Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 171 of 279
Found at i:56658242 original size:39 final size:39
Alignment explanation
Indices: 56658188--56658264 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
56658178 ATTGTTCCGA
56658188 AAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTC
1 AAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTC
*
56658227 AAGAGTGTGTCACTTGGGATTTCTTTCAGACAGAATTT
1 AAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTT
56658265 TGCAAAAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (39 bp):
AAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTC
Found at i:56663663 original size:28 final size:28
Alignment explanation
Indices: 56663617--56663742 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
56663607 TGACTTTCGA
56663617 CACTAAGTGTGCGTA-TTTAATTGTAAAG
1 CACTAAGTGTGCG-AGTTTAATTGTAAAG
*
56663645 CACTAAGTGTGCTAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
56663673 CACTAAGTGTACGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
56663701 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
56663729 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
56663743 ACTTATTAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 1 0.01
28 84 0.99
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:56664528 original size:70 final size:70
Alignment explanation
Indices: 56664439--56664954 Score: 686
Period size: 70 Copynumber: 7.3 Consensus size: 70
56664429 ATGTTCATGT
* * *
56664439 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGC
56664504 TGTCC
66 TGTCC
* * * * *
56664509 AATTTTGATG-TAAAAATGCTG-CTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACATAT
1 AATTTTTATGCT-AAAATGCTGTC-CAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATAT
*
56664572 GCTGTCA
64 GCTGTCC
* * *
56664579 AATTTTTATGCTAAAATGCTGTCCAATTTGTTATATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGC
56664644 TGTCC
66 TGTCC
* * * * *
56664649 AATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAACTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGC
56664714 TGTCC
66 TGTCC
* * *
56664719 AATTTTGATG-TAAAAATGCTG-CTCAATTTGGTATATATATAGGCTGCCCAAATTGTTGTATAT
1 AATTTTTATGCT-AAAATGCTGTC-CAATTT-GT-TGTATATATGCTGCCCAAATTGTTGTATAT
56664782 ATGCTGTCC
62 ATGCTGTCC
*
56664791 AATTTTTATGCTAAAATGCTGTTCAATTTGATTG-ATATATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGTCCAATTTG-TTGTATATATGCTGCCCAAATTGTTGTATATATG
56664855 CTGTCC
65 CTGTCC
*
56664861 AATTTTTATGCTAAAATGCTGTTCAATTTGATTG-ATATATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGTCCAATTTG-TTGTATATATGCTGCCCAAATTGTTGTATATATG
56664925 CTGTCC
65 CTGTCC
*
56664931 AATTTTTGGTG-TGAAAATGCTGTC
1 AATTTTT-ATGCT-AAAATGCTGTC
56664955 TAGTTTGGTA
Statistics
Matches: 402, Mismatches: 31, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
69 4 0.01
70 320 0.80
71 18 0.04
72 59 0.15
73 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (70 bp):
AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCCCAAATTGTTGTATATATGC
TGTCC
Found at i:56664620 original size:47 final size:48
Alignment explanation
Indices: 56664439--56664935 Score: 217
Period size: 47 Copynumber: 10.6 Consensus size: 48
56664429 ATGTTCATGT
* * * *
56664439 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCA
1 AATTTGTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
* * * *
56664487 AA-TTGT-TGC-ATATATGCTGTCCAATTTTGATGTAAAAATGCTGCTC-
1 AATTTGTATGCTA-AAATGCTGTCCAA-TTTGTTGTATATATGCTGCTCA
* * * * * *
56664533 AATTTGGTAT-AT-ATATGCTGCCCAAATTGTTGCACATATGCTG-TCA
1 AATTT-GTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
* * * *
56664579 AATTTTTATGCTAAAATGCTGTCCAATTTGTTATATTTATGCTGCCCA
1 AATTTGTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
* * * *
56664627 AA-TTGT-TGC-ATATATGCTGTCCAATTTTTATGCT-TAAATGCTGC-CC
1 AATTTGTATGCTA-AAATGCTGTCCAATTTGT-TG-TATATATGCTGCTCA
** ** ** *
56664673 AATTTGT-TG-TATTTATGCTACCCAAACTGTTGTATATATGCTG-TCC
1 AATTTGTATGCTA-AAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
* * *
56664719 AATTT-TGATG-TAAAAATGCTG-CTCAATTTGGTATATATATAGGCTGCCCA
1 AATTTGT-ATGCT-AAAATGCTGTC-CAATTT-GT-TGTATATATGCTGCTCA
* * * *
56664769 AA-TTGT-TG-TATATATGCTGTCCAATTTTTATGCTA-AAATGCTGTTC-
1 AATTTGTATGCTA-AAATGCTGTCCAATTTGT-TG-TATATATGCTGCTCA
* * * * *
56664815 AATTTG-ATTGAT-ATATGCTGCCCAAATTGTTGTATATATGCTG-TCC
1 AATTTGTA-TGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
* * *
56664861 AATTTTTATGCTAAAATGCTGTTCAATTTGATTG-ATATATGCTGCCCA
1 AATTTGTATGCTAAAATGCTGTCCAATTTG-TTGTATATATGCTGCTCA
*
56664909 AA-TTGT-TG-TATATATGCTGTCCAATTT
1 AATTTGTATGCTA-AAATGCTGTCCAATTT
56664936 TTGGTGTGAA
Statistics
Matches: 340, Mismatches: 70, Indels: 80
0.69 0.14 0.16
Matches are distributed among these distances:
45 14 0.04
46 111 0.33
47 157 0.46
48 38 0.11
49 16 0.05
50 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (48 bp):
AATTTGTATGCTAAAATGCTGTCCAATTTGTTGTATATATGCTGCTCA
Found at i:56664764 original size:25 final size:25
Alignment explanation
Indices: 56664736--56664783 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
56664726 ATGTAAAAAT
* *
56664736 GCTGCTCAATTTGGTATATATATAG
1 GCTGCCCAAATTGGTATATATATAG
* *
56664761 GCTGCCCAAATTGTTGTATATAT
1 GCTGCCCAAATTGGTATATATAT
56664784 GCTGTCCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (25 bp):
GCTGCCCAAATTGGTATATATATAG
Found at i:56664860 original size:212 final size:209
Alignment explanation
Indices: 56664439--56664984 Score: 830
Period size: 212 Copynumber: 2.6 Consensus size: 209
56664429 ATGTTCATGT
*
56664439 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
56664504 TGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACA
66 TGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACA
56664569 TATGCTGTCAAATTTTTATGCTAAAATGCTGTCCAATTTGTTATATTTATGCTGCCCAAATTGTT
131 TATGCTGTCAAATTTTTATGCTAAAATGCTGTCCAATTTGTTATA-TTATGCTGCCCAAATTGTT
56664634 GCATATATGCTGTCC
195 GCATATATGCTGTCC
* * *
56664649 AATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTACCCAAACTGTTGTATATATGC
1 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
56664714 TGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATAGGCTGCCCAAATTGTTGTA
66 TGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATAT--GCTGCCCAAATTGTTGCA
* * *
56664779 TATATGCTGTCCAATTTTTATGCTAAAATGCTGTTCAATTTGATTGATA-TATGCTGCCCAAATT
129 CATATGCTGTCAAATTTTTATGCTAAAATGCTGTCCAATTTG-TT-ATATTATGCTGCCCAAATT
*
56664843 GTTGTATATATGCTGTCC
192 GTTGCATATATGCTGTCC
* * *
56664861 AATTTTTATGCTAAAATGCTGTTCAATTTGATTG-ATATATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTTAAATGCTGTCCAATTTG-TTGTATTTATGCTGCCCAAATTGTTGTATATATG
* * * **
56664925 CTGTCCAATTTTTGGTGTGAAAATGCTG-TCTAGTTTGGTATATGA-ATGCTATCCAAATTG
65 CTGTCCAA-TTTTGATGTAAAAATGCTGCTC-AATTTGGTATAT-ATATGCTGCCCAAATTG
56664985 ATGTAAAAAG
Statistics
Matches: 308, Mismatches: 20, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
210 106 0.34
211 11 0.04
212 152 0.49
213 35 0.11
214 4 0.01
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (209 bp):
AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
TGTCCAATTTTGATGTAAAAATGCTGCTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACA
TATGCTGTCAAATTTTTATGCTAAAATGCTGTCCAATTTGTTATATTATGCTGCCCAAATTGTTG
CATATATGCTGTCC
Found at i:56668956 original size:43 final size:42
Alignment explanation
Indices: 56668887--56669004 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
56668877 AGCTCGTACA
* *
56668887 ATGCCAAC-GTCCCAGAC-GTGGACTTACATGTAATCAAATATCG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAAATA-CG
* * *
56668930 ATGCCACTGTCCCAGACAGGGTCTTACGCGAAATCATATACG
1 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATACG
* * *
56668972 ATGCCAATGTCTCAGACATGGTCTTACACGTAA
1 ATGCCACTGTCCCAGACAGGGTCTTACACGTAA
56669005 ATCTCAAATC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 32 0.51
43 30 0.48
44 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATACG
Found at i:56668988 original size:42 final size:44
Alignment explanation
Indices: 56668887--56669044 Score: 141
Period size: 43 Copynumber: 3.7 Consensus size: 44
56668877 AGCTCGTACA
* * *
56668887 ATGCCAACGTCCCAGAC-GTGGACTTACATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAAATCAAATATCG
* * *
56668930 ATGCCACTGTCCCAGACAGGGTCTTACGCG-AAATCATATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCAAATATCG
* * *
56668972 ATGCCAATGTCTCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATC-AAATATCG
* *
56669016 A-ACCAATGTCCTAGAC-GTGGTCTTACACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG
56669045 AGATCACATC
Statistics
Matches: 93, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
42 28 0.30
43 60 0.65
44 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAAATCAAATATCG
Found at i:56670574 original size:43 final size:43
Alignment explanation
Indices: 56670526--56670616 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
56670516 AGTACTTTTG
*
56670526 AAAAAAAAGAGGAGAAACTAAAATTTTTAGTTTTTCTTCTCTC
1 AAAAAAAAAAGGAGAAACTAAAATTTTTAGTTTTTCTTCTCTC
56670569 AAAAAAAAAAGGAGAAACTAAAATTTTTAGTTTTTCTTCTCTC
1 AAAAAAAAAAGGAGAAACTAAAATTTTTAGTTTTTCTTCTCTC
56670612 AAAAA
1 AAAAA
56670617 TACTTTTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (43 bp):
AAAAAAAAAAGGAGAAACTAAAATTTTTAGTTTTTCTTCTCTC
Found at i:56670861 original size:43 final size:38
Alignment explanation
Indices: 56670814--56670913 Score: 87
Period size: 41 Copynumber: 2.5 Consensus size: 38
56670804 AAATATTTAA
56670814 AATTTATAT-TTCATATAATAAAATATTAATAATAAGTTATACT
1 AATTTATATATTC-T-TAATAAAATA-TAATAAT-A-TTA-ACT
* *
56670857 AATTT-TTTATTCTTACTAAAATATAATAATATTAACT
1 AATTTATATATTCTTAATAAAATATAATAATATTAACT
* *
56670894 AATTTAAACATTACTTAATA
1 AATTTATATATT-CTTAATA
56670914 CATATTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
37 8 0.17
38 6 0.12
39 7 0.15
40 7 0.15
41 9 0.19
42 3 0.06
43 8 0.17
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (38 bp):
AATTTATATATTCTTAATAAAATATAATAATATTAACT
Found at i:56671676 original size:16 final size:16
Alignment explanation
Indices: 56671648--56671695 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
56671638 CGTCTGGTTC
56671648 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
56671664 GCTTTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
56671680 GCTGTAATGAAATAGA
1 GCTGTAATGGAATAGA
56671696 AATGTAATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:56674865 original size:3 final size:3
Alignment explanation
Indices: 56674857--56674939 Score: 112
Period size: 3 Copynumber: 27.3 Consensus size: 3
56674847 TGTTTAATTA
* *
56674857 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
56674905 ATT ATA ATT ATT ACT ACT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
56674940 GCTTTATTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:56680427 original size:44 final size:44
Alignment explanation
Indices: 56680283--56681301 Score: 1037
Period size: 44 Copynumber: 23.0 Consensus size: 44
56680273 AAGACTTGTA
** * *
56680283 TCTTCGATCTACTTCACTGCTGATACAGGAAGACAATATCTGCTT
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
* * *** *
56680328 TCTTCGATCTACTTTGC-CACCAGTATGGGAAGATAAGATCTGCTAT
1 TCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCT-T
** * * *
56680374 T-TTTTATCTACTTCACGCCAATACATGAATATAAGATCTACTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
56680417 TCTTCGATCTACTT--CGCCACTAGTATGGGAAAACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATA-CAT--GAAGACAAGATCTGCTT
*
56680462 TCTTCGATCTACCTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
56680506 TCTTCGATCTACTTCACGCCAATCCATAAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
56680550 TCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCCGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
56680594 TCTTCGATCTACTTCATGCCAGTACATGAAGACAAGAT-TCGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT-GCTT
* * * *
56680638 TCTTCGATCTACTTCATGCCAATACATGAAGACAATATTTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *** *
56680682 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
56680727 TATTTGATCTACTTCACGCCAATACATGAAGATAAGATCTACTC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
56680771 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCAGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* **
56680815 TCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *** *
56680859 TCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTG
1 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
* * * *
56680904 TATTTGATCTACTTCACGCCAATACATGAAGATAAGATCTACTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
56680948 TCTTTGATCCACTTCACGCCAATACATGAAGACAAGATCCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
56680992 TCTTCGATCTACTTCA--CCACTAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATA-CAT--GAAGACAAGATCTGCTT
* * *
56681037 TCTTTGATCTACTTCACGCCAATACATGAAGATAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * * *
56681081 TCTTCGATCTACTTTGC-CACCAGTATAGGAAGACAAAATTTGCTA
1 TCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTT
* *
56681126 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * *
56681170 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* * *
56681215 TCTTTGATCTATTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
56681259 TCTTGGACCTACTTCACGCCAATACATGAAGACAAGATCTGCT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
56681302 ATCCTTTCTA
Statistics
Matches: 795, Mismatches: 156, Indels: 47
0.80 0.16 0.05
Matches are distributed among these distances:
42 12 0.02
43 8 0.01
44 527 0.66
45 225 0.28
46 10 0.01
47 13 0.02
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:56680524 original size:133 final size:131
Alignment explanation
Indices: 56680283--56681301 Score: 1010
Period size: 133 Copynumber: 7.7 Consensus size: 131
56680273 AAGACTTGTA
** * * *
56680283 TCTTCGATCTACTTCACTGCTGATACAGGAAGACAATATCTGCTTTCTTCGATCTACTTTGC-CA
1 TCTTCGATCTACTT-AC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC-TT-CACG
* *** * * * *
56680347 CCAGTATGGGAAGATAAGATCTGCTATT-TTTTATCTACTTCACGCCAATACATGAATATAAGAT
62 CCAATACATGAAGACAAGATCTGCT-TTCTTTGATCTACTTCACGCCAATACATGAAGACAAGAT
*
56680411 CTACTT
126 CTGCTT
* * * * *
56680417 TCTTCGATCTACTT-CGCCACTAGTATGGGAAAACAAGATCTGCTATCTTCGATCTACCTCACGC
1 TCTTCGATCTACTTACGCCAATA-CAT--GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGC
* * *
56680481 CAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATCCATAAAGACAAGATCT
63 CAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
56680546 GCTT
128 GCTT
* * *
56680550 TCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCCGCTTTCTTCGATCTACTTCATGCCA
1 TCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
* * * * *
56680615 GTACATGAAGACAAGAT-TCGCTTTCTTCGATCTACTTCATGCCAATACATGAAGACAATATTTG
65 ATACATGAAGACAAGATCT-GCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
*
56680679 TTT
129 CTT
* *** * * *
56680682 TCTTTGATCTACTT-CGCCACCAGTATGGGAAGACAAGATCTGCTATATTTGATCTACTTCACGC
1 TCTTCGATCTACTTACGCCA--A-TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGC
* * * *
56680746 CAATACATGAAGATAAGATCTACTCTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCA
63 CAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCT
56680811 GCTT
128 GCTT
* ** * *
56680815 TCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTATTTTCTTCAATCTACTTCACCACC
1 TCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCA-CGCC
* *** * * * *
56680880 AGTATGGGAAGACAAGATCTGCTGTATTTGATCTACTTCACGCCAATACATGAAGATAAGATCTA
64 AATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
56680945 CTT
129 CTT
* * * *
56680948 TCTTTGATCCACTTCACGCCAATACATGAAGACAAGATCCGTTTTCTTCGATCTACTTCA--CCA
1 TCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
* * * *
56681011 CTAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGATAAGATC
65 ATA-CAT--GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
*
56681076 TGTTT
127 TGCTT
* * * * * * *
56681081 TCTTCGATCTACTT-TGCCACCAGTATAGGAAGACAAAATTTGCTATCTTTGATCTACTTCACGC
1 TCTTCGATCTACTTACGCCA--A-TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGC
* * * * * * *
56681145 CAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATC
63 CAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATC
*
56681210 TGCTA
127 TGCTT
* * * * *
56681215 TCTTTGATCTATTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTGGACCTACTTCACGCCA
1 TCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
56681280 ATACATGAAGACAAGATCTGCT
65 ATACATGAAGACAAGATCTGCT
56681302 ATCCTTTCTA
Statistics
Matches: 730, Mismatches: 129, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
130 10 0.01
131 10 0.01
132 137 0.19
133 443 0.61
134 107 0.15
135 14 0.02
136 9 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (131 bp):
TCTTCGATCTACTTACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAA
TACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT
T
Found at i:56681024 original size:89 final size:86
Alignment explanation
Indices: 56680283--56681301 Score: 923
Period size: 89 Copynumber: 11.5 Consensus size: 86
56680273 AAGACTTGTA
* * * * *
56680283 TCTTCGATCTACTTCACTGCTGATACAGGAAGACAATATCTGCTTTCTTCGATCTACTTTGC-CA
1 TCTTCGATCTACTTCAC--C-AATACATGAAGACAAGATCTGCTTTCTTTGATCTAC-TT-CACG
* *** *
56680347 CCAGTATGGGAAGATAAGATCTGCTAT
61 CCAATACATGAAGACAAGATCTGCT-T
** * * * *
56680374 T-TTTTATCTACTTCACGCCAATACATGAATATAAGATCTACTTTCTTCGATCTACTT--CGCCA
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCA
* * * *
56680436 CTAGTATGGGAAAACAAGATCTGCTA
64 ATA-CAT--GAAGACAAGATCTGCTT
* *
56680462 TCTTCGATCTACCTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCA
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCA
* *
56680527 ATCCATAAAGACAAGATCTGCTT
64 ATACATGAAGACAAGATCTGCTT
* * * *
56680550 TCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCCGCTTTCTTCGATCTACTTCATGCCA
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCA
*
56680615 GTACATGAAGACAAGAT-TCGCTT
64 ATACATGAAGACAAGATCT-GCTT
* * * * *
56680638 TCTTCGATCTACTTCATGCCAATACATGAAGACAATATTTGTTTTCTTTGATCTACTTCGCCACC
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTC-ACGCC
* *** *
56680703 AGTATGGGAAGACAAGATCTGCTA
63 AATACATGAAGACAAGATCTGCTT
* * * * *
56680727 TATTTGATCTACTTCACGCCAATACATGAAGATAAGATCTACTCTCTTTGATCTACTTCACGCCA
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCA
*
56680792 ATACATGAAGACAAGATCAGCTT
64 ATACATGAAGACAAGATCTGCTT
* ** ** *
56680815 TCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTATTTTCTTCAATCTACTTCACCACC
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCA-CGCC
* *** *
56680880 AGTATGGGAAGACAAGATCTGCTG
63 AATACATGAAGACAAGATCTGCTT
* * * * *
56680904 TATTTGATCTACTTCACGCCAATACATGAAGATAAGATCTACTTTCTTTGATCCACTTCACGCCA
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCA
* *
56680969 ATACATGAAGACAAGATCCGTTT
64 ATACATGAAGACAAGATCTGCTT
* * *
56680992 TCTTCGATCTACTTCACCACTAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCACCAATA-CAT--GAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCC
* *
56681057 AATACATGAAGATAAGATCTGTTT
63 AATACATGAAGACAAGATCTGCTT
* * * * * *
56681081 TCTTCGATCTACTTTGCCACCAGTATAGGAAGACAAAATTTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTAC-TT--CACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCC
*
56681146 AATACATGAAGACAAGATCTGTTT
63 AATACATGAAGACAAGATCTGCTT
* * * * *
56681170 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTTGATCTATTTCACGCC
1 TCTTCGATCTACTT---CACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCC
*
56681235 AATACATGAAGACAAGATCTGTTT
63 AATACATGAAGACAAGATCTGCTT
* *
56681259 TCTTGGACCTACTTCACGCCAATACATGAAGACAAGATCTGCT
1 TCTTCGATCTACTTCA--CCAATACATGAAGACAAGATCTGCT
56681302 ATCCTTTCTA
Statistics
Matches: 788, Mismatches: 119, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
86 13 0.02
87 4 0.01
88 279 0.35
89 457 0.58
90 18 0.02
91 9 0.01
92 8 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (86 bp):
TCTTCGATCTACTTCACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAAT
ACATGAAGACAAGATCTGCTT
Found at i:56683573 original size:18 final size:18
Alignment explanation
Indices: 56683547--56683589 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
56683537 GTTTGGTAGG
*
56683547 GAAAAAATCCAAAAGAAT
1 GAAAGAATCCAAAAGAAT
**
56683565 GAAAGAATCGTAAAGAAT
1 GAAAGAATCCAAAAGAAT
*
56683583 AAAAGAA
1 GAAAGAA
56683590 CATTTACTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.07, G:0.16, T:0.12
Consensus pattern (18 bp):
GAAAGAATCCAAAAGAAT
Found at i:56685301 original size:24 final size:24
Alignment explanation
Indices: 56685256--56685302 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56685246 TTGGGATTCC
*
56685256 TGCATCTTCTCCGACATATCCTGT
1 TGCATCTTCTCCAACATATCCTGT
*
56685280 TGCATCTTGTCCAACCAT-TCCTG
1 TGCATCTTCTCCAA-CATATCCTG
56685303 CACTTGTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (24 bp):
TGCATCTTCTCCAACATATCCTGT
Found at i:56690418 original size:5 final size:5
Alignment explanation
Indices: 56690408--56690438 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
56690398 TTACTTTAAA
56690408 TAATT TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT TAATT T
56690439 GAAGAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TAATT
Found at i:56696778 original size:17 final size:17
Alignment explanation
Indices: 56696756--56696793 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
56696746 TAGCAAACAA
56696756 GGTAAACAAGAACTGTT
1 GGTAAACAAGAACTGTT
56696773 GGTAAACAAGAACTGTT
1 GGTAAACAAGAACTGTT
56696790 GGTA
1 GGTA
56696794 GATAAGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (17 bp):
GGTAAACAAGAACTGTT
Found at i:56696821 original size:13 final size:13
Alignment explanation
Indices: 56696803--56696827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56696793 AGATAAGTTG
56696803 AATAAAATATAAT
1 AATAAAATATAAT
56696816 AATAAAATATAA
1 AATAAAATATAA
56696828 GTCTTTAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAATATAAT
Found at i:56702649 original size:42 final size:42
Alignment explanation
Indices: 56702590--56702761 Score: 125
Period size: 42 Copynumber: 4.1 Consensus size: 42
56702580 ACATCATTTT
* *
56702590 CAGAAGCCCA-AA-GGCTGAACAGAAGATCATGAGAGCTAAA
1 CAGAAACCCATAAGGGCTGAACAGAAGATCATAAGAGCTAAA
** * *
56702630 CAGAAACCCATAAGGGCTGAATGGAAGCTCATAAGAGCTGAA
1 CAGAAACCCATAAGGGCTGAACAGAAGATCATAAGAGCTAAA
* * * ** * *
56702672 CGGAAACCCATAAGGGTTAAATGGAAGCTCAAAAGAGCTAAA
1 CAGAAACCCATAAGGGCTGAACAGAAGATCATAAGAGCTAAA
** * * * * * *
56702714 TGGAAACTCATATA-AGTTAAACAGAAGTTCGTAAGAGCTAAA
1 CAGAAACCCATA-AGGGCTGAACAGAAGATCATAAGAGCTAAA
56702756 CAGAAA
1 CAGAAA
56702762 GTAAAACATG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
40 9 0.08
41 2 0.02
42 96 0.89
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (42 bp):
CAGAAACCCATAAGGGCTGAACAGAAGATCATAAGAGCTAAA
Found at i:56702664 original size:21 final size:21
Alignment explanation
Indices: 56702616--56702725 Score: 94
Period size: 21 Copynumber: 5.2 Consensus size: 21
56702606 GAACAGAAGA
* **
56702616 TCATGAGAGCTAAACAGAAAC
1 TCATAAGAGCTAAATGGAAAC
* * * *
56702637 CCATAAGGGCTGAATGGAAGC
1 TCATAAGAGCTAAATGGAAAC
* *
56702658 TCATAAGAGCTGAACGGAAAC
1 TCATAAGAGCTAAATGGAAAC
* * * *
56702679 CCATAAGGGTTAAATGGAAGC
1 TCATAAGAGCTAAATGGAAAC
*
56702700 TCAAAAGAGCTAAATGGAAAC
1 TCATAAGAGCTAAATGGAAAC
56702721 TCATA
1 TCATA
56702726 TAAGTTAAAC
Statistics
Matches: 66, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (21 bp):
TCATAAGAGCTAAATGGAAAC
Found at i:56705921 original size:31 final size:31
Alignment explanation
Indices: 56705886--56705973 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
56705876 ACTCAGGCAT
56705886 CAAATTAAATATTAAAGTCAAACTTAGGTAC
1 CAAATTAAATATTAAAGTCAAACTTAGGTAC
* * * *
56705917 CAAATTGAA-A--AAA---AAACTCAAGTAT
1 CAAATTAAATATTAAAGTCAAACTTAGGTAC
56705942 CAAATTAAATATTAAAGTCAAACTTAGGTAC
1 CAAATTAAATATTAAAGTCAAACTTAGGTAC
56705973 C
1 C
56705974 GAATGATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
25 17 0.40
26 1 0.02
28 6 0.14
30 1 0.02
31 18 0.42
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (31 bp):
CAAATTAAATATTAAAGTCAAACTTAGGTAC
Found at i:56706184 original size:31 final size:31
Alignment explanation
Indices: 56706129--56706194 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
56706119 TTTTGAACTA
* * *
56706129 AATTTGACCTTCAACCTTTTAAAAAGA-TTAG
1 AATTTGACCATCAACATTTCAAAAAGAGTT-G
*
56706160 AATTTGACCATCAATATTTCAAAAAGAGTTG
1 AATTTGACCATCAACATTTCAAAAAGAGTTG
56706191 AATT
1 AATT
56706195 GTTTTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (31 bp):
AATTTGACCATCAACATTTCAAAAAGAGTTG
Found at i:56706813 original size:17 final size:17
Alignment explanation
Indices: 56706791--56706828 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
56706781 TTTAAAAAAT
56706791 ATTTTTAAAAAATTTTA
1 ATTTTTAAAAAATTTTA
**
56706808 ATTTTTTTAAAATTTTA
1 ATTTTTAAAAAATTTTA
56706825 ATTT
1 ATTT
56706829 ATGAAGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAAAAAATTTTA
Found at i:56709795 original size:2 final size:2
Alignment explanation
Indices: 56709788--56709814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56709778 GGGTCTCACA
56709788 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56709815 AGAAATGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56714121 original size:25 final size:28
Alignment explanation
Indices: 56714087--56714140 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
56714077 TCTAATAAAC
*
56714087 TTTTAATAAATAAT-T-A-AAATATTAT
1 TTTTAATAAAAAATCTGATAAATATTAT
*
56714112 TTTTATTAAAAAATCTGATAAATATTAT
1 TTTTAATAAAAAATCTGATAAATATTAT
56714140 T
1 T
56714141 AGCAAGCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 1 0.04
27 1 0.04
28 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTTAATAAAAAATCTGATAAATATTAT
Found at i:56716608 original size:35 final size:35
Alignment explanation
Indices: 56716562--56716629 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
56716552 AGGTGAAAAA
56716562 GAGTTCCAAGCAGAAATGCGAGCAACTGGTAGAAG
1 GAGTTCCAAGCAGAAATGCGAGCAACTGGTAGAAG
* *
56716597 GAGTTCCAAGCAGAAATGCGTGCAATTGGTAGA
1 GAGTTCCAAGCAGAAATGCGAGCAACTGGTAGA
56716630 GCTCACCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (35 bp):
GAGTTCCAAGCAGAAATGCGAGCAACTGGTAGAAG
Found at i:56718576 original size:16 final size:16
Alignment explanation
Indices: 56718555--56718585 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56718545 CCGCTCGGTT
56718555 CCTCCTTCGTCTGTTG
1 CCTCCTTCGTCTGTTG
56718571 CCTCCTTCGTCTGTT
1 CCTCCTTCGTCTGTT
56718586 ATTCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.39, G:0.16, T:0.45
Consensus pattern (16 bp):
CCTCCTTCGTCTGTTG
Found at i:56725666 original size:30 final size:30
Alignment explanation
Indices: 56725632--56725696 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
56725622 GTGGGTGACC
* *
56725632 AAAATG-AAATAGTTTTTAATGACAATGCCT
1 AAAATGAAAAT-GGTTTTAATGACAATACCT
*
56725662 AAAATGAAAATGGTTTTAATGGCAATACCT
1 AAAATGAAAATGGTTTTAATGACAATACCT
56725692 AAAAT
1 AAAAT
56725697 CAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (30 bp):
AAAATGAAAATGGTTTTAATGACAATACCT
Found at i:56727100 original size:3 final size:3
Alignment explanation
Indices: 56727092--56727121 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56727082 ACAAAAACAA
56727092 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56727122 GGATTCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56730022 original size:23 final size:22
Alignment explanation
Indices: 56729990--56730051 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
56729980 CCCGGCCCGT
*
56729990 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
56730014 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
56730036 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
56730052 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:56730046 original size:16 final size:16
Alignment explanation
Indices: 56730025--56730081 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
56730015 TTTTATTAAA
*
56730025 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
56730041 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
56730057 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
56730073 ATTAAAATT
1 ATTAAAATT
56730082 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:56730175 original size:28 final size:27
Alignment explanation
Indices: 56730135--56730191 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
56730125 ATCTATCATT
* * *
56730135 TTGTTAGTAAAATTATTAATTGTATTAA
1 TTGTTACTAAAATTATCAAAT-TATTAA
56730163 TTGTTACTAAAATTATCAAATTATTAA
1 TTGTTACTAAAATTATCAAATTATTAA
56730190 TT
1 TT
56730192 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (27 bp):
TTGTTACTAAAATTATCAAATTATTAA
Found at i:56730211 original size:76 final size:82
Alignment explanation
Indices: 56730131--56730288 Score: 229
Period size: 83 Copynumber: 2.0 Consensus size: 82
56730121 TAAAATCTAT
56730131 CATTTTGTTAGT-AAA-ATT-A-TTAATTGTATTAATTGTTACTAAAATTATCAAATTAT-T-AA
1 CATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATATAAA
56730190 TTATTAATTGTTACTAA
66 TTATTAATTGTTACTAA
*
56730207 CATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATAT
1 CATTTTGTTAGTAAAA-TATTAA-T-TTAATTGTATTAATTGTTACTAAAATTATCAAATTATAT
56730272 CAAATTATTAATTGTTA
63 -AAATTATTAATTGTTA
56730289 ATTGTATTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
76 12 0.17
77 3 0.04
79 3 0.04
80 1 0.01
83 36 0.51
84 1 0.01
86 15 0.21
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (82 bp):
CATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATATAAA
TTATTAATTGTTACTAA
Found at i:56730237 original size:40 final size:40
Alignment explanation
Indices: 56730131--56730240 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
56730121 TAAAATCTAT
56730131 CATTTTGTTAGTAAAATTATTAATTGTATTAATTGTTACTAA
1 CATTTTGTTAGTAAAATTATTAATTG--TTAATTGTTACTAA
* * *
56730173 -A----ATTA-TCAAATTATTAATTATTAATTGTTACTAA
1 CATTTTGTTAGTAAAATTATTAATTGTTAATTGTTACTAA
56730207 CATTTTGTTAGTAAAATTATTAATTGTTAATTGT
1 CATTTTGTTAGTAAAATTATTAATTGTTAATTGT
56730241 ATTAATTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
34 14 0.25
35 1 0.02
36 13 0.23
37 3 0.05
39 3 0.05
40 21 0.38
41 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (40 bp):
CATTTTGTTAGTAAAATTATTAATTGTTAATTGTTACTAA
Found at i:56730366 original size:22 final size:22
Alignment explanation
Indices: 56730335--56730381 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
56730325 TAACTTAAAA
* *
56730335 TAAAACTAAAACTAGTATAT-TT
1 TAAAAATAAAAATA-TATATATT
56730357 TAAAAATAAAAATATATATATT
1 TAAAAATAAAAATATATATATT
56730379 TAA
1 TAA
56730382 TATATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATAAAAATATATATATT
Found at i:56737890 original size:49 final size:48
Alignment explanation
Indices: 56737734--56738599 Score: 300
Period size: 49 Copynumber: 17.6 Consensus size: 48
56737724 GTTTCCAATT
* * * *
56737734 AAAAGATTGAGGCCACAACGGTAAATCTTATTCCCAGGCAGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAG-TG
* * * * * * * * * *
56737783 AACATATTGAAGCTACAATGGCAAATTTTGCTTCCC-CGATATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* * *
56737832 AAAAAATTGAAGCCACAACGGTAAATCTTATTCCCAGGAGGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAGT-G
* * * * * * * * * *
56737881 AATAGATTGAAGCTACGACAGCGAATTTTGATTCCC-TGACATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* * * *
56737930 AAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTACAGCAG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAG-TG
* * * * * * * * * *
56737979 AACAGATTGAAACTACAATGGCGAATCTTGCTTCCC-CGACATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* * * ** *
56738028 AAAAAATTGAGGCCACAACGGCAAATCTTACTTCCCAAGCGGTGCAGCG
1 AAAAGATTGAAGCCACAACGGCAAATCTTA-TTCCCAGGAAGTGCAGTG
* * ** * * * * *
56738077 AAATAGATTGAAGCTATAACGGTGAATCTTGTTTCCC-CGACATTGCAATT
1 AAA-AGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* ** *
56738127 AAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGGCGGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAG-TG
* * * ** * * * * *
56738176 AATAGATTGAAACTACAACGGTGAATCTTGCTTCCC-TGACATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* * * * *
56738225 AAAAGATTGAGGCCACAACGGCAAATCTTACTTCGCAAGCAGTGCAGCGG
1 AAAAGATTGAAGCCACAACGGCAAATCTTA-TTCCCAGGAAGTGCAG-TG
* * ** * * * * *
56738275 AACAGATTGAAGCTACAACGGTGAATCTTGTTTCCC-CGACATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT-ATTCCCAGGA-AGTGCAGTG
* * *
56738324 AAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGG-CGATGCAGCGG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAG-TGCAG-TG
* * * * * * * *
56738373 AACAGATTGAAGCTACAACGATG-AATTTCATT-TTCCC-CGACATTACAATT
1 AAAAGATTGAAGCCACAACG--GCAA-ATC-TTATTCCCAGGA-AGTGCAGTG
* * * *
56738423 AAAAGATTGATGCCACAACGGCGAATCTTATTTCCAGGCAGTGCAGTAG
1 AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAGT-G
* * * * * * * * *
56738472 AACATATTGAAGCTACGACGGCAAATCTTGCTTTCTC--GACATTGCAATT
1 AAAAGATTGAAGCCACAACGGCAAATCTT--ATTCCCAGGA-AGTGCAGTG
* * * *
56738521 AAAATATT-AAGGCCACAACGGCAAATCTTACTTCTCAGGCAGTGCAGCG
1 AAAAGATTGAA-GCCACAACGGCAAATCTTA-TTCCCAGGAAGTGCAGTG
* * *
56738570 AAATAGATTGAAGCTACAATGACAAATCTT
1 AAA-AGATTGAAGCCACAACGGCAAATCTT
56738600 GTTTTCTCCG
Statistics
Matches: 560, Mismatches: 211, Indels: 91
0.65 0.24 0.11
Matches are distributed among these distances:
47 2 0.00
48 57 0.10
49 331 0.59
50 152 0.27
51 16 0.03
52 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (48 bp):
AAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGAAGTGCAGTG
Found at i:56738127 original size:99 final size:98
Alignment explanation
Indices: 56737729--56738699 Score: 1140
Period size: 98 Copynumber: 9.8 Consensus size: 98
56737719 CCATAGTTTC
* * *
56737729 CAATTAAAAGATTGAGGCCACAACGGTAAATCTTATTCCCAGGCAGTGCAGCGGAACATATTGAA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAATAGATTGAA
* * * * *
56737794 GCTACAATGGCAAATTTTGCTTCCCCGATATTG
66 GCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * * *
56737827 CAATTAAAAAATTGAAGCCACAACGGTAAATCTTATTCCCAGG-AGGTGCAGTGGAATAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCA-GTGCAGCGGAATAGATTGA
* * * * *
56737891 AGCTACGACAGCGAATTTTGATTCCCTGACATTG
65 AGCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * *
56737925 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTACAGCAGAACAGATTGAA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAATAGATTGAA
* * *
56737990 ACTACAATGGCGAATCTTGCTTCCCCGACATTG
66 GCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * * *
56738023 CAATTAAAAAATTGAGGCCACAACGGCAAATCTTACTTCCCAAGCGGTGCAGCGAAATAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTCCCAGGCAGTGCAGCGGAATAGATTGA
* *
56738088 AGCTATAACGGTGAATCTTGTTTCCCCGACATTG
65 AGCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * *
56738122 CAATTAAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGGCGGTGCAGCGGAATAGATTGAA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAATAGATTGAA
* * * *
56738187 ACTACAACGGTGAATCTTGCTTCCCTGACATTG
66 GCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * *
56738220 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTACTTCGCAAGCAGTGCAGCGGAACAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTCCCAGGCAGTGCAGCGGAATAGATTGA
*
56738285 AGCTACAACGGTGAATCTTGTTTCCCCGACATTG
65 AGCTACAACGGCGAATCTTGTTTCCCCGACATTG
* * *
56738319 CAATTAAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGGC-GATGCAGCGGAACAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAG-TGCAGCGGAATAGATTGA
** * *
56738383 AGCTACAACGATGAAT-TTCATTTTCCCCGACATTA
65 AGCTACAACGGCGAATCTT--GTTTCCCCGACATTG
* * * ** * *
56738418 CAATTAAAAGATTGATGCCACAACGGCGAATCTTATTTCCAGGCAGTGCAGTAGAACATATTGAA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAATAGATTGAA
* * *
56738483 GCTACGACGGCAAATCTTGCTTT-CTCGACATTG
66 GCTACAACGGCGAATCTTG-TTTCCCCGACATTG
* * * *
56738516 CAATTAAAATATTAAGGCCACAACGGCAAATCTTACTTCTCAGGCAGTGCAGCGAAATAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTCCCAGGCAGTGCAGCGGAATAGATTGA
* * * *
56738581 AGCTACAATGACAAATCTTGTTTTCTCCGACATTG
65 AGCTACAACGGCGAATCTTG-TTTCCCCGACATTG
* * * * ** * * * *
56738616 CAATTTAAAGATTGAAGTCACAATGGTGAATCTTATTTCCTAGGCGGTGCAGTGGGATAGATTGA
1 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTA-TTCCCAGGCAGTGCAGCGGAATAGATTGA
*
56738681 AGCTACAACGACGAATCTT
65 AGCTACAACGGCGAATCTT
56738700 AATGCCCTGA
Statistics
Matches: 750, Mismatches: 111, Indels: 22
0.85 0.13 0.02
Matches are distributed among these distances:
97 4 0.01
98 369 0.49
99 299 0.40
100 78 0.10
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (98 bp):
CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAATAGATTGAA
GCTACAACGGCGAATCTTGTTTCCCCGACATTG
Found at i:56738185 original size:197 final size:196
Alignment explanation
Indices: 56737729--56738699 Score: 1169
Period size: 197 Copynumber: 4.9 Consensus size: 196
56737719 CCATAGTTTC
* * *
56737729 CAATTAAAAGATTGAGGCCACAACGGTAAATCTTATTCCCAGGCAGTGCAGCGGAACATATTGAA
1 CAATTAAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAACAGATTGAA
* * * * *
56737794 GCTACAATGGCAAATTTTGCTTCCCCGATATTGCAATTAAAAAATTGAAGCCACAACGGTAAATC
66 GCTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAAATC
* * * * * * *
56737859 TTATTCCCAGGAGGTGCAGTGGAATAGATTGAAGCTACGACAGCGAATTTTGATTCCCTGACATT
131 TTATTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACATT
56737924 G
196 G
* * *
56737925 CAATTAAAAGATTGAGGCCACAACGGCAAATCTTATTCCCAGGCAGTACAGCAGAACAGATTGAA
1 CAATTAAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAACAGATTGAA
* * *
56737990 ACTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAATTGAGGCCACAACGGCAAATC
66 GCTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAAATC
* * * *
56738055 TTACTTCCCAAGCGGTGCAGCGAAATAGATTGAAGCTATAACGGTGAATCTTGTTTCCCCGACAT
131 TTA-TTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAT
56738120 TG
195 TG
* * *
56738122 CAATTAAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGGCGGTGCAGCGGAATAGATTGAA
1 CAATTAAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAACAGATTGAA
* * * * *
56738187 ACTACAACGGTGAATCTTGCTTCCCTGACATTGCAATTAAAAGATTGAGGCCACAACGGCAAATC
66 GCTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAAATC
* * * * *
56738252 TTACTTCGCAAGCAGTGCAGCGGAACAGATTGAAGCTACAACGGTGAATCTTGTTTCCCCGACAT
131 TTA-TTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACAT
56738317 TG
195 TG
*
56738319 CAATTAAAAGATTGAAGCCACAACAGCAAATCTTATTCCCAGGC-GATGCAGCGGAACAGATTGA
1 CAATTAAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGCAG-TGCAGCGGAACAGATTGA
* ** * * *
56738383 AGCTACAACGATGAAT-TT-CATTTTCCCCGACATTACAATTAAAAGATTGATGCCACAACGGCG
65 AGCTACAATGGCGAATCTTGC---TTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCA
* * ** * * * * *
56738446 AATCTTATTTCCAGGCAGTGCAGTAGAACATATTGAAGCTACGACGGCAAATCTTGCTTT-CTCG
127 AATCTTATTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTTG-TTTCCCCG
56738510 ACATTG
191 ACATTG
* * * *
56738516 CAATTAAAATATT-AAGGCCACAACGGCAAATCTTACTTCTCAGGCAGTGCAGCGAAATAGATTG
1 CAATTAAAAGATTGAA-GCCACAACGGCAAATCTTA-TTCCCAGGCAGTGCAGCGGAACAGATTG
* * * * * * * **
56738580 AAGCTACAATGACAAATCTTGTTTTCTCCGACATTGCAATTTAAAGATTGAAGTCACAATGGTGA
64 AAGCTACAATGGCGAATCTTG-CTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAA
* * * *
56738645 ATCTTATTTCCTAGGCGGTGCAGTGGGATAGATTGAAGCTACAACGACGAATCTT
128 ATCTTA-TTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTT
56738700 AATGCCCTGA
Statistics
Matches: 683, Mismatches: 79, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
195 1 0.00
196 128 0.19
197 388 0.57
198 125 0.18
199 41 0.06
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (196 bp):
CAATTAAAAGATTGAAGCCACAACGGCAAATCTTATTCCCAGGCAGTGCAGCGGAACAGATTGAA
GCTACAATGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCAAATC
TTATTCCCAGGCGGTGCAGCGGAATAGATTGAAGCTACAACGGCGAATCTTGTTTCCCCGACATT
G
Found at i:56738937 original size:88 final size:83
Alignment explanation
Indices: 56738787--56738979 Score: 217
Period size: 88 Copynumber: 2.3 Consensus size: 83
56738777 CCACAGATCT
* * *
56738787 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGAACCCAGTCTTATCTCCCTGAAGTTACAGTGGAG
*
56738852 CAGACAGAAGAATCCAATCC
66 AAGACAGAAG-AT-CAATCC
* * * *
56738872 TATCTCTCTGAAGTTGCGGTGGAGCGGATTGAAACCACAGATCTTATCTCCCTGAAGTTACAGTG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCG-AACC-CAG-TCTTATCTCCCTGAAGTTACAGTG
** *
56738937 GAGAAGATTGAAGATGAATCC
63 GAGAAGACAGAAGATCAATCC
*
56738958 TATAC-CTCTGAAGTTGTAGTAG
1 TAT-CTCTCTGAAGTTGCAGTAG
56738980 GTCAGATTAA
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
85 27 0.30
86 24 0.27
87 6 0.07
88 33 0.37
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (83 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATCGAACCCAGTCTTATCTCCCTGAAGTTACAGTGGAG
AAGACAGAAGATCAATCC
Found at i:56738946 original size:44 final size:43
Alignment explanation
Indices: 56738750--56738948 Score: 188
Period size: 44 Copynumber: 4.6 Consensus size: 43
56738740 TCCTATATCT
* * * *
56738750 CTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTGAAACC-CAGATCTTATCTCC
* * * *
56738794 CTGAAGTTGCAGTAGAGCAGATCG-CATCCAG-TCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAACCCAGATCTTATCTCC
** * * *
56738835 CTGAAGTTGCAGTGGAGCAGACAGAAGAATCCA-ATCCTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTG-A-AACCCAGATCTTATCTCC
* *
56738879 CTGAAGTTGCGGTGGAGCGGATTGAAACCACAGATCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTGAAACC-CAGATCTTATCTCC
* *
56738923 CTGAAGTTACAGTGGAGAAGATTGAA
1 CTGAAGTTGCAGTGGAGCAGATTGAA
56738949 GATGAATCCT
Statistics
Matches: 124, Mismatches: 25, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
41 30 0.24
42 6 0.05
43 5 0.04
44 83 0.67
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (43 bp):
CTGAAGTTGCAGTGGAGCAGATTGAAACCCAGATCTTATCTCC
Found at i:56739362 original size:4 final size:4
Alignment explanation
Indices: 56739353--56739378 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
56739343 AAAATAAACA
56739353 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
56739379 CCTAACCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:56740549 original size:3 final size:3
Alignment explanation
Indices: 56740535--56740570 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
56740525 TGTTATTTCT
56740535 TTA TTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56740571 TACCCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56740756 original size:3 final size:3
Alignment explanation
Indices: 56740748--56740788 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
56740738 TCTATTTGTC
56740748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56740789 TGTTTGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:56742524 original size:26 final size:26
Alignment explanation
Indices: 56742493--56742546 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
56742483 ATAATAATAA
*
56742493 TTAAATCTTAGTTTTTATCTTTAAAT
1 TTAAATCTTAATTTTTATCTTTAAAT
56742519 TTAAATCTTAATTTTTATCTTTAAAT
1 TTAAATCTTAATTTTTATCTTTAAAT
56742545 TT
1 TT
56742547 TTAACATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (26 bp):
TTAAATCTTAATTTTTATCTTTAAAT
Found at i:56742545 original size:14 final size:14
Alignment explanation
Indices: 56742504--56742549 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
56742494 TAAATCTTAG
56742504 TTTTTATCTTTAAA
1 TTTTTATCTTTAAA
**
56742518 TTTAAATC-TT-AA
1 TTTTTATCTTTAAA
56742530 TTTTTATCTTTAAA
1 TTTTTATCTTTAAA
56742544 TTTTTA
1 TTTTTA
56742550 ACATAATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTATCTTTAAA
Found at i:56746104 original size:26 final size:25
Alignment explanation
Indices: 56746034--56746122 Score: 105
Period size: 26 Copynumber: 3.7 Consensus size: 25
56746024 TTATTATATA
*
56746034 TAATTATATATA-AAAATATAAA-T
1 TAATCATATATATAAAATATAAAGT
* *
56746057 TAA-CCTCT-TATAAAATATAAAGT
1 TAATCATATATATAAAATATAAAGT
*
56746080 TAATTATATATATAAATATATAAAGT
1 TAATCATATATATAAA-ATATAAAGT
56746106 TAATCATATATATAAAA
1 TAATCATATATATAAAA
56746123 AACAAATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.04
22 12 0.22
23 7 0.13
24 2 0.04
25 7 0.13
26 24 0.44
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TAATCATATATATAAAATATAAAGT
Found at i:56755782 original size:10 final size:10
Alignment explanation
Indices: 56755767--56755791 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56755757 CTTAACTACC
56755767 ACTAAGAACA
1 ACTAAGAACA
56755777 ACTAAGAACA
1 ACTAAGAACA
56755787 ACTAA
1 ACTAA
56755792 AATAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.08, T:0.12
Consensus pattern (10 bp):
ACTAAGAACA
Found at i:56758920 original size:25 final size:25
Alignment explanation
Indices: 56758892--56758940 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
56758882 TCACGTCACT
56758892 AACACATAATTTTGATAATTTTTTA
1 AACACATAATTTTGATAATTTTTTA
56758917 AACACATAATTTTGATAATTTTTT
1 AACACATAATTTTGATAATTTTTT
56758941 TACTCTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (25 bp):
AACACATAATTTTGATAATTTTTTA
Found at i:56759350 original size:5 final size:5
Alignment explanation
Indices: 56759340--56759365 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56759330 TTATTTTAAA
56759340 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
56759366 GAAGAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:56759559 original size:12 final size:12
Alignment explanation
Indices: 56759542--56759566 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56759532 GGTGTTCATT
56759542 CGGTTAACCGAC
1 CGGTTAACCGAC
56759554 CGGTTAACCGAC
1 CGGTTAACCGAC
56759566 C
1 C
56759567 CGAAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:56759740 original size:9 final size:9
Alignment explanation
Indices: 56759726--56759793 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
56759716 TTTGGTTAAA
56759726 AATTACCCG
1 AATTACCCG
56759735 AATTACCCG
1 AATTACCCG
*
56759744 AATTAACCG
1 AATTACCCG
*
56759753 AATTAACCG
1 AATTACCCG
*
56759762 AATTACCGCA
1 AATTACC-CG
*
56759772 AAATACCCG
1 AATTACCCG
56759781 AATTACCCG
1 AATTACCCG
56759790 AATT
1 AATT
56759794 TTTTTATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
9 45 0.87
10 7 0.13
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:56760046 original size:23 final size:20
Alignment explanation
Indices: 56760005--56760048 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
56759995 AGTAATACAC
*
56760005 ATTTTTTTTTTAAATTTTTA
1 ATTTTTTTTTTAAAATTTTA
56760025 ATTTTTTTCTCTTAAAAATTTTA
1 ATTTTTTT-T-TT-AAAATTTTA
56760048 A
1 A
56760049 ATTCAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 2 0.10
23 9 0.45
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTTTTTAAAATTTTA
Found at i:56764860 original size:31 final size:30
Alignment explanation
Indices: 56764804--56764874 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
56764794 TTTAAATAGT
*
56764804 AAATG-TAAAATTGTATTTTAGTCTTTTTAA
1 AAATGATAAAATTGTATTTTAATC-TTTTAA
*
56764834 AAATGATAAAATTTTGA-TTTAATCTTTTAA
1 AAATGATAAAATTGT-ATTTTAATCTTTTAA
*
56764864 AAATTATAAAA
1 AAATGATAAAA
56764875 ATATAAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 21 0.58
31 14 0.39
32 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (30 bp):
AAATGATAAAATTGTATTTTAATCTTTTAA
Found at i:56774990 original size:75 final size:75
Alignment explanation
Indices: 56774867--56775016 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
56774857 TTGAGGACGA
56774867 AAAGTCCTAAGGGGGAGAGTTATAACGGCCCATTTACAGTGAAATCGAAACAGTGGTTTTAGGAC
1 AAAGTCCTAAGGGGGAGAGTTATAACGGCCCATTTACAGTGAAATCGAAACAGTGGTTTTAGGAC
56774932 CACAAATTTG
66 CACAAATTTG
* *
56774942 AAAGTCCTAAGGGGGAGAGTTGTAACGGCCTATTTACAGTGAAATCGAAACAGTGGTTTTAGGAC
1 AAAGTCCTAAGGGGGAGAGTTATAACGGCCCATTTACAGTGAAATCGAAACAGTGGTTTTAGGAC
56775007 CACAAATTTG
66 CACAAATTTG
56775017 GAGTCAAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (75 bp):
AAAGTCCTAAGGGGGAGAGTTATAACGGCCCATTTACAGTGAAATCGAAACAGTGGTTTTAGGAC
CACAAATTTG
Found at i:56776220 original size:33 final size:33
Alignment explanation
Indices: 56776180--56776298 Score: 89
Period size: 33 Copynumber: 3.6 Consensus size: 33
56776170 CATTATTATG
56776180 TAAGACCATAGTTGGGCTATGGCATTCTCATGA
1 TAAGACCATAGTTGGGCTATGGCATTCTCATGA
** * * **
56776213 TAAGACCATAACTGGGTTATGGCACTACGAATG-
1 TAAGACCATAGTTGGGCTATGGCA-TTCTCATGA
* * * * *
56776246 TAAGACCATGGTAGGGCCATGGCATTTTGCGT-A
1 TAAGACCATAGTTGGGCTATGGCATTCT-CATGA
* *
56776279 AAAGACCATAGTTGGACTAT
1 TAAGACCATAGTTGGGCTAT
56776299 AGCACAAGGA
Statistics
Matches: 61, Mismatches: 22, Indels: 6
0.69 0.25 0.07
Matches are distributed among these distances:
32 1 0.02
33 55 0.90
34 5 0.08
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCTATGGCATTCTCATGA
Found at i:56778847 original size:26 final size:27
Alignment explanation
Indices: 56778816--56778869 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
56778806 TCGAATCAAT
56778816 ACCCCCCTCAAATAAAGCTTCTAACAA
1 ACCCCCCTCAAATAAAGCTTCTAACAA
56778843 ACCCCCCTCAAATAAAGCTTCTAACAA
1 ACCCCCCTCAAATAAAGCTTCTAACAA
56778870 TGTTCTCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.37, G:0.04, T:0.19
Consensus pattern (27 bp):
ACCCCCCTCAAATAAAGCTTCTAACAA
Found at i:56781778 original size:31 final size:31
Alignment explanation
Indices: 56781740--56781800 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
56781730 TTTTTAAACT
* *
56781740 AAATTTGACCTTCAACCTTTTAAAAAGAGTA
1 AAATTTGACCATCAACCTTTCAAAAAGAGTA
*
56781771 AAATTTGACCATCAATCTTTCAAAAAGAGT
1 AAATTTGACCATCAACCTTTCAAAAAGAGT
56781801 TGAATTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
AAATTTGACCATCAACCTTTCAAAAAGAGTA
Found at i:56783641 original size:21 final size:21
Alignment explanation
Indices: 56783615--56783656 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
56783605 ACGCGCTGTC
56783615 AGGGTTTTGGG-TTTTGGGTTT
1 AGGG-TTTGGGTTTTTGGGTTT
56783636 AGGGTTTGGGTTTTTGGGTTT
1 AGGGTTTGGGTTTTTGGGTTT
56783657 TTAGGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.05, C:0.00, G:0.43, T:0.52
Consensus pattern (21 bp):
AGGGTTTGGGTTTTTGGGTTT
Found at i:56783645 original size:13 final size:14
Alignment explanation
Indices: 56783616--56783671 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
56783606 CGCGCTGTCA
*
56783616 GGGTTTTGGGTTTT
1 GGGTTTAGGGTTTT
56783630 GGGTTTAGGG-TTT
1 GGGTTTAGGGTTTT
*
56783643 GGGTTTTTGGGTTTTT
1 GGG-TTTAGGG-TTTT
*
56783659 AGGTTTA-GGTTTT
1 GGGTTTAGGGTTTT
56783672 TAAAGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 10 0.29
14 17 0.49
15 3 0.09
16 5 0.14
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.55
Consensus pattern (14 bp):
GGGTTTAGGGTTTT
Found at i:56783658 original size:8 final size:7
Alignment explanation
Indices: 56783616--56783657 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
56783606 CGCGCTGTCA
56783616 GGGTTTT
1 GGGTTTT
56783623 GGGTTTT
1 GGGTTTT
*
56783630 GGGTTTA
1 GGGTTTT
56783637 GGG-TTT
1 GGGTTTT
56783643 GGGTTTTT
1 GGG-TTTT
56783651 GGGTTTT
1 GGGTTTT
56783658 TAGGTTTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.02, C:0.00, G:0.43, T:0.55
Consensus pattern (7 bp):
GGGTTTT
Found at i:56783804 original size:95 final size:95
Alignment explanation
Indices: 56783698--56784002 Score: 461
Period size: 96 Copynumber: 3.2 Consensus size: 95
56783688 TAAATAAGGG
* *
56783698 ATTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTTCAAAATTAGATTAGGGTTTAGT
1 ATTAGGGTTTAGGGTTTCTTAAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
56783763 GTTTAAGGTTTTTAAGGAAAAATCAAATAA
66 GTTTAAGGTTTTTAAGGAAAAATCAAATAA
* * * * * *
56783793 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAAAATTTTAAAAATCAGATTAAGGTTTAG
1 ATTAGGGTTTAGGGTTTCTTAAGTAAATTAATT-ATAAATTTTTAAAAATTAGATTAGGGTTTAG
56783858 TG-TTAAGGGTTTTTAAGGAAAAATCAAATAA
65 TGTTTAA-GGTTTTTAAGGAAAAATCAAATAA
*
56783889 ATTAGGGTTTAGGGTTAT-TTAAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTT-TCTTAAGTAAATTAATTATAAATTTT-TAAAAATTAGATTAGGGTTTA
56783953 GTGTTTAAGGTTTTTAAGGAAAAACTCAAATAA
64 GTGTTTAAGGTTTTTAAGGAAAAA-TCAAATAA
*
56783986 ATTAGGGTTTGGGGTTT
1 ATTAGGGTTTAGGGTTT
56784003 AAGATTACTT
Statistics
Matches: 188, Mismatches: 16, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
95 41 0.22
96 120 0.64
97 27 0.14
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTTCTTAAGTAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGT
GTTTAAGGTTTTTAAGGAAAAATCAAATAA
Found at i:56784264 original size:126 final size:126
Alignment explanation
Indices: 56784036--56784329 Score: 489
Period size: 126 Copynumber: 2.3 Consensus size: 126
56784026 GTTAATTTAG
*
56784036 AAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAAATTCGAGGAGACGT
1 AAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAAATTCGAGGAGACGT
*
56784101 TTTTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTATTGAA
66 TTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTATTGAA
* * *
56784162 AAAAGCTCCCACGTGGACGCGCTTTTACTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGT
1 AAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAAATTCGAGGAGACGT
* * *
56784227 TTCTGAGTAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTATTGAA
66 TTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTATTGAA
* * *
56784288 AGAAGCTCCCCCGTGGACGAGCTTTTGCTACAGTAGCTCCTG
1 AAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
56784330 TTTGGCCTGA
Statistics
Matches: 156, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 156 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (126 bp):
AAAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAAATTCGAGGAGACGT
TTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTATTGAA
Found at i:56785858 original size:34 final size:34
Alignment explanation
Indices: 56785819--56785915 Score: 185
Period size: 34 Copynumber: 2.9 Consensus size: 34
56785809 TGTAAAAGTA
*
56785819 AATTTCTATTTTATTACATGAAATAATATAGAAG
1 AATTTCTATTTTATTACATTAAATAATATAGAAG
56785853 AATTTCTATTTTATTACATTAAATAATATAGAAG
1 AATTTCTATTTTATTACATTAAATAATATAGAAG
56785887 AATTTCTATTTTATTACATTAAATAATAT
1 AATTTCTATTTTATTACATTAAATAATAT
56785916 CAAAATATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (34 bp):
AATTTCTATTTTATTACATTAAATAATATAGAAG
Found at i:56789009 original size:13 final size:11
Alignment explanation
Indices: 56788970--56789012 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
56788960 TCTTTCAATA
*
56788970 TTCTCCCAAAT
1 TTCTCTCAAAT
56788981 TTCTCTCAAAT
1 TTCTCTCAAAT
56788992 TTCTCTCAAAT
1 TTCTCTCAAAT
*
56789003 TCCTCTCAAA
1 TTCTCTCAAA
56789013 GCTCTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:56789036 original size:23 final size:24
Alignment explanation
Indices: 56789010--56789054 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56789000 AATTCCTCTC
56789010 AAAGCTCT-ATTTAATTTTTTTAA
1 AAAGCTCTAATTTAATTTTTTTAA
*
56789033 AAAGCTCTAATTTTATTTTTTT
1 AAAGCTCTAATTTAATTTTTTT
56789055 GGATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (24 bp):
AAAGCTCTAATTTAATTTTTTTAA
Found at i:56790181 original size:20 final size:20
Alignment explanation
Indices: 56790156--56790193 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
56790146 AATGAGATAA
56790156 TCAATTCGTATTTAGTATAG
1 TCAATTCGTATTTAGTATAG
56790176 TCAATTCGTATTTAGTAT
1 TCAATTCGTATTTAGTAT
56790194 TTAGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (20 bp):
TCAATTCGTATTTAGTATAG
Found at i:56790195 original size:7 final size:7
Alignment explanation
Indices: 56790183--56790208 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
56790173 TAGTCAATTC
56790183 GTATTTA
1 GTATTTA
56790190 GTATTTA
1 GTATTTA
56790197 GTATTTA
1 GTATTTA
56790204 GTATT
1 GTATT
56790209 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:56791840 original size:33 final size:33
Alignment explanation
Indices: 56791794--56791993 Score: 123
Period size: 33 Copynumber: 5.5 Consensus size: 33
56791784 ATGTGAAAGG
*
56791794 GGTTGCTATGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
56791827 GGTTGCTAAGTGCTGA-TCCCACCATATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCC-CGA-ATC----AT-TG---GT
* *
56791869 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
56791902 GGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A---AT-CAT-TG---GT
* *
56791945 GGTTACTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
56791978 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
56791994 ATCCATCGAT
Statistics
Matches: 130, Mismatches: 16, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
32 4 0.03
33 53 0.41
34 6 0.05
35 1 0.01
36 4 0.03
37 3 0.02
38 5 0.04
39 4 0.03
40 2 0.02
41 3 0.02
42 21 0.16
43 24 0.18
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:56791967 original size:76 final size:75
Alignment explanation
Indices: 56791715--56791993 Score: 441
Period size: 75 Copynumber: 3.7 Consensus size: 75
56791705 TGATTCCCCC
* * *
56791715 AAGGGGTTGCTAAGTGCTGATTCCTCGAACCATTGGTGGTTGTTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
56791780 TTAAATGTGA
66 TTAAATGTGA
* *
56791790 AAGGGGTTGCTATGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
56791855 TTAAATGTGA
66 TTAAATGTGA
* * *
56791865 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTA-T
* *
56791930 TTTGAATGTGA
65 CTTAAATGTGA
* *
56791941 AAGGGGTTACTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGA
56791994 ATCCATCGAT
Statistics
Matches: 187, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
75 128 0.68
76 59 0.32
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
TTAAATGTGA
Found at i:56797188 original size:17 final size:17
Alignment explanation
Indices: 56797166--56797231 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 17
56797156 TCCTTAAAAC
56797166 AAATAAATAATAGTTTA
1 AAATAAATAATAGTTTA
*
56797183 AAATAAATAATA-TAATAAA
1 AAATAAATAATAGT--T-TA
*
56797202 AACATATATAATAGTTTA
1 AA-ATAAATAATAGTTTA
56797220 AAATAAATAATA
1 AAATAAATAATA
56797232 TAATAAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 21 0.52
18 4 0.10
19 4 0.10
20 9 0.22
21 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATAAATAATAGTTTA
Found at i:56797238 original size:17 final size:17
Alignment explanation
Indices: 56797166--56797239 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
56797156 TCCTTAAAAC
*
56797166 AAATAAATAATAGT-TTA
1 AAATAAATAATA-TAATA
56797183 AAATAAATAATATAATA
1 AAATAAATAATATAATA
* *
56797200 AAA-ACATATATAATAGTTTA
1 AAATAAATA-AT-ATA--ATA
56797220 AAATAAATAATATAATA
1 AAATAAATAATATAATA
56797237 AAA
1 AAA
56797240 ACTTTTAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 5 0.11
17 24 0.52
18 3 0.07
19 3 0.07
20 7 0.15
21 4 0.09
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (17 bp):
AAATAAATAATATAATA
Found at i:56797319 original size:49 final size:52
Alignment explanation
Indices: 56797214--56797319 Score: 137
Period size: 50 Copynumber: 2.1 Consensus size: 52
56797204 CATATATAAT
* * *
56797214 AGTTTAAAATAAATAATATAATAAAAACTTTTAAACAAATATTAAGTAAAAC
1 AGTTTAAAATAAATAATATAATAAAAACCTTAAAACAAATAATAAGTAAAAC
* * *
56797266 AGTTTAGAATAAATGATA-AAT-AAAACCTTAAAACAAATAAT-AGTAAAAG
1 AGTTTAAAATAAATAATATAATAAAAACCTTAAAACAAATAATAAGTAAAAC
56797315 AGTTT
1 AGTTT
56797320 TTTTTTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 12 0.25
50 17 0.35
51 3 0.06
52 16 0.33
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.29
Consensus pattern (52 bp):
AGTTTAAAATAAATAATATAATAAAAACCTTAAAACAAATAATAAGTAAAAC
Found at i:56799162 original size:126 final size:125
Alignment explanation
Indices: 56798936--56799226 Score: 456
Period size: 126 Copynumber: 2.3 Consensus size: 125
56798926 TCAGGCCAAA
* * *
56798936 TAGAAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGCCATTGC
1 TAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGC
* *
56799001 ATCCTGCTTGAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
66 ATCCTACTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
* * *
56799061 TCAGAAATTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGACAATG
1 T-AGAAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATG
* * *
56799126 CATCCTACTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTTAAAATTATTTTT
65 CATCCTACTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
* *
56799187 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTT
1 TAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
56799227 TTTTAAATTA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 36 0.24
126 114 0.76
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (125 bp):
TAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGC
ATCCTACTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
Found at i:56799394 original size:96 final size:96
Alignment explanation
Indices: 56799273--56799501 Score: 363
Period size: 96 Copynumber: 2.4 Consensus size: 96
56799263 AACTCCAAAT
*
56799273 CCTAATTTATTTGATTTTTCCTTAAAAACTCTAAACACTAAACCCTAATCTAATTT-TTTAAAAT
1 CCTAATTTATTTGATTTTTTCTTAAAAACTCTAAACACTAAACCCTAATCTAATTTCTTTAAAA-
56799337 TTTATAATTAATTTACTCAAGTAACCCTAAAC
65 TTTATAATTAATTTACTCAAGTAACCCTAAAC
* * * * *
56799369 CCTAATTTATATAATTTTTTCTTAAAAACCCTAAACACTAAACCCTAATTTGATTTCTTTAAAAT
1 CCTAATTTATTTGATTTTTTCTTAAAAACTCTAAACACTAAACCCTAATCTAATTTCTTTAAAAT
56799434 TTATAATTAATTTACTCAAGTAACCCTAAAC
66 TTATAATTAATTTACTCAAGTAACCCTAAAC
56799465 CCTAATTTATTTGATTTTTTCCTTAAAAA-TCATAAAC
1 CCTAATTTATTTGATTTTTT-CTTAAAAACTC-TAAAC
56799502 TAATTTTCTA
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
96 101 0.83
97 20 0.17
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.41
Consensus pattern (96 bp):
CCTAATTTATTTGATTTTTTCTTAAAAACTCTAAACACTAAACCCTAATCTAATTTCTTTAAAAT
TTATAATTAATTTACTCAAGTAACCCTAAAC
Found at i:56799593 original size:16 final size:17
Alignment explanation
Indices: 56799567--56799613 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
56799557 TTAATTTTTT
* *
56799567 TCCTTAAAACCTTAAAA
1 TCCTAAAAACCCTAAAA
56799584 T-CTAAAAACCCTAAAA
1 TCCTAAAAACCCTAAAA
56799600 TCCT-AAAACCCTAA
1 TCCTAAAAACCCTAA
56799614 CCCTAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 24 0.89
17 3 0.11
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (17 bp):
TCCTAAAAACCCTAAAA
Found at i:56805908 original size:46 final size:46
Alignment explanation
Indices: 56805855--56805943 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
56805845 GGTTGTTTTT
*
56805855 TTTAATGGCGCCTATCTGAGAGGCG-CTAATAAATATTATATATATA
1 TTTAATGGCGCCTATCTGACAGGCGTC-AATAAATATTATATATATA
* * *
56805901 TTTAATGGTGCCTATCTGACAGGCGTCAATCAATATTTTATAT
1 TTTAATGGCGCCTATCTGACAGGCGTCAATAAATATTATATAT
56805944 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 37 0.97
47 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (46 bp):
TTTAATGGCGCCTATCTGACAGGCGTCAATAAATATTATATATATA
Found at i:56813747 original size:22 final size:22
Alignment explanation
Indices: 56813722--56813769 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
56813712 TTAATTAAAT
56813722 AAATGTTAATCTTTA-AATTTTA
1 AAAT-TTAATCTTTATAATTTTA
* * *
56813744 AAATTTATTTTTTATTATTTTA
1 AAATTTAATCTTTATAATTTTA
56813766 AAAT
1 AAAT
56813770 AAAATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
AAATTTAATCTTTATAATTTTA
Found at i:56813810 original size:24 final size:24
Alignment explanation
Indices: 56813763--56813810 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56813753 TTTTATTATT
* * **
56813763 TTAAAATAAAATTAATAGTTATAA
1 TTAAAATAAAATAAAAAGGGATAA
56813787 TTAAAATAAAATAAAAAGGGATAA
1 TTAAAATAAAATAAAAAGGGATAA
56813811 ATTAGTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (24 bp):
TTAAAATAAAATAAAAAGGGATAA
Found at i:56814361 original size:16 final size:16
Alignment explanation
Indices: 56814340--56814370 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56814330 CCGCTCGGTT
56814340 CCTCCTTCGTCTGTTG
1 CCTCCTTCGTCTGTTG
56814356 CCTCCTTCGTCTGTT
1 CCTCCTTCGTCTGTT
56814371 ATTCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.39, G:0.16, T:0.45
Consensus pattern (16 bp):
CCTCCTTCGTCTGTTG
Found at i:56817289 original size:13 final size:13
Alignment explanation
Indices: 56817271--56817297 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56817261 CAGCCAGCGG
56817271 TGGTAACTGCTAA
1 TGGTAACTGCTAA
56817284 TGGTAACTGCTAA
1 TGGTAACTGCTAA
56817297 T
1 T
56817298 CATACTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TGGTAACTGCTAA
Found at i:56819392 original size:20 final size:21
Alignment explanation
Indices: 56819367--56819412 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
56819357 ATCTTGAAAT
56819367 TTATAATTTAC-TTTCTAAAA
1 TTATAATTTACTTTTCTAAAA
* *
56819387 TTATAATTTTCTTTTTTAAAA
1 TTATAATTTACTTTTCTAAAA
56819408 TTATA
1 TTATA
56819413 GGCATATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATAATTTACTTTTCTAAAA
Found at i:56822615 original size:17 final size:16
Alignment explanation
Indices: 56822580--56822611 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56822570 CTATTTTAAT
56822580 TATTAAAAATAAAAAA
1 TATTAAAAATAAAAAA
56822596 TATTAAAAATAAAAAA
1 TATTAAAAATAAAAAA
56822612 ATATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TATTAAAAATAAAAAA
Found at i:56824193 original size:24 final size:22
Alignment explanation
Indices: 56824150--56824193 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
56824140 AGTGATGATC
* *
56824150 TAAATTGCATATAAATTTTGGT
1 TAAATTGCATACAAACTTTGGT
56824172 TAAATGTGACATACAAACTTTG
1 TAAAT-TG-CATACAAACTTTG
56824194 AATTACAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
TAAATTGCATACAAACTTTGGT
Found at i:56828702 original size:21 final size:23
Alignment explanation
Indices: 56828631--56828696 Score: 64
Period size: 25 Copynumber: 2.9 Consensus size: 23
56828621 GTAAGACGAA
* *
56828631 ATTTTAAATTTAGTTATTTTTAATT
1 ATTTTAAAATTAATT-TTTTTAA-T
**
56828656 AAGTTAAAATTAATTTTTTTAAT
1 ATTTTAAAATTAATTTTTTTAAT
56828679 ATTTTAAAA-T-ATTTTTTT
1 ATTTTAAAATTAATTTTTTT
56828697 GTTATTATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 8 0.23
22 1 0.03
23 8 0.23
24 7 0.20
25 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (23 bp):
ATTTTAAAATTAATTTTTTTAAT
Found at i:56828707 original size:21 final size:21
Alignment explanation
Indices: 56828668--56828707 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56828658 GTTAAAATTA
*
56828668 ATTTTTTTAATATTTTAAAAT
1 ATTTTTTTAATATTATAAAAT
**
56828689 ATTTTTTTGTTATTATAAA
1 ATTTTTTTAATATTATAAA
56828708 TAGGTGGATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTTTTTAATATTATAAAAT
Found at i:56837289 original size:23 final size:23
Alignment explanation
Indices: 56837252--56837295 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56837242 ATGTACTCAT
56837252 GCCATTACAAATTTACTCAAATTA
1 GCCATTACAAATTTAC-CAAATTA
*
56837276 GCCATTTC-AATTTACCAAAT
1 GCCATTACAAATTTACCAAAT
56837296 ATTCATAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
GCCATTACAAATTTACCAAATTA
Found at i:56838779 original size:41 final size:45
Alignment explanation
Indices: 56838659--56838836 Score: 151
Period size: 41 Copynumber: 4.0 Consensus size: 45
56838649 GATACTCGAA
* *
56838659 TAATCACATATATCGGACAATGCCAACGTCCCAGAC-GTGGTCTTACATG
1 TAATCACATATATC-G---ATGCCAATGTCCCAGACAG-GGTCTTACACG
* *
56838708 CT-ATCTC--ATATCGATGCCATTGTCCCAGACAGGGTCTTACACG
1 -TAATCACATATATCGATGCCAATGTCCCAGACAGGGTCTTACACG
* **
56838751 -AATCA-A-ATA-CGATGCCAATGTCCTAGACATTGTCTTACACG
1 TAATCACATATATCGATGCCAATGTCCCAGACAGGGTCTTACACG
56838792 TAATCACATATATCGATGCC-ATCGTCCCAGAC-GTGGTCTTACACG
1 TAATCACATATATCGATGCCAAT-GTCCCAGACAG-GGTCTTACACG
56838837 GGAACACATA
Statistics
Matches: 107, Mismatches: 12, Indels: 23
0.75 0.08 0.16
Matches are distributed among these distances:
41 28 0.26
42 11 0.10
43 26 0.24
44 6 0.06
45 25 0.23
46 1 0.01
47 5 0.05
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (45 bp):
TAATCACATATATCGATGCCAATGTCCCAGACAGGGTCTTACACG
Found at i:56838845 original size:45 final size:44
Alignment explanation
Indices: 56838678--56838850 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 44
56838668 ATATCGGACA
* * ** *
56838678 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTC-ATATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACGGAATCACAATATCG
*
56838721 ATGCCATTGTCCCAGACAG-GGTCTTACAC-GAATCA-AATA-CG
1 ATGCCATCGTCCCAGAC-GTGGTCTTACACGGAATCACAATATCG
* * * *
56838762 ATGCCAAT-GTCCTAGACATTGTCTTACACGTAATCACATATATCG
1 ATGCC-ATCGTCCCAGACGTGGTCTTACACGGAATCACA-ATATCG
56838807 ATGCCATCGTCCCAGACGTGGTCTTACACGGGAA-CAC-ATATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACAC-GGAATCACAATATCG
56838850 A
1 A
56838851 AAATCCTATG
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
41 24 0.23
42 13 0.12
43 32 0.30
44 6 0.06
45 28 0.26
46 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCATCGTCCCAGACGTGGTCTTACACGGAATCACAATATCG
Found at i:56845918 original size:15 final size:14
Alignment explanation
Indices: 56845877--56845919 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
56845867 GTTTTAGTCA
56845877 AAAACCTTAAACCT
1 AAAACCTTAAACCT
* *
56845891 AAAACATTAAAACTT
1 AAAACCTT-AAACCT
56845906 AAAACCCTTAAACC
1 AAAA-CCTTAAACC
56845920 CTAATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.30
15 13 0.57
16 3 0.13
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAACCTTAAACCT
Found at i:56849341 original size:31 final size:31
Alignment explanation
Indices: 56849297--56849358 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
56849287 TTATGTACTG
56849297 GTTTCTTAGTATGAATATTCAGTTGCATTAT
1 GTTTCTTAGTATGAATATTCAGTTGCATTAT
* *
56849328 GTTTGTTATTATGAATATTCAGTTGCATTAT
1 GTTTCTTAGTATGAATATTCAGTTGCATTAT
56849359 TATTACTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (31 bp):
GTTTCTTAGTATGAATATTCAGTTGCATTAT
Found at i:56853646 original size:15 final size:15
Alignment explanation
Indices: 56853622--56853656 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56853612 TTTGGAATTC
* *
56853622 AATATTATATATTGA
1 AATATCATATAGTGA
56853637 AATATCATATAGTGA
1 AATATCATATAGTGA
56853652 AATAT
1 AATAT
56853657 ATCAAAGCTT
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:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (15 bp):
AATATCATATAGTGA
Found at i:56855326 original size:500 final size:492
Alignment explanation
Indices: 56854284--56855418 Score: 1180
Period size: 500 Copynumber: 2.3 Consensus size: 492
56854274 GTATCGATCA
* * * * * * * * *
56854284 ATTGTACATTTCTATGA-TACTAACATAATTGAATGAATTATGACATCAGTTGTAGAATCATTGA
1 ATTGTACATTTCTCTAATTATTAACGTAATTGAATGAGTTATGACATTAATTGTACAATCATTTA
* * * * *
56854348 TCTAATTGAATAAATCTATGTATGAAA-CTTAT-GACATTATAGTGTTATAAGTGTTTTTAAAAG
66 TCTAATTGAATGAATCTATGTATGAAAGGTAATAG-CATTGTAGTG-TATAAGTATTTTTAAAAG
* * * * * *
56854411 TATTTATCAATTCTATATTCCTTTAATTACTAGCAAAATCGAATGAATTGTCACATTAATCGTAG
129 TATTTATCAATTGTATATTCCTCTAATCACTAGCAAAATCGAATAAATTCTCACATTAATCGTAC
* *
56854476 ATCCAATGAACCAATGGAATAAATTGTATAATAACTCGTACAATCATTTATCCAATTAAATCAGT
194 ATCCAATGAACCAATGGAATAAATTGTATAATAACTCATACAATCATTGATCCAATTAAATCAGT
*** * * *
56854541 CCATGTAAACATAGTGTTTAGTATAAATGTTTGGAATTCAATACCGTACAGTGAAAACTTTAGAC
259 CCATGTAAACATAACATTGAGTATAAATGTTTAGAATTCAATACCATACAGTGAAAACTTTAGAC
* * *
56854606 CATCAATGTTTAATTGGAAAATTTTGATCAACTTAAGAGTATTTATCAATTATGCATTCCTTTAA
324 CACCAATGTTTAATTGGAAAATTTTAATCAACTTAAGAGTATTTATCAATTATGCATTCCTCTAA
* * * * * *
56854671 CTACTAACAAATTTGAATAATTATGATATCGAACCAGTTGAATCGAATCTATATATGAGTGTATT
389 CTACTAACAAATTTGAATAATTATGACATCGAACCAATTAAATCGAATCTATATATGAATGCAGT
* * * * *
56854736 AACATTGTGTTGTACAAGTAACTTGAAATGTATTAATGT
454 AACATTGTGGTCTACAAGTAACTTGAAAAGTAATAATGC
* * * * * * **
56854775 ATTGTATATTTCTTTAATTATTAATGTAATTGAATAAGTTATTATATTAATTGTACAGCCATTTA
1 ATTGTACATTTCTCTAATTATTAACGTAATTGAATGAGTTATGACATTAATTGTACAATCATTTA
56854840 TCTAATTGAATGAATCTATGTA-GAAAGGTAATAGCATTGTAGTGTATAAGTATTTTTAAAAGTA
66 TCTAATTGAATGAATCTATGTATGAAAGGTAATAGCATTGTAGTGTATAAGTATTTTTAAAAGTA
* * *** * * * *
56854904 TTTATTAATTGTATGTTCCTCTAATCACTAGTGCAATTGAATAAATTCTGACATTAGTTGTACAG
131 TTTATCAATTGTATATTCCTCTAATCACTAGCAAAATCGAATAAATTCTCACATTAATCGTACA-
* * * * * * * *
56854969 T-TATTGATCTAATTGAATAAATTGTATAATTAA-TCATACAATCATTGGTCTAATTGAATCAGT
195 TCCAATGAACCAATGGAATAAATTGTATAA-TAACTCATACAATCATTGATCCAATTAAATCAGT
* * *
56855032 CTATGTAAAC-TCAACATTGAGTATACATGTTTAGAATTCAATATCATACAGTGAAATATATCAA
259 CCATGTAAACAT-AACATTGAGTATAAATGTTTAGAATTCAATACCATACAGTG---------AA
* ** *
56855096 AACTTTGGACCACCAATGTTTAATT-TCAAATGTTTAATCAACTTCAGAGTATTTATCAATTATG
314 AACTTTAGACCACCAATGTTTAATTGGAAAAT-TTTAATCAACTTAAGAGTATTTATCAATTATG
* * * * * * * *
56855160 TATTCCTCTAACTGCTAACGTAA-TTGAATGATTATGACATTGAACTAATTAAATTGAGTCTATA
378 CATTCCTCTAACTACTAAC-AAATTTGAATAATTATGACATCGAACCAATTAAATCGAATCTATA
* * *
56855224 TATGAATGCAGTAACATTGTGGTCTACAAGTGATTTGAAAAGTAATGAT-C
442 TATGAATGCAGTAACATTGTGGTCTACAAGTAACTTGAAAAGTAATAATGC
* *
56855274 ACTTTTACATTTCTCTAATTTTTAACGTAATTGAATGAGTTATGACATTAATTGTACAATC-TTT
1 A-TTGTACATTTCTCTAATTATTAACGTAATTGAATGAGTTATGACATTAATTGTACAATCATTT
* * * *
56855338 GATCTAATTGAACGAATCTATGCATG-AAGGTAATTA-CATTGTAGTGTATAAGTATTTGTAAGA
65 -ATCTAATTGAATGAATCTATGTATGAAAGGTAA-TAGCATTGTAGTGTATAAGTATTTTTAAAA
*
56855401 GTATTGATCAATTGTATA
128 GTATTTATCAATTGTATA
56855419 ATCCATTGTA
Statistics
Matches: 522, Mismatches: 101, Indels: 33
0.80 0.15 0.05
Matches are distributed among these distances:
490 1 0.00
491 176 0.34
492 71 0.14
493 1 0.00
499 8 0.02
500 260 0.50
501 5 0.01
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (492 bp):
ATTGTACATTTCTCTAATTATTAACGTAATTGAATGAGTTATGACATTAATTGTACAATCATTTA
TCTAATTGAATGAATCTATGTATGAAAGGTAATAGCATTGTAGTGTATAAGTATTTTTAAAAGTA
TTTATCAATTGTATATTCCTCTAATCACTAGCAAAATCGAATAAATTCTCACATTAATCGTACAT
CCAATGAACCAATGGAATAAATTGTATAATAACTCATACAATCATTGATCCAATTAAATCAGTCC
ATGTAAACATAACATTGAGTATAAATGTTTAGAATTCAATACCATACAGTGAAAACTTTAGACCA
CCAATGTTTAATTGGAAAATTTTAATCAACTTAAGAGTATTTATCAATTATGCATTCCTCTAACT
ACTAACAAATTTGAATAATTATGACATCGAACCAATTAAATCGAATCTATATATGAATGCAGTAA
CATTGTGGTCTACAAGTAACTTGAAAAGTAATAATGC
Found at i:56857527 original size:23 final size:22
Alignment explanation
Indices: 56857495--56857556 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
56857485 CCCGGCCCAT
*
56857495 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
56857519 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
56857541 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
56857557 TTGTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:56857551 original size:16 final size:16
Alignment explanation
Indices: 56857530--56857586 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
56857520 TTTTATTAAA
*
56857530 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
56857546 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
56857562 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
56857578 ATTAAAATT
1 ATTAAAATT
56857587 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:56857647 original size:70 final size:70
Alignment explanation
Indices: 56857569--56857710 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
56857559 GTTATCAAAA
56857569 TTAATTATTATTAAAATTGTATCAAATTATATATTTTTTGTACCAATCAACATTTTATAAAATCT
1 TTAATTATTATTAAAATTGTATCAAATTATATATTTTTTGTACCAATCAACATTTTATAAAATCT
56857634 AACAT
66 AACAT
56857639 TTAATTATTATTAAAATTGTATCAAATTATATATTTTTTGTACCAATCAACATTTTATAAAATCT
1 TTAATTATTATTAAAATTGTATCAAATTATATATTTTTTGTACCAATCAACATTTTATAAAATCT
56857704 AACAT
66 AACAT
56857709 TT
1 TT
56857711 TGTTAGTAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (70 bp):
TTAATTATTATTAAAATTGTATCAAATTATATATTTTTTGTACCAATCAACATTTTATAAAATCT
AACAT
Found at i:56857898 original size:22 final size:22
Alignment explanation
Indices: 56857867--56857913 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
56857857 TAACTTAAAA
* *
56857867 TAAAACTAAAACTAGTATAT-TT
1 TAAAAATAAAAATA-TATATATT
56857889 TAAAAATAAAAATATATATATT
1 TAAAAATAAAAATATATATATT
56857911 TAA
1 TAA
56857914 TATATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATAAAAATATATATATT
Found at i:56859662 original size:20 final size:19
Alignment explanation
Indices: 56859621--56859668 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
56859611 AAACATAAAA
* *
56859621 TTTGAAATTTTATAAATAT
1 TTTGAATTTTTAAAAATAT
56859640 TTTGAATTTTTAAAAATTAT
1 TTTGAATTTTTAAAAA-TAT
56859660 TTTGAATTT
1 TTTGAATTT
56859669 GTTTTGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTGAATTTTTAAAAATAT
Found at i:56861016 original size:24 final size:22
Alignment explanation
Indices: 56860989--56861045 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
56860979 GTGAGTACTA
56860989 TATTCAATTACACATATGATAATG
1 TATTCAA--ACACATATGATAATG
56861013 TATTC-AACACATATGATAATG
1 TATTCAAACACATATGATAATG
56861034 TATTC-AACACAT
1 TATTCAAACACAT
56861046 CAGATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 27 0.82
23 1 0.03
24 5 0.15
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (22 bp):
TATTCAAACACATATGATAATG
Found at i:56861024 original size:21 final size:21
Alignment explanation
Indices: 56860998--56861045 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
56860988 ATATTCAATT
56860998 ACACATATGATAATGTATTCA
1 ACACATATGATAATGTATTCA
56861019 ACACATATGATAATGTATTCA
1 ACACATATGATAATGTATTCA
56861040 ACACAT
1 ACACAT
56861046 CAGATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (21 bp):
ACACATATGATAATGTATTCA
Found at i:56870919 original size:46 final size:46
Alignment explanation
Indices: 56870901--56871103 Score: 207
Period size: 46 Copynumber: 4.3 Consensus size: 46
56870891 TGACAAGTGG
* * *
56870901 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
56870947 AAAGTGATAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGAT-A--GCTA---T-AGCTACACTTATCTGATCAAGTGAC
* * *
56871000 -AAGTGGA-AAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 AAAGT-GATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* *
56871045 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
56871091 AAAGTGATAAGTG
1 AAAGTGATAAGTG
56871104 GCTACACTTA
Statistics
Matches: 136, Mismatches: 10, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
45 26 0.19
46 65 0.48
47 2 0.01
49 4 0.03
51 1 0.01
52 11 0.08
53 27 0.20
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:56870955 original size:98 final size:91
Alignment explanation
Indices: 56870909--56871092 Score: 260
Period size: 98 Copynumber: 1.9 Consensus size: 91
56870899 GGAAAGTGAT
*
56870909 AAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAAGTGATAGCTT
1 AAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAA--G-T--G-G-TAGCTT
*
56870974 CAGCTACACTTATCTGATCAAGTGACAAGTGGA
59 TAGCTACACTTATCTGATCAAGTGACAAGTGGA
* *
56871007 AAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTAC
1 AAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
*
56871072 ACTTATCTGATCAAGAGACAA
66 ACTTATCTGATCAAGTGACAA
56871093 AGTGATAAGT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
91 32 0.40
93 1 0.01
95 1 0.01
96 1 0.01
98 46 0.57
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (91 bp):
AAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTAC
ACTTATCTGATCAAGTGACAAGTGGA
Found at i:56871010 original size:105 final size:98
Alignment explanation
Indices: 56870850--56871140 Score: 335
Period size: 105 Copynumber: 3.1 Consensus size: 98
56870840 TCAAGTGACA
* *
56870850 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTAA
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAA--G-T--G--A
*
56870915 TAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGAT
59 TAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGAT
56870955 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAGCTTC
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAGCTTC
56871020 GGCTATACTTATCTGATCAAGAGAC------A-
66 GGCTATACTTATCTGATCAAGAGACAAAGTGAT
* *
56871046 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC------AAAGTGATAAG--T
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGAT-AGCTT
* *
56871103 -GGCTACACTTATCTGATCAAGAAACAAAGTGAT
65 CGGCTATACTTATCTGATCAAGAGACAAAGTGAT
56871136 AAGTG
1 AAGTG
56871141 GCTACACTTA
Statistics
Matches: 171, Mismatches: 7, Indels: 31
0.82 0.03 0.15
Matches are distributed among these distances:
83 23 0.13
84 1 0.01
85 8 0.05
86 2 0.01
89 1 0.01
90 5 0.03
91 43 0.25
92 1 0.01
98 32 0.19
100 1 0.01
102 1 0.01
103 1 0.01
105 52 0.30
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAGCTTC
GGCTATACTTATCTGATCAAGAGACAAAGTGAT
Found at i:56871070 original size:91 final size:83
Alignment explanation
Indices: 56871020--56871214 Score: 250
Period size: 74 Copynumber: 2.5 Consensus size: 83
56871010 TGATAGCTTC
* * *
56871020 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCA
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCA
56871085 AGAGACAAAGTGATAAGT
66 AGAGACAAAGTGATAAGT
56871103 GGCTACACTTATCTGATCAAGAAACAAAGTGATAA--G-T-G-----GCTACACTTATCTGATCA
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCA
* *
56871159 AGAAACAAAGTGATAGGT
66 AGAGACAAAGTGATAAGT
**
56871177 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTGAT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGAT
56871215 CATACGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
72 9 0.09
73 4 0.04
74 53 0.51
75 1 0.01
79 1 0.01
80 1 0.01
81 1 0.01
83 33 0.32
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (83 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCA
AGAGACAAAGTGATAAGT
Found at i:56871111 original size:37 final size:37
Alignment explanation
Indices: 56871067--56871212 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
56871057 GATAGCTTTA
*
56871067 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
56871104 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
56871141 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
56871178 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
56871213 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:56871929 original size:18 final size:18
Alignment explanation
Indices: 56871903--56871949 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
56871893 TTTTAAAAAC
56871903 ATAAA-ATTTGAAATTTT
1 ATAAATATTTGAAATTTT
*
56871920 ATAAATATTTTGAATTTTT
1 ATAAATA-TTTGAAATTTT
*
56871939 AAAAATTATTT
1 ATAAA-TATTT
56871950 TGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 5 0.20
18 1 0.04
19 17 0.68
20 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATAAATATTTGAAATTTT
Found at i:56871950 original size:20 final size:19
Alignment explanation
Indices: 56871909--56871956 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
56871899 AAACATAAAA
* *
56871909 TTTGAAATTTTATAAATAT
1 TTTGAATTTTTAAAAATAT
56871928 TTTGAATTTTTAAAAATTAT
1 TTTGAATTTTTAAAAA-TAT
56871948 TTTGAATTT
1 TTTGAATTT
56871957 GTTTTGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTGAATTTTTAAAAATAT
Found at i:56876374 original size:21 final size:22
Alignment explanation
Indices: 56876345--56876391 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
56876335 CAGAAGGAGT
*
56876345 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
56876367 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
56876388 GAGT
1 GAGT
56876392 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:56879134 original size:11 final size:11
Alignment explanation
Indices: 56879118--56879163 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
56879108 CACGGTTTTT
56879118 TACAAAAATAA
1 TACAAAAATAA
56879129 TACAAAAA-AA
1 TACAAAAATAA
* *
56879139 TAAAAAAAAAA
1 TACAAAAATAA
56879150 T-C-AAAATAA
1 TACAAAAATAA
56879159 TACAA
1 TACAA
56879164 GTATTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 7 0.24
10 10 0.34
11 12 0.41
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (11 bp):
TACAAAAATAA
Found at i:56879154 original size:20 final size:21
Alignment explanation
Indices: 56879121--56879160 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56879111 GGTTTTTTAC
*
56879121 AAAAATAATACAAAAAAATAA
1 AAAAAAAATACAAAAAAATAA
*
56879142 AAAAAAAAT-CAAAATAATA
1 AAAAAAAATACAAAAAAATA
56879161 CAAGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAAAATACAAAAAAATAA
Found at i:56879328 original size:15 final size:16
Alignment explanation
Indices: 56879296--56879331 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
56879286 TTCGTATTTT
56879296 TTTTATTTTCAGATTA
1 TTTTATTTTCAGATTA
*
56879312 TTTTATTTT-ATATTA
1 TTTTATTTTCAGATTA
56879327 TTTTA
1 TTTTA
56879332 GTACATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTATTTTCAGATTA
Found at i:56879663 original size:30 final size:30
Alignment explanation
Indices: 56879627--56879684 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
56879617 TAAATTAAAT
56879627 TAAATAATAAAACATAGAATGTACATAACA
1 TAAATAATAAAACATAGAATGTACATAACA
56879657 TAAATAATAAAACATAGAATGTACATAA
1 TAAATAATAAAACATAGAATGTACATAA
56879685 GACAAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.24
Consensus pattern (30 bp):
TAAATAATAAAACATAGAATGTACATAACA
Found at i:56889232 original size:21 final size:22
Alignment explanation
Indices: 56889206--56889246 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
56889196 AATAAATGCC
56889206 AAAAAA-TTATTTTAAAAATTA
1 AAAAAATTTATTTTAAAAATTA
56889227 AAAAAATTTATTTTAAAAAT
1 AAAAAATTTATTTTAAAAAT
56889247 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAAATTTATTTTAAAAATTA
Found at i:56889251 original size:11 final size:11
Alignment explanation
Indices: 56889235--56889375 Score: 87
Period size: 11 Copynumber: 13.9 Consensus size: 11
56889225 TAAAAAAATT
56889235 TATTTTAAAAA
1 TATTTTAAAAA
*
56889246 TATTTT--TAA
1 TATTTTAAAAA
56889255 -A-TT-AAAAA
1 TATTTTAAAAA
* *
56889263 AATTTTACAAAG
1 TATTTTA-AAAA
56889275 TATTTTAAAAA
1 TATTTTAAAAA
56889286 TATTTT--AAA
1 TATTTTAAAAA
56889295 -A--TTAAAAA
1 TATTTTAAAAA
*
56889303 AATTTTAAAAA
1 TATTTTAAAAA
*
56889314 GTATTTTAAAAG
1 -TATTTTAAAAA
56889326 TATTTT--AAA
1 TATTTTAAAAA
56889335 -A--TTAAAAA
1 TATTTTAAAAA
*
56889343 AATTTTAAAAA
1 TATTTTAAAAA
*
56889354 GTATTTTAAAAG
1 -TATTTTAAAAA
56889366 TATTTTAAAA
1 TATTTTAAAA
56889376 TTAAAAAAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
6 4 0.04
7 2 0.02
8 11 0.11
9 10 0.10
10 2 0.02
11 46 0.45
12 27 0.26
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:56889253 original size:17 final size:17
Alignment explanation
Indices: 56889221--56889268 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
56889211 ATTATTTTAA
56889221 AAATTAAAAAAATTTATT
1 AAATTAAAAAAATTT-TT
*
56889239 ---TTAAAAATATTTTT
1 AAATTAAAAAAATTTTT
56889253 AAATTAAAAAAATTTT
1 AAATTAAAAAAATTTT
56889269 ACAAAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
17 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTAAAAAAATTTTT
Found at i:56889279 original size:40 final size:40
Alignment explanation
Indices: 56889235--56889385 Score: 266
Period size: 40 Copynumber: 3.8 Consensus size: 40
56889225 TAAAAAAATT
* *
56889235 TATTTTAAAAATATTTTTAAATTAAAAAAATTTTACAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAG
56889275 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAG
*
56889315 TATTTTAAAAGTATTTTAAAATTAAAAAAATTTTAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAG
*
56889355 TATTTTAAAAGTATTTTAAAATTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
56889386 AAAATATTTA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 108 1.00
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAG
Found at i:56889339 original size:29 final size:29
Alignment explanation
Indices: 56889307--56889364 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
56889297 TAAAAAAATT
*
56889307 TTAAAAAGTATTTT-AAAAGTATTTTAAAA
1 TTAAAAA-AATTTTAAAAAGTATTTTAAAA
56889336 TTAAAAAAATTTTAAAAAGTATTTTAAAA
1 TTAAAAAAATTTTAAAAAGTATTTTAAAA
56889365 GTATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
TTAAAAAAATTTTAAAAAGTATTTTAAAA
Found at i:56889403 original size:80 final size:79
Alignment explanation
Indices: 56889219--56889403 Score: 257
Period size: 80 Copynumber: 2.3 Consensus size: 79
56889209 AAATTATTTT
* *
56889219 AAAAATTAAAAAAATTTATTTTAAAAATATTTTTAAATTAAAAAAATTTTACAAAGTATTTTAAA
1 AAAAATT--AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAGTATTTTAAA
56889284 AATATTTTAAAATTAA
64 AATATTTTAAAATTAA
* *
56889300 AAAAATTTTAAAAA-GTATTTTAAAAGTATTTTAAAATTAAAAAAATTTTAAAAAGTATTTTAAA
1 AAAAA--TTAAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAGTATTTTAAA
*
56889364 AGTATTTTAAAATTAA
64 AATATTTTAAAATTAA
56889380 AAAAA-TAAAATATTTATTATTAAA
1 AAAAATTAAAA-ATTTATT-TTAAA
56889404 TTCGGGCCGG
Statistics
Matches: 93, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
77 5 0.05
78 1 0.01
79 4 0.04
80 71 0.76
81 10 0.11
83 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (79 bp):
AAAAATTAAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAGTATTTTAAAAA
TATTTTAAAATTAA
Found at i:56892148 original size:71 final size:72
Alignment explanation
Indices: 56892071--56892249 Score: 206
Period size: 71 Copynumber: 2.5 Consensus size: 72
56892061 ATCTACCCTG
* * * *
56892071 TTTGGACAGCTTTTATACATCAATTTGGATAGCATTTATATACCA-AATTAGA-CAACATTTTCA
1 TTTGGACAGCATATATACAACAATTTGGA-AGCATTTATATACAACAATTAGAGCAACATTTTCA
56892134 CACCAAAA
65 CACCAAAA
* * *
56892142 TTTGGACAGCATAAATACAACAATTTAGGAAGCA--TATATACAACAATTTGAGCAACATTTTTA
1 TTTGGACAGCATATATACAACAATTT-GGAAGCATTTATATACAACAATTAGAGCAACATTTTCA
56892205 CACCAAAA
65 CACCAAAA
* * *
56892213 -TTGGACAGCGTATATACAACAAATTGGGCAGCATTTA
1 TTTGGACAGCATATATACAAC-AATTTGGAAGCATTTA
56892250 AACATCAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
69 8 0.09
70 30 0.33
71 48 0.53
72 5 0.05
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (72 bp):
TTTGGACAGCATATATACAACAATTTGGAAGCATTTATATACAACAATTAGAGCAACATTTTCAC
ACCAAAA
Done.