Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 117 of 190
Found at i:35422648 original size:24 final size:24
Alignment explanation
Indices: 35422598--35422648 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
35422588 TACATATATT
*
35422598 AAAAAAATAATATGAAAAAGAATA
1 AAAAAAATAATATGAAAAAGAAGA
35422622 AAAAAAACTAA-ATGTAAAAA-AAGA
1 AAAAAAA-TAATATG-AAAAAGAAGA
35422646 AAA
1 AAA
35422649 TGGAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (24 bp):
AAAAAAATAATATGAAAAAGAAGA
Found at i:35424184 original size:20 final size:20
Alignment explanation
Indices: 35424161--35424202 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
35424151 AAATATAATG
*
35424161 ATAAT-AACAATAATATTAAA
1 ATAATGAACAA-AATAATAAA
35424181 ATAATGAACAAAATAATAAA
1 ATAATGAACAAAATAATAAA
35424201 AT
1 AT
35424203 TACTAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAATGAACAAAATAATAAA
Found at i:35425599 original size:44 final size:44
Alignment explanation
Indices: 35425531--35425691 Score: 171
Period size: 44 Copynumber: 3.6 Consensus size: 44
35425521 GTGGTTTTAG
* * * * *
35425531 TCTGTTCCACTGTAACGTT-AGGGAGATAGGACTAGTAACTTCAA
1 TCTGCTCCACTGCAAC-TTCAGGGAGATAAGATTTGTAACTTCAA
** * *
35425575 TCTGCTCCACTGCATTTTCAGGGAGATAACATTTGTAACATCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAA
* ** *
35425619 TCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGTTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAA
*
35425664 TCTGCTCTACTGCAACTTCAGGGAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATA
35425692 TTATTAGCCA
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.02
44 63 0.66
45 31 0.32
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAA
Found at i:35425923 original size:89 final size:89
Alignment explanation
Indices: 35425768--35426616 Score: 1106
Period size: 89 Copynumber: 9.6 Consensus size: 89
35425758 AACGTTATTT
** *
35425768 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTATTATCTTCAGTCTACTCCGCTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
* * *
35425833 GTACAGGAAGGCAAGGCTAGTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * * * * * * **
35425857 CTCCATCTGCTTCGCTGCAAGTACCGGAAGGCATGATCTGTTATCTTCAATCTGCTTCTTTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
* * * * **
35425922 GTACAGGAAAGCAAGGTTAATGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * * * * * *
35425946 TTCAATCTGCTTCGATGCCAGTATAGGAAGACATGATTTGCTATCTTCAATCTGCTCCACTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
* *
35426011 GTACAGGGAGGCAAGGCTGTTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* *
35426035 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
35426100 GTACAGGGAGGCAAAGCTGGTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * * * **
35426124 TTCGATCCGCTTTGCTTCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTTCGCTACCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
*
35426189 GTA-AGGGAGACAAAGCTGGTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * * *
35426212 TTTGATCCGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTTAATCTGCTCCGCTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
* *
35426277 GTATAGGGAGGCAAGGCTGGTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * *
35426301 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATAATCTGCTATCTTTAGTCTGCTCCACTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
**
35426366 GTACAGGGAGGCAAAATTGGTGTC
66 GTACAGGGAGGCAAAGCTGGTGTC
* **
35426390 TTCGATCTGCTTCGCTGCCAGTACAGGAGGGCATGATCTGCTATCTTTTGTCTGCTCCGCTGTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
** *
35426455 GTACAGGGAGGCAAAATTGGTATC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * * *
35426479 TTCAATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
* *
35426544 GTACAAGGAGGCAAAGCTGGTGCC
66 GTACAGGGAGGCAAAGCTGGTGTC
* * *
35426568 TTCGATCTACTTCGCTGCCAGTACAGGAAGGCATGATTTGCAATCTTCA
1 TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCA
35426617 TTGATCTGTT
Statistics
Matches: 669, Mismatches: 90, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
88 79 0.12
89 590 0.88
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (89 bp):
TTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGTCA
GTACAGGGAGGCAAAGCTGGTGTC
Found at i:35426616 original size:444 final size:444
Alignment explanation
Indices: 35425771--35426616 Score: 1233
Period size: 444 Copynumber: 1.9 Consensus size: 444
35425761 GTTATTTTTC
* * *
35425771 GATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTATTATCTTCAGTCTACTCCGCTGTCAGTA
1 GATCCGCTTCGCTGCCAGTACAGGAAGGCATGATCTACTATCTTCAATCTACTCCGCTGTCAGTA
* * *
35425836 CAGGAAGGCAAGGCTAGTGTCCTCCATCTGCTTCGCTGCAAGTACCGGAAGGCATGATCTGTTAT
66 CAGGAAGGCAAGGCTAGTGTCCTCCATCTGCTTCGCTGCAAGTACAGGAAGGCATAATCTGCTAT
* ** **
35425901 CTTCAATCTGCTTCTTTGTCAGTACAGGAAAGCAAGGTTAATGTCTTCAATCTGCTTCGATGCCA
131 CTTCAATCTGCTCCACTGTCAGTACAGGAAAGCAAAATTAATGTCTTCAATCTGCTTCGATGCCA
* * ** *
35425966 GTATAGGAAGACATGATTTGCTATCTTCAATCTGCTCCACTGTCAGTACAGGGAGGCAAGGCTGT
196 GTACAGGAAGACATGATCTGCTATCTTCAATCTGCTCCACTGTCAGTACAGGGAGGCAAAACTGG
* * *
35426031 TGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCT
261 TATCTTCAATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCT
* * * * *
35426096 GCCAGTACAGGGAGGCAAAGCTGGTGTCTTCGATCCGCTTTGCTTCCAGTACAGGAAGGCATGAT
326 GCCAGTACAAGGAGGCAAAGCTGGTGCCTTCGATCCACTTCGCTGCCAGTACAGGAAGGCATGAT
*
35426161 CTGCTATCTTCAGTCTGCTTCGCTACCAGTAAGGGAGACAAAGCTGGTGTCTTT
391 CTGCAATCTTCAGTCTGCTTCGCTACCAGTAAGGGAGACAAAGCTGGTGTCTTT
* * *
35426215 GATCCGCTTCGCTGCCAGTACAGGAAGGCATGATCTGCTATCTTTAATCTGCTCCGCTGTCAGTA
1 GATCCGCTTCGCTGCCAGTACAGGAAGGCATGATCTACTATCTTCAATCTACTCCGCTGTCAGTA
* * * * * *
35426280 TAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATAATCTGCTAT
66 CAGGAAGGCAAGGCTAGTGTCCTCCATCTGCTTCGCTGCAAGTACAGGAAGGCATAATCTGCTAT
* * * * ** * *
35426345 CTTTAGTCTGCTCCACTGTCAGTACAGGGAGGCAAAATTGGTGTCTTCGATCTGCTTCGCTGCCA
131 CTTCAATCTGCTCCACTGTCAGTACAGGAAAGCAAAATTAATGTCTTCAATCTGCTTCGATGCCA
* * *** * *
35426410 GTACAGGAGGGCATGATCTGCTATCTTTTGTCTGCTCCGCTGTCAGTACAGGGAGGCAAAATTGG
196 GTACAGGAAGACATGATCTGCTATCTTCAATCTGCTCCACTGTCAGTACAGGGAGGCAAAACTGG
35426475 TATCTTCAATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCT
261 TATCTTCAATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCT
*
35426540 GCCAGTACAAGGAGGCAAAGCTGGTGCCTTCGATCTACTTCGCTGCCAGTACAGGAAGGCATGAT
326 GCCAGTACAAGGAGGCAAAGCTGGTGCCTTCGATCCACTTCGCTGCCAGTACAGGAAGGCATGAT
*
35426605 TTGCAATCTTCA
391 CTGCAATCTTCA
35426617 TTGATCTGTT
Statistics
Matches: 351, Mismatches: 51, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
444 351 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (444 bp):
GATCCGCTTCGCTGCCAGTACAGGAAGGCATGATCTACTATCTTCAATCTACTCCGCTGTCAGTA
CAGGAAGGCAAGGCTAGTGTCCTCCATCTGCTTCGCTGCAAGTACAGGAAGGCATAATCTGCTAT
CTTCAATCTGCTCCACTGTCAGTACAGGAAAGCAAAATTAATGTCTTCAATCTGCTTCGATGCCA
GTACAGGAAGACATGATCTGCTATCTTCAATCTGCTCCACTGTCAGTACAGGGAGGCAAAACTGG
TATCTTCAATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCT
GCCAGTACAAGGAGGCAAAGCTGGTGCCTTCGATCCACTTCGCTGCCAGTACAGGAAGGCATGAT
CTGCAATCTTCAGTCTGCTTCGCTACCAGTAAGGGAGACAAAGCTGGTGTCTTT
Found at i:35426935 original size:24 final size:24
Alignment explanation
Indices: 35426885--35426941 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
35426875 CAGATTGCCC
35426885 CCACTGTAATCTTCAAACTTCAAT
1 CCACTGTAATCTTCAAACTTCAAT
* **
35426909 CCATTGTAATCTTCAAGGTT-AAGT
1 CCACTGTAATCTTCAAACTTCAA-T
35426933 CCACTGTAA
1 CCACTGTAA
35426942 CTTTAGGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAACTTCAAT
Found at i:35428479 original size:21 final size:21
Alignment explanation
Indices: 35428429--35428479 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
35428419 AGTTCGGGCC
35428429 CAAATAA-AAAAATAAACAAA
1 CAAATAATAAAAATAAACAAA
35428449 CAGAAT-ATAAAAATAAA-AAA
1 CA-AATAATAAAAATAAACAAA
35428469 TCAAATAATAA
1 -CAAATAATAA
35428480 GAGTACAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAATAATAAAAATAAACAAA
Found at i:35434452 original size:19 final size:20
Alignment explanation
Indices: 35434413--35434452 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
35434403 CAAGGTCGTA
*
35434413 TATGTAAAATGTATCCGTTT
1 TATGTAAAATGGATCCGTTT
*
35434433 TATGTAAAA-GGATTCGTTT
1 TATGTAAAATGGATCCGTTT
35434452 T
1 T
35434453 CTAGTAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (20 bp):
TATGTAAAATGGATCCGTTT
Found at i:35441627 original size:45 final size:44
Alignment explanation
Indices: 35441527--35441933 Score: 298
Period size: 44 Copynumber: 8.9 Consensus size: 44
35441517 CACCGTAGCG
* ** * **
35441527 AATCTTATCCCCCTGAAGTTGCAGCAGAGTAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* **
35441571 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATCGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
*
35441616 AATCTTATCTCCCTGAAGTTAG-AGTGGAGCAGATTAAAGATAAAA
1 AATCTTATCTCCCTGAAGTT-GCAGTGGAGCAGATTAAAGAT-ACA
* * * *
35441661 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * *
35441705 AATCTTATTTTCCTGAAGTTGCAGTGGAACATATTAAAGCTACTAGTCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-----A-T-ACA
* * * * * *
35441756 AATCTTATCTCCTTAAAGTTACA-TCAGAGCAAATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGATACA
* * * * * *
35441800 AATCTTATTTCCCTAAAGTTACATTGGAACAGATTAAAGCTACAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-----A--TACA
*
35441851 AATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-ACTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGA-TACA
** ** *
35441895 AGCCTTATCTCTTTAAAGTTGCAGTGGAGCAGATTAAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
35441934 CGAACTTTAT
Statistics
Matches: 289, Mismatches: 53, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
44 140 0.48
45 79 0.27
46 2 0.01
50 2 0.01
51 66 0.23
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
Found at i:35441653 original size:89 final size:89
Alignment explanation
Indices: 35441522--35441934 Score: 264
Period size: 95 Copynumber: 4.5 Consensus size: 89
35441512 GAAGTCACCG
* ** * * * *
35441522 TAGCGAATCTTATCCCCCTGAAGTTGCAGCAGAGTAGATTAAAGCCACAAATCTTATCTCCCTGA
1 TAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAAAAATCTTATCTCCCTAA
*
35441587 AGTTGCAGTGAAGCAGATCGAAGA
66 AGTTGCAGTGAAGCAGATCAAAGA
* *
35441611 TAGCAAATCTTATCTCCCTGAAGTTAG-AGTGGAGCAGATTAAAGATAAAAAATCTTATCTCCCT
1 TAGCGAATCTTATCTCCCTGAAGTT-GCAGTGGAGCAGATTAAAG-CAAAAAATCTTATCTCCCT
* * * *
35441675 AAAGTTGTAGTGGAGCAGATTAAAGC
64 AAAGTTGCAGTGAAGCAGATCAAAGA
* * * *
35441701 TA-CGAATCTTATTTTCCTGAAGTTGCAGTGGAACATATTAAAGCTACTAGTCACAAATCTTATC
1 TAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-A--A---A-AAATCTTATC
* * * * * *
35441765 TCCTTAAAGTTACA-TCAGAGCAAATTAAAGT
59 TCCCTAAAGTTGCAGTGA-AGCAGATCAAAGA
* * * * * *
35441796 TA-CAAATCTTATTTCCCTAAAGTTACATTGGAACAGATTAAAGCTACAAGTTGCAAATCTTATC
1 TAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-A-AA-----AAATCTTATC
* * * *
35441860 TCTCTGAAGTTGCAGTGGAGCAGATTAAA-A
59 TCCCTAAAGTTGCAGTGAAGCAGATCAAAGA
* ** *
35441890 CTA-C-AAGCCTTATCTCTTTAAAGTTGCAGTGGAGCAGATTAAAGC
1 -TAGCGAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
35441935 GAACTTTATC
Statistics
Matches: 257, Mismatches: 49, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
88 1 0.00
89 72 0.28
90 39 0.15
91 2 0.01
94 5 0.02
95 137 0.53
96 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (89 bp):
TAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAAAAATCTTATCTCCCTAA
AGTTGCAGTGAAGCAGATCAAAGA
Found at i:35441792 original size:95 final size:95
Alignment explanation
Indices: 35441567--35441934 Score: 302
Period size: 95 Copynumber: 3.9 Consensus size: 95
35441557 AGATTAAAGC
* * * ** * * *
35441567 CACAAATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATCGAAGATAGCAAATCTTATCTCCCTG
1 CACAAATCTTATCTCCCTAAAGTTACAGTAG-AGCAAATTAAAGCTA-CAAATCTTATTTCCCTA
* * *
35441631 AAGTTAGAGTGGAGCAGATTAAAG--ATAA--
64 AAGTTACAGTGGAACAGATTAAAGCTACAAGT
** * * * * *
35441659 -A-AAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGCTACGAATCTTATTTTCCTGAA
1 CACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAAATTAAAGCTACAAATCTTATTTCCCTAAA
* * *
35441722 GTTGCAGTGGAACATATTAAAGCTACTAGT
66 GTTACAGTGGAACAGATTAAAGCTACAAGT
* *
35441752 CACAAATCTTATCTCCTTAAAGTTACA-TCAGAGCAAATTAAAGTTACAAATCTTATTTCCCTAA
1 CACAAATCTTATCTCCCTAAAGTTACAGT-AGAGCAAATTAAAGCTACAAATCTTATTTCCCTAA
*
35441816 AGTTACATTGGAACAGATTAAAGCTACAAGT
65 AGTTACAGTGGAACAGATTAAAGCTACAAGT
** * * * * * * ** * **
35441847 TGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACTACAAGCCTTATCTCTTTAAA
1 CACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAAATTAAAGCTACAAATCTTATTTCCCTAAA
* *
35441912 GTTGCAGTGGAGCAGATTAAAGC
66 GTTACAGTGGAACAGATTAAAGC
35441935 GAACTTTATC
Statistics
Matches: 222, Mismatches: 45, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
89 34 0.15
90 36 0.16
91 4 0.02
94 2 0.01
95 145 0.65
96 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (95 bp):
CACAAATCTTATCTCCCTAAAGTTACAGTAGAGCAAATTAAAGCTACAAATCTTATTTCCCTAAA
GTTACAGTGGAACAGATTAAAGCTACAAGT
Found at i:35441884 original size:51 final size:51
Alignment explanation
Indices: 35441792--35441934 Score: 156
Period size: 51 Copynumber: 2.9 Consensus size: 51
35441782 GAGCAAATTA
* * * * * *
35441792 AAGTTACAAATCTTATTTCCCTAAAGTTACATTGGAACAGATTAAAGCTAC
1 AAGTTGCAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTAC
* *
35441843 AAGTTGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACTAC
1 AAGTTGCAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTAC
*
35441894 AA---GC----CTTATCTCTTTAAAGTTGCAGTGGAGCAGATTAAAGC
1 AAGTTGCAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGC
35441935 GAACTTTATC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
44 34 0.42
48 2 0.02
51 45 0.56
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (51 bp):
AAGTTGCAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTAC
Found at i:35443525 original size:4 final size:4
Alignment explanation
Indices: 35443516--35443610 Score: 61
Period size: 4 Copynumber: 23.8 Consensus size: 4
35443506 ATTGTTTCCT
* * *
35443516 TTTA TTTA TTTA TTTA -TTA TTCCT- TTTA TTTTA TTCA TTTA CTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA -TTTA TTTA TTTA TTTA TTTA
* * * * * *
35443565 TTTA CTTA TTTA TTTA TATA -TTA TTCA TTCA TTCA TTTT TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
35443611 TAATTCCTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
3 6 0.08
4 60 0.82
5 6 0.08
6 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:35448189 original size:9 final size:9
Alignment explanation
Indices: 35448183--35448207 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35448173 TAAGATAATC
35448183 ATAATAACA
1 ATAATAACA
35448192 ATAATAACA
1 ATAATAACA
35448201 ATAATAA
1 ATAATAA
35448208 GGATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:35449943 original size:44 final size:44
Alignment explanation
Indices: 35449854--35450019 Score: 131
Period size: 44 Copynumber: 3.8 Consensus size: 44
35449844 ACGTTAACCC
* * * ** * *
35449854 GCTCCACTACAACCTCAGGGAGATAGGACTAT-CGACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-TGCTTCCTCAGTCT
* * *
35449898 GCTCCACTGCAACCTCTGGGAGATAAGATTTGCTTCCTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCCTCAGTCT
** * *
35449942 GC-CCTACTGTGACTTCAAGGG-GATAAGACTTGTTTTCTCAGTCT
1 GCTCC-ACTGCAACTTC-AGGGAGATAAGACTTGCTTCCTCAGTCT
* * *
35449986 GCTCCGCTGCAACTTCAAGGAGATAAGACCTGCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGCT
35450020 GCGATCCATT
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
43 6 0.06
44 85 0.89
45 5 0.05
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCCTCAGTCT
Found at i:35463310 original size:12 final size:12
Alignment explanation
Indices: 35463293--35463374 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 12
35463283 TAACCATTTA
35463293 ATTATTTTTATT
1 ATTATTTTTATT
**
35463305 ATTATTGCTATT
1 ATTATTTTTATT
*
35463317 ATTATTTTTATC
1 ATTATTTTTATT
*
35463329 ACTA--TTTATT
1 ATTATTTTTATT
* *
35463339 ATTGTTCTTATT
1 ATTATTTTTATT
*
35463351 ATTATATTTGATT
1 ATTAT-TTTTATT
*
35463364 -TTATTTCTATT
1 ATTATTTTTATT
35463375 TATTTATATG
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
10 7 0.13
11 5 0.10
12 35 0.67
13 5 0.10
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:35467652 original size:35 final size:35
Alignment explanation
Indices: 35467611--35467695 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
35467601 GATTTTCTTC
*
35467611 CAAATTATTATTCATTCATTCATAATCATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGATA
35467646 CAAATTATTATTCATTCATTCATAATCATATGATA
1 CAAATTATTATTCATTCATTCATAATCATATGATA
*
35467681 CAAATAATTATTCAT
1 CAAATTATTATTCAT
35467696 GAATTTATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (35 bp):
CAAATTATTATTCATTCATTCATAATCATATGATA
Found at i:35468773 original size:19 final size:18
Alignment explanation
Indices: 35468744--35468790 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
35468734 CAACCAAGAG
35468744 GCAAGAAAAAAGAAAAAA
1 GCAAGAAAAAAGAAAAAA
35468762 GCAAGCAAAAAAGAAAAAA
1 GCAAG-AAAAAAGAAAAAA
35468781 G-AAGAAAAAA
1 GCAAGAAAAAA
35468791 AAACCGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
GCAAGAAAAAAGAAAAAA
Found at i:35468792 original size:19 final size:19
Alignment explanation
Indices: 35468744--35468791 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
35468734 CAACCAAGAG
35468744 GCAAG-AAAAAAGAAAAAA
1 GCAAGAAAAAAAGAAAAAA
*
35468762 GCAAGCAAAAAAGAAAAAA
1 GCAAGAAAAAAAGAAAAAA
35468781 G-AAGAAAAAAA
1 GCAAGAAAAAAA
35468792 AACCGAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (19 bp):
GCAAGAAAAAAAGAAAAAA
Found at i:35469052 original size:18 final size:18
Alignment explanation
Indices: 35468975--35469128 Score: 93
Period size: 17 Copynumber: 8.3 Consensus size: 18
35468965 ATACGCCTTT
35468975 AAAAAACATTTCGTGTTTC
1 AAAAAA-ATTTCGTGTTTC
*
35468994 -AAAAAATCTCGTGTTTTC
1 AAAAAAATTTCGTG-TTTC
**
35469012 AATTCAAAAATTTTCGCACTTTC
1 AA---AAAAA-TTTCG-TGTTTC
*
35469035 AAAAAAATCTCGTGTTTC
1 AAAAAAATTTCGTGTTTC
35469053 AAAAAAAATTTTGCGT-TTTC
1 -AAAAAAA-TTT-CGTGTTTC
**
35469073 AAAAATTTTTCGTGTTT-
1 AAAAAAATTTCGTGTTTC
* *
35469090 TAAAAATTTTCGTG-TT-
1 AAAAAAATTTCGTGTTTC
**
35469106 AAAAAAAACTCGTGTTTC
1 AAAAAAATTTCGTGTTTC
35469124 AAAAA
1 AAAAA
35469129 TTTTCACATT
Statistics
Matches: 106, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
16 12 0.11
17 24 0.23
18 24 0.23
19 17 0.16
20 11 0.10
21 3 0.03
22 5 0.05
23 10 0.09
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (18 bp):
AAAAAAATTTCGTGTTTC
Found at i:35469164 original size:18 final size:18
Alignment explanation
Indices: 35468976--35469163 Score: 84
Period size: 18 Copynumber: 10.2 Consensus size: 18
35468966 TACGCCTTTA
35468976 AAAAACATT-TCGTGTTTC
1 AAAAA-ATTCTCGTGTTTC
35468994 AAAAAA-TCTCGTGTTTTC
1 AAAAAATTCTCGTG-TTTC
* **
35469012 AATTCAAAAATTTTCGCACTTTC
1 -A---AAAAATTCTCG-TGTTTC
*
35469035 AAAAAAATCTCGTGTTTC
1 AAAAAATTCTCGTGTTTC
*
35469053 AAAAAAAATTTTGCGT-TTTC
1 --AAAAAATTCT-CGTGTTTC
* *
35469073 AAAAATTTTTCGTGTTT-
1 AAAAAATTCTCGTGTTTC
* *
35469090 TAAAAATTTTCGTG-TT-
1 AAAAAATTCTCGTGTTTC
**
35469106 AAAAAAAACTCGTGTTTC
1 AAAAAATTCTCGTGTTTC
* * * *
35469124 AAAAATTTTCACAT-TTTG
1 AAAAA-ATTCTCGTGTTTC
*
35469142 AAAATATTCTCGTGTTTC
1 AAAAAATTCTCGTGTTTC
35469160 AAAA
1 AAAA
35469164 TCTTCGTGTC
Statistics
Matches: 127, Mismatches: 27, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
16 13 0.10
17 28 0.22
18 44 0.35
19 13 0.10
20 12 0.09
21 3 0.02
22 6 0.05
23 8 0.06
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (18 bp):
AAAAAATTCTCGTGTTTC
Found at i:35474857 original size:6 final size:6
Alignment explanation
Indices: 35474846--35474933 Score: 85
Period size: 6 Copynumber: 14.8 Consensus size: 6
35474836 TATGCCTTAA
*
35474846 AAAAAC AAAAAC AACAAAC AAAAA- AAACAAC AAACAC AAAAA- AACAAAC
1 AAAAAC AAAAAC AA-AAAC AAAAAC AAA-AAC AAAAAC AAAAAC AA-AAAC
* * *
35474895 AAAAAC AAAAAC AGAAA- AAAGA- AAAAAC AAAAAG AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
35474934 AAATCAAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.17
6 46 0.67
7 11 0.16
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:35474861 original size:9 final size:9
Alignment explanation
Indices: 35474844--35474902 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
35474834 ATTATGCCTT
35474844 AAAAA-AAC
1 AAAAACAAC
35474852 AAAAACAAC
1 AAAAACAAC
*
35474861 --AAACAAA
1 AAAAACAAC
35474868 AAAAACAAC
1 AAAAACAAC
*
35474877 AAACACAA-
1 AAAAACAAC
35474885 AAAAACAAAC
1 AAAAAC-AAC
35474895 AAAAACAA
1 AAAAACAA
35474903 AAACAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
7 6 0.14
8 10 0.24
9 20 0.48
10 6 0.14
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAC
Found at i:35474873 original size:16 final size:15
Alignment explanation
Indices: 35474845--35474936 Score: 89
Period size: 16 Copynumber: 5.7 Consensus size: 15
35474835 TTATGCCTTA
35474845 AAAAAACAAAAACAAC
1 AAAAAA-AAAAACAAC
35474861 AAACAAAAAAAACAAC
1 AAA-AAAAAAAACAAC
35474877 AAACACAAAAAAACAAAC
1 AAA-A-AAAAAAAC-AAC
*
35474895 AAAAACAAAAACAGA-
1 AAAAAAAAAAACA-AC
35474910 AAAAAGAAAAAACAA-
1 AAAAA-AAAAAACAAC
35474925 AAAGAAAAAAAA
1 AAA-AAAAAAAA
35474937 TCAAGATGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
15 16 0.24
16 34 0.50
17 12 0.18
18 6 0.09
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACAAC
Found at i:35474891 original size:33 final size:31
Alignment explanation
Indices: 35474844--35474936 Score: 86
Period size: 33 Copynumber: 2.9 Consensus size: 31
35474834 ATTATGCCTT
35474844 AAAAAA-ACAAAAACAACAAACAAAAAAAACA-
1 AAAAAAGA-AAAAACAACAAA-AAAAAAAACAG
*
35474875 ACAAACACA-AAAAAACAAACAAAAACAAAAACAG
1 A-AAA-A-AGAAAAAAC-AACAAAAAAAAAAACAG
35474909 AAAAAAGAAAAAACAA-AAAGAAAAAAAA
1 AAAAAAGAAAAAACAACAAA-AAAAAAAA
35474937 TCAAGATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
30 3 0.06
31 11 0.21
32 11 0.21
33 19 0.36
34 9 0.17
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (31 bp):
AAAAAAGAAAAAACAACAAAAAAAAAAACAG
Found at i:35474919 original size:14 final size:12
Alignment explanation
Indices: 35474844--35474936 Score: 71
Period size: 13 Copynumber: 7.3 Consensus size: 12
35474834 ATTATGCCTT
35474844 AAAAAAACAAAA
1 AAAAAAACAAAA
*
35474856 ACAACAAACAAAA
1 A-AAAAAACAAAA
*
35474869 AAAACAACAAACA
1 AAAAAAACAAA-A
35474882 CAAAAAAACAAACA
1 -AAAAAAACAAA-A
*
35474896 AAAACAAA-AACA
1 AAAA-AAACAAAA
* *
35474908 GAAAAAAGAAAA
1 AAAAAAACAAAA
*
35474920 AACAAAAAGAAAA
1 AA-AAAAACAAAA
35474933 AAAA
1 AAAA
35474937 TCAAGATGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
11 3 0.04
12 19 0.28
13 30 0.45
14 15 0.22
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:35476211 original size:78 final size:76
Alignment explanation
Indices: 35475783--35476551 Score: 952
Period size: 76 Copynumber: 9.9 Consensus size: 76
35475773 TTTCAAGAAA
*
35475783 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
*
35475848 TCACGTTGAGG
66 TCACGCTGAGG
* * *
35475859 CATTTTTAATTTCTGTTGTTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
35475924 TCACGCTGAGG
66 TCACGCTGAGG
* *
35475935 TATTTTTAATTTCTATTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
35476000 TCACGCTGAGG
66 TCACGCTGAGG
* * *
35476011 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAGTACGAGATGTGAGTTGAGCTTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
35476076 TCACGCTGAGG
66 TCACGCTGAGG
*
35476087 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
* *
35476152 TCACACTAAGG
66 TCACGCTGAGG
* * *
35476163 TATTTTTTAAATTTCTATTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCG
1 TA-TTTTT-AATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
35476228 GGTCGCACGCTGAGG
64 GGT--CACGCTGAGG
* *** *
35476243 TATTTTAAATTTCTGTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
35476308 TTGCACGCTGAGG
66 -T-CACGCTGAGG
**** *
35476321 TATTTCTTTTAAATTTCTTGTTAGTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TA--T-TTTT-AATTTC-TGTT--TTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAG
** * *
35476386 CCTCGGACCATGCCGAGG
59 CCTCGGGTCACGCTGAGG
* * ** *
35476404 TATTTCTTTTAAATTTATGTTTTTCATAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TA--T-TTTT-AATTTCTGTTTTT-TTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCC
* *
35476469 TC-GGACACATGCCGAGG
61 TCGGGTCAC--GCTGAGG
*
35476486 TATTTCTTTTAAATTTCTG---TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TA--T-TTTT-AATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
35476548 CGGG
62 CGGG
35476552 GCACATGTCG
Statistics
Matches: 632, Mismatches: 45, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
76 289 0.46
77 5 0.01
78 160 0.25
79 9 0.01
80 17 0.03
81 44 0.07
82 35 0.06
83 28 0.04
85 45 0.07
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (76 bp):
TATTTTTAATTTCTGTTTTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGG
Found at i:35476649 original size:75 final size:75
Alignment explanation
Indices: 35475801--35476663 Score: 381
Period size: 76 Copynumber: 11.1 Consensus size: 75
35475791 ATTTCTGTTT
* * * **
35475801 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC-GGG-TCACGTTGAGGC-ATT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGA-GCTATT
**
35475863 TTTAATTTCTGTTG
65 TTCGA-TT-T-TTG
* * * * * *
35475877 TTTTTCAAAAATCAACTCATAGTACGAGAGGTGAGTTGAGCCTC-GGG-TCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
** *
35475940 TTAATTTCTATTT
66 TCGA-TT-T-TTG
* * * * *
35475953 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTC-GGG-TCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
** *
35476016 TTAATTTCTGTTT
66 TCGA-TT-T-TTG
* * * * * * * *
35476029 TTTTTCAAAAATCAACTCATAGTACGAGATGTGAGTTGAGCTTC-GGG-TCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
** *
35476092 TTAATTTCTGTTT
66 TCGA-TT-T-TTG
* * * ** *
35476105 TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACA--CTAAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA--T
** *
35476168 TTTAAATTTCTATTT
64 TTTCGA-TT-T-TTG
* * * * * * *
35476183 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
** *
35476248 TAAATTTCTG
66 TCGATTTTTG
* * *** * *
35476258 TTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTTGCACGCTGAGGTA
1 -TTTTTC--AAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTA
**
35476323 TTTCTTTTAAATTTCTTG
63 ----TTTTCGATTT-TTG
* * * * * *
35476341 TTAGTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGG
1 TT--TTT---CAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGC
** *
35476404 TATTTCTTTTAAATTTATG
61 TA----TTTTCGATTTTTG
* * * * *
35476423 TTTTTCATAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGT
1 TTTTTC----AAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCT
** *
35476487 ATTTCTTTTAAATTTCTG
62 A----TTTTCGATTTTTG
* * * * *
35476505 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATGTCGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
35476570 TCGATTTTTG
66 TCGATTTTTG
* * * * * *
35476580 TTTTTCGAAGATCAACTCATAAT-CAAAGAGGTGAGTTTAGCTTCGGGTCGCACGCCGAGCT-TT
1 TTTTTCAAAAATCAACTCATAATGC-AAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATT
*
35476643 TCTCGATTTTTA
65 T-TCGATTTTTG
35476655 TTTTTCAAA
1 TTTTTCAAA
35476664 TAAAAAGAAA
Statistics
Matches: 705, Mismatches: 54, Indels: 57
0.86 0.07 0.07
Matches are distributed among these distances:
74 4 0.01
75 77 0.11
76 271 0.38
77 4 0.01
78 163 0.23
79 15 0.02
80 10 0.01
81 42 0.06
82 50 0.07
83 26 0.04
84 5 0.01
85 38 0.05
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (75 bp):
TTTTTCAAAAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTCGGGGCACACGCCGAGCTATTT
TCGATTTTTG
Found at i:35476860 original size:31 final size:32
Alignment explanation
Indices: 35476824--35476891 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
35476814 TAGCCCTCGA
35476824 ATTTTTCAAAAATTACATTTTGA-CCCCTAAT
1 ATTTTTCAAAAATTACATTTTGACCCCCTAAT
* * *
35476855 TTTTTTCTAAATTTACATTTTGACCCCCTAAT
1 ATTTTTCAAAAATTACATTTTGACCCCCTAAT
35476887 ATTTT
1 ATTTT
35476892 GTAATTACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTTTTCAAAAATTACATTTTGACCCCCTAAT
Found at i:35477328 original size:27 final size:25
Alignment explanation
Indices: 35477298--35477366 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
35477288 ACCAAGAGGC
35477298 AAGAAAAAAAGAAAAAAGCAAGCAAAA
1 AAGAAAAAAAGAAAAAAG--AGCAAAA
*
35477325 AAGAAAAAAGAAGAAAAAAGAGCAAAG
1 AAG-AAAAA-AAGAAAAAAGAGCAAAA
*
35477352 AA-TAAAAAAGAAAAA
1 AAGAAAAAAAGAAAAA
35477367 GGGGAAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 8 0.21
25 4 0.11
27 11 0.29
28 5 0.13
29 10 0.26
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (25 bp):
AAGAAAAAAAGAAAAAAGAGCAAAA
Found at i:35477341 original size:17 final size:17
Alignment explanation
Indices: 35477302--35477366 Score: 85
Period size: 17 Copynumber: 3.7 Consensus size: 17
35477292 AGAGGCAAGA
35477302 AAAAAAGAAAAAAGCAAG
1 AAAAAAGAAAAAAG-AAG
35477320 CAAAAAAGAAAAAAGAAG
1 -AAAAAAGAAAAAAGAAG
** *
35477338 AAAAAAGAGCAAAGAAT
1 AAAAAAGAAAAAAGAAG
35477355 AAAAAAGAAAAA
1 AAAAAAGAAAAA
35477367 GGGGAAAGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
17 24 0.59
18 3 0.07
19 14 0.34
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAAAGAAG
Found at i:35478271 original size:17 final size:17
Alignment explanation
Indices: 35478249--35478436 Score: 83
Period size: 18 Copynumber: 10.2 Consensus size: 17
35478239 CGCCTTTAAA
35478249 AAAAAATTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
35478266 AAAAAATCTCGTGTTTTC
1 AAAAAATTTCGTG-TTTC
* *
35478284 AATTCAAAAATTTTTGCGCTTTC
1 -A---AAAAA-TTTCGTG-TTTC
* *
35478307 AAAAAAAATCTCGTGTTTTAA
1 --AAAAAATTTCGTG-TTT-C
*
35478328 AAAAAATTTCGCGTTTTC
1 AAAAAATTTCGTG-TTTC
* *
35478346 AAAAATTTTTCGTGTTTT
1 AAAAA-ATTTCGTGTTTC
* *
35478364 AAAAATTTTCGTG-TTA
1 AAAAAATTTCGTGTTTC
**
35478380 AAAAAAACTCGTGTTTC
1 AAAAAATTTCGTGTTTC
* *
35478397 AAAAATTTTCGCAT-TTTG
1 AAAAAATTTCG--TGTTTC
*
35478415 AAAATATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
35478433 AAAA
1 AAAA
35478437 TCTTCGTGTC
Statistics
Matches: 129, Mismatches: 28, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.09
17 31 0.24
18 33 0.26
19 26 0.20
20 7 0.05
21 5 0.04
22 5 0.04
23 8 0.06
24 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:35478271 original size:18 final size:19
Alignment explanation
Indices: 35478248--35478378 Score: 99
Period size: 19 Copynumber: 6.8 Consensus size: 19
35478238 TCGCCTTTAA
35478248 AAAAAAATTTCGTG-TTTC
1 AAAAAAATTTCGTGTTTTC
*
35478266 -AAAAAATCTCGTGTTTTC
1 AAAAAAATTTCGTGTTTTC
* * *
35478284 AATTCAAAAATTTTTGCGCTTTC
1 AA---AAAAA-TTTCGTGTTTTC
* *
35478307 AAAAAAAATCTCGTGTTTTA
1 -AAAAAAATTTCGTGTTTTC
*
35478327 AAAAAAATTTCGCGTTTTC
1 AAAAAAATTTCGTGTTTTC
**
35478346 AAAAATTTTTCGTGTTTT-
1 AAAAAAATTTCGTGTTTTC
*
35478364 -AAAAATTTTCGTGTT
1 AAAAAAATTTCGTGTT
35478379 AAAAAAAACT
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
17 26 0.29
18 4 0.04
19 32 0.36
20 7 0.08
21 5 0.06
22 5 0.06
23 8 0.09
24 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAAAAATTTCGTGTTTTC
Found at i:35479781 original size:7 final size:7
Alignment explanation
Indices: 35479769--35479816 Score: 80
Period size: 7 Copynumber: 7.0 Consensus size: 7
35479759 CTGAGTCAAA
35479769 AAAAATG
1 AAAAATG
35479776 AAAAATG
1 AAAAATG
35479783 AAAAATG
1 AAAAATG
*
35479790 -AGAATG
1 AAAAATG
35479796 AAAAATG
1 AAAAATG
35479803 AAAAATG
1 AAAAATG
35479810 AAAAATG
1 AAAAATG
35479817 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:35479797 original size:20 final size:20
Alignment explanation
Indices: 35479772--35479810 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35479762 AGTCAAAAAA
35479772 AATGAAAAATGAAAAATGAG
1 AATGAAAAATGAAAAATGAG
35479792 AATGAAAAATGAAAAATGA
1 AATGAAAAATGAAAAATGA
35479811 AAAATGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (20 bp):
AATGAAAAATGAAAAATGAG
Found at i:35481114 original size:87 final size:87
Alignment explanation
Indices: 35480968--35481275 Score: 440
Period size: 87 Copynumber: 3.5 Consensus size: 87
35480958 AGATCAGTGG
* **
35480968 AGATAGCAAATCTTGCCCGCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
35481033 CGGTTGCAGTGGAGCTAGTTAA
66 CGGTTGCAGTGGAGCTAGTTAA
* *
35481055 AGATAGCAGATCTTGCCTTCCTGCATTGATAGCGGAGCAGATCGAAAACAAAGCCTTGCCTCCAT
1 AGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
*
35481120 CGGTTGCAGTGGAGCTGGTTAA
66 CGGTTGCAGTGGAGCTAGTTAA
* * *
35481142 AGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAAGATAC-CAGCCTTGCCTCC
1 AGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCC
* * *
35481206 CTCAGTTGCAGTGGAG-TAGGTTGA
64 ATCGGTTGCAGTGGAGCTA-GTTAA
* * *
35481230 AGATAGCAGATATTGCCTTCCTGCATCGACAGTGAAGCAGATCGAA
1 AGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA
35481276 GATTACAAGT
Statistics
Matches: 198, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
87 124 0.63
88 72 0.36
89 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.22
Consensus pattern (87 bp):
AGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCAT
CGGTTGCAGTGGAGCTAGTTAA
Found at i:35481246 original size:44 final size:44
Alignment explanation
Indices: 35481022--35481247 Score: 117
Period size: 44 Copynumber: 5.2 Consensus size: 44
35481012 AAAACAAAGC
* * *
35481022 CTTGCCTCCATCGGTTGCAGTGGAGCTA-GTTAAAGATAGCAGAT
1 CTTGCCTCCCTCAGTTGCAGTGGAG-TAGGTTGAAGATAGCAGAT
* * * * * * * *
35481066 CTTGCCTTCCTGCA-TTGATAGCGGAGCAGATCGAA-A-A-CAAAGC
1 CTTGCCTCCCT-CAGTTG-CAGTGGAGTAGGTTGAAGATAGCAGA-T
* * *
35481109 CTTGCCTCCATCGGTTGCAGTGGAGCT-GGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCAGTTGCAGTGGAG-TAGGTTGAAGATAGCAGAT
* * * * * * * * *
35481153 CTTGCCTTCCTACA-CTGACAGCGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTCCCT-CAGTTG-CAGTGGAGTAGGTTGAAGATAGCAGAT
35481197 CTTGCCTCCCTCAGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTCAGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
*
35481241 ATTGCCT
1 CTTGCCT
35481248 TCCTGCATCG
Statistics
Matches: 124, Mismatches: 44, Indels: 28
0.63 0.22 0.14
Matches are distributed among these distances:
42 14 0.11
43 35 0.28
44 44 0.35
45 31 0.25
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (44 bp):
CTTGCCTCCCTCAGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
Found at i:35481277 original size:45 final size:44
Alignment explanation
Indices: 35481141--35481278 Score: 129
Period size: 45 Copynumber: 3.1 Consensus size: 44
35481131 GAGCTGGTTA
*
35481141 AAGATAGCAGATCTTGCCTTCCTACA-CTGACAGCGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCT-CATC-GACAGTGAAGCAGATCG
* * * * * * * *
35481186 AAGATACCAG-CCTTGCCTCCCTCAGTTG-CAGTGGAGTAGGTTG
1 AAGATAGCAGATCTTGCCTTCCTCA-TCGACAGTGAAGCAGATCG
*
35481229 AAGATAGCAGATATTGCCTTCCTGCATCGACAGTGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCT-CATCGACAGTGAAGCAGATCG
35481274 AAGAT
1 AAGAT
35481279 TACAAGTTCT
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
43 21 0.30
44 22 0.31
45 27 0.39
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (44 bp):
AAGATAGCAGATCTTGCCTTCCTCATCGACAGTGAAGCAGATCG
Found at i:35481844 original size:100 final size:100
Alignment explanation
Indices: 35481671--35482074 Score: 684
Period size: 100 Copynumber: 4.0 Consensus size: 100
35481661 CGAAGAAGCA
* *
35481671 AATCTTATCCCTCAGGCAATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
1 AATCTTATCCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
*
35481736 ACATTGCAGTTCAAAAGATTAAAGCTACAATAGCG
66 ACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
* *
35481771 AATCTTATCCCCCATGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCG
1 AATCTTATCCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
35481836 ACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
66 ACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
*
35481871 AATCTTATCCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGTTTCCCCG
1 AATCTTATCCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* *
35481936 GCATTGCAGTTCAAAAGATTAAAGCTACAATAGCG
66 ACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
* * *
35481971 AATCTTA-CCTCCCAGGCGATGCAGTGTAGCAGATTAAAGCCACATCGGTGAATCATGCTTCCCC
1 AATCTTATCC-CCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
*
35482035 GACATTGCAGTTCAAAAGATTAAAGCCACAACAGCG
65 GACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
35482071 AATC
1 AATC
35482075 GTGCTTCCCC
Statistics
Matches: 286, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
99 2 0.01
100 284 0.99
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (100 bp):
AATCTTATCCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
ACATTGCAGTTCAAAAGATTAAAGCTACAACAGCG
Found at i:35482115 original size:50 final size:50
Alignment explanation
Indices: 35481701--35482126 Score: 364
Period size: 50 Copynumber: 8.5 Consensus size: 50
35481691 GCAGTGGAAC
* *
35481701 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* ** * * ** *
35481751 AGATTAAAGCTACAATAGCGAATCTT--ATCCCCCATGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGA--C-ATTGCAGTTCAAA
** *
35481801 AGATTAAAGCCACATTGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* * * * * ** *
35481851 AGATTAAAGCTACAACAGCGAATCTT-ATCCCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCC-GAC-ATTGCAGTTCAAA
* * * *
35481901 AGATTAAAGCCACATCGGTGAATCTTGTTTCCCCGGCATTGCAGTTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* ** * * * * **
35481951 AGATTAAAGCTACAATAGCGAATCTTACCTCCCAGGCGA-TGCAGTGT-AGC
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGAC-ATTGCAGT-TCAAA
* * *
35482001 AGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* *
35482051 AGATTAAAGCCACAACAGCGAATCGTGCTTCCCCGACATTGCAGTT-AAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
*
35482100 ATGATTAAAGCCACAATGGCGAATCTT
1 A-GATTAAAGCCACAACGGCGAATCTT
35482127 ACTTTCTAAA
Statistics
Matches: 292, Mismatches: 69, Indels: 30
0.75 0.18 0.08
Matches are distributed among these distances:
48 6 0.02
49 13 0.04
50 258 0.88
51 9 0.03
52 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTCAAA
Found at i:35483611 original size:12 final size:12
Alignment explanation
Indices: 35483594--35483628 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35483584 TAACAGTTTA
35483594 ATTATTTTTATT
1 ATTATTTTTATT
**
35483606 ATTATTGCTATT
1 ATTATTTTTATT
35483618 ATTATTTTTAT
1 ATTATTTTTAT
35483629 CACTAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:35486775 original size:16 final size:17
Alignment explanation
Indices: 35486740--35486775 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35486730 TTCAATCATT
* *
35486740 AAAAAAACGAATATGAA
1 AAAAAAACAAACATGAA
35486757 AAAAAAACAAACATGAA
1 AAAAAAACAAACATGAA
35486774 AA
1 AA
35486776 CATCACAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAACAAACATGAA
Found at i:35487581 original size:20 final size:20
Alignment explanation
Indices: 35487556--35487594 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35487546 TGATATGTAT
35487556 TTAAAT-ATAAAATAAATTAC
1 TTAAATAATAAAA-AAATTAC
35487576 TTAAATCAATAAAAAAATT
1 TTAAAT-AATAAAAAAATT
35487595 GAAAATTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAATAATAAAAAAATTAC
Found at i:35487669 original size:14 final size:13
Alignment explanation
Indices: 35487650--35487684 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
35487640 TTTACTAATT
35487650 TTTTATTTATTTTA
1 TTTTATTT-TTTTA
35487664 TTTTATTTTTTTA
1 TTTTATTTTTTTA
35487677 TTATTATT
1 TT-TTATT
35487685 GAATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:35490756 original size:107 final size:109
Alignment explanation
Indices: 35490601--35490885 Score: 436
Period size: 107 Copynumber: 2.6 Consensus size: 109
35490591 AGCTATTGTG
35490601 ACGAGAAAATCGACACCCAGTA-CTTAGGGCATGTTTCTCGAATTTCCAAACGCAAAACATTGCC
1 ACGAGAAAATCGACACCCAGTACCTTAGGGCATGTTTCTCGAATTTCCAAACGCAAAACATTGCC
35490665 TTA-TTTGAAAA-TTTTTGAAAAGGATATTAAG-TCATTTGGTCGA
66 TTATTTTGAAAAGTTTTT-AAAAGGATATTAAGCT-ATTTGGTCGA
* * * *
35490708 ACGAG-AAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTACC
1 ACGAGAAAATCGACACCCAGTACCTTAGGGCATGTTTCTCGAATTTCCAAACGCAAAACATTGCC
*
35490772 TTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGA
66 TTA-TTTTGAAAAGTTTTTAAAAGGATATTAAGCTATTTGGTCGA
*
35490817 ACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTG
1 ACGAG-AAAATCGACACCCAGTACCTTAGGGCATG-TTTCTCGAATTTCCAAACGCAAAACATTG
35490882 CCTT
64 CCTT
35490886 TATTATTTTT
Statistics
Matches: 160, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
106 15 0.09
107 47 0.29
109 36 0.22
110 6 0.04
111 25 0.16
112 31 0.19
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (109 bp):
ACGAGAAAATCGACACCCAGTACCTTAGGGCATGTTTCTCGAATTTCCAAACGCAAAACATTGCC
TTATTTTGAAAAGTTTTTAAAAGGATATTAAGCTATTTGGTCGA
Found at i:35491581 original size:35 final size:34
Alignment explanation
Indices: 35491524--35491596 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
35491514 ACATATTTTA
*
35491524 ATATATGTAAAAAAAACCATGAGAATATATATAT
1 ATATATGTAAAAAAAAACATGAGAATATATATAT
* * * *
35491558 ATATATGTATAAAAAAAATATGAGTATTTATGTAT
1 ATATATGTA-AAAAAAAACATGAGAATATATATAT
35491593 ATAT
1 ATAT
35491597 TAAATAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.36
Consensus pattern (34 bp):
ATATATGTAAAAAAAAACATGAGAATATATATAT
Found at i:35493326 original size:2 final size:2
Alignment explanation
Indices: 35493319--35493344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35493309 ATGACTATGC
35493319 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
35493345 TGATAGGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35494016 original size:18 final size:18
Alignment explanation
Indices: 35493993--35494035 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35493983 ATTTTACAAT
35493993 TCGAATAGCTCAAATAAC
1 TCGAATAGCTCAAATAAC
* *
35494011 TCGAATAGTTCGAATAAC
1 TCGAATAGCTCAAATAAC
*
35494029 TCAAATA
1 TCGAATA
35494036 ACAAATTTGT
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:0.44, C:0.19, G:0.12, T:0.26
Consensus pattern (18 bp):
TCGAATAGCTCAAATAAC
Found at i:35499148 original size:25 final size:25
Alignment explanation
Indices: 35499114--35499165 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
35499104 ATGAATGTCA
*
35499114 TTAAAAAGGTCCACTAGAGAAAGGG
1 TTAAAAAGGTCAACTAGAGAAAGGG
35499139 TTAAAAAGGTCAACTAGAGAAAGGG
1 TTAAAAAGGTCAACTAGAGAAAGGG
35499164 TT
1 TT
35499166 TCTAATTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (25 bp):
TTAAAAAGGTCAACTAGAGAAAGGG
Found at i:35500054 original size:13 final size:13
Alignment explanation
Indices: 35500036--35500061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35500026 GGACTTTGTA
35500036 CTTTTAAATGCTT
1 CTTTTAAATGCTT
35500049 CTTTTAAATGCTT
1 CTTTTAAATGCTT
35500062 TTATAGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTTTAAATGCTT
Found at i:35500231 original size:25 final size:25
Alignment explanation
Indices: 35500197--35500244 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
35500187 AAAGACATGT
35500197 TTAGGGTTATGGTCCCCAAATTATA
1 TTAGGGTTATGGTCCCCAAATTATA
**
35500222 TTAGGGTTATGGTTTCCAAATTA
1 TTAGGGTTATGGTCCCCAAATTA
35500245 CACACAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (25 bp):
TTAGGGTTATGGTCCCCAAATTATA
Found at i:35502643 original size:41 final size:41
Alignment explanation
Indices: 35502588--35502737 Score: 219
Period size: 41 Copynumber: 3.7 Consensus size: 41
35502578 TTTAACATAT
* * * *
35502588 TCACCGGCATTTAGCCTGCTAAGCTTATAGCCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * *
35502629 TCACCGACACTTAGCCTGCTAGGTTTATAACCGGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
35502670 TAACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
35502711 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
35502738 AAGTCCGAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:35503173 original size:12 final size:12
Alignment explanation
Indices: 35503145--35503177 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35503135 AGCTCATCAA
35503145 ATATACA-ATAG
1 ATATACATATAG
*
35503156 ATATACATATAT
1 ATATACATATAG
35503168 ATATACATAT
1 ATATACATAT
35503178 TCGAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAG
Found at i:35503221 original size:114 final size:112
Alignment explanation
Indices: 35503098--35503405 Score: 526
Period size: 114 Copynumber: 2.7 Consensus size: 112
35503088 ACTAATTTCA
35503098 ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACA
1 ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACA
*
35503163 TATATATATACATATTCGAACTTCATTTATGTGTATATATATAACATTC
66 TATATATATACATATTCGAACTTCATTTA--TGCATATATATAACATTC
35503212 ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACA
1 ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATAC-
*
35503277 TATATATATATACATATTCGAACTTCATTTATGCATATATATATCATTC
65 -ATATATATATACATATTCGAACTTCATTTATGCATATATATAACATTC
* * *
35503326 ATACTTAACTAATTTCAATTCGTATACTTTTAATTATAGCTCATCAAATGTACAATAGTTATACA
1 ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACA
*
35503391 TATATATATATATAT
66 TATATATATACATAT
35503406 ATATGCTGAT
Statistics
Matches: 186, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
112 15 0.08
114 141 0.76
116 30 0.16
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (112 bp):
ATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAGATATACA
TATATATATACATATTCGAACTTCATTTATGCATATATATAACATTC
Found at i:35504400 original size:13 final size:13
Alignment explanation
Indices: 35504382--35504406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35504372 CAATCAAATG
35504382 CACACAAAATAAA
1 CACACAAAATAAA
35504395 CACACAAAATAA
1 CACACAAAATAA
35504407 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:35506162 original size:33 final size:33
Alignment explanation
Indices: 35506125--35506361 Score: 100
Period size: 33 Copynumber: 7.1 Consensus size: 33
35506115 TTTTAATGAA
*
35506125 AAGACCATAATTGGGTTATGGCACTATGAACGT
1 AAGACCATAATTGGGCTATGGCACTATGAACGT
** * * ** * * * *
35506158 AAGACCATGGTTGGACCATGATAGTGTTTATATGT
1 AAGACCATAATTGGGCTATGGCACT-ATGA-ACGT
** * * *
35506193 AAGACCATAGCTGGGCTATGGCATTCTG-ATGAT
1 AAGACCATAATTGGGCTATGGCACTATGAACG-T
*
35506226 AAGACCATAATTGGGTTATGGCACTATGAACGT
1 AAGACCATAATTGGGCTATGGCACTATGAACGT
** * * * * * *
35506259 AAGACCATGGTTGGACCATGGCAGTGTTTATATGT
1 AAGACCATAATTGGGCTATGGCACT-ATGA-ACGT
** * * *
35506294 AAGACCATAGCTGGGCTATGGCATTCTG-ATGAT
1 AAGACCATAATTGGGCTATGGCACTATGAACG-T
* * * *
35506327 AAGACCATAACTGGGTTATGGCACTACGAATGT
1 AAGACCATAATTGGGCTATGGCACTATGAACGT
35506360 AA
1 AA
35506362 AGGATGAATT
Statistics
Matches: 149, Mismatches: 47, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
32 6 0.04
33 88 0.59
34 11 0.07
35 44 0.30
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (33 bp):
AAGACCATAATTGGGCTATGGCACTATGAACGT
Found at i:35506261 original size:101 final size:101
Alignment explanation
Indices: 35506058--35506361 Score: 511
Period size: 101 Copynumber: 3.0 Consensus size: 101
35506048 ATTGACGGAG
* * * *
35506058 AAGACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCATAGCTGGG-TATGGCATTTTAAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
*
35506122 GAAAAGACCATAATTGGGTTATGGCACTATGAACGT
66 GATAAGACCATAATTGGGTTATGGCACTATGAACGT
**
35506158 AAGACCATGGTTGGACCATGATAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
35506223 GATAAGACCATAATTGGGTTATGGCACTATGAACGT
66 GATAAGACCATAATTGGGTTATGGCACTATGAACGT
35506259 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* * *
35506324 GATAAGACCATAACTGGGTTATGGCACTACGAATGT
66 GATAAGACCATAATTGGGTTATGGCACTATGAACGT
35506360 AA
1 AA
35506362 AGGATGAATT
Statistics
Matches: 191, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
100 46 0.24
101 145 0.76
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (101 bp):
AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
GATAAGACCATAATTGGGTTATGGCACTATGAACGT
Found at i:35506404 original size:25 final size:25
Alignment explanation
Indices: 35506355--35506420 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
35506345 TGGCACTACG
* *
35506355 AATGTAAAGGATGA-ATTGACGGAA
1 AATGTAAAAGATGATATTGACAGAA
35506379 AATGTAAAAGATGATATATGA-AGAA
1 AATGTAAAAGATGATAT-TGACAGAA
*
35506404 ACA-ATAAAAGATGATAT
1 A-ATGTAAAAGATGATAT
35506421 GTATCATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.36
25 19 0.53
26 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.23
Consensus pattern (25 bp):
AATGTAAAAGATGATATTGACAGAA
Found at i:35508430 original size:19 final size:17
Alignment explanation
Indices: 35508394--35508437 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
35508384 ATATTAAAAA
35508394 TATATTTTTTAATATTT
1 TATATTTTTTAATATTT
*
35508411 TATACTTTTTTGAATTTTT
1 TATA-TTTTTT-AATATTT
35508430 TATATTTT
1 TATATTTT
35508438 AAAAACAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATATTTTTTAATATTT
Found at i:35516942 original size:2 final size:2
Alignment explanation
Indices: 35516935--35516981 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35516925 CCTTAATGTT
35516935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35516977 TA TA T
1 TA TA T
35516982 TGTCAATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35519131 original size:108 final size:110
Alignment explanation
Indices: 35518960--35519163 Score: 340
Period size: 108 Copynumber: 1.9 Consensus size: 110
35518950 AATTTGGCTA
* * *
35518960 AACGTGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAATGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
35519025 TTA-TTTTGA-AAATTTTTGAAAAGGATATTAAGTCATTTGGTGG
66 TTATTTTTGAGAAATTTTTGAAAAGGATATTAAGTCATTTGGTGG
*
35519068 AACGAGAAGTCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
* *
35519133 TTATTTTTGAGAAGTTTTTTAAAAGGATATT
66 TTATTTTTGAGAAATTTTTGAAAAGGATATT
35519164 TAGCTATNNN
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 64 0.73
109 6 0.07
110 18 0.20
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (110 bp):
AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
TTATTTTTGAGAAATTTTTGAAAAGGATATTAAGTCATTTGGTGG
Found at i:35519728 original size:13 final size:13
Alignment explanation
Indices: 35519710--35519790 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
35519700 GAATCATAAA
35519710 ATATAAAATACAT
1 ATATAAAATACAT
35519723 ATATAAAATACAT
1 ATATAAAATACAT
* * * *
35519736 TTTTAAAAAAAAT
1 ATATAAAATACAT
*
35519749 ATGT-AAAT--AT
1 ATATAAAATACAT
* *
35519759 ATAT-ATATATAT
1 ATATAAAATACAT
*
35519771 AAATAAAATACAT
1 ATATAAAATACAT
35519784 ATATAAA
1 ATATAAA
35519791 TATGTATATG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
10 8 0.15
12 8 0.15
13 36 0.69
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:35519910 original size:3 final size:3
Alignment explanation
Indices: 35519902--35519959 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
35519892 ATATAAGAGC
35519902 AAT AAT 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 AAT AAT
35519950 AAT AAT AAT A
1 AAT AAT AAT A
35519960 GGACTAAATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35520623 original size:21 final size:22
Alignment explanation
Indices: 35520597--35520640 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
35520587 CAAACAGAAG
35520597 TAAAAAATAAATAAAT-AAAAA
1 TAAAAAATAAATAAATGAAAAA
* *
35520618 T-AAAAATAGATTAATGAAAAA
1 TAAAAAATAAATAAATGAAAAA
35520639 TA
1 TA
35520641 GAATGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAAAATAAATAAATGAAAAA
Found at i:35526190 original size:11 final size:11
Alignment explanation
Indices: 35526174--35526213 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
35526164 TTCAAAAATT
35526174 CTCTTAAGTTC
1 CTCTTAAGTTC
35526185 CTCTTAAGTTC
1 CTCTTAAGTTC
*
35526196 CTCTTAAGTTT
1 CTCTTAAGTTC
35526207 CTCTTAA
1 CTCTTAA
35526214 CTCCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCTTAAGTTC
Found at i:35526258 original size:12 final size:12
Alignment explanation
Indices: 35526219--35526262 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
35526209 CTTAACTCCC
*
35526219 TTTTTTTAAATA
1 TTTTTTAAAATA
* *
35526231 ATTTTAAAAATA
1 TTTTTTAAAATA
35526243 TTTTTTAAAAT-
1 TTTTTTAAAATA
35526254 TTTTTTAAA
1 TTTTTTAAA
35526263 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:35527374 original size:7 final size:7
Alignment explanation
Indices: 35527362--35527386 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35527352 AGTCGATTGA
35527362 TATTTAG
1 TATTTAG
35527369 TATTTAG
1 TATTTAG
35527376 TATTTAG
1 TATTTAG
35527383 TATT
1 TATT
35527387 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:35528356 original size:25 final size:25
Alignment explanation
Indices: 35528328--35528375 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
35528318 TATTTTGATA
35528328 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
35528353 TTATTTGATTTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
35528376 ATTTTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:35528493 original size:45 final size:43
Alignment explanation
Indices: 35528419--35528730 Score: 220
Period size: 45 Copynumber: 7.0 Consensus size: 43
35528409 TTAATACCTT
* * *
35528419 TAAA-TTAAAAACCCTAACCTAATTTACTTAAAAACCTTAAACCC
1 TAAACTTAAAAACCCTAACCCAATTAACTTAAAAACCCT-AA-CC
**
35528463 TAAACTTAAAAACCCTAACCCCCTTAACTTAAAAACCCTAACC
1 TAAACTTAAAAACCCTAACCCAATTAACTTAAAAACCCTAACC
* * *
35528506 TAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACT
1 T-A--AACTTAAAAACCCTAACCCAATTAACTTAAAAACCCTAACC
* * * *
35528552 TAATTTAATTAAAAATCCTAAACCC--TAAACTTAAAAACCCTAATC
1 TAA---ACTTAAAAACCCT-AACCCAATTAACTTAAAAACCCTAACC
* * *
35528597 TAATTTAATTAAAAACCGTAAACCC--TAAACTTAAAAACCCTAACC
1 TAA---ACTTAAAAACCCT-AACCCAATTAACTTAAAAACCCTAACC
* * * * * *
35528642 TAATTAAATTAAAAATCATAACCTAATTAAATTTAAAACCCTGAACCC
1 T-A--AACTTAAAAACCCTAACCCAATTAACTTAAAAACCCT-AA-CC
* *
35528690 TAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 TAAACTTAAAAACCCTAACCCAATTAACTTAAAAACCCTAA
35528731 ACTANNNNNN
Statistics
Matches: 223, Mismatches: 30, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
43 4 0.02
44 13 0.06
45 133 0.60
46 62 0.28
47 7 0.03
48 4 0.02
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (43 bp):
TAAACTTAAAAACCCTAACCCAATTAACTTAAAAACCCTAACC
Found at i:35528503 original size:68 final size:66
Alignment explanation
Indices: 35528418--35528730 Score: 305
Period size: 68 Copynumber: 4.6 Consensus size: 66
35528408 ATTAATACCT
* * * *
35528418 TTAAATTAAAAACCCTAACCTAATTTACTTAAAAACCTTAAACCCT-A-AACTTAAAAACCCTAA
1 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCT-AA-CCTAATAAATTAAAAACCCTAA
35528481 CCCCC
64 --CCC
35528486 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
1 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAA-TAAATTAAAAACCCTAAC
**
35528551 TTAAT
65 ---CC
* * * *
35528556 TTAA-TTAAAAATCCTAAACCCT-A--AACTTAAAAACCCTAATCTAATTTAATTAAAAACCGTA
1 TTAACTTAAAAACCCT-AA-CCTAATTAACTTAAAAACCCTAACCTAA-TAAATTAAAAACCCT-
35528617 AACCC
62 AACCC
* * * * *
35528622 TAAACTTAAAAACCCTAACCTAATTAAATTAAAAATCATAACCTAATTAAATTTAAAACCCTGAA
1 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAA-TAAATTAAAAACCCT-AA
35528687 CCC
64 CCC
* *
35528690 TAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAA
35528731 ACTANNNNNN
Statistics
Matches: 208, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
65 3 0.01
66 9 0.04
67 14 0.07
68 144 0.69
69 28 0.13
70 7 0.03
71 3 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.27
Consensus pattern (66 bp):
TTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATAAATTAAAAACCCTAACC
C
Found at i:35528538 original size:28 final size:23
Alignment explanation
Indices: 35528418--35528730 Score: 285
Period size: 23 Copynumber: 13.8 Consensus size: 23
35528408 ATTAATACCT
*
35528418 TTAAATTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
35528441 TTTACTTAAAAACCTTAAACCCT-A
1 TTAACTTAAAAACCCT-AA-CCTAA
***
35528465 --AACTTAAAAACCCTAACCCCC
1 TTAACTTAAAAACCCTAACCTAA
35528486 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
35528509 TTAACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
35528532 TTAAATTAAAAACCCTAACTTAA
1 TTAACTTAAAAACCCTAACCTAA
*
35528555 TTTAA-TTAAAAATCCTAAACCCT-A
1 -TTAACTTAAAAACCCT-AA-CCTAA
*
35528579 --AACTTAAAAACCCTAATCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
35528600 TTTAA-TTAAAAACCGTAAACCCT-A
1 -TTAACTTAAAAACCCT-AA-CCTAA
35528624 --AACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* * *
35528645 TTAAATTAAAAATCATAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
* *
35528668 TTAAATTTAAAACCCTGAACCCT-A
1 TTAACTTAAAAACCCT-AA-CCTAA
35528692 --AACTTAAAAACCCTAACCTAA
1 TTAACTTAAAAACCCTAACCTAA
*
35528713 TTAAATTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
35528731 ACTANNNNNN
Statistics
Matches: 238, Mismatches: 28, Indels: 48
0.76 0.09 0.15
Matches are distributed among these distances:
20 10 0.04
21 15 0.06
22 44 0.18
23 141 0.59
24 18 0.08
25 10 0.04
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.27
Consensus pattern (23 bp):
TTAACTTAAAAACCCTAACCTAA
Found at i:35528870 original size:23 final size:23
Alignment explanation
Indices: 35528835--35529382 Score: 627
Period size: 23 Copynumber: 23.9 Consensus size: 23
35528825 NNNNNNNNNN
*
35528835 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTAAATT
*
35528858 -AAAACCCTAAACCTAATTTAATT
1 AAAAACCCT-AACCTAATTAAATT
* *
35528881 TAAAACCCTAAACCT-ACTAAACTT
1 AAAAACCCT-AACCTAATTAAA-TT
35528905 AAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
35528928 AAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
35528951 AAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
*
35528974 AAAAACCCTAACCTAATTAACTT
1 AAAAACCCTAACCTAATTAAATT
* *
35528997 AAAAACTCTAACCTAATTAACTT
1 AAAAACCCTAACCTAATTAAATT
*
35529020 AAAAACTCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
35529043 AAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
* * *
35529066 AAAAATCATAAACCCT-A--AACTT
1 AAAAACCCT-AA-CCTAATTAAATT
*
35529088 AAAAACCCTAACCCT--CTAAACTT
1 AAAAACCCTAA-CCTAATTAAA-TT
*
35529111 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTAAATT
*
35529134 AAAAACCCTAAACCCT-A--AACTT
1 AAAAACCCT-AA-CCTAATTAAATT
*
35529156 AAAAACCCTAACCTAATTTAATT
1 AAAAACCCTAACCTAATTAAATT
*
35529179 AAAAACTCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
*** *
35529202 AAAAACCCTAACCCCCTTAACTT
1 AAAAACCCTAACCTAATTAAATT
*
35529225 AAAAACCCTAACCTAATTAACTT
1 AAAAACCCTAACCTAATTAAATT
*
35529248 AAAAACTCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
35529271 AAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
* *
35529294 AAGAACCCTAAACCCT-A--AACTT
1 AAAAACCCT-AA-CCTAATTAAATT
** *
35529316 AAAAACCCTAACCCCATTAACTT
1 AAAAACCCTAACCTAATTAAATT
**
35529339 AAAAAATCTAACCTAATTAAATT
1 AAAAACCCTAACCTAATTAAATT
*
35529362 AAAAACCCTAAACTAAATTAA
1 AAAAACCCTAACCT-AATTAA
35529383 TAATTTTACT
Statistics
Matches: 458, Mismatches: 45, Indels: 43
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.01
21 12 0.03
22 48 0.10
23 337 0.74
24 47 0.10
25 9 0.02
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAACCCTAACCTAATTAAATT
Found at i:35529323 original size:228 final size:227
Alignment explanation
Indices: 35528922--35529382 Score: 766
Period size: 228 Copynumber: 2.0 Consensus size: 227
35528912 CTAACCTAAT
35528922 TAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
1 TAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
* *
35528987 TAATTAACTTAAAAACTCTAACCTAATTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCT
66 CAATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCT
*
35529052 AACCTAATTAAATTAAAAATCATAAACCCTAAACTTAAAAACCCTAACCCTC-TAAACTTAAAAA
131 AACCTAATTAAATTAAAAACCATAAACCCTAAACTTAAAAACCCTAACCC-CATAAACTTAAAAA
* *
35529116 CCCTAACCTAATTTAATTAAAAACCCTAAACCC
195 ACCTAACCTAATTAAATTAAAAACCCTAAACCC
* *
35529149 TAAACTTAAAAACCCTAACCTAATTTAATTAAAAACTCTAACCTAATTAAATTAAAAACCCTAAC
1 TAAA-TTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
**
35529214 CCCCTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCC
65 CCAATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCC
* * *
35529279 TAACCTAATTAAATTAAGAACCCTAAACCCTAAACTTAAAAACCCTAACCCCATTAACTTAAAAA
130 TAACCTAATTAAATTAAAAACCATAAACCCTAAACTTAAAAACCCTAACCCCATAAACTTAAAAA
*
35529344 ATCTAACCTAATTAAATTAAAAACCCTAAA--C
195 ACCTAACCTAATTAAATTAAAAACCCTAAACCC
35529375 TAAATTAA
1 TAAATTAA
35529383 TAATTTTACT
Statistics
Matches: 219, Mismatches: 13, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
225 4 0.02
226 5 0.02
227 5 0.02
228 205 0.94
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (227 bp):
TAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
CAATTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCCT
AACCTAATTAAATTAAAAACCATAAACCCTAAACTTAAAAACCCTAACCCCATAAACTTAAAAAA
CCTAACCTAATTAAATTAAAAACCCTAAACCC
Found at i:35529586 original size:116 final size:116
Alignment explanation
Indices: 35529377--35529620 Score: 427
Period size: 116 Copynumber: 2.1 Consensus size: 116
35529367 CCCTAAACTA
* **
35529377 AATTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAAT
* *
35529442 TAATAATTTTATATAATTTGATAATTTTACTAATCATTAATACAGTTTATC
66 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTATC
35529493 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATG-TTTTGACTGGTACTAACAAT
1 AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAAT
35529557 TAATAATTTTATATAATTTGATAATTTTTACTAACCATTAATACAATTTATC
66 TAATAATTTTATATAATTTGATAA-TTTTACTAACCATTAATACAATTTATC
35529609 AATTAATAATTT
1 AATTAATAATTT
35529621 CACAAACTTA
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
115 42 0.34
116 80 0.66
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (116 bp):
AATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTTGACTGGTACTAACAAT
TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTATC
Found at i:35532788 original size:125 final size:125
Alignment explanation
Indices: 35532631--35533003 Score: 597
Period size: 124 Copynumber: 3.0 Consensus size: 125
35532621 CAAACATGCT
*
35532631 ACTGTAGCAAAAGCGCGTCTACGAGGGAGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGAGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
35532696 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
* *
35532756 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAACATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGAGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
* * *
35532820 AGAAACGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTCCATGACCT
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
* * *
35532880 ACTGTAGCAAAAGCACGTCCATGAGGGTGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGAGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
* *** *
35532944 AGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGACC
35533004 TAAAAACCCT
Statistics
Matches: 229, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
123 3 0.01
124 174 0.76
125 52 0.23
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGAGCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGACCG
Found at i:35534145 original size:2 final size:2
Alignment explanation
Indices: 35534138--35534202 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
35534128 TGCTTAAACT
35534138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35534180 TA T- TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35534203 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35538522 original size:2 final size:2
Alignment explanation
Indices: 35538510--35538594 Score: 154
Period size: 2 Copynumber: 43.0 Consensus size: 2
35538500 TTTTATTTTC
*
35538510 AT AT AT CT AT AT AT -T 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 AT AT AT AT AT
35538551 AT AT AT AT AT 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 AT AT AT AT AT
35538593 AT
1 AT
35538595 CTTGGTGAGG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35560447 original size:20 final size:19
Alignment explanation
Indices: 35560421--35560502 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 19
35560411 TCATTCTTAA
*
35560421 AAAAATTTTAAAAAAAACCT
1 AAAAATTTTAAAAAAAA-AT
*
35560441 TAAAATTTTGAAAATAAAAAT
1 AAAAATTTT-AAAA-AAAAAT
*
35560462 AAAAATTGTTAAAAAAATAT
1 AAAAATT-TTAAAAAAAAAT
35560482 AAGAAATCTTTCAAAAAAAAA
1 AA-AAAT-TTT-AAAAAAAAA
35560503 AGGAATATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 15 0.29
21 21 0.41
22 15 0.29
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAATTTTAAAAAAAAAT
Found at i:35560958 original size:10 final size:11
Alignment explanation
Indices: 35560932--35560956 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35560922 AATTTTAGAA
35560932 TTTTAATTTTT
1 TTTTAATTTTT
35560943 TTTTAATTTTT
1 TTTTAATTTTT
35560954 TTT
1 TTT
35560957 AAGAATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:35562802 original size:13 final size:13
Alignment explanation
Indices: 35562786--35562811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35562776 ATTGATCTCA
35562786 AATATGTTCAAAG
1 AATATGTTCAAAG
35562799 AATATGTTCAAAG
1 AATATGTTCAAAG
35562812 TCGAGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AATATGTTCAAAG
Found at i:35570003 original size:2 final size:2
Alignment explanation
Indices: 35569996--35570040 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35569986 CCCTTCAAGT
35569996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35570038 TA T
1 TA T
35570041 GAATGATACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35570275 original size:5 final size:5
Alignment explanation
Indices: 35570265--35570292 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35570255 AATTAAGAGT
35570265 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
35570293 GTCTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:35570389 original size:4 final size:4
Alignment explanation
Indices: 35570380--35570409 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
35570370 AATAATAGTC
35570380 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
35570410 AAATGGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:35574322 original size:3 final size:3
Alignment explanation
Indices: 35574314--35574387 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
35574304 TAATTCTCAC
35574314 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
35574362 TAA TAA TAA TAT TAA TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
35574388 CTTACCTCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35575253 original size:4 final size:4
Alignment explanation
Indices: 35575244--35575274 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35575234 TCTCAAGATA
35575244 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
35575275 ATTTTAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:35575937 original size:157 final size:158
Alignment explanation
Indices: 35575748--35576062 Score: 465
Period size: 160 Copynumber: 2.0 Consensus size: 158
35575738 GTCATTACAC
* * *
35575748 CTTTTTTTGCTTCTAGTTCTTGTACTCGTACCAGACTAAG-GA-AAAAAATCACAACCCCAAATT
1 CTTTTTTTGCTTCTAGTTCTTGTACTCATACCAGACTAAGAAAGAAAAAATCACAAACCCAAATT
* *
35575811 AGATTTAAATATTTTGAAACTTGACAGT-AAAAAATGTTTATAATATACTTGTGATCCAGTTGTA
66 AGATTTAAATATTTTGAAACTTGACAATGAAAAAATGTTTA-AATATACCTGTGATCCAGTTGTA
* * * *
35575875 TTAGGTTGAATGCATGGTCTTTTGTTGTT
130 TTAGGTCGAAGGCATGATCTTCTGTTGTT
*
35575904 CTTTTTTTGGCTTCTAGTTCTTGTACTCATACCAGACTAAGACAAGAAAAAATCACAAACGCAAA
1 CTTTTTTT-GCTTCTAGTTCTTGTACTCATACCAGACTAAGA-AAGAAAAAATCACAAACCCAAA
* *
35575969 TTAGATTTAAATATTTTGAAACTTGACAATGAAAAAGTGTTTACATATACCTGTGATCCAGTTGT
64 TTAGATTTAAATATTTTGAAACTTGACAATGAAAAAATGTTTAAATATACCTGTGATCCAGTTGT
*
35576034 GTTAGGTCGAAGGCATGATCTTCTGTTGT
129 ATTAGGTCGAAGGCATGATCTTCTGTTGT
35576063 GACCCTCACC
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
156 8 0.06
157 31 0.22
159 1 0.01
160 90 0.64
161 11 0.08
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (158 bp):
CTTTTTTTGCTTCTAGTTCTTGTACTCATACCAGACTAAGAAAGAAAAAATCACAAACCCAAATT
AGATTTAAATATTTTGAAACTTGACAATGAAAAAATGTTTAAATATACCTGTGATCCAGTTGTAT
TAGGTCGAAGGCATGATCTTCTGTTGTT
Found at i:35578356 original size:18 final size:18
Alignment explanation
Indices: 35578333--35578375 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
35578323 AACCATCTAA
*
35578333 ACCTTCAACACCCTTACC
1 ACCTTCAACACCCTCACC
*
35578351 ACCTTCACCACCCTCACC
1 ACCTTCAACACCCTCACC
35578369 ACCTTCA
1 ACCTTCA
35578376 TTGCCAGCAA
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:0.53, G:0.00, T:0.21
Consensus pattern (18 bp):
ACCTTCAACACCCTCACC
Found at i:35578415 original size:24 final size:23
Alignment explanation
Indices: 35578384--35578429 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
35578374 CATTGCCAGC
*
35578384 AACCTCAACACCCTCCCCACCTA
1 AACCTCAACACCCTCACCACCTA
35578407 AACCTTCAACACCCTCACCACCT
1 AACC-TCAACACCCTCACCACCT
35578430 TTACTGCCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.30, C:0.54, G:0.00, T:0.15
Consensus pattern (23 bp):
AACCTCAACACCCTCACCACCTA
Found at i:35578421 original size:57 final size:57
Alignment explanation
Indices: 35578351--35578614 Score: 269
Period size: 57 Copynumber: 4.8 Consensus size: 57
35578341 CACCCTTACC
* * *
35578351 ACCTTCACCACCCTCACCACCTTCATTGCCAGCAACCTCAACACCCTCCCCACCTAA
1 ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAA
* * * ** **
35578408 ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAGCACACTCTCCATTTTC
1 ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAA
* *
35578465 ACCTTCAACACTCGT-ACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAA
1 ACCTTCAACAC-CCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAA
* * * **
35578522 ACC-T--------TCACCACCTTCACTGCCAGCAACCTCAACACCCTTCTCATTTAA
1 ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAA
* **
35578570 ACCTTCAACACCCTCACCACTTTTACTGCCAGCAATTTCAACACC
1 ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACC
35578615 TTCATTACCA
Statistics
Matches: 167, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
47 1 0.01
48 39 0.23
49 1 0.01
56 1 0.01
57 123 0.74
58 2 0.01
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.22
Consensus pattern (57 bp):
ACCTTCAACACCCTCACCACCTTTACTGCCAGCAACCTCAACACCCTCCCCACCTAA
Found at i:35578541 original size:48 final size:48
Alignment explanation
Indices: 35578480--35578586 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
35578470 CAACACTCGT
*
35578480 ACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTC
1 ACCACCTTCACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTC
* * * **
35578528 ACCACCTTCACTGCCAGCAACCTCAACACCCTTCTCATTTAAACCTTC
1 ACCACCTTCACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTC
* *
35578576 AACACCCTCAC
1 ACCACCTTCAC
35578587 CACTTTTACT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.29, C:0.48, G:0.03, T:0.21
Consensus pattern (48 bp):
ACCACCTTCACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTC
Found at i:35578574 original size:105 final size:105
Alignment explanation
Indices: 35578351--35578614 Score: 289
Period size: 105 Copynumber: 2.4 Consensus size: 105
35578341 CACCCTTACC
* * * *
35578351 ACCTTCACCACCCTCACCACCTTCATTGCCAGCAACCTCAACACCCTCCCCACCTAAACCTTCAA
1 ACCTTCAACACCCTCACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAAACC-T---
* * **
35578416 CACCCTCACCACCTTTACTGCCAGCAACCTCAGCACACTCTCCATTTTC
62 -----TCACCACCTTCACTGCCAGCAACCTCAACACACTCTCCATTTAA
*
35578465 ACCTTCAACACTCGT-ACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTCA
1 ACCTTCAACAC-CCTCACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTCA
*
35578529 CCACCTTCACTGCCAGCAACCTCAACACCCT-TCTCATTTAA
65 CCACCTTCACTGCCAGCAACCTCAACACACTCTC-CATTTAA
* * **
35578570 ACCTTCAACACCCTCACCACTTTTACTGCCAGCAATTTCAACACC
1 ACCTTCAACACCCTCACCACCTTTACTGCCAACAACCTCAACACC
35578615 TTCATTACCA
Statistics
Matches: 132, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
104 4 0.03
105 73 0.55
113 1 0.01
114 52 0.39
115 2 0.02
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.22
Consensus pattern (105 bp):
ACCTTCAACACCCTCACCACCTTTACTGCCAACAACCTCAACACCCTCCCCACCTAAACCTTCAC
CACCTTCACTGCCAGCAACCTCAACACACTCTCCATTTAA
Found at i:35579787 original size:2 final size:2
Alignment explanation
Indices: 35579780--35579843 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
35579770 TCATTGCCTG
*
35579780 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35579822 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
35579844 TTTATTAACT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:35583568 original size:17 final size:17
Alignment explanation
Indices: 35583542--35583588 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
35583532 TAATAATTTA
35583542 TGTATATATG-AAAAAT
1 TGTATATATGTAAAAAT
35583558 TGTATTATATGTAAAAA-
1 TGTA-TATATGTAAAAAT
35583575 TGT-TATTATGTAAA
1 TGTATA-TATGTAAA
35583589 TATTTGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
16 12 0.43
17 9 0.32
18 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (17 bp):
TGTATATATGTAAAAAT
Found at i:35583583 original size:18 final size:17
Alignment explanation
Indices: 35583542--35583575 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35583532 TAATAATTTA
35583542 TGTA-TATATGAAAAAT
1 TGTATTATATGAAAAAT
35583558 TGTATTATATGTAAAAAT
1 TGTATTATATG-AAAAAT
35583576 GTTATTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TGTATTATATGAAAAAT
Found at i:35585836 original size:131 final size:131
Alignment explanation
Indices: 35585602--35586320 Score: 931
Period size: 131 Copynumber: 5.5 Consensus size: 131
35585592 CCTTACACTT
* * *
35585602 GAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTC
* *
35585667 CAACCTATTTCACTGCTGGTCAGGGACATATGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
35585732 G
131 G
* * *
35585733 GAAGATAAGATTCGCCATCTTCGATCTGCTCCACTATTGCTTAGGGAGAAAAGATCTGCAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTC
* * *
35585798 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTCAAATTTGTTTCCCTACTCCTGG
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
35585863 G
131 G
* * * *
35585864 GAAGATAAGATTCACTGTCTTCGACCTGCTCCACTACTGCTTAGGAAGATAAGATCTGCAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTC
35585929 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
*
35585994 T
131 G
* * * * *
35585995 GAATATAAAATTCGCCGTCTTCAATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTC
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTC
* * * *
35586060 CAACCTATTCCACTGCTGGTCAGGGACATAGGACTCGGTGGCCTAAATCTGCTTCCC-ACTATCT
66 CAACCTATTCCACTGCTGGTCAGGGACATAGGACT-TGTGGCTTAAATCTGTTTCCCTACT-CCT
*
35586124 TGG
129 AGG
* * * * *
35586127 AAAGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTT
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT-TT
** * * * * * * * * *
35586192 -CAACCTGCTCCGCTGCTGCTCAGGGAGACAAGACTCGGTGGCCTAAATCTGCTTCCC-ACTATC
65 CCAACCTATTCCACTGCTGGTCAGGGACATAGGACT-TGTGGCTTAAATCTGTTTCCCTACT-CC
*
35586255 TTGG
128 TAGG
* * ** * *
35586259 AAAGATAAGATTTGCCGTCTTTAATTTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
1 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAT
35586321 ATTCACCGAT
Statistics
Matches: 529, Mismatches: 56, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
131 335 0.63
132 192 0.36
133 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (131 bp):
GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTC
CAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAG
G
Found at i:35586177 original size:44 final size:44
Alignment explanation
Indices: 35586129--35586313 Score: 133
Period size: 44 Copynumber: 4.2 Consensus size: 44
35586119 TATCTTGGAA
*
35586129 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
35586173 AGATAAGATCTACAATCTTCAACCTGCTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * **** * * *
35586217 AGACAAGACTCGGTGGCCTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
35586261 AGATAAGATTTGCCGTCTTTAATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
35586305 AGATAAGAT
1 AGATAAGAT
35586314 CTACAATATT
Statistics
Matches: 100, Mismatches: 35, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
44 82 0.82
45 4 0.04
46 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:35587556 original size:7 final size:7
Alignment explanation
Indices: 35587544--35587584 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
35587534 CCGTCATTAC
35587544 TTTTCAT
1 TTTTCAT
35587551 TTTTCAT
1 TTTTCAT
35587558 TTTTCA-
1 TTTTCAT
35587564 TTTTCAT
1 TTTTCAT
35587571 TTTTCAT
1 TTTTCAT
35587578 TTTTCAT
1 TTTTCAT
35587585 CCCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:35587567 original size:13 final size:13
Alignment explanation
Indices: 35587544--35587580 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
35587534 CCGTCATTAC
35587544 TTTTCATTTTTCAT
1 TTTTCA-TTTTCAT
35587558 TTTTCATTTTCAT
1 TTTTCATTTTCAT
35587571 TTTTCATTTT
1 TTTTCATTTT
35587581 TCATCCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:35587569 original size:20 final size:20
Alignment explanation
Indices: 35587544--35587584 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35587534 CCGTCATTAC
35587544 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
35587564 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
35587584 T
1 T
35587585 CCCTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:35588560 original size:27 final size:28
Alignment explanation
Indices: 35588500--35588572 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
35588490 CATATTTTTA
35588500 TTTTGACTTTAATTGATTTCTCTTTTTTGC
1 TTTTGACTTTAATT--TTTCTCTTTTTTGC
*
35588530 TTTTGACTTTGATTTTT-TCTTTTTT-C
1 TTTTGACTTTAATTTTTCTCTTTTTTGC
*
35588556 TTTTTGATTTTAATTTT
1 -TTTTGACTTTAATTTT
35588573 GATTTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 22 0.56
28 3 0.08
30 13 0.33
ACGTcount: A:0.12, C:0.10, G:0.08, T:0.70
Consensus pattern (28 bp):
TTTTGACTTTAATTTTTCTCTTTTTTGC
Found at i:35588586 original size:33 final size:33
Alignment explanation
Indices: 35588523--35588587 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
35588513 TGATTTCTCT
* * *
35588523 TTTTTGCTTTTGACTTTGATTTTTTCTTTTTTC
1 TTTTTGATTTTAACTTTGATTTTATCTTTTTTC
*
35588556 TTTTTGATTTTAATTTTGATTTTGAT-TTTTTT
1 TTTTTGATTTTAACTTTGATTTT-ATCTTTTTT
35588588 GATTGAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (33 bp):
TTTTTGATTTTAACTTTGATTTTATCTTTTTTC
Found at i:35597366 original size:15 final size:15
Alignment explanation
Indices: 35597346--35597403 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
35597336 TTAACTGGAC
35597346 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
*
35597361 ATTTTATTATTA-TT
1 ATTTTATTTTTATTT
* *
35597375 ATATATATTTTTTATAT
1 AT-TTTA-TTTTTATTT
*
35597392 ATTTTAGTTTTA
1 ATTTTATTTTTA
35597404 ATACTTGGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.12
15 19 0.56
16 8 0.24
17 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
ATTTTATTTTTATTT
Found at i:35600955 original size:18 final size:18
Alignment explanation
Indices: 35600934--35601064 Score: 94
Period size: 18 Copynumber: 7.4 Consensus size: 18
35600924 CTTCTCACCA
*
35600934 TCTTTCTTGGTTTCATCT
1 TCTTTCTTGGCTTCATCT
** *
35600952 TCTTTCTTACCTTCTTCT
1 TCTTTCTTGGCTTCATCT
35600970 TCCTTT-TTGGCTTCATCT
1 T-CTTTCTTGGCTTCATCT
35600988 T-TCTT-TT-G-TTCATCT
1 TCT-TTCTTGGCTTCATCT
* * *
35601003 TCCTTCTTGGGTTCACCT
1 TCTTTCTTGGCTTCATCT
* *
35601021 TCTTTCTTTTG-TTCATCC
1 TCTTTC-TTGGCTTCATCT
* *
35601039 TCTTTTTTGGCTTCACCT
1 TCTTTCTTGGCTTCATCT
35601057 TCTTTCTT
1 TCTTTCTT
35601065 TGGTTCCTCT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
15 10 0.11
16 4 0.05
17 8 0.09
18 58 0.67
19 7 0.08
ACGTcount: A:0.05, C:0.27, G:0.08, T:0.59
Consensus pattern (18 bp):
TCTTTCTTGGCTTCATCT
Found at i:35600985 original size:36 final size:34
Alignment explanation
Indices: 35600935--35601064 Score: 111
Period size: 36 Copynumber: 3.7 Consensus size: 34
35600925 TTCTCACCAT
* * * *
35600935 CTTTCTTGGTTTCATCTTCTTTCTTACCTTCTTCTTC
1 CTTT-TTGGCTTCACCTTCTTTCTT--GTTCATCTTC
*
35600972 CTTTTTGGCTTCATCTT-TCTT-TTGTTCATCTTC
1 CTTTTTGGCTTCACCTTCT-TTCTTGTTCATCTTC
* * *
35601005 CTTCTTGGGTTCACCTTCTTTCTTTTGTTCATCCTC
1 CTTTTTGGCTTCACCTTCTTTC--TTGTTCATCTTC
*
35601041 TTTTTTGGCTTCACCTTCTTTCTT
1 CTTTTTGGCTTCACCTTCTTTCTT
35601065 TGGTTCCTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
33 24 0.31
34 3 0.04
35 3 0.04
36 44 0.56
37 4 0.05
ACGTcount: A:0.05, C:0.28, G:0.08, T:0.58
Consensus pattern (34 bp):
CTTTTTGGCTTCACCTTCTTTCTTGTTCATCTTC
Found at i:35600999 original size:15 final size:15
Alignment explanation
Indices: 35600981--35601037 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 15
35600971 CCTTTTTGGC
35600981 TTCATCTTTCTTTTG
1 TTCATCTTTCTTTTG
*
35600996 TTCATCTTCCTTCTTGGG
1 TTCATCTTTCTT-TT--G
35601014 TTCACCTTCTTTCTTTTG
1 TTCA---TCTTTCTTTTG
35601032 TTCATC
1 TTCATC
35601038 CTCTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 13 0.38
16 2 0.06
18 10 0.29
20 2 0.06
21 7 0.21
ACGTcount: A:0.07, C:0.26, G:0.09, T:0.58
Consensus pattern (15 bp):
TTCATCTTTCTTTTG
Found at i:35601046 original size:69 final size:70
Alignment explanation
Indices: 35600937--35601081 Score: 166
Period size: 69 Copynumber: 2.1 Consensus size: 70
35600927 CTCACCATCT
* * * * *
35600937 TTCTTGGTTTCATCTTCTTTCTTACCTTCTTCTTCCTTTTTGGCTTCA-TCTTTCTTTTGTTCAT
1 TTCTTGGGTTCACCTTCTTTCTTACCTTCATCCTCCTTTTTGGCTTCACTCTTTCTTTGGTTCAT
35601001 CTTCC
66 CTTCC
*** *
35601006 TTCTTGGGTTCACCTTCTTTCTTTTGTTCATCCTCTTTTTTGGCTTCACCTTCTTTCTTTGGTTC
1 TTCTTGGGTTCACCTTCTTTCTTACCTTCATCCTCCTTTTTGGCTTCA-C-TCTTTCTTTGGTTC
* *
35601071 CTCTTTC
64 ATCTTCC
35601078 TTCT
1 TTCT
35601082 CTGGTTCTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
69 40 0.65
72 22 0.35
ACGTcount: A:0.05, C:0.28, G:0.09, T:0.59
Consensus pattern (70 bp):
TTCTTGGGTTCACCTTCTTTCTTACCTTCATCCTCCTTTTTGGCTTCACTCTTTCTTTGGTTCAT
CTTCC
Found at i:35601065 original size:36 final size:36
Alignment explanation
Indices: 35600970--35601070 Score: 136
Period size: 36 Copynumber: 2.9 Consensus size: 36
35600960 ACCTTCTTCT
*
35600970 TCCTTTTTGGCTTCA---TCTTTCTTTTGTTCATCT
1 TCCTTTTTGGCTTCACCTTCTTTCTTTTGTTCATCC
* *
35601003 TCCTTCTTGGGTTCACCTTCTTTCTTTTGTTCATCC
1 TCCTTTTTGGCTTCACCTTCTTTCTTTTGTTCATCC
* *
35601039 TCTTTTTTGGCTTCACCTTCTTTCTTTGGTTC
1 TCCTTTTTGGCTTCACCTTCTTTCTTTTGTTC
35601071 CTCTTTCTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
33 13 0.22
36 45 0.78
ACGTcount: A:0.05, C:0.27, G:0.11, T:0.57
Consensus pattern (36 bp):
TCCTTTTTGGCTTCACCTTCTTTCTTTTGTTCATCC
Found at i:35602566 original size:3 final size:3
Alignment explanation
Indices: 35602552--35602596 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
35602542 TTTTGAATTT
*
35602552 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35602597 TTTAAGGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35603269 original size:23 final size:23
Alignment explanation
Indices: 35603243--35603288 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
35603233 AGTTTTTAAG
35603243 TAAATCTT-TAAAAAATTAATTTA
1 TAAAT-TTATAAAAAATTAATTTA
* *
35603266 TAAATTTATAATAATTTAATTTA
1 TAAATTTATAAAAAATTAATTTA
35603289 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATTTATAAAAAATTAATTTA
Found at i:35607823 original size:13 final size:13
Alignment explanation
Indices: 35607805--35607833 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
35607795 GCGAAACACC
35607805 TATAACAATGCAT
1 TATAACAATGCAT
35607818 TATAACAATGCAT
1 TATAACAATGCAT
35607831 TAT
1 TAT
35607834 GTGTGAATGA
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:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (13 bp):
TATAACAATGCAT
Found at i:35629184 original size:124 final size:123
Alignment explanation
Indices: 35628791--35629196 Score: 598
Period size: 124 Copynumber: 3.3 Consensus size: 123
35628781 AACATGCTAT
* *
35628791 TGTAGCAAAAGCGCGTCCACGTGTGAGCGATTTCAAAAATTCTTCTAATAAAGCATCTTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGA
* * *
35628856 AGCGTTTTTATACTATTTGCTTAGAAACGTCAACTCAAAATTATTTTTCAGGACCTAC
66 AGCGTTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCAGGACCTAC
* * *
35628914 TGTAGCAAAAGCGCATCCACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGA
* * *
35628979 AGCATTTTT-TATGCTATTTGCTCAGAAACATCAACTCGAAATTATTTTTTTAGGACCTAC
66 AGCGTTTTTATAT--TATTTGCTCAGAAACGTCAACTCGAAATTA-TTTTTCAGGACCTAC
* * *
35629039 TGTAGCAAAAGCACGTTCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGA
* * *
35629104 ATCGTTTTTATATTATTTGCTCAGTAACGTCAACTCGAAATTATTTTCTCAGGACCTAT
66 AGCGTTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTT-TCAGGACCTAC
* *
35629163 TGTATCAAAAACGCGTCCACGTGGGAGCGATTTC
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
35629197 CTTAATAAAT
Statistics
Matches: 251, Mismatches: 27, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
122 2 0.01
123 72 0.29
124 94 0.37
125 80 0.32
126 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (123 bp):
TGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTAATAAAGCATCCTGCTTGA
AGCGTTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCAGGACCTAC
Found at i:35636080 original size:29 final size:30
Alignment explanation
Indices: 35636027--35636086 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35636017 ACAGGGCATT
*
35636027 GGGGCAAAAATGTAATTATGCAAAAATTTA
1 GGGGCAAAAATATAATTATGCAAAAATTTA
* *
35636057 GGGGCAAAATTATAATTTTG-AAAAATTTA
1 GGGGCAAAAATATAATTATGCAAAAATTTA
35636086 G
1 G
35636087 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAATATAATTATGCAAAAATTTA
Found at i:35636494 original size:50 final size:50
Alignment explanation
Indices: 35636419--35636609 Score: 283
Period size: 50 Copynumber: 3.8 Consensus size: 50
35636409 ATTTGGGTAA
35636419 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
35636469 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
35636519 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35636569 AGAACATCCCATGTAAGACCATCTCTGGGACATGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
35636610 TATGTTATTA
Statistics
Matches: 126, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 95 0.75
51 31 0.25
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35645416 original size:15 final size:15
Alignment explanation
Indices: 35645378--35645417 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
35645368 TGGGTTTTGA
35645378 ATTTCGATTTTTAAAG
1 ATTT-GATTTTTAAAG
*
35645394 ATTT-ATTTTTAGAG
1 ATTTGATTTTTAAAG
35645408 ATTTGATTTT
1 ATTTGATTTT
35645418 CAGGGTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 13 0.59
15 5 0.23
16 4 0.18
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (15 bp):
ATTTGATTTTTAAAG
Found at i:35654179 original size:3 final size:3
Alignment explanation
Indices: 35654173--35654219 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
35654163 AATAATAATA
* *
35654173 ATG ATG ATG TTG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
35654220 TAAGAAGTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:35654603 original size:11 final size:11
Alignment explanation
Indices: 35654587--35654632 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
35654577 ATCAGTTAAA
35654587 TATTATTTTAT
1 TATTATTTTAT
35654598 TATTATTTTACT
1 TATTATTTTA-T
*
35654610 TA-GATATTTAT
1 TATTAT-TTTAT
35654621 TATTATTTTAT
1 TATTATTTTAT
35654632 T
1 T
35654633 TAGAAAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:35654619 original size:23 final size:23
Alignment explanation
Indices: 35654593--35654636 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
35654583 TAAATATTAT
35654593 TTTATTATTATTTTACTTAGATA
1 TTTATTATTATTTTACTTAGATA
*
35654616 TTTATTATTATTTTATTTAGA
1 TTTATTATTATTTTACTTAGA
35654637 AAATGGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTATTATTATTTTACTTAGATA
Found at i:35656106 original size:13 final size:15
Alignment explanation
Indices: 35656083--35656124 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
35656073 AATTCATCCT
35656083 TAAAATTTAAAATATA
1 TAAAA-TTAAAATATA
35656099 T-AAA-TAAAATA-A
1 TAAAATTAAAATATA
35656111 TAAAATTAAAATAT
1 TAAAATTAAAATAT
35656125 TGTTTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.09
13 10 0.43
14 7 0.30
15 3 0.13
16 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATTAAAATATA
Found at i:35656122 original size:14 final size:14
Alignment explanation
Indices: 35656083--35656123 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
35656073 AATTCATCCT
35656083 TAAAATTTAAAAT-A
1 TAAAA-TTAAAATAA
35656097 TATAAA-TAAAATAA
1 TA-AAATTAAAATAA
35656111 TAAAATTAAAATA
1 TAAAATTAAAATA
35656124 TTGTTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.38
14 12 0.50
15 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAATTAAAATAA
Found at i:35665189 original size:33 final size:33
Alignment explanation
Indices: 35665128--35665190 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
35665118 ATGTATTTAC
*
35665128 TTTTTATTAATAATTATAGATTATTATATTAAT
1 TTTTTATTAAAAATTATAGATTATTATATTAAT
35665161 TTTTTA-TAAAAATTATTA-ATTATATATATT
1 TTTTTATTAAAAATTA-TAGATTAT-TATATT
35665191 TGAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
TTTTTATTAAAAATTATAGATTATTATATTAAT
Done.