Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 144 of 173
Found at i:43653983 original size:133 final size:133
Alignment explanation
Indices: 43653471--43654010 Score: 875
Period size: 133 Copynumber: 4.1 Consensus size: 133
43653461 AGGAAAATAG
* * *
43653471 GATCTG-TTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAAATCTGCATCTTCGATCCA
1 GATCTGCTT-TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCA
* * * *
43653535 CTTCACTACTAATATAGGAAGATAGGATCTGTTATCTTCGATCTACTTCATGCCAATACATGAAG
65 CTTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAG
43653600 ACAA
130 ACAA
* * *
43653604 GATTTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCAATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
* **
43653669 TTCGCTACCAATATAGGAAGACGGGATCTACTATCTTCGATCTACTTCACGCCAATACATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
43653734 CAA
131 CAA
* *
43653737 TATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
* *
43653802 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTTGATCTACTTCACGCTAATACATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
43653867 CAA
131 CAA
* * *
43653870 GATCTGCTTTCTTCGATCTACTTCGCCTCCAATATGGGAAGACAAGATCTGCATCTTCGGTCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
*
43653935 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCCACTTCACGCCAATACATGAAGA
66 TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
43654000 CAA
131 CAA
43654003 GATCTGCT
1 GATCTGCT
43654011 ATTTTCTAGT
Statistics
Matches: 375, Mismatches: 31, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
133 373 0.99
134 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (133 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCAC
TTCGCTACCAATATAGGAAGACAGGATCTGTTATCTTCGATCTACTTCACGCCAATACATGAAGA
CAA
Found at i:43665904 original size:15 final size:15
Alignment explanation
Indices: 43665884--43665918 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
43665874 TATATATGCC
43665884 ACAATAAGAAATACA
1 ACAATAAGAAATACA
* *
43665899 ACAATAATAAATATA
1 ACAATAAGAAATACA
43665914 ACAAT
1 ACAAT
43665919 GTCATAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (15 bp):
ACAATAAGAAATACA
Found at i:43666326 original size:24 final size:24
Alignment explanation
Indices: 43666297--43666347 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
43666287 ATATACGTAT
43666297 AAATAT-AAAAATATTCATTTAAAA
1 AAATATAAAAAATATTCA-TTAAAA
*
43666321 AAATATAGAAAAATATTTATTAAAA
1 AAATATA-AAAAATATTCATTAAAA
43666346 AA
1 AA
43666348 TAGAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 8 0.33
26 10 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATATAAAAAATATTCATTAAAA
Found at i:43667941 original size:24 final size:24
Alignment explanation
Indices: 43667891--43667947 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
43667881 AAGATTTAAT
* *
43667891 ATTTATTAGTATAATGTTTTTAGC
1 ATTTATTAGTATAATATTTTGAGC
43667915 ATTTATTAGTATAATATATTTGA-C
1 ATTTATTAGTATAATAT-TTTGAGC
*
43667939 ATTAATTAG
1 ATTTATTAG
43667948 AATTAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (24 bp):
ATTTATTAGTATAATATTTTGAGC
Found at i:43675363 original size:50 final size:49
Alignment explanation
Indices: 43675309--43675477 Score: 212
Period size: 50 Copynumber: 3.4 Consensus size: 49
43675299 CTCTATGGCA
* *
43675309 AGTCCTCTGTAAAGCCTTTGTGGCGATTTATTTGGGAAACCTCTGTTGCG
1 AGTCC-CTGTAAAGCCTTTGTAGCGATTTATTTGGGAAACCTCTGTAGCG
* * * *
43675359 AGTCCTCTATAAAACCTTTGTAGCAATTTATTTGGGAAACCTCTGTAGCA
1 AGTCC-CTGTAAAGCCTTTGTAGCGATTTATTTGGGAAACCTCTGTAGCG
* * * *
43675409 AGTCCCTTGTAAAGCCTCTGTTGCGATTTATTTGAGAAGCCTCTGTAGCG
1 AGTCCC-TGTAAAGCCTTTGTAGCGATTTATTTGGGAAACCTCTGTAGCG
43675459 AGTCACCTGTAAAGCCTTT
1 AGTC-CCTGTAAAGCCTTT
43675478 ATGGTAGGGT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 99 0.97
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (49 bp):
AGTCCCTGTAAAGCCTTTGTAGCGATTTATTTGGGAAACCTCTGTAGCG
Found at i:43675473 original size:25 final size:25
Alignment explanation
Indices: 43675398--43675475 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
43675388 ATTTGGGAAA
*
43675398 CCTCTGTAGCAAGTC-CCTTGTAAAG
1 CCTCTGTAGCGAGTCACC-TGTAAAG
* * * **
43675423 CCTCTGTTGCGATTTATTTG-AGAAG
1 CCTCTGTAGCGAGTCACCTGTA-AAG
43675448 CCTCTGTAGCGAGTCACCTGTAAAG
1 CCTCTGTAGCGAGTCACCTGTAAAG
43675473 CCT
1 CCT
43675476 TTATGGTAGG
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
24 1 0.03
25 37 0.95
26 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (25 bp):
CCTCTGTAGCGAGTCACCTGTAAAG
Found at i:43679259 original size:862 final size:870
Alignment explanation
Indices: 43677167--43679367 Score: 3014
Period size: 882 Copynumber: 2.5 Consensus size: 870
43677157 ACGACACACC
* * *
43677167 ACCAATAAAACGATTAAGGAAAACTTCAATGAAACATAATAA-ATAATAATAATAAACAAGATGC
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATATAATAATAAAAAACGAGATGC
* * * *
43677231 TAGTTCGAGGTTCCTCCCATGCTAA-TCCATGTCCTAGTTTTCTGTGTTACCTGAGAGTTAAGGA
66 TAGTCCGAGGTTCCTCCGATGCTAATTCGA-GTCCTAGTTTTCTGTGTTACCTGAGAGGTAA-GA
* * * * * *
43677295 AAATA-GGGAGTGGGCTTATGATAACCCAATGCGAGTCTAATTTTTAAACCATTAGATATAATTG
129 AAAAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTCTAATTTTTAAA-CATTACATATAATTG
* * *
43677359 TTCAAACGACAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGAGACATTTA
193 TTCAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCA
*
43677424 GTAAATCAATGCTTGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTC
258 GTAAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTC
* ** * * * * **
43677489 ATCCATCCTATTTGCCCTCGAGCATCGCTCGACACTCGAAAACACATTTTAGTAATTGACTGTCT
323 ATCCATCTTATCCGCCCTCGAGCATCACTCGACACTCTAAAACACATTTCAGTAACTGACCATCT
* * * *
43677554 TGGATTTCCCGGTGACGATGGTCGTTCACTTATCATCCGTGACGATGAATTTTAATACAATAACT
388 TGGATTTCCAGATGACGATGGTCGTTCACTTGTCATCCGTGACGATGAATTTTACTACAATAACT
* * * * * *
43677619 TACCAAATGTAACACCCCCGATCTAGATTAGGAGTTTCGAGTAAGTTAAATGCGTTACATTGATC
453 TACCAAATGTAAAACCCCCGAACCAGATTAGGAGTTTCGACTAAGTCAAAGGCGTTACATTGATC
*
43677684 ACCGAAGTAATCCAGTAAAGCCATTCTTTTGCTTGAGTTGAATTGTATGAAAATCACTCTTTTGT
518 ACCGAAGTAATCCAGTAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTTTTGT
* * *
43677749 TTTTAGGAAAGACATTCATTAATTAATTCCGCTTTACTTAGTAATCTATCTACAATATTATGAAC
583 TTTTAAGAAAGACATTCATTAATTAATTCCGCTTTACTCAGTAACCTATCTACAATATTATGAAC
* * * * *
43677814 GTGAAGTTTTTTTTTTAGAAAACGGTTTATGATTTTAAAAGCCTTATCAAAACTTTAAGTATTTT
648 ATGAAGTTTATTTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGTATTTT
** * * * *
43677879 GGAAAGCTACAGAAACCAATAATAAGGATAATAATTTTCTAAACCAATTAGCATGCAATAATTAG
713 ACAAAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATAATCAA
* *
43677944 AGTAATAACTAAATGTCATGCTTAAAAATTTATAAGCTAAATAATCCCAAACCACAATTATGAAA
778 AGTAATAACTAAATGTCATGATTAAAAATTTATAAGCTAAATAATCCCAAACCACAAGTAT-AAA
43678009 GCAATAAATAATTAATAGCTTACGACCCAATTAACAA
842 GC-------AA-TAATAGCTTACGACCCAATTAACAA
* *
43678046 ACCAATAAAATGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAATAAAAAATGAGAT
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAAT--ATAATAATAAAAAACGAGAT
* * * *
43678111 GCTAGTCCAAGGTTCCTCCGATGCCAATCCGAGTCCTAGTTTTCTGTGTTACCTGAGAGGTAAGG
64 GCTAGTCCGAGGTTCCTCCGATGCTAATTCGAGTCCTAGTTTTCTGTGTTACCTGAGAGGTAAGA
* * * *
43678176 AAAATGGGGAGTAAGCTTATGACAGCCTAATATGAGTCTAATTTTTAAACTATTACATATAATTG
129 AAAAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTCTAATTTTTAAAC-ATTACATATAATTG
* * * * *
43678241 TTCAAACCG-TAAAGAATTTAATTTAAAACATCATAACAAATTAAACATAATATTAGAGG-CATT
193 TTCAAA-CGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAG-GGACATT
* ** **
43678304 CAGTTAATCAATGCATGTACTCGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTGTCAC
256 CAGTAAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCAC
* *
43678369 CCATCCATCTTATCCGCTCTCGAGCATCACTCGACACTCTAAAACACATTTCAGTAACTGACCAT
321 TCATCCATCTTATCCGCCCTCGAGCATCACTCGACACTCTAAAACACATTTCAGTAACTGACCAT
** * * * * **
43678434 CCCGAATTGCCTGATGACGATGGTCATTCACTTGTCATCCGTGGTGAT-AACTTTTACTACAATA
386 CTTGGATTTCCAGATGACGATGGTCGTTCACTTGTCATCCGTGACGATGAA-TTTTACTACAATA
* * *
43678498 ACTTACCAAATGTAAAACCCCC-AACCAGGCTTAGGAGTTTTGACTAAGTCAAAGGTGTTACATT
450 ACTTACCAAATGTAAAACCCCCGAACCA-GATTAGGAGTTTCGACTAAGTCAAAGGCGTTACATT
* * * **
43678562 GATCACTGAAGTGATCCAGTAAAGTCATTCTTTTGATTGAGTTGAATTGTATGAAAATTGCTCTT
514 GATCACCGAAGTAATCCAGTAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTT
*
43678627 TTGTTTTTAAGAAAGACATTCATTAATTAA-TCTGACTTTACTCAGTAACCTATCTACAATATTA
579 TTGTTTTTAAGAAAGACATTCATTAATTAATTCCG-CTTTACTCAGTAACCTATCTACAATATTA
* * * *
43678691 TTAACATGAAG-TTATTTTTGAGCAAGCGATTTATGGTTTTAAAAGACTTATCAAAACTTTAAGT
643 TGAACATGAAGTTTATTTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGT
** **
43678755 ATTTTACAAAGCAACAGAAATTAATAATAAGAATAATGGTTTTCTAAACCAATTAGCATGCAATA
708 ATTTTACAAAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATA
* * *
43678820 ATCAAAGTAATAACTAAATTTCATGATT-AAATTTTATAAGCTAAGTAATCCCAAACCAC-AGT-
773 ATCAAAGTAATAACTAAATGTCATGATTAAAAATTTATAAGCTAAATAATCCCAAACCACAAGTA
43678882 T-AA-C-A-AATAGCTTACGACCCAATTAACAA
838 TAAAGCAATAATAGCTTACGACCCAATTAACAA
* * *
43678911 ACCAATAAAACGATTAAGGAATACTTTAATGGAACATAATAATA-AATAATAAAAAACGATATGC
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATATAATAATAAAAAACGAGATGC
* *
43678975 TAGTCCGAGGTTCCTTCGATGCTAATTCGAGTCCTAGTTTTTTGTGTTACCTGAGAGGTAAGAAA
66 TAGTCCGAGGTTCCTCCGATGCTAATTCGAGTCCTAGTTTTCTGTGTTACCTGAGAGGTAAGAAA
*
43679040 AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAATCATTACATATAATTGTT
131 AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTCTAATTTTTAAA-CATTACATATAATTGTT
* * *
43679105 CAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATACTATAAGGGATATTCAAT
195 CAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCAGT
* * * *
43679170 AAATCAATGCATGTACAAGTTTTGTTCATAATGTAATGAAATTATAATTTTAAATTCCCACTCAT
260 AAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTCAT
*
43679235 CCATCTTATCCGCCCTCGAGCATCACTCGACATTCTAAAACACATTTCAGTAACTGACCATCTTG
325 CCATCTTATCCGCCCTCGAGCATCACTCGACACTCTAAAACACATTTCAGTAACTGACCATCTTG
* **
43679300 GATTTCCAAATGACGATGGTCGTTCACTTGTCATCAATGACGATGAATTTTACTACAATAACTTA
390 GATTTCCAGATGACGATGGTCGTTCACTTGTCATCCGTGACGATGAATTTTACTACAATAACTTA
43679365 CCA
455 CCA
43679368 TCCTGGTTTG
Statistics
Matches: 1158, Mismatches: 149, Indels: 47
0.86 0.11 0.03
Matches are distributed among these distances:
861 4 0.00
862 358 0.31
863 4 0.00
865 64 0.06
867 1 0.00
875 1 0.00
876 2 0.00
878 1 0.00
879 42 0.04
880 29 0.03
881 140 0.12
882 507 0.44
883 5 0.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (870 bp):
ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATATAATAATAAAAAACGAGATGC
TAGTCCGAGGTTCCTCCGATGCTAATTCGAGTCCTAGTTTTCTGTGTTACCTGAGAGGTAAGAAA
AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTCTAATTTTTAAACATTACATATAATTGTTC
AAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCAGTA
AATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTCATC
CATCTTATCCGCCCTCGAGCATCACTCGACACTCTAAAACACATTTCAGTAACTGACCATCTTGG
ATTTCCAGATGACGATGGTCGTTCACTTGTCATCCGTGACGATGAATTTTACTACAATAACTTAC
CAAATGTAAAACCCCCGAACCAGATTAGGAGTTTCGACTAAGTCAAAGGCGTTACATTGATCACC
GAAGTAATCCAGTAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTTTTGTTTT
TAAGAAAGACATTCATTAATTAATTCCGCTTTACTCAGTAACCTATCTACAATATTATGAACATG
AAGTTTATTTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGTATTTTACA
AAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATAATCAAAGT
AATAACTAAATGTCATGATTAAAAATTTATAAGCTAAATAATCCCAAACCACAAGTATAAAGCAA
TAATAGCTTACGACCCAATTAACAA
Found at i:43679835 original size:13 final size:13
Alignment explanation
Indices: 43679819--43679897 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
43679809 TTGCATGTAG
43679819 GGTTCGCATATAA
1 GGTTCGCATATAA
*
43679832 GGTTCGCACATACAA
1 GGTTCG--CATATAA
* * *
43679847 AGTTCGCATGTAG
1 GGTTCGCATATAA
* *
43679860 GGTTTGCACATACA
1 GGTTCGCATATA-A
* *
43679874 GGGTTCACATTTAA
1 -GGTTCGCATATAA
43679888 GGTTCGCATA
1 GGTTCGCATA
43679898 CTAAATCACA
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
13 26 0.57
14 1 0.02
15 19 0.41
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (13 bp):
GGTTCGCATATAA
Found at i:43679852 original size:28 final size:28
Alignment explanation
Indices: 43679820--43679895 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
43679810 TGCATGTAGG
43679820 GTTCGCATATAAGGTTCGCACATACAAA
1 GTTCGCATATAAGGTTCGCACATACAAA
* * * **
43679848 GTTCGCATGTAGGGTTTGCACATACAGG
1 GTTCGCATATAAGGTTCGCACATACAAA
* *
43679876 GTTCACATTTAAGGTTCGCA
1 GTTCGCATATAAGGTTCGCA
43679896 TACTAAATCA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
GTTCGCATATAAGGTTCGCACATACAAA
Found at i:43679939 original size:24 final size:24
Alignment explanation
Indices: 43679888--43680063 Score: 87
Period size: 24 Copynumber: 7.4 Consensus size: 24
43679878 TCACATTTAA
* *
43679888 GGTTCGCATACTAAATCACATGAT
1 GGTTCGCATAATAAATCACATGAG
*
43679912 GGTTTGCATAATAAATCACATTG-G
1 GGTTCGCATAATAAATCACA-TGAG
* **
43679936 GGTT--CATATACACAATCGTATGAG
1 GGTTCGCATA-ATA-AATCACATGAG
* *
43679960 GGTTCGCATATTAAATC-CATAAG
1 GGTTCGCATAATAAATCACATGAG
* * * *
43679983 GGTTCGTATACTAAATCATATTAG
1 GGTTCGCATAATAAATCACATGAG
* * * *
43680007 GGTTTGCATATTAAAACATAT-AGG
1 GGTTCGCATAATAAATCACATGA-G
* * *
43680031 GGTTCTCATACTAAATC-CATAAG
1 GGTTCGCATAATAAATCACATGAG
43680054 GGCTT-GCATA
1 GG-TTCGCATA
43680064 TAGGGTTCGC
Statistics
Matches: 118, Mismatches: 24, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
22 4 0.03
23 33 0.28
24 74 0.63
25 3 0.03
26 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (24 bp):
GGTTCGCATAATAAATCACATGAG
Found at i:43679988 original size:23 final size:24
Alignment explanation
Indices: 43679958--43680064 Score: 98
Period size: 24 Copynumber: 4.5 Consensus size: 24
43679948 CAATCGTATG
43679958 AGGGTTCGCATATTAAATCCATA-
1 AGGGTTCGCATATTAAATCCATAT
* *
43679981 AGGGTTCGTATACTAAAT-CATATT
1 AGGGTTCGCATATTAAATCCATA-T
* *
43680005 AGGGTTTGCATATTAAA-ACATAT
1 AGGGTTCGCATATTAAATCCATAT
* *
43680028 AGGGGTTCTCATACTAAATCCATA-
1 A-GGGTTCGCATATTAAATCCATAT
43680052 AGGGCTT-GCATAT
1 AGGG-TTCGCATAT
43680065 AGGGTTCGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
22 4 0.06
23 25 0.37
24 34 0.51
25 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (24 bp):
AGGGTTCGCATATTAAATCCATAT
Found at i:43679993 original size:47 final size:48
Alignment explanation
Indices: 43679895--43680064 Score: 161
Period size: 47 Copynumber: 3.6 Consensus size: 48
43679885 TAAGGTTCGC
* * * **
43679895 ATACTAAATCACATGATGGTTTGCATAATAAATCACATTGGGGTTCAT
1 ATACTAAATCATATGAGGGTTTGCATATTAAATCACATAAGGGTTCAT
* * *
43679943 ATAC-ACAATCGTATGAGGGTTCGCATATTAAATC-CATAAGGGTTCGT
1 ATACTA-AATCATATGAGGGTTTGCATATTAAATCACATAAGGGTTCAT
* * * *
43679990 ATACTAAATCATATTAGGGTTTGCATATTAAAACATATAGGGGTTC-T
1 ATACTAAATCATATGAGGGTTTGCATATTAAATCACATAAGGGTTCAT
*
43680037 CATACTAAATCCATA--AGGGCTTGCATAT
1 -ATACTAAAT-CATATGAGGGTTTGCATAT
43680065 AGGGTTCGCA
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
47 52 0.51
48 46 0.45
49 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (48 bp):
ATACTAAATCATATGAGGGTTTGCATATTAAATCACATAAGGGTTCAT
Found at i:43680101 original size:58 final size:58
Alignment explanation
Indices: 43680037--43680257 Score: 266
Period size: 58 Copynumber: 3.8 Consensus size: 58
43680027 TAGGGGTTCT
* * * * *
43680037 CATACTAAATC-CATAAGGGCTTGCATATAGGGTTCGCATTATATATAGTAAGAGATCA
1 CATACTAAATCATATAAGGGTTTGCATAT-GGGTTCGCATAATATATGGTAAGAGATCG
* *
43680095 CATACTAAGTCATATAAGGGTTTGCATATGGGTTAG-ACTAATATATGGTAAGAGATCG
1 CATACTAAATCATATAAGGGTTTGCATATGGGTTCGCA-TAATATATGGTAAGAGATCG
* * * *
43680153 TATACTAAATCATATAAAGGTTTTCATATGGGTTCGCATAATTTATGGTAAGAGATCG
1 CATACTAAATCATATAAGGGTTTGCATATGGGTTCGCATAATATATGGTAAGAGATCG
* * * *
43680211 CATACTAAATCATATAAAAGGTTTTCATATAGGTCCGCATAATATAT
1 CATACTAAATCATAT-AAGGGTTTGCATATGGGTTCGCATAATATAT
43680258 AGGGTTCACA
Statistics
Matches: 142, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
57 1 0.01
58 97 0.68
59 44 0.31
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (58 bp):
CATACTAAATCATATAAGGGTTTGCATATGGGTTCGCATAATATATGGTAAGAGATCG
Found at i:43680293 original size:18 final size:18
Alignment explanation
Indices: 43680237--43680295 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
43680227 AAAGGTTTTC
*
43680237 ATATA-GGTCCGCATAAT
1 ATATAGGGTTCGCATAAT
* *
43680254 ATATAGGGTTCACATAAG
1 ATATAGGGTTCGCATAAT
*
43680272 ATATAGGGTTCGCATTAT
1 ATATAGGGTTCGCATAAT
43680290 ATATAG
1 ATATAG
43680296 TAAGAGGCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
17 5 0.14
18 30 0.86
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (18 bp):
ATATAGGGTTCGCATAAT
Found at i:43680465 original size:16 final size:16
Alignment explanation
Indices: 43680428--43680469 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
43680418 TTAATAGTTC
*
43680428 ACCTAA-GGTTCGCAT
1 ACCTAAGGGTTCACAT
* *
43680443 TCATAAGGGTTCACAT
1 ACCTAAGGGTTCACAT
43680459 ACCTAAGGGTT
1 ACCTAAGGGTT
43680470 TGTATACATG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (16 bp):
ACCTAAGGGTTCACAT
Found at i:43680485 original size:15 final size:15
Alignment explanation
Indices: 43680465--43680535 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
43680455 ACATACCTAA
*
43680465 GGGTTTGTATACATG
1 GGGTTTGCATACATG
*
43680480 GGGTTTTGCATATATG
1 GGG-TTTGCATACATG
*
43680496 GAGTTTGCATACATG
1 GGGTTTGCATACATG
* *
43680511 GGGTTCGCATATAT-
1 GGGTTTGCATACATG
43680525 GGGTTTGCATA
1 GGGTTTGCATA
43680536 ACAGATTACC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 10 0.21
15 25 0.53
16 12 0.26
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (15 bp):
GGGTTTGCATACATG
Found at i:43680523 original size:30 final size:30
Alignment explanation
Indices: 43680465--43680535 Score: 108
Period size: 31 Copynumber: 2.4 Consensus size: 30
43680455 ACATACCTAA
* *
43680465 GGGTTTGTATACATGGGGTTTTGCATATAT
1 GGGTTTGCATACATGGGGTTTCGCATATAT
43680495 GGAGTTTGCATACATGGGG-TTCGCATATAT
1 GG-GTTTGCATACATGGGGTTTCGCATATAT
43680525 GGGTTTGCATA
1 GGGTTTGCATA
43680536 ACAGATTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 9 0.24
30 14 0.37
31 15 0.39
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (30 bp):
GGGTTTGCATACATGGGGTTTCGCATATAT
Found at i:43682611 original size:20 final size:21
Alignment explanation
Indices: 43682579--43682627 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
43682569 ATGTAATATA
*
43682579 TAAA-TAATAAAATTTAAAAT
1 TAAAGTAATAAAATTTAAAAG
43682599 TAAAGTAAT-AAATTTAAAAG
1 TAAAGTAATAAAATTTAAAAG
*
43682619 AAAAGTAAT
1 TAAAGTAAT
43682628 TCAACATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
TAAAGTAATAAAATTTAAAAG
Found at i:43693387 original size:16 final size:16
Alignment explanation
Indices: 43693363--43693416 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
43693353 TTTGGTTCGT
* *
43693363 TGTACTGGATTAGAGA
1 TGTAATGGAATAGAGA
*
43693379 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGA
* * *
43693395 CGTAATGGAATAAAGG
1 TGTAATGGAATAGAGA
43693411 TGTAAT
1 TGTAAT
43693417 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.31, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:43693461 original size:45 final size:44
Alignment explanation
Indices: 43693396--43693485 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
43693386 GAATAGAGGC
*
43693396 GTAATGGAATAAAGGTGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAAAGGCGTAATAG-AAATCAACTGTTTGGTTGAAT
* * ***
43693441 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAAT
43693485 G
1 G
43693486 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAAAGGCGTAATAGAAATCAACTGTTTGGTTGAAT
Found at i:43693659 original size:25 final size:25
Alignment explanation
Indices: 43693627--43693681 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
43693617 TAATTTAATC
*
43693627 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
43693651 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
43693676 ATATAT
1 ATATAT
43693682 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:43693765 original size:107 final size:108
Alignment explanation
Indices: 43693654--43693853 Score: 366
Period size: 107 Copynumber: 1.9 Consensus size: 108
43693644 TTATTAAATA
*
43693654 TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTCATAT
1 TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATAT
*
43693719 GAATTTACTCAAATCATAATATA-GATAATTTAACATAATTAT
66 GAATTTACTAAAATCATAATATATGATAATTTAACATAATTAT
*
43693761 TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATAT
1 TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATAT
43693826 GAATTTACTAAAATCATAATATATGATA
66 GAATTTACTAAAATCATAATATATGATA
43693854 CTATAAAATA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 85 0.96
108 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (108 bp):
TATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATAT
GAATTTACTAAAATCATAATATATGATAATTTAACATAATTAT
Found at i:43693786 original size:16 final size:16
Alignment explanation
Indices: 43693743--43693788 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
43693733 CATAATATAG
*
43693743 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
43693759 ATTATT-AAATATATT
1 ATAATTAAAATATATT
43693774 ATAATTAAAATATAT
1 ATAATTAAAATATAT
43693789 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:43693795 original size:14 final size:15
Alignment explanation
Indices: 43693743--43693797 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
43693733 CATAATATAG
43693743 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
43693759 ATTATTAAATATATT
1 ATAATTAAATATATT
43693774 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
43693787 ATAATTTAATA
1 ATAATTAAATA
43693798 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:43693899 original size:107 final size:107
Alignment explanation
Indices: 43693658--43693904 Score: 346
Period size: 107 Copynumber: 2.3 Consensus size: 107
43693648 TAAATATATT
*
43693658 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTCATATGAAT
1 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATATGAAT
* * * * *
43693723 TTACTCAAATCATAATATAGATAATTTAACATAATTATTATT
66 TTACTAAAATCATAATATAGATAATATAAAATAATAATTATG
*
43693765 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAAT
1 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATATGAAT
*
43693830 TTACTAAAATCATAATATATGATACTATAAAAT-ATAATT-TG
66 TTACTAAAATCATAATATA-GATAATATAAAATAATAATTATG
43693871 AAATA-ATTA-ATATT-AAATATAT--TTTAATTAAAAT
1 AAATATATTATA-ATTAAAATATATAATTTAA-TAAAAT
43693905 ATATGATTTA
Statistics
Matches: 129, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
102 5 0.04
103 6 0.05
104 9 0.07
105 7 0.05
106 6 0.05
107 86 0.67
108 10 0.08
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (107 bp):
AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTCATATGAAT
TTACTAAAATCATAATATAGATAATATAAAATAATAATTATG
Found at i:43693973 original size:47 final size:45
Alignment explanation
Indices: 43693904--43694171 Score: 191
Period size: 47 Copynumber: 5.9 Consensus size: 45
43693894 TTAATTAAAA
*
43693904 TATATG-ATTTAATAAAATTTAAAATAATTATACCTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATA--TAATAAATTTTCT
* * *
43693951 TATATGAATTTGTATAATTTAAAATAATTA-ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATATAATAAAT-T-TTCT
* * *
43693996 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-AT-ATAATAAATTTTCT
* * *
43694042 TGTATGAATTTATATAATTTAAAATAATTA-ATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATATAATAAAT-T-TTCT
* * *
43694087 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-AT-ATAATAAATTTTCT
*
43694133 TATATGAATTTATATAATTTAAAATAATTA-ATATTAAAT
1 TATATGAATTTATATAATTTAAAATAATTATATAATAAAT
43694172 ATAATTTAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 49
0.70 0.11 0.20
Matches are distributed among these distances:
43 6 0.03
44 54 0.31
45 15 0.09
46 16 0.09
47 71 0.41
48 10 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (45 bp):
TATATGAATTTATATAATTTAAAATAATTATATAATAAATTTTCT
Found at i:43693995 original size:16 final size:16
Alignment explanation
Indices: 43693965--43694013 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
43693955 TGAATTTGTA
43693965 TAAT-TTAAA-ATAAT
1 TAATATTAAATATAAT
43693979 TAATATTAAATATAATT
1 TAATATTAAATATAA-T
*
43693996 TAATAATAATATATAAT
1 TAATATTAA-ATATAAT
43694013 T
1 T
43694014 TCATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 5 0.17
16 4 0.13
17 11 0.37
18 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTAAATATAAT
Found at i:43694011 original size:18 final size:17
Alignment explanation
Indices: 43693970--43694019 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
43693960 TTGTATAATT
*
43693970 TAAA-ATAA-TTAATAT
1 TAAATATAATTTAATAA
43693985 TAAATATAATTTAATAA
1 TAAATATAATTTAATAA
*
43694002 TAATATATAATTTCATAA
1 TAA-ATATAATTTAATAA
43694020 AATTCTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 9 0.30
18 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATAATTTAATAA
Found at i:43694013 original size:44 final size:43
Alignment explanation
Indices: 43693963--43694197 Score: 197
Period size: 44 Copynumber: 5.2 Consensus size: 43
43693953 TATGAATTTG
43693963 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * ** *
43694007 TATAATTTCATAAAATTCTTGATAATAAATTTTCTTGT-ATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAATT-TAAT-AATATA
43694054 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
43694098 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
43694145 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
43694189 TATAATTTA
1 TATAATTTA
43694198 TACATTTAAC
Statistics
Matches: 147, Mismatches: 28, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
43 7 0.05
44 62 0.42
45 9 0.06
46 9 0.06
47 53 0.36
48 7 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:43694034 original size:91 final size:91
Alignment explanation
Indices: 43693938--43694196 Score: 491
Period size: 91 Copynumber: 2.8 Consensus size: 91
43693928 TAATTATACC
*
43693938 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
43694003 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
*
43694029 TAATAAATTTTCTTGTATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
43694094 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
43694120 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
43694185 GATATATAATTT
66 GATATATAATTT
43694197 ATACATTTAA
Statistics
Matches: 164, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 164 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:43695709 original size:16 final size:17
Alignment explanation
Indices: 43695683--43695715 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
43695673 TAAATTTTCA
43695683 GATATAAGTGACAAAGT
1 GATATAAGTGACAAAGT
*
43695700 GATA-AAGTGAGAAAGT
1 GATATAAGTGACAAAGT
43695716 AGGGGGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.27, T:0.21
Consensus pattern (17 bp):
GATATAAGTGACAAAGT
Found at i:43699810 original size:20 final size:20
Alignment explanation
Indices: 43699785--43699825 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43699775 TAGGACTAAA
* *
43699785 TAGGAAACATTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
43699805 TAGGAAAAAGTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
43699825 T
1 T
43699826 GGACTGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (20 bp):
TAGGAAAAAGTTGAAAATTT
Found at i:43700742 original size:40 final size:39
Alignment explanation
Indices: 43700694--43700897 Score: 167
Period size: 40 Copynumber: 5.1 Consensus size: 39
43700684 CATACTAGAT
* * *
43700694 AGAAGCTCATAAGAGCTGATCTACCCGAAGCACACTAGAC
1 AGAAGCTCATAAGAGCTGATCTAACCGAA-CACACCAAAC
* * * **
43700734 AGAAGCTCATAAAAGTTGATCCAACCGTAACATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCTAACCG-AACACACCAAAC
* * **
43700774 AGAAGATCATAAGAGCTGATTTAATAGAAACACACCAAAC
1 AGAAGCTCATAAGAGCTGATCTAACCG-AACACACCAAAC
* * * *
43700814 AGTAGCTCAGAAGAGCTGATCCAACTGAA-ACATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCTAACCGAACACA--CCAAAC
* * * *
43700854 AGAAGCTCATAAGAGTTGATCCAACCGTAACACGCCTAAC
1 AGAAGCTCATAAGAGCTGATCTAACCG-AACACACCAAAC
43700894 AGAA
1 AGAA
43700898 AGTATAACAC
Statistics
Matches: 128, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
38 3 0.02
39 2 0.02
40 117 0.91
41 4 0.03
42 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (39 bp):
AGAAGCTCATAAGAGCTGATCTAACCGAACACACCAAAC
Found at i:43700821 original size:80 final size:80
Alignment explanation
Indices: 43700694--43700897 Score: 228
Period size: 80 Copynumber: 2.5 Consensus size: 80
43700684 CATACTAGAT
* * * * * * *
43700694 AGAAGCTCATAAGAGCTGATCTACCCGAAGCACACTAGACAGAAGCTCATAAAAGTTGATCCAAC
1 AGAAGCTCATAAGAGCTGATCTAACAGAAACACACCAAACAGAAGCTCAGAAAAGCTGATCCAAC
*
43700759 CGTAACATGCCAAAC
66 CGAAACATGCCAAAC
* * * * *
43700774 AGAAGATCATAAGAGCTGATTTAATAGAAACACACCAAACAGTAGCTCAGAAGAGCTGATCCAAC
1 AGAAGCTCATAAGAGCTGATCTAACAGAAACACACCAAACAGAAGCTCAGAAAAGCTGATCCAAC
*
43700839 TGAAACATGCCAAAC
66 CGAAACATGCCAAAC
* * * * * *
43700854 AGAAGCTCATAAGAGTTGATCCAACCGTAACACGCCTAACAGAA
1 AGAAGCTCATAAGAGCTGATCTAACAGAAACACACCAAACAGAA
43700898 AGTATAACAC
Statistics
Matches: 100, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 100 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (80 bp):
AGAAGCTCATAAGAGCTGATCTAACAGAAACACACCAAACAGAAGCTCAGAAAAGCTGATCCAAC
CGAAACATGCCAAAC
Found at i:43709711 original size:19 final size:20
Alignment explanation
Indices: 43709684--43709723 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43709674 GTAAATACAC
* *
43709684 ATATGTTTATAAT-TGATCA
1 ATATATTTAAAATATGATCA
43709703 ATATATTTAAAATATGATCA
1 ATATATTTAAAATATGATCA
43709723 A
1 A
43709724 CATCATATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
ATATATTTAAAATATGATCA
Found at i:43712719 original size:43 final size:43
Alignment explanation
Indices: 43712630--43712721 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
43712620 CTTGTGGTTG
* * * *
43712630 CTTCCTTTTTTGTTGTTTCTTGGTTGTGGTTGCTTCCATGTTA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
** *
43712673 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTTTTTCTACGTAA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
43712716 CTTCCT
1 CTTCCT
43712722 CTGTCTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.07, C:0.18, G:0.18, T:0.57
Consensus pattern (43 bp):
CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
Found at i:43713337 original size:21 final size:22
Alignment explanation
Indices: 43713299--43713340 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43713289 AATAAATGAA
**
43713299 AAGAAAAATTTTATCCACAACC
1 AAGAAAAATTACATCCACAACC
43713321 AAGAAAAATTACA-CCACAAC
1 AAGAAAAATTACATCCACAAC
43713341 TGGCAAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.17
Consensus pattern (22 bp):
AAGAAAAATTACATCCACAACC
Found at i:43715308 original size:27 final size:27
Alignment explanation
Indices: 43715233--43715309 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
43715223 GTATCTCACA
** *
43715233 TTTAACGTCCCGTCAAACTATCCCGTG
1 TTTAACGTCCCGTCGGACTATCTCGTG
* * *
43715260 TTTAACGTCTCGTTGGAATATCTCGTG
1 TTTAACGTCCCGTCGGACTATCTCGTG
*
43715287 TTTAATGTCCCGTCGGACTATCT
1 TTTAACGTCCCGTCGGACTATCT
43715310 ATGATGCCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (27 bp):
TTTAACGTCCCGTCGGACTATCTCGTG
Found at i:43715482 original size:45 final size:43
Alignment explanation
Indices: 43715433--43715547 Score: 126
Period size: 45 Copynumber: 2.6 Consensus size: 43
43715423 TTCCATGGTT
* * *
43715433 TCTTTCAACCATTGTCTTACTTATTTAT-ATGATGACATCATAGCA
1 TCTTTCAGCCATAGTCTTACTCATTTATCATGATG-C--CATAGCA
* *
43715478 TCTTTCAGCTATGGTCTTACTCATCCTTATCATGATGCCATAGCA
1 TCTTTCAGCCATAGTCTTACTCAT--TTATCATGATGCCATAGCA
43715523 TC-TTCAGCCATAGTCTTACTCATTT
1 TCTTTCAGCCATAGTCTTACTCATTT
43715548 TCAGGCATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 2 0.03
44 19 0.31
45 29 0.48
47 5 0.08
48 6 0.10
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (43 bp):
TCTTTCAGCCATAGTCTTACTCATTTATCATGATGCCATAGCA
Found at i:43720654 original size:106 final size:106
Alignment explanation
Indices: 43720516--43720727 Score: 370
Period size: 106 Copynumber: 2.0 Consensus size: 106
43720506 CATATCAAAT
* * * *
43720516 GACACGAAACATAACCAATTGGTCACAAACATACATTTACCAAAACCCTATTTACGTGCCACTTA
1 GACACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTA
43720581 AAATTAAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
66 AAATTAAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
*
43720622 GACACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGTCACTTA
1 GACACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTA
*
43720687 AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
66 AAATTAAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
43720728 CGGATAGTGC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (106 bp):
GACACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTA
AAATTAAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
Found at i:43729086 original size:12 final size:12
Alignment explanation
Indices: 43729069--43729122 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
43729059 CTCAAAAGCT
43729069 TATATATATACA
1 TATATATATACA
*
43729081 TATATATATTCGAA
1 TATATATATAC--A
*
43729095 TATTATACATACA
1 TA-TATATATACA
43729108 TATATATATACA
1 TATATATATACA
43729120 TAT
1 TAT
43729123 CTTTGTCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:43729593 original size:15 final size:15
Alignment explanation
Indices: 43729573--43729604 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
43729563 CAAAATAAGC
43729573 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
43729588 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
43729603 TA
1 TA
43729605 CATTCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TAGTTTAAATATAAT
Found at i:43733557 original size:30 final size:30
Alignment explanation
Indices: 43733498--43733577 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
43733488 ACACAAAGTG
*
43733498 CTTGGAAACTATAA-CACTAGTACATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* * *
43733527 CTTGGAAACTGTAATCACCGGTATATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* *
43733557 CCTGGAAACTAAAATCACCAG
1 CTTGGAAACTATAATCACCAG
43733578 CACCTAGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (30 bp):
CTTGGAAACTATAATCACCAGTACATAGTA
Found at i:43737141 original size:26 final size:26
Alignment explanation
Indices: 43737097--43737169 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
43737087 TATCATCCTT
**
43737097 ATTTTACCCTTAGCGAAATTTTAACG
1 ATTTTACCCTTAGTAAAATTTTAACG
* * *
43737123 ATTTTACCCTTGGTAAAATTTTGATG
1 ATTTTACCCTTAGTAAAATTTTAACG
* *
43737149 ATTTTGCCCCTAGTAAAATTT
1 ATTTTACCCTTAGTAAAATTT
43737170 CGAGAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTAACG
Found at i:43737333 original size:6 final size:6
Alignment explanation
Indices: 43737318--43737393 Score: 89
Period size: 6 Copynumber: 12.5 Consensus size: 6
43737308 GCAAATGAAT
* * * * *
43737318 CATTTA CATTTC CATTTT CATTTT CATTTC CATTTC CATTTT CATTTTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CA-TTTC
*
43737367 CATTTC CATTTC CATTTT CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CAT
43737394 ATCTAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
6 56 0.90
7 6 0.10
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (6 bp):
CATTTC
Found at i:43737339 original size:12 final size:12
Alignment explanation
Indices: 43737318--43737393 Score: 98
Period size: 12 Copynumber: 6.2 Consensus size: 12
43737308 GCAAATGAAT
*
43737318 CATTTACATTTC
1 CATTTTCATTTC
*
43737330 CATTTTCATTTT
1 CATTTTCATTTC
*
43737342 CATTTCCATTTC
1 CATTTTCATTTC
*
43737354 CATTTTCATTTTT
1 CATTTTCA-TTTC
*
43737367 CATTTCCATTTC
1 CATTTTCATTTC
43737379 CATTTTCATTTC
1 CATTTTCATTTC
43737391 CAT
1 CAT
43737394 ATCTAATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
12 44 0.81
13 10 0.19
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (12 bp):
CATTTTCATTTC
Found at i:43737340 original size:18 final size:18
Alignment explanation
Indices: 43737318--43737393 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
43737308 GCAAATGAAT
* *
43737318 CATTTACATTTCCATTTT
1 CATTTTCATTTCCATTTC
43737336 CATTTTCATTTCCATTTC
1 CATTTTCATTTCCATTTC
*
43737354 CATTTTCATTTTTCATTTC
1 CATTTTCA-TTTCCATTTC
* *
43737373 CATTTCCATTTTCATTTC
1 CATTTTCATTTCCATTTC
43737391 CAT
1 CAT
43737394 ATCTAATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 37 0.70
19 16 0.30
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (18 bp):
CATTTTCATTTCCATTTC
Found at i:43748787 original size:21 final size:21
Alignment explanation
Indices: 43748761--43748817 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
43748751 TTATCGCTTT
*
43748761 CCACACGGGCGTGTGCCTTAGA
1 CCACACGGGCGTGTGCCTCA-A
* *
43748783 -CACACGGTCGTGTTCCTCAA
1 CCACACGGGCGTGTGCCTCAA
*
43748803 CCACATGGGCGTGTG
1 CCACACGGGCGTGTG
43748818 AGTTAGCCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTGCCTCAA
Found at i:43748946 original size:21 final size:21
Alignment explanation
Indices: 43748922--43748969 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
43748912 CACATGGGCG
43748922 TGTGTCTCAGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
* **
43748943 TGTGCCTTTGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
43748964 TGTGTC
1 TGTGTC
43748970 ACTCTCCGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (21 bp):
TGTGTCTCAGCCACACGGCCA
Found at i:43766706 original size:51 final size:52
Alignment explanation
Indices: 43766644--43766812 Score: 205
Period size: 53 Copynumber: 3.2 Consensus size: 52
43766634 GGGTGTTGGC
* *
43766644 ACACTAATGGCCGGCACCCTTGTGCCAGATTTTAAAAAAATTGG-TGCTGGG
1 ACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAATTGGATGCTGGG
* * *
43766695 ATACTAATGGCCGACATCCTTGTACCAGAATTTAAAAAAAATTGGATGCTGGG
1 ACACTAATGGCCGGCACCCTTGTACCAG-ATTTAAAAAAAATTGGATGCTGGG
* * * * * * *
43766748 ACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAATTGGGGTGTTGAG
1 ACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAATT-GGATGCTGGG
43766801 ACACTAATGGCC
1 ACACTAATGGCC
43766813 AGCAACCACT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 24 0.24
52 29 0.30
53 45 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (52 bp):
ACACTAATGGCCGGCACCCTTGTACCAGATTTAAAAAAAATTGGATGCTGGG
Found at i:43769761 original size:28 final size:29
Alignment explanation
Indices: 43769737--43769797 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
43769727 CATTTTTATT
43769737 TTTTATTAC-TTTATTT-ATTTATTTTAAC
1 TTTTA-TACTTTTATTTAATTTATTTTAAC
*
43769765 TTTTATACTTTTATTTAATTTAATTTACAC
1 TTTTATACTTTTATTTAATTTATTTTA-AC
43769795 TTT
1 TTT
43769798 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 9 0.31
30 5 0.17
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATACTTTTATTTAATTTATTTTAAC
Found at i:43769798 original size:29 final size:27
Alignment explanation
Indices: 43769737--43769811 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 27
43769727 CATTTTTATT
*
43769737 TTTTATTACTTTATTTATTTATTTTAAC
1 TTTTA-TACTTTATTTATTTAATTTAAC
43769765 TTTTATAC--T-TTTATTTAATTTAA-
1 TTTTATACTTTATTTATTTAATTTAAC
* *
43769788 -TTTACACTTTATTTATTTATTTTA
1 TTTTATACTTTATTTATTTAATTTA
43769812 CTCTATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
24 14 0.34
25 13 0.32
27 3 0.07
28 5 0.12
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATACTTTATTTATTTAATTTAAC
Found at i:43775171 original size:30 final size:31
Alignment explanation
Indices: 43775135--43775194 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
43775125 AAACCTTTTA
*
43775135 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
43775165 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
43775195 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:43780461 original size:20 final size:20
Alignment explanation
Indices: 43780419--43780465 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
43780409 CTACCCACAT
*
43780419 TAGGGCTCCAAATCTAGTGC
1 TAGGGCTCCAAATCTACTGC
*
43780439 TAGGGCTCTAAATCTGACT-C
1 TAGGGCTCCAAATCT-ACTGC
43780459 TAGGGCT
1 TAGGGCT
43780466 TGGCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
TAGGGCTCCAAATCTACTGC
Found at i:43782161 original size:25 final size:24
Alignment explanation
Indices: 43782130--43782188 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
43782120 TTTGTTTATG
43782130 TTTTAATT-TTATGTGATTTAATAA
1 TTTTAATTATTATGTG-TTTAATAA
* *
43782154 TTATTAATTAATTTTGTGTTTCATAA
1 TT-TTAATT-ATTATGTGTTTAATAA
43782180 TTTTAATTA
1 TTTTAATTA
43782189 GGTACAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 12 0.40
26 9 0.30
27 6 0.20
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTAATTATTATGTGTTTAATAA
Found at i:43782164 original size:29 final size:25
Alignment explanation
Indices: 43782132--43782188 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 25
43782122 TGTTTATGTT
43782132 TTAATTTTATGTGATTTAATAATTATTAA
1 TTAA-TTT-TGTG-TTTAATAATT-TTAA
*
43782161 TTAATTTTGTGTTTCATAATTTTAA
1 TTAATTTTGTGTTTAATAATTTTAA
43782186 TTA
1 TTA
43782189 GGTACAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
26 9 0.33
27 4 0.15
28 3 0.11
29 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (25 bp):
TTAATTTTGTGTTTAATAATTTTAA
Found at i:43782332 original size:20 final size:20
Alignment explanation
Indices: 43782307--43782356 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43782297 AAAAAGGCCA
43782307 AGCCCTAG-AGCCAGATTTGG
1 AGCCCTAGCA-CCAGATTTGG
*
43782327 AGCCCTAGCACTAGATTTGG
1 AGCCCTAGCACCAGATTTGG
*
43782347 AGCCCCAGCA
1 AGCCCTAGCA
43782357 TGGGTAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (20 bp):
AGCCCTAGCACCAGATTTGG
Found at i:43787277 original size:34 final size:35
Alignment explanation
Indices: 43787229--43787295 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
43787219 CAGTAAAATA
*
43787229 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* * *
43787263 TTTTCTGTATAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
43787296 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:43789854 original size:29 final size:30
Alignment explanation
Indices: 43789822--43789898 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
43789812 AAGTTGTAGA
*
43789822 TTTAGTCCTTATACTTT-AATTTGATCAAT
1 TTTAGTCCTTGTACTTTCAATTTGATCAAT
* * *
43789851 TTTAGTCCTTGTAGTTTTCAATTTGGTTAAT
1 TTTAGTCCTTGTA-CTTTCAATTTGATCAAT
*
43789882 GTTAGTCCTTGTACTTT
1 TTTAGTCCTTGTACTTT
43789899 TCAAAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.30
30 6 0.15
31 22 0.55
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (30 bp):
TTTAGTCCTTGTACTTTCAATTTGATCAAT
Found at i:43793160 original size:18 final size:18
Alignment explanation
Indices: 43793137--43793171 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43793127 TAATATTATA
43793137 AAATATAATTATTATTTC
1 AAATATAATTATTATTTC
43793155 AAATATAATTATTATTT
1 AAATATAATTATTATTT
43793172 TTATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATAATTATTATTTC
Found at i:43794195 original size:21 final size:22
Alignment explanation
Indices: 43794170--43794210 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
43794160 TTGGACATGT
43794170 ATTTTTAGTAC-TTTTTTAAAG
1 ATTTTTAGTACGTTTTTTAAAG
**
43794191 ATTTTTTTTACGTTTTTTAA
1 ATTTTTAGTACGTTTTTTAA
43794211 TTTTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (22 bp):
ATTTTTAGTACGTTTTTTAAAG
Found at i:43802793 original size:6 final size:6
Alignment explanation
Indices: 43802784--43802882 Score: 58
Period size: 6 Copynumber: 16.7 Consensus size: 6
43802774 AGATTCAAAA
* ** ** *
43802784 AAAATC AAAATC AAAGTC AAAAAG AAGAAAA AAAATC AAAATC AAAGTC
1 AAAATC AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC
* * ** * * *
43802833 AAAA-- AGAATA AAAAGA AAAATC AAAATC AAAGTC AAAATG AAAATG
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
43802879 AAAA
1 AAAA
43802883 AGAGAGAAGA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
4 3 0.04
6 65 0.89
7 5 0.07
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:43802818 original size:31 final size:33
Alignment explanation
Indices: 43802780--43802870 Score: 150
Period size: 31 Copynumber: 2.8 Consensus size: 33
43802770 GTTCAGATTC
*
43802780 AAAAAAAATCAAAATCAAAGTCAAAAAG-A-AG
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAATAA
43802811 AAAAAAAATCAAAATCAAAGTCAAAAAGAATAA
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAATAA
43802844 AAAGAAAAATCAAAATCAAAGTCAAAA
1 AAA-AAAAATCAAAATCAAAGTCAAAA
43802871 TGAAAATGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 28 0.50
32 1 0.02
33 4 0.07
34 23 0.41
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.11
Consensus pattern (33 bp):
AAAAAAAATCAAAATCAAAGTCAAAAAGAATAA
Found at i:43802894 original size:13 final size:13
Alignment explanation
Indices: 43802873--43802914 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
43802863 AGTCAAAATG
*
43802873 AAAATGAAAAAGA
1 AAAAGGAAAAAGA
*
43802886 GAGAA-GAAAAAGA
1 -AAAAGGAAAAAGA
43802899 AAAAGGAAAAAGA
1 AAAAGGAAAAAGA
43802912 AAA
1 AAA
43802915 GGAGAGGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAGGAAAAAGA
Found at i:43802898 original size:6 final size:6
Alignment explanation
Indices: 43802867--43802914 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
43802857 AATCAAAGTC
* * *
43802867 AAAATG AAAATG AAAAAG AGAGAAG AAAAAG AAAAAGG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAA-G AAAAAG AAAA
43802915 GGAGAGGCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:43802911 original size:19 final size:18
Alignment explanation
Indices: 43802867--43802914 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
43802857 AATCAAAGTC
* *
43802867 AAAATGAAAATGAAAAAG
1 AAAAAGAAAAAGAAAAAG
*
43802885 AGAGAAGAAAAAGAAAAAGG
1 A-AAAAGAAAAAGAAAAA-G
43802905 AAAAAGAAAA
1 AAAAAGAAAA
43802915 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:43803804 original size:13 final size:14
Alignment explanation
Indices: 43803786--43803819 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
43803776 TTTGAGTCAA
*
43803786 AAAAATGAAAATG-
1 AAAAATGAAAAAGT
43803799 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
43803813 AAAAATG
1 AAAAATG
43803820 GAGACGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:43805161 original size:44 final size:43
Alignment explanation
Indices: 43805111--43805248 Score: 122
Period size: 42 Copynumber: 3.2 Consensus size: 43
43805101 AAAACAAAGC
43805111 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATATCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATA-CAGAT
* * * * * * * *
43805155 CTTGCCTTCC-T-GCATTAACAGCGAAGCAGATTAAA-A-ACAAAGC
1 CTTGCC-TCCATCG-GTT-GCAGTGGAGCGGGTTAAAGATACAGA-T
43805198 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATA-CAGAT
43805242 CTTGCCT
1 CTTGCCT
43805249 TCTTGTACTG
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
42 19 0.28
43 12 0.17
44 19 0.28
45 19 0.28
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (43 bp):
CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATACAGAT
Found at i:43805204 original size:43 final size:42
Alignment explanation
Indices: 43805068--43805204 Score: 109
Period size: 42 Copynumber: 3.2 Consensus size: 42
43805058 GATAGCAGAT
*
43805068 CTTGCCTTCCTGCATTGACAGTGAAGCAGATCAAAAACAAAGC
1 CTTGCCTTCCTGCATT-ACAGTGAAGCAGATTAAAAACAAAGC
* * * * * * *
43805111 CTTGCC-TCCAT-CGGTTGCAGTGGAGCGGGTTAAAGATATCAGA-T
1 CTTGCCTTCC-TGC-ATTACAGTGAAGCAGATTAAA-A-A-CAAAGC
*
43805155 CTTGCCTTCCTGCATTAACAGCGAAGCAGATTAAAAACAAAGC
1 CTTGCCTTCCTGCATT-ACAGTGAAGCAGATTAAAAACAAAGC
43805198 CTTGCCT
1 CTTGCCT
43805205 CCATCGGTTG
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
42 20 0.29
43 18 0.26
44 11 0.16
45 20 0.29
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCATTACAGTGAAGCAGATTAAAAACAAAGC
Found at i:43805330 original size:88 final size:87
Alignment explanation
Indices: 43805054--43805361 Score: 418
Period size: 87 Copynumber: 3.5 Consensus size: 87
43805044 AACAGATCAG
*
43805054 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCAAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
43805119 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * *
43805141 TAAAGATATCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTAAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
43805206 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * * * * * *
43805228 TAAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACA-AAGCCTTGCCT
* **
43805293 CCCTCGGTTGCAGTGGAGTAGGT
65 CCATCGGTTGCAGTGGAGCGGGT
* * * * * * *
43805316 TGAATATAGTAGATCTTGCCTTCCCGCATCGACAGTGAAGTAGATC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC
43805362 GAAGATTACA
Statistics
Matches: 194, Mismatches: 26, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
87 127 0.65
88 67 0.35
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
CATCGGTTGCAGTGGAGCGGGT
Found at i:43805751 original size:44 final size:44
Alignment explanation
Indices: 43805618--43805756 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 44
43805608 GTAAGGAAAT
* **
43805618 AGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAAT
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGC
*** ** * * * *
43805662 AGACCAAAGATATTCAAATCTTATCTCCCTGAGATTATAGCGGAGC
1 AGATTGAAGCCAGT--AATCCTATCTCCCTGAGATTACAGTGGAGC
*
43805708 AGATTGAAGCCAGTAATCCTATCTTCCTGAGATTACAGTGGAGC
1 AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGC
*
43805752 GGATT
1 AGATT
43805757 AAAAGGATCT
Statistics
Matches: 70, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
44 37 0.53
46 33 0.47
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGC
Found at i:43810738 original size:16 final size:17
Alignment explanation
Indices: 43810702--43810742 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
43810692 TTTGCTAAGG
*
43810702 GAAATAAATGGAAAGAA
1 GAAAAAAATGGAAAGAA
*
43810719 GAAAAAAATGTAAA-AA
1 GAAAAAAATGGAAAGAA
43810735 GAAAAAAA
1 GAAAAAAA
43810743 GTAGGGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (17 bp):
GAAAAAAATGGAAAGAA
Found at i:43814942 original size:18 final size:19
Alignment explanation
Indices: 43814921--43814962 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
43814911 TGGTTAATTT
43814921 TTAATTAAGCTA-GTTTAA
1 TTAATTAAGCTAGGTTTAA
*
43814939 TTAATTTAGCTATGGTTTAA
1 TTAATTAAGCTA-GGTTTAA
43814959 TTAA
1 TTAA
43814963 GCTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (19 bp):
TTAATTAAGCTAGGTTTAA
Found at i:43815625 original size:19 final size:19
Alignment explanation
Indices: 43815599--43815648 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
43815589 AAACTTAAAA
*
43815599 AATA-TTTTTTGTAATTTT
1 AATACTTTTTTATAATTTT
* *
43815617 TATACTTTTTAATAATTTT
1 AATACTTTTTTATAATTTT
43815636 AATACTTTTTTAT
1 AATACTTTTTTAT
43815649 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
AATACTTTTTTATAATTTT
Found at i:43815671 original size:27 final size:27
Alignment explanation
Indices: 43815598--43815687 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
43815588 AAAACTTAAA
43815598 AAAT-ATTTTTTGTAATTTTTATACTTTTT
1 AAATAATTTTTTG-AATTTTT-TA-TTTTT
* *
43815627 -AATAATTTTAAT-ACTTTTTTATTTTT
1 AAATAATTTT-TTGAATTTTTTATTTTT
* *
43815653 AAATAATTTTTTGAATTTTTAAATTTT
1 AAATAATTTTTTGAATTTTTTATTTTT
*
43815680 AAAAAATT
1 AAATAATT
43815688 AATTACTGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.12
27 29 0.58
28 9 0.18
29 5 0.10
30 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
AAATAATTTTTTGAATTTTTTATTTTT
Found at i:43821067 original size:2 final size:2
Alignment explanation
Indices: 43821060--43821097 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
43821050 CTGTTTCTTT
* *
43821060 TC TC TC TC CC TC TC AC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43821098 GGGATTGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:43836896 original size:15 final size:15
Alignment explanation
Indices: 43836866--43836899 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
43836856 TAACTCATCA
43836866 TTTAATTTTAATTTT
1 TTTAATTTTAATTTT
43836881 TTTAACTTTTAATTTT
1 TTTAA-TTTTAATTTT
43836897 TTT
1 TTT
43836900 TTCAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTAATTTTAATTTT
Found at i:43838752 original size:59 final size:60
Alignment explanation
Indices: 43838679--43838806 Score: 231
Period size: 60 Copynumber: 2.1 Consensus size: 60
43838669 ATCTAGTAGA
*
43838679 CAAGTTCAGGTACCAAAGTGAACG-AAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
*
43838738 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTATAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
43838798 CAAGTTCAG
1 CAAGTTCAG
43838807 GGGCTAAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 23 0.35
60 43 0.65
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (60 bp):
CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTGGACTTAGTTGC
Found at i:43840531 original size:95 final size:95
Alignment explanation
Indices: 43840368--43840559 Score: 323
Period size: 95 Copynumber: 2.0 Consensus size: 95
43840358 AATATAATGC
* *
43840368 TTAGACCCAACCCACACCCTACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
1 TTAGACCCAACCCAAACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
*
43840433 AAATGTTGTGATAGTGCTTGGACTTTTCTT
66 AAATGTTGTGATAATGCTTGGACTTTTCTT
* *
43840463 TTAGACCCAGCCCAAACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGATAA-GT
1 TTAGACCCAACCCAAACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGA-AAGGT
43840527 GAAATGTTGTGATAATGCTTGGACTTTTCTT
65 GAAATGTTGTGATAATGCTTGGACTTTTCTT
43840558 TT
1 TT
43840560 TCTTTTATAG
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 89 0.98
96 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (95 bp):
TTAGACCCAACCCAAACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
AAATGTTGTGATAATGCTTGGACTTTTCTT
Found at i:43842481 original size:18 final size:19
Alignment explanation
Indices: 43842454--43842490 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43842444 TTGCTATACT
*
43842454 TTTAT-TTTTTTTGAGCAA
1 TTTATATTTTTTCGAGCAA
43842472 TTTATATTTTTTCGAGCAA
1 TTTATATTTTTTCGAGCAA
43842491 GGCGAGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTATATTTTTTCGAGCAA
Found at i:43857924 original size:17 final size:16
Alignment explanation
Indices: 43857906--43857944 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
43857896 TTAAACTTTA
43857906 AAAATTCAAAAAATTT
1 AAAATTCAAAAAATTT
* *
43857922 AAAATTGAAAAAAATAT
1 AAAATT-CAAAAAATTT
43857939 AAAATT
1 AAAATT
43857945 GTTCATAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAATTCAAAAAATTT
Found at i:43857945 original size:17 final size:17
Alignment explanation
Indices: 43857913--43857945 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43857903 TTAAAAATTC
*
43857913 AAAAAATTTAAAATTGA
1 AAAAAATATAAAATTGA
43857930 AAAAAATATAAAATTG
1 AAAAAATATAAAATTG
43857946 TTCATAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAAAATATAAAATTGA
Found at i:43867429 original size:10 final size:10
Alignment explanation
Indices: 43867416--43867449 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
43867406 GAAAAATTCT
*
43867416 TTAAAAATTG
1 TTAAAAATTA
43867426 TTAAAAATTA
1 TTAAAAATTA
*
43867436 TTAAGAATTA
1 TTAAAAATTA
43867446 TTAA
1 TTAA
43867450 TTTCTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:43868003 original size:20 final size:20
Alignment explanation
Indices: 43867964--43868007 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43867954 CAAAACAAAA
*
43867964 TTTTAAATTTTTTTACTAAT
1 TTTTAAATTTATTTACTAAT
43867984 TTTTATAATTTATTTA-TAAT
1 TTTTA-AATTTATTTACTAAT
43868004 TTTT
1 TTTT
43868008 GCATTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATTTATTTACTAAT
Found at i:43868019 original size:20 final size:21
Alignment explanation
Indices: 43867964--43868019 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
43867954 CAAAACAAAA
43867964 TTTTA-AATTTTTTTACTAAT
1 TTTTACAATTTTTTTACTAAT
* *
43867984 TTTTATAATTTATTTA-TAAT
1 TTTTACAATTTTTTTACTAAT
* *
43868004 TTTTGCATTTTTTTTA
1 TTTTACAATTTTTTTA
43868020 AAAAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTACAATTTTTTTACTAAT
Found at i:43868145 original size:40 final size:40
Alignment explanation
Indices: 43868074--43868149 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
43868064 AAGCGCAATT
* * *
43868074 AATATACCATGTCACTAGTCACCTTGTCATGTCATCGGTC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
*
43868114 AATACACCATGTCACTTGTCAACTTGCCATGTCATC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATC
43868150 AATGATGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (40 bp):
AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
Found at i:43883364 original size:15 final size:15
Alignment explanation
Indices: 43883346--43883394 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
43883336 CTATAAAACC
43883346 TTTATTATTAAAATA
1 TTTATTATTAAAATA
*
43883361 TTTATAATTGTAATAAATA
1 TTTATTA-T-T-A-AAATA
43883380 TTTATTATTAAAATA
1 TTTATTATTAAAATA
43883395 ATATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 2 0.07
18 2 0.07
19 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTATTATTAAAATA
Found at i:43883394 original size:19 final size:19
Alignment explanation
Indices: 43883356--43883399 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
43883346 TTTATTATTA
**
43883356 AAATATTTATAATTGTAAT
1 AAATATTTATAATTAAAAT
*
43883375 AAATATTTATTATTAAAAT
1 AAATATTTATAATTAAAAT
43883394 -AATATT
1 AAATATT
43883400 AAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATATTTATAATTAAAAT
Found at i:43883465 original size:13 final size:14
Alignment explanation
Indices: 43883427--43883468 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
43883417 ATATGAAGAA
43883427 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
43883442 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
43883457 -TATTATTAAAAT
1 ATATTATTAAAAT
43883469 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:43883508 original size:75 final size:78
Alignment explanation
Indices: 43883374--43883518 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 78
43883364 ATAATTGTAA
* * * *
43883374 TAAATATTTATTATTAAAATAATATTAAATATTTTTCAATAATATATGAAGAAATATTAT-TT-A
1 TAAATATTTATTATTAAAATAAAATTAAATATTATTAAATAATATATGAAAAAATATTATATTGA
43883437 AAATTATCATTTT
66 AAATTATCATTTT
* *
43883450 TAAA-ATTTATTATTAAAATAAAATTAAA-A-TATTAAATAATTTATTAAAAAATAAATTATATT
1 TAAATATTTATTATTAAAATAAAATTAAATATTATTAAATAATATATGAAAAAAT--ATTATATT
43883512 GAAAATT
64 GAAAATT
43883519 TATTTTATGA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
73 18 0.31
74 1 0.02
75 28 0.47
76 6 0.10
77 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (78 bp):
TAAATATTTATTATTAAAATAAAATTAAATATTATTAAATAATATATGAAAAAATATTATATTGA
AAATTATCATTTT
Found at i:43884890 original size:18 final size:18
Alignment explanation
Indices: 43884842--43884901 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
43884832 GAAAAATTAT
* * *
43884842 AAAATATTTAAAACATTA
1 AAAATATTAAAAAAAATA
* *
43884860 TAAAT-TTATAAAAAATA
1 AAAATATTAAAAAAAATA
43884877 AAAATATTAAAAAAACTATA
1 AAAATATTAAAAAAA--ATA
43884897 AAAAT
1 AAAAT
43884902 TCAAGAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
20 8 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATTAAAAAAAATA
Found at i:43887225 original size:124 final size:124
Alignment explanation
Indices: 43886986--43887355 Score: 605
Period size: 124 Copynumber: 3.0 Consensus size: 124
43886976 TTTTAGGGCT
*** * *
43886986 TGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAAGATGC
1 TGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
43887051 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
65 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
*
43887111 TGGAAGAAATAATTTTTTTTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTAGCAGGATGCT
1 TGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* *
43887176 ATTTGAGAAGAATTTATAAAATCGCGCTCTCGTGGACGCGCTTTTGCTACAGTCGGTCA
66 ATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
*
43887235 TGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATGGTATAAAATCGCTTCTAGCAGGATGCT
1 TGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* *
43887300 ATTTGAGAAGAATTTATGAAAATCGCGCCCTTGTGGACGCACTTTTGCTACAGTAG
66 ATTTGAGAAGAATTTAT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
43887356 CATGTTTGGG
Statistics
Matches: 228, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
124 179 0.79
125 49 0.21
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
TGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
ATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
Found at i:43890512 original size:17 final size:17
Alignment explanation
Indices: 43890445--43890512 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
43890435 TATGTGAATG
*
43890445 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
43890461 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
43890480 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
43890499 TAAAATTATTAATT
1 TAAAATTATTAATT
43890513 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:43890535 original size:116 final size:116
Alignment explanation
Indices: 43890331--43890574 Score: 427
Period size: 116 Copynumber: 2.1 Consensus size: 116
43890321 TAAGTTTGTG
*
43890331 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** * *
43890396 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAGCATTATGTGAATGTA
66 TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
43890447 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
43890511 TTGTTAGTACCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
43890563 AAATTATTAATT
1 AAATTATTAATT
43890575 TAGTTTAGGG
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
115 41 0.34
116 81 0.66
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:43890689 original size:68 final size:66
Alignment explanation
Indices: 43890600--43891530 Score: 730
Period size: 68 Copynumber: 13.7 Consensus size: 66
43890590 AATTAAATTA
* *
43890600 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGAGTTAGGATTTTTAAGCTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGG-GTTAGGGTTTTTAAGTTT
43890665 AG
65 AG
43890667 GGTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTA-GGTTAGGGTTTTTAAGT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--AGGGTTAGGGTTTTTAAGT
*
43890731 TAAGG
63 TTA-G
* * * *
43890736 GGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGGATTTTAA-TTAAATTAGGTTAGGGTTTTTAAG
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGTTAAA--GGGTTAGGGTTTTTAA-
*
43890797 GTTAAG
61 GTTTAG
* * *
43890803 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTA-GGTTAGGGTTTTTAAGTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--AGGGTTAGGGTTTTTAAG-T
43890867 AATTA-
63 --TTAG
* *** * *
43890872 GGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAA-TTTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGTTAGGGTTTTTAAGTTT-
*
43890936 ATTA
65 A--G
* **
43890940 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-TAGGGTTTATGATTTTAATTAA-
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGG-TTA-GGGTTT--TTAAG
*
43891003 ATTA-
62 TTTAG
* *
43891007 GGTTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGT
1 GGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAAA--GGGTTAGGGTTTTTAAGT
*
43891068 TAAGGGG
63 TTA---G
* * * * *
43891075 GTTAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTT-TAGGATTTAGAGTTTTTAAT
1 G---GTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGG-GTTAGGGTTTTTAAG
43891139 TAAATTA-
62 T---TTAG
* * *
43891146 GGTTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGTGTTTTTTAAG
1 GGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTTAAA--GGGTTAG-GGTTTTTAAG
43891207 TTTAG
62 TTTAG
* * * ** *
43891212 GGTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTT-TAGGGTTTAATGTTTTTAATTA
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGG-TTAGGGTTTTTAAGT-
43891276 AATTA-
63 --TTAG
* *
43891281 GGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA-GGTTAGGGTTTTTAAGTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA--AGGGTTAGGGTTTTTAAGTT
43891345 TAG
64 TAG
* * * * *
43891348 GGTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGTT-TAGTGTTTAGGG-TTTTAAATT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAG-GGTTAGGGTTTTTAAGTT
*
43891411 TAATTA
64 T-A--G
*
43891417 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGAGGGTTAGGGTTTTTAAGTTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAA-AGGGTTAGGGTTTTTAAGTTT
43891482 AG
65 AG
* * *
43891484 GGTTTAAGG-TTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAAGGGT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGT
43891531 ATTAATGGTT
Statistics
Matches: 698, Mismatches: 89, Indels: 156
0.74 0.09 0.17
Matches are distributed among these distances:
63 4 0.01
64 12 0.02
65 35 0.05
66 44 0.06
67 131 0.19
68 295 0.42
69 90 0.13
70 27 0.04
71 24 0.03
72 13 0.02
73 14 0.02
74 7 0.01
75 2 0.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (66 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGGTTAGGGTTTTTAAGTTTA
G
Found at i:43890696 original size:45 final size:45
Alignment explanation
Indices: 43890577--43891530 Score: 1105
Period size: 45 Copynumber: 21.0 Consensus size: 45
43890567 TATTAATTTA
*
43890577 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--GG
** * *
43890624 G-TTAGGGTTTTTAAGTTAAAGGA-GTTAGGATTTTTAAGCTTAGG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
43890668 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGG
**
43890715 G-TTAGGGTTTTTAAGTT-AA-GGGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* * * *
43890758 GTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGGTTAAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
43890803 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--GG
*
43890850 G-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAGGG
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTA-GG
* * *
43890895 GGTTAGGGTTTTTAAGTT---TAAGGTTTAGGGTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAA-TTAAATTAGG-TTAGGGTTTTTAAGTTT-A--GG
*
43890941 G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43890985 GTTTA-TGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
43891028 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA--GG
43891075 GTTAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
1 G-T--TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891123 ATTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
*
43891167 GTTTAGGGTTTTTAATTAAATTAGGTTAGTGTTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAG-GGTTTTTAAGTTTAGG
*
43891213 GTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
** * *
43891258 GTTTAATGTTTTTAATTAAATTAGGTTAGAGTTTTTAA-TTTAATTAG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-A--GG
*
43891305 G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891349 GTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGTTTAGT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891394 GTTTAGGGTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAATTA-G
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGG
*
43891441 G-TTAGGGTTTTTAAGTTAAGA--GGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTTAA-TTAA-ATTAGGTTAGGGTTTTTAAGTTTAGG
*
43891485 GTTTAAGG-TTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAAGG
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTT-AGG
43891529 GT
1 GT
43891531 ATTAATGGTT
Statistics
Matches: 793, Mismatches: 64, Indels: 103
0.83 0.07 0.11
Matches are distributed among these distances:
42 4 0.01
43 20 0.03
44 162 0.20
45 319 0.40
46 199 0.25
47 39 0.05
48 10 0.01
50 40 0.05
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (45 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGG
Found at i:43890732 original size:91 final size:92
Alignment explanation
Indices: 43890577--43891526 Score: 1083
Period size: 91 Copynumber: 10.5 Consensus size: 92
43890567 TATTAATTTA
*
43890577 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAAGTT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAA-TT
** * *
43890641 AAAGGA-GTTAGGATTTTTAAGCTTAGG
65 AAATTAGGTTAGGGTTTTTAAGTTTAGG
*
43890668 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAGTT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAA-TT
**
43890732 -AA-GGGGTTAGGGTTTTTAAGTTTAGG
65 AAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43890758 GTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGGTT-A--AGGTTTAGGGTTTTTAATT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-GTTAATTAGGTTTAGGGTTTTTAATT
*
43890820 AAATTAGGTTAGGGTTTTTAA-TTTAATTAG
65 AAATTAGGTTAGGGTTTTTAAGTTT-A--GG
** *
43890850 G-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAA-GGGGGTTAGGGTTTTTAAGT
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAA-T
* *
43890912 T---TAAGGTTTAGGGTTTTTAA-TTTAATTAG
64 TAAATTAGG-TTAGGGTTTTTAAGTTT-A--GG
* * *
43890941 G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG-T--TTAGGGTTTA-TGATTTTAATT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTA-GGTTTAGGGTTTTTAATT
43891001 AAATTAGGTTAGGGTTTTTAAGTTTA-G
65 AAATTAGGTTAGGGTTTTTAAGTTTAGG
***
43891028 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGTTAGGGTTTTTAA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGG-T--TTAGGGTTTTTAA
43891093 TTAAATTAGGTTAGGGTTTTTAAGTTTAGG
63 TTAAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891123 ATTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGGTTTAGGGTTTTTAATTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAATTA
*
43891185 AATTAGGTTAGTGTTTTTTAAGTTTAGG
66 AATTAGGTTAG-GGTTTTTAAGTTTAGG
* **
43891213 GTTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGGGTTTAATGTTTTTAATT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTA-GGTTTAGGGTTTTTAATT
* *
43891275 AAATTAGGTTAGAGTTTTTAA-TTTAATTAG
65 AAATTAGGTTAGGGTTTTTAAGTTT-A--GG
*
43891305 G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG-T--TTAGGGTTTAGGGTTTTTAATT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTA-GGTTTAGGGTTTTTAATT
* *
43891366 AAATTAGGTTGGGGTTTTTAAGTTTAGT
65 AAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891394 GTTTAGGGTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAGTT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAA-TT
*
43891458 AAGA--GGGTTAGGGTTTTTAAGTTTAGG
65 AA-ATTAGGTTAGGGTTTTTAAGTTTAGG
* *
43891485 GTTTAAGG-TTTTAATTAAATTAGGTTAGGGTTTTTAATTTAA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA
43891527 GGGTATTAAT
Statistics
Matches: 760, Mismatches: 58, Indels: 83
0.84 0.06 0.09
Matches are distributed among these distances:
87 2 0.00
88 43 0.06
89 58 0.08
90 234 0.31
91 308 0.41
92 32 0.04
93 9 0.01
94 36 0.05
95 38 0.05
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (92 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTTAGGGTTTTTAATTA
AATTAGGTTAGGGTTTTTAAGTTTAGG
Found at i:43890733 original size:28 final size:23
Alignment explanation
Indices: 43890569--43891526 Score: 829
Period size: 23 Copynumber: 42.2 Consensus size: 23
43890559 AGTAAAATTA
*
43890569 TTAATTTAGTTTAGGGTTTTTAA-
1 TTAA-TTAGGTTAGGGTTTTTAAG
*
43890592 TTAAATTAGGTTAGGGTTTTTAAT
1 TT-AATTAGGTTAGGGTTTTTAAG
43890616 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
43890639 TTAA--AGGAGTTAGGATTTTTAAG
1 TTAATTA-G-GTTAGGGTTTTTAAG
* *
43890662 CTT-A--GGGTTTAGGGTTTTTAAT
1 -TTAATTAGG-TTAGGGTTTTTAAG
43890684 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
43890707 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
**
43890730 TTAA-GGGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
43890752 -T--TTAGGGTTTAAGGATTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
43890773 TTAAATTAGGTTAGGGTTTTTAAGG
1 TT-AATTAGGTTAGGGTTTTTAA-G
43890798 TT-A--AGGTTTAGGGTTTTTAA-
1 TTAATTAGG-TTAGGGTTTTTAAG
*
43890818 TTAAATTAGGTTAGGGTTTTTAAT
1 TT-AATTAGGTTAGGGTTTTTAAG
43890842 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
43890865 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
***
43890888 TTAAGGGGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
43890911 TT--TAAGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAG
*
43890933 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
43890956 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
43890979 -T--TTAGGGTTTA-TGATTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
43890999 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
43891023 -T--TTAGGTTTAGGGTTTTTAA-
1 TTAATTAGG-TTAGGGTTTTTAAG
43891043 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
43891067 TTAAGGGGGTTA-GTTAGGGTTTTTAA-
1 TTAA-----TTAGGTTAGGGTTTTTAAG
43891093 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
*
43891117 -T--TTAGGATTTAGAGTTTTTAA-
1 TTAATTAGG--TTAGGGTTTTTAAG
43891138 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
43891162 -T--TTAGGTTTAGGGTTTTTAA-
1 TTAATTAGG-TTAGGGTTTTTAAG
*
43891182 TTAAATTAGGTTAGTGTTTTTTAAG
1 TT-AATTAGGTTAG-GGTTTTTAAG
*
43891207 -T--TTAGGGTTTAAGGTTTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
43891228 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
**
43891252 -T--TTAGGGTTTAATGTTTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
* *
43891273 TTAAATTAGGTTAGAGTTTTTAAT
1 TT-AATTAGGTTAGGGTTTTTAAG
*
43891297 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
43891320 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
43891343 -T--TTAGGGTTTAGGGTTTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
*
43891364 TTAAATTAGGTTGGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
* * * * *
43891388 TTTAGT-GTTTAGGGTTTTAAAT
1 TTAATTAGGTTAGGGTTTTTAAG
43891410 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
43891433 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
43891456 TTAA-GAGGGTTAGGGTTTTTAAG
1 TTAATTA-GGTTAGGGTTTTTAAG
*
43891479 -T--TTAGGGTTTAAGG-TTTTAA-
1 TTAATTA-GG-TTAGGGTTTTTAAG
*
43891499 TTAAATTAGGTTAGGGTTTTTAAT
1 TT-AATTAGGTTAGGGTTTTTAAG
43891523 TTAA
1 TTAA
43891527 GGGTATTAAT
Statistics
Matches: 783, Mismatches: 58, Indels: 188
0.76 0.06 0.18
Matches are distributed among these distances:
20 26 0.03
21 68 0.09
22 161 0.21
23 430 0.55
24 58 0.07
25 19 0.02
26 2 0.00
27 16 0.02
28 3 0.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAG
Found at i:43891599 original size:25 final size:25
Alignment explanation
Indices: 43891569--43891616 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
43891559 TATCAAAAAT
43891569 TTTTATTTTATTACATCAAATAAAC
1 TTTTATTTTATTACATCAAATAAAC
43891594 TTTTATTTTATTACATCAAATAA
1 TTTTATTTTATTACATCAAATAA
43891617 TATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTATTTTATTACATCAAATAAAC
Found at i:43891969 original size:18 final size:18
Alignment explanation
Indices: 43891946--43891981 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43891936 CGGAAAAGGG
*
43891946 TACATACAAGGGTTAGGA
1 TACATACAAGGGCTAGGA
*
43891964 TACATATAAGGGCTAGGA
1 TACATACAAGGGCTAGGA
43891982 AACGCACCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TACATACAAGGGCTAGGA
Found at i:43892634 original size:7 final size:7
Alignment explanation
Indices: 43892624--43892648 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43892614 TTATATACAT
43892624 AATACTA
1 AATACTA
43892631 AATACTA
1 AATACTA
43892638 AATACTA
1 AATACTA
43892645 AATA
1 AATA
43892649 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:43892856 original size:20 final size:20
Alignment explanation
Indices: 43892819--43892856 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43892809 TTTATTTTTA
*
43892819 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
43892839 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
43892857 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:43893790 original size:12 final size:11
Alignment explanation
Indices: 43893748--43893790 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
43893738 ATTTTTATGG
*
43893748 TTTAAAAAAAA
1 TTTAAAAAATA
43893759 TTTAAAAAATA
1 TTTAAAAAATA
* *
43893770 TTTTTAAAATTA
1 -TTTAAAAAATA
43893782 TTTAAAAAA
1 TTTAAAAAA
43893791 GGGAGTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:43893812 original size:11 final size:11
Alignment explanation
Indices: 43893796--43893837 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
43893786 AAAAAGGGAG
43893796 TTAAGAGAAAC
1 TTAAGAGAAAC
*
43893807 TTAAGAGGAAC
1 TTAAGAGAAAC
*
43893818 TTAAGAGGAAC
1 TTAAGAGAAAC
43893829 TTAAGAGAA
1 TTAAGAGAA
43893838 TTTTTGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:43898880 original size:20 final size:20
Alignment explanation
Indices: 43898855--43898908 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
43898845 TCTTTCTTAA
43898855 CAAAAATTAAAAATAATTTT
1 CAAAAATTAAAAATAATTTT
* *
43898875 CAAAAATTCAAAATGATTTT
1 CAAAAATTAAAAATAATTTT
*
43898895 -TAAAATTAAAAATA
1 CAAAAATTAAAAATA
43898909 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
CAAAAATTAAAAATAATTTT
Found at i:43919144 original size:20 final size:20
Alignment explanation
Indices: 43919121--43919189 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
43919111 GTTAGATATT
*
43919121 TTGATAAATCTTTAAAAATA
1 TTGATAAATCTTTAGAAATA
*
43919141 TTGATAAAT-TATTAGATATA
1 TTGATAAATCT-TTAGAAATA
*
43919161 TTGATAAATCCTTT-GAAATT
1 TTGATAAAT-CTTTAGAAATA
43919181 TTGATAAAT
1 TTGATAAAT
43919190 TGTTATATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.02
20 38 0.90
21 2 0.05
22 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (20 bp):
TTGATAAATCTTTAGAAATA
Found at i:43919165 original size:40 final size:40
Alignment explanation
Indices: 43919105--43919190 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
43919095 ATTATCTTGG
* *
43919105 TAAATTGTTAGATATTTTGATAAAT-CTTTAAAAATATTGA
1 TAAATTATTAGATATATTGATAAATCCTTT-AAAATATTGA
* *
43919145 TAAATTATTAGATATATTGATAAATCCTTTGAAATTTTGA
1 TAAATTATTAGATATATTGATAAATCCTTTAAAATATTGA
43919185 TAAATT
1 TAAATT
43919191 GTTATATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (40 bp):
TAAATTATTAGATATATTGATAAATCCTTTAAAATATTGA
Found at i:43920485 original size:30 final size:29
Alignment explanation
Indices: 43920421--43920476 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
43920411 CCCAAATCGA
* *
43920421 TTAAAAATAATTTTTCTAATAAAAATTAC
1 TTAAAAATAAATTTTCTAACAAAAATTAC
43920450 TTAAAAATAAATTTTC-AACAAACAATT
1 TTAAAAATAAATTTTCTAACAAA-AATT
43920477 GATATAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAAATTTTCTAACAAAAATTAC
Found at i:43922224 original size:18 final size:19
Alignment explanation
Indices: 43922201--43922239 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
43922191 GAAACTCTAT
43922201 ATCCTTC-AGGGATTTT-AA
1 ATCCTTCTA-GGATTTTCAA
43922219 ATCCTTCTAGGATTTTCAA
1 ATCCTTCTAGGATTTTCAA
43922238 AT
1 AT
43922240 AAATTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (19 bp):
ATCCTTCTAGGATTTTCAA
Found at i:43929823 original size:2 final size:2
Alignment explanation
Indices: 43929816--43929886 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
43929806 TCTTATAATT
43929816 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43929858 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43929887 AAATATATAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:43933774 original size:18 final size:18
Alignment explanation
Indices: 43933746--43933793 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
43933736 ATTTTTCGAA
43933746 AAATAAA-TTTTTTGTTC
1 AAATAAATTTTTTTGTTC
43933763 AAATAAATTTTTTTGTTC
1 AAATAAATTTTTTTGTTC
*
43933781 AAAT-TATTTTTTT
1 AAATAAATTTTTTT
43933794 CCAGTTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
AAATAAATTTTTTTGTTC
Found at i:43962516 original size:49 final size:49
Alignment explanation
Indices: 43962459--43962558 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
43962449 TCCTTTACAT
* *
43962459 CACCAAGCCCAAATCCTAGTAAACCCAACTAGCCTGAAGTTTTAAGACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
*
43962508 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAATACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
43962557 CA
1 CA
43962559 GCCCAAGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (49 bp):
CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
Found at i:43962533 original size:25 final size:25
Alignment explanation
Indices: 43962459--43962534 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
43962449 TCCTTTACAT
43962459 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
* * * * *
43962484 CAACTAGCCTGAAGT--T-TTAAGACC
1 CACCAAGCC-CAAATCCTAGTAA-ACC
43962508 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
43962533 CA
1 CA
43962535 ACTAACCTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
23 6 0.17
24 11 0.31
25 13 0.36
26 6 0.17
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.16
Consensus pattern (25 bp):
CACCAAGCCCAAATCCTAGTAAACC
Found at i:43967651 original size:11 final size:11
Alignment explanation
Indices: 43967635--43967666 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
43967625 TGGCGAACTT
*
43967635 TGTCAAATTAC
1 TGTCAAATTAA
43967646 TGTCAAATTAA
1 TGTCAAATTAA
43967657 TGTCAAATTA
1 TGTCAAATTA
43967667 TTGTGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (11 bp):
TGTCAAATTAA
Found at i:43970537 original size:43 final size:42
Alignment explanation
Indices: 43970469--43970579 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 42
43970459 AGATCGTACA
43970469 ATGCCTAC-GTCCCAGACGAGGTCTTACA-TGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGAC-AGGTCTTACACT-TAAATCAAATA-CG
*
43970512 ATGCCACTGTCCCAGACAGGATCTTACACTTAAATCATATACG
1 ATGCCACTGTCCCAGACAGG-TCTTACACTTAAATCAAATACG
*
43970555 ATGCCAATGTCCCAGACATGGTCTT
1 ATGCCACTGTCCCAGACA-GGTCTT
43970580 TCTCAATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
42 5 0.08
43 45 0.74
44 11 0.18
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGTCTTACACTTAAATCAAATACG
Found at i:43971787 original size:16 final size:17
Alignment explanation
Indices: 43971766--43971797 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43971756 TGTTCATACT
43971766 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
43971782 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
43971798 GTCTTACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:43972551 original size:3 final size:3
Alignment explanation
Indices: 43972539--43972617 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
43972529 TAATGTGTGC
* * * * *
43972539 TAT TATT TAT TAT TAT TAT ATAT TAT TCT TAA CAC TAT TAT AAT TAT
1 TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
43972586 TAT TAT TAG CAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43972618 AATACCTTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:43977540 original size:6 final size:6
Alignment explanation
Indices: 43977525--43977563 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
43977515 ATGAAAATGA
*
43977525 AAAAGAG AAAAGG AAAAGG AAAAGG AAAAAG AAAAGG AA
1 AAAAG-G AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AA
43977564 TGGCCAAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:43977546 original size:26 final size:24
Alignment explanation
Indices: 43977512--43977563 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
43977502 AATCAAAGTC
*
43977512 AAAATGAAAATGAAAAAGAGAAAAGG
1 AAAAGGAAAA-GAAAAA-AGAAAAGG
*
43977538 AAAAGGAAAAGGAAAAAGAAAAGG
1 AAAAGGAAAAGAAAAAAGAAAAGG
43977562 AA
1 AA
43977564 TGGCCAAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 5 0.21
26 9 0.38
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (24 bp):
AAAAGGAAAAGAAAAAAGAAAAGG
Found at i:43977949 original size:21 final size:22
Alignment explanation
Indices: 43977909--43977953 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
43977899 GGATTTCAAG
*
43977909 AACAAAAAAGAAAGAGATGAAA
1 AACAAAAAAGAAAGAAATGAAA
*
43977931 AACAAAAATGAAA-AAATGAAA
1 AACAAAAAAGAAAGAAATGAAA
43977952 AA
1 AA
43977954 TGAAAGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (22 bp):
AACAAAAAAGAAAGAAATGAAA
Done.