACAAAAGC
28871729 AT
1 AT
28871731 TCTTATTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (30 bp):
ATGTTGGACATAAGCCTATCCCACAAAAGC
Found at i:28873556 original size:10 final size:9
Alignment explanation
Indices: 28873539--28873563 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28873529 ATTTTAAACA
28873539 TATTTTTTT
1 TATTTTTTT
28873548 TATTTTTTT
1 TATTTTTTT
28873557 TATTTTT
1 TATTTTT
28873564 AAAATATTTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:28873559 original size:41 final size:39
Alignment explanation
Indices: 28873494--28873605 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 39
28873484 CTGAATGTAA
28873494 TAAATATATTTTTTTTATTTTTTATTTTTAAAAATA-TTT
1 TAAA-ATATTTTTTTTATTTTTTATTTTTAAAAATATTTT
28873533 TAAACATATTTTTTTTATTTTTTTTATTTTT-AAAATATTTT
1 TAAA-ATATTTTTTTTA--TTTTTTATTTTTAAAAATATTTT
*
28873574 TAAAATAAATTTTTTTAATTTTTTAGTTTTTA
1 TAAAAT--ATTTTTTTTATTTTTTA-TTTTTA
28873606 TTAAAAAATG
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
39 16 0.25
40 15 0.23
41 24 0.38
42 9 0.14
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (39 bp):
TAAAATATTTTTTTTATTTTTTATTTTTAAAAATATTTT
Found at i:28875259 original size:50 final size:53
Alignment explanation
Indices: 28875162--28875258 Score: 130
Period size: 50 Copynumber: 1.9 Consensus size: 53
28875152 ATTTTAAGAT
*
28875162 AAATAGATACACACATAATATTAAATTTAAATATCTTAAAAGTAAAAATGAAC
1 AAATAGATACACACATAATATTAAACTTAAATATCTTAAAAGTAAAAATGAAC
* * *
28875215 AAATAGATA-A-A-ATAATATTAAACTTAGATAT-TTTAGAGTAAAAA
1 AAATAGATACACACATAATATTAAACTTAAATATCTTAAAAGTAAAAA
28875259 AAATGATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 11 0.28
50 18 0.45
51 1 0.03
52 1 0.03
53 9 0.22
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (53 bp):
AAATAGATACACACATAATATTAAACTTAAATATCTTAAAAGTAAAAATGAAC
Found at i:28885881 original size:18 final size:18
Alignment explanation
Indices: 28885855--28885897 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
28885845 CTGCATCTCT
*
28885855 TCATCATATGTAAGTGGG
1 TCATTATATGTAAGTGGG
*
28885873 TCATTATATGTGAGTGGG
1 TCATTATATGTAAGTGGG
28885891 TCATTAT
1 TCATTAT
28885898 CTTCCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (18 bp):
TCATTATATGTAAGTGGG
Found at i:28891749 original size:20 final size:21
Alignment explanation
Indices: 28891705--28891752 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
28891695 GAACATGTTA
28891705 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
28891727 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
28891747 ATTTTT
1 ATTTTT
28891753 GACAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:28893541 original size:14 final size:14
Alignment explanation
Indices: 28893524--28893553 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28893514 AGTAAGAGAG
*
28893524 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
28893538 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
28893552 GA
1 GA
28893554 ATGAGGGACA
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:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:28901001 original size:109 final size:111
Alignment explanation
Indices: 28900800--28901024 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 111
28900790 TCCATGATGA
28900800 GGGAACATTCGTAATAACTCTTTGTACCTTTCCCATGCTTCATACAGGGACTCATCATCCATTTG
1 GGGAACATTCGTAATAACTCTTTGTACCTTTCCCATGCTTCATACAGGGACTCATCATCCATTTG
*
28900865 TTGGAAGGCAGTGATCTCATTCCTCAACTTGGCATTCTTGCTCGGT
66 TTGGAAGGCAGTGATCTCATTCCTCAACTTGGCATTCTTGCTCGGC
*
28900911 GGGAAC-TT-GTAATAACTCTTTGTACCTTTCCCATGCTTCATACAGGGACTCATCATCCATTTT
1 GGGAACATTCGTAATAACTCTTTGTACCTTTCCCATGCTTCATACAGGGACTCATCATCCATTTG
28900974 TTGGAAGGCAGTGATCTCATTCCTCAACTTGGCATTCTTGCTCGGC
66 TTGGAAGGCAGTGATCTCATTCCTCAACTTGGCATTCTTGCTCGGC
28901020 GGGAA
1 GGGAA
28901025 ATACTTCATG
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
109 104 0.93
110 2 0.02
111 6 0.05
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (111 bp):
GGGAACATTCGTAATAACTCTTTGTACCTTTCCCATGCTTCATACAGGGACTCATCATCCATTTG
TTGGAAGGCAGTGATCTCATTCCTCAACTTGGCATTCTTGCTCGGC
Found at i:28909467 original size:137 final size:137
Alignment explanation
Indices: 28909193--28909460 Score: 387
Period size: 137 Copynumber: 2.0 Consensus size: 137
28909183 AAGCTATAAA
* *
28909193 TGGGCCTGCTTACACAAGCTGTCAATTGGAATGTAGCTACACAGTGCTGCTCACACAAGCTGTCG
1 TGGGCCTGCTCACACAAGCTGTCAATTGGAACGTAGCTACACAGTGCTGCTCACACAAGCTGTCG
* * *
28909258 AGTATCTGCAACAAATGCTGGAACTCAGCCACCGGAAGGACATTCAGCACCAACACCTGAAAGAT
66 AGTATCTGCAACAAATGCTAGAACTCAGCCACCGGAAGGACATTCAGCACCAACACCCGAAACAT
28909323 GATAACC
131 GATAACC
* ** *
28909330 TGGGTCTGCTCACACAAGCTGTCGGTTGGAACGTAGCTACACAGTGCTGCTCACACAAGTTGTCG
1 TGGGCCTGCTCACACAAGCTGTCAATTGGAACGTAGCTACACAGTGCTGCTCACACAAGCTGTCG
* * **
28909395 AGTATCTGCAACAAATG-TCAGAACTCAGCCACC-GATAGGACATTTAGGACCAGTACCCGAAAC
66 AGTATCTGCAACAAATGCT-AGAACTCAGCCACCGGA-AGGACATTCAGCACCAACACCCGAAAC
28909458 ATG
129 ATG
28909461 GAAACCTAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
136 3 0.03
137 113 0.97
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (137 bp):
TGGGCCTGCTCACACAAGCTGTCAATTGGAACGTAGCTACACAGTGCTGCTCACACAAGCTGTCG
AGTATCTGCAACAAATGCTAGAACTCAGCCACCGGAAGGACATTCAGCACCAACACCCGAAACAT
GATAACC
Found at i:28912613 original size:41 final size:41
Alignment explanation
Indices: 28912556--28912636 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
28912546 ATGAGGGTCT
* *
28912556 TTTGGGCCTTTCCCGTATCGTGTTCAATTATAAGTGTTTCC
1 TTTGGGCCTCTCCCGTATCGTGTCCAATTATAAGTGTTTCC
*
28912597 TTTGGGCCTCTCCCGTATTGTGTCCAATTATAAGTGTTTC
1 TTTGGGCCTCTCCCGTATCGTGTCCAATTATAAGTGTTTC
28912637 TTGGACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (41 bp):
TTTGGGCCTCTCCCGTATCGTGTCCAATTATAAGTGTTTCC
Found at i:28912729 original size:4 final size:4
Alignment explanation
Indices: 28912714--28912751 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
28912704 AAGCATCATG
28912714 AATT AATT --TT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
28912752 TCCTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
AATT
Found at i:28912758 original size:16 final size:14
Alignment explanation
Indices: 28912714--28912769 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 14
28912704 AAGCATCATG
28912714 AATTAATTTTAATT
1 AATTAATTTTAATT
28912728 AATTAATTAATTAATT
1 AATTAATT--TTAATT
28912744 AATTAATTTCCTAATT
1 AATTAATTT--TAATT
*
28912760 AAATAATTTT
1 AATTAATTTT
28912770 CTCAACTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 10 0.27
16 27 0.73
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:28912942 original size:4 final size:4
Alignment explanation
Indices: 28912898--28912923 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28912888 ATTTTGAACT
28912898 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
28912924 GAAAAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:28929721 original size:29 final size:25
Alignment explanation
Indices: 28929660--28929717 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
28929650 AGCAAAAATA
28929660 AAATGAATCCTAAGTATATATAACC
1 AAATGAATCCTAAGTATATATAACC
*
28929685 AAATGAATCCTAAGTATATATGACC
1 AAATGAATCCTAAGTATATATAACC
*
28929710 TAATGAAT
1 AAATGAAT
28929718 GAATGCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (25 bp):
AAATGAATCCTAAGTATATATAACC
Found at i:28930608 original size:17 final size:18
Alignment explanation
Indices: 28930585--28930627 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
28930575 TTAATTAATT
28930585 AACTAAATTAA-TTTCTC
1 AACTAAATTAATTTTCTC
*
28930602 AATTAAA-TAATTTTCTC
1 AACTAAATTAATTTTCTC
28930619 AACTAAATT
1 AACTAAATT
28930628 CTAATTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (18 bp):
AACTAAATTAATTTTCTC
Found at i:28935195 original size:32 final size:32
Alignment explanation
Indices: 28935159--28935270 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
28935149 AAGCTTGCAT
28935159 ATTATGTCTTGCATTATATGTTTGTAGCTTTA
1 ATTATGTCTTGCATTATATGTTTGTAGCTTTA
** * * *
28935191 ATTATGAGTTGCATTATGTGTTTGCATCTTTAA
1 ATTATGTCTTGCATTATATGTTTGTAGCTTT-A
28935224 ATTATGTCTTGCATTATATG--TGTAGCATTTA
1 ATTATGTCTTGCATTATATGTTTGTAGC-TTTA
* *
28935255 ATTAGGTCATGCATTA
1 ATTATGTCTTGCATTA
28935271 AAGCATCTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
31 19 0.29
32 29 0.44
33 18 0.27
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (32 bp):
ATTATGTCTTGCATTATATGTTTGTAGCTTTA
Found at i:28936806 original size:15 final size:16
Alignment explanation
Indices: 28936783--28936812 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28936773 GGTAAAAAAT
28936783 AATTGAAAAAAATTTG
1 AATTGAAAAAAATTTG
28936799 AATT-AAAAAAATTT
1 AATTGAAAAAAATTT
28936813 AGATTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
AATTGAAAAAAATTTG
Found at i:28937645 original size:12 final size:13
Alignment explanation
Indices: 28937623--28937653 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28937613 AGTGTGGAGC
28937623 AAAAGAAATTGAG
1 AAAAGAAATTGAG
28937636 AAAA-AAATTGAG
1 AAAAGAAATTGAG
28937648 AAAAGA
1 AAAAGA
28937654 GAGAGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (13 bp):
AAAAGAAATTGAG
Found at i:28939143 original size:24 final size:23
Alignment explanation
Indices: 28939080--28939176 Score: 106
Period size: 23 Copynumber: 4.2 Consensus size: 23
28939070 TCTACCCTGT
*
28939080 TTGGACAGC-TCTTATACATCAAA
1 TTGGACAGCAT-TTATACACCAAA
** *
28939103 TCAGACACCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
28939126 TTGGATAGCAGTTTATACACCAAA
1 TTGGACAGCA-TTTATACACCAAA
* *
28939150 TTGGACAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
28939173 TTGG
1 TTGG
28939177 CCAACATATA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
23 38 0.62
24 23 0.38
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (23 bp):
TTGGACAGCATTTATACACCAAA
Found at i:28939173 original size:23 final size:23
Alignment explanation
Indices: 28939092--28939188 Score: 95
Period size: 23 Copynumber: 4.2 Consensus size: 23
28939082 GGACAGCTCT
* ** * *
28939092 TATACATCAAATCAGACACCATT
1 TATACACCAAATTGGACAGCATA
* *
28939115 TATACACCAAATTGGATAGCAGTT
1 TATACACCAAATTGGACAGCA-TA
28939139 TATACACCAAATTGGACAGCATA
1 TATACACCAAATTGGACAGCATA
* * *
28939162 TATACACTAAATTGGCCAACATA
1 TATACACCAAATTGGACAGCATA
28939185 TATA
1 TATA
28939189 TATACCCAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 41 0.65
24 22 0.35
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (23 bp):
TATACACCAAATTGGACAGCATA
Found at i:28940207 original size:43 final size:42
Alignment explanation
Indices: 28940152--28940278 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
28940142 ATATCATACA
28940152 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATAACG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAA-CACATAACG
** * *
28940195 ATGCC-ACTGTCCCAGACAAGGTCTTAGATGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACATGT-AACACATA-ACG
* * *
28940238 ATGCCAACATCCCAGATGTGGTCTTACACGATAACACATAA
1 ATGCCAACGTCCCAGACGTGGTCTTACATG-TAACACATAA
28940279 TGGAATCCTA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
42 3 0.04
43 58 0.87
44 6 0.09
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAACACATAACG
Found at i:28941697 original size:23 final size:23
Alignment explanation
Indices: 28941661--28941707 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28941651 TATTAACATA
* *
28941661 ATAACTTTTCTATG-TAAAATATC
1 ATAACATTTATATGTTAAAA-ATC
28941684 ATAACATTTATATGTTAAAAATC
1 ATAACATTTATATGTTAAAAATC
28941707 A
1 A
28941708 CAATCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAACATTTATATGTTAAAAATC
Found at i:28954939 original size:21 final size:21
Alignment explanation
Indices: 28954915--28954969 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
28954905 ATCAATTTAG
* *
28954915 GGTTCGCATATAAACAAGTAT
1 GGTTCACATATAAACAAGTAC
* *
28954936 GGTTCCCATAACTAAACATGTAC
1 GGTTCACAT-A-TAAACAAGTAC
28954959 GGTTCACATAT
1 GGTTCACATAT
28954970 TATAGAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 17 0.61
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
GGTTCACATATAAACAAGTAC
Found at i:28954962 original size:23 final size:23
Alignment explanation
Indices: 28954925--28954968 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28954915 GGTTCGCATA
* *
28954925 TAAACAAGTATGGTTCCCATAAC
1 TAAACAAGTACGGTTCACATAAC
*
28954948 TAAACATGTACGGTTCACATA
1 TAAACAAGTACGGTTCACATA
28954969 TTATAGAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (23 bp):
TAAACAAGTACGGTTCACATAAC
Found at i:28956357 original size:21 final size:21
Alignment explanation
Indices: 28956332--28956377 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
28956322 TTGAGAAGAA
*
28956332 AGAATCAAAGATTAATATTGT
1 AGAATCAAAGAGTAATATTGT
28956353 AGAATCAAAGAGTAATATTGT
1 AGAATCAAAGAGTAATATTGT
28956374 AGAA
1 AGAA
28956378 AAACCAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (21 bp):
AGAATCAAAGAGTAATATTGT
Found at i:28961163 original size:17 final size:17
Alignment explanation
Indices: 28961141--28961174 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28961131 ATTTGGGCCA
*
28961141 TGTGGGCCACACGGGCG
1 TGTGGGCCACACAGGCG
28961158 TGTGGGCCACACAGGCG
1 TGTGGGCCACACAGGCG
28961175 AACATCATGG
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:0.15, C:0.29, G:0.44, T:0.12
Consensus pattern (17 bp):
TGTGGGCCACACAGGCG
Found at i:28962210 original size:20 final size:20
Alignment explanation
Indices: 28962172--28962212 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28962162 GTATTTAGCA
*
28962172 AAGTTACGGTTTCCCAACAC
1 AAGTTACGGTTTCCAAACAC
*
28962192 AAGTTACGGTTTTCAAACAC
1 AAGTTACGGTTTCCAAACAC
28962212 A
1 A
28962213 CTACCATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (20 bp):
AAGTTACGGTTTCCAAACAC
Found at i:28964156 original size:50 final size:50
Alignment explanation
Indices: 28964085--28964253 Score: 184
Period size: 50 Copynumber: 3.4 Consensus size: 50
28964075 TTAAGGGAAT
* *
28964085 GAGATCCCATGTAAGACCATGTCAGGGACATGGCGTTGGCACTGAGATGA
1 GAGATCCCATGTAAGACCATGTCAGGGACATAGCGTTGGCACCGAGATGA
28964135 GAGATCCCATGTAAGACCATGTCTA-GGACATAGCGTTGGCACCGAGATGA
1 GAGATCCCATGTAAGACCATGTC-AGGGACATAGCGTTGGCACCGAGATGA
* * * * * * * *
28964185 GAGGTCCC-TCGTAAAACCAT-TCTGGGACATATCATGGGCACCGATATCA
1 GAGATCCCAT-GTAAGACCATGTCAGGGACATAGCGTTGGCACCGAGATGA
*
28964234 -AAACTCCCATGTAAGACCAT
1 GAGA-TCCCATGTAAGACCAT
28964254 ATTTGGGATA
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
48 1 0.01
49 36 0.36
50 63 0.62
51 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (50 bp):
GAGATCCCATGTAAGACCATGTCAGGGACATAGCGTTGGCACCGAGATGA
Found at i:28964540 original size:12 final size:12
Alignment explanation
Indices: 28964523--28964561 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28964513 ATGAGTTATT
28964523 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
28964535 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
28964547 TAAGTGAGTAAG
1 TAAGTAAGCAAG
28964559 TAA
1 TAA
28964562 AGAAGTGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:28964549 original size:20 final size:20
Alignment explanation
Indices: 28964524--28964567 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28964514 TGAGTTATTT
28964524 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
** *
28964544 AAGTAAGTGAGTAAGTAAAG
1 AAGTAAGCAAGTAAGTAAAC
28964564 AAGT
1 AAGT
28964568 GAGTAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:28965997 original size:56 final size:50
Alignment explanation
Indices: 28965901--28966147 Score: 176
Period size: 50 Copynumber: 4.8 Consensus size: 50
28965891 ATTTGGGTAA
* * * **
28965901 AGAGATCCCATGTAAGACCATGTCTAGGACATGTCTTTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA-C--CCA-A--ATG
*
28965957 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCCAAATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCCAAATG
* * *
28966007 AGAGGTCCCCA-GTAAGACCATGTCTAGGACATGGCATGGGTA-CCAATATG
1 AGAGGT-CCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCCAA-ATG
** * * * * * ** * *
28966057 AGAACTCCCATGTAAGAACATATCTGGGATATGGCATTGGCA-GTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCCAAATG
* ** * *
28966106 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA
28966148 TGTTATTATC
Statistics
Matches: 159, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
49 45 0.28
50 69 0.43
51 4 0.03
52 1 0.01
53 1 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCCAAATG
Found at i:28966010 original size:50 final size:49
Alignment explanation
Indices: 28965954--28966147 Score: 201
Period size: 50 Copynumber: 3.9 Consensus size: 49
28965944 CATTGAGATT
*
28965954 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCCAA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CCAA
* * *
28966004 ATGAGAGGTCCCCA-GTAAGACCATGTCTAGGACATGGCATGGGTACCAA
1 ATGAGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
** * * * ** *
28966053 TATGAGAACTCCCATGTAAGAACATATCTGGGATATGGCATTGGCAGTAC
1 -ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* * ** *
28966103 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28966148 TGTTATTATC
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
49 45 0.38
50 69 0.58
51 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
Found at i:28979578 original size:17 final size:18
Alignment explanation
Indices: 28979545--28979598 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
28979535 TCGTCATATC
*
28979545 TTTATTATTTTATTTTAT
1 TTTATTATTTAATTTTAT
28979563 TTTATT-TTTAATTTTATCT
1 TTTATTATTTAATTTTA--T
*
28979582 TTCTATTATTCAATTTT
1 TT-TATTATTTAATTTT
28979599 TTGACTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 3 0.10
20 4 0.13
21 8 0.27
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTATTTAATTTTAT
Found at i:28980112 original size:18 final size:18
Alignment explanation
Indices: 28980089--28980126 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28980079 CCCTAAACTG
28980089 AATTGCAATTTACTTCCC
1 AATTGCAATTTACTTCCC
*
28980107 AATTGCAATTTACTTTCC
1 AATTGCAATTTACTTCCC
28980125 AA
1 AA
28980127 GTTACCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (18 bp):
AATTGCAATTTACTTCCC
Found at i:28988950 original size:49 final size:47
Alignment explanation
Indices: 28988813--28989464 Score: 1124
Period size: 47 Copynumber: 13.7 Consensus size: 47
28988803 AGGATTCTAC
*
28988813 GTGATGAATGTGAAAATGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
28988860 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28988907 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28988956 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28989005 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28989054 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28989101 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28989150 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
28989197 GTGATGAATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28989244 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28989291 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28989338 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * *
28989385 GTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
28989432 GTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAG
28989465 TCCCGAAGGG
Statistics
Matches: 584, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
47 393 0.67
49 191 0.33
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
Found at i:28989638 original size:36 final size:37
Alignment explanation
Indices: 28989583--28989660 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
28989573 CCGAGCTCTA
* *
28989583 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
28989619 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28989656 AAGAC
1 AAGAC
28989661 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28991237 original size:40 final size:40
Alignment explanation
Indices: 28990874--28991225 Score: 542
Period size: 40 Copynumber: 8.8 Consensus size: 40
28990864 GAGAATTGAG
* *
28990874 AGTGATGTATCCAGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
28990914 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
28990954 AGTAATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
28990994 AGTAATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
*
28991034 AGTAATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
28991074 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
* *
28991114 AGTGATGTATCCGGACTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
* * ** * *
28991154 AGTGATATATCCGTGCTAAACCCCAAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
* * * * *
28991194 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCA
28991226 ATCATGCTGG
Statistics
Matches: 291, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 291 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
Found at i:28995156 original size:49 final size:47
Alignment explanation
Indices: 28995066--28995720 Score: 1130
Period size: 47 Copynumber: 13.7 Consensus size: 47
28995056 AGGATTCTAC
28995066 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28995113 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28995162 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28995211 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCTGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC-GAT
28995259 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
*
28995308 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATCGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28995355 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28995404 GTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGAT
28995453 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28995500 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28995547 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
28995594 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * * * * *
28995641 GTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
28995688 GTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 GTGATGAATGTGAAAGTGTATATATGTGATAAG
28995721 TCCCGAAGGG
Statistics
Matches: 589, Mismatches: 12, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
47 330 0.56
48 21 0.04
49 212 0.36
50 26 0.04
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
Found at i:28999655 original size:46 final size:46
Alignment explanation
Indices: 28999583--28999713 Score: 217
Period size: 46 Copynumber: 2.8 Consensus size: 46
28999573 ACAAAATGAT
* *
28999583 TAAGACCATAGTTGATAGACATTATGGCACTATACCAGAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAGAATAAA
* *
28999629 TAAGACCATAGTTGAAAGGCACTATGGCACTATATCAGAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAGAATAAA
*
28999675 TAAGACCATAGTTGAAAGACACTATGGCACCATACCAGA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGA
28999714 AACGAGTATG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAGAATAAA
Found at i:28999801 original size:44 final size:45
Alignment explanation
Indices: 28999716--28999843 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 45
28999706 ATACCAGAAA
* * * *
28999716 CGAGTATGGCCATGACTGAAAGACGTTACGGTATCACGATTCTAT
1 CGAGTAAGACCATAACTGAAAGACGTTACGGCATCACGATTCTAT
* * *
28999761 CGAGTAAGACCATAACT-AAAGACTTTATGGCATCATGATTCTAT
1 CGAGTAAGACCATAACTGAAAGACGTTACGGCATCACGATTCTAT
* * ** * *
28999805 TGAGTAAGACCTTAGTTGAAAGATGTTATGGCATCACGA
1 CGAGTAAGACCATAACTGAAAGACGTTACGGCATCACGA
28999844 ATCAAACGAA
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 36 0.53
45 32 0.47
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
CGAGTAAGACCATAACTGAAAGACGTTACGGCATCACGATTCTAT
Found at i:29000942 original size:41 final size:41
Alignment explanation
Indices: 29000883--29001229 Score: 426
Period size: 41 Copynumber: 8.5 Consensus size: 41
29000873 TGAGCTTTCG
* * *
29000883 GGGCTTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
29000924 GGGCTTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
*
29000965 GGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCA
1 GGGC-TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
29001007 GGGATTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
29001048 GGGATTTAGCGACGTTTTTTAGAAAGCTCCGCTAATGTTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
** * * *
29001089 GTACTTTAGCGGTGTTTTTGA-AAAGCGCTGCTAATACTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * *
29001129 GGGATTTAGCGGCGTTTTTGAGAATGCGCCACTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* * * * *
29001170 GGGCTTTAGCGGCGTTTTTGGGAAAACGTCGCTAATTCTCG
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
29001211 GGGCTTTAGCGGCGTTTTT
1 GGGCTTTAGCGGCGTTTTT
29001230 CAGGTAGCAC
Statistics
Matches: 259, Mismatches: 45, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
40 32 0.12
41 189 0.73
42 38 0.15
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:29001031 original size:83 final size:82
Alignment explanation
Indices: 29000887--29001299 Score: 404
Period size: 81 Copynumber: 5.0 Consensus size: 82
29000877 CTTTCGGGGC
* * * * *
29000887 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGAGAAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
*
29000952 CCGCTAATGCTCAGGGCT
66 CCGCTAATGCTCAGGG-A
* * * *
29000970 TTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCAGCATTTTTAAGAAAGCG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
*
29001035 CCGCTAATGCTTAGGGA
66 CCGCTAATGCTCAGGGA
* * * * * *
29001052 TTTAGCGACGTTTTTTAGAAAGCTCCGCTAATGTTCA-GTACTTTAGCGGTGTTTTTGA-AAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA-TTTAGCGGCGTTTTTGAGAAAGC
* *
29001115 GCTGCTAATACTCAGGGA
65 GCCGCTAATGCTCAGGGA
* * * * *
29001133 TTTAGCGGCGTTTTTGAGAATGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAACG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
* * * *
29001198 TCGCTAATTCTCGGGGC
66 CCGCTAATGCTCAGGGA
* ** * * * * ** *
29001215 TTTAGCGGCGTTTTTCAGGTAGCACTGCGAATACTCTA--TTTTTAGCGGCGTTTTCT-AAAAAG
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC-AGGGATTTAGCGGCGTTTT-TGAGAAAG
*
29001277 CACCGCTAATGCTCAGGGA
64 CGCCGCTAATGCTCAGGGA
29001296 TTTA
1 TTTA
29001300 AAATAATTTA
Statistics
Matches: 266, Mismatches: 59, Indels: 12
0.79 0.18 0.04
Matches are distributed among these distances:
81 103 0.39
82 91 0.34
83 72 0.27
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
CCGCTAATGCTCAGGGA
Found at i:29001218 original size:122 final size:123
Alignment explanation
Indices: 29000887--29001229 Score: 458
Period size: 122 Copynumber: 2.8 Consensus size: 123
29000877 CTTTCGGGGC
*
29000887 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGAGAAAGCG
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
* * *
29000952 CCGCTAATGCTCAGGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
66 TCGCTAATTCTCAGGGC-TTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATACTCAGGGA
* * * *
29001011 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTTAGGGATTTAGCGACGTTTTTTAGAAAGC-
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
** *
29001075 TCCGCTAATGT-TCAGTACTTTAGCGGTGTTTTTGA-AAAGCGCTGCTAATACTCAGGGA
66 T-CGCTAAT-TCTCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATACTCAGGGA
* * * * * * *
29001133 TTTAGCGGCGTTTTTGAGAATGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAACG
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
* *
29001198 TCGCTAATTCTCGGGGCTTTAGCGGCGTTTTT
66 TCGCTAATTCTCAGGGCTTTAGCGGTGTTTTT
29001230 CAGGTAGCAC
Statistics
Matches: 189, Mismatches: 26, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
121 1 0.01
122 99 0.52
123 18 0.10
124 71 0.38
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (123 bp):
TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCG
TCGCTAATTCTCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATACTCAGGGA
Found at i:29001259 original size:122 final size:122
Alignment explanation
Indices: 29000887--29001299 Score: 449
Period size: 122 Copynumber: 3.4 Consensus size: 122
29000877 CTTTCGGGGC
* *
29000887 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGAGAAAGCG
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
* * * *
29000952 CCGCTAATGCTCAGGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGA
66 TCGCTAATTCTCAGGGC-TTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATACTCA-GGA
* * *
29001011 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTTAGGGATTTAGCGACGTTTTTTAGAAAGC-
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
**
29001075 TCCGCTAATGT-TCAGTACTTTAGCGGTGTTTTTGA-AAAGCGCTGCTAATACTCAGGGA
66 T-CGCTAAT-TCTCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATACTCA-GGA
* * * * * * * *
29001133 TTTAGCGGCGTTTTTGAGAATGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAACG
1 TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
* * * ** * * **
29001198 TCGCTAATTCTCGGGGCTTTAGCGGCGTTTTTCAGGTAGCACTGCGAATACTCTA-TT
66 TCGCTAATTCTCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATACTC-AGGA
* * *
29001255 TTTAGCGGCGTTTTCTAA-AAAGCACCGCTAATGCTCAGGGATTTA
1 TTTAGCAGCATTTT-TAAGAAAGCGCCGCTAATGCTCAGGGATTTA
29001300 AAATAATTTA
Statistics
Matches: 244, Mismatches: 38, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
121 1 0.00
122 137 0.56
123 34 0.14
124 72 0.30
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (122 bp):
TTTAGCAGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAGAAAGCG
TCGCTAATTCTCAGGGCTTTAGCGGTGTTTTTGAGAAAGCGCTGCTAATACTCAGGA
Found at i:29001294 original size:163 final size:163
Alignment explanation
Indices: 29000897--29001299 Score: 414
Period size: 163 Copynumber: 2.5 Consensus size: 163
29000887 TTTAGCAGCA
* * * * ** * *
29000897 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGTGGCGTTTTTGAGAAAGCGCCGCTAATGC
1 TTTTTCAGAAAGCACCGCGAATACTCAGTACTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGC
* * *
29000962 TCAGGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTCAGGGATTTAGCAGCATTTTTA
65 TCAGGG-ATTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTCAGGGATTTAGCAGCATTTTTA
* *
29001027 AGAAAGCGCCGCTAATGCTTAGGGATTTAGCGACG
129 AGAAAACGCCGCTAATGCTCAGGGATTTAGCGACG
* * * ** * * * *
29001062 TTTTTTAGAAAGCTCCGCTAATGTTCAGTACTTTAGCGGTGTTTTTGAAAAGCGCTGCTAATACT
1 TTTTTCAGAAAGCACCGCGAATACTCAGTACTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCT
* * * * **
29001127 CAGGGATTTAGCGGCGTTTTTGAGAATGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
66 CAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTCAGGGATTTAGCAGCATTTTTAAG
* * * * *
29001192 AAAACGTCGCTAATTCTCGGGGCTTTAGCGGCG
131 AAAACGCCGCTAATGCTCAGGGATTTAGCGACG
** * * *
29001225 TTTTTCAGGTAGCACTGCGAATACTC--TATTTTTAGCGGCGTTTTCTAAAAAGCACCGCTAATG
1 TTTTTCAGAAAGCACCGCGAATACTCAGTA-CTTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATG
29001288 CTCAGGGATTTA
64 CTCAGGGATTTA
29001300 AAATAATTTA
Statistics
Matches: 195, Mismatches: 41, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
161 2 0.01
162 13 0.07
163 121 0.62
164 20 0.10
165 39 0.20
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (163 bp):
TTTTTCAGAAAGCACCGCGAATACTCAGTACTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCT
CAGGGATTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTCAGGGATTTAGCAGCATTTTTAAG
AAAACGCCGCTAATGCTCAGGGATTTAGCGACG
Found at i:29001492 original size:14 final size:14
Alignment explanation
Indices: 29001473--29001520 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
29001463 TATCACTATA
*
29001473 GTTTAGAGTTTTTG
1 GTTTAGAGTTTATG
* *
29001487 GTTTAGGGTATATG
1 GTTTAGAGTTTATG
*
29001501 GTTTAGAGTTTAAG
1 GTTTAGAGTTTATG
29001515 GTTTAG
1 GTTTAG
29001521 GTGTTACCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
GTTTAGAGTTTATG
Found at i:29001556 original size:22 final size:21
Alignment explanation
Indices: 29001531--29001578 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
29001521 GTGTTACCAT
* *
29001531 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTACGGATTAT-GG
*
29001553 TTTAAGGATTACGGTTTATGG
1 TTTAAGGATTACGGATTATGG
29001574 TTTAA
1 TTTAA
29001579 AGGCTGGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.25, C:0.02, G:0.27, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTACGGATTATGG
Found at i:29001568 original size:29 final size:29
Alignment explanation
Indices: 29001536--29001670 Score: 107
Period size: 29 Copynumber: 4.7 Consensus size: 29
29001526 ACCATTTTAA
*
29001536 GGTTTATGGATTATGGGTTTAAGGATTAC
1 GGTTTATGGATTATGGGTTTAAGGATTAT
* ** * ** *
29001565 GGTTTATGGTTTAAAGG-CTGGGGTTTAT
1 GGTTTATGGATTATGGGTTTAAGGATTAT
*
29001593 GGTTTATGGATTATGGGTTTAGGGATTAT
1 GGTTTATGGATTATGGGTTTAAGGATTAT
* * *
29001622 GGTTTAT-GATTTATGGTTTTAAGGTTTTAG
1 GGTTTATGGA-TTATGGGTTTAAGG-ATTAT
*
29001652 GGTTTA-GGTTTAT-GGTTTA
1 GGTTTATGGATTATGGGTTTA
29001671 GGGTTTAGAT
Statistics
Matches: 82, Mismatches: 20, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
28 27 0.33
29 45 0.55
30 10 0.12
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (29 bp):
GGTTTATGGATTATGGGTTTAAGGATTAT
Found at i:29001596 original size:7 final size:7
Alignment explanation
Indices: 29001531--29001677 Score: 91
Period size: 7 Copynumber: 20.6 Consensus size: 7
29001521 GTGTTACCAT
*
29001531 TTTAAGG
1 TTTATGG
29001538 TTTATGG
1 TTTATGG
*
29001545 ATTATGGG
1 TTTAT-GG
*
29001553 TTTAAGG
1 TTTATGG
* *
29001560 ATTACGG
1 TTTATGG
29001567 TTTATGG
1 TTTATGG
*
29001574 TTTAAAGG
1 TTT-ATGG
* **
29001582 -CTGGGG
1 TTTATGG
29001588 TTTATGG
1 TTTATGG
29001595 TTTATGG
1 TTTATGG
*
29001602 ATTATGGG
1 TTTAT-GG
*
29001610 TTTAGGG
1 TTTATGG
*
29001617 ATTATGG
1 TTTATGG
*
29001624 TTTATGA
1 TTTATGG
29001631 TTTATGG
1 TTTATGG
*
29001638 TTTTAAGG
1 -TTTATGG
*
29001646 TTTTAGGG
1 -TTTATGG
29001654 TTTA-GG
1 TTTATGG
29001660 TTTATGG
1 TTTATGG
*
29001667 TTTAGGG
1 TTTATGG
29001674 TTTA
1 TTTA
29001678 GATTAACTAG
Statistics
Matches: 108, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
6 8 0.07
7 74 0.69
8 26 0.24
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:29001676 original size:36 final size:37
Alignment explanation
Indices: 29001586--29001676 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 37
29001576 TAAAGGCTGG
* *
29001586 GGTTTATGGTTTATGG-ATTATGGGTTTAGGGATTAT
1 GGTTTATGGTTTATGGTTTTAAGGGTTTAGGGATTAT
* * *
29001622 GGTTTATGATTTATGGTTTTAAGGTTTTAGGGTTTA-
1 GGTTTATGGTTTATGGTTTTAAGGGTTTAGGGATTAT
*
29001658 GGTTTATGGTTTAGGGTTT
1 GGTTTATGGTTTATGGTTT
29001677 AGATTAACTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 32 0.68
37 15 0.32
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.51
Consensus pattern (37 bp):
GGTTTATGGTTTATGGTTTTAAGGGTTTAGGGATTAT
Found at i:29002348 original size:20 final size:20
Alignment explanation
Indices: 29002326--29002388 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
29002316 TTCGTGATTT
29002326 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
29002347 AAAGATTTT-AAATTTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
29002367 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
29002387 AA
1 AA
29002389 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:29002356 original size:10 final size:10
Alignment explanation
Indices: 29002329--29002388 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
29002319 GTGATTTAAA
29002329 ATTTTAAAATG
1 ATTTTAAAA-G
29002340 AATTTTAAAAG
1 -ATTTTAAAAG
**
29002351 ATTTTAAATT
1 ATTTTAAAAG
*
29002361 TTTTTAAAA-
1 ATTTTAAAAG
29002370 ATTTTAAAAAG
1 ATTTT-AAAAG
29002381 ATTTTAAA
1 ATTTTAAA
29002389 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:29003233 original size:13 final size:13
Alignment explanation
Indices: 29003217--29003246 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29003207 AAAAATTTTA
*
29003217 GCTTTTCAGAAGT
1 GCTTTTCAAAAGT
29003230 GCTTTTCAAAAGT
1 GCTTTTCAAAAGT
29003243 GCTT
1 GCTT
29003247 CTGAAAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (13 bp):
GCTTTTCAAAAGT
Found at i:29007052 original size:42 final size:43
Alignment explanation
Indices: 29006987--29007226 Score: 197
Period size: 43 Copynumber: 5.6 Consensus size: 43
29006977 TATCTTCTTT
* * *
29006987 TAAAGGTTATGTTTTTAGCGGCGTTTTTG-TGAAAAGCGTCGC
1 TAAAGGTTATGTTTTTAGCGGCGTTTGTGATAAAAAGCGCCGC
*
29007029 TAAAGGTT-TGTTTTATAGTGGCGTTTGTGATAAAAAGCGCCGC
1 TAAAGGTTATGTTTT-TAGCGGCGTTTGTGATAAAAAGCGCCGC
* ** * * *
29007072 TAAAGGTCATGACATTTAGCGGCATTTTTGAT-AGAAGCGCCGC
1 TAAAGGTTATG-TTTTTAGCGGCGTTTGTGATAAAAAGCGCCGC
* * * * *
29007115 TAAAGGTCATGATCTTTAGCGGCGTTTGTGAT-AGAAGTGTCGC
1 TAAAGGTTATG-TTTTTAGCGGCGTTTGTGATAAAAAGCGCCGC
* *
29007158 TAAAGGTCAT-TATCTTTAGC-GCGTTTGTGAT-AAAAGCACCGC
1 TAAAGGTTATGT-T-TTTAGCGGCGTTTGTGATAAAAAGCGCCGC
** *
29007200 TAAAGGCCATGATCTTTAGCGGCGTTT
1 TAAAGGTTATG-TTTTTAGCGGCGTTT
29007227 TTTCACATAA
Statistics
Matches: 165, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
41 7 0.04
42 53 0.32
43 87 0.53
44 16 0.10
45 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
TAAAGGTTATGTTTTTAGCGGCGTTTGTGATAAAAAGCGCCGC
Found at i:29007159 original size:86 final size:87
Alignment explanation
Indices: 29006987--29007226 Score: 269
Period size: 86 Copynumber: 2.8 Consensus size: 87
29006977 TATCTTCTTT
* * * * * *
29006987 TAAAGGTTATG-TTTTTAGCGGCGTTTTTG-TGAAAAGCGTCGCTAAAGGT-TTG-TTTTATAGT
1 TAAAGGTCATGATCTTTAGCGGCGTTTTTGAT-AAAAGCGCCGCTAAAGGTCATGATCTT-TAGC
29007048 GGCGTTTGTGATAAAAAGCGCCGC
64 GGCGTTTGTGATAAAAAGCGCCGC
* *
29007072 TAAAGGTCATGA-CATTTAGCGGCATTTTTGATAGAAGCGCCGCTAAAGGTCATGATCTTTAGCG
1 TAAAGGTCATGATC-TTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCG
* * *
29007136 GCGTTTGTGAT-AGAAGTGTCGC
65 GCGTTTGTGATAAAAAGCGCCGC
* * * *
29007158 TAAAGGTCATTATCTTTAGC-GCGTTTGTGATAAAAGCACCGCTAAAGGCCATGATCTTTAGCGG
1 TAAAGGTCATGATCTTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGG
29007222 CGTTT
66 CGTTT
29007227 TTTCACATAA
Statistics
Matches: 132, Mismatches: 17, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
85 54 0.41
86 56 0.42
87 19 0.14
88 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (87 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTTTGATAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGG
CGTTTGTGATAAAAAGCGCCGC
Found at i:29007211 original size:85 final size:87
Alignment explanation
Indices: 29007048--29007226 Score: 247
Period size: 85 Copynumber: 2.1 Consensus size: 87
29007038 GTTTTATAGT
* * *
29007048 GGCGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGACATTTAGCGGCATTTTTGATAGAAGCGCC
1 GGCGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGACATTTAGCGGCATTTGTGATAAAAGCACC
*
29007113 GCTAAAGGTCATGATCTTTAGC
66 GCTAAAGGCCATGATCTTTAGC
* * * * *
29007135 GGCGTTTGTGAT-AGAAGTGTCGCTAAAGGTCATTATC-TTTAGC-GCGTTTGTGATAAAAGCAC
1 GGCGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGA-CATTTAGCGGCATTTGTGATAAAAGCAC
29007197 CGCTAAAGGCCATGATCTTTAGC
65 CGCTAAAGGCCATGATCTTTAGC
29007220 GGCGTTT
1 GGCGTTT
29007227 TTTCACATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
85 44 0.54
86 25 0.30
87 13 0.16
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (87 bp):
GGCGTTTGTGATAAAAAGCGCCGCTAAAGGTCATGACATTTAGCGGCATTTGTGATAAAAGCACC
GCTAAAGGCCATGATCTTTAGC
Found at i:29007419 original size:20 final size:20
Alignment explanation
Indices: 29007394--29007438 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
29007384 TATTAAGCTA
29007394 AAGTAAATGCAATGGAAAGT
1 AAGTAAATGCAATGGAAAGT
29007414 AAGTAAATGCAATGGAAAGT
1 AAGTAAATGCAATGGAAAGT
29007434 AAGTA
1 AAGTA
29007439 TATGGAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGTAAATGCAATGGAAAGT
Found at i:29008950 original size:9 final size:9
Alignment explanation
Indices: 29008936--29009110 Score: 87
Period size: 9 Copynumber: 18.8 Consensus size: 9
29008926 CAAGTAACTT
29008936 TTTTTATAA
1 TTTTTATAA
29008945 -TTTT-T-A
1 TTTTTATAA
29008951 TTTTTATAA
1 TTTTTATAA
29008960 TTTATT-TGAA
1 TTT-TTAT-AA
29008970 TTTTT-T-A
1 TTTTTATAA
29008977 TTATTTATAA
1 TT-TTTATAA
*
29008987 GTTTTTTTTGAA
1 --TTTTTAT-AA
* *
29008999 TTTTAATATG
1 TTTTTATA-A
29009009 TTTTTAATAA
1 TTTTT-ATAA
*
29009019 TTTATAATAA
1 TTT-TTATAA
29009029 TTTTTATAA
1 TTTTTATAA
*
29009038 TATTTATAA
1 TTTTTATAA
*
29009047 GTTTTCCAT-A
1 -TTTT-TATAA
*
29009057 TTTGTATAA
1 TTTTTATAA
29009066 TTTTATATAA
1 TTTT-TATAA
*
29009076 ATTTTA-ATA
1 TTTTTATA-A
29009085 TTTTTAATAA
1 TTTTT-ATAA
*
29009095 ATTTTATAA
1 TTTTTATAA
29009104 TTTTTAT
1 TTTTTAT
29009111 GAAAAAAATT
Statistics
Matches: 127, Mismatches: 18, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 8 0.06
8 11 0.09
9 47 0.37
10 45 0.35
11 11 0.09
12 4 0.03
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29008996 original size:29 final size:26
Alignment explanation
Indices: 29008945--29009002 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 26
29008935 TTTTTTATAA
29008945 TTTTTATTTTTATAATTTATTTGAAT
1 TTTTTATTTTTATAATTTATTTGAAT
*
29008971 TTTTTATTATTTATAAGTTTTTTTTGAAT
1 TTTTTATT-TTTATAA--TTTATTTGAAT
29009000 TTT
1 TTT
29009003 AATATGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.29
27 7 0.25
29 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (26 bp):
TTTTTATTTTTATAATTTATTTGAAT
Found at i:29009026 original size:21 final size:22
Alignment explanation
Indices: 29008997--29009046 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
29008987 GTTTTTTTTG
29008997 AATTT-TAAT-ATGTTTT-TAAT
1 AATTTATAATAAT-TTTTATAAT
29009017 AATTTATAATAATTTTTATAAT
1 AATTTATAATAATTTTTATAAT
29009039 -ATTTATAA
1 AATTTATAA
29009047 GTTTTCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTTATAATAATTTTTATAAT
Found at i:29009059 original size:28 final size:27
Alignment explanation
Indices: 29009017--29009109 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
29009007 TGTTTTTAAT
29009017 AATTTATAATAATTTTTATAATATTTATA
1 AATTT-TAAT-ATTTTTATAATATTTATA
* * * *
29009046 AGTTTTCCATATTTGTATAATTTTATATA
1 AATTTT-AATATTTTTATAATATT-TATA
29009075 AATTTTAATATTTTTAATAA-ATTTTATA
1 AATTTTAATATTTTT-ATAATA-TTTATA
*
29009103 ATTTTTA
1 AATTTTA
29009110 TGAAAAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
28 30 0.59
29 21 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
AATTTTAATATTTTTATAATATTTATA
Found at i:29009108 original size:19 final size:18
Alignment explanation
Indices: 29008935--29009109 Score: 78
Period size: 19 Copynumber: 9.3 Consensus size: 18
29008925 TCAAGTAACT
*
29008935 TTTTTTATAATTTT-T-A
1 TTTTTAATAATTTTATAA
*
29008951 TTTTT-ATAATTTATTTGAA
1 TTTTTAATAATTT-TAT-AA
* *
29008970 TTTTTTATTA-TTTATAA
1 TTTTTAATAATTTTATAA
** *
29008987 GTTTTTTTTGAATTTTAATATG
1 -TTTTTAAT-AATTTT-ATA-A
29009009 TTTTTAATAATTTATAATAA
1 TTTTTAATAATTT-T-ATAA
29009029 TTTTT-ATAATATTTATAA
1 TTTTTAATAAT-TTTATAA
**
29009047 GTTTTCCAT-ATTTGTATAA
1 -TTTTTAATAATTT-TATAA
29009066 -TTTTATATAAATTTTA-ATA
1 TTTTTA-AT-AATTTTATA-A
29009085 TTTTTAATAAATTTTATAA
1 TTTTTAAT-AATTTTATAA
29009104 TTTTTA
1 TTTTTA
29009110 TGAAAAAAAT
Statistics
Matches: 127, Mismatches: 11, Indels: 39
0.72 0.06 0.22
Matches are distributed among these distances:
15 7 0.06
16 6 0.05
17 6 0.05
18 18 0.14
19 46 0.36
20 30 0.24
21 14 0.11
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTAATAATTTTATAA
Found at i:29009712 original size:22 final size:22
Alignment explanation
Indices: 29009684--29009739 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
29009674 TTAATTTTAT
29009684 TTTTAATTACAAAATAATGAAA
1 TTTTAATTACAAAATAATGAAA
*
29009706 TTTTAATTATAAAATAATGAAA
1 TTTTAATTACAAAATAATGAAA
29009728 TTTTAATTACAA
1 TTTTAATTACAA
29009740 TGGCCATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTTAATTACAAAATAATGAAA
Found at i:29016289 original size:37 final size:37
Alignment explanation
Indices: 29016234--29016309 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
29016224 AAGCTGAAGT
*
29016234 GTAACAACCTTGGAACTTGAATCGATTAGGCATCTTC
1 GTAACAACCTTGGAACTTGAATCGATTAGGCATCATC
*
29016271 GTAACAACCTTGGCACTTGAATCGATTAGGCATCATC
1 GTAACAACCTTGGAACTTGAATCGATTAGGCATCATC
29016308 GT
1 GT
29016310 GACGAGCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (37 bp):
GTAACAACCTTGGAACTTGAATCGATTAGGCATCATC
Found at i:29016837 original size:27 final size:26
Alignment explanation
Indices: 29016802--29016879 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
29016792 GGCAGAAACT
* *
29016802 AGTTTGCAACTCAACTGGCGAACTCCC
1 AGTTCGCAAC-CAACTGGCGAACACCC
* * *
29016829 AGTTCGCAACGAAACTGGTGAACACCT
1 AGTTCGCAAC-CAACTGGCGAACACCC
*
29016856 AGTTCGTCAAACCAACTAGCGAAC
1 AGTTCG-C-AACCAACTGGCGAAC
29016880 CCAACTTGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
27 27 0.68
28 10 0.25
29 3 0.08
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (26 bp):
AGTTCGCAACCAACTGGCGAACACCC
Found at i:29021629 original size:85 final size:85
Alignment explanation
Indices: 29021486--29021664 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
29021476 GGCCGGCCAT
29021486 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29021551 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
29021571 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29021636 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
29021656 GGGCATGGG
1 GAGCATGGG
29021665 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:29022917 original size:47 final size:47
Alignment explanation
Indices: 29022865--29023656 Score: 1223
Period size: 47 Copynumber: 16.7 Consensus size: 47
29022855 AGTGTATATA
*
29022865 TGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
** *
29022912 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
29022959 TGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
29023006 TGTGATAAGGCCGAATGGCCAATATGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
** *
29023053 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
29023100 TGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
29023147 TGTGATAAGGCCGAATGGCCAATATGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
* *
29023194 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--TGTATG
29023243 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
* *
29023290 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--TGTATG
29023339 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
** *
29023386 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
* * *
29023433 TGAGATAAAGCCGAATGGACAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
29023480 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGATGA-ATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA--ACATGTGTATG
** *
29023528 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
* * *
29023575 TGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATA
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGTGTATG
*
29023622 TGTGATAAGGCCGAATGGCCAATGTGATGGATGTG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
29023657 GAAGTGTATA
Statistics
Matches: 685, Mismatches: 48, Indels: 24
0.90 0.06 0.03
Matches are distributed among these distances:
46 4 0.01
47 547 0.80
48 45 0.07
49 87 0.13
50 2 0.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
Found at i:29023552 original size:24 final size:24
Alignment explanation
Indices: 29023477--29023553 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
29023467 GAACATGTGT
29023477 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* ** *
29023501 ATGTGATGA-ATGTGATGAATGTG--T
1 ATGTG-TGATAAG-GCCGAATG-GCCA
29023525 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
29023549 ATGTG
1 ATGTG
29023554 ATGAATGTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 1 0.03
23 9 0.23
24 19 0.49
25 9 0.23
26 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.34, T:0.27
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:29034055 original size:40 final size:40
Alignment explanation
Indices: 29034018--29034281 Score: 324
Period size: 40 Copynumber: 6.7 Consensus size: 40
29034008 GCTACTCGTT
*
29034018 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
29034058 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
29034097 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
29034137 CAAATGCCTTC-AGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * *
29034177 CAAATGCCTTTGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
29034216 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
29034257 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29034282 CATCATTCAA
Statistics
Matches: 195, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 67 0.34
40 114 0.58
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:29034121 original size:79 final size:80
Alignment explanation
Indices: 29034018--29034280 Score: 347
Period size: 79 Copynumber: 3.3 Consensus size: 80
29034008 GCTACTCGTT
* **
29034018 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
29034082 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
29034097 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCAGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
*
29034161 GATTTAGTAACTCGTA
65 GATTTAGTAACTCGCA
* * *
29034177 CAAATGCCTTTGGG-CTTAGCCCGG-AATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
* * * *
29034240 GATATGGTCACTTAGCA
65 GATTTAGTAAC-TCGCA
29034257 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
29034281 ACATCATTCA
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
79 107 0.66
80 54 0.34
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
ATTTAGTAACTCGCA
Found at i:29034144 original size:119 final size:120
Alignment explanation
Indices: 29034018--29034281 Score: 331
Period size: 119 Copynumber: 2.2 Consensus size: 120
29034008 GCTACTCGTT
*
29034018 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
* * *
29034082 ATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
65 AATTAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATATAGTAACTTAGCA
* * * * * *
29034137 CAAATGCCTTC-AGATCTTAGTCCGGATTTAGTAACTCGTACAAATGCCTTTGGGCTTAGCCCGG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAACCCGG
* ** * *
29034201 AATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
65 AATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCA
29034257 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29034282 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 5 0.04
119 106 0.86
120 12 0.10
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGA
ATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATATAGTAACTTAGCA
Found at i:29046922 original size:67 final size:67
Alignment explanation
Indices: 29046839--29047177 Score: 360
Period size: 67 Copynumber: 5.1 Consensus size: 67
29046829 GTAGGGCCAG
* * *
29046839 AGCTCGACTATGGCAACATAGAGAGTCCGCCAGGACATTAAACATGGGGTATGATGTGTAAGATC
1 AGCTTGACTATGGCAACATAGAGAGTCTGCCAGGACATTAAACATGAGGTATGATGTGTAAGATC
29046904 AT
66 AT
* * * * *
29046906 AACTTGGCTATGGCAACATAGAGAGTCTGCCATGACATTAAACATGAGGCATGATGT-TCAAGAC
1 AGCTTGACTATGGCAACATAGAGAGTCTGCCAGGACATTAAACATGAGGTATGATGTGT-AAGAT
29046970 CAT
65 CAT
* **** ** * * * * * *
29046973 AGCTCGACTACAATAATGTAGTGAATCTACTAGGACATTAAACATGAGGCATGATGTGTAAGATT
1 AGCTTGACTATGGCAACATAGAGAGTCTGCCAGGACATTAAACATGAGGTATGATGTGTAAGATC
29047038 AT
66 AT
* ** * * * *
29047040 AGCTAGACTATGATAATATAGAGAGTCCGCTAGGACATTAAACATGAGGTATGATGTGTAAGACC
1 AGCTTGACTATGGCAACATAGAGAGTCTGCCAGGACATTAAACATGAGGTATGATGTGTAAGATC
29047105 AT
66 AT
* *
29047107 AGCTTGGCTATGGCAACATAGAGAGTCTGCTCA-GACATTAATCATTG-GGTATGATGTGTAAGA
1 AGCTTGACTATGGCAACATAGAGAGTCTGC-CAGGACATTAAACA-TGAGGTATGATGTGTAAGA
29047170 TCAT
64 TCAT
29047174 AGCT
1 AGCT
29047178 CAGCTATAGC
Statistics
Matches: 224, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.00
67 219 0.98
68 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (67 bp):
AGCTTGACTATGGCAACATAGAGAGTCTGCCAGGACATTAAACATGAGGTATGATGTGTAAGATC
AT
Found at i:29052120 original size:18 final size:19
Alignment explanation
Indices: 29052083--29052120 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
29052073 CAAGGTCTTG
29052083 AGTTTAATCCTTTGCAAAAT
1 AGTTTAAT-CTTTGCAAAAT
*
29052103 AGTTTAAT-TTTGCTAAAT
1 AGTTTAATCTTTGCAAAAT
29052121 TATCTCCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
AGTTTAATCTTTGCAAAAT
Found at i:29053548 original size:20 final size:21
Alignment explanation
Indices: 29053523--29053564 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
29053513 ACCTGTAAAC
*
29053523 TTTAGTGTTTAAATT-ATATT
1 TTTAGTGGTTAAATTGATATT
29053543 TTTAGTGGTTAAATTGATATT
1 TTTAGTGGTTAAATTGATATT
29053564 T
1 T
29053565 AAGCTTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
TTTAGTGGTTAAATTGATATT
Found at i:29056092 original size:18 final size:18
Alignment explanation
Indices: 29056069--29056107 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
29056059 CAATACTTAA
29056069 CTTAGAATTCACCCATTT
1 CTTAGAATTCACCCATTT
29056087 CTTAGAATTCACCCATTT
1 CTTAGAATTCACCCATTT
29056105 CTT
1 CTT
29056108 CGTTACTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.05, T:0.41
Consensus pattern (18 bp):
CTTAGAATTCACCCATTT
Found at i:29056514 original size:28 final size:28
Alignment explanation
Indices: 29056374--29056693 Score: 317
Period size: 28 Copynumber: 11.4 Consensus size: 28
29056364 GTTTGGCACG
*
29056374 AGGCATTCATTTAACAGAGATAGCCACAA
1 AGGC-TTCCTTTAACAGAGATAGCCACAA
* * * *
29056403 AGACATGCTTTTAA-ATGAGGTAGCCACAA
1 AGGC-TTCCTTTAACA-GAGATAGCCACAA
** *
29056432 AGGAATCCTTTTAATAGAGATAGCCACAA
1 AGGCTTCC-TTTAACAGAGATAGCCACAA
* *
29056461 AGACTTCCTTTTAACAGAAATAGCCACAA
1 AGGCTTCC-TTTAACAGAGATAGCCACAA
* *
29056490 AGGCTTCCTTTAATAGAGATCGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
29056518 AGGCTTCTTTTAACAGAGATCA-CCACAA
1 AGGCTTCCTTTAACAGAGAT-AGCCACAA
* ***
29056546 AGGCTTCCTTTAATAGAGATCTTCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
* *
29056574 AAGCTTCCTTTAACAGAGATCA-CCATAA
1 AGGCTTCCTTTAACAGAGAT-AGCCACAA
* * *
29056602 AGGCTTCCTTTAATAGGGATTGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
29056630 AGGCTTCCTTTAACAGAGATAGCCACGA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
29056658 AGGCATCCTTT--CAGAGATAGCCACAA
1 AGGCTTCCTTTAACAGAGATAGCCACAA
*
29056684 AGGATTCCTT
1 AGGCTTCCTT
29056694 GCAAAAACTA
Statistics
Matches: 240, Mismatches: 44, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
26 22 0.09
28 144 0.60
29 73 0.30
30 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (28 bp):
AGGCTTCCTTTAACAGAGATAGCCACAA
Found at i:29056549 original size:56 final size:56
Alignment explanation
Indices: 29056306--29056686 Score: 335
Period size: 56 Copynumber: 6.8 Consensus size: 56
29056296 TCATTTCCAA
* ** * * * *
29056306 AGATAGCCACAAAGGCTTTCCTTTTATAG-TCTTGCCACGAAGGCGTACTTTTAATAG
1 AGATAGCCACAAAGGC-TTCCTTTAATAGAGATAGCCACAAAGGC-TTCTTTTAACAG
* * * * * * * *
29056363 AGTTTGGCAC-GAGGCATTCATTTAACAGAGATAGCCACAAAGACATGCTTTTAA-ATG
1 AGATAGCCACAAAGGC-TTCCTTTAATAGAGATAGCCACAAAGGC-TTCTTTTAACA-G
* ** *
29056420 AGGTAGCCACAAAGGAATCCTTTTAATAGAGATAGCCACAAAGACTTCCTTTTAACAG
1 AGATAGCCACAAAGGCTTCC-TTTAATAGAGATAGCCACAAAGGCTT-CTTTTAACAG
* *
29056478 AAATAGCCACAAAGGCTTCCTTTAATAGAGATCGCCACAAAGGCTTCTTTTAACAG
1 AGATAGCCACAAAGGCTTCCTTTAATAGAGATAGCCACAAAGGCTTCTTTTAACAG
*** * *
29056534 AGATCA-CCACAAAGGCTTCCTTTAATAGAGATCTTCACAAAAGCTTCCTTTAACAG
1 AGAT-AGCCACAAAGGCTTCCTTTAATAGAGATAGCCACAAAGGCTTCTTTTAACAG
* * * *
29056590 AGATCA-CCATAAAGGCTTCCTTTAATAGGGATTGCCACAAAGGCTTCCTTTAACAG
1 AGAT-AGCCACAAAGGCTTCCTTTAATAGAGATAGCCACAAAGGCTTCTTTTAACAG
* * *
29056646 AGATAGCCACGAAGGCATCCTTT--CAGAGATAGCCACAAAGG
1 AGATAGCCACAAAGGCTTCCTTTAATAGAGATAGCCACAAAGG
29056687 ATTCCTTGCA
Statistics
Matches: 269, Mismatches: 47, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
54 15 0.06
55 1 0.00
56 141 0.52
57 61 0.23
58 50 0.19
59 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (56 bp):
AGATAGCCACAAAGGCTTCCTTTAATAGAGATAGCCACAAAGGCTTCTTTTAACAG
Found at i:29072246 original size:39 final size:39
Alignment explanation
Indices: 29072161--29072249 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
29072151 GTACTGATTA
*
29072161 CTGATACTGTAATGGGCTAAGGCCTAATGCATGACTGCAC
1 CTGATACTG-AATGGGCTAAGGCCTAATGCATAACTGCAC
* *
29072201 CT-ATACTGAATGGGCTAAGGCCATAACTG-A-AACTGGAT
1 CTGATACTGAATGGGCTAAGGCC-TAA-TGCATAACTGCAC
29072239 CTGATACTGAA
1 CTGATACTGAA
29072250 AAAGGGCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 21 0.49
39 18 0.42
40 4 0.09
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
CTGATACTGAATGGGCTAAGGCCTAATGCATAACTGCAC
Found at i:29075010 original size:39 final size:39
Alignment explanation
Indices: 29074925--29075013 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 39
29074915 GTACTGATTA
*
29074925 CTGATACTGTAATGGGCTAAGGCCTAATGCATGACTGCAC
1 CTGATACTG-AATGGGCTAAGGCCTAATGCATAACTGCAC
* *
29074965 CT-ATACTGAATGGGCTAAGGCCATAATTG-A-AACTGGAT
1 CTGATACTGAATGGGCTAAGGCC-TAA-TGCATAACTGCAC
29075003 CTGATACTGAA
1 CTGATACTGAA
29075014 AAAGGGCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
38 21 0.49
39 18 0.42
40 4 0.09
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (39 bp):
CTGATACTGAATGGGCTAAGGCCTAATGCATAACTGCAC
Found at i:29077907 original size:27 final size:27
Alignment explanation
Indices: 29077869--29077921 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29077859 TCTTCAGTCC
*
29077869 ACTTGAAAGGTGCACTTTTCCTCAAAA
1 ACTTGAAAGGTGCACTTTTCCACAAAA
29077896 ACTTGAAAGGTGCACTTTTCCACAAA
1 ACTTGAAAGGTGCACTTTTCCACAAA
29077922 CCTCTTATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (27 bp):
ACTTGAAAGGTGCACTTTTCCACAAAA
Found at i:29079396 original size:20 final size:21
Alignment explanation
Indices: 29079359--29079407 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
29079349 AACTAGTATT
29079359 CTGCAACAGTGAGGGTTGTCC
1 CTGCAACAGTGAGGGTTGTCC
29079380 CTGCAACAGTG-GGGTTGT-C
1 CTGCAACAGTGAGGGTTGTCC
29079399 CTAGCAACA
1 CT-GCAACA
29079408 CCATTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 11 0.41
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (21 bp):
CTGCAACAGTGAGGGTTGTCC
Found at i:29079845 original size:16 final size:16
Alignment explanation
Indices: 29079814--29079866 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
29079804 AGTCTTGTCA
29079814 CTATAGTTTT-AGAAT
1 CTATAGTTTTCAGAAT
29079829 CTATAGTTTTCAGAAT
1 CTATAGTTTTCAGAAT
* * *
29079845 CTAGAG-TTTCACAGT
1 CTATAGTTTTCAGAAT
29079860 CTATAGT
1 CTATAGT
29079867 ATTCTATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 22 0.69
16 10 0.31
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (16 bp):
CTATAGTTTTCAGAAT
Found at i:29080027 original size:18 final size:19
Alignment explanation
Indices: 29080006--29080045 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
29079996 ATGGCATGGA
29080006 TTTTTCACAAA-ATACATT
1 TTTTTCACAAATATACATT
* *
29080024 TTTTTCTCAAATATGCATT
1 TTTTTCACAAATATACATT
29080043 TTT
1 TTT
29080046 GAAAATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTTCACAAATATACATT
Found at i:29095495 original size:18 final size:19
Alignment explanation
Indices: 29095469--29095505 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29095459 AATTTTGGAA
29095469 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
29095487 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
29095506 ATGTGATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:29096435 original size:22 final size:22
Alignment explanation
Indices: 29096376--29096437 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
29096366 TAGTTTAATG
29096376 TGGTGAT-GTTACGGTGGTTGAA
1 TGGTGATGGTT-CGGTGGTTGAA
* * * *
29096398 TAGTGGTGGAGT-GGTGGTTGTA
1 TGGTGATGG-TTCGGTGGTTGAA
29096420 TGGTGATGGTTCGGTGGT
1 TGGTGATGGTTCGGTGGT
29096438 GATTTGGTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 1 0.03
24 1 0.03
ACGTcount: A:0.13, C:0.03, G:0.47, T:0.37
Consensus pattern (22 bp):
TGGTGATGGTTCGGTGGTTGAA
Found at i:29098110 original size:35 final size:35
Alignment explanation
Indices: 29098063--29098159 Score: 104
Period size: 35 Copynumber: 2.8 Consensus size: 35
29098053 TTTATCACAG
* *
29098063 TGGCATGTTTAACATGTGAATTAGAATCAGAATAA
1 TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
* * * * *
29098098 TGGCATGCTTAACATACGAATCATAGTCAGAATGA
1 TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
* * *
29098133 TAGCATGCTCAACATGCAAATTAGAAT
1 TGGCATGCTTAACATGCGAATTAGAAT
29098160 ATCAATAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (35 bp):
TGGCATGCTTAACATGCGAATTAGAATCAGAATAA
Found at i:29102255 original size:31 final size:32
Alignment explanation
Indices: 29102199--29102265 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
29102189 TTATTTATAT
*
29102199 AGGTTGGCCGAATGTGTGGGATCA-TTTAACA
1 AGGTTAGCCGAATGTGTGGGATCATTTTAACA
*
29102230 AGGTTAGCCGAAT-T-TGGAGATTCATTTTAGCA
1 AGGTTAGCCGAATGTGTGG-GA-TCATTTTAACA
29102262 AGGT
1 AGGT
29102266 GTATGCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 3 0.10
31 15 0.48
32 10 0.32
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (32 bp):
AGGTTAGCCGAATGTGTGGGATCATTTTAACA
Found at i:29103089 original size:22 final size:22
Alignment explanation
Indices: 29103058--29103101 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29103048 TTTTGAACCA
*
29103058 TTACCTTTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
29103080 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
29103102 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:29103937 original size:16 final size:17
Alignment explanation
Indices: 29103911--29103944 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29103901 TTAGATTGGG
*
29103911 TTGATAAAATTATTTAA
1 TTGATAAAATTAATTAA
29103928 TTGA-AAAATTAATTAA
1 TTGATAAAATTAATTAA
29103944 T
1 T
29103945 ATAAGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TTGATAAAATTAATTAA
Found at i:29105620 original size:12 final size:11
Alignment explanation
Indices: 29105602--29105641 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
29105592 TATTTCATGC
29105602 TAATTTTTTTA
1 TAATTTTTTTA
29105613 TGAATTTTTTTA
1 T-AATTTTTTTA
29105625 TAATTTTTTTA
1 TAATTTTTTTA
29105636 T-ATTTT
1 TAATTTT
29105642 GAGTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.18
11 12 0.43
12 11 0.39
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:29106053 original size:19 final size:19
Alignment explanation
Indices: 29106032--29106067 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
29106022 TAAAAAAATA
29106032 AAAAATTATT-AATTTTAG
1 AAAAATTATTAAATTTTAG
29106050 AAAAATTATTAAATTTTA
1 AAAAATTATTAAATTTTA
29106068 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAAATTATTAAATTTTAG
Found at i:29106140 original size:11 final size:12
Alignment explanation
Indices: 29106116--29106140 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29106106 AATTTTTTAT
29106116 AAAAATTGTAAA
1 AAAAATTGTAAA
29106128 AAAAATTGTAAA
1 AAAAATTGTAAA
29106140 A
1 A
29106141 TTTTATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAATTGTAAA
Found at i:29106402 original size:28 final size:28
Alignment explanation
Indices: 29106356--29106462 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 28
29106346 CTAACGAATT
29106356 TATAAAATTTTATAATTTTTTTATATTTC
1 TATAAAATTTTATAA-TTTTTTATATTTC
* * *
29106385 TAT-ATATTTTATAATTTTTTACGATTTT
1 TATAAAATTTTATAATTTTTTA-TATTTC
* *
29106413 TATAAAATTTTACAATTTTTTATATTTT
1 TATAAAATTTTATAATTTTTTATATTTC
* * *
29106441 TTTACAATTTTTATATTTTTTT
1 TATA-AAATTTTATAATTTTTT
29106463 CTAATTTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
27 7 0.11
28 25 0.38
29 33 0.51
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (28 bp):
TATAAAATTTTATAATTTTTTATATTTC
Found at i:29106404 original size:10 final size:10
Alignment explanation
Indices: 29106363--29106471 Score: 75
Period size: 10 Copynumber: 11.3 Consensus size: 10
29106353 ATTTATAAAA
29106363 TTTTATAATT
1 TTTTATAATT
29106373 TTTT-T-ATAT
1 TTTTATAAT-T
* *
29106382 TTCTAT-ATA
1 TTTTATAATT
29106391 TTTTATAATT
1 TTTTATAATT
**
29106401 TTTTACGA-T
1 TTTTATAATT
**
29106410 TTTTATAAAA
1 TTTTATAATT
*
29106420 TTTTACAATT
1 TTTTATAATT
*
29106430 TTTTATATTT
1 TTTTATAATT
*
29106440 TTTTACAA-T
1 TTTTATAATT
*
29106449 TTTTATATTT
1 TTTTATAATT
*
29106459 TTTTCTAATT
1 TTTTATAATT
29106469 TTT
1 TTT
29106472 AATATTTGAA
Statistics
Matches: 74, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
8 2 0.03
9 24 0.32
10 48 0.65
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:29106413 original size:19 final size:19
Alignment explanation
Indices: 29106391--29106472 Score: 94
Period size: 19 Copynumber: 4.3 Consensus size: 19
29106381 TTTCTATATA
*
29106391 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACAAT
**
29106410 TTTTATAAAATTTTACAATT
1 TTTTATAATTTTTTACAA-T
*
29106430 TTTTATATTTTTTTACAAT
1 TTTTATAATTTTTTACAAT
*
29106449 TTTTAT-ATTTTTTTCTAAT
1 TTTTATAATTTTTTAC-AAT
29106468 TTTTA
1 TTTTA
29106473 ATATTTGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.13
19 30 0.57
20 16 0.30
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:29106417 original size:57 final size:58
Alignment explanation
Indices: 29106319--29106466 Score: 158
Period size: 57 Copynumber: 2.5 Consensus size: 58
29106309 ATTTTACGAA
* *
29106319 ATATTTCTTTACATTTTATATAATTTTCTAACGAATTTATAAAATTTTATAATTTTTTT
1 ATATTTCTATACATTTTATATAATTTTCTAACGAATTTATAAAATTTTACAA-TTTTTT
* * *
29106378 ATATTTCTATATA-TTT-TATAATTTT-TTACGATTTTTATAAAATTTTACAATTTTTT
1 ATATTTCTATACATTTTATATAATTTTCTAACGA-ATTTATAAAATTTTACAATTTTTT
* * **
29106434 ATATTTTTTTACAATTTTTATATTTTTTTCTAA
1 ATATTTCTATAC-A-TTTTATATAATTTTCTAA
29106467 TTTTTAATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
56 20 0.28
57 26 0.36
58 3 0.04
59 14 0.19
60 7 0.10
61 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (58 bp):
ATATTTCTATACATTTTATATAATTTTCTAACGAATTTATAAAATTTTACAATTTTTT
Found at i:29106442 original size:11 final size:10
Alignment explanation
Indices: 29106428--29106478 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
29106418 AATTTTACAA
29106428 TTTTTTATAT
1 TTTTTTATAT
*
29106438 TTTTTTACA-
1 TTTTTTATAT
*
29106447 ATTTTTATAT
1 TTTTTTATAT
* *
29106457 TTTTTTCTAA
1 TTTTTTATAT
*
29106467 TTTTTAATAT
1 TTTTTTATAT
29106477 TT
1 TT
29106479 GAAATTTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:29106469 original size:39 final size:40
Alignment explanation
Indices: 29106381--29106478 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 40
29106371 TTTTTTTATA
* * *
29106381 TTTCTATATATTTTATAATTTTTTACGATTTTTATAAAATT
1 TTTCTA-ATTTTTTATATTTTTTTACAATTTTTATAAAATT
* **
29106422 TTAC-AATTTTTTATATTTTTTTACAATTTTTAT-ATTTT
1 TTTCTAATTTTTTATATTTTTTTACAATTTTTATAAAATT
*
29106460 TTTCTAATTTTTAATATTT
1 TTTCTAATTTTTTATATTT
29106479 GAAATTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
38 6 0.12
39 38 0.79
40 1 0.02
41 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (40 bp):
TTTCTAATTTTTTATATTTTTTTACAATTTTTATAAAATT
Found at i:29106546 original size:20 final size:20
Alignment explanation
Indices: 29106521--29106559 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29106511 AATTTTATTG
*
29106521 ATTCTAATTTTTTATAAAAA
1 ATTCTAATTTTTAATAAAAA
29106541 ATTCTAATTTTTAATAAAA
1 ATTCTAATTTTTAATAAAA
29106560 CAAGGGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTCTAATTTTTAATAAAAA
Found at i:29106732 original size:88 final size:87
Alignment explanation
Indices: 29106562--29106763 Score: 266
Period size: 88 Copynumber: 2.3 Consensus size: 87
29106552 TAATAAAACA
* *
29106562 AGGG-CTTAATTGCTTTTTTTGTAAAAAGTTTGAAGGTCTTGTTGATGCATTTTGAAAGTTCAAG
1 AGGGACTTAATTGCTTTTTTT-T-AAAAGTTTGAAGGCCTTGTTGATGCATTTTGAAAATTCAAG
29106626 TAACCAATGGAGTACAAAAAAAAG
64 TAACCAATGGAGTACAAAAAAAAG
* * *
29106650 TAGGGGA-TTAATTGCTTTTTTTTAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAATTCAAG
1 -A-GGGACTTAATTGCTTTTTTTTAAAAGTTTGAAGGCCTTGTTGATGCATTTTGAAAATTCAAG
* * *
29106714 T-GCTCAATTGAGTGCAAAAAAAAG
64 TAAC-CAATGGAGTACAAAAAAAAG
29106738 AGGGACTTAATTGCTTTTTTTTAAAA
1 AGGGACTTAATTGCTTTTTTTTAAAA
29106764 AAAATTGAGG
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
86 4 0.04
87 21 0.21
88 55 0.55
89 2 0.02
90 18 0.18
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (87 bp):
AGGGACTTAATTGCTTTTTTTTAAAAGTTTGAAGGCCTTGTTGATGCATTTTGAAAATTCAAGTA
ACCAATGGAGTACAAAAAAAAG
Found at i:29108113 original size:13 final size:13
Alignment explanation
Indices: 29108095--29108121 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29108085 AAAATAATAT
29108095 AAATGTTTTATAA
1 AAATGTTTTATAA
29108108 AAATGTTTTATAA
1 AAATGTTTTATAA
29108121 A
1 A
29108122 TTGTCTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AAATGTTTTATAA
Found at i:29111355 original size:22 final size:22
Alignment explanation
Indices: 29111299--29111342 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29111289 CTTTTGTTCG
** *
29111299 ATTAAATAAAATTTTATTTTTA
1 ATTAAATTCAATTTTAATTTTA
29111321 ATTAAATTCAATTTTAATTTTA
1 ATTAAATTCAATTTTAATTTTA
29111343 TATAATTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAATTCAATTTTAATTTTA
Found at i:29114602 original size:23 final size:22
Alignment explanation
Indices: 29114543--29114602 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
29114533 TGGATCTAAC
29114543 CTAAAAGAAGAAATACAAAAAA
1 CTAAAAGAAGAAATACAAAAAA
* ** * *
29114565 TTAGAATTAAAAAATACGAAAACA
1 CTA-AAAGAAGAAATAC-AAAAAA
29114589 CTAAAAGAAGAAAT
1 CTAAAAGAAGAAAT
29114603 TTAATAGCTA
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
22 2 0.07
23 18 0.67
24 7 0.26
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (22 bp):
CTAAAAGAAGAAATACAAAAAA
Found at i:29121299 original size:3 final size:3
Alignment explanation
Indices: 29121291--29121321 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29121281 TTTTTAGATT
29121291 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29121322 TTAACATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29122416 original size:13 final size:13
Alignment explanation
Indices: 29122398--29122426 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29122388 CTAAAGTAAC
29122398 AATTAAACCATTT
1 AATTAAACCATTT
29122411 AATTAAACCATTT
1 AATTAAACCATTT
29122424 AAT
1 AAT
29122427 AAATGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAAACCATTT
Found at i:29124588 original size:19 final size:19
Alignment explanation
Indices: 29124561--29124600 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29124551 ACAGCCTAGC
*
29124561 CACACGGGCGTGTGCCACA
1 CACACGGGCATGTGCCACA
* *
29124580 CACATGGGCATGTGTCACA
1 CACACGGGCATGTGCCACA
29124599 CA
1 CA
29124601 AGGGCAACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (19 bp):
CACACGGGCATGTGCCACA
Found at i:29126590 original size:33 final size:33
Alignment explanation
Indices: 29126553--29126663 Score: 179
Period size: 33 Copynumber: 3.4 Consensus size: 33
29126543 GCCAATCCAT
29126553 CCATCACACCAATGCTCATAAGAGCTAAACCAA
1 CCATCACACCAATGCTCATAAGAGCTAAACCAA
*
29126586 CCATCACACCAATGCTTATAAGAG-TCAAACCAA
1 CCATCACACCAATGCTCATAAGAGCT-AAACCAA
*
29126619 CCATCACACCAATGCTCATAAGAGCTAATCCAA
1 CCATCACACCAATGCTCATAAGAGCTAAACCAA
*
29126652 CCAGCACACCAA
1 CCATCACACCAA
29126664 ATAAAGAGTA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
32 1 0.01
33 70 0.97
34 1 0.01
ACGTcount: A:0.41, C:0.34, G:0.09, T:0.15
Consensus pattern (33 bp):
CCATCACACCAATGCTCATAAGAGCTAAACCAA
Found at i:29132660 original size:114 final size:114
Alignment explanation
Indices: 29132460--29132692 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
29132450 CTTTCTGTAC
** * * *
29132460 TATTTTCTACGGTGTAATTGAGATCGAAGTAGTTCTAGCAGTTACTTCAATAACAATTTCAACTT
1 TATTTTCTACGGTGTAATCAAGATCGAAGCAGTTCCAACAGTTACTTCAATAACAATTTCAACTT
29132525 TTCTCACCGTGACGGTAAACCTCGCAATCCTTTAGGAAATACATCAGTG
66 TTCTCACCGTGACGGTAAACCTCGCAATCCTTTAGGAAATACATCAGTG
*
29132574 TATTTTCTACGGTGTAATCAAGATCGAAGCAGTTCCAACTGTTACTTCAATAACAATTTCAACTT
1 TATTTTCTACGGTGTAATCAAGATCGAAGCAGTTCCAACAGTTACTTCAATAACAATTTCAACTT
* *
29132639 TTCTCACCTTGACGGTAAACCTCGCAATCCTTTAGGAAATACATTAGTG
66 TTCTCACCGTGACGGTAAACCTCGCAATCCTTTAGGAAATACATCAGTG
29132688 TATTT
1 TATTT
29132693 AGAACTGTCA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TATTTTCTACGGTGTAATCAAGATCGAAGCAGTTCCAACAGTTACTTCAATAACAATTTCAACTT
TTCTCACCGTGACGGTAAACCTCGCAATCCTTTAGGAAATACATCAGTG
Found at i:29133670 original size:24 final size:27
Alignment explanation
Indices: 29133632--29133680 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
29133622 TTATTCCTCA
29133632 ATTACAAATTTTACCA-ATTAGGGTCG
1 ATTACAAATTTTACCAGATTAGGGTCG
*
29133658 ATTA-AAA-TTTACCAGATTTGGGT
1 ATTACAAATTTTACCAGATTAGGGT
29133681 TTTGAGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (27 bp):
ATTACAAATTTTACCAGATTAGGGTCG
Found at i:29137834 original size:22 final size:22
Alignment explanation
Indices: 29137804--29137859 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
29137794 CTGTGGTGTA
29137804 GTGGAAAGGTGGCGACACAGGT
1 GTGGAAAGGTGGCGACACAGGT
*
29137826 GTGGCAAGGAGGTGGCGTCACAGGT
1 GTGG-AA--AGGTGGCGACACAGGT
*
29137851 GTGGTAAGG
1 GTGGAAAGG
29137860 AGGTCAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 1 0.03
25 19 0.66
ACGTcount: A:0.23, C:0.12, G:0.48, T:0.16
Consensus pattern (22 bp):
GTGGAAAGGTGGCGACACAGGT
Done.