Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 188 of 211
Found at i:58165538 original size:25 final size:25
Alignment explanation
Indices: 58165516--58165662 Score: 140
Period size: 25 Copynumber: 5.8 Consensus size: 25
58165506 GTCTCGATAT
58165516 ATGGCTC-CCTGGAGCTTCCCGATTA
1 ATGGCTCTCCT-GAGCTTCCCGATTA
* *
58165541 AAGGCTCTTTCATGAGCTTCCCGATTA
1 ATGGCTC--TCCTGAGCTTCCCGATTA
58165568 ATGGCTCT-CTAGAGCTTCCCGATTA
1 ATGGCTCTCCT-GAGCTTCCCGATTA
* *
58165593 AAGGCTCTTTCATGAGCTTCCCG-TTA
1 ATGGCTC--TCCTGAGCTTCCCGATTA
*
58165619 ATGGCTCTCCGGAGCTTCCCGA-TA
1 ATGGCTCTCCTGAGCTTCCCGATTA
* *
58165643 CATGGCTCACATGAGCTTCC
1 -ATGGCTCTCCTGAGCTTCC
58165663 TGTTATATGA
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.15
25 43 0.43
26 9 0.09
27 31 0.31
28 3 0.03
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (25 bp):
ATGGCTCTCCTGAGCTTCCCGATTA
Found at i:58165562 original size:27 final size:27
Alignment explanation
Indices: 58165527--58165626 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
58165517 TGGCTCCCTG
58165527 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAAAGGCTCTTTCAT
* *
58165554 GAGCTTCCCGATTAATGGCTCTCT-A-
1 GAGCTTCCCGATTAAAGGCTCTTTCAT
58165579 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAAAGGCTCTTTCAT
*
58165606 GAGCTTCCCG-TTAATGGCTCT
1 GAGCTTCCCGATTAAAGGCTCT
58165627 CCGGAGCTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
25 22 0.33
26 12 0.18
27 32 0.48
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (27 bp):
GAGCTTCCCGATTAAAGGCTCTTTCAT
Found at i:58165641 original size:51 final size:52
Alignment explanation
Indices: 58165516--58165641 Score: 211
Period size: 52 Copynumber: 2.4 Consensus size: 52
58165506 GTCTCGATAT
58165516 ATGGCTC-CCTGGAGCTTCCCGATTAAAGGCTCTTTCATGAGCTTCCCGATTA
1 ATGGCTCTCC-GGAGCTTCCCGATTAAAGGCTCTTTCATGAGCTTCCCGATTA
**
58165568 ATGGCTCTCTAGAGCTTCCCGATTAAAGGCTCTTTCATGAGCTTCCCG-TTA
1 ATGGCTCTCCGGAGCTTCCCGATTAAAGGCTCTTTCATGAGCTTCCCGATTA
58165619 ATGGCTCTCCGGAGCTTCCCGAT
1 ATGGCTCTCCGGAGCTTCCCGAT
58165642 ACATGGCTCA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 24 0.35
52 44 0.64
53 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.31
Consensus pattern (52 bp):
ATGGCTCTCCGGAGCTTCCCGATTAAAGGCTCTTTCATGAGCTTCCCGATTA
Found at i:58167725 original size:3 final size:3
Alignment explanation
Indices: 58167683--58167713 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
58167673 AACGTGCACC
58167683 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
58167714 AAGCTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58171170 original size:31 final size:30
Alignment explanation
Indices: 58171108--58171172 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
58171098 ATTAGGATTG
* * *
58171108 AAAATTTAAAATTTAAAACGTATAAATACT
1 AAAATTTAAAATTTAAAACATACAAAGACT
* *
58171138 AAAATTTACCAATTTAAAATATACAAAGACT
1 AAAATTTA-AAATTTAAAACATACAAAGACT
58171169 AAAA
1 AAAA
58171173 CTGACCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.29
Consensus pattern (30 bp):
AAAATTTAAAATTTAAAACATACAAAGACT
Found at i:58171180 original size:31 final size:31
Alignment explanation
Indices: 58171117--58171180 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
58171107 GAAAATTTAA
* * * * *
58171117 AATTTAAAACGTATAAATACTAAAATTTACC
1 AATTTAAAACATACAAAGACTAAAACTGACC
*
58171148 AATTTAAAATATACAAAGACTAAAACTGACC
1 AATTTAAAACATACAAAGACTAAAACTGACC
58171179 AA
1 AA
58171181 ATTATATAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.27
Consensus pattern (31 bp):
AATTTAAAACATACAAAGACTAAAACTGACC
Found at i:58171630 original size:11 final size:11
Alignment explanation
Indices: 58171614--58171638 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58171604 GTATATAAAT
58171614 TTATTAAAAAA
1 TTATTAAAAAA
58171625 TTATTAAAAAA
1 TTATTAAAAAA
58171636 TTA
1 TTA
58171639 AATGAATGTC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTATTAAAAAA
Found at i:58173841 original size:38 final size:41
Alignment explanation
Indices: 58173763--58173851 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 41
58173753 AAAAAAGTAT
* *
58173763 TTATATTAAAAAACACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
* *
58173804 TTATATTAAAAAA-AC-A-AATAAATATAATGAGTATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
* *
58173842 CTGTATTAAA
1 TTATATTAAA
58173852 TATAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 26 0.62
39 1 0.02
40 2 0.05
41 13 0.31
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:58179185 original size:45 final size:46
Alignment explanation
Indices: 58179028--58179186 Score: 200
Period size: 46 Copynumber: 3.5 Consensus size: 46
58179018 AACCTAATGT
* * * *
58179028 CATATTGTCTTTCAACTATGATCTTATTCATTTTCCGTCATGTTGC
1 CATAGTGTCTTTCAACTATGGTATTATTCATTTTCTGTCATGTTGC
*
58179074 CATAATGTCTTTCAACTATGGTATTATTCATTTTCTGTCATGTTGC
1 CATAGTGTCTTTCAACTATGGTATTATTCATTTTCTGTCATGTTGC
58179120 CATAGTGTCTTTCAACTATGGTCA-TATTCATTTT-TGAT-ATAG-TGC
1 CATAGTGTCTTTCAACTATGGT-ATTATTCATTTTCTG-TCAT-GTTGC
* *
58179165 TATAGTGTCTTTCAGCTATGGT
1 CATAGTGTCTTTCAACTATGGT
58179187 GTTACTCGTT
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
45 27 0.26
46 75 0.73
47 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (46 bp):
CATAGTGTCTTTCAACTATGGTATTATTCATTTTCTGTCATGTTGC
Found at i:58179220 original size:45 final size:45
Alignment explanation
Indices: 58179166--58179287 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
58179156 ATATAGTGCT
* * *
58179166 ATAGTGTCTTTCAGCTATGGTGTTACTCGTTTGATTCGTGATGTC
1 ATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGATTCGTGATGCC
58179211 ATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGATTCGTGATGCC
1 ATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGATTCGTGATGCC
*
58179256 ATAGCGTCTTTTAGCTATGGTCTTACTCGTTT
1 ATAGCGTCTTTCAGCTATGGTCTTACTCGTTT
58179288 TTCAACCAAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (45 bp):
ATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGATTCGTGATGCC
Found at i:58189893 original size:15 final size:16
Alignment explanation
Indices: 58189873--58189903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58189863 GGATGAGTTG
58189873 ATTCGG-TTTAAATTA
1 ATTCGGATTTAAATTA
58189888 ATTCGGATTTAAATTA
1 ATTCGGATTTAAATTA
58189904 TTTGAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
ATTCGGATTTAAATTA
Found at i:58189958 original size:15 final size:15
Alignment explanation
Indices: 58189920--58189965 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
58189910 TTTAAAGTTA
*
58189920 TTTAATTTTTTT-AG
1 TTTAATTTTTTTGGG
* *
58189934 TTGAAATTTTTTGGG
1 TTTAATTTTTTTGGG
58189949 TTTAATTTTTTTGGG
1 TTTAATTTTTTTGGG
58189964 TT
1 TT
58189966 GGTTGGAGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.65
Consensus pattern (15 bp):
TTTAATTTTTTTGGG
Found at i:58194693 original size:73 final size:72
Alignment explanation
Indices: 58194574--58194717 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 72
58194564 TCTTTTCAAA
* *
58194574 CTCAAGTTTTAAATGATCTAGGGAATTAAGAAGAAATCGTGTCCTAACTTATTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTAGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGAT-CC
58194639 CTTTTTTT
65 CTTTTTTT
* *
58194647 CTCAAGTTTTAAACGATCTCGGGAATTAAGAA-AAGATCGTGTCCTAACTTACTGGGCATGATCT
1 CTCAAGTTTTAAACGATCTAGGGAATTAAGAAGAA-ATCGTGTCCTAACTTACTGGGCATGATCC
58194711 CTTTTTT
65 CTTTTTT
58194718 AAATCCAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
72 10 0.15
73 56 0.85
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTAGGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTT
Found at i:58198032 original size:40 final size:40
Alignment explanation
Indices: 58197977--58198056 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
58197967 TTATTAGATA
58197977 TTCACCCTTATAAATTCGCATACATATTTTTCTTATACTC
1 TTCACCCTTATAAATTCGCATACATATTTTTCTTATACTC
*
58198017 TTCACCCTTATAAATTTGCATACATATTTTTCTTATACTC
1 TTCACCCTTATAAATTCGCATACATATTTTTCTTATACTC
58198057 ACACATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.03, T:0.46
Consensus pattern (40 bp):
TTCACCCTTATAAATTCGCATACATATTTTTCTTATACTC
Found at i:58198188 original size:14 final size:15
Alignment explanation
Indices: 58198171--58198199 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58198161 ACGTATTAAA
58198171 ATATGTATAT-TTTT
1 ATATGTATATATTTT
58198185 ATATGTATATATTTT
1 ATATGTATATATTTT
58198200 TCATCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
ATATGTATATATTTT
Found at i:58198568 original size:18 final size:18
Alignment explanation
Indices: 58198547--58198592 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
58198537 TCATATGTCC
58198547 ATTTTTATGT-TTTAGTTT
1 ATTTTTATGTATTTA-TTT
*
58198565 ATTTTTATTTATTTATTT
1 ATTTTTATGTATTTATTT
58198583 ATTTGTTATG
1 ATTT-TTATG
58198593 ATATATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (18 bp):
ATTTTTATGTATTTATTT
Found at i:58198644 original size:15 final size:15
Alignment explanation
Indices: 58198626--58198655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58198616 GTTATTCTTT
*
58198626 TTTGTTCATATTATC
1 TTTGTTCACATTATC
58198641 TTTGTTCACATTATC
1 TTTGTTCACATTATC
58198656 ATATTTATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTGTTCACATTATC
Found at i:58198872 original size:110 final size:110
Alignment explanation
Indices: 58198716--58199220 Score: 838
Period size: 110 Copynumber: 4.6 Consensus size: 110
58198706 AAATTTTTCT
* *
58198716 AAATGAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
58198780 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
*
58198825 AAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
58198890 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
*
58198935 AAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
*
58199000 TTTTCTCGTTCAACCAAATGGCTTAATATCATTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
* *
58199045 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCAAGAAAACATGCCCTAAGGTGTTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
* * *
58199110 TTTTCTCATTCAACCAAATGGCTAAATATACTTTTAAAAATTTTCA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTT-A
* * * *
58199156 AAATAAGGTAATGTTTTGCGTTT-GGAAA-TCTGAG-AAACGTGCCCTAATGTGCTGGGTTTCGA
1 AAATAAGGCAATGTTTTGCGTTTGGGAAATTC-GAGAAAACATGCCCTAAGGTGCTGGGTGTCGA
58199218 TTT
65 TTT
58199221 CTCGATTGAC
Statistics
Matches: 376, Mismatches: 17, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
109 50 0.13
110 303 0.81
111 23 0.06
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (110 bp):
AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
Found at i:58204321 original size:43 final size:43
Alignment explanation
Indices: 58204246--58204331 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
58204236 GACTGTTCAT
*
58204246 CGCCTTGTCACTTCATCTGCCTTCCTTCTTCAAGACGCTTCCA
1 CGCCTTGTCACTTCATCTACCTTCCTTCTTCAAGACGCTTCCA
* *
58204289 CGCCTTGTCACTTCATCTACCTTTCTTTTTCAAGACGCTTCCA
1 CGCCTTGTCACTTCATCTACCTTCCTTCTTCAAGACGCTTCCA
58204332 TACTCCCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.15, C:0.37, G:0.10, T:0.37
Consensus pattern (43 bp):
CGCCTTGTCACTTCATCTACCTTCCTTCTTCAAGACGCTTCCA
Found at i:58213445 original size:16 final size:16
Alignment explanation
Indices: 58213418--58213455 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58213408 ATATTTTTAC
*
58213418 AATTTTTAAAAAATTA
1 AATTTTTAAAAAAATA
58213434 TAATTTTT-AAAAAATA
1 -AATTTTTAAAAAAATA
58213450 AATTTT
1 AATTTT
58213456 AGAATTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTTTAAAAAAATA
Found at i:58213470 original size:18 final size:19
Alignment explanation
Indices: 58213447--58213482 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58213437 TTTTTAAAAA
58213447 ATAAAT-TTTAGAATTTGT
1 ATAAATATTTAGAATTTGT
*
58213465 ATAAATATTTTGAATTTG
1 ATAAATATTTAGAATTTG
58213483 CTCATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
ATAAATATTTAGAATTTGT
Found at i:58217600 original size:14 final size:16
Alignment explanation
Indices: 58217563--58217600 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
58217553 TCAAATATTT
*
58217563 TATAAAACATAAATAA
1 TATAAAATATAAATAA
58217579 TATAAAATATAAA-AA
1 TATAAAATATAAATAA
58217594 T-TAAAAT
1 TATAAAAT
58217601 TACATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAAATATAAATAA
Found at i:58220247 original size:15 final size:15
Alignment explanation
Indices: 58220227--58220264 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
58220217 CTACATCTTT
58220227 TATAATAAT-TTATA
1 TATAATAATATTATA
58220241 GTATAATAATACTTATA
1 -TATAATAATA-TTATA
58220258 TATAATA
1 TATAATA
58220265 GTAATACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TATAATAATATTATA
Found at i:58220291 original size:14 final size:15
Alignment explanation
Indices: 58220272--58220300 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58220262 ATAGTAATAC
58220272 ATTATATATT-TATT
1 ATTATATATTATATT
58220286 ATTATATATTATATT
1 ATTATATATTATATT
58220301 GCTTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATATATTATATT
Found at i:58220492 original size:30 final size:30
Alignment explanation
Indices: 58220458--58220534 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 30
58220448 TATATTATAA
58220458 TAATAGTTATATATGTATTAATA-ATTTTA-G
1 TAATAGTTATATAT-TA-TAATATATTTTATG
58220488 TAATAGTTATATATTATAATATTATTTTATG
1 TAATAGTTATATATTATAATA-TATTTTATG
* *
58220519 TATTAGTAATATATTA
1 TAATAGTTATATATTA
58220535 ATTTAGTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 5 0.12
29 2 0.05
30 20 0.48
31 15 0.36
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TAATAGTTATATATTATAATATATTTTATG
Found at i:58220663 original size:17 final size:16
Alignment explanation
Indices: 58220615--58220663 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
58220605 ATTGTCATTA
58220615 AATTTTAAT-TTTA-T
1 AATTTTAATATTTATT
*
58220629 ATATTTTAATAATTATT
1 A-ATTTTAATATTTATT
58220646 AATTTTATATATTTATT
1 AATTTTA-ATATTTATT
58220663 A
1 A
58220664 TACAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 1 0.03
15 8 0.28
16 9 0.31
17 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTAATATTTATT
Found at i:58220672 original size:27 final size:25
Alignment explanation
Indices: 58220613--58220674 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
58220603 ATATTGTCAT
*
58220613 TAAATTTTAATTTTATATATTTTAA
1 TAAATATTAATTTTATATATTTTAA
* *
58220638 TAATTATTAATTTTATATATTTATTA
1 TAAATATTAATTTTATATATTT-TAA
58220664 TACAATATTAA
1 TA-AATATTAA
58220675 AAATATTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 20 0.65
26 4 0.13
27 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAATATTAATTTTATATATTTTAA
Found at i:58237810 original size:111 final size:111
Alignment explanation
Indices: 58237622--58237831 Score: 280
Period size: 111 Copynumber: 1.9 Consensus size: 111
58237612 AATTAAATTG
*** **
58237622 TAAAATTTTTAGGGGTTAAAATAAAATTTTATCTTTTTTATTAATTATAAAATTACAAATGTTAA
1 TAAAATTTTTAGGGACAAAAATAAAATTTTATCCATTTTATTAATTATAAAATTACAAATGTTAA
* *
58237687 GGGCCTAAAAGATAATTCTACCAAATCAAGGGGGGAAATTGGATTA
66 AGGCCTAAAAGATAATTCGACCAAATCAAGGGGGGAAATTGGATTA
*
58237733 TAAAATTTTTAAGGGACAAAAATAAAAATTTTA-CCATTTTATT-ATTATAAAATTATAAATGTT
1 TAAAATTTTT-AGGGACAAAAAT-AAAATTTTATCCATTTTATTAATTATAAAATTACAAATGTT
* ** *
58237796 AAAGGCTTGGAAGATAATTCGACCAAATCAATGGGG
64 AAAGGCCTAAAAGATAATTCGACCAAATCAAGGGGG
58237832 CCAAGTTTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
111 59 0.69
112 17 0.20
113 9 0.11
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (111 bp):
TAAAATTTTTAGGGACAAAAATAAAATTTTATCCATTTTATTAATTATAAAATTACAAATGTTAA
AGGCCTAAAAGATAATTCGACCAAATCAAGGGGGGAAATTGGATTA
Found at i:58251261 original size:3 final size:3
Alignment explanation
Indices: 58251255--58251280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58251245 GTTGTTGGGT
58251255 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
58251281 TTCGATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:58261950 original size:28 final size:29
Alignment explanation
Indices: 58261913--58261983 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
58261903 AAAAATAAAA
58261913 ATTTACCAAAATATTAC-AATTTTTTTTT
1 ATTTACCAAAATATTACAAATTTTTTTTT
58261941 ATTTACCAAAATATTACAAATTTTTTTTT
1 ATTTACCAAAATATTACAAATTTTTTTTT
58261970 ATTTACCAAAATAT
1 ATTTACCAAAATAT
58261984 ATCAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTACCAAAATATTACAAATTTTTTTTT
Found at i:58262083 original size:27 final size:27
Alignment explanation
Indices: 58262053--58262119 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
58262043 CCCCAATGGT
*
58262053 ATTGGCGGCACCAAAGGTGCCAAAACG
1 ATTGGCGGCACCAAAGGTGCCAAAACC
** *
58262080 ATTGGCGGCACCAATTGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
58262107 ATTGGCGGCACCA
1 ATTGGCGGCACCA
58262120 CTGGTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:58262501 original size:18 final size:18
Alignment explanation
Indices: 58262480--58262542 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
58262470 AATATATTTC
58262480 ATAAAATATATATGCTAA
1 ATAAAATATATATGCTAA
* ***
58262498 ATAAAATA-ACAAAATAA
1 ATAAAATATATATGCTAA
58262515 CTATAAAATATATATGCTAA
1 --ATAAAATATATATGCTAA
58262535 ATAAAATA
1 ATAAAATA
58262543 ATAAAATAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 5 0.15
18 16 0.47
19 8 0.24
20 5 0.15
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAATATATATGCTAA
Found at i:58262522 original size:37 final size:37
Alignment explanation
Indices: 58262480--58262557 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
58262470 AATATATTTC
58262480 ATAAAATATATATGCTAAATAAAATAACAAAATAACT
1 ATAAAATATATATGCTAAATAAAATAACAAAATAACT
*
58262517 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATATATATGCTAAATAAAATAACAAAATAACT
58262554 ATAA
1 ATAA
58262558 TATACATTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (37 bp):
ATAAAATATATATGCTAAATAAAATAACAAAATAACT
Found at i:58262573 original size:37 final size:37
Alignment explanation
Indices: 58262480--58262573 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
58262470 AATATATTTC
* *
58262480 ATAAAATATATATGCTAAATAAAATAACAAAATAACT
1 ATAAAATACATATACTAAATAAAATAACAAAATAACT
* * *
58262517 ATAAAATATATATGCTAAATAAAATAATAAAATAACT
1 ATAAAATACATATACTAAATAAAATAACAAAATAACT
*
58262554 ATAATATACAT-TACATAAAT
1 ATAAAATACATATAC-TAAAT
58262574 TTTAAACACA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 2 0.04
37 50 0.96
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (37 bp):
ATAAAATACATATACTAAATAAAATAACAAAATAACT
Found at i:58262768 original size:28 final size:28
Alignment explanation
Indices: 58262712--58262808 Score: 160
Period size: 29 Copynumber: 3.4 Consensus size: 28
58262702 TTTTTATATT
58262712 TTTTGGTAAATAATAAAAAAGTT-TAAATA
1 TTTTGGTAAATAA-AAAAAAGTTGT-AATA
58262741 TTTTGGTAAATAAAAAAAAGTTGTAATA
1 TTTTGGTAAATAAAAAAAAGTTGTAATA
58262769 TTTTGGTAAATAAAAAAAAAGTTGTAATA
1 TTTTGGTAAAT-AAAAAAAAGTTGTAATA
58262798 TTTTGGTAAAT
1 TTTTGGTAAAT
58262809 TTTTATTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
28 24 0.36
29 42 0.64
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38
Consensus pattern (28 bp):
TTTTGGTAAATAAAAAAAAGTTGTAATA
Found at i:58263507 original size:24 final size:24
Alignment explanation
Indices: 58263474--58263528 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
58263464 CCTAAAATGA
* *
58263474 AATTTTAATATTATTATAAT-TTT
1 AATTTTAATATAAATATAATATTT
58263497 AATTATTAATATAAATATAATATTT
1 AATT-TTAATATAAATATAATATTT
*
58263522 AAATTTA
1 AATTTTA
58263529 TTATTATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.63
25 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTTTAATATAAATATAATATTT
Found at i:58263509 original size:18 final size:17
Alignment explanation
Indices: 58263474--58263520 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
58263464 CCTAAAATGA
*
58263474 AATTTTAATATTATTAT
1 AATTTTAATATTAATAT
58263491 AATTTTAATTATTAATAT
1 AATTTTAA-TATTAATAT
* *
58263509 AAATATAATATT
1 AATTTTAATATT
58263521 TAAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAATATTAATAT
Found at i:58272629 original size:21 final size:21
Alignment explanation
Indices: 58272605--58272644 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58272595 GTAAACTTTT
58272605 TTTTTTA-AATTTTTTACAATC
1 TTTTTTATAA-TTTTTACAATC
58272626 TTTTTTATAATTTTTACAA
1 TTTTTTATAATTTTTACAA
58272645 AACTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTATAATTTTTACAATC
Found at i:58272650 original size:22 final size:21
Alignment explanation
Indices: 58272605--58272650 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
58272595 GTAAACTTTT
*
58272605 TTTTTTAAATTTTTTACAATC
1 TTTTTTAAATTTTTTACAAAC
58272626 TTTTTTATAA-TTTTTACAAAAC
1 TTTTTTA-AATTTTTTAC-AAAC
58272648 TTT
1 TTT
58272651 ACATTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTAAATTTTTTACAAAC
Found at i:58275545 original size:13 final size:13
Alignment explanation
Indices: 58275527--58275551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58275517 TTCATGGCGG
58275527 AACCCAAAAATTA
1 AACCCAAAAATTA
58275540 AACCCAAAAATT
1 AACCCAAAAATT
58275552 TTCCCCAAAA
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:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCAAAAATTA
Found at i:58278750 original size:106 final size:106
Alignment explanation
Indices: 58278560--58278753 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
58278550 AACCGCTGAG
* * *
58278560 ACCGCCGTGTCAAGTGGCGGTTTCAGACTCAGACACGGGCGCACCTCCCAACCAACACGACACCC
1 ACCGCCGAGTCAAGTGGCGGTTTCAGACCCAGACACGGGCGCACCTCCCAACCAACACAACACCC
*
58278625 ACCGACACTTCCTGCCAAAACCCCCTTCTTCTACTGCTGCA
66 ACCGACACTTCCCGCCAAAACCCCCTTCTTCTACTGCTGCA
* * *
58278666 ACCGCCGAGT-AAGATGGCGGTTTCAGACCCCGACACGGGCGCACCTGCCAACCACCACAAACAC
1 ACCGCCGAGTCAAG-TGGCGGTTTCAGACCCAGACACGGGCGCACCTCCCAACCAACAC-AACAC
* *
58278730 CCATCGACTCTTCCCG-CAAAACCC
64 CCACCGACACTTCCCGCCAAAACCC
58278754 AACACTCCCC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 3 0.04
106 57 0.74
107 17 0.22
ACGTcount: A:0.25, C:0.42, G:0.19, T:0.14
Consensus pattern (106 bp):
ACCGCCGAGTCAAGTGGCGGTTTCAGACCCAGACACGGGCGCACCTCCCAACCAACACAACACCC
ACCGACACTTCCCGCCAAAACCCCCTTCTTCTACTGCTGCA
Found at i:58279942 original size:34 final size:35
Alignment explanation
Indices: 58279887--58279953 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
58279877 CAAACACCAG
*
58279887 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
58279922 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
58279954 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:58280479 original size:6 final size:6
Alignment explanation
Indices: 58280470--58280561 Score: 52
Period size: 6 Copynumber: 16.0 Consensus size: 6
58280460 TTAATTACAA
* * * *
58280470 AATATT AATATT AATATA AATA-T AAAATT ATTTATTT AA-ATT TA-ATT
1 AATATT AATATT AATATT AATATT AATATT A-ATA-TT AATATT AATATT
** * *
58280517 -ATAAA AATATT AATATT AATATT AATA-T AAT-TT TATATT TATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
58280562 TTAAATTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
4 1 0.01
5 17 0.25
6 45 0.67
7 1 0.01
8 3 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATATT
Found at i:58280491 original size:12 final size:12
Alignment explanation
Indices: 58280469--58280546 Score: 59
Period size: 12 Copynumber: 6.2 Consensus size: 12
58280459 TTTAATTACA
58280469 AAATATTAATAT
1 AAATATTAATAT
* *
58280481 TAATATAAATAT
1 AAATATTAATAT
* *
58280493 AAAATTATTTATTT
1 -AAA-TATTAATAT
58280507 AAAT-TTAATTAT
1 AAATATTAA-TAT
58280519 AAAAATATTAATAT
1 --AAATATTAATAT
*
58280533 TAATATTAATAT
1 AAATATTAATAT
58280545 AA
1 AA
58280547 TTTTATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
11 3 0.06
12 25 0.50
13 5 0.10
14 13 0.26
15 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:58280530 original size:52 final size:51
Alignment explanation
Indices: 58280449--58280546 Score: 169
Period size: 52 Copynumber: 1.9 Consensus size: 51
58280439 AATAATAAAT
*
58280449 TTTATTTAAATTTAATTACAAAATATTAATATTAATATAAATATAAAATTA
1 TTTATTTAAATTTAATTAAAAAATATTAATATTAATATAAATATAAAATTA
*
58280500 TTTATTTAAATTTAATTATAAAAATATTAATATTAATATTAATATAA
1 TTTATTTAAATTTAATTA-AAAAATATTAATATTAATATAAATATAA
58280547 TTTTATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 18 0.41
52 26 0.59
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (51 bp):
TTTATTTAAATTTAATTAAAAAATATTAATATTAATATAAATATAAAATTA
Found at i:58280545 original size:26 final size:26
Alignment explanation
Indices: 58280460--58280546 Score: 99
Period size: 26 Copynumber: 3.3 Consensus size: 26
58280450 TTATTTAAAT
58280460 TTAAT-TACAAAATATTAATATTAATA
1 TTAATATA-AAAATATTAATATTAATA
* * *
58280486 TAAATATAAAATTATTTAT-TTAA-A
1 TTAATATAAAAATATTAATATTAATA
58280510 TTTAATTATAAAAATATTAATATTAATA
1 -TTAA-TATAAAAATATTAATATTAATA
58280538 TTAATATAA
1 TTAATATAA
58280547 TTTTATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 31 0.62
27 10 0.20
28 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATAAAAATATTAATATTAATA
Found at i:58280570 original size:52 final size:51
Alignment explanation
Indices: 58280449--58280562 Score: 162
Period size: 52 Copynumber: 2.3 Consensus size: 51
58280439 AATAATAAAT
*
58280449 TTTATTTAAATTTAATTA-CAAAATATTAATATTAATATAAATATAAAATTA
1 TTTATTTAAATTTAATTATAAAAATATTAATATTAATATAAATAT-AAATTA
*
58280500 TTTATTTAAATTTAATTATAAAAATATTAATATTAATATTAATAT-AATT-
1 TTTATTTAAATTTAATTATAAAAATATTAATATTAATATAAATATAAATTA
*
58280549 TTATATTTATATTT
1 TT-TATTTAAATTT
58280563 TAAATTATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
49 2 0.03
50 14 0.24
51 18 0.31
52 24 0.41
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (51 bp):
TTTATTTAAATTTAATTATAAAAATATTAATATTAATATAAATATAAATTA
Found at i:58297968 original size:100 final size:100
Alignment explanation
Indices: 58297839--58298026 Score: 322
Period size: 100 Copynumber: 1.9 Consensus size: 100
58297829 CCCATGTTTA
* *
58297839 TTGTTATTGTTATTGTTGTTGTGGCTAATGTAATAAAACAAAGGAATAAATAAGAGAACGGAAAG
1 TTGTTATTGTTATTGTGGTTGTGGCTAATGTAATAAAACAAAGGAATAAATAAGAGAACAGAAAG
58297904 GACAATGAATTAGAAAGAGTTAATGTTGAATGTTG
66 GACAATGAATTAGAAAGAGTTAATGTTGAATGTTG
* * * *
58297939 TTGTTATTGTTGTTGTGGTTGTGGTTAATGTAATAAAACAAAGGGATAAATAAGAGAATAGAAAG
1 TTGTTATTGTTATTGTGGTTGTGGCTAATGTAATAAAACAAAGGAATAAATAAGAGAACAGAAAG
58298004 GACAATGAATTAGAAAGAGTTAA
66 GACAATGAATTAGAAAGAGTTAA
58298027 GGAAGGAGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (100 bp):
TTGTTATTGTTATTGTGGTTGTGGCTAATGTAATAAAACAAAGGAATAAATAAGAGAACAGAAAG
GACAATGAATTAGAAAGAGTTAATGTTGAATGTTG
Found at i:58301653 original size:19 final size:20
Alignment explanation
Indices: 58301623--58301662 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
58301613 TAAATATTAT
*
58301623 ATATATTATTATTACCTTTA
1 ATATATTATTATTAACTTTA
58301643 ATATA-TATTATTAACTTTA
1 ATATATTATTATTAACTTTA
58301662 A
1 A
58301663 GCTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTATTAACTTTA
Found at i:58302744 original size:33 final size:33
Alignment explanation
Indices: 58302681--58302745 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
58302671 AACCTTACAT
58302681 ACCAAACAATAAATTAAATTGTTTACTTATTTAC
1 ACCAAACAATAAATTAAATTGTTTA-TTATTTAC
*
58302715 ACCAAA-AATGAATTAACATTGCTTT-TTATTT
1 ACCAAACAATAAATTAA-ATTG-TTTATTATTT
58302746 CATATTATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 15 0.54
34 10 0.36
35 3 0.11
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (33 bp):
ACCAAACAATAAATTAAATTGTTTATTATTTAC
Found at i:58305326 original size:12 final size:12
Alignment explanation
Indices: 58305309--58305343 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58305299 ATATATTTTT
*
58305309 AAAAATTATATA
1 AAAAATAATATA
58305321 AAAAATAATATA
1 AAAAATAATATA
*
58305333 AAAATTAATAT
1 AAAAATAATAT
58305344 GGGCTGGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:58309236 original size:24 final size:24
Alignment explanation
Indices: 58309204--58309249 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
58309194 TCATTTAACT
*
58309204 TAATTGAACATGTTCATGAACATA
1 TAATTGAACATGTTCACGAACATA
58309228 TAATTGAACATGTTCACGAACA
1 TAATTGAACATGTTCACGAACA
58309250 ATGTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
TAATTGAACATGTTCACGAACATA
Found at i:58311615 original size:14 final size:14
Alignment explanation
Indices: 58311598--58311627 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
58311588 ATATATAATT
*
58311598 ATTTTAATATTTTA
1 ATTTTAAAATTTTA
58311612 ATTTTAAAATTTTA
1 ATTTTAAAATTTTA
58311626 AT
1 AT
58311628 CAAAGTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTTAAAATTTTA
Found at i:58316664 original size:7 final size:7
Alignment explanation
Indices: 58316650--58316680 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
58316640 AAAAAAAGGA
58316650 TTTA-TT
1 TTTATTT
58316656 TTTATTT
1 TTTATTT
58316663 TTTATTT
1 TTTATTT
58316670 TTTATTT
1 TTTATTT
58316677 TTTA
1 TTTA
58316681 AAATCTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:58326185 original size:25 final size:23
Alignment explanation
Indices: 58326155--58326208 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 23
58326145 ACGCATTTTA
58326155 ATTTTTAAAAGTCAAAAATAAAAACT
1 ATTTTTAAAA-T-AAAAATAAAAA-T
*
58326181 ATTTTTAAAATGAAAATAAAAAT
1 ATTTTTAAAATAAAAATAAAAAT
58326204 ATTTT
1 ATTTT
58326209 CATAAACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 10 0.37
25 1 0.04
26 10 0.37
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
ATTTTTAAAATAAAAATAAAAAT
Found at i:58326696 original size:29 final size:30
Alignment explanation
Indices: 58326661--58326738 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
58326651 GGACTCCAAA
*
58326661 AAGTTTAAGTACCAACTTA-AAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAATGTC
* * *
58326690 AAGTTTAGGTACTAAATTAGGAAAAATTGTC
1 AAGTTTAAGTACCAAATTA-GAAAAAATGTC
*
58326721 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
58326739 GGGCCAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.40
31 24 0.60
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAGAAAAAATGTC
Found at i:58326761 original size:88 final size:89
Alignment explanation
Indices: 58326609--58326774 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 89
58326599 AAAAAAGATT
*
58326609 GGTACCAAAATAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACTCCAAAAAGTTTAAGTACC
1 GGTACCAAAATAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACTCCAAAAAATTTAAGTACC
*
58326674 AACTTAA-AAAAATGTCAAGTTTA
66 AAATTAAGAAAAATGTCAAGTTTA
* * ** * * * *
58326697 GGTACTAAATTAGGAAAAATTGTCAAGTT-TGAGTACCAAATTGGGC-CAGAAAAAATTTAGGTA
1 GGTACCAAAATAGGAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACTC-CAAAAAATTTAAGTA
58326760 CCAAATTAAGAAAAA
64 CCAAATTAAGAAAAA
58326775 AATAATTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
87 2 0.03
88 58 0.89
89 5 0.08
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (89 bp):
GGTACCAAAATAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACTCCAAAAAATTTAAGTACC
AAATTAAGAAAAATGTCAAGTTTA
Found at i:58331547 original size:26 final size:26
Alignment explanation
Indices: 58331516--58331567 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
58331506 CTTTATTTAT
58331516 TTTTACATAATACTTTTATAAATATA
1 TTTTACATAATACTTTTATAAATATA
**
58331542 TTTTACATAATTTTTTTATAAATATA
1 TTTTACATAATACTTTTATAAATATA
58331568 AAATATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTACATAATACTTTTATAAATATA
Found at i:58335983 original size:5 final size:5
Alignment explanation
Indices: 58335975--58336015 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
58335965 CCAATAGAAG
** *
58335975 ATAAA ATAAA ATAAA ATAAA ATAAA GCAAC ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
58336016 ACGAGCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:58348552 original size:30 final size:30
Alignment explanation
Indices: 58348516--58348576 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
58348506 ATTCAAACAA
*
58348516 CTTTCTTCTCTAATCTCCAAGACAGACCAT
1 CTTTCTTCTCTAATCTCCAACACAGACCAT
58348546 CTTTCTTCTCTAATCTCCAACACAGACCAT
1 CTTTCTTCTCTAATCTCCAACACAGACCAT
58348576 C
1 C
58348577 ATATCAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (30 bp):
CTTTCTTCTCTAATCTCCAACACAGACCAT
Found at i:58353536 original size:21 final size:21
Alignment explanation
Indices: 58353497--58353537 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58353487 GACAATTAGA
* *
58353497 TTTATCTTGATATTTAATTTC
1 TTTATCTTGATAATAAATTTC
*
58353518 TTTATTTTGATAATAAATTT
1 TTTATCTTGATAATAAATTT
58353538 ATTTTAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTATCTTGATAATAAATTTC
Found at i:58356034 original size:42 final size:42
Alignment explanation
Indices: 58355975--58356077 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
58355965 GGCTAGATTC
* * *
58355975 TTGTACTAATATATCAATTATTGAGCTATCTGAATTCAATTG
1 TTGTAATAATAGATCAATTATTGAGCTATCTGAATCCAATTG
* *
58356017 TTGTAATAATAGATCAATTATTGAGTTATTTGAATCCAATTG
1 TTGTAATAATAGATCAATTATTGAGCTATCTGAATCCAATTG
58356059 TTGTAATAATAGATCAATT
1 TTGTAATAATAGATCAATT
58356078 CAGGCACTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (42 bp):
TTGTAATAATAGATCAATTATTGAGCTATCTGAATCCAATTG
Found at i:58356035 original size:20 final size:20
Alignment explanation
Indices: 58356010--58356077 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
58356000 CTATCTGAAT
58356010 TCAATTGTTGTAATAATAGA
1 TCAATTGTTGTAATAATAGA
* * * *
58356030 TCAATTATTG-AGTTATTTGAA
1 TCAATTGTTGTA-ATAATAG-A
58356051 TCCAATTGTTGTAATAATAGA
1 T-CAATTGTTGTAATAATAGA
58356072 TCAATT
1 TCAATT
58356078 CAGGCACTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 18 0.50
21 4 0.11
22 12 0.33
23 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (20 bp):
TCAATTGTTGTAATAATAGA
Found at i:58356201 original size:31 final size:30
Alignment explanation
Indices: 58356137--58356215 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
58356127 CTAAGGGATC
* *
58356137 TAATCAAAATTTTCAAAATTTTTGAAGATT
1 TAATCAAAATTTTCAAAATTTTAGAAGAGT
* * *
58356167 TAATTAAAATTTTTAGAAATTTTAGAAGGGT
1 TAATCAAAATTTTCA-AAATTTTAGAAGAGT
* *
58356198 TAATGAGAATTTTCAAAA
1 TAATCAAAATTTTCAAAA
58356216 AATAATGAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 16 0.40
31 24 0.60
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (30 bp):
TAATCAAAATTTTCAAAATTTTAGAAGAGT
Found at i:58356223 original size:20 final size:21
Alignment explanation
Indices: 58356198--58356238 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
58356188 TTAGAAGGGT
58356198 TAATGAG-AATTTTCAAAAAA
1 TAATGAGAAATTTTCAAAAAA
58356218 TAATGAGAAATTTTCAAAAAA
1 TAATGAGAAATTTTCAAAAAA
58356239 AGATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
TAATGAGAAATTTTCAAAAAA
Found at i:58358767 original size:22 final size:23
Alignment explanation
Indices: 58358742--58358801 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
58358732 TAAAAATAAT
*
58358742 AAAATTTTAATTTAAATATT-TA
1 AAAATTTAAATTTAAATATTATA
*
58358764 AAAA-TTAAATTTATACTATTATA
1 AAAATTTAAATTTA-AATATTATA
58358787 AAAA-TTACAATTTAA
1 AAAATTTA-AATTTAA
58358802 TTTCCTTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.24
22 9 0.27
23 10 0.30
24 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATTTAAATTTAAATATTATA
Found at i:58359921 original size:23 final size:23
Alignment explanation
Indices: 58359894--58359939 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
58359884 ATTTTCACGA
*
58359894 AACATTAACCATGTAAATTTTTT
1 AACATTAACAATGTAAATTTTTT
*
58359917 AACATTAACAATGTAGATTTTTT
1 AACATTAACAATGTAAATTTTTT
58359940 GAGTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (23 bp):
AACATTAACAATGTAAATTTTTT
Found at i:58360064 original size:40 final size:39
Alignment explanation
Indices: 58360008--58360117 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
58359998 AACGTCACTA
* * *
58360008 AAAATCAAGCAATAGCGGCGCTCTTCT-AAAAATGCCGCT
1 AAAATGAAGCATTAGCGGCGCT-TTCTGAAAAACGCCGCT
* * * *
58360047 AAAGATGGAGCATTAGCGACGCTTTTTGGAAAACGCCGCT
1 AAA-ATGAAGCATTAGCGGCGCTTTCTGAAAAACGCCGCT
* *
58360087 AAAATTAAGCATTAGCGGCGTTTTCTGAAAA
1 AAAATGAAGCATTAGCGGCGCTTTCTGAAAA
58360118 GCGCTGCAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
39 28 0.50
40 28 0.50
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (39 bp):
AAAATGAAGCATTAGCGGCGCTTTCTGAAAAACGCCGCT
Found at i:58360308 original size:41 final size:40
Alignment explanation
Indices: 58360165--58360314 Score: 192
Period size: 41 Copynumber: 3.6 Consensus size: 40
58360155 TGAGTTTTTG
* * * *
58360165 GGGCTTTTAGCGTCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAA-AAGCACCACTAATGCTC
*
58360206 GGGCCTTTAGCGGCGTTTTTAAAAATGCACCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAA-GCACCACTAATGCTC
* **
58360247 GGGCCTTTCGTTGCGTTTTTGAAATAGCACCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAA-AGCACCACTAATGCTC
58360288 GGGCCTTTAGCGGCGTTTTTGAGAAAG
1 GGGCCTTTAGCGGCGTTTTTGA-AAAG
58360315 TGCCGCTAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.02
41 89 0.95
42 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (40 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAGCACCACTAATGCTC
Found at i:58360918 original size:17 final size:17
Alignment explanation
Indices: 58360855--58360924 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
58360845 GGGGTTATGC
58360855 TTTAAGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
* *
58360872 TTT-AGGAATTAGGGGCTATGC
1 TTTAAGG-GTTAGGGG----GA
*
58360893 TTTAGGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
58360910 TTTAAGGGTTAGGGG
1 TTTAAGGGTTAGGGG
58360925 TTTAGGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
16 3 0.07
17 25 0.61
21 11 0.27
22 2 0.05
ACGTcount: A:0.21, C:0.03, G:0.44, T:0.31
Consensus pattern (17 bp):
TTTAAGGGTTAGGGGGA
Found at i:58360922 original size:38 final size:38
Alignment explanation
Indices: 58360834--58360924 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 38
58360824 AGATTTAAGG
*
58360834 TTTAAGGGTTAGGGGTTATGCTTTAAGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGCTATGCTTTAAGGGTTAGGGGGA
* *
58360872 TTT-AGGAATTAGGGGCTATGCTTTAGGGGTTAGGGGGA
1 TTTAAGG-GTTAGGGGCTATGCTTTAAGGGTTAGGGGGA
58360910 TTTAAGGGTTAGGGG
1 TTTAAGGGTTAGGGG
58360925 TTTAGGGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
37 3 0.06
38 41 0.87
39 3 0.06
ACGTcount: A:0.21, C:0.03, G:0.43, T:0.33
Consensus pattern (38 bp):
TTTAAGGGTTAGGGGCTATGCTTTAAGGGTTAGGGGGA
Found at i:58361924 original size:20 final size:22
Alignment explanation
Indices: 58361878--58361925 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
58361868 AATTTTTAAC
58361878 TATTAAATATTATTTAATAGAT
1 TATTAAATATTATTTAATAGAT
* *
58361900 T-TTAACTA-TATTTTAT-GAT
1 TATTAAATATTATTTAATAGAT
58361919 TATTAAA
1 TATTAAA
58361926 GATTTAGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.18
20 11 0.50
21 6 0.27
22 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTAAATATTATTTAATAGAT
Found at i:58362038 original size:17 final size:17
Alignment explanation
Indices: 58362016--58362092 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
58362006 GGGGTTATGC
58362016 TTTAGGGGTTAGGGAGA
1 TTTAGGGGTTAGGGAGA
* *
58362033 TTTAGGAGTTAGGGGCTATGC
1 TTTAGGGGTTA-GGG--A-GA
*
58362054 TTTAGGGGTTAGGGGGA
1 TTTAGGGGTTAGGGAGA
*
58362071 TTTAAGGGTTAGGG-G-
1 TTTAGGGGTTAGGGAGA
58362086 TTTAGGG
1 TTTAGGG
58362093 TTTTAACGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 6 0.12
16 1 0.02
17 24 0.49
18 3 0.06
20 4 0.08
21 11 0.22
ACGTcount: A:0.19, C:0.03, G:0.45, T:0.32
Consensus pattern (17 bp):
TTTAGGGGTTAGGGAGA
Found at i:58362062 original size:38 final size:38
Alignment explanation
Indices: 58361994--58362085 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
58361984 AGATTTAAGG
* *
58361994 TTTAAGGGTTTGGGGGTTATGCTTTAGGGGTTAGGGAGA
1 TTTAAGGG-TTAGGGGCTATGCTTTAGGGGTTAGGGAGA
*
58362033 TTT-AGGAGTTAGGGGCTATGCTTTAGGGGTTAGGGGGA
1 TTTAAGG-GTTAGGGGCTATGCTTTAGGGGTTAGGGAGA
58362071 TTTAAGGGTTAGGGG
1 TTTAAGGGTTAGGGG
58362086 TTTAGGGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 41 0.85
39 7 0.15
ACGTcount: A:0.18, C:0.03, G:0.45, T:0.34
Consensus pattern (38 bp):
TTTAAGGGTTAGGGGCTATGCTTTAGGGGTTAGGGAGA
Found at i:58362467 original size:14 final size:14
Alignment explanation
Indices: 58362432--58362471 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
58362422 GTATAGGACC
58362432 AAAATAT-AA-GAA
1 AAAATATAAATGAA
58362444 AAAATA-AAATGAA
1 AAAATATAAATGAA
58362457 AAAATATAAATGAA
1 AAAATATAAATGAA
58362471 A
1 A
58362472 TAAAAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 8 0.32
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAATATAAATGAA
Found at i:58365002 original size:65 final size:65
Alignment explanation
Indices: 58364918--58365041 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
58364908 CGTTTGTGAA
* * * *
58364918 AAAAGCGTCGCGAAAGAACATGACCTTTATCGGCGTTTGTGGGAATAGCGCCGCTAAAGGTCAGG
1 AAAAGCGCCGCGAAAGAACATGACCTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCAGG
*
58364983 AAAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAG
1 AAAAGCGCCGCGAAAGAACATGACCTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAG
58365042 AGCATGACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (65 bp):
AAAAGCGCCGCGAAAGAACATGACCTTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCAGG
Found at i:58366824 original size:31 final size:31
Alignment explanation
Indices: 58366753--58366824 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
58366743 AACTTAATTG
* * * *
58366753 CTTAATAATTTAAATGAAAACTTTCAAATAG
1 CTTAATGACTTAAATGAAAACCTTCAAATAA
* *
58366784 CTTAGTGACTTAAATGAAAACCTTCGAATAA
1 CTTAATGACTTAAATGAAAACCTTCAAATAA
*
58366815 TTTAATGACT
1 CTTAATGACT
58366825 ATTTTATAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (31 bp):
CTTAATGACTTAAATGAAAACCTTCAAATAA
Found at i:58370947 original size:17 final size:17
Alignment explanation
Indices: 58370925--58370958 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58370915 TTTTTAATTG
58370925 TTTTTTAATATTATACT
1 TTTTTTAATATTATACT
*
58370942 TTTTTTAATATTTTACT
1 TTTTTTAATATTATACT
58370959 ATATTCTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTAATATTATACT
Found at i:58393780 original size:21 final size:21
Alignment explanation
Indices: 58393754--58393805 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
58393744 TCACTTCGTT
58393754 TCTTTTTGTCCAAGTTACTTC
1 TCTTTTTGTCCAAGTTACTTC
*
58393775 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTGTCCAAGTTACTTC
58393796 TCTTTTTGTC
1 TCTTTTTGTC
58393806 TAACTCACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.56
Consensus pattern (21 bp):
TCTTTTTGTCCAAGTTACTTC
Found at i:58393816 original size:21 final size:21
Alignment explanation
Indices: 58393734--58393816 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
58393724 ACAAAAAAGA
*
58393734 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
58393758 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
**
58393779 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
* *
58393800 TTTGTCTAACTCACTTC
1 TTTGTCCAAGTCACTTC
58393817 CTTAGGGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 37 0.71
24 15 0.29
ACGTcount: A:0.13, C:0.24, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:58393890 original size:19 final size:19
Alignment explanation
Indices: 58393866--58393905 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
58393856 AAGCTCCATA
58393866 GTAAGTGATTCCAAGCCCC
1 GTAAGTGATTCCAAGCCCC
58393885 GTAAGTGATTCCAAGCCCC
1 GTAAGTGATTCCAAGCCCC
58393904 GT
1 GT
58393906 TTTTAACGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (19 bp):
GTAAGTGATTCCAAGCCCC
Found at i:58394262 original size:16 final size:16
Alignment explanation
Indices: 58394241--58394292 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
58394231 GTTTTGGGGA
58394241 AAAAGTGTAAATATGC
1 AAAAGTGTAAATATGC
* **
58394257 AAAAGT-TTAA-GGGC
1 AAAAGTGTAAATATGC
58394271 AAAAGTGTAAATATGC
1 AAAAGTGTAAATATGC
58394287 AAAAGT
1 AAAAGT
58394293 TTAGGGGCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (16 bp):
AAAAGTGTAAATATGC
Found at i:58394264 original size:30 final size:30
Alignment explanation
Indices: 58394230--58394304 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
58394220 TTAATTTACG
* *
58394230 AGTTTTGGGGAAAAAGTGTAAATATGCAAA
1 AGTTTAGGGGCAAAAGTGTAAATATGCAAA
*
58394260 AGTTTAAGGGCAAAAGTGTAAATATGCAAA
1 AGTTTAGGGGCAAAAGTGTAAATATGCAAA
58394290 AGTTTAGGGGCAAAA
1 AGTTTAGGGGCAAAA
58394305 TAGTAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (30 bp):
AGTTTAGGGGCAAAAGTGTAAATATGCAAA
Found at i:58394543 original size:18 final size:17
Alignment explanation
Indices: 58394510--58394548 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
58394500 TTTTATAAAT
58394510 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
58394528 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
58394545 TGTG
1 TGTG
58394549 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:58394818 original size:23 final size:23
Alignment explanation
Indices: 58394766--58394818 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
58394756 AGTGTTATTG
*
58394766 ATCAGTGCTAGCTTCGGCTACAT
1 ATCAGTGCTAGCTTCAGCTACAT
* * *
58394789 GTTAGTGGTAGCTTCAGCTACAT
1 ATCAGTGCTAGCTTCAGCTACAT
58394812 ATCAGTG
1 ATCAGTG
58394819 TGGCACTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGCTAGCTTCAGCTACAT
Found at i:58412640 original size:18 final size:16
Alignment explanation
Indices: 58412619--58412663 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
58412609 ATTTTGGGTG
58412619 TTTTATTTTTTCGTTTTC
1 TTTT-TTTTTTC-TTTTC
*
58412637 TTTTTTTTCTCTTTTC
1 TTTTTTTTTTCTTTTC
*
58412653 TCTTTTTTTTC
1 TTTTTTTTTTC
58412664 CTTGTGGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 6 0.25
18 4 0.17
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTTCTTTTC
Found at i:58412643 original size:16 final size:16
Alignment explanation
Indices: 58412624--58412663 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
58412614 GGGTGTTTTA
58412624 TTTTTTCGTTTTCT-TT
1 TTTTTTC-TTTTCTCTT
58412640 TTTTTCTCTTTTCTCTT
1 TTTTT-TCTTTTCTCTT
58412657 TTTTTTC
1 TTTTTTC
58412664 CTTGTGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTCTCTT
Found at i:58414407 original size:9 final size:9
Alignment explanation
Indices: 58414388--58414424 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58414378 TGAGTTTTCG
*
58414388 AATTTGAAT
1 AATTCGAAT
*
58414397 AACTCGAAT
1 AATTCGAAT
58414406 AATTCGAAT
1 AATTCGAAT
58414415 AATTCGAAT
1 AATTCGAAT
58414424 A
1 A
58414425 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:58414815 original size:17 final size:17
Alignment explanation
Indices: 58414776--58414821 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
58414766 ACTCACCCTA
58414776 TTTACTTTCCCTC-AAACT
1 TTTA-TTTCCC-CAAAACT
58414794 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAAC-T
58414811 TTTATTTCCCC
1 TTTATTTCCCC
58414822 CCTAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 5 0.20
18 10 0.40
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATTTCCCCAAAACT
Found at i:58421009 original size:11 final size:11
Alignment explanation
Indices: 58420993--58421019 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
58420983 TGACTCATAA
58420993 CATCCCAATTG
1 CATCCCAATTG
58421004 CATCCCAATTG
1 CATCCCAATTG
58421015 CATCC
1 CATCC
58421020 TTGACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.41, G:0.07, T:0.26
Consensus pattern (11 bp):
CATCCCAATTG
Found at i:58424496 original size:156 final size:155
Alignment explanation
Indices: 58424228--58424518 Score: 431
Period size: 156 Copynumber: 1.9 Consensus size: 155
58424218 CATAAACTTT
* * *
58424228 AAGCACTTAAAATTTTCAGTATCATTTCTTTAGCACATGCTTACTAACAAAGGGAACAGAAAAAC
1 AAGCACTTAAAACTTTCAATATCATTTCTTTAGCACATACTTACTAACAAAGGGAACAGAAAAAC
* * * **
58424293 TATTTATATTATTATCAGGAAATTTTCCAAAGATCTATCATTTTCATGTATGGAA-AAACTTGAG
66 AATTTATATTATTATCAGAAAATTCTCCAAAGATCTATCATAATCATGTATGGAAGAAACTTGAG
58424357 CCTAAACATCTCGATCCTCAACCGA
131 CCTAAACATCTCGATCCTCAACCGA
* * ** *
58424382 AAGCACTTTAAACTTTGAATATCATTTCTTTAGCATGTACTTTACTAACAAAGGGAACGGAAAAA
1 AAGCACTTAAAACTTTCAATATCATTTCTTTAGCACATAC-TTACTAACAAAGGGAACAGAAAAA
*
58424447 GAATTTTATATTATTATCAGAAAATTCTCCAAAGATCTATCATAATCATGTATGGAAGAAACTTG
65 CAA-TTTATATTATTATCAGAAAATTCTCCAAAGATCTATCATAATCATGTATGGAAGAAACTTG
58424512 AGCCTAA
129 AGCCTAA
58424519 CAAATCGACA
Statistics
Matches: 120, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
154 33 0.28
155 24 0.20
156 49 0.41
157 14 0.12
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (155 bp):
AAGCACTTAAAACTTTCAATATCATTTCTTTAGCACATACTTACTAACAAAGGGAACAGAAAAAC
AATTTATATTATTATCAGAAAATTCTCCAAAGATCTATCATAATCATGTATGGAAGAAACTTGAG
CCTAAACATCTCGATCCTCAACCGA
Found at i:58427698 original size:124 final size:125
Alignment explanation
Indices: 58427308--58427719 Score: 655
Period size: 125 Copynumber: 3.3 Consensus size: 125
58427298 ATTTATTAAG
* * *
58427308 GAAATCGCTCCAACGTGGACGCGCTTTTGCTACAGCAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
*
58427373 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
*
58427433 GAAATCGCTCCCACGTGAACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* * *
58427498 GCTTCTAAGCAAATAGTATAAAAAACGCTTGAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* * * *
58427558 AAAATCACTCCCACGTGGGCACGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
* *
58427623 GCTTCTGAGCAAATAGTAT-AAAAACGCTTCAAACAAGATGCTTTATCAGAAAAATTTCT
66 GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
* ** *
58427682 GAAATCGTTCCCACGTGGACGCATTTTTACTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
58427720 CATGTTTGAG
Statistics
Matches: 261, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
124 66 0.25
125 195 0.75
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAC
GCTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTTTATCAGAAGAATTTCT
Found at i:58430980 original size:49 final size:49
Alignment explanation
Indices: 58430927--58431191 Score: 458
Period size: 49 Copynumber: 5.4 Consensus size: 49
58430917 TAAGAATATT
*
58430927 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
* *
58430976 AACTATTTTCTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
* * *
58431025 AACTATTTTGTATTTTATTACATCAAATAATATCAAATTATTTAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
*
58431074 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
*
58431123 AACTATTTTGTATTTTATTATATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
58431172 AACTATTTTGTATTTTATTA
1 AACTATTTTGTATTTTATTA
58431192 CATTAATATA
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 207 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTAAATCAAATAATATCAAAATATTCAAAATA
Found at i:58431358 original size:21 final size:21
Alignment explanation
Indices: 58431313--58431352 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58431303 TTGTCCAGCT
* *
58431313 TCCGACGGGGGTTGTGGTTGC
1 TCCGACGGGGATTCTGGTTGC
58431334 TCCGACGGGGATTCTGGTT
1 TCCGACGGGGATTCTGGTT
58431353 CATCCGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.42, T:0.30
Consensus pattern (21 bp):
TCCGACGGGGATTCTGGTTGC
Found at i:58431774 original size:30 final size:31
Alignment explanation
Indices: 58431740--58431807 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
58431730 GTGCTGTTGC
* *
58431740 TGGGCCTGA-TGAAGTTATGGGCGTTGATGA
1 TGGGCCTGAGTGAAGTTATGGGCCTCGATGA
* * *
58431770 TGGGCC-GAGTGAATTTCTGGGCCTCGTTGA
1 TGGGCCTGAGTGAAGTTATGGGCCTCGATGA
58431800 TGGGCCTG
1 TGGGCCTG
58431808 CGTTGTCGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.06
30 28 0.90
31 1 0.03
ACGTcount: A:0.15, C:0.16, G:0.40, T:0.29
Consensus pattern (31 bp):
TGGGCCTGAGTGAAGTTATGGGCCTCGATGA
Found at i:58433455 original size:10 final size:10
Alignment explanation
Indices: 58433410--58433457 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
58433400 TTTTTACGAT
*
58433410 TTAAAAAAAA
1 TTAAAAATAA
58433420 TTAAAAA-AA
1 TTAAAAATAA
* *
58433429 TTAAAACTATT
1 TTAAAAATA-A
58433440 TTAAAAATAA
1 TTAAAAATAA
58433450 TTAAAAAT
1 TTAAAAAT
58433458 TTGAAGCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:58439989 original size:29 final size:28
Alignment explanation
Indices: 58439957--58440036 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 28
58439947 AATCAAAAAA
58439957 TACATTTTGACCCCTGAAATTTTTGAAAT
1 TACATTTTGACCCCT-AAATTTTTGAAAT
* *
58439986 TACATTTTGACCCACCAACTTTTTGAAAT
1 TACATTTTGACCC-CTAAATTTTTGAAAT
*
58440015 TACATTTTGAACCCTAAATTTT
1 TACATTTTGACCCCTAAATTTT
58440037 CTCAAAATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.16
29 37 0.82
30 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (28 bp):
TACATTTTGACCCCTAAATTTTTGAAAT
Found at i:58440413 original size:16 final size:16
Alignment explanation
Indices: 58440383--58440429 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
58440373 CGAACGGAGA
*
58440383 AGAAGAGAAAAAAAAAG
1 AGAA-AGAAAGAAAAAG
58440400 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAG
58440416 A-AAA-AAAGAGAAAA
1 AGAAAGAAAGA-AAAA
58440430 AAATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 12 0.43
17 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAG
Found at i:58440415 original size:10 final size:10
Alignment explanation
Indices: 58440382--58440432 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
58440372 CCGAACGGAG
58440382 AAGAAGAGAAA
1 AAGAA-AGAAA
* *
58440393 AAAAAAGAGA
1 AAGAAAGAAA
58440403 AAGAAAGAAA
1 AAGAAAGAAA
58440413 AAGAAA-AAA
1 AAGAAAGAAA
58440422 AGAGAAA-AAA
1 A-AGAAAGAAA
58440432 A
1 A
58440433 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 4 0.11
10 27 0.77
11 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:58440706 original size:14 final size:13
Alignment explanation
Indices: 58440689--58440731 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
58440679 GCAGCAAGCC
58440689 AAAAAAAGAG-GA
1 AAAAAAAGAGAGA
*
58440701 GAAAAAAGAGAGA
1 AAAAAAAGAGAGA
58440714 AAAAAAA-AGAGA
1 AAAAAAAGAGAGA
58440726 AAAAAA
1 AAAAAA
58440732 GGAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:58440707 original size:12 final size:12
Alignment explanation
Indices: 58440690--58440743 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 12
58440680 CAGCAAGCCA
58440690 AAAAAAGAGGAG
1 AAAAAAGAGGAG
58440702 AAAAAAGA-GAG
1 AAAAAAGAGGAG
* *
58440713 AAAAAAAAAGAG
1 AAAAAAGAGGAG
*
58440725 AAAAAA-AGGAA
1 AAAAAAGAGGAG
58440736 AAAAAAGA
1 AAAAAAGA
58440744 AAAGTTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 19 0.51
12 18 0.49
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAAGAGGAG
Found at i:58440713 original size:11 final size:11
Alignment explanation
Indices: 58440690--58440739 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
58440680 CAGCAAGCCA
58440690 AAAAAAGAGGAG
1 AAAAAAGA-GAG
58440702 AAAAAAGAGAG
1 AAAAAAGAGAG
*
58440713 AAAAAAAAAGAG
1 -AAAAAAGAGAG
58440725 AAAAAA-AG-G
1 AAAAAAGAGAG
58440734 AAAAAA
1 AAAAAA
58440740 AAGAAAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
11 9 0.25
12 18 0.50
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:58440728 original size:10 final size:10
Alignment explanation
Indices: 58440699--58440746 Score: 55
Period size: 9 Copynumber: 4.7 Consensus size: 10
58440689 AAAAAAAGAG
58440699 GAGAAAAAAGA
1 GAGAAAAAA-A
58440710 GAGAAAAAAAAA
1 GAG--AAAAAAA
58440722 GAGAAAAAAA
1 GAGAAAAAAA
58440732 G-GAAAAAAA
1 GAGAAAAAAA
58440741 -AGAAAA
1 GAGAAAA
58440747 GTTCAATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 13 0.38
10 8 0.24
11 3 0.09
12 4 0.12
13 6 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
GAGAAAAAAA
Found at i:58441080 original size:17 final size:17
Alignment explanation
Indices: 58441060--58441193 Score: 67
Period size: 18 Copynumber: 7.6 Consensus size: 17
58441050 TCAAAAATAC
58441060 TAAAAAAATTCGTGTTT
1 TAAAAAAATTCGTGTTT
58441077 T-AAAAAATTCCGATG-TT
1 TAAAAAAATT-CG-TGTTT
*
58441094 TCAAAAAATTCCCGTGTTT
1 TAAAAAAATT--CGTGTTT
*
58441113 T-CAAAAATTCCCGTGTTT
1 TAAAAAAATT--CGTGTTT
** **
58441131 TAAAAATTTTTTATGTTT
1 TAAAAA-AATTCGTGTTT
***
58441149 TCAAAAAAATAATTGTTT
1 T-AAAAAAATTCGTGTTT
* **
58441167 CAAAAATCTTCGTGTTT
1 TAAAAAAATTCGTGTTT
58441184 TAAAAAAATT
1 TAAAAAAATT
58441194 TGTATTTTGA
Statistics
Matches: 89, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
16 8 0.09
17 24 0.27
18 41 0.46
19 14 0.16
20 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (17 bp):
TAAAAAAATTCGTGTTT
Found at i:58441093 original size:18 final size:18
Alignment explanation
Indices: 58441062--58441136 Score: 102
Period size: 18 Copynumber: 4.3 Consensus size: 18
58441052 AAAAATACTA
58441062 AAAAAATT--CGTGTTTT
1 AAAAAATTCCCGTGTTTT
*
58441078 AAAAAATT-CCGATGTTTC
1 AAAAAATTCCCG-TGTTTT
58441096 AAAAAATTCCCGTGTTTT
1 AAAAAATTCCCGTGTTTT
*
58441114 CAAAAATTCCCGTGTTTT
1 AAAAAATTCCCGTGTTTT
58441132 AAAAA
1 AAAAA
58441137 TTTTTTATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
16 8 0.15
17 2 0.04
18 39 0.75
19 3 0.06
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAATTCCCGTGTTTT
Found at i:58446886 original size:41 final size:41
Alignment explanation
Indices: 58446841--58446926 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
58446831 ACTTCATCTA
* *
58446841 CTAGGTTTAAAGTCTAATTCAGTTCACCGGCACTTAGCCTG
1 CTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGCCTG
* *
58446882 CTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTG
1 CTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGCCTG
58446923 CTAG
1 CTAG
58446927 ACATATAGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
CTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGCCTG
Found at i:58446934 original size:41 final size:41
Alignment explanation
Indices: 58446857--58446934 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
58446847 TTAAAGTCTA
* *
58446857 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACATATAGCCTG
58446898 ATTCAGTTCACCGGCACTTAGCCTGCTAGACATATAG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGACATATAG
58446935 TCTAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGACATATAGCCTG
Found at i:58446949 original size:41 final size:41
Alignment explanation
Indices: 58446861--58446954 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
58446851 AGTCTAATTC
* * * * *
58446861 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGACATATAGCCTAAATA
*
58446902 AGTTCACCGGCACTTAGCCTGCTAGACATATAGTCTAAATA
1 AGTTCACCGGCACTTAGCCTGCTAGACATATAGCCTAAATA
* *
58446943 ATTTCACTGGCA
1 AGTTCACCGGCA
58446955 ATAAATCCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
AGTTCACCGGCACTTAGCCTGCTAGACATATAGCCTAAATA
Found at i:58448699 original size:13 final size:13
Alignment explanation
Indices: 58448681--58448705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58448671 ACCAACGATA
58448681 AAATTTTCACACG
1 AAATTTTCACACG
58448694 AAATTTTCACAC
1 AAATTTTCACAC
58448706 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:58451774 original size:17 final size:17
Alignment explanation
Indices: 58451754--58451810 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
58451744 AAAAATACTA
58451754 AAAAAATTCGTGTTTTC
1 AAAAAATTCGTGTTTTC
*
58451771 AAAAATTTCGATG-TTTC
1 AAAAAATTCG-TGTTTTC
58451788 AAAAAATTCCCGTGTTTT-
1 AAAAAATT--CGTGTTTTC
58451806 AAAAA
1 AAAAA
58451811 TTTTTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 20 0.59
18 9 0.26
19 5 0.15
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAAAATTCGTGTTTTC
Found at i:58451774 original size:18 final size:18
Alignment explanation
Indices: 58451753--58451867 Score: 62
Period size: 17 Copynumber: 6.5 Consensus size: 18
58451743 CAAAAATACT
58451753 AAAAAAATTCGTGTTTTC
1 AAAAAAATTCGTGTTTTC
*
58451771 -AAAAATTTCGATG-TTTC
1 AAAAAAATTCG-TGTTTTC
58451788 -AAAAAATTCCCGTGTTTT-
1 AAAAAAATT--CGTGTTTTC
** **
58451806 AAAAATTTTTTATGTTTTC
1 AAAAA-AATTCGTGTTTTC
***
58451825 AAAAAAATAATTG-TTTC
1 AAAAAAATTCGTGTTTTC
**
58451842 AAAAATCTTCGTGTTTT-
1 AAAAAAATTCGTGTTTTC
58451859 AAAAAAATT
1 AAAAAAATT
58451868 TGTATTTTAA
Statistics
Matches: 71, Mismatches: 18, Indels: 17
0.67 0.17 0.16
Matches are distributed among these distances:
17 39 0.55
18 16 0.23
19 14 0.20
20 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (18 bp):
AAAAAAATTCGTGTTTTC
Found at i:58451811 original size:17 final size:16
Alignment explanation
Indices: 58451755--58451812 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
58451745 AAAATACTAA
58451755 AAAAATT-CGTGTTTT
1 AAAAATTCCGTGTTTT
* *
58451770 CAAAAATTTCGATGTTTCA
1 -AAAAATTCCG-TGTTT-T
58451789 AAAAATTCCCGTGTTTT
1 AAAAATT-CCGTGTTTT
58451806 AAAAATT
1 AAAAATT
58451813 TTTTATGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 7 0.20
17 9 0.26
18 17 0.49
19 2 0.06
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (16 bp):
AAAAATTCCGTGTTTT
Found at i:58455373 original size:42 final size:42
Alignment explanation
Indices: 58455308--58455404 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
58455298 CTATATGAAT
* *
58455308 GGCACTAAGTGTGCGAAACTAAAATGACAATGTTGAATAATG
1 GGCACTAAGTGTGAGAAACTAAAATGACAATGTTGAATAACG
* * **
58455350 GGCACTAAATGTGAGAAATTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGAGAAACTAAAATGACAATGTTGAATAACG
58455392 GGCACTAAGTGTG
1 GGCACTAAGTGTG
58455405 CGACACCGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.25
Consensus pattern (42 bp):
GGCACTAAGTGTGAGAAACTAAAATGACAATGTTGAATAACG
Found at i:58460392 original size:17 final size:18
Alignment explanation
Indices: 58460370--58460414 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
58460360 TAACTATTAA
58460370 TGAAATTAATATA-TATT
1 TGAAATTAATATAGTATT
58460387 TGAAA-T-AT-TAGTATT
1 TGAAATTAATATAGTATT
58460402 TCGAAATTAATAT
1 T-GAAATTAATAT
58460415 TTTTATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.09
15 7 0.30
16 5 0.22
17 6 0.26
18 2 0.09
19 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (18 bp):
TGAAATTAATATAGTATT
Found at i:58475756 original size:20 final size:20
Alignment explanation
Indices: 58475712--58475757 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
58475702 ACCCATTCTC
*
58475712 GTTTGTATAAAATTGAATTA
1 GTTTGTATAAAATTGAATAA
* *
58475732 GTTTGTATAAATTTTAATAA
1 GTTTGTATAAAATTGAATAA
*
58475752 TTTTGT
1 GTTTGT
58475758 GAGGTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (20 bp):
GTTTGTATAAAATTGAATAA
Found at i:58477127 original size:21 final size:21
Alignment explanation
Indices: 58477101--58477156 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 21
58477091 TTAAATCATG
58477101 TCTCTCAAATTCTCTCATACT
1 TCTCTCAAATTCTCTCATACT
*
58477122 TCTCTCCAATATTCTCTCATATT
1 TCTCT-CAA-ATTCTCTCATACT
58477145 TCTCTCAAATTC
1 TCTCTCAAATTC
58477157 CTCTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.28
22 6 0.19
23 17 0.53
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (21 bp):
TCTCTCAAATTCTCTCATACT
Found at i:58477160 original size:11 final size:10
Alignment explanation
Indices: 58477101--58477167 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
58477091 TTAAATCATG
58477101 TCTCTCAAAT
1 TCTCTCAAAT
*
58477111 TCTCTCATACT
1 TCTCTCA-AAT
58477122 TCTCTCCAATAT
1 TCTCT-CAA-AT
*
58477134 TCTCTCATATT
1 TCTCTCA-AAT
58477145 TCTCTCAAAT
1 TCTCTCAAAT
*
58477155 TCCTCTAAAAT
1 T-CTCTCAAAT
58477166 TC
1 TC
58477168 CTCTTAAAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
10 11 0.23
11 27 0.57
12 9 0.19
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.43
Consensus pattern (10 bp):
TCTCTCAAAT
Found at i:58478877 original size:18 final size:18
Alignment explanation
Indices: 58478841--58478883 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
58478831 TACCAGGTGC
* *
58478841 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
*
58478859 GTATCCTAACTCTTATAT
1 GTATCCTAACCCTTATAT
*
58478877 GTTTCCT
1 GTATCCT
58478884 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:58480081 original size:126 final size:126
Alignment explanation
Indices: 58479856--58480146 Score: 442
Period size: 126 Copynumber: 2.3 Consensus size: 126
58479846 CAGGCCAAAT
58479856 AGGAACTAC-GTTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAATACTTTTGCTGACAAAGC
1 AGGAACTACTG-TAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAATACTTTTGCTGACAAAGC
* *
58479920 ATCCTGCTTAAAGCGTTTTTGGCACTATTTGCTCAGAAACGTCTTCTCGAAATTATTGTTTC
65 ACCCTGCTTAAAGCGTTTTTGGCACTATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTC
* * * *
58479982 AGGAACTATTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGA-ACTTTTGCTGACAATGC
1 AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCA-ATACTTTTGCTGACAAAGC
* * * *
58480046 ACCCTGCTTAAAGCGTTTTTGTCACTATTTGCTCAGAAATGTCTTCTCAAAATTATTTTTTT
65 ACCCTGCTTAAAGCGTTTTTGGCACTATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTC
* *
58480108 AGTAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTT
1 AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
58480147 TTTTAAATTA
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
126 147 0.99
127 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (126 bp):
AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTATTTCAATACTTTTGCTGACAAAGCA
CCCTGCTTAAAGCGTTTTTGGCACTATTTGCTCAGAAACGTCTTCTCAAAATTATTGTTTC
Found at i:58480280 original size:46 final size:47
Alignment explanation
Indices: 58480228--58480387 Score: 132
Period size: 48 Copynumber: 3.4 Consensus size: 47
58480218 AAAACCCCTA
58480228 AACCCTAA-TCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
1 AACCCTAACTCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
* * * ** ** * *
58480274 AACCCTAAGCCCTAATTTATTT--AATTTTTTCTTAA-AAACCCTTAACACT
1 AACCCTAA-CTCTAATTTTTTTAAAATTTATAATTAATTTA--C-TCA-AGT
*
58480323 AAACCCTAA-TCTAATTTTTTAAAAATTTATAATTAATTTACTCAAGT
1 -AACCCTAACTCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
58480370 AACCCTAAACTCTAATTT
1 AACCCT-AACTCTAATTT
58480388 AATTGATTTT
Statistics
Matches: 83, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
45 1 0.01
46 24 0.29
47 5 0.06
48 31 0.37
49 3 0.04
50 18 0.22
51 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (47 bp):
AACCCTAACTCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGT
Done.