Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 103 of 145
Found at i:34774480 original size:13 final size:13
Alignment explanation
Indices: 34774464--34774488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34774454 TTTTCTTGTT
34774464 TTATTATTATTTA
1 TTATTATTATTTA
34774477 TTATTATTATTT
1 TTATTATTATTT
34774489 TCACTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:34774723 original size:14 final size:13
Alignment explanation
Indices: 34774696--34774731 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
34774686 TTATATTATT
*
34774696 AAAAAATTATATA
1 AAAAAATAATATA
34774709 AAAATAATAATATA
1 AAAA-AATAATATA
34774723 AAAAAATAA
1 AAAAAATAA
34774732 AATGGACGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAAAATAATATA
Found at i:34775397 original size:9 final size:9
Alignment explanation
Indices: 34775380--34775416 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34775370 TGAGTTTTCG
34775380 AATTCGAAT
1 AATTCGAAT
*
34775389 AACTCGAAT
1 AATTCGAAT
34775398 AATTCGAAT
1 AATTCGAAT
34775407 AATTCGAAT
1 AATTCGAAT
34775416 A
1 A
34775417 CAAACTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34776213 original size:5 final size:5
Alignment explanation
Indices: 34776203--34776227 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34776193 CTCGAAAATT
34776203 TTCGA TTCGA TTCGA TTCGA TTCGA
1 TTCGA TTCGA TTCGA TTCGA TTCGA
34776228 CCGAATGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TTCGA
Found at i:34779154 original size:68 final size:68
Alignment explanation
Indices: 34779045--34779211 Score: 226
Period size: 68 Copynumber: 2.5 Consensus size: 68
34779035 GCGAACTTCT
* * * * *
34779045 TATGTTGCCATAGCCTAGCTATGGTCTTACATAGTATTAACCGATGTTTACTGTCCTACTAGACT
1 TATGTTACCATAGCCTAGTTATGGTCTTACACAATATTAACCGATGTTTACTATCCTACTAGACT
34779110 CCA
66 CCA
* * * * * *
34779113 TATGTTATCATAGCCTAGTTATGGTATTACACAATATTAACCTATGTTTACTATCTTAGTGGACT
1 TATGTTACCATAGCCTAGTTATGGTCTTACACAATATTAACCGATGTTTACTATCCTACTAGACT
34779178 CCA
66 CCA
*
34779181 TATGTTGCCATAGCCTAGTTATGGTCTTACA
1 TATGTTACCATAGCCTAGTTATGGTCTTACA
34779212 TATTAGACCT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 85 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (68 bp):
TATGTTACCATAGCCTAGTTATGGTCTTACACAATATTAACCGATGTTTACTATCCTACTAGACT
CCA
Found at i:34782178 original size:89 final size:89
Alignment explanation
Indices: 34782072--34782242 Score: 243
Period size: 89 Copynumber: 1.9 Consensus size: 89
34782062 GAATTGTAGT
* *
34782072 TTCAATCTACTCCACTGCAACTTTAGGGAAAGAAAATTTGTAGCTTCAATATGCTCTACTGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAAAGAAAATTTGTAGCTTCAATATGCTCCACTGTAAC
34782137 TTCAGAGAAGTAAGATTCGCTATC
66 TTCAGAGAAGTAAGATTCGCTATC
* * * * * *
34782161 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCCACTGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAAAGAAAATTTGTAGCTTCAATATGCTCCACTGTAAC
* * *
34782226 TTCGGGGAGGTAAGATT
66 TTCAGAGAAGTAAGATT
34782243 TGTGACTTGA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (89 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAAAGAAAATTTGTAGCTTCAATATGCTCCACTGTAAC
TTCAGAGAAGTAAGATTCGCTATC
Found at i:34782315 original size:90 final size:93
Alignment explanation
Indices: 34782205--34782435 Score: 261
Period size: 95 Copynumber: 2.5 Consensus size: 93
34782195 GATTTGTAGC
* * * * *
34782205 TTCAATCTGTTCCACTGTAACTTCGGGGAGGTAAGATTTGTGACTTGA-TTTAATCCGACCCACT
1 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTTGACTTCAATCCGACCCACT
*
34782269 GTAACTTCAAAGGTATAGGA-T-TTAGT
66 GCAACTTCAAAGGTATAGGATTGTTAGT
* * * ** * *
34782295 TTCAATCTACTCCACTGTAACTTCAAGGAGATAATATTTGCCACGATGACTTCAATCCGTCCCAC
1 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAAC-TTGACTTCAATCCGACCCAC
** *
34782360 TGCAACTTCAGGGGTATAGGATTTGTTATT
65 TGCAACTTCAAAGGTATAGGA-TTGTTAGT
* *
34782390 TTCAATATGCTCTACTGTAACTTCAGGGAGATAAGATTTGTAACTT
1 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
34782436 CAATCTATTC
Statistics
Matches: 113, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
90 36 0.32
91 3 0.03
92 31 0.27
94 2 0.02
95 41 0.36
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (93 bp):
TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTTGACTTCAATCCGACCCACT
GCAACTTCAAAGGTATAGGATTGTTAGT
Found at i:34783231 original size:44 final size:44
Alignment explanation
Indices: 34782041--34783241 Score: 660
Period size: 44 Copynumber: 26.6 Consensus size: 44
34782031 GTTCCAACTT
* * * *
34782041 ACTGCAACTTCAAGGG-TATAGGAATTGTAG-TTTCAATCTACTCC
1 ACTGCAACTTC-AGGGAGATAAGATTTGTAGCTTT-AATCTGCTCC
* * * * * * *
34782085 ACTGCAACTTTAGGGAAAGAAAATTTGTAGCTTCAATATGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * * *
34782129 ACTGTAACTTCAGAGA-AGTAAGATTCGCTATCTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGA-TAAGATTTG-TAGCTTTAATCTGCTCC
* *
34782174 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * * *
34782218 ACTGTAACTTCGGGGAGGTAAGATTTGTGACTTGATTTAATCCGAC-CC
1 ACTGCAACTTCAGGGAGATAAGATTTGT-A---GCTTTAATCTG-CTCC
* * * * *
34782266 ACTGTAACTTCAAAGG-TATAGGA-TT-TAG-TTTCAATCTACTCC
1 ACTGCAACTTC-AGGGAGATAAGATTTGTAGCTTT-AATCTGCTCC
* * * * * *
34782308 ACTGTAACTTCAAGGAGATAATATTTGCCACGATGACTTCAATCCG-TCCC
1 ACTGCAACTTCAGGGAGATAAGATTTG----TA-G-CTTTAATCTGCT-CC
* * * *
34782358 ACTGCAACTTCAGGG-GTATAGGATTTGTTA-TTTTCAATATGCTCT
1 ACTGCAACTTCAGGGAG-ATAAGATTTG-TAGCTTT-AATCTGCTCC
* * * **
34782403 ACTGTAACTTCAGGGAGATAAGATTTGTAACTTCAATCTATTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * * * * **
34782447 ACTGTAACTTTAGGGAAATAAGATTTATAGCTTGTAGCTTTAATCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTT-TA-ATCTGCTCC
* * ** * * *
34782493 -CTTCCGACTTCAAAGAAATAAGACTCGCTACGGTAGATTTAATCTGAC-CC
1 AC-TGCAACTTCAGGGAGATAAGA-T---T--TGTAGCTTTAATCTG-CTCC
* * * * *
34782543 ACTACAACTTCAGAGG-TATAGGATTTGTCGCTTTAATATGCTCC
1 ACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * ** * *
34782587 ACTACAACTTCAAGGAGATAAGATTTACTATATTCACTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTT-GTAGCTTTAATCTGCTCC
* * * * * *
34782632 ACTACAACTTTAGGGAGATAAGATTTGCTATCTTCACTCTGTTCC
1 ACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCC
* *
34782677 ACTACAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* *** **
34782721 ATTGCAACTTCAGGGAGATAAGATTTACGGCTTTAATCTATTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * * * *
34782765 ACTACAACTTCATGGAGATAAGATTTATGGTTTTAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * * *
34782809 ACTGCAACTTTAGAGAGATAAGATTTGATATCTTCAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCC
* * * *
34782854 ACTGCAACTTCAGGGAGATAAGATTTTCTATCTTCAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGA-TTTGTAGCTTTAATCTGCTCC
* * * * *
34782899 ACTGCAACTTTAAGGAGATAAGATTTGTGGCTTTAATCTTCTTC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * *
34782943 ACTGCAACTTTAGGGAGATAAAATTCATGT--TTTTAATCTGCTTC
1 ACTGCAACTTCAGGGAGATAAGATT--TGTAGCTTTAATCTGCTCC
* * *
34782987 A-TCACAACTTCAGGGAGATAAGATTTGCCACGATGACTTCAATCTG-TCC
1 ACT-GCAACTTCAGGGAGATAAGATTTG----TA-G-CTTTAATCTGCTCC
* * * * *
34783036 TACTGCAACTTAAGAGG-TATAGGGTTTGCTA-TTTTCAATCTGCTCC
1 -ACTGCAACTTCAG-GGAGATAAGATTTG-TAGCTTT-AATCTGCTCC
* * * * *
34783082 ACTGTAACTTCAGGAAGATAAGATTTGTAACTTTAATCTACTCT
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* * * *
34783126 ACTGCAACTTCAGAGAGATAAGATTTGTTATCTTCAATCTGATCC
1 ACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCC
*
34783171 ACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
* *
34783215 ACTACAACTTCAGGGAGATAAAATTTG
1 ACTGCAACTTCAGGGAGATAAGATTTG
34783242 CCACCATAAC
Statistics
Matches: 897, Mismatches: 194, Indels: 132
0.73 0.16 0.11
Matches are distributed among these distances:
41 8 0.01
42 24 0.03
43 11 0.01
44 408 0.45
45 287 0.32
46 35 0.04
47 6 0.01
48 26 0.03
49 8 0.01
50 70 0.08
51 9 0.01
52 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCC
Found at i:34783241 original size:89 final size:89
Alignment explanation
Indices: 34782533--34783241 Score: 594
Period size: 89 Copynumber: 7.9 Consensus size: 89
34782523 CGGTAGATTT
* * * * *
34782533 AATCTGAC-CCACTACAACTTCAGAGG-TATAGGATTTGTCGCTTTAATATGCTCCACTACAACT
1 AATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACT
* ** *
34782596 TCAAGGAGATAAGATTTACTATATTC
64 TCAGGGAGATAAGATTTGTTATCTTC
* * * ** * * *
34782622 ACTCTGCTCCACTACAACTTTAGGGAGATAAGATTTGCTATCTTCACTCTGTTCCACTACAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGGCTTTAATCTGCTCCACTACAACTT
* * *
34782687 TAGGGAGATAAGATTTG-TAGCTTT
65 CAGGGAGATAAGATTTGTTATCTTC
* ** **
34782711 AATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTACGGCTTTAATCTATTCCACTACAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
* * ** *
34782776 ATGGAGATAAGATTTATGGT-TTT
66 AGGGAGATAAGATTTGTTATCTTC
* * * ** * * *
34782799 AATCTGCTCTACTGCAACTTTAGAGAGATAAGATTTGATATCTTCAATCTGCTCTACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGGCTTTAATCTGCTCCACTACAACTT
34782864 CAGGGAGATAAGATTT-TCTATCTTC
65 CAGGGAGATAAGATTTGT-TATCTTC
* * * * * * *
34782889 AATCTGCTCTACTGCAACTTTAAGGAGATAAGATTTGTGGCTTTAATCTTCTTCACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
*
34782954 AGGGAGATAAAATTCATGTT-T-TT-
66 AGGGAGATAAGATT--TGTTATCTTC
* * * *
34782977 AATCTGCTTCA-TCACAACTTCAGGGAGATAAGATTTGCCACGATGACTTCAATCTG-TCCTACT
1 AATCTGCTCCACT-GCAACTTCAGGGAGATAAGATTT-----G-TGGCTTTAATCTGCTCC-ACT
* * * * * * *
34783040 GCAACTTAAGAGG-TATAGGGTTTGCTATTTTC
58 ACAACTTCAG-GGAGATAAGATTTGTTATCTTC
* * ** * * *
34783072 AATCTGCTCCACTGTAACTTCAGGAAGATAAGATTTGTAACTTTAATCTACTCTACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
*
34783137 AGAGAGATAAGATTTGTTATCTTC
66 AGGGAGATAAGATTTGTTATCTTC
*
34783161 AATCTGATCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
*
34783226 AGGGAGATAAAATTTG
66 AGGGAGATAAGATTTG
34783242 CCACCATAAC
Statistics
Matches: 495, Mismatches: 100, Indels: 50
0.77 0.16 0.08
Matches are distributed among these distances:
87 1 0.00
88 104 0.21
89 242 0.49
90 76 0.15
91 2 0.00
92 4 0.01
93 4 0.01
94 29 0.06
95 32 0.06
96 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (89 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTC
AGGGAGATAAGATTTGTTATCTTC
Found at i:34791166 original size:19 final size:19
Alignment explanation
Indices: 34791144--34791194 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
34791134 GGGTCTTTTT
*
34791144 ATGAAATTTAATGCATATG-
1 ATGAAATGTAATGC-TATGA
34791163 ATGAAATGTAATGCTATGA
1 ATGAAATGTAATGCTATGA
34791182 ATGAAATG-AATGC
1 ATGAAATGTAATGC
34791195 AAAAAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (19 bp):
ATGAAATGTAATGCTATGA
Found at i:34793007 original size:9 final size:8
Alignment explanation
Indices: 34792972--34793018 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
34792962 TAAAATGATA
34792972 AATAATA-
1 AATAATAT
*
34792979 AATAATAG
1 AATAATAT
*
34792987 AATACTAT
1 AATAATAT
34792995 AATAATGAT
1 AATAAT-AT
34793004 AATAATATT
1 AATAATA-T
34793013 AATAAT
1 AATAAT
34793019 GTAAAATAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 15 0.44
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (8 bp):
AATAATAT
Found at i:34814162 original size:18 final size:18
Alignment explanation
Indices: 34814139--34814173 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34814129 TAAAAAAAAA
34814139 AAATTATAAACCTACAAG
1 AAATTATAAACCTACAAG
34814157 AAATTATAAACCTACAA
1 AAATTATAAACCTACAA
34814174 AGATCATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATTATAAACCTACAAG
Found at i:34830456 original size:26 final size:26
Alignment explanation
Indices: 34830410--34830460 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
34830400 TAGAAGTACA
*
34830410 TAATTTTAGTTGCTTATTCTACAAGT
1 TAATTTTAGTTGCTTAGTCTACAAGT
*
34830436 TAATTTTAGCTT-TTTAGTCTACAAG
1 TAATTTTAG-TTGCTTAGTCTACAAG
34830461 AATAAAGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (26 bp):
TAATTTTAGTTGCTTAGTCTACAAGT
Found at i:34832352 original size:2 final size:2
Alignment explanation
Indices: 34832345--34832380 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34832335 GCTTATCAAG
34832345 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34832381 AGGTATGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34835685 original size:102 final size:102
Alignment explanation
Indices: 34835509--34835698 Score: 254
Period size: 102 Copynumber: 1.9 Consensus size: 102
34835499 CTGGTTTCAC
* * * * * * * *
34835509 TATCATCTAATTTCTTTAAATTATTAAGCTAGAATTCTTTTCATTTTCAAAGAGATACAGAAACA
1 TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAACA
*
34835574 TAAATACGGCTAAATGGCAAGAACATGACCGCTAGTT
66 TAAATACGGCTAAATGACAAGAACATGACCGCTAGTT
* ****
34835611 TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAACGAGATAAAGATGTT
1 TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAACA
34835676 TAAATACGGCTAAATGACAAGAA
66 TAAATACGGCTAAATGACAAGAA
34835699 TGTTCATGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (102 bp):
TATCATCTAATTCCTTAAAATCATTAAGCTAAAAATCTTTCCATTGTCAAAGAGATAAAGAAACA
TAAATACGGCTAAATGACAAGAACATGACCGCTAGTT
Found at i:34837902 original size:14 final size:14
Alignment explanation
Indices: 34837879--34837917 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
34837869 TTTTTCAACA
34837879 TTTTACCTTTTCTT
1 TTTTACCTTTTCTT
* *
34837893 TTTTAACTTTACTT
1 TTTTACCTTTTCTT
34837907 TTTTACCTTTT
1 TTTTACCTTTT
34837918 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTACCTTTTCTT
Found at i:34841234 original size:4 final size:4
Alignment explanation
Indices: 34841220--34841254 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
34841210 AGGAAATATG
*
34841220 ATGA TTGA ATGA ATGA ATGA ATGA ATGA ATGA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATG
34841255 CAGACATCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (4 bp):
ATGA
Found at i:34842609 original size:16 final size:16
Alignment explanation
Indices: 34842584--34842652 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
34842574 TTGGTTCGCT
*
34842584 GTAATGGAATAGAGGC
1 GTAATGGAATAAAGGC
*
34842600 GTAATAGAATAAAGGC
1 GTAATGGAATAAAGGC
* **
34842616 TTAATGGAATAAAGAT
1 GTAATGGAATAAAGGC
* *
34842632 ATAATGGAATAGAGGC
1 GTAATGGAATAAAGGC
34842648 GTAAT
1 GTAAT
34842653 AGTATTCTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAAAGGC
Found at i:34842794 original size:20 final size:22
Alignment explanation
Indices: 34842769--34842828 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
34842759 TGTTTTGTTA
*
34842769 TAAAAT-TTTAATA-AGATTAT
1 TAAAATATATAATATAGATTAT
34842789 TAAAATAATATAATATAGATTAT
1 TAAAAT-ATATAATATAGATTAT
34842812 TAAAATAATATAATATA
1 TAAAAT-ATATAATATA
34842829 AATATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 6 0.17
22 6 0.17
23 24 0.67
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAAATATATAATATAGATTAT
Found at i:34842812 original size:23 final size:23
Alignment explanation
Indices: 34842777--34842828 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
34842767 TATAAAATTT
34842777 TAATA-AGATTATTAAAATAATA
1 TAATATAGATTATTAAAATAATA
34842799 TAATATAGATTATTAAAATAATA
1 TAATATAGATTATTAAAATAATA
34842822 TAATATA
1 TAATATA
34842829 AATATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TAATATAGATTATTAAAATAATA
Found at i:34846452 original size:18 final size:19
Alignment explanation
Indices: 34846431--34846466 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34846421 AGAAATCTAG
34846431 AGAAAAAAAATG-GAGAAA
1 AGAAAAAAAATGTGAGAAA
*
34846449 AGAAAAGAAATGTGAGAA
1 AGAAAAAAAATGTGAGAA
34846467 GAAAAGAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (19 bp):
AGAAAAAAAATGTGAGAAA
Found at i:34854590 original size:67 final size:67
Alignment explanation
Indices: 34854479--34854605 Score: 236
Period size: 67 Copynumber: 1.9 Consensus size: 67
34854469 AGGAACATCC
* *
34854479 AAATACATACCTAGATCCTTTACCTTTGTAAATCCAAGATTGTTACATAAATTAGTTGATAACAC
1 AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGATAACAC
34854544 CT
66 CT
34854546 AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGAT
1 AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGAT
34854606 TCTTCCTATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (67 bp):
AAATACATACCTAGATCCCTTACCTTTGTAAATCCAAGACTGTTACATAAATTAGTTGATAACAC
CT
Found at i:34855268 original size:14 final size:15
Alignment explanation
Indices: 34855242--34855271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34855232 AAACACGGTC
34855242 CATAAAAACCCATAT
1 CATAAAAACCCATAT
34855257 CATAAAAA-CCATAT
1 CATAAAAACCCATAT
34855271 C
1 C
34855272 CAAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAAAAACCCATAT
Found at i:34858385 original size:22 final size:22
Alignment explanation
Indices: 34858326--34858382 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 22
34858316 ATCTTCAAGT
34858326 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAGAAGATATG
34858345 ATATGCAATCTTAGAAGATATG
1 ATATGCAATCTTAGAAGATATG
* *
34858367 ATTTTGTAATCTTAGA
1 A-TATGCAATCTTAGA
34858383 GATTTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
22 8 0.25
23 12 0.38
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATGCAATCTTAGAAGATATG
Found at i:34860239 original size:14 final size:14
Alignment explanation
Indices: 34860220--34860259 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34860210 TTGATTGCCA
34860220 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
34860234 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
34860248 GGAAAATGTTTT
1 GTAAAATGTTTT
34860260 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:34860268 original size:20 final size:20
Alignment explanation
Indices: 34860243--34860282 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34860233 CGTAAAATGA
*
34860243 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
34860263 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
34860283 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:34860272 original size:34 final size:35
Alignment explanation
Indices: 34860228--34860294 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
34860218 CAGTAAAATG
*
34860228 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
34860262 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
34860295 CAGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:34862666 original size:6 final size:6
Alignment explanation
Indices: 34862657--34862705 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
34862647 TCAAGGATAA
* * *
34862657 GGGAAG GGGAAG GGGAAA GGGAAG GGGAAG GGGAAG GGAAAG GGAAAG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG
34862705 G
1 G
34862706 AAAATTTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:34862705 original size:18 final size:17
Alignment explanation
Indices: 34862655--34862708 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
34862645 TGTCAAGGAT
34862655 AAGGGAAGGGGAAGGGGA
1 AAGGGAAGGGGAA-GGGA
*
34862673 AAGGGAAGGGGAAGGGG
1 AAGGGAAGGGGAAGGGA
* *
34862690 AAGGGAAAGGGAAAGGA
1 AAGGGAAGGGGAAGGGA
34862707 AA
1 AA
34862709 ATTTTCCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (17 bp):
AAGGGAAGGGGAAGGGA
Found at i:34871590 original size:11 final size:11
Alignment explanation
Indices: 34871570--34871647 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
34871560 CAAAAATTAA
34871570 AAAAAGTATTTT
1 AAAAA-TATTTT
34871582 AAAAATATTTT
1 AAAAATATTTT
34871593 --AAA-A--TT
1 AAAAATATTTT
* **
34871599 AAAAAAATTAA
1 AAAAATATTTT
34871610 AAAAATATTTT
1 AAAAATATTTT
34871621 AAAAAGTATTTT
1 AAAAA-TATTTT
* *
34871633 AAAAAAAGTTT
1 AAAAATATTTT
34871644 AAAA
1 AAAA
34871648 TTTAAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
11 27 0.51
12 16 0.30
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:34871635 original size:51 final size:52
Alignment explanation
Indices: 34871550--34871677 Score: 177
Period size: 51 Copynumber: 2.4 Consensus size: 52
34871540 ATTTATTTTG
* ** * *
34871550 AAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAAA
1 AAAATTAAAA-AAATATTTTAAAAAGTATTTTAAAAAAAGTTTAAAATTTAAA
34871602 AAAATTAAAAAAATATTTTAAAAAGTATTTTAAAAAAAGTTTAAAATTTAAA
1 AAAATTAAAAAAATATTTTAAAAAGTATTTTAAAAAAAGTTTAAAATTTAAA
*
34871654 AAATTTAAAAAAAGTATTTTAAAA
1 AAAATTAAAAAAA-TATTTTAAAA
34871678 TTGAAAAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 31 0.46
52 27 0.40
53 10 0.15
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (52 bp):
AAAATTAAAAAAATATTTTAAAAAGTATTTTAAAAAAAGTTTAAAATTTAAA
Found at i:34873906 original size:630 final size:630
Alignment explanation
Indices: 34872698--34873943 Score: 1807
Period size: 630 Copynumber: 2.0 Consensus size: 630
34872688 ACTTTATTTA
* ** * *
34872698 TAATTTAGTCCTTTTCTATTTTAGTTAATTAATTAGGTTAATTAACCTTTAACTTATGTTTTGTT
1 TAATTTAGTCCTTTTCTATTTCAGTTAATTAATTACCTTAATTAACCTTTAAATTATGTTTTGTC
* * * *
34872763 GTAATATAGACATTAGTGAGTAGCTAGCTAGATTCCTTTCTTGCATGCTTGATTGAATAGAAAAC
66 GTAATATAGACATCAGTGAGTAGCTAGCTAGACTCCTTTCTTGCATGCTTAATTGAATACAAAAC
* * * * *
34872828 ATTAAATCGCTGACTCATTTGGGTTCAACCCTTTGGAATACTTCGTGTTCCATCGGATTATAAAT
131 ATTAAACCGCTAACTCATTTGGGTTCAACCCCTTGAAATACTTCGTGTTCCATCGAATTATAAAT
* * * * * *
34872893 ATTACAACTGACATTGTACGATTGCAGTTAAAACTGTTCTTTAAAATAGTTTTTTTTATAAAATC
196 ATTACAACTAAAACTGTACGATTGCAGTTAAAACTGCTCCTTAAAATAGTTTTTTTTATAAAAGC
* * ** * * *
34872958 AGTTACTTTTACGTGCATGCGATATAGCGGTCAACTGAGCAATAGAGCTCAATGTTATTTCCATG
261 AATCACTTTTACGTGCACACGAGATAGCGGTCAACTAAGCAATAGAGCTCAATGGTATTTCCATG
* * *
34873023 ATTCAAATTATTATAATACGAAATCCAAATCAATTGCATATAACTAATTTCAAATGCAAATATTA
326 ATTCAAATCATTATAATACAAAATCCAAATCAATTGCATATAACTAATTTCAAATG-----A-GA
* *
34873088 ACTAATTCACATATAAATTATGCAAATCTTCAAATCATACAACAATATACATATGTAAAAAATAC
385 ACTAATTCACATACAAATTATGCAAATCTTCAAATCATACAACAATATACAAATGTAAAAAATAC
*
34873153 ACTAGTTATGTCAATTGATTCAACTAAGCATATTGTCTTAATTAATAACTAAATGAACATACTAT
450 ACTAGTTATGTCAATTGATTCAACTAAGCATATTGTCTTAATTAACAACTAAATGAACATACTAT
*
34873218 ACCGATTTGATTTAAATTCACATTTCTTTCACTTTTATGCATTCAATAAAGTTTACATATCA-TT
515 ACCGATTTGATTTAAATTCACATTTCTTTCACTTTTATGCATTCAATAAAGTTTACATATAATTT
* * *
34873282 TCTGAACTGAAAACAATTCAAA-CATTGTCTTTAAATTAGCTTAATTAACCTT
580 TC-AAACCGAAAACAATT-AAACCATTATCTTTAAATTAGCTTAATTAACCTT
*
34873334 TAATTTAGTCCTTTTCTGTTTCAGTTAATTAATTACCTTAATTAACCTTTAAATTATGTTTTGTC
1 TAATTTAGTCCTTTTCTATTTCAGTTAATTAATTACCTTAATTAACCTTTAAATTATGTTTTGTC
* * *
34873399 GTAATATAGACGTCAGTGAGTAGCTAGCTAGACTCCTTTCTTGCATGTTTAATTGAATACAAATC
66 GTAATATAGACATCAGTGAGTAGCTAGCTAGACTCCTTTCTTGCATGCTTAATTGAATACAAAAC
* **
34873464 ATTAAACCGCTAACTCCTTTGGGTTTGACCCCTTGAAATACTTCGTGTTCCATCAGAATTATAAA
131 ATTAAACCGCTAACTCATTTGGGTTCAACCCCTTGAAATACTTCGTGTTCCATC-GAATTATAAA
* *
34873529 TATTACAACTAAAACTGTACGCTTGCAGTTAAAATTGCTCCTTAAAATAGTTTTTTTTATAAAAG
195 TATTACAACTAAAACTGTACGATTGCAGTTAAAACTGCTCCTTAAAATAGTTTTTTTTATAAAAG
** * ** ** * *
34873594 CAATCGGTTTTACGTGCACACGCGATAGCTTTCAGTTAAGTAATAGAGCTTAATGGTATTTCCAT
260 CAATCACTTTTACGTGCACACGAGATAGCGGTCAACTAAGCAATAGAGCTCAATGGTATTTCCAT
** *
34873659 GATTCAAATCATTATAATACAAAATCTGAATCAATTGTATATAACTAATTTCAAATG-GAACTAA
325 GATTCAAATCATTATAATACAAAATCCAAATCAATTGCATATAACTAATTTCAAATGAGAACTAA
*
34873723 TTCACATACAAATTATGCAAATCTTCAAATCATACAACAATATGCAAATGTAAAAAATACACTAG
390 TTCACATACAAATTATGCAAATCTTCAAATCATACAACAATATACAAATGTAAAAAATACACTAG
*
34873788 TTATG-CTAATTGATTCAACTAAGCATATTGTTTTAATTAACAACTAAATGAACATACTATACCG
455 TTATGTC-AATTGATTCAACTAAGCATATTGTCTTAATTAACAACTAAATGAACATACTATACCG
* * *
34873852 ATTTGATTTACATTCACATTTCTTTCACTTTTATGCATTTAATAATGTTTACATATAATTTTCAA
519 ATTTGATTTAAATTCACATTTCTTTCACTTTTATGCATTCAATAAAGTTTACATATAATTTTCAA
34873917 ACCGAAAACAATTAAACCATTATCTTT
584 ACCGAAAACAATTAAACCATTATCTTT
34873944 CCATATCGGT
Statistics
Matches: 543, Mismatches: 63, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
629 4 0.01
630 204 0.38
631 4 0.01
636 164 0.30
637 167 0.31
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (630 bp):
TAATTTAGTCCTTTTCTATTTCAGTTAATTAATTACCTTAATTAACCTTTAAATTATGTTTTGTC
GTAATATAGACATCAGTGAGTAGCTAGCTAGACTCCTTTCTTGCATGCTTAATTGAATACAAAAC
ATTAAACCGCTAACTCATTTGGGTTCAACCCCTTGAAATACTTCGTGTTCCATCGAATTATAAAT
ATTACAACTAAAACTGTACGATTGCAGTTAAAACTGCTCCTTAAAATAGTTTTTTTTATAAAAGC
AATCACTTTTACGTGCACACGAGATAGCGGTCAACTAAGCAATAGAGCTCAATGGTATTTCCATG
ATTCAAATCATTATAATACAAAATCCAAATCAATTGCATATAACTAATTTCAAATGAGAACTAAT
TCACATACAAATTATGCAAATCTTCAAATCATACAACAATATACAAATGTAAAAAATACACTAGT
TATGTCAATTGATTCAACTAAGCATATTGTCTTAATTAACAACTAAATGAACATACTATACCGAT
TTGATTTAAATTCACATTTCTTTCACTTTTATGCATTCAATAAAGTTTACATATAATTTTCAAAC
CGAAAACAATTAAACCATTATCTTTAAATTAGCTTAATTAACCTT
Found at i:34877570 original size:4 final size:4
Alignment explanation
Indices: 34877556--34877602 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
34877546 ATCTTTTCAT
* *
34877556 GTTA ATTA GTTA GTTA GTTA GTTA GTTA CTTA GTTA GTTA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT
34877603 GATAAGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (4 bp):
GTTA
Found at i:34881911 original size:20 final size:21
Alignment explanation
Indices: 34881887--34881942 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
34881877 TTAAAATTTA
34881887 AAAAATTAAAAAAATATTTTT
1 AAAAATTAAAAAAATATTTTT
34881908 AAAAAATTAAAAAAATATTTTT
1 -AAAAATTAAAAAAATATTTTT
*
34881930 AAAAGTATAAAAA
1 AAAAAT-TAAAAA
34881943 TTAGTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAATTAAAAAAATATTTTT
Found at i:34881942 original size:22 final size:22
Alignment explanation
Indices: 34881883--34881933 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
34881873 TTTTTTAAAA
34881883 TTTAAAAAATTAAAAAAATATT
1 TTTAAAAAATTAAAAAAATATT
34881905 TTTAAAAAATTAAAAAAATATT
1 TTTAAAAAATTAAAAAAATATT
34881927 TTTAAAA
1 TTTAAAA
34881934 GTATAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAAAATTAAAAAAATATT
Found at i:34886991 original size:59 final size:58
Alignment explanation
Indices: 34886883--34887008 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 58
34886873 AGGCTTGAGT
* * * *
34886883 TTTTTTTATCAAAGTTAAGTCTTGAACTTGTCAATTGTTCCCACATTGAGATCTAAAAC
1 TTTTTTTATCAAAGTTAAGTCCTGAACTTGACAAATGTTCCCACATTGAG-CCTAAAAC
* ** **
34886942 TTTTTTTATCCAAGTTAAGTCCTGAACTTGACAAATGTTCCCATGTTGAGCCTTCAAC
1 TTTTTTTATCAAAGTTAAGTCCTGAACTTGACAAATGTTCCCACATTGAGCCTAAAAC
34887000 TTTTTTTAT
1 TTTTTTTAT
34887009 TATTATCTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
58 14 0.24
59 44 0.76
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (58 bp):
TTTTTTTATCAAAGTTAAGTCCTGAACTTGACAAATGTTCCCACATTGAGCCTAAAAC
Found at i:34898148 original size:18 final size:18
Alignment explanation
Indices: 34898125--34898162 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34898115 TCCAAGACCG
34898125 GCGGTTTGCGAGACTTAA
1 GCGGTTTGCGAGACTTAA
*
34898143 GCGGTTTGTGAGACTTAA
1 GCGGTTTGCGAGACTTAA
34898161 GC
1 GC
34898163 TCTAGCCCTG
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:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (18 bp):
GCGGTTTGCGAGACTTAA
Found at i:34907525 original size:23 final size:23
Alignment explanation
Indices: 34907483--34907541 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
34907473 AGTTCTTTAT
*
34907483 GAGCTTCCTGTTATATGACTCTCTA
1 GAGCTTCCTG--ATATGACTCGCTA
*
34907508 GAGCTTCCTGATATGACTCGCTT
1 GAGCTTCCTGATATGACTCGCTA
*
34907531 GAACTTCCTGA
1 GAGCTTCCTGA
34907542 CATATGGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (23 bp):
GAGCTTCCTGATATGACTCGCTA
Found at i:34907622 original size:26 final size:26
Alignment explanation
Indices: 34907593--34907643 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
34907583 GCTTCCCGTT
* * *
34907593 TAAAGGATCTTTGTGAGCTTCCTGAG
1 TAAAAGATCTTTATGAACTTCCTGAG
*
34907619 TAAAAGTTCTTTATGAACTTCCTGA
1 TAAAAGATCTTTATGAACTTCCTGA
34907644 TTATGGCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (26 bp):
TAAAAGATCTTTATGAACTTCCTGAG
Found at i:34907755 original size:26 final size:26
Alignment explanation
Indices: 34907715--34907774 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
34907705 AAGCTTCTCG
* *
34907715 ATAT-GCTTTTTGTGAGCTTCTTGATT
1 ATATGGCTCTTTGTGAGCTTCCTG-TT
*
34907741 A-ATGGCTCTTTGTGAGTTTCCTGTT
1 ATATGGCTCTTTGTGAGCTTCCTGTT
34907766 ATATGGCTC
1 ATATGGCTC
34907775 GAGAGAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (26 bp):
ATATGGCTCTTTGTGAGCTTCCTGTT
Found at i:34911042 original size:51 final size:51
Alignment explanation
Indices: 34910983--34911086 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
34910973 TCCAAAAAAG
34910983 TATGTAAACTCACCTACCAATGGATGTTGAATCTACCAAAAATAATATTTT
1 TATGTAAACTCACCTACCAATGGATGTTGAATCTACCAAAAATAATATTTT
34911034 TATGTAAACTCACCTACCAATGGATGTTGAATCTACCAAAAATAATATTTT
1 TATGTAAACTCACCTACCAATGGATGTTGAATCTACCAAAAATAATATTTT
34911085 TA
1 TA
34911087 CTCCTAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (51 bp):
TATGTAAACTCACCTACCAATGGATGTTGAATCTACCAAAAATAATATTTT
Found at i:34911866 original size:9 final size:9
Alignment explanation
Indices: 34911849--34911882 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
34911839 TATAGTTTGA
*
34911849 TATTTGAAT
1 TATTCGAAT
34911858 TATTCGAAT
1 TATTCGAAT
*
34911867 TATTCGAGT
1 TATTCGAAT
34911876 TATTCGA
1 TATTCGA
34911883 TTTCGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:34911954 original size:9 final size:9
Alignment explanation
Indices: 34911937--34911967 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34911927 TCGAGTTGAT
34911937 TCGAATAAC
1 TCGAATAAC
*
34911946 TCGATTAAC
1 TCGAATAAC
34911955 TCGAATAAC
1 TCGAATAAC
34911964 TCGA
1 TCGA
34911968 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:34912048 original size:16 final size:16
Alignment explanation
Indices: 34912027--34912061 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34912017 TCACCCCTAC
*
34912027 GCCAAACAGCTGTCGT
1 GCCAAACAGCTGTCAT
*
34912043 GCCAAACAGTTGTCAT
1 GCCAAACAGCTGTCAT
34912059 GCC
1 GCC
34912062 CACGATGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (16 bp):
GCCAAACAGCTGTCAT
Found at i:34913170 original size:21 final size:21
Alignment explanation
Indices: 34913146--34913189 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
34913136 ATCGGATTTT
34913146 AAAGAACCCACATCACCTCCG
1 AAAGAACCCACATCACCTCCG
34913167 AAAGAACCCACATCACCTCCG
1 AAAGAACCCACATCACCTCCG
34913188 AA
1 AA
34913190 CTCTATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.41, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAGAACCCACATCACCTCCG
Found at i:34917400 original size:26 final size:27
Alignment explanation
Indices: 34917370--34917420 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
34917360 GTGAAGAAAC
34917370 AAACTCAG-AAGC-AAAAACAGAAAATG
1 AAACT-AGCAAGCGAAAAACAGAAAATG
*
34917396 AAACTAGCAAGCGAATAACAGAAAA
1 AAACTAGCAAGCGAAAAACAGAAAA
34917421 GAGAGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.08
Consensus pattern (27 bp):
AAACTAGCAAGCGAAAAACAGAAAATG
Found at i:34920706 original size:26 final size:28
Alignment explanation
Indices: 34920677--34920742 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
34920667 CTTTTATTTG
* *
34920677 TTTTGTTTTAATT-ATAA-TAATATATA
1 TTTTGTTTTAATTAATAAGCAATAAATA
*
34920703 TTTT-TACTTAATTAATAAGCAATAAATA
1 TTTTGT-TTTAATTAATAAGCAATAAATA
34920731 TTTTGTTATTAA
1 TTTTGTT-TTAA
34920743 ATACATATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 1 0.03
26 10 0.32
27 4 0.13
28 11 0.35
29 5 0.16
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTTGTTTTAATTAATAAGCAATAAATA
Found at i:34920750 original size:19 final size:20
Alignment explanation
Indices: 34920723--34920761 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34920713 ATTAATAAGC
*
34920723 AATAAATAT-TTTGTTATTA
1 AATAAATATGTTTATTATTA
*
34920742 AATACATATGTTTATTATTA
1 AATAAATATGTTTATTATTA
34920762 TTCCACATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
AATAAATATGTTTATTATTA
Found at i:34923631 original size:19 final size:18
Alignment explanation
Indices: 34923587--34923632 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
34923577 GAGTTAAACG
* * *
34923587 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAATC
34923605 AATCGAATTATTCGAATC
1 AATCGAATTATTCGAATC
34923623 AACTCGAATT
1 AA-TCGAATT
34923633 TTTTTTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCGAATC
Found at i:34923689 original size:9 final size:9
Alignment explanation
Indices: 34923672--34923708 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34923662 TGAGTTTTCG
34923672 AATTCGAAT
1 AATTCGAAT
*
34923681 AACTCGAAT
1 AATTCGAAT
34923690 AATTCGAAT
1 AATTCGAAT
34923699 AATTCGAAT
1 AATTCGAAT
34923708 A
1 A
34923709 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34924854 original size:23 final size:24
Alignment explanation
Indices: 34924828--34924875 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
34924818 AGATTGAAAG
*
34924828 CCAAA-ACGTGCTAGGTTAGCAGA
1 CCAAAGACGTGCTAGGGTAGCAGA
*
34924851 CCAAAGACGTGCTAGGGTAGTAGA
1 CCAAAGACGTGCTAGGGTAGCAGA
34924875 C
1 C
34924876 TTTTAGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (24 bp):
CCAAAGACGTGCTAGGGTAGCAGA
Found at i:34927047 original size:22 final size:21
Alignment explanation
Indices: 34927009--34927068 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
34926999 TAATATTATA
*
34927009 TTTATATTTTAAGTTTATTTC
1 TTTATATTTTAAATTTATTTC
34927030 TTTATATTTTAAAATTTATTTC
1 TTTATATTTT-AAATTTATTTC
34927052 TTT-TAGTATTTAAATTT
1 TTTATA-T-TTTAAATTT
34927069 CATGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
21 12 0.34
22 20 0.57
23 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATATTTTAAATTTATTTC
Found at i:34928248 original size:29 final size:29
Alignment explanation
Indices: 34928215--34928273 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
34928205 TTTGATCTCT
*
34928215 ATATTTTTAAAATATTTTTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
*
34928244 ATATTTTTATAATATTATTAATTAGTTCA
1 ATATTTTTAAAATATTATTAATTAGTTCA
34928273 A
1 A
34928274 ATGGTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATTTTTAAAATATTATTAATTAGTTCA
Found at i:34939766 original size:18 final size:18
Alignment explanation
Indices: 34939740--34939782 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34939730 GACTGGGAAA
* *
34939740 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
34939758 AGGATACATATCAGGGCT
1 AGGATACATATAAGGGCT
34939776 AGGATAC
1 AGGATAC
34939783 GTATTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:34941627 original size:30 final size:30
Alignment explanation
Indices: 34941593--34941657 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
34941583 ATTAATTAAA
34941593 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
* * *
34941623 GAGAGCTTTGATAAATTTAGGGGGAAATTT
1 GAGAGCTTTGAAAAATTTAAGGAGAAATTT
34941653 GAGAG
1 GAGAG
34941658 TTTTTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAAAAATTTAAGGAGAAATTT
Found at i:34945355 original size:22 final size:23
Alignment explanation
Indices: 34945312--34945356 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
34945302 TTTCAATAAA
*
34945312 TAAAAAAATAAAATTATTAATAT
1 TAAAAAAATAAAATTATAAATAT
* *
34945335 TAAAACAATATAA-TATAAATAT
1 TAAAAAAATAAAATTATAAATAT
34945357 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAAATAAAATTATAAATAT
Found at i:34946317 original size:8 final size:8
Alignment explanation
Indices: 34946300--34946330 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
34946290 CCTTTTACTA
*
34946300 TATATTTG
1 TATATATG
34946308 TATATATG
1 TATATATG
34946316 TATATATG
1 TATATATG
34946324 TATATAT
1 TATATAT
34946331 AGCAAACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATATATG
Found at i:34951335 original size:41 final size:41
Alignment explanation
Indices: 34951283--34951364 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
34951273 ATATTTTATT
* * *
34951283 TTATGTTTTAGTAGTTTATTAGAATAAGTGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
34951324 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
34951365 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATATTCC
Found at i:34959803 original size:3 final size:3
Alignment explanation
Indices: 34959795--34959866 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
34959785 GGACTCGTAT
* * *
34959795 TCA TCA TCA TCA TCA TCG T-A ACAA TAA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA
* *
34959840 TCA TCA TCA TAA TCA CCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
34959867 AAAGAAGTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
3 56 0.98
4 1 0.02
ACGTcount: A:0.38, C:0.31, G:0.01, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:34961049 original size:10 final size:9
Alignment explanation
Indices: 34961031--34961074 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
34961021 ACTATTTTTT
34961031 AAAAT-TTA
1 AAAATATTA
34961039 AAAATCATTA
1 AAAAT-ATTA
*
34961049 AAATTATTA
1 AAAATATTA
*
34961058 AAAATAATA
1 AAAATATTA
34961067 AAAATATT
1 AAAATATT
34961075 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 5 0.17
9 18 0.60
10 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAATATTA
Found at i:34969302 original size:12 final size:12
Alignment explanation
Indices: 34969285--34969309 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34969275 GCTCATACTC
34969285 TCAAATCTTTTA
1 TCAAATCTTTTA
34969297 TCAAATCTTTTA
1 TCAAATCTTTTA
34969309 T
1 T
34969310 TGGTTCAGAA
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TCAAATCTTTTA
Found at i:34970049 original size:9 final size:9
Alignment explanation
Indices: 34970032--34970077 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
34970022 TGAGTTTTCG
34970032 AATTCGAAT
1 AATTCGAAT
*
34970041 AACTCGAAT
1 AATTCGAAT
34970050 AATTCGAAT
1 AATTCGAAT
34970059 AATTCGAAT
1 AATTCGAAT
34970068 AATTCGAAT
1 AATTCGAAT
34970077 A
1 A
34970078 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34984431 original size:16 final size:16
Alignment explanation
Indices: 34984410--34984440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34984400 CAAAATTCTT
34984410 GGACAATCTTCTCATG
1 GGACAATCTTCTCATG
*
34984426 GGACAATCTTTTCAT
1 GGACAATCTTCTCAT
34984441 TCCATATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (16 bp):
GGACAATCTTCTCATG
Found at i:34985074 original size:31 final size:31
Alignment explanation
Indices: 34985036--34985099 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
34985026 GCCAAACAAT
34985036 TTAGTGTAATTACTACTACCATACGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
* *
34985067 TTAGTGTAATTACTACTAGCATATGCAAATA
1 TTAGTGTAATTACTACTACCATACGCAAATA
34985098 TT
1 TT
34985100 GCTCTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (31 bp):
TTAGTGTAATTACTACTACCATACGCAAATA
Found at i:34993103 original size:9 final size:9
Alignment explanation
Indices: 34993091--34993140 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
34993081 AAAAACAATA
34993091 AAAAATTAT
1 AAAAATTAT
34993100 AAAAATTAT
1 AAAAATTAT
34993109 AAAAA-TAT
1 AAAAATTAT
*
34993117 TAAAATTGAT
1 AAAAATT-AT
* *
34993127 TAAATTTAT
1 AAAAATTAT
34993136 AAAAA
1 AAAAA
34993141 AATATAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 7 0.20
9 20 0.57
10 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:34993103 original size:19 final size:20
Alignment explanation
Indices: 34993081--34993118 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
34993071 AAAATCCTTA
34993081 AAAAACAATAAAAA-ATTAT
1 AAAAACAATAAAAATATTAT
**
34993100 AAAAATTATAAAAATATTA
1 AAAAACAATAAAAATATTA
34993119 AAATTGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAACAATAAAAATATTAT
Found at i:34993104 original size:11 final size:10
Alignment explanation
Indices: 34992988--34993118 Score: 58
Period size: 10 Copynumber: 13.1 Consensus size: 10
34992978 ATATTTTCTC
*
34992988 ATAAAAATTT
1 ATAAAAAATT
34992998 ATAAAAAA-T
1 ATAAAAAATT
*
34993007 AAAATAAAATT
1 ATAA-AAAATT
34993018 ATAAAAAA-T
1 ATAAAAAATT
* *
34993027 ATTAAAATTGAT
1 ATAAAAAAT--T
*
34993039 ATAAAAAAAT
1 ATAAAAAATT
****
34993049 ATTTCGAATT
1 ATAAAAAATT
34993059 A-AAAAAATT
1 ATAAAAAATT
*
34993068 AT-TAAAATCCT
1 ATAAAAAAT--T
**
34993079 -TAAAAAACA
1 ATAAAAAATT
34993088 ATAAAAAATT
1 ATAAAAAATT
34993098 AT-AAAAATT
1 ATAAAAAATT
34993107 ATAAAAATATT
1 ATAAAAA-ATT
34993118 A
1 A
34993119 AAATTGATTA
Statistics
Matches: 86, Mismatches: 23, Indels: 23
0.65 0.17 0.17
Matches are distributed among these distances:
9 30 0.35
10 36 0.42
11 13 0.15
12 7 0.08
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:34993567 original size:9 final size:9
Alignment explanation
Indices: 34993555--34993744 Score: 71
Period size: 10 Copynumber: 20.0 Consensus size: 9
34993545 TTTTATGATT
34993555 TTTTTATAA
1 TTTTTATAA
34993564 TTTTTATAA
1 TTTTTATAA
**
34993573 GTTCATATCAA
1 -TTTTTAT-AA
* *
34993584 TTTTAATAC
1 TTTTTATAA
* *
34993593 TATTTATGA
1 TTTTTATAA
*
34993602 TTTTAATAGAA
1 TTTT--TATAA
* *
34993613 TTTTAATACG
1 TTTTTATA-A
34993623 TTTTTATAAA
1 TTTTTAT-AA
*
34993633 TTTTTAAATA
1 TTTTTATA-A
*
34993643 TGTTTTATTA
1 T-TTTTATAA
*
34993653 CTTTTATAAA
1 TTTTTAT-AA
*
34993663 TTTTATAGAA
1 TTTT-TATAA
*
34993673 TTTTTAT-G
1 TTTTTATAA
34993681 TTTTTGATAA
1 TTTTT-ATAA
*
34993691 TATTTATAA
1 TTTTTATAA
*
34993700 GTTTATATCAA
1 -TTTTTAT-AA
*
34993711 TTTTCAT-A
1 TTTTTATAA
34993719 TTTTT-TAA
1 TTTTTATAA
* *
34993727 TATTTATAT
1 TTTTTATAA
34993736 TTTTTATAA
1 TTTTTATAA
34993745 AGATTTTCTG
Statistics
Matches: 127, Mismatches: 38, Indels: 32
0.64 0.19 0.16
Matches are distributed among these distances:
7 1 0.01
8 15 0.12
9 44 0.35
10 48 0.38
11 19 0.15
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34993831 original size:22 final size:22
Alignment explanation
Indices: 34993803--34993847 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
34993793 AAATCAAAAG
34993803 TTGTCACGTGTCACAATTTGAT
1 TTGTCACGTGTCACAATTTGAT
34993825 TTGTCACGTGTCACAATTTGAT
1 TTGTCACGTGTCACAATTTGAT
34993847 T
1 T
34993848 GGTCTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (22 bp):
TTGTCACGTGTCACAATTTGAT
Found at i:34997006 original size:93 final size:92
Alignment explanation
Indices: 34996896--34997063 Score: 264
Period size: 92 Copynumber: 1.8 Consensus size: 92
34996886 ATAAAGATGG
* *
34996896 GATGGAATGTAAAATTATTTAGTACACTATCGGGTATGTAATATTATCTTATTTGATTCATTTAG
1 GATGGAATGTAAAATTATTCAGTAAAC-ATCGGGTATGTAATATTATCTTATTTGATTCATTTAG
*
34996961 TTGGAGGGTAAAATTTTACTATTTGGTT
65 CTGGAGGGTAAAATTTTACTATTTGGTT
* * * *
34996989 GATGGAATGTAAGATTATTCAGTAAACCTCGGGTATGTAATATTTTCTTATTTGTTTCATTTAGC
1 GATGGAATGTAAAATTATTCAGTAAACATCGGGTATGTAATATTATCTTATTTGATTCATTTAGC
34997054 TGGAGGGTAA
66 TGGAGGGTAA
34997064 TTTTTTTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
92 44 0.65
93 24 0.35
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (92 bp):
GATGGAATGTAAAATTATTCAGTAAACATCGGGTATGTAATATTATCTTATTTGATTCATTTAGC
TGGAGGGTAAAATTTTACTATTTGGTT
Found at i:35004665 original size:67 final size:68
Alignment explanation
Indices: 35004557--35004691 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 68
35004547 CAAAATTAAA
35004557 TGAATAATAATATTTATTTATTTATTGATAAAGACACCTATTGAAAGATGTCTCTAT-AAGAGAC
1 TGAATAATAATATTTATTTATTTATTGATAAAGACACCTATTGAAAGATGTCTCTATGAAGAGAC
35004621 ATG
66 ATG
35004624 TGAATAATAATATTTATTTATTTATTGATAAAGACACCTATTGAAAGATGTCTCTATGAAGAGAC
1 TGAATAATAATATTTATTTATTTATTGATAAAGACACCTATTGAAAGATGTCTCTATGAAGAGAC
35004689 ATG
66 ATG
35004692 AAAATTCCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 57 0.85
68 10 0.15
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (68 bp):
TGAATAATAATATTTATTTATTTATTGATAAAGACACCTATTGAAAGATGTCTCTATGAAGAGAC
ATG
Found at i:35013138 original size:44 final size:45
Alignment explanation
Indices: 35013047--35013139 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
35013037 TTCACTGTAT
* *
35013047 TGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAATGTAA
1 TGGAATAGAAGCGTAATAGCAAATCAATTGTTTGGTTGAATGGAA
* *
35013092 TGGAATAGAAGCGTAATAGC-ATTC-TTGTGTTTGGTTGAATGGAA
1 TGGAATAGAAGCGTAATAGCAAATCAAT-TGTTTGGTTGAATGGAA
35013136 TGGA
1 TGGA
35013140 GGTGTAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (45 bp):
TGGAATAGAAGCGTAATAGCAAATCAATTGTTTGGTTGAATGGAA
Found at i:35013350 original size:15 final size:15
Alignment explanation
Indices: 35013322--35013362 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
35013312 NTAAAATATA
35013322 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35013337 TATTAAATATATTAT
1 AATTAAATATATTAT
35013352 AATTAAA-ATAT
1 AATTAAATATAT
35013363 CATGAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35013587 original size:24 final size:25
Alignment explanation
Indices: 35013541--35013588 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
35013531 TATGAATTTG
35013541 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
35013567 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
35013589 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:35020828 original size:6 final size:6
Alignment explanation
Indices: 35020805--35020840 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
35020795 ATATACATAG
* *
35020805 TCAGAT TTAGAA TCAGAT TCAGAT TCAGAT TCAGAT
1 TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT TCAGAT
35020841 AACAGAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (6 bp):
TCAGAT
Found at i:35028928 original size:3 final size:3
Alignment explanation
Indices: 35028922--35028953 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35028912 ATCATGAGAA
35028922 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35028954 CAAACGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35029725 original size:46 final size:46
Alignment explanation
Indices: 35029652--35029758 Score: 137
Period size: 46 Copynumber: 2.3 Consensus size: 46
35029642 GTAAAAGTAT
* * *
35029652 ATTT-ATAATATTTT-ATAAATATAGTAAATAACAGATATCAACTTG
1 ATTTAATAAT-TTTTAATGAATATAGTAAAGAACAGATACCAACTTG
* * *
35029697 ATTTAATACTTTTTAATGAATATGGTAAAGAACAGATACCAGCTTG
1 ATTTAATAATTTTTAATGAATATAGTAAAGAACAGATACCAACTTG
35029743 ATTTAATAATTTTTAA
1 ATTTAATAATTTTTAA
35029759 CGAAAATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 8 0.15
46 45 0.85
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (46 bp):
ATTTAATAATTTTTAATGAATATAGTAAAGAACAGATACCAACTTG
Found at i:35033265 original size:24 final size:25
Alignment explanation
Indices: 35033228--35033278 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
35033218 CACGTTAGCG
35033228 AACAAAAATATATAAATAT-AAATA
1 AACAAAAATATATAAATATAAAATA
* * *
35033252 AACAAATATTTATATATATAAAATA
1 AACAAAAATATATAAATATAAAATA
35033277 AA
1 AA
35033279 ATAAATTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AACAAAAATATATAAATATAAAATA
Found at i:35033604 original size:15 final size:15
Alignment explanation
Indices: 35033584--35033613 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35033574 AAACAGAGGG
35033584 GATTTCTTTTGATTT
1 GATTTCTTTTGATTT
*
35033599 GATTTCTTTTTATTT
1 GATTTCTTTTGATTT
35033614 TCTCGGCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.07, G:0.10, T:0.70
Consensus pattern (15 bp):
GATTTCTTTTGATTT
Found at i:35040724 original size:132 final size:132
Alignment explanation
Indices: 35040550--35041682 Score: 1467
Period size: 132 Copynumber: 8.6 Consensus size: 132
35040540 TAGACAGCGA
** *
35040550 AGCAGATCAAAGATGAAAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAATAA
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAA
*
35040614 TTCTA-CTTCCCTGGGCAACAGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
65 TTCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
35040678 GTGG
129 GTGG
* ** *
35040682 AGCGGATCAAAGATGGCAGATTTTACCTTTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
35040747 TTTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCTTAAGCAGTAGT
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
35040812 GG
131 GG
* * ** * **
35040814 AACAGATCTAAGATGGTGGACTTTACCTCCCTGAGGTTTTAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * * ** *
35040879 TCTATTTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCT--GCA-TAGA
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG-
*
35040941 CAGCG
130 -TG-G
* * *
35040946 AAGCAGATCATAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 -AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * *
35041011 TTCTATTTCTCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
65 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
35041076 TGG
130 TGG
* *
35041079 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * * * ** * *
35041144 TCTATTTCTCTGGGCAGCAGTGGAATAGACTGAAGATTTTAAATCTTGCCT-TCT-TGCA-TAGA
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG-
*
35041206 CAGCG
130 -TG-G
* *
35041211 AAGCAGATCAAAGATGGCAGATTTTACCTTCCTGAGGTTACAGTGGAGTACATTGAAACCAGTAA
1 -AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * *
35041276 TTCTATCTCCCTGGGCAGCAGCGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAG-AGTAG
65 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
35041340 TGG
130 TGG
* * * * *
35041343 AGTAGATCGAAGATGACAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
35041408 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTAT-AGATCTTATTTCCCTAAGCATTAG
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCTAAGCAGTAG
35041472 TGG
130 TGG
* *
35041475 AGCATATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
35041540 TCTATCTCCCAGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGT
66 TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
35041605 GG
131 GG
* * * *
35041607 AACAGATCAAAGATGGCAAATTTTACCTCCCTGAAGTTACAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
35041672 TCTATCTCCCT
66 TCTATCTCCCT
35041683 AGTCGGCGTG
Statistics
Matches: 869, Mismatches: 113, Indels: 38
0.85 0.11 0.04
Matches are distributed among these distances:
129 6 0.01
130 6 0.01
131 114 0.13
132 520 0.60
133 209 0.24
134 4 0.00
135 7 0.01
136 3 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:35041027 original size:265 final size:263
Alignment explanation
Indices: 35040552--35041682 Score: 1502
Period size: 265 Copynumber: 4.3 Consensus size: 263
35040542 GACAGCGAAG
* ** *
35040552 CAGATCAAAGATGAAAGATTTTACCTCCCT-ATGGTTACAGTGGAGTACATTGAAGCCAATAATT
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATT
* * * * ** * *
35040616 CTACTTCCCTGGGCAACAGTGGAGTAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
65 CTATTTCCCTGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCT-AGCAGTAGAG
* ** *
35040681 GAGCGGATCAAAGATGGCAGATTTTACCTTTCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
129 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
35040746 TTTTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCTTAAGCAGTAG
194 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
35040811 TGGAA
259 TGGAA
* ** * **
35040816 CAGATCTAAGATGGTGGACTTTACCTCCCTGAGGTTTTAGTGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* *
35040881 TATTTCCCTAGGCAGCAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCT-GCA-TAGACAG
66 TATTTCCCTGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTAGCAGTAG--AG
* * *
35040944 CGAAGCAGATCATAGACGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
129 -G-AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT
* * * * *
35041009 AATTCTATTTCTCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGT
192 AATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
*
35041074 AGTGGAG
257 AGTGGAA
*
35041081 CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAATGGAGTACATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * *
35041146 TATTTCTCTGGGCAGCAGTGGAATAGACTGAAGATTTTAAATCTTGCCTT-CTTGCA-TAGACAG
66 TATTTCCCTGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTAGCAGTAG--AG
* *
35041209 CGAAGCAGATCAAAGATGGCAGATTTTACCTTCCTGAGGTTACAGTGGAGTACATTGAAACCAGT
129 -G-AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT
* * *
35041274 AATTCTATCTCCCTGGGCAGCAGCGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAG-AGT
192 AATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
*
35041338 AGTGGAG
257 AGTGGAA
* * * *
35041345 TAGATCGAAGATGACAGATTTTACCTCCCTGGGGTTACAGTGGAGTACATTGAAGCTAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
* * * ** * *
35041410 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTATAGATCTT-ATTTCCCTAAGCATTAGTG
66 TATTTCCCTGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTGCCTT-CCT-AGCAGTAGAG
* *
35041474 GAGCATATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
129 GAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
35041539 TTCTATCTCCCAGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAG
194 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
35041604 TGGAA
259 TGGAA
* * * *
35041609 CAGATCAAAGATGGCAAATTTTACCTCCCTGAAGTTACAGTGGAGTATATTGAAGCCAGTAATTC
1 CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
*
35041674 TATCTCCCT
66 TATTTCCCT
35041683 AGTCGGCGTG
Statistics
Matches: 770, Mismatches: 86, Indels: 22
0.88 0.10 0.03
Matches are distributed among these distances:
261 3 0.00
262 3 0.00
263 118 0.15
264 286 0.37
265 354 0.46
266 3 0.00
267 3 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (263 bp):
CAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC
TATTTCCCTGGGCAACAGTGGAATAGACTGAAGATTTTAGATCTTGCCTTCCTAGCAGTAGAGGA
GCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT
CTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
GAA
Found at i:35047113 original size:241 final size:242
Alignment explanation
Indices: 35046690--35047173 Score: 961
Period size: 241 Copynumber: 2.0 Consensus size: 242
35046680 TCATTTCTTT
35046690 TAAATTTACATTACTTTTTTAACGCTACAAGACAATAATCAAATTTCAATTTTAAATTTTAGAGT
1 TAAATTTACATTACTTTTTTAACGCTACAAGACAATAATCAAATTTCAATTTTAAATTTTAGAGT
35046755 ATAATGATAATTTTACCAAATATATAAAAATGACTTGAAATATTTAAGCATATGGCATGTTTTAA
66 ATAATGATAATTTTACCAAATATATAAAAATGACTTGAAATATTTAAGCATATGGCATGTTTTAA
35046820 TTTTAATCTTATTGATAAATTATTATATATTATTTTAAATGGTTTTGAATAAGAATTATACATAA
131 TTTTAATCTTATTGATAAATTATTATATATTATTTTAAATGGTTTTGAATAAGAATTATACATAA
35046885 TAATTTCAACATAAAATTAACTTGATAAATTGCTA-TTACTTATTTA
196 TAATTTCAACATAAAATTAACTTGATAAATTGCTATTTACTTATTTA
35046931 TAAATTTACATTACTTTTTTAACGCTACAAGACAATAATCAAATTTCAATTTTAAATTTTAGAGT
1 TAAATTTACATTACTTTTTTAACGCTACAAGACAATAATCAAATTTCAATTTTAAATTTTAGAGT
35046996 ATAATGATAATTTTACCAAATATATAAAAATGACTTGAAATATTTAAGCATATGGCATGTTTTAA
66 ATAATGATAATTTTACCAAATATATAAAAATGACTTGAAATATTTAAGCATATGGCATGTTTTAA
35047061 TTTTAATCTTATTGATAAATTATTATATATTATTTTAAATGGTTTTGAATAAGAATTATACATAA
131 TTTTAATCTTATTGATAAATTATTATATATTATTTTAAATGGTTTTGAATAAGAATTATACATAA
35047126 TAATTTCAACATAAAATTAACTTGATAAATTGCTATTTACTTATTTA
196 TAATTTCAACATAAAATTAACTTGATAAATTGCTATTTACTTATTTA
35047173 T
1 T
35047174 TCAATTTAAA
Statistics
Matches: 242, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
241 230 0.95
242 12 0.05
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (242 bp):
TAAATTTACATTACTTTTTTAACGCTACAAGACAATAATCAAATTTCAATTTTAAATTTTAGAGT
ATAATGATAATTTTACCAAATATATAAAAATGACTTGAAATATTTAAGCATATGGCATGTTTTAA
TTTTAATCTTATTGATAAATTATTATATATTATTTTAAATGGTTTTGAATAAGAATTATACATAA
TAATTTCAACATAAAATTAACTTGATAAATTGCTATTTACTTATTTA
Found at i:35047946 original size:42 final size:42
Alignment explanation
Indices: 35047900--35047983 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
35047890 CAAATTGACG
35047900 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
*
35047942 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAGAACTACCC
1 GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
35047984 AATTCCGACT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (42 bp):
GAGTTAACTAAACTGAGCTAAAACTAAAAGTAAAAACTACCC
Found at i:35052951 original size:16 final size:16
Alignment explanation
Indices: 35052906--35052940 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35052896 TAGATAAATA
* *
35052906 CATACATACAGACATG
1 CATACATAAATACATG
35052922 CATACATAAATACATG
1 CATACATAAATACATG
35052938 CAT
1 CAT
35052941 GCATGCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (16 bp):
CATACATAAATACATG
Found at i:35063570 original size:33 final size:34
Alignment explanation
Indices: 35063528--35063594 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
35063518 TAGTATAAAA
*
35063528 ATTATGAAAATGCAACATTCTAC-CATCAAGCTC
1 ATTATGAAAAAGCAACATTCTACTCATCAAGCTC
35063561 ATTATGAAAAAGCAACATTCTACTCATCAAGCTC
1 ATTATGAAAAAGCAACATTCTACTCATCAAGCTC
35063595 CGGTCATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (34 bp):
ATTATGAAAAAGCAACATTCTACTCATCAAGCTC
Found at i:35076294 original size:48 final size:48
Alignment explanation
Indices: 35076226--35076385 Score: 259
Period size: 48 Copynumber: 3.3 Consensus size: 48
35076216 AAGGTATATT
* * *
35076226 TGTCTTTCACTATTTGCACTCTTAGAGTTGGTAC-TTTATTGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTA-TGTATGGCA
35076274 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
* *
35076322 TGTCATTCATTATTTTCACTCTTAGATTTTGTACTTTTATGTATGGCA
1 TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
35076370 TGTCATTCATTATTTT
1 TGTCATTCATTATTTT
35076386 TATTGATAAA
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
48 102 0.96
49 4 0.04
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (48 bp):
TGTCATTCATTATTTTCACTCTTAGAGTTGGTACTTTTATGTATGGCA
Found at i:35080639 original size:2 final size:2
Alignment explanation
Indices: 35080632--35080663 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35080622 TTTTCTTTTA
35080632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35080664 TAGCTAAANN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35080745 original size:2 final size:2
Alignment explanation
Indices: 35080738--35080772 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35080728 ATCTTGTTTT
35080738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35080773 TAGGACTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35081497 original size:3 final size:3
Alignment explanation
Indices: 35081489--35081530 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35081479 AATACACCAA
35081489 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35081531 GGTAAGAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35087490 original size:13 final size:14
Alignment explanation
Indices: 35087465--35087498 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
35087455 TAAAGGTGTT
35087465 TCTTTATTTTAATA
1 TCTTTATTTTAATA
35087479 TCTTTA-TTTAATA
1 TCTTTATTTTAATA
35087492 TCATTTA
1 TC-TTTA
35087499 GAAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTTATTTTAATA
Found at i:35089024 original size:34 final size:34
Alignment explanation
Indices: 35088949--35089025 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
35088939 GACAAAAAAT
* * * *
35088949 CTACTATTTTCTTGTGTGTTTTTTTACTATTTTG
1 CTACTATTTTATTGTGTGTTTTCTCACTATTTTA
* *
35088983 CTGCTATTTTATTGT-TGTTTTCTCACTTGTTTTA
1 CTACTATTTTATTGTGTGTTTTCTCAC-TATTTTA
35089017 CTACTATTT
1 CTACTATTT
35089026 CACTATTATG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
33 9 0.26
34 26 0.74
ACGTcount: A:0.13, C:0.14, G:0.10, T:0.62
Consensus pattern (34 bp):
CTACTATTTTATTGTGTGTTTTCTCACTATTTTA
Found at i:35093890 original size:13 final size:13
Alignment explanation
Indices: 35093845--35093878 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
35093835 CTTTGCTTTT
35093845 GAAAAGTGCTGTG
1 GAAAAGTGCTGTG
35093858 GAAAAGTGCTGTG
1 GAAAAGTGCTGTG
35093871 GAAAAGTG
1 GAAAAGTG
35093879 TTTTTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.38, T:0.21
Consensus pattern (13 bp):
GAAAAGTGCTGTG
Found at i:35102198 original size:3 final size:3
Alignment explanation
Indices: 35102190--35102221 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35102180 ACCGTGCATG
35102190 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35102222 ATTGTAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35104170 original size:18 final size:18
Alignment explanation
Indices: 35104147--35104189 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
35104137 TAATAGATTT
35104147 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
35104165 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
35104183 TTAATTA
1 TTAATTA
35104190 CACTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:35105925 original size:132 final size:131
Alignment explanation
Indices: 35105565--35105996 Score: 441
Period size: 132 Copynumber: 3.3 Consensus size: 131
35105555 GTTAGAAGCT
* * * * *
35105565 CGCTATGAGAAGGATCAAAATACATCCAGAGATAGTGATGGTAATGGTGAAATGCTTGATGAAAA
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
** * * * * * * * *
35105630 TAGATCTACTGGCTCTCATAGTGAGGAGCAAGATCAGCACTTATTGGTTGAAGGGCGACGTAATG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAA-GGCCACGTAATG
*
35105695 GT
130 GA
* * * * * *
35105697 TGCTATGAGAAGGAACAAAATGCATCCAGAGA---T-A--GTGATGGTGATATGCTCGATGAAAA
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
** * * *
35105756 TAGATCTACTGATTCTTTTAGCAAGAAGCACGGTGAGAACTTATCGATAGAAGGCCAACGTAATG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCC-ACGTAATG
35105821 GA
130 GA
* * * *
35105823 CGCTACGAGAAAGATCAAGATACTTCCAGAGATGGTGATGGTGATGGTGATATGGTTGATGAAAG
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
* *
35105888 TAGGTCTATTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCA--TAATGG
66 TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG
35105951 TA
131 -A
** * *
35105953 -GCTACGAGGCAGATCAAATTGCATCCAGAGATGGTGATGGTGAT
1 CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGAT
35105997 ATGGTTGATG
Statistics
Matches: 247, Mismatches: 45, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
125 3 0.01
126 94 0.38
128 1 0.00
129 46 0.19
130 2 0.01
131 1 0.00
132 100 0.40
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (131 bp):
CGCTACGAGAAAGATCAAAATACATCCAGAGATGGTGATGGTGATGGTGATATGCTTGATGAAAA
TAGATCTACTGATTCTCATAGCGAGGAGCACGGTGAGAACTTATCGGTAGAAGGCCACGTAATGG
A
Found at i:35114084 original size:28 final size:28
Alignment explanation
Indices: 35114053--35114132 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
35114043 AGATTAATTG
* *
35114053 ACGAGTAGTGATCATTTTTATTACTAAT
1 ACGAGTAATGATCATTTTCATTACTAAT
* *
35114081 ACGAGTAATGATTATTTTCATTACTAGT
1 ACGAGTAATGATCATTTTCATTACTAAT
35114109 ACGAGTAATGATCATTTTCATTAC
1 ACGAGTAATGATCATTTTCATTAC
35114133 AAAAGATACA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (28 bp):
ACGAGTAATGATCATTTTCATTACTAAT
Found at i:35116353 original size:21 final size:21
Alignment explanation
Indices: 35116327--35116390 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
35116317 TTTTGGTGGA
35116327 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* **
35116348 TCAGCTCTCACAAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* *
35116369 TCATCTCGTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
35116390 T
1 T
35116391 AGCGTGTTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.41
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:35123445 original size:17 final size:17
Alignment explanation
Indices: 35123423--35123456 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35123413 AAATATAACA
*
35123423 TTTTTGAATAATACTTG
1 TTTTTGAATAAAACTTG
35123440 TTTTTGAATAAAACTTG
1 TTTTTGAATAAAACTTG
35123457 ATAAATTTCA
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:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTTTGAATAAAACTTG
Found at i:35124628 original size:21 final size:21
Alignment explanation
Indices: 35124582--35124621 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35124572 TTAAATTACA
*
35124582 TTTTGGTCACTAAACTTTATG
1 TTTTGGTCACTAAACATTATG
35124603 TTTTGGTCACT-AACATTAT
1 TTTTGGTCACTAAACATTAT
35124622 TAATTTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTTGGTCACTAAACATTATG
Found at i:35125813 original size:20 final size:18
Alignment explanation
Indices: 35125768--35125813 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
35125758 AAGATGAAAG
35125768 AAAGAAAGGAAATAAAAA
1 AAAGAAAGGAAATAAAAA
*
35125786 AAACGAAAGTGAAATAAATTA
1 AAA-GAAAG-GAAATAAA-AA
35125807 AAAGAAA
1 AAAGAAA
35125814 AAGAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 12 0.50
21 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (18 bp):
AAAGAAAGGAAATAAAAA
Found at i:35126063 original size:53 final size:53
Alignment explanation
Indices: 35125968--35126074 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
35125958 GTTATAAATT
* * * *
35125968 AATAAAGTTAATAATTAAAATTTGAAAAATTAAATTTTAGTAATCAAAATATA
1 AATAAAATTAATAATTAAAATTAGAAAAATTAAAATTGAGTAATCAAAATATA
*
35126021 AATAAAATTAATAATTAAAATATAGCAAAA-TAAAATTGAGTAATCAAAATATA
1 AATAAAATTAATAATTAAAAT-TAGAAAAATTAAAATTGAGTAATCAAAATATA
35126074 A
1 A
35126075 TTTAGTAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 42 0.88
54 6 0.12
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.32
Consensus pattern (53 bp):
AATAAAATTAATAATTAAAATTAGAAAAATTAAAATTGAGTAATCAAAATATA
Found at i:35126068 original size:19 final size:19
Alignment explanation
Indices: 35126046--35126083 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35126036 TAAAATATAG
35126046 CAAAATAAAATTGAGTAAT
1 CAAAATAAAATTGAGTAAT
* *
35126065 CAAAATATAATTTAGTAAT
1 CAAAATAAAATTGAGTAAT
35126084 ATTGTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
CAAAATAAAATTGAGTAAT
Found at i:35126071 original size:29 final size:25
Alignment explanation
Indices: 35126004--35126074 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 25
35125994 AAATTAAATT
35126004 TTAGTAATCAAAATAT-AAATAAAA
1 TTAGTAATCAAAATATAAAATAAAA
* *
35126028 TTAATAATTAAAATATAGCAAAATAAAA
1 TTAGTAATCAAAATAT---AAAATAAAA
35126056 TTGAGTAATCAAAATATAA
1 TT-AGTAATCAAAATATAA
35126075 TTTAGTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 14 0.37
26 2 0.05
28 10 0.26
29 12 0.32
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (25 bp):
TTAGTAATCAAAATATAAAATAAAA
Found at i:35132773 original size:31 final size:31
Alignment explanation
Indices: 35132729--35132821 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
35132719 GGGAATTAGT
*
35132729 CATTCATATTTGCATATCCATACCTTGTAATA
1 CATTCATATTTGCATATTCATACCTTGTAA-A
* * *
35132761 -ATTCGTATTTGCAAATTCATACCCTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
* *
35132791 CATTCATATTTACATATTCATATCTTGTAAA
1 CATTCATATTTGCATATTCATACCTTGTAAA
35132822 GTCACATATC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (31 bp):
CATTCATATTTGCATATTCATACCTTGTAAA
Found at i:35150832 original size:24 final size:24
Alignment explanation
Indices: 35150800--35150846 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
35150790 TTCTAATATC
35150800 AAAATTTAATTTCAGCATATGAAT
1 AAAATTTAATTTCAGCATATGAAT
35150824 AAAATTTAATTTCAGCATATGAA
1 AAAATTTAATTTCAGCATATGAA
35150847 ATTACCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (24 bp):
AAAATTTAATTTCAGCATATGAAT
Found at i:35153759 original size:40 final size:40
Alignment explanation
Indices: 35153666--35153773 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
35153656 GTTTGGACAA
* * *
35153666 AAAACGCCGCAAAAAATCGAGCATTAGCGACGCTTTATGG
1 AAAACGCCGCTAAAGATCGAGCATTTGCGACGCTTTATGG
*
35153706 AAAACGCCGCTAAAGATCGAGCATTTGCGGCGCTTTATGG
1 AAAACGCCGCTAAAGATCGAGCATTTGCGACGCTTTATGG
* *
35153746 AAAACGCCACTAAAGATCGAACATTTGC
1 AAAACGCCGCTAAAGATCGAGCATTTGC
35153774 AGCGTTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTTGCGACGCTTTATGG
Found at i:35169276 original size:9 final size:9
Alignment explanation
Indices: 35169234--35169301 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
35169224 ATAATTTTAA
35169234 AAAAATTAT
1 AAAAATTAT
* *
35169243 AAAATTTGTT
1 AAAAATT-AT
*
35169253 AAAAGTTACT
1 AAAAATTA-T
35169263 AAAAATTAT
1 AAAAATTAT
35169272 AAAAATT-T
1 AAAAATTAT
*
35169280 AAATATGTA-
1 AAAAAT-TAT
35169289 AAAAA-TAT
1 AAAAATTAT
35169297 AAAAA
1 AAAAA
35169302 AAATATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
7 2 0.04
8 11 0.23
9 19 0.40
10 15 0.32
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35172481 original size:25 final size:26
Alignment explanation
Indices: 35172452--35172523 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
35172442 TTTAGGCCAG
*
35172452 TTGGGCTAGGGT-ATTGGGCTTAG-GT
1 TTGGGCTAGGTTAATTGGG-TTAGAGT
*
35172477 TTGGGCTAGGTTAATTGGGTTAGATT
1 TTGGGCTAGGTTAATTGGGTTAGAGT
35172503 TTGGGCTAGGTTAATTGGGTT
1 TTGGGCTAGGTTAATTGGGTT
35172524 TGTAAAAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 15 0.35
26 28 0.65
ACGTcount: A:0.15, C:0.06, G:0.39, T:0.40
Consensus pattern (26 bp):
TTGGGCTAGGTTAATTGGGTTAGAGT
Found at i:35172494 original size:14 final size:13
Alignment explanation
Indices: 35172452--35172521 Score: 65
Period size: 14 Copynumber: 5.4 Consensus size: 13
35172442 TTTAGGCCAG
*
35172452 TTGGGCTAGGGTA
1 TTGGGCTAGGTTA
35172465 TTGGGCTTAGG-T-
1 TTGGGC-TAGGTTA
35172477 TTGGGCTAGGTTAA
1 TTGGGCTAGGTT-A
* *
35172491 TTGGGTTAGATT-
1 TTGGGCTAGGTTA
35172503 TTGGGCTAGGTTAA
1 TTGGGCTAGGTT-A
35172517 TTGGG
1 TTGGG
35172522 TTTGTAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.09
12 17 0.36
13 7 0.15
14 19 0.40
ACGTcount: A:0.16, C:0.06, G:0.40, T:0.39
Consensus pattern (13 bp):
TTGGGCTAGGTTA
Found at i:35174306 original size:25 final size:25
Alignment explanation
Indices: 35174253--35174306 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
35174243 CGACCCGTTT
* * *
35174253 TTAATTAAAATTAAAATTAGTTTTT
1 TTAATTAAAATTAAAACTAATTTTA
35174278 TTAA-TAAAATTAAAACTAATTGTTA
1 TTAATTAAAATTAAAACTAATT-TTA
35174303 TTAA
1 TTAA
35174307 AATTAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAATTAAAATTAAAACTAATTTTA
Found at i:35174325 original size:16 final size:16
Alignment explanation
Indices: 35174288--35174327 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
35174278 TTAATAAAAT
* *
35174288 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
35174304 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
35174320 TAAAATTA
1 TAAAATTA
35174328 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:35174433 original size:9 final size:9
Alignment explanation
Indices: 35174400--35174427 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35174390 TTTATCAAAT
35174400 TATTAATTG
1 TATTAATTG
35174409 TATTAATTG
1 TATTAATTG
35174418 TATTAATTG
1 TATTAATTG
35174427 T
1 T
35174428 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:35174437 original size:68 final size:66
Alignment explanation
Indices: 35174316--35174459 Score: 261
Period size: 68 Copynumber: 2.2 Consensus size: 66
35174306 AAATTAATTG
*
35174316 TTAGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
35174381 A
66 A
35174382 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
35174447 TGA
64 TGA
35174450 TTAGTAAATT
1 TTAGTAAATT
35174460 GCCCGAGGCC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 26 0.35
68 49 0.65
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (66 bp):
TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
A
Found at i:35175534 original size:29 final size:29
Alignment explanation
Indices: 35175486--35175542 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
35175476 CCGAAATAAA
* * *
35175486 TTAATTTTTCTATTACT-AAATAAATTAAT
1 TTAATTTTTATAGTAATAAAAT-AATTAAT
35175515 TTAATTTTTATAGTAATAAAATAATTAA
1 TTAATTTTTATAGTAATAAAATAATTAA
35175543 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAATTTTTATAGTAATAAAATAATTAAT
Found at i:35181208 original size:15 final size:15
Alignment explanation
Indices: 35181190--35181220 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35181180 ATTTAGTAAA
35181190 AGGTCAAAATCATGT
1 AGGTCAAAATCATGT
35181205 AGGTCAAAATCATGT
1 AGGTCAAAATCATGT
35181220 A
1 A
35181221 TGCTTGTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (15 bp):
AGGTCAAAATCATGT
Found at i:35182800 original size:20 final size:20
Alignment explanation
Indices: 35182775--35182815 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
35182765 AACTATACTA
*
35182775 TATATCAAATTACTTTTAAT
1 TATATCAAATGACTTTTAAT
35182795 TATATCAAATGACTTTTAAT
1 TATATCAAATGACTTTTAAT
35182815 T
1 T
35182816 GTGATGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATCAAATGACTTTTAAT
Found at i:35200197 original size:16 final size:16
Alignment explanation
Indices: 35200176--35200245 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
35200166 TTGATTTGCT
*
35200176 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
* *
35200192 ATTACACCTCCATTCC
1 ATTACACCTCTAATCC
35200208 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
35200224 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
35200240 AATACA
1 ATTACA
35200246 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:35202501 original size:35 final size:35
Alignment explanation
Indices: 35202427--35202501 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
35202417 TGAAAATTTT
* * * *
35202427 TCATATATTTAGAGGATCCTATTCCTAAATATGTT
1 TCATATATTTAGAGGATCCAATACCCAAATATGTA
* *
35202462 TCATATATTTAGAGGATTCAATACCCAGAT-TGATA
1 TCATATATTTAGAGGATCCAATACCCAAATATG-TA
35202497 TCATA
1 TCATA
35202502 CTTAAGACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (35 bp):
TCATATATTTAGAGGATCCAATACCCAAATATGTA
Found at i:35203917 original size:24 final size:24
Alignment explanation
Indices: 35203880--35203936 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
35203870 CTATTGTTGA
*
35203880 AGTTTTCAATTGAAAATGGTTTCTGT
1 AGTTTTC--TTGAAAATGGTTTCTAT
*
35203906 ATTTTTCTTGAAAATGGTTTCTAT
1 AGTTTTCTTGAAAATGGTTTCTAT
35203930 AGTTTTC
1 AGTTTTC
35203937 AATTTGTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 22 0.79
26 6 0.21
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (24 bp):
AGTTTTCTTGAAAATGGTTTCTAT
Found at i:35205002 original size:66 final size:66
Alignment explanation
Indices: 35204896--35205026 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
35204886 CAAAAGGTTT
*
35204896 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTCTGAGTATAATTTGAACCCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
35204961 G
66 G
*
35204962 TGGTAGTGTTGGCATTGGCATTAGTAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
1 TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
35205027 CACATTTGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (66 bp):
TGGTAGTGTTGGCATTGGCATTAATAAAAGTTTGAGCTTACTATGAGTATAATTTGAACCCAAAT
G
Done.