Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 43 of 185
Found at i:12733122 original size:10 final size:10
Alignment explanation
Indices: 12733107--12733131 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12733097 GCATCCCATA
12733107 ATAATATCCT
1 ATAATATCCT
12733117 ATAATATCCT
1 ATAATATCCT
12733127 ATAAT
1 ATAAT
12733132 TAGGAATCAA
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATATCCT
Found at i:12733747 original size:20 final size:21
Alignment explanation
Indices: 12733714--12733762 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
12733704 ATTAATTATA
* *
12733714 TTTTATTAAGTGAAAATA-AT
1 TTTTAATAAATGAAAATACAT
*
12733734 TTTTAATAAATGAAATTACAT
1 TTTTAATAAATGAAAATACAT
*
12733755 TTTAAATA
1 TTTTAATA
12733763 TGATTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
TTTTAATAAATGAAAATACAT
Found at i:12733762 original size:21 final size:19
Alignment explanation
Indices: 12733707--12733759 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
12733697 GAATAATATT
* *
12733707 AATTATATTTTATTAAGTGA
1 AATTA-ATTTTAATAAATGA
*
12733727 AAATAATTTTTAATAAATGA
1 AATTAA-TTTTAATAAATGA
12733747 AATTACATTTTAA
1 AATTA-ATTTTAA
12733760 ATATGATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
AATTAATTTTAATAAATGA
Found at i:12736943 original size:15 final size:15
Alignment explanation
Indices: 12736897--12736944 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
12736887 TTGATAAACT
*
12736897 AAAATATTAAGTACTG
1 AAAA-ATTAAGTATTG
*
12736913 AAAAATTAAATATTG
1 AAAAATTAAGTATTG
*
12736928 AAAAATTAAGTGTTG
1 AAAAATTAAGTATTG
12736943 AA
1 AA
12736945 TTTAAGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:12743302 original size:31 final size:31
Alignment explanation
Indices: 12743264--12743326 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
12743254 TTATACAAAC
*
12743264 ATGTAAACGGGAAGCTCTTCCAAGCCATATA
1 ATGTAAACGGGAAGCTCTCCCAAGCCATATA
* *
12743295 ATGTAAACGGGAATCTCTCCCGAGCCATATA
1 ATGTAAACGGGAAGCTCTCCCAAGCCATATA
12743326 A
1 A
12743327 CGGGAAGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (31 bp):
ATGTAAACGGGAAGCTCTCCCAAGCCATATA
Found at i:12743369 original size:25 final size:25
Alignment explanation
Indices: 12743321--12743411 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
12743311 CTCCCGAGCC
* * *
12743321 ATATAACGGGAAGCTCACGTGAGTT
1 ATATAACAGGAAGCTCAAGAGAGTT
* *
12743346 GTATAACAGGAAGCTCAAGAGAGTC
1 ATATAACAGGAAGCTCAAGAGAGTT
* *
12743371 AT-TAATCAGGAAGCTCATGAGAGCT
1 ATATAA-CAGGAAGCTCAAGAGAGTT
* *
12743396 AAATAACGGGAAGCTC
1 ATATAACAGGAAGCTC
12743412 GTGAGAGCCA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 3 0.06
25 47 0.89
26 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (25 bp):
ATATAACAGGAAGCTCAAGAGAGTT
Found at i:12743416 original size:25 final size:25
Alignment explanation
Indices: 12743379--12743450 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
12743369 TCATTAATCA
* *
12743379 GGAAGCTCATGAGAGCTAAATAACG
1 GGAAGCTCGTGAGAGCCAAATAACG
* **
12743404 GGAAGCTCGTGAGAGCCAAGTATTG
1 GGAAGCTCGTGAGAGCCAAATAACG
*
12743429 GGAAGCTTGTGAGAGCCAAATA
1 GGAAGCTCGTGAGAGCCAAATA
12743451 TCAAGACGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (25 bp):
GGAAGCTCGTGAGAGCCAAATAACG
Found at i:12749980 original size:14 final size:14
Alignment explanation
Indices: 12749949--12749979 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
12749939 TCTCTCTCTC
12749949 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
12749963 TTTTCTTT-TTTCT
1 TTTTCTTTCTTTCT
12749976 TTTT
1 TTTT
12749980 TTTAAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:12754798 original size:60 final size:62
Alignment explanation
Indices: 12754725--12754849 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 62
12754715 AATTATAATT
* * *
12754725 TTTTTAAATGTATAATTATAACAATTTTTGTTTTA-ATTAGTTTTTTA-TTTTTAATGTGAA
1 TTTTTAAATGTATAATTATAACAAATTTTATTTTATATTAATTTTTTATTTTTTAATGTGAA
*
12754785 TTTTTAAATGTATAATTATAACAAATTTTATTTTATTTTAATTTTTTATTTTTTAATGTGAA
1 TTTTTAAATGTATAATTATAACAAATTTTATTTTATATTAATTTTTTATTTTTTAATGTGAA
12754847 TTT
1 TTT
12754850 AGTAATACGA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 33 0.56
61 10 0.17
62 16 0.27
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (62 bp):
TTTTTAAATGTATAATTATAACAAATTTTATTTTATATTAATTTTTTATTTTTTAATGTGAA
Found at i:12764125 original size:36 final size:36
Alignment explanation
Indices: 12764078--12764148 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
12764068 ACACCGTTAG
* *
12764078 AATTTTAATAACAACTTTTCCTTTCTTTTCAAGATT
1 AATTTTAATAACAACTCTTCCTTTATTTTCAAGATT
*
12764114 AATTTTAATAACAACTCTTCTTTTATTTTCAAGAT
1 AATTTTAATAACAACTCTTCCTTTATTTTCAAGAT
12764149 GGCCAATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.49
Consensus pattern (36 bp):
AATTTTAATAACAACTCTTCCTTTATTTTCAAGATT
Found at i:12767108 original size:55 final size:56
Alignment explanation
Indices: 12767024--12767136 Score: 192
Period size: 55 Copynumber: 2.0 Consensus size: 56
12767014 TAAAAAAATT
12767024 AACTTAATAATTCTTTTACATCGTTACAAT-CCCCAACAATGGTGCCAACAATTTG
1 AACTTAATAATTCTTTTACATCGTTACAATGCCCCAACAATGGTGCCAACAATTTG
**
12767079 AACTTAATAATTCTTTTACATCGTTACAATGGTGCCAACAATGGTGCCAACAATTTG
1 AACTTAATAATTCTTTTACATCGTTACAAT-GCCCCAACAATGGTGCCAACAATTTG
12767136 A
1 A
12767137 CCATGCTATG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 30 0.56
57 24 0.44
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (56 bp):
AACTTAATAATTCTTTTACATCGTTACAATGCCCCAACAATGGTGCCAACAATTTG
Found at i:12767121 original size:12 final size:12
Alignment explanation
Indices: 12767104--12767132 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12767094 TTACATCGTT
12767104 ACAATGGTGCCA
1 ACAATGGTGCCA
12767116 ACAATGGTGCCA
1 ACAATGGTGCCA
12767128 ACAAT
1 ACAAT
12767133 TTGACCATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (12 bp):
ACAATGGTGCCA
Found at i:12767766 original size:16 final size:16
Alignment explanation
Indices: 12767745--12767775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12767735 ATCGAATATC
*
12767745 AATAAAAACTTAATCA
1 AATAAAAAATTAATCA
12767761 AATAAAAAATTAATC
1 AATAAAAAATTAATC
12767776 CATGCAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAAATTAATCA
Found at i:12769117 original size:27 final size:27
Alignment explanation
Indices: 12769068--12769238 Score: 123
Period size: 27 Copynumber: 6.3 Consensus size: 27
12769058 GGAAGAAACA
* * * *
12769068 CCTTTGTGGCAGTCTTTGTAAAGGAAG
1 CCTTTGTGACAATCTCTATAAAGGAAG
* *
12769095 CCTTTGTGACAATATCTGA-AAAGGGAG
1 CCTTTGTGACAATCTCT-ATAAAGGAAG
*
12769122 TCTTTGTGACAATCTCTATAAATGG-AG
1 CCTTTGTGACAATCTCTATAAA-GGAAG
* * * *
12769149 CTTTTGTGGCAATATCTATAAAGGATG
1 CCTTTGTGACAATCTCTATAAAGGAAG
* * *
12769176 CCTTTGTGGCGATCTCTATTAAAGAAAG
1 CCTTTGTGACAATCTCTA-TAAAGGAAG
* * *
12769204 CGTTTATGACTATCTCTGA-AAAGGAAG
1 CCTTTGTGACAATCTCT-ATAAAGGAAG
12769231 ACCTTTGT
1 -CCTTTGT
12769239 AGCGCAGTTT
Statistics
Matches: 112, Mismatches: 25, Indels: 13
0.75 0.17 0.09
Matches are distributed among these distances:
26 3 0.03
27 81 0.72
28 27 0.24
29 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (27 bp):
CCTTTGTGACAATCTCTATAAAGGAAG
Found at i:12778994 original size:10 final size:9
Alignment explanation
Indices: 12778973--12779082 Score: 51
Period size: 10 Copynumber: 11.1 Consensus size: 9
12778963 GCCCATTTTT
12778973 ATTTTAAAA
1 ATTTTAAAA
12778982 ATTTTAGAAA
1 ATTTTA-AAA
**
12778992 ATTAAAAAA
1 ATTTTAAAA
12779001 GTATTTTAAAAA
1 --ATTTT-AAAA
12779013 TATTTTAAAA
1 -ATTTTAAAA
*
12779023 ATATTTTAAA
1 AT-TTTAAAA
**
12779033 ATTAAAAAAA
1 ATT-TTAAAA
**
12779043 ATTAAAAAAA
1 ATT-TTAAAA
12779053 GTATTTTAAAA
1 --ATTTTAAAA
12779064 ATATTTAAAA
1 AT-TTTAAAA
12779074 A-TTTAAAA
1 ATTTTAAAA
12779082 A
1 A
12779083 AAATTAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
8 8 0.10
9 14 0.17
10 40 0.49
11 13 0.16
12 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:12779011 original size:11 final size:11
Alignment explanation
Indices: 12778972--12779115 Score: 78
Period size: 11 Copynumber: 13.9 Consensus size: 11
12778962 GGCCCATTTT
12778972 TATTTT-AAAA
1 TATTTTAAAAA
*
12778982 -ATTTTAGAAA
1 TATTTTAAAAA
*
12778992 -A-TTAAAAAA
1 TATTTTAAAAA
12779001 GTATTTTAAAAA
1 -TATTTTAAAAA
12779013 TATTTTAAAAA
1 TATTTTAAAAA
12779024 TATTTT--AAA
1 TATTTTAAAAA
*
12779033 -A-TTAAAAAA
1 TATTTTAAAAA
* **
12779042 AATTAAAAAAA
1 TATTTTAAAAA
12779053 GTATTTTAAAAA
1 -TATTTTAAAAA
12779065 TA-TTT-AAAA
1 TATTTTAAAAA
12779074 -A-TTTAAAAA
1 TATTTTAAAAA
* * *
12779083 AAATTAAAAAA
1 TATTTTAAAAA
* *
12779094 GTATGTAAAAAA
1 -TATTTTAAAAA
12779106 TATTTTAAAA
1 TATTTTAAAA
12779116 TTAAAAAAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
7 2 0.02
8 5 0.05
9 25 0.24
10 9 0.08
11 42 0.40
12 23 0.22
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:12779019 original size:41 final size:41
Alignment explanation
Indices: 12778972--12779124 Score: 195
Period size: 41 Copynumber: 3.7 Consensus size: 41
12778962 GGCCCATTTT
* **
12778972 TATTTTAAAAAT-TTTAGAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTTA-AAAATTAAAAAA-AATTAAAAAAAG
*
12779013 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTAAAAATTAAAAAAAATTAAAAAAAG
12779054 TATTTTAAAAATATTTAAAAATTTAAAAAAAATT-AAAAAAG
1 TATTTTAAAAATATTTAAAAA-TTAAAAAAAATTAAAAAAAG
* * *
12779095 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
12779125 TAAATATATT
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
40 17 0.17
41 69 0.68
42 15 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (41 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAATTAAAAAAAG
Found at i:12779075 original size:82 final size:82
Alignment explanation
Indices: 12778974--12779124 Score: 218
Period size: 82 Copynumber: 1.8 Consensus size: 82
12778964 CCCATTTTTA
* * * *
12778974 TTTTAAAAATTTTAGAAAA-TTAAAAAAGTATTTTAAAAA-TATTTTAAAAATATTTTAAAATTA
1 TTTTAAAAATTTTAGAAAATTTAAAAAA--AATTAAAAAAGTATGTAAAAAATATTTTAAAATTA
12779037 AAAAAAATTAAAAAAAGTA
64 AAAAAAATTAAAAAAAGTA
12779056 TTTTAAAAATATTTA-AAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAA
1 TTTTAAAAAT-TTTAGAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAA
12779120 AAAAA
65 AAAAA
12779125 TAAATATATT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
81 8 0.13
82 42 0.68
83 12 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (82 bp):
TTTTAAAAATTTTAGAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
AAAAATTAAAAAAAGTA
Found at i:12779086 original size:52 final size:51
Alignment explanation
Indices: 12778989--12779115 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 51
12778979 AAAATTTTAG
**
12778989 AAAATTAAAAAAGTATTTTAAAAATATTTTAAAAATATTTTAAAATTAAAA
1 AAAATTAAAAAAGTATTTTAAAAATATTTTAAAAATATTAAAAAATTAAAA
12779040 AAAATTAAAAAAAGTATTTTAAAAATA-TTTAAAAAT-TTAAAAAAAATTAAAA
1 AAAATT-AAAAAAGTATTTTAAAAATATTTTAAAAATATT--AAAAAATTAAAA
*
12779092 AAGTATGTAAAAAA-TATTTTAAAA
1 AA-AAT-TAAAAAAGTATTTTAAAA
12779116 TTAAAAAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
50 2 0.03
51 15 0.22
52 42 0.62
53 8 0.12
54 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (51 bp):
AAAATTAAAAAAGTATTTTAAAAATATTTTAAAAATATTAAAAAATTAAAA
Found at i:12790961 original size:43 final size:43
Alignment explanation
Indices: 12790897--12790983 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
12790887 GGTGAGATTG
* *
12790897 ATTGCCAATAGAATTGCCATGGCAATTTCGGGAAGATGACTTA
1 ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
*
12790940 ATTGCCAACAGAATTGTCATGGCAATTTCGGGAAGATAACTTA
1 ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
12790983 A
1 A
12790984 CACTTTATCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (43 bp):
ATTGCCAACAGAATTGCCATGGCAATTTCGGGAAGATAACTTA
Found at i:12791481 original size:25 final size:25
Alignment explanation
Indices: 12791447--12791495 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
12791437 TATTAGGGTG
*
12791447 AATGTTTTATCATCTTTAATGCTCA
1 AATGCTTTATCATCTTTAATGCTCA
12791472 AATGCTTTATCATCTTTAATGCTC
1 AATGCTTTATCATCTTTAATGCTC
12791496 GTGATTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (25 bp):
AATGCTTTATCATCTTTAATGCTCA
Found at i:12797850 original size:41 final size:41
Alignment explanation
Indices: 12797790--12798077 Score: 314
Period size: 41 Copynumber: 7.0 Consensus size: 41
12797780 AAGATTATTG
* ** *
12797790 TGAATTGCACCTATGTGCCCCCGTTTGTACTTCAGTACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
* *
12797831 TAAATTGCACATACATGCCCCCGTTTGTACTTTGGTACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
**
12797872 T-AATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTA-CCCC
* *** * *
12797913 TGAATTGCACCTATGCGCCCCCGTTTATACGTT-GGTACCCT
1 TGAATTGCACATACATGCCCCCGTTTGTAC-TTCGGTACCCC
* * * *
12797954 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
* *
12797995 TGAATTGCACATAC--GCTCCCCTATTTGTACTTCGGTACCCT
1 TGAATTGCACATACATGC-CCCC-GTTTGTACTTCGGTACCCC
* *
12798036 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
12798077 T
1 T
12798078 AAATACACTT
Statistics
Matches: 206, Mismatches: 33, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.01
40 37 0.18
41 135 0.66
42 28 0.14
43 4 0.02
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.33
Consensus pattern (41 bp):
TGAATTGCACATACATGCCCCCGTTTGTACTTCGGTACCCC
Found at i:12797951 original size:82 final size:81
Alignment explanation
Indices: 12797790--12798077 Score: 355
Period size: 82 Copynumber: 3.5 Consensus size: 81
12797780 AAGATTATTG
* ** * * **
12797790 TGAATTGCACCTATGTGCCCCCGTTTGTACTTC-AGTACCCCTAAATTGCACATACATGCCCCCG
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGA-TACCCCTGAATTGCACATACGCGCCCCCG
*
12797854 TTTGTACTTTGGTACCCC
65 TTTGTAC-TTGGTACCCT
* * * *
12797872 T-AATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCCTGAATTGCACCTATGCGCCCCCG
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATA-CCCCTGAATTGCACATACGCGCCCCCG
*
12797936 TTTATACGTTGGTACCCT
65 TTTGTAC-TTGGTACCCT
* * * **
12797954 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGAATTGCACATACGCTCCCCTAT
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGCGCCCCCGT
12798019 TTGTACTTCGGTACCCT
66 TTGTACTT-GGTACCCT
12798036 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCT
1 TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCT
12798078 AAATACACTT
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 30 0.17
82 115 0.65
83 31 0.18
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.33
Consensus pattern (81 bp):
TGAATTGCACATACATGCCCCTGTTTGTACTTCGATACCCCTGAATTGCACATACGCGCCCCCGT
TTGTACTTGGTACCCT
Found at i:12798040 original size:123 final size:123
Alignment explanation
Indices: 12797790--12798081 Score: 376
Period size: 123 Copynumber: 2.4 Consensus size: 123
12797780 AAGATTATTG
* *
12797790 TGAATTGCACCTATGTGCCCCCGTTTGTACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
1 TGAATTGCACCTATGCGCCCCCGTTTATACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
*
12797855 TTGTACTTTGGTACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
66 TTGTACTTTGATACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
* * * * *
12797913 TGAATTGCACCTATGCGCCCCCGTTTATACGTT-GGTACCCTTGAATTGCACATACGTGCCCCTG
1 TGAATTGCACCTATGCGCCCCCGTTTATAC-TTCAGTACCCCTAAATTGCACATACATGCCCCCG
* *
12797977 TTTGTACTTTGATACCCCTGAATTGCACATACGCT-CCCCTATTTGTACTTCGGTA-CCCT
65 TTTGTACTTTGATACCCCT-AATTGCACATAC-ATGCCCCTATTTGTACTTCGGTACCCCC
* *** * *
12798036 TGAATTGCACATACATGCCCCTGTTTGTACTTC-GATACCCCTAAAT
1 TGAATTGCACCTATGCGCCCCCGTTTATACTTCAG-TACCCCTAAAT
12798082 ACACTTTTGT
Statistics
Matches: 146, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
122 3 0.02
123 108 0.74
124 34 0.23
125 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.33
Consensus pattern (123 bp):
TGAATTGCACCTATGCGCCCCCGTTTATACTTCAGTACCCCTAAATTGCACATACATGCCCCCGT
TTGTACTTTGATACCCCTAATTGCACATACATGCCCCTATTTGTACTTCGGTACCCCC
Found at i:12821080 original size:31 final size:31
Alignment explanation
Indices: 12821045--12821108 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
12821035 TATCTAAACT
* *
12821045 TTTTTTA-TCCAATTAGGTACCTGAACTTGGC
1 TTTTTTATTCCAATTA-GTACCTAAACTTAGC
12821076 TTTTTTATTCCAATTAGTACCTAAACTTAGC
1 TTTTTTATTCCAATTAGTACCTAAACTTAGC
12821107 TT
1 TT
12821109 CATGGTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (31 bp):
TTTTTTATTCCAATTAGTACCTAAACTTAGC
Found at i:12824198 original size:40 final size:40
Alignment explanation
Indices: 12824154--12824233 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12824144 AGGGAAATCA
12824154 AAGTAGGTTTGGCTTTTCCTTTCTTATCAGACATTTTGAT
1 AAGTAGGTTTGGCTTTTCCTTTCTTATCAGACATTTTGAT
12824194 AAGTAGGTTTGGCTTTTCCTTTCTTATCAGACATTTTGAT
1 AAGTAGGTTTGGCTTTTCCTTTCTTATCAGACATTTTGAT
12824234 TGAAGTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (40 bp):
AAGTAGGTTTGGCTTTTCCTTTCTTATCAGACATTTTGAT
Found at i:12825745 original size:82 final size:82
Alignment explanation
Indices: 12825608--12825934 Score: 645
Period size: 82 Copynumber: 4.0 Consensus size: 82
12825598 TTTCATTACA
12825608 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
12825673 CATATTTTTTTCTAATC
66 CATATTTTTTTCTAATC
12825690 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
12825755 CATATTTTTTTCTAATC
66 CATATTTTTTTCTAATC
12825772 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
12825837 CATATTTTTTTCTAATC
66 CATATTTTTTTCTAATC
*
12825854 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTACATGCTAATTTGA
1 AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
12825919 CATATTTTTTTCTAAT
66 CATATTTTTTTCTAAT
12825935 TTGACACAGT
Statistics
Matches: 244, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 244 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (82 bp):
AATTTGTAAAGTAAGACAAAATTAAAGATGAAATTTTAATCTTACTTATTTAAATGCTAATTTGA
CATATTTTTTTCTAATC
Found at i:12826517 original size:43 final size:43
Alignment explanation
Indices: 12826450--12826534 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
12826440 ATAGAGAGAA
*
12826450 ATTTGCTATTTGTTTCATTAATCACACACTTATCATATCTTCC
1 ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTCC
*
12826493 ATTTGCTATTTGTTTAATTCATCACACACTTATCATATCTTC
1 ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTC
12826535 TCCCTTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.47
Consensus pattern (43 bp):
ATTTGCTATTTGTTTAATTAATCACACACTTATCATATCTTCC
Found at i:12833024 original size:53 final size:53
Alignment explanation
Indices: 12832960--12833062 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
12832950 ATTTTACACA
* * *
12832960 CTTTCGTTCACCTTATTTTCTAAAGAAAATGTTCTAATCCATATAATCTCACT
1 CTTTCGCTCACCTTATTTTCTAAACAAAATGTTCTAATCCACATAATCTCACT
* * *
12833013 CTTTCGCTCACCTTGTTTTTTAAACAAAATGTTCTAATCCGCATAATCTC
1 CTTTCGCTCACCTTATTTTCTAAACAAAATGTTCTAATCCACATAATCTC
12833063 TTCATTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (53 bp):
CTTTCGCTCACCTTATTTTCTAAACAAAATGTTCTAATCCACATAATCTCACT
Found at i:12834849 original size:25 final size:26
Alignment explanation
Indices: 12834820--12834896 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
12834810 ACGAATTTTC
12834820 TCAAAATTTTAAC-AGGGTAAAATTG
1 TCAAAATTTTAACAAGGGTAAAATTG
* * *
12834845 TCAAAACTTTATCAAGGGTTAAATTG
1 TCAAAATTTTAACAAGGGTAAAATTG
*
12834871 TCAGAATTTT-ACAATGGGTAAAATTG
1 TCAAAATTTTAACAA-GGGTAAAATTG
12834897 GGATGAGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 14 0.33
26 29 0.67
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTAACAAGGGTAAAATTG
Found at i:12839394 original size:94 final size:94
Alignment explanation
Indices: 12839233--12839420 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
12839223 AGGGTTTTAG
*
12839233 ATTCTTCCTCTCCTGACCAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
1 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
12839298 TCCACTTGCTAATCCCCCCATAGGAGGAT
66 TCCACTTGCTAATCCCCCCATAGGAGGAT
12839327 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
1 ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
12839392 TCCACTTGCTAATCCCCCCATAGGAGGAT
66 TCCACTTGCTAATCCCCCCATAGGAGGAT
12839421 CAGTTCCTCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (94 bp):
ATTCTTCCTCTCCTGAACAGCTAATGCATTAAGAAATACCTACAAAATAGCTAATTATTCATACC
TCCACTTGCTAATCCCCCCATAGGAGGAT
Found at i:12857935 original size:32 final size:32
Alignment explanation
Indices: 12857861--12857938 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
12857851 GCAATGTTTA
* * *
12857861 AATGTAAGACCATAGCTGGGCTATGGCATTTT
1 AATGTAAGACCATAACTGGGCTATGGCACTTG
12857893 AAT-TAAAAGACCATAACTGGG-TATGGCACCTTG
1 AATGT--AAGACCATAACTGGGCTATGGCA-CTTG
12857926 AATGTAAGACCAT
1 AATGTAAGACCAT
12857939 CGTTGGACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
31 1 0.03
32 18 0.46
33 19 0.49
34 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (32 bp):
AATGTAAGACCATAACTGGGCTATGGCACTTG
Found at i:12858007 original size:104 final size:100
Alignment explanation
Indices: 12857830--12858018 Score: 252
Period size: 104 Copynumber: 1.9 Consensus size: 100
12857820 AATTGACGGA
* * * * * *
12857830 TAAGACCATGGTTGGAACATGGCAATGTTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATCGTTGGAACATGGCAATGATAAAATGTAAGACCATAGCTAGGCTATGACATTCTAA
*
12857895 TTAAAAGACCATAACTGGGTATGGCACCTTGAATG
66 TGAAAAGACCATAACTGGGTATGGCACCTTGAATG
*
12857930 TAAGACCATCGTTGGACCATGGCAGTATAGATAAATATGTAAGACCATAGCTAGGCTATGACATT
1 TAAGACCATCGTTGGAACATGGCA--AT-GATAAA-ATGTAAGACCATAGCTAGGCTATGACATT
* *
12857995 CTGATGATAAGACCATAACTGGGT
62 CTAATGAAAAGACCATAACTGGGT
12858019 TATAGCACTA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
100 22 0.29
102 2 0.03
103 4 0.05
104 47 0.63
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (100 bp):
TAAGACCATCGTTGGAACATGGCAATGATAAAATGTAAGACCATAGCTAGGCTATGACATTCTAA
TGAAAAGACCATAACTGGGTATGGCACCTTGAATG
Found at i:12859720 original size:20 final size:20
Alignment explanation
Indices: 12859678--12859720 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12859668 TTTACATGCT
* *
12859678 AATTTGACATATTTTGTTCC
1 AATTTGACATAGTTTGGTCC
* *
12859698 AATTTGACGTAGTTTGGTGC
1 AATTTGACATAGTTTGGTCC
12859718 AAT
1 AAT
12859721 AGAAGAAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (20 bp):
AATTTGACATAGTTTGGTCC
Found at i:12869541 original size:57 final size:57
Alignment explanation
Indices: 12869452--12869620 Score: 216
Period size: 57 Copynumber: 3.0 Consensus size: 57
12869442 AAAATACAAA
* *
12869452 ATCTTAACTAA-ATTAGAATATCAATATTTTAGGTAACTAAT-TTCTTGAGAATCAGTT
1 ATCTTAACTAATA-TAGAATATCAATATTTTAGGTAACTAATCTTC-TAAGAATCAGCT
* * *
12869509 GTCTTAACTAATATAAAATATCAATATTTTAGGTAATTAATCTTCTAAGAATCAGCT
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAGCT
** * * *
12869566 ATCTTAACTTGTATAGAATATCATTATTTTAGGTAACTATTCTCCTAAGAATCAG
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAG
12869621 GTATATAGTG
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 93 0.96
58 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (57 bp):
ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTTCTAAGAATCAGCT
Found at i:12877996 original size:57 final size:56
Alignment explanation
Indices: 12877909--12878023 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 56
12877899 GACATGCAAA
* * *
12877909 ATCTTAACTATATAGAATATCAGTATTTTAGGTAATTAATTTCCTAAGAATCATCT
1 ATCTTAACTATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
*
12877965 ATCTTAACTAATATAGAATATCAGTATTTTAGGTAACTAATTTACTATGAATCAACT
1 ATCTTAACT-ATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
12878022 AT
1 AT
12878024 ATAGTGTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 9 0.17
57 45 0.83
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (56 bp):
ATCTTAACTATATAGAATATCAGTATTTTAGGTAACTAATTTACTAAGAATCAACT
Found at i:12884626 original size:23 final size:22
Alignment explanation
Indices: 12884583--12884633 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
12884573 AATTCCTTCA
* *
12884583 AATTAATTTTTATATATTTAAAT
1 AATTTATTTTTAAATATTT-AAT
12884606 AATTTATTTTTAAAT-TATTAAT
1 AATTTATTTTTAAATAT-TTAAT
12884628 AATTTA
1 AATTTA
12884634 GACAAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTATTTTTAAATATTTAAT
Found at i:12886414 original size:23 final size:20
Alignment explanation
Indices: 12886365--12886416 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
12886355 ATGAATACAC
*
12886365 CAATTTATAATTATATTAGA
1 CAATATATAATTATATTAGA
*
12886385 TAA-ATATAATTATTTATGTAGA
1 CAATATATAATTA--TAT-TAGA
12886407 CAATATATAA
1 CAATATATAA
12886417 ACATAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 3 0.12
22 6 0.24
23 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (20 bp):
CAATATATAATTATATTAGA
Found at i:12890246 original size:49 final size:50
Alignment explanation
Indices: 12890174--12890359 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
12890164 GTGAAGTTGC
*
12890174 TAGGTCACGTGTGTAGTACTATGTGCAAGCTACTACG-GTACCGAAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCG-AATGAA
* * * **
12890223 TAGGTCACATGTGTAGTACTATGTGCAGGCTATTATGCGTACCGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAAT-GAA
* * * * * *
12890274 TCGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAATGAA
* *
12890324 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 TA-GGTCACATGTGTAGTACTATGTGCAAGCTACTA
12890360 TGTGAACTGT
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 36 0.32
50 8 0.07
51 68 0.61
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAAGCTACTACGCGTACCGAATGAA
Found at i:12894064 original size:68 final size:68
Alignment explanation
Indices: 12893977--12894105 Score: 258
Period size: 68 Copynumber: 1.9 Consensus size: 68
12893967 AATTTACATC
12893977 TTTTTTATTCATATGCATGCATATTTATATAGGAATGAAATAAATCAACAATAATCTTGTTAACA
1 TTTTTTATTCATATGCATGCATATTTATATAGGAATGAAATAAATCAACAATAATCTTGTTAACA
12894042 GAA
66 GAA
12894045 TTTTTTATTCATATGCATGCATATTTATATAGGAATGAAATAAATCAACAATAATCTTGTT
1 TTTTTTATTCATATGCATGCATATTTATATAGGAATGAAATAAATCAACAATAATCTTGTT
12894106 GTATAAGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (68 bp):
TTTTTTATTCATATGCATGCATATTTATATAGGAATGAAATAAATCAACAATAATCTTGTTAACA
GAA
Found at i:12900047 original size:25 final size:26
Alignment explanation
Indices: 12899981--12900037 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
12899971 ATCCATCGAA
12899981 TTTTCCTTCTATTCAATCGGGATTTT
1 TTTTCCTTCTATTCAATCGGGATTTT
12900007 TTTTCCTTCTATTCAATCGGGATTTT
1 TTTTCCTTCTATTCAATCGGGATTTT
12900033 TTTTC
1 TTTTC
12900038 TTTTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (26 bp):
TTTTCCTTCTATTCAATCGGGATTTT
Found at i:12903366 original size:49 final size:49
Alignment explanation
Indices: 12903309--12903453 Score: 209
Period size: 49 Copynumber: 2.9 Consensus size: 49
12903299 TATTTTCTCA
* * *
12903309 ATGCCATAGTCCAACTATGGTCTTACACGTAATCACATATCACATACCG
1 ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
* * *
12903358 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTACTG
1 ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
*
12903407 ATGCCATAGCCCAGCTATGGCCTTACACGGAAATCACATAATCACAT
1 ATGCCATAGCCCAGCTATGGTCTTACAC-GAAATCACAT-ATCACAT
12903454 TTTCAATTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
49 71 0.83
50 9 0.10
51 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (49 bp):
ATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACATACCG
Found at i:12907315 original size:16 final size:17
Alignment explanation
Indices: 12907288--12907322 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12907278 AATAATTAGG
*
12907288 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
12907305 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
12907321 TT
1 TT
12907323 TAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:12908812 original size:12 final size:12
Alignment explanation
Indices: 12908795--12908819 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12908785 GCGAATCCAA
12908795 ATTAAAATAATT
1 ATTAAAATAATT
12908807 ATTAAAATAATT
1 ATTAAAATAATT
12908819 A
1 A
12908820 AATTACTAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAATAATT
Found at i:12912456 original size:6 final size:6
Alignment explanation
Indices: 12912445--12912470 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12912435 AGATGTAGAG
12912445 CTTCTA CTTCTA CTTCTA CTTCTA CT
1 CTTCTA CTTCTA CTTCTA CTTCTA CT
12912471 CCTAGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTCTA
Found at i:12929467 original size:24 final size:24
Alignment explanation
Indices: 12929440--12929490 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12929430 GACGATCTAA
12929440 AAGGGAAGGAAAACTAACGAAAGT
1 AAGGGAAGGAAAACTAACGAAAGT
12929464 AAGGGAAGGAAAACTAACGAAAGT
1 AAGGGAAGGAAAACTAACGAAAGT
12929488 AAG
1 AAG
12929491 CATATAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.29, T:0.08
Consensus pattern (24 bp):
AAGGGAAGGAAAACTAACGAAAGT
Found at i:12930541 original size:27 final size:26
Alignment explanation
Indices: 12930510--12930569 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
12930500 ATTATAAATC
12930510 AATAAAGT-ATACATACAAAAATTTTAA
1 AATAAA-TAATACATACAAAAA-TTTAA
* *
12930537 AATAAATAATATATACGAAAATTTAA
1 AATAAATAATACATACAAAAATTTAA
12930563 AATAAAT
1 AATAAAT
12930570 CAAAAATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
AATAAATAATACATACAAAAATTTAA
Found at i:12932754 original size:45 final size:45
Alignment explanation
Indices: 12932679--12932810 Score: 124
Period size: 45 Copynumber: 2.9 Consensus size: 45
12932669 ACTTGTAGCG
* * * *
12932679 TCAATTTGCTCCGCCACAACCTGA-AGGAGATAAGATTTGCT-ATCT
1 TCAATCTGCTCCGCTACAACTTCAGA-GAGATAAGATTTGCTGAT-T
* * * * *
12932724 TCAGTCTGCTCCGCTATAACTTCAGAGAGATAAGGTTTGGTGGTT
1 TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTGATT
* * *
12932769 TCAATCTGCTCCTCTGCAACTTCAGGGAGATAAGATTTGCTG
1 TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTG
12932811 TCTGTAGCTT
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
45 67 0.97
46 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (45 bp):
TCAATCTGCTCCGCTACAACTTCAGAGAGATAAGATTTGCTGATT
Found at i:12932997 original size:143 final size:141
Alignment explanation
Indices: 12932702--12933037 Score: 440
Period size: 143 Copynumber: 2.4 Consensus size: 141
12932692 CCACAACCTG
* * * * * *
12932702 AAGGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTATAACTTCAGAGAGATAAGGTTTGGTGG
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
* * * * * ** *
12932767 TTTCAATCTGCTCCTCTGCAACTTCAGGGAGATAAGATTTGCTGTCTGTAGCTTTAATTTGTTCC
66 CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATTAGCTAACTGTAGCTTTAATATGTTCC
*
12932832 ACTGCAACGCT
131 ACTGCAACGCC
* * *
12932843 AGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGATGTAACTTTAGGGAGATAAGG-CTGGTGG
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
*
12932907 CTTCAATCTGCTCCACTCCAACTTTAGGAAGATAAGATTCAGCATAACTTGTAGCTTTAATATGT
66 CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATT-AGC-TAAC-TGTAGCTTTAATATGT
12932972 TCCACTGCAACGCC
128 TCCACTGCAACGCC
* * *
12932986 AAGGAAATAAGATTCGCTGTCTTTAGTTTGCTCCGCTGCAACTTCAGGGAGA
1 AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGA
12933038 CTTCTGGAAG
Statistics
Matches: 167, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
140 40 0.24
141 51 0.31
142 2 0.01
143 74 0.44
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (141 bp):
AAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGGAGATAAGGTCTGGTGG
CTTCAATCTGCTCCACTCCAACTTCAGGAAGATAAGATTAGCTAACTGTAGCTTTAATATGTTCC
ACTGCAACGCC
Found at i:12939985 original size:27 final size:26
Alignment explanation
Indices: 12939954--12940015 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
12939944 ATTATAAATC
12939954 AATAAAGT-ATACATACAAAAATTTTAA
1 AATAAA-TAATACATACAAAAA-TTTAA
* * *
12939981 AATAAATAATATATACGAAAATTTGA
1 AATAAATAATACATACAAAAATTTAA
12940007 AATAAATAA
1 AATAAATAA
12940016 AAAATAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.45
27 17 0.55
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
AATAAATAATACATACAAAAATTTAA
Found at i:12948389 original size:25 final size:26
Alignment explanation
Indices: 12948360--12948409 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12948350 CCGTCAGAAA
*
12948360 ATACTCAAG-AAACAACTCGAAAAAC
1 ATACTCAAGAAAACAACTCAAAAAAC
12948385 ATACTCAAGAAAACAACTCAAAAAA
1 ATACTCAAGAAAACAACTCAAAAAA
12948410 TATCATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.60, C:0.22, G:0.06, T:0.12
Consensus pattern (26 bp):
ATACTCAAGAAAACAACTCAAAAAAC
Found at i:12948403 original size:13 final size:12
Alignment explanation
Indices: 12948362--12948409 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
12948352 GTCAGAAAAT
*
12948362 ACTCAAGAAACA
1 ACTCAAAAAACA
*
12948374 ACTCGAAAAACA
1 ACTCAAAAAACA
12948386 TACTCAAGAAAACA
1 -ACTCAA-AAAACA
12948400 ACTCAAAAAA
1 ACTCAAAAAA
12948410 TATCATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 14 0.45
13 11 0.35
14 6 0.19
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.10
Consensus pattern (12 bp):
ACTCAAAAAACA
Found at i:12956553 original size:11 final size:11
Alignment explanation
Indices: 12956534--12956575 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
12956524 CCTTCAAAAA
12956534 TTCTCTTAAGT
1 TTCTCTTAAGT
*
12956545 TTTTCTTAAGT
1 TTCTCTTAAGT
*
12956556 TCCTCTTAAGT
1 TTCTCTTAAGT
12956567 TTCTCTTAA
1 TTCTCTTAA
12956576 CTCCATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (11 bp):
TTCTCTTAAGT
Found at i:12956596 original size:13 final size:13
Alignment explanation
Indices: 12956580--12956614 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
12956570 TCTTAACTCC
12956580 ATTTTTTAAAATA
1 ATTTTTTAAAATA
12956593 A-TTTTTAAAATA
1 ATTTTTTAAAATA
12956605 ATTTTTTAAA
1 ATTTTTTAAA
12956615 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:12956609 original size:11 final size:12
Alignment explanation
Indices: 12956582--12956624 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
12956572 TTAACTCCAT
12956582 TTTTTAAAATAA
1 TTTTTAAAATAA
12956594 TTTTTAAAATAA
1 TTTTTAAAATAA
* *
12956606 TTTTTTAAAT-T
1 TTTTTAAAATAA
12956617 TTTTTAAA
1 TTTTTAAA
12956625 CTGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTAAAATAA
Found at i:12958428 original size:18 final size:18
Alignment explanation
Indices: 12958402--12958436 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12958392 AGGTGCGTTT
*
12958402 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
12958420 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
12958437 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:12958882 original size:44 final size:45
Alignment explanation
Indices: 12958833--12958919 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
12958823 ATATTTTGAA
*
12958833 TATTTTGATATTATTTTATGTAA-AAGAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAA-AATAGAAATTTATTTGAGT
*
12958877 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
12958920 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
44 32 0.82
45 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:12958921 original size:25 final size:25
Alignment explanation
Indices: 12958887--12959049 Score: 196
Period size: 25 Copynumber: 6.7 Consensus size: 25
12958877 TATTTTGATA
12958887 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
12958912 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* * *
12958937 CTATTTGATGTGATAAAAAAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
12958962 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
12958987 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
12959006 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
12959032 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
12959050 ATCCTAACCT
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 8 0.07
22 1 0.01
23 1 0.01
24 8 0.07
25 91 0.78
26 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:12959110 original size:29 final size:29
Alignment explanation
Indices: 12959065--12959886 Score: 1096
Period size: 29 Copynumber: 29.4 Consensus size: 29
12959055 AACCTAATTT
12959065 AACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
12959095 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* * ****
12959124 AACCCTAAACCCTAACTTAA--AAACCCTA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
* ** ** *
12959152 AACCTTAACTTTAAAAACCTTAACCTAATT--T
1 AACCCTAACCCT---AACC-TAATTTAATTAAA
*
12959183 TACCCTAAACCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
12959213 AAACCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959242 AACCCT-A----AACC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
* *
12959263 AACCCTAAACCT----TAA-CT--TTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959285 AACCCT-A-----ACCTAATTTAACCTT--A
1 AACCCTAACCCTAACCTAATTTAA--TTAAA
12959308 AACCCTAA--C----CTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
12959331 AACCCT-A--C---CCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959354 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959383 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959412 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959441 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959470 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959499 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959528 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959557 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959586 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959615 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959644 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959673 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959702 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959731 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959760 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959789 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12959818 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
12959847 AACCCTAAACCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
12959876 AATCCTAACCC
1 AACCCTAACCC
12959887 CTTAACTTAA
Statistics
Matches: 723, Mismatches: 29, Indels: 81
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.01
21 13 0.02
22 14 0.02
23 40 0.06
24 8 0.01
25 3 0.00
26 1 0.00
27 4 0.01
28 17 0.02
29 577 0.80
30 25 0.03
31 7 0.01
32 4 0.01
33 2 0.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:12959145 original size:21 final size:22
Alignment explanation
Indices: 12959119--12959292 Score: 101
Period size: 21 Copynumber: 7.6 Consensus size: 22
12959109 CCTAATTTAA
12959119 TTAAAAACCCTAAACCCTAAC-
1 TTAAAAACCCTAAACCCTAACT
*
12959140 TTAAAAACCCTAAACCTTAACT
1 TTAAAAACCCTAAACCCTAACT
* *
12959162 TTAAAAA-CCTTAA-CCTAATT
1 TTAAAAACCCTAAACCCTAACT
* *
12959182 TTACCCTAAACCCT-AA-CCTAATT
1 TTA---AAAACCCTAAACCCTAACT
*
12959205 TAATTAAAAAACCT-AACCCTAACCTAATT
1 T--T-AAAAACCCTAAACCCTAA-C----T
*
12959234 TAATTAAAAACCCTAAACCTTAAC-
1 T--T-AAAAACCCTAAACCCTAACT
*
12959258 TTAAAAACCCTAAACCTTAACT
1 TTAAAAACCCTAAACCCTAACT
12959280 TTAAAAACCCTAA
1 TTAAAAACCCTAA
12959293 CCTAATTTAA
Statistics
Matches: 127, Mismatches: 10, Indels: 31
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.06
21 44 0.35
22 21 0.17
23 21 0.17
24 9 0.07
25 1 0.01
26 1 0.01
29 15 0.12
30 7 0.06
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAAACCCTAAACCCTAACT
Found at i:12959188 original size:59 final size:58
Alignment explanation
Indices: 12959124--12959316 Score: 169
Period size: 59 Copynumber: 3.3 Consensus size: 58
12959114 TTTAATTAAA
12959124 AACCCTAAACCCTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCTTAACCTAATTT
1 AACCCTAAACCCTAACTTAAAAACCCTAAACCTTAACTTTAAAAACC-TAACCTAATTT
* * ***** ** ** *
12959183 TACCCTAAACCCTAACCTAATTTAATTAAAAAACC-TAACCCT---AACCTAATTTAATTAAA
1 AACCCTAAACCCTAACTTAA---AAACCCTAAACCTTAACTTTAAAAACCTAACCTAATT--T
*
12959242 AACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTT
1 AACCCTAAACCCTAACTTAAAAACCCTAAACCTTAACTTTAAAAA-CCTAACCTAATTT
*
12959301 AACCTTAAACCCTAAC
1 AACCCTAAACCCTAAC
12959317 CTAATTTAAT
Statistics
Matches: 97, Mismatches: 27, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
56 7 0.07
57 13 0.13
58 4 0.04
59 49 0.51
60 2 0.02
61 15 0.15
62 7 0.07
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (58 bp):
AACCCTAAACCCTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCTAACCTAATTT
Found at i:12959295 original size:21 final size:21
Alignment explanation
Indices: 12959233--12959292 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
12959223 CTAACCTAAT
12959233 TTAA-TTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
12959253 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
12959274 TTAACTTTAAAAACCCTAA
1 TTAAC-TTAAAAACCCTAA
12959293 CCTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.11
21 21 0.55
22 13 0.34
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:12959898 original size:21 final size:22
Alignment explanation
Indices: 12959871--12959927 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
12959861 CCTAATTTAA
12959871 TTAAAAATCCTAACCCCTTAAC-
1 TTAAAAA-CCTAACCCCTTAACT
12959893 TTAAAAACCTAA-CCCTTAACT
1 TTAAAAACCTAACCCCTTAACT
*
12959914 TTAAAACCCTAACC
1 TTAAAAACCTAACC
12959928 TAATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (22 bp):
TTAAAAACCTAACCCCTTAACT
Found at i:12959958 original size:23 final size:23
Alignment explanation
Indices: 12959916--12959959 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12959906 CCTTAACTTT
* * *
12959916 AAAACCCTAACCTAATTTAATTA
1 AAAACCCTAAACAAAGTTAATTA
12959939 AAAACCCTAAACAAAGTTAAT
1 AAAACCCTAAACAAAGTTAAT
12959960 AATTTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAACCCTAAACAAAGTTAATTA
Found at i:12960102 original size:116 final size:116
Alignment explanation
Indices: 12959953--12960308 Score: 653
Period size: 116 Copynumber: 3.1 Consensus size: 116
12959943 CCCTAAACAA
*
12959953 AGTTAATAATTTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAATT
1 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAATT
*
12960018 AATAATTTTATATAATTTGATGATTTTACTAACCATTAATACAATTTTTAG
66 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAG
12960069 AGTTAGA-AATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAAT
1 AGTTA-ATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAAT
12960133 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAG
65 TAATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAG
*
12960185 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATT
1 AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAATT
12960250 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTA-
66 AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAA-TTTTTAG
12960301 AGTTAATA
1 AGTTAATA
12960309 CAATTTATCA
Statistics
Matches: 234, Mismatches: 3, Indels: 6
0.96 0.01 0.02
Matches are distributed among these distances:
115 1 0.00
116 226 0.97
117 7 0.03
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (116 bp):
AGTTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGCTACTAACAATT
AATAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTAG
Found at i:12960325 original size:17 final size:17
Alignment explanation
Indices: 12960284--12960325 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
12960274 TTTACTAACC
* *
12960284 ATTAATACAATTTTTTA
1 ATTAATACAATTTATCA
12960301 AGTTAATACAATTTATCA
1 A-TTAATACAATTTATCA
12960319 ATTAATA
1 ATTAATA
12960326 ATTGCACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTAATACAATTTATCA
Found at i:12963572 original size:125 final size:125
Alignment explanation
Indices: 12963329--12963555 Score: 409
Period size: 125 Copynumber: 1.8 Consensus size: 125
12963319 CCCAAACATG
* *
12963329 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
*
12963394 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
12963454 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
* *
12963519 TAGAAGTGATTTTATACTATTTGATTAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
12963556 CTCGAAATTA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 97 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAATAATTATTTCTTCTGTGAC
Found at i:12974017 original size:7 final size:7
Alignment explanation
Indices: 12974005--12974037 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
12973995 AGAAGTGTCT
12974005 GTTAGTA
1 GTTAGTA
12974012 GTTAGTA
1 GTTAGTA
12974019 GTTAGTA
1 GTTAGTA
12974026 GTTAGTA
1 GTTAGTA
12974033 -TTAGT
1 GTTAGT
12974038 TGTGGTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (7 bp):
GTTAGTA
Found at i:12978159 original size:16 final size:16
Alignment explanation
Indices: 12978132--12978185 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
12978122 AGATTTACCT
*
12978132 ATTACACCTCTATTCC
1 ATTACACATCTATTCC
*
12978148 ATTACGCATCTATTCC
1 ATTACACATCTATTCC
* *
12978164 ATTACACCTCTATTTC
1 ATTACACATCTATTCC
12978180 ATTACA
1 ATTACA
12978186 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACATCTATTCC
Found at i:12979300 original size:19 final size:20
Alignment explanation
Indices: 12979278--12979315 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12979268 ATTAATGATT
12979278 TAAATT-TGATTA-AATGTTA
1 TAAATTGTG-TTAGAATGTTA
12979297 TAAATTGTGTTAGAATGTT
1 TAAATTGTGTTAGAATGTT
12979316 TCGGTAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (20 bp):
TAAATTGTGTTAGAATGTTA
Found at i:12988104 original size:24 final size:24
Alignment explanation
Indices: 12988068--12988157 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
12988058 CTCTGAAACA
*
12988068 ATGGAAAGGTTGAAAAGGATAACC
1 ATGGAAAGATTGAAAAGGATAACC
*
12988092 ATGGAAAGATTGAAAAGG-TTACC
1 ATGGAAAGATTGAAAAGGATAACC
* * *
12988115 GATGAAAAGGTCGAAAAGGATAACC
1 -ATGGAAAGATTGAAAAGGATAACC
*
12988140 ATGGAAAGATTGGAAAGG
1 ATGGAAAGATTGAAAAGG
12988158 TTACCAATGA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 4 0.07
24 46 0.85
25 4 0.07
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.17
Consensus pattern (24 bp):
ATGGAAAGATTGAAAAGGATAACC
Found at i:12988171 original size:24 final size:24
Alignment explanation
Indices: 12988079--12988197 Score: 98
Period size: 24 Copynumber: 5.0 Consensus size: 24
12988069 TGGAAAGGTT
* * *
12988079 GAAAAGGATAACC-ATGGAAAGATT
1 GAAAAGG-TTACCAATGAAAAGATC
* *
12988103 GAAAAGGTTACCGATGAAAAGGTC
1 GAAAAGGTTACCAATGAAAAGATC
* * *
12988127 GAAAAGGATAACC-ATGGAAAGATT
1 GAAAAGG-TTACCAATGAAAAGATC
* *
12988151 GGAAAGGTTACCAATGAAAAGGTC
1 GAAAAGGTTACCAATGAAAAGATC
* *
12988175 GAAAATGATACCAATGAAAAGAT
1 GAAAAGGTTACCAATGAAAAGAT
12988198 AAAAAAGGAT
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.11
24 63 0.84
25 4 0.05
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (24 bp):
GAAAAGGTTACCAATGAAAAGATC
Found at i:12988205 original size:48 final size:48
Alignment explanation
Indices: 12988066--12988197 Score: 194
Period size: 48 Copynumber: 2.8 Consensus size: 48
12988056 ATCTCTGAAA
* *
12988066 CAATGGAAAGGTTGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
1 CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
* *
12988114 CGATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGGAAAGGTTAC
1 CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
* *
12988162 CAATGAAAAGGTCGAAAATGAT-ACCAATGAAAAGAT
1 CAATGAAAAGGTCGAAAAGGATAACC-ATGGAAAGAT
12988198 AAAAAAGGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
47 3 0.04
48 73 0.96
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (48 bp):
CAATGAAAAGGTCGAAAAGGATAACCATGGAAAGATTGAAAAGGTTAC
Found at i:12991669 original size:20 final size:18
Alignment explanation
Indices: 12991640--12991676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
12991630 TTGTGTGTTT
12991640 TCTTTTCATTTTAATTTTA
1 TCTTTTCATTTT-ATTTTA
12991659 TCTTGTTCATTTTATTTT
1 TCTT-TTCATTTTATTTT
12991677 CTATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTCATTTTATTTTA
Found at i:12996720 original size:54 final size:54
Alignment explanation
Indices: 12996633--12996822 Score: 231
Period size: 54 Copynumber: 3.5 Consensus size: 54
12996623 TCGTTAACTG
* *
12996633 TACCGAAATACCCTCGATAGGTAAAATTATCGAAATACTCTCGATGGGTAAAAT
1 TACCAAAATACCCTCGATGGGTAAAATTATCGAAATACTCTCGATGGGTAAAAT
*
12996687 TACCAAAATACCCTCGATGGGTAAAATTATCGAAATACTCTCGATGGATAAAAT
1 TACCAAAATACCCTCGATGGGTAAAATTATCGAAATACTCTCGATGGGTAAAAT
* * * * *
12996741 TA-CAGAAATACTCTCGATGGATAAAATTATCGAAATAC-CCCTAATGGGTAAATT
1 TACCA-AAATACCCTCGATGGGTAAAATTATCGAAATACTCTC-GATGGGTAAAAT
* * * *
12996795 TACTATAATACCCCCGTTAGGGTAAAAT
1 TACCAAAATACCCTCGAT-GGGTAAAAT
12996823 GACTGCTAGG
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 4 0.03
54 104 0.89
55 9 0.08
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (54 bp):
TACCAAAATACCCTCGATGGGTAAAATTATCGAAATACTCTCGATGGGTAAAAT
Found at i:12996792 original size:27 final size:27
Alignment explanation
Indices: 12996636--12996778 Score: 207
Period size: 27 Copynumber: 5.3 Consensus size: 27
12996626 TTAACTGTAC
* *
12996636 CGAAATACCCTCGATAGGTAAAATTAT
1 CGAAATACTCTCGATGGGTAAAATTAT
*
12996663 CGAAATACTCTCGATGGGTAAAATTAC
1 CGAAATACTCTCGATGGGTAAAATTAT
* *
12996690 CAAAATACCCTCGATGGGTAAAATTAT
1 CGAAATACTCTCGATGGGTAAAATTAT
*
12996717 CGAAATACTCTCGATGGATAAAATTA-
1 CGAAATACTCTCGATGGGTAAAATTAT
*
12996743 CAGAAATACTCTCGATGGATAAAATTAT
1 C-GAAATACTCTCGATGGGTAAAATTAT
12996771 CGAAATAC
1 CGAAATAC
12996779 CCCTAATGGG
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
CGAAATACTCTCGATGGGTAAAATTAT
Found at i:12996976 original size:27 final size:27
Alignment explanation
Indices: 12996946--12996997 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12996936 AGTACTATTT
12996946 CTGGTGGCTCTGCCACA-ATTACTGTTA
1 CTGGTGGCTCTGCCACATA-TACTGTTA
*
12996973 CTGGTGGCTTTGCCACATATACTGT
1 CTGGTGGCTCTGCCACATATACTGT
12996998 GCTGGCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATACTGTTA
Found at i:13007327 original size:40 final size:40
Alignment explanation
Indices: 13007165--13007325 Score: 214
Period size: 40 Copynumber: 4.0 Consensus size: 40
13007155 CACACCCGAA
** * *
13007165 AAAAGCTCATAAAAGTTGGTCCAACCGAAACACGCCAAAC
1 AAAAGCTCATAAGTGCTGATCCAACCGAAACACGCCAAAC
* *
13007205 AAAAGCTCATAAGTGTTGATCCAACCAAAACACGCCAAAC
1 AAAAGCTCATAAGTGCTGATCCAACCGAAACACGCCAAAC
* *
13007245 AAAAGCTCATAAGTTCTGATCTAACCGAAACACGCCAAAC
1 AAAAGCTCATAAGTGCTGATCCAACCGAAACACGCCAAAC
* * * *
13007285 AGAAGCTTATAAGAGCTGATCCAACTGAAACACGCCAAAC
1 AAAAGCTCATAAGTGCTGATCCAACCGAAACACGCCAAAC
13007325 A
1 A
13007326 GAGAGTATAA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.44, C:0.27, G:0.14, T:0.15
Consensus pattern (40 bp):
AAAAGCTCATAAGTGCTGATCCAACCGAAACACGCCAAAC
Found at i:13014453 original size:28 final size:28
Alignment explanation
Indices: 13014390--13014515 Score: 191
Period size: 28 Copynumber: 4.5 Consensus size: 28
13014380 ATATTAAGTC
*
13014390 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
13014417 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
13014445 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
13014473 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
13014502 CGCACACTTAGTGC
1 CGCACACTTAGTGC
13014516 CAATCTCATG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.24
28 51 0.55
29 19 0.21
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13026381 original size:23 final size:21
Alignment explanation
Indices: 13026347--13026398 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
13026337 AATACAAAAA
* *
13026347 TAAAAAACTAAAACTATTAGGTT
1 TAAAAAAATAAAAATATTA--TT
*
13026370 TAAAAAAATAAAAATCTTATT
1 TAAAAAAATAAAAATATTATT
13026391 TAAAAAAA
1 TAAAAAAA
13026399 AGAAGTTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
23 16 0.62
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAAAAATAAAAATATTATT
Found at i:13030242 original size:22 final size:22
Alignment explanation
Indices: 13030217--13030260 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13030207 TACTCAAGGT
13030217 ATGATCATATGCAATTTTACCA
1 ATGATCATATGCAATTTTACCA
*
13030239 ATGATCATATGCGATTTTACCA
1 ATGATCATATGCAATTTTACCA
13030261 GGTGACACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
ATGATCATATGCAATTTTACCA
Found at i:13030745 original size:21 final size:21
Alignment explanation
Indices: 13030721--13030762 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13030711 AAAATCATGG
*
13030721 CTACGAACTAAATTACAAACA
1 CTACCAACTAAATTACAAACA
*
13030742 CTACCAAGTAAATTACAAACA
1 CTACCAACTAAATTACAAACA
13030763 TGCATGGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (21 bp):
CTACCAACTAAATTACAAACA
Found at i:13030870 original size:138 final size:138
Alignment explanation
Indices: 13030615--13030891 Score: 482
Period size: 138 Copynumber: 2.0 Consensus size: 138
13030605 GGTTTACATC
* *
13030615 ATTATAAACATGCATGGGTCCTCCCACAAACCAGTTACCAAAATAAGAAACCATGAAATAGTTAT
1 ATTACAAACATGCATGGGTCCTCCCACAAACCAATTACCAAAATAAGAAACCATGAAATAGTTAT
13030680 GCTTGAAAAGCTCCAAAACTAGTCATCCAAGAAAATCATGGCTACGAACTAAATTACAAACACTA
66 GCTTGAAAAGCTCCAAAACTAGTCATCCAAGAAAATCATGGCTACGAACTAAATTACAAACACTA
13030745 CCAAGTAA
131 CCAAGTAA
* * *
13030753 ATTACAAACATGCATGGGTCCTCCCTCAAACCAATTAGCAAAATAAGAAACTATGAAATAGTTAT
1 ATTACAAACATGCATGGGTCCTCCCACAAACCAATTACCAAAATAAGAAACCATGAAATAGTTAT
* *
13030818 GCTTGAAAAGCTCCAACACTAGTCATCCAAGAAAATCATGGCTACGAGCTAAATTACAAACACTA
66 GCTTGAAAAGCTCCAAAACTAGTCATCCAAGAAAATCATGGCTACGAACTAAATTACAAACACTA
*
13030883 CTAAGTAA
131 CCAAGTAA
13030891 A
1 A
13030892 AGAAGCAGTG
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.22
Consensus pattern (138 bp):
ATTACAAACATGCATGGGTCCTCCCACAAACCAATTACCAAAATAAGAAACCATGAAATAGTTAT
GCTTGAAAAGCTCCAAAACTAGTCATCCAAGAAAATCATGGCTACGAACTAAATTACAAACACTA
CCAAGTAA
Found at i:13038092 original size:34 final size:36
Alignment explanation
Indices: 13038010--13038100 Score: 100
Period size: 34 Copynumber: 2.6 Consensus size: 36
13038000 CTGTACAAAA
*
13038010 GTGCAAACTATGTTTGCAAGTGAAAGCCTGTTCTGT
1 GTGCAAACTATGTTCGCAAGTGAAAGCCTGTTCTGT
* * * * *
13038046 ATG-AAA-TGTGTTCACAAGTGGAAGCTTGTT-T-T
1 GTGCAAACTATGTTCGCAAGTGAAAGCCTGTTCTGT
13038078 GTGCAAACTATGTTCGCAAGTGA
1 GTGCAAACTATGTTCGCAAGTGA
13038101 GTTTGGTAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
32 3 0.07
33 4 0.09
34 31 0.72
35 3 0.07
36 2 0.05
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (36 bp):
GTGCAAACTATGTTCGCAAGTGAAAGCCTGTTCTGT
Found at i:13040562 original size:40 final size:40
Alignment explanation
Indices: 13040461--13040568 Score: 189
Period size: 40 Copynumber: 2.7 Consensus size: 40
13040451 GCAAACACAT
* *
13040461 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
13040501 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
13040541 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
13040569 TCCAATGCTC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:13049051 original size:28 final size:28
Alignment explanation
Indices: 13048939--13049062 Score: 106
Period size: 28 Copynumber: 4.5 Consensus size: 28
13048929 CGTGTTTCAA
* * * *
13048939 GCCACACAGGTTTCCATTT-CATAGATC
1 GCCACAAAGGCTTCCCTTTCCATAGATT
* * * *
13048966 CCCATAAATGCTTCCCTTTCCATAGATC
1 GCCACAAAGGCTTCCCTTTCCATAGATT
* *
13048994 GCCACAAAGGCTTCCCTTTCTATAGGTT
1 GCCACAAAGGCTTCCCTTTCCATAGATT
* * * *
13049022 GCAACAAAGGTTTCCCTTACCATAAATT
1 GCCACAAAGGCTTCCCTTTCCATAGATT
*
13049050 GCCACAAAAGCTT
1 GCCACAAAGGCTT
13049063 TCCTATTCTT
Statistics
Matches: 75, Mismatches: 21, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
27 13 0.17
28 62 0.83
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.29
Consensus pattern (28 bp):
GCCACAAAGGCTTCCCTTTCCATAGATT
Found at i:13053082 original size:7 final size:7
Alignment explanation
Indices: 13053070--13053094 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13053060 CTTTCATATT
13053070 ATATAAC
1 ATATAAC
13053077 ATATAAC
1 ATATAAC
13053084 ATATAAC
1 ATATAAC
13053091 ATAT
1 ATAT
13053095 CCCATTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (7 bp):
ATATAAC
Found at i:13056022 original size:3 final size:3
Alignment explanation
Indices: 13056014--13056042 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13056004 GGAGACTGCA
13056014 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13056043 AGAAATTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13061806 original size:22 final size:21
Alignment explanation
Indices: 13061766--13061807 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
13061756 AATTTATGAT
**
13061766 AATAAATTTATAATTTTAATG
1 AATAAATTTATAAGATTAATG
13061787 AATATAATTTATAAGATTAAT
1 AATA-AATTTATAAGATTAAT
13061808 ATTAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAAATTTATAAGATTAATG
Found at i:13066457 original size:26 final size:28
Alignment explanation
Indices: 13066407--13066462 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 28
13066397 TATAGTTTTT
13066407 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
13066435 ATAAT-ATTATAAA-GTTATTATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
13066461 AT
1 AT
13066463 CAAATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 14 0.52
27 8 0.30
28 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:13066657 original size:44 final size:44
Alignment explanation
Indices: 13066594--13066683 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
13066584 GTTTTTGATA
*
13066594 ATTTTTACGTTTTTGAGATCGTTGCTTCGTGTTCTTCAAAACCT
1 ATTTTTACGTTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCT
13066638 ATTTTTACGTTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCT
1 ATTTTTACGTTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCT
13066682 AT
1 AT
13066684 GCTTGAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (44 bp):
ATTTTTACGTTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCT
Found at i:13066695 original size:44 final size:44
Alignment explanation
Indices: 13066603--13066695 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
13066593 AATTTTTACG
* * * *
13066603 TTTTTGAGATCGTTGCTTCGTGTTCTTCAAAACCTATTTTTACG
1 TTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCTATCTTGACA
13066647 TTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCTATGCTTGA-A
1 TTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCTAT-CTTGACA
13066691 TTTTT
1 TTTTT
13066696 TATTTTGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.93
45 3 0.07
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.48
Consensus pattern (44 bp):
TTTTTGAGATCATTGCTTCGTGTTCTTCAAAACCTATCTTGACA
Found at i:13073483 original size:50 final size:50
Alignment explanation
Indices: 13073359--13073488 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 50
13073349 ATAATGGTCA
* * * * * *
13073359 CACATGT-AGTACTATGTGTAGGCTACTATGTGTACTGAAAGGCTTTGGT
1 CACATGTGAGTACTATGTGAAGGCTACTACGTGAACCGAAAGACTTTGAT
*
13073408 CACATGTGTAGTACTATGT-ACAGGCTACTACGTGAACCGAAA-ATTTTGAT
1 CACATGTG-AGTACTATGTGA-AGGCTACTACGTGAACCGAAAGACTTTGAT
*
13073458 CACATGTGGAGTACTATATGAAGGCTACTAC
1 CACATGT-GAGTACTATGTGAAGGCTACTAC
13073489 ATGTATCGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
49 7 0.10
50 31 0.46
51 30 0.44
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (50 bp):
CACATGTGAGTACTATGTGAAGGCTACTACGTGAACCGAAAGACTTTGAT
Found at i:13077100 original size:28 final size:28
Alignment explanation
Indices: 13077054--13077110 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
13077044 TATAGTTTTT
13077054 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
*
13077082 ATAATATATTATAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
13077110 A
1 A
13077111 ACAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:13077118 original size:28 final size:29
Alignment explanation
Indices: 13077060--13077118 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
13077050 TTTTATAATA
*
13077060 ATTATAAAGGTTATAATAATAAATAATAT
1 ATTATAAAGGTTATAATAATAAATAAAAT
*
13077089 ATTATAAA-GTTATTATAATAAA-ACAAAT
1 ATTATAAAGGTTATAATAATAAATA-AAAT
13077117 AT
1 AT
13077119 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 18 0.67
29 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTATAAAGGTTATAATAATAAATAAAAT
Found at i:13078063 original size:44 final size:43
Alignment explanation
Indices: 13077999--13078116 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 43
13077989 GTGTGTTATC
* *
13077999 ATGTAAGACCACGTCTGGGACGTTGGCATTGATTTGTAATTTAC
1 ATGTAAGACCACGTCTGGGACGTTGGCATTGATATGTAA-TTAA
* * * *
13078043 GTGTAAGACCATGTCTGGGACAG-TGGCATCGATATGTGATTAA
1 ATGTAAGACCACGTCTGGGAC-GTTGGCATTGATATGTAATTAA
*
13078086 ATGTAAGACCACGTCTGGGGCGTTGGCATTG
1 ATGTAAGACCACGTCTGGGACGTTGGCATTG
13078117 TACGAGCTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.02
43 28 0.45
44 32 0.52
45 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (43 bp):
ATGTAAGACCACGTCTGGGACGTTGGCATTGATATGTAATTAA
Found at i:13081370 original size:21 final size:21
Alignment explanation
Indices: 13081344--13081403 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
13081334 TTATCGTTTT
13081344 TCTTTTCTTTCTCTTTTTCAA
1 TCTTTTCTTTCTCTTTTTCAA
*
13081365 TCTTTT-TTT-TC-TTTT-AC
1 TCTTTTCTTTCTCTTTTTCAA
*
13081382 T-TTTTCTTTCTTTTCTTTCAA
1 TCTTTTCTTTCTCTT-TTTCAA
13081403 T
1 T
13081404 TTCAATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
16 4 0.13
17 5 0.16
18 5 0.16
19 3 0.10
20 6 0.19
21 8 0.26
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (21 bp):
TCTTTTCTTTCTCTTTTTCAA
Found at i:13081372 original size:37 final size:38
Alignment explanation
Indices: 13081331--13081403 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
13081321 TTTTCCTTTC
*
13081331 TTTTTATCGTTTTTC-TTTTCTTTCTCTT-TTTCAATCT
1 TTTTTATC-TTTTACTTTTTCTTTCTCTTCTTTCAATCT
* *
13081368 TTTTTTTCTTTTACTTTTTCTTTCTTTTCTTTCAAT
1 TTTTTATCTTTTACTTTTTCTTTCTCTTCTTTCAAT
13081404 TTCAATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 19 0.61
38 7 0.23
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (38 bp):
TTTTTATCTTTTACTTTTTCTTTCTCTTCTTTCAATCT
Found at i:13081386 original size:16 final size:15
Alignment explanation
Indices: 13081342--13081399 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
13081332 TTTTATCGTT
*
13081342 TTTCTTTTCTTTCTC
1 TTTCTTTTCTTTTTC
*
13081357 TTT-TTCAATCTTTTT-
1 TTTCTT--TTCTTTTTC
13081372 TTTCTTTTACTTTTTC
1 TTTCTTTT-CTTTTTC
13081388 TTTCTTTTCTTT
1 TTTCTTTTCTTT
13081400 CAATTTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 3 0.09
15 16 0.46
16 16 0.46
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTTTTTC
Found at i:13081400 original size:25 final size:25
Alignment explanation
Indices: 13081341--13081400 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
13081331 TTTTTATCGT
13081341 TTTTCTTTTCTTTCTCTTTTTCAATC
1 TTTTC-TTTCTTTCTCTTTTTCAATC
* **
13081367 TTTTTTTTCTTT-TACTTTTTCTTTC
1 TTTTCTTTCTTTCT-CTTTTTCAATC
13081392 TTTTCTTTC
1 TTTTCTTTC
13081401 AATTTCAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.03
25 24 0.83
26 4 0.14
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCTTTCTTTCTCTTTTTCAATC
Found at i:13083315 original size:96 final size:96
Alignment explanation
Indices: 13083146--13083336 Score: 328
Period size: 96 Copynumber: 2.0 Consensus size: 96
13083136 TACTTGCTTG
13083146 AATAGTCTCACTTTCTCTTGCCTTTTTCCGCTCACTCTGCCTCTCTAAGTTCTCAAAAGAACTAG
1 AATAGTCTCACTTTCTCTTGCCTTTTTCCGCTCACTCTGCCTCTCTAAGTTCTCAAAAGAACTAG
*
13083211 TTACACTTAAAAGCATTCATTGTGGGTCGAC
66 TTACACTTAAAAGCAGTCATTGTGGGTCGAC
* *
13083242 AATAGTCTCACTTTCTCTTGCCTTTTTCCGCTCACTCTGCCTCTTTAAGTTCTCAAAAGGACTAG
1 AATAGTCTCACTTTCTCTTGCCTTTTTCCGCTCACTCTGCCTCTCTAAGTTCTCAAAAGAACTAG
* * *
13083307 TTAGACTTAGAAGCAGTCGTTGTGGGTCGA
66 TTACACTTAAAAGCAGTCATTGTGGGTCGA
13083337 TTTGCAAAGC
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.36
Consensus pattern (96 bp):
AATAGTCTCACTTTCTCTTGCCTTTTTCCGCTCACTCTGCCTCTCTAAGTTCTCAAAAGAACTAG
TTACACTTAAAAGCAGTCATTGTGGGTCGAC
Found at i:13084667 original size:22 final size:23
Alignment explanation
Indices: 13084655--13084697 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13084645 ACTTAATAAG
13084655 CTTAA-TTAATAAACTGTAAACA
1 CTTAATTTAATAAACTGTAAACA
13084677 CTTAATTTAATAAACTGTAAA
1 CTTAATTTAATAAACTGTAAA
13084698 TAAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (23 bp):
CTTAATTTAATAAACTGTAAACA
Found at i:13086675 original size:32 final size:32
Alignment explanation
Indices: 13086639--13086702 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
13086629 TACCAGTTTC
13086639 CTCTTGCACACAAAAATATCACCATAAACATG
1 CTCTTGCACACAAAAATATCACCATAAACATG
13086671 CTCTTGCACACAAAAATATCACCATAAACATG
1 CTCTTGCACACAAAAATATCACCATAAACATG
13086703 TTTTGTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (32 bp):
CTCTTGCACACAAAAATATCACCATAAACATG
Found at i:13088187 original size:17 final size:18
Alignment explanation
Indices: 13088159--13088192 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13088149 TGAATAAAAT
13088159 AATAATAATATTTTTTTG
1 AATAATAATATTTTTTTG
13088177 AATAA-AATATTTTTTT
1 AATAATAATATTTTTTT
13088193 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AATAATAATATTTTTTTG
Found at i:13088657 original size:19 final size:19
Alignment explanation
Indices: 13088633--13088866 Score: 123
Period size: 19 Copynumber: 12.2 Consensus size: 19
13088623 TTTGGATTAG
*
13088633 AATTTTGTATGAATATTCT
1 AATTTTGTATGAATATTGT
13088652 AATTTTTTTTGTATGAATATTGT
1 AA----TTTTGTATGAATATTGT
*
13088675 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
13088694 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
13088717 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
*
13088737 -ATTTTGCATGAATATTGT
1 AATTTTGTATGAATATTGT
*
13088755 AATTTTGTGTGAATATTGT
1 AATTTTGTATGAATATTGT
*
13088774 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* * *
13088788 AATATTG--T-AATTTTAT
1 AATTTTGTATGAATATTGT
* *
13088804 AATTTTATATGAATATTGC
1 AATTTTGTATGAATATTGT
13088823 AATTTTTTTGTATGAATATTGT
1 AA---TTTTGTATGAATATTGT
13088845 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
13088864 AAT
1 AAT
13088867 GTCGGGATAT
Statistics
Matches: 166, Mismatches: 23, Indels: 52
0.69 0.10 0.22
Matches are distributed among these distances:
13 1 0.01
14 6 0.04
15 3 0.02
16 7 0.04
17 4 0.02
18 8 0.05
19 74 0.45
20 14 0.08
21 1 0.01
22 22 0.13
23 22 0.13
24 3 0.02
25 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:13088661 original size:23 final size:23
Alignment explanation
Indices: 13088635--13088682 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
13088625 TGGATTAGAA
13088635 TTTTGTATGAATATTCTAATTTT
1 TTTTGTATGAATATTCTAATTTT
*
13088658 TTTTGTATGAATATTGTAATTTT
1 TTTTGTATGAATATTCTAATTTT
13088681 TT
1 TT
13088683 ATGAATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.62
Consensus pattern (23 bp):
TTTTGTATGAATATTCTAATTTT
Found at i:13088730 original size:103 final size:100
Alignment explanation
Indices: 13088616--13088799 Score: 264
Period size: 103 Copynumber: 1.8 Consensus size: 100
13088606 ATATTTAGTG
*
13088616 TTTATAGTTTGGATTAGAATTTTGTATGAATATTCTAATTTTTTTTGTATGAATATTGTAA-TTT
1 TTTATAGTTTGGATTAGAATTTTGCATGAATATTCTAA----TTTTGTATGAATATTGTAATTTT
13088680 TT-TATGAATATTGTAATTATTTTATAATTAAATTTGTA
62 TTGTATGAATATTGTAATTATTTTATAATTAAATTTGTA
* * *
13088718 TTTATAGTTTTGGATTAGTATTTTGCATGAATATTGTAATTTTGTGTGAATATTGTAATTTTTTT
1 TTTATAG-TTTGGATTAGAATTTTGCATGAATATTCTAATTTTGTATGAATATTGTAA-TTTTTT
13088783 GTATGAATATTGTAATT
64 GTATGAATATTGTAATT
13088800 TTATAATTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
99 18 0.24
101 5 0.07
102 23 0.31
103 28 0.38
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.55
Consensus pattern (100 bp):
TTTATAGTTTGGATTAGAATTTTGCATGAATATTCTAATTTTGTATGAATATTGTAATTTTTTGT
ATGAATATTGTAATTATTTTATAATTAAATTTGTA
Found at i:13088789 original size:41 final size:41
Alignment explanation
Indices: 13088738--13088866 Score: 150
Period size: 49 Copynumber: 3.0 Consensus size: 41
13088728 TGGATTAGTA
* *
13088738 TTTTGCATGAATATTGTAATTTTGTGTGAATATTGTAATTT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTT
* *
13088779 TTTTGTATGAATATTGTAATTTTATAATTTTATATGAATATTGCAATTT
1 TTTTGTATGAATATTG--------TAATTTTGTATGAATATTGTAATTT
13088828 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAAT
13088867 GTCGGGATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
41 36 0.49
49 38 0.51
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (41 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTT
Found at i:13088807 original size:49 final size:49
Alignment explanation
Indices: 13088754--13088850 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
13088744 ATGAATATTG
* * *
13088754 TAATTTTGTGTGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTA
1 TAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTA
13088803 TAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTT
1 TAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTT
13088851 GTATGAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (49 bp):
TAATTTTATATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTA
Found at i:13088815 original size:27 final size:24
Alignment explanation
Indices: 13088757--13088850 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 24
13088747 AATATTGTAA
*
13088757 TTTTGTGTGAATATTGTAA--TTT
1 TTTTGTATGAATATTGTAATTTTT
13088779 TTTTGTATGAATATTGTAATTTTAT
1 TTTTGTATGAATATTGTAATTTT-T
* *
13088804 AATTTTATATGAATATTGCAA--TTT
1 --TTTTGTATGAATATTGTAATTTTT
13088828 TTTTGTATGAATATTGTAATTTT
1 TTTTGTATGAATATTGTAATTTT
13088851 GTATGAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
22 35 0.58
24 5 0.08
25 3 0.05
27 17 0.28
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (24 bp):
TTTTGTATGAATATTGTAATTTTT
Found at i:13088832 original size:103 final size:99
Alignment explanation
Indices: 13088619--13088807 Score: 233
Period size: 99 Copynumber: 1.9 Consensus size: 99
13088609 TTTAGTGTTT
*
13088619 ATAG-TTTGGATTAGAATTTTGTATGAATATTCTAATTTTTTTTGTATGAATATTGTAATTTTTT
1 ATAGTTTTGGATTAGAATTTTGCATGAATATTCTAA---TTTTTGTATGAATATTGTAATTTTTT
* *
13088683 ATGAATATTGTAATTATTTTATAATTAAATTTGTATTT
63 ATGAATATTGTAA-TATTTTATAATTAAATATGTATTA
* * *
13088721 ATAGTTTTGGATTAGTATTTTGCATGAATATTGTAA-TTTTGTGTGAATATTGTAATTTTTTTGT
1 ATAGTTTTGGATTAGAATTTTGCATGAATATTCTAATTTTTGTATGAATATTGTAA--TTTTT-T
13088785 ATGAATATTGT-A-ATTTTATAATT
63 ATGAATATTGTAATATTTTATAATT
13088808 TTATATGAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
99 29 0.37
101 6 0.08
102 16 0.20
103 28 0.35
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (99 bp):
ATAGTTTTGGATTAGAATTTTGCATGAATATTCTAATTTTTGTATGAATATTGTAATTTTTTATG
AATATTGTAATATTTTATAATTAAATATGTATTA
Found at i:13088988 original size:60 final size:60
Alignment explanation
Indices: 13088907--13089028 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
13088897 TGTATGAATA
* * * * *
13088907 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
*
13088967 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
13089027 TT
1 TT
13089029 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:13089113 original size:37 final size:37
Alignment explanation
Indices: 13089062--13089142 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
13089052 CATATAAAGT
13089062 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGTTTAA
13089100 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
13089137 TTATAA
1 TTATAA
13089143 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 39 0.91
38 4 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
Found at i:13089336 original size:122 final size:122
Alignment explanation
Indices: 13089194--13089440 Score: 413
Period size: 122 Copynumber: 2.0 Consensus size: 122
13089184 TTTTATATAA
13089194 TGTAACTTTTATAAAATTTAATTTAATTTGATTTTGTATTTATTTAACAGTAATTATTGATTTTT
1 TGTAACTTTTATAAAATTTAATTTAATTTGATTTTGTATTTATTTAACAGTAATTATTGATTTTT
*
13089259 AAAAACAAATTAACTGAATTCATTTTTTTGATTGCAGATTTGCAGGATCAATAAAAC
66 AAAAACAAATTAACTGAATTCATTTTTTTGATTGCAGATTTGCAAGATCAATAAAAC
* * *
13089316 TGTAACTTTTATATAATTTAATTTTATTTGATTTTGTATTTATTTAACAGTATTTATTGATTTTT
1 TGTAACTTTTATAAAATTTAATTTAATTTGATTTTGTATTTATTTAACAGTAATTATTGATTTTT
** * * *
13089381 TGAAACAAATTAATTGAATTTATTTTTTTGATTGCATATTTGCAAGATCAATAAAAC
66 AAAAACAAATTAACTGAATTCATTTTTTTGATTGCAGATTTGCAAGATCAATAAAAC
13089438 TGT
1 TGT
13089441 TTTATTGAAT
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (122 bp):
TGTAACTTTTATAAAATTTAATTTAATTTGATTTTGTATTTATTTAACAGTAATTATTGATTTTT
AAAAACAAATTAACTGAATTCATTTTTTTGATTGCAGATTTGCAAGATCAATAAAAC
Found at i:13089645 original size:37 final size:38
Alignment explanation
Indices: 13089604--13089684 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 38
13089594 AAAAAGTCAA
13089604 TTATAATTAAACTTTTAATAAAATAATTTTTAA-TTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
*
13089641 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
13089679 TTATAA
1 TTATAA
13089685 ACTTTATATG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 32 0.76
38 10 0.24
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATAATTTTTAATTTTT
Found at i:13089794 original size:60 final size:60
Alignment explanation
Indices: 13089718--13089839 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
13089708 ATACTAAACT
* * * * *
13089718 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
13089778 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
13089838 AA
1 AA
13089840 TATTCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:13089867 original size:8 final size:8
Alignment explanation
Indices: 13089854--13089985 Score: 53
Period size: 8 Copynumber: 16.4 Consensus size: 8
13089844 CATACAAAAA
13089854 ATTACAAT
1 ATTACAAT
13089862 ATTACAAT
1 ATTACAAT
* * *
13089870 ATATCCCGAC
1 AT-T-ACAAT
13089880 ATTACAAT
1 ATTACAAT
*
13089888 ATTCATACAAA
1 A-T--TACAAT
13089899 ATTACAAT
1 ATTACAAT
13089907 ATTACAAT
1 ATTACAAT
*
13089915 ATTCATACAAA
1 A-T--TACAAT
13089926 ATTACAAT
1 ATTACAAT
13089934 ATT-C-AT
1 ATTACAAT
** * *
13089940 ACAAAAAA
1 ATTACAAT
13089948 ATTACAAT
1 ATTACAAT
13089956 ATT-C-AT
1 ATTACAAT
13089962 A-TA-AA-
1 ATTACAAT
*
13089967 ATTATAAT
1 ATTACAAT
13089975 ATTACAAT
1 ATTACAAT
13089983 ATT
1 ATT
13089986 CATACAAAAA
Statistics
Matches: 90, Mismatches: 19, Indels: 30
0.65 0.14 0.22
Matches are distributed among these distances:
5 2 0.02
6 9 0.10
7 4 0.04
8 53 0.59
9 4 0.04
10 6 0.07
11 12 0.13
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:13089962 original size:68 final size:69
Alignment explanation
Indices: 13089880--13090016 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 69
13089870 ATATCCCGAC
13089880 ATTACAATATTCATACAAAATTACAATATTACAATATTCATAC-AAAATTACAATATTCATACAA
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAATTACAATATTCATACAA
13089944 AAAA
66 AAAA
* * *
13089948 ATTACAATATTCATATAAAATTATAATATTACAATATTCATACAAAAAAATTAGAATATTCATAC
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATAC--AAAAATTACAATATTCATAC
13090013 AAAA
64 AAAA
13090017 TTCTAATCCA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
68 41 0.65
71 22 0.35
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (69 bp):
ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAATTACAATATTCATACAA
AAAA
Found at i:13089979 original size:49 final size:48
Alignment explanation
Indices: 13089833--13090007 Score: 189
Period size: 49 Copynumber: 3.7 Consensus size: 48
13089823 TTATAAAATA
* ** * *
13089833 ATTACAATATTCATACAAAAAATTACAATATTACAAT-ATATCCCGAC
1 ATTACAATATTCATACAAAAAATTACAATATTACAATAAAATTACAAT
** *
13089880 ATTACAATATTCATAC--AAAATTACAATATTACAATATTCA-TACAAA
1 ATTACAATATTCATACAAAAAATTACAATATTACAATA-AAATTACAAT
*
13089926 ATTACAATATTCATACAAAAAAATTACAATATT-CATATAAAATTATAAT
1 ATTACAATATTCATAC-AAAAAATTACAATATTACA-ATAAAATTACAAT
*
13089975 ATTACAATATTCATACAAAAAAATTAGAATATT
1 ATTACAATATTCATAC-AAAAAATTACAATATT
13090008 CATACAAAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
45 19 0.17
46 18 0.16
47 17 0.15
48 3 0.03
49 53 0.48
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.33
Consensus pattern (48 bp):
ATTACAATATTCATACAAAAAATTACAATATTACAATAAAATTACAAT
Found at i:13090018 original size:19 final size:19
Alignment explanation
Indices: 13089901--13089977 Score: 100
Period size: 19 Copynumber: 3.9 Consensus size: 19
13089891 CATACAAAAT
*
13089901 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
13089920 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
13089939 TACAAAAAAATTACAATATTCA
1 TAC---AAAATTACAATATTCA
* *
13089961 TATAAAATTATAATATT
1 TACAAAATTACAATATT
13089978 ACAATATTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
19 34 0.65
22 18 0.35
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Done.